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Susitna-Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
Title:
Fish and aquatics instream flow study, Study plan Section 8.5 : Final study
plan SuWa 200
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Alaska Energy Authority
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Final study plan
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Series (ARLIS-assigned report number):
Susitna-Watana Hydroelectric Project document number 200
Existing numbers on document:
Published by:
[Anchorage : Alaska Energy Authority, 2013]
Date published:
July 2013
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Date or date range of report:
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Study plan Section 8.5
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Pagination:
167 p.
Related work(s):
Pages added/changed by ARLIS:
Notes:
All reports in the Susitna-Watana Hydroelectric Project Document series include an ARLIS-
produced cover page and an ARLIS-assigned number for uniformity and citability. All reports
are posted online at http://www.arlis.org/resources/susitna-watana/
Susitna-Watana Hydroelectric Project
(FERC No. 14241)
Fish and Aquatics Instream Flow Study
Study Plan Section 8.5
Final Study Plan
Alaska Energy Authority
July 2013
FINAL STUDY PLAN FISH AND AQUATICS INSTREAM FLOW STUDY 8.5
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FERC Project No. 14241 Page 8-1 July 2013
8. INSTREAM FLOW STUDY: FISH, AQUATICS, AND RIPARIAN
8.5. Fish and Aquatics Instream Flow Study
On December 14, 2012, Alaska Energy Authority (AEA) filed with the Federal Energy
Regulatory Commission (FERC or Commission) its Revised Study Plan (RSP), which included
58 individual study plans (AEA 2012). Included within the RSP was the Fish and Aquatics
Instream Flow Study (IFS), Section 8.5. RSP Section 8.5 focuses on establishing an
understanding of important biological communities and associated habitats, and the hydrologic,
physical, and chemical processes in the Susitna River that directly influence those resources.
On February 1, 2013, FERC staff issued its study determination (February 1 SPD) for 44 of the
58 studies, approving 31 studies as filed and 13 with modifications. FERC requested additional
information before issuing a SPD on the remaining studies. The Draft Focus Areas Technical
Memorandum (TM) was filed with FERC on January 31, 2013 and was subsequently presented
and discussed during a Technical Work Group (TWG) meeting on February 14, 2013. With
consideration of the comments and suggestions received from licensing participants, a Final
Focus Area TM was filed with FERC on March 1, 2013. On April 1, 2013 FERC issued its
study determination (April 1 SPD) for the remaining 14 studies; approving 1 study as filed and
13 with modifications. RSP Section 8.5 was one of the 13 approved with modifications. In its
April 1 SPD, FERC recommended the following:
Microhabitat Types, HSC and HSI Development
- We recommend that AEA file with the Initial Study Report, a detailed evaluation of the
comparison of fish abundance measures (e.g., number of individuals by species and age
class) with specific microhabitat variable measurements where sampling overlaps, to
determine whether a relationship between a specific microhabitat variable and fish
abundance is evident. We expect the majority of locations where fish sampling and the eight
additional microhabitat variable sampling efforts would overlap at a scale where they could
be related would occur in focus areas where these sampling efforts are concentrated. If
results from these initial comparisons indicate strong relationships may exist between a
specific microhabitat parameter and fish abundance for a target species and life stage,
expanded sampling may be necessary in 2014 to investigate these microhabitat relationships
further. Accordingly, we recommend that AEA include in the evaluation to be filed with the
Initial Study Report, any proposals to develop HSC curves for any of the 8 additional
parameters as part of the 2014 study season.
Upwelling and Downwelling
- We recommend that AEA test the feasibility of measuring vertical hydraulic gradient as a
site-specific microhabitat variable using field measurements, and if determined feasible and
effective at describing upwelling, incorporate the methods into the site-specific HSC
development process. The results of the feasibility test (regardless of whether a feasible or
infeasible finding is made) should be summarized in the Initial Study Report.
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Water Quality Monitoring at Salmon Spawning Locations
- We recommend that AEA monitor temperature, dissolved oxygen, and water level
monitoring data at one or more select Chinook, pink, and coho spawning locations within
Middle River focus areas.
AEA already planned on and has collected water temperature, dissolved oxygen and water level
data at selected salmon spawning sites as part of the 2012-2013 pilot winter studies conducted
within two focus areas (FA 104 (Whiskers Slough) and FA – 128 (Skull Creek) in the Middle
River. Information obtained from those studies will be used to define additional areas for
monitoring of these parameters at the same and other focus areas in 2013-2014. See Section
8.5.4.5.1.2.1 of this Final Study Plan for more details concerning the monitoring of these
parameters.
Instream Flow Study Areas and Study Sites
- We recommend that AEA: (1) consult with the TWG and select an appropriate focus area
within MR-2 to eliminate from the study; (2) consult with the TWG and establish an
additional focus area in geomorphic reach MR-7 that is sufficient for conducting
interdisciplinary studies, possibly near Lower McKenzie Creek or below Curry on old
Oxbow II; and (3) file a detailed description of the changes to the proposed focus area
locations in MR-2 and MR-7 by May 31, 2013, and include in the filing documentation of
consultation with NMFS, FWS, and Alaska DFG, including how the agency comments were
addressed.
In accordance with the April 1 SPD, an Instream Flow Technical Team meeting was held on
April 26, 2013 and AEA conferred with the TWG representatives concerning the changes to the
Focus Area locations. On May 31, 2013 AEA filed with FERC the Adjustments to Middle River
Focus Areas TM, providing the details requested in the April 1 SPD. Information in the Final
Focus Areas TM provides supplemental information concerning the final selection of Focus
Areas presented in this Final Study Plan. This Final Study Plan reflects all other FERC
requested modifications.
8.5.1. General Description of the Study
8.5.1.1. Focus of IFS
The 2013–2014 IFS plan is specifically directed toward establishing an understanding of
important biological communities and associated habitats, and the hydrologic, physical, and
chemical processes in the Susitna River that directly influence those resources. The focus of
much of this work will be on establishing a set of analytical tools/models based on the best
available information and data that can be used for defining both existing or base conditions, i.e.,
without Project, and how these resources and processes will respond to alternative Project
operational scenarios.
8.5.1.2. Study Objectives
The goal of the IFS and its component study efforts is to provide quantitative indices of existing
aquatic habitats that enable a determination of the effects of alternative Project operational
scenarios. Achievement of this goal will require close coordination with a number of interrelated
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studies (e.g., Fish Distribution/Abundance [see Section 9.6], Characterization of Aquatic
Habitats [see Section 9.9], Geomorphology [see Section 6.0], Water Quality [see Section 5.0],
etc.) that will provide important inputs into an overall Project effects analysis (see Figure 8.5-1).
Specific objectives of this and associated companion studies include the following:
1. Map the current aquatic habitat in main channel and off-channel habitats of the Susitna
River affected by Project operations. This objective will be completed as part of the
Characterization of Aquatic Habitats Study (see Section 9.9) (see Figure 8.5-1).
2. Select study areas and sampling procedures to collect data and information that can be
used to characterize, quantify, and model mainstem and lateral Susitna River habitat
types at different scales. This objective will be completed via a collaborative process
involving this study, Riparian Instream Flow (see Section 8.6), Groundwater (see Section
7.5), Geomorphology (see Section 6.0), Water Quality (see Section 5.0), and Fish and
Aquatics (see Section 9.0).
3. Develop a Mainstem Open-water Flow Routing Model that estimates water surface
elevations and average water velocity along modeled transects on an hourly basis under
alternative operational scenarios.
4. Develop site-specific Habitat Suitability Criteria (HSC) and Habitat Suitability Indices
(HSI) for various species and life stages of fish for biologically relevant time periods
selected in consultation with the TWG. Criteria will include observed physical
phenomena that may be a factor in fish preference (e.g., depth, velocity, substrate,
embeddedness, proximity to cover, groundwater influence, turbidity, etc.). If study efforts
are unable to develop robust site-specific data, HSC/HSI will be developed using the best
available information and selected in consultation with the TWG.
5. Develop integrated aquatic habitat models that produce a time series of data for a variety
of biological metrics under existing conditions and alternative operational scenarios.
These metrics may include (but are not limited to) the following:
• Water surface elevation at selected river locations
• Water velocity within study areas subdivisions (cells or transects) over a range of
flows during seasonal conditions
• Length of edge habitats in main channel and off-channel habitats
• Habitat area associated with off-channel habitats
• Clear water area zones
• Effective spawning and incubation habitats
• Varial zone area
• Frequency and duration of exposure/inundation of the varial zone at selected river
locations
• Habitat suitability indices
6. Evaluate existing conditions and alternative operational scenarios using a hydrologic
database that includes specific years or portions of annual hydrographs for wet, average,
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and dry hydrologic conditions and warm and cold Pacific Decadal Oscillation (PDO)
phases.
7. Coordinate instream flow modeling and evaluation procedures with complementary study
efforts including Riparian (see Section 8.6), Geomorphology (see Sections 6.5 and 6.6),
Groundwater (see Section 7.5), Baseline Water Quality (see Section 5.5), Fish Passage
Barriers (see Section 9.12), and Ice Processes (see Section 7.6) (see Figure 8.5-1). If
channel conditions are expected to change over the license period, instream flow habitat
modeling efforts will incorporate changes identified and quantified by riverine process
studies.
8. Develop a Decision Support System-type framework to conduct a variety of post-
processing comparative analyses derived from the output metrics estimated under aquatic
habitat models. These include (but are not limited to) the following:
• Seasonal juvenile and adult fish rearing
• Habitat connectivity
• Spawning and egg incubation
• Juvenile fish stranding and trapping
• Ramping rates
• Distribution and abundance of benthic macroinvertebrates
8.5.2. Existing Information and Need for Additional Information
8.5.2.1. Summary of Existing Susitna River Information
Substantial physical, hydrologic, and biological information is available for the Susitna River as
a result of previous hydropower licensing efforts conducted during the 1970s and 1980s. The
extent and details of many of those studies were provided in the Draft Environmental Impact
Statement (FERC 1984) for the previously-proposed Susitna-Hydroelectric (Su-Hydro) Project
(FERC No. 7114) along with companion appendices and attachments in the way of Alaska
Department of Fish and Game (ADF&G) reports. A gap analysis conducted by HDR (2011)
summarized some of the data. The gap analysis provided an initial listing of salient reports and
data that warranted more detailed evaluations.
A more focused review of existing reports and data specific to the Su-Hydro Project proposed in
the 1980s was initiated by Alaska Energy Authority (AEA) in 2012. This has included the
identification, acquisition, and compilation of study plans, reports, data, maps, drawings,
photographs, and technical correspondence pertaining to the 1980s Su-Hydro Project. Although a
substantial amount of this information had already been provided to and made available through
the Alaska Resources Library and Information Services (ARLIS), AEA has identified and is
working with ARLIS in acquiring the majority of original files, documents, maps, drawings, and
other information that had been archived in several locations in Alaska. These documents are in a
variety of formats including textual, microfiche, and maps. The majority of documents will be
housed in the ARLIS library in Anchorage, Alaska (some are available online through the
University of Alaska, Fairbanks library) and will be made available either electronically or by
on-site review to interested parties, licensing participants, and Project team members.
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As part of the 2012 effort, AEA also commissioned the targeted review of reports, data, and
other information specific to the 1980s studies of fish, fish habitats, and instream flow-related
assessments. This work is nearing completion and will result in the preparation of Technical
Memoranda (TMs) that summarize the salient fish and instream flow-related information from
those studies. To date, over 60 reports from the 1980s and earlier have been identified and
reviewed. These documents include 83 separate volumes containing descriptions of field studies
and reports with tabular data, figures, and maps. The reports describe studies that were focused
on a wide range of interrelated topics designed to provide information that would allow for an
evaluation of the potential effects of the Su-Hydro Project operations on downstream fish and
aquatic resources and habitats. These included studies focused on the following:
• Adult salmon passage in sloughs and side channels
• Adult salmon spawn timing and distribution
• Salmon Habitat Suitability Criteria
• Salmon spawning habitat evaluation
• Juvenile salmon abundance and distribution including winter studies
• Resident fish abundance, distribution, and life history
• Channel geometry investigations
• Groundwater upwelling detection
• Hydrological investigations and modeling of anadromous and resident fish habitat
The documents are well organized and rich in detail regarding study rationale, site descriptions,
methods applied, and results. With respect to instream flow analysis, the studies generally
followed the Instream Flow Incremental Methodology (IFIM) described by Bovee (1982), and
therefore careful consideration was given to study design, site selection, data collection, and data
analysis and modeling. In addition, recognizing the spatial variability in the diversity and
complexity of habitat types within different segments of the Susitna River, substantial effort was
spent on developing approaches that could be used for expansion/extrapolation of flow-habitat
model results obtained from one location to unmeasured sites (Aaserude et al. 1985). Overall, the
documents represent a remarkable source of information that is directly relevant to the types of
studies that are proposed in this RSP. Indeed, many of the study components presented in the
RSP have been founded on certain elements provided in one or more of the earlier reports.
However, the studies presented in the RSP are not simply repeating or duplicating those
conducted in the 1980s. Rather, the earlier studies have been appropriately used to make
informed decisions regarding study design, methods selection, and modeling approaches that are
best suited to address the specific objectives of the RSP as stated in Section 8.5.1.2.
One consideration that was taken into account relative to the applicability of the earlier studies
was that the 1980s Su-Hydro Project was envisioned as a two-dam project, with an upper dam,
reservoir, and powerhouse near river mile (RM) 184 (Watana Dam). It was envisioned that the
upper development would be operated in load-following mode to meet power demands. A lower
dam, reservoir, and powerhouse (Devils Canyon Dam) would provide additional power
generation, but would also re-regulate flow releases from the upper development. Downstream
flow releases from the Devils Canyon Dam would not have the daily flow fluctuations associated
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with load-following operations of the upper development. In addition, because the Devils
Canyon Dam would create a reservoir that would inundate much of the river between the two
dams, the instream flow and riparian study efforts in the 1980s focused on the effects of flow
releases to the Susitna River downstream of the Devils Canyon Dam site, and the reach between
the Devils Canyon Dam and Watana Dam sites was not modeled as part of the instream flow
study. Instream flow-related issues that were the focus of studies completed in the 1980s were
thus more concerned with determining the effects of changes in the timing and magnitude of
flows on the quantity and quality of fish habitats that would occur with the two dams as
configured, rather than flow fluctuations.
The Project, as currently proposed, without the re-regulation of flows that a second dam would
allow, will require the evaluation of downstream effects of load-following operations on fish and
wildlife resources downstream of the Watana Dam site, in addition to an assessment of overall
effects due to shifts and changes in flow timing and magnitude. These are important differences
between the current proposal and that of the 1980s, and have directly factored into the design of
studies proposed in the RSP. In particular, the proposed studies now include the development of
a flow routing model that will predict water surface elevation changes at different locations in
the river under variable flow conditions. Linkage of this model with those developed as part of
this RSP that are focused on defining habitat-flow relationships in different habitat types of the
river will allow for an integrated evaluation of Project effects under different operational
scenarios, including load-following. Other related resource studies (e.g., Riparian [see Section
8.6], Geomorphology [see Section 6.0], Water Quality [see Section 5.0], and Ice Processes [see
Section 7.6]) will also rely on this model and will use it to evaluate Project operational effects on
their respective resources.
As background and to provide context for the studies that are contained in this RSP, some of the
salient information from the 1980s studies is summarized below.
8.5.2.2. Habitat Distribution
The spatial distribution and characterization of existing habitat conditions in the Susitna River
are important aspects of 2013–2014 instream flow studies. Fish species in the Susitna River
basin rely on a range of aquatic habitats, and specific habitat types may be selectively used by
different species and life stages (Jennings 1985; Sundet and Pachek 1985). Furthermore, fish
utilization of specific habitats may vary seasonally or spatially within the basin (Suchanek et al.
1985). The distribution of aquatic habitats in the Susitna River will be an important consideration
during instream flow studies to evaluate potential effects of stream flow fluctuations on habitat
and fish communities.
Habitat distribution mapping was performed during 1980s studies at the macro-habitat scale (i.e.,
main channel, side channel, side slough, upland slough, tributary mouth, tributary, and lake) (see
Section 9.9). The character and distribution of habitat during the 1980s were mapped using aerial
photography based on hydrology and channel morphology (Trihey 1982; ADF&G 1983). The
aerial photos were recorded at various stream flow levels to identify the effect of Susitna River
discharge on habitat distribution (Figure 8.5-2) (Klinger-Kingsley et al. 1985). Most of the
mapping effort targeted the Middle River Segment and relatively less for the Lower River
Segment; very little habitat data are available for the Upper River Segment from the 1980s
(Klinger-Kingsley et al. 1985; Buckwalter 2011). A more complete summary of the existing
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information relating to habitat distribution in the Susitna River is provided in Section 9.9
(Characterization of Aquatic Habitats in the Susitna River).
8.5.2.3. Fish Distribution and Abundance
The distribution and abundance of fish species in the Susitna River will play an important role in
evaluating the potential flow-induced effects of the Project, particularly in the Middle and Lower
Susitna River. The distribution of fish species among Susitna River segments (Upper, Middle,
and Lower) and among main channel, off-channel, and tributary habitats is essential information
for 2013–2014 instream flow studies to identify species and life stages that may be affected by
Susitna River stream flow fluctuations. Relative abundance of fish species among river segments
and habitats will similarly provide a basis for evaluating the effects of hydrologic changes on
fish in the Susitna River.
Extensive studies were conducted during the 1980s related to fish distribution and abundance
and more recent fish distribution studies performed during the 2000s have supplemented data
collected during the earlier efforts (see Section 9.0). At least 20 anadromous and resident fish
species are known to inhabit the Susitna River between headwater areas and Cook Inlet (RM 0.0)
(Jennings 1985; Delaney et al. 1981a, 1981b). Species richness is greatest in the Lower River
Segment and declines in the Middle and Upper River segments (Jennings 1985; Delaney et al.
1981b). Steep, high-velocity cascades in Devils Canyon (RM 152 – 160) represent the upstream
extent of distribution for many species (Jennings 1985; Delaney et al. 1981a). Fish species found
in the Middle and Lower River segments include, but are not limited to, Pacific salmon species
(Chinook, sockeye, chum, coho, and pink), Arctic grayling, rainbow trout, Dolly Varden,
humpback whitefish, round whitefish, and burbot (Jennings 1985; Delaney et al. 1981b, 1981c ).
Within the Middle and Lower River segments, these fish species utilize main channel, off-
channel, and tributary habitats (Jennings 1985; Delaney et al. 1981b, 1981c). In terms of
instream flow studies, fish utilization in main channel and off-channel habitats is of principal
importance because these areas are influenced by Susitna River stream flow fluctuations. A more
detailed synthesis of fish distribution and abundance is provided in Section 9.0 (Fish and
Aquatics).
8.5.2.4. Salmonid Spawning and Incubation
Salmonid spawning and egg incubation are critical life history phases and are important
considerations for development of Susitna River instream flow studies. Water depth, velocity,
and temperature of surface stream flow are important habitat characteristics for spawning adult
salmonids, while intergravel flow and water quality can be critical for salmonid egg incubation
and emergent fry survival. As a result, each biological process is sensitive to stream flow
fluctuations. As part of Susitna River instream flow studies, it is important to identify the
distribution and timing of salmonid spawning in the Susitna River (see Section 9.0). Main
channel (main channels, side channels, and tributary mouths), off-channel (side sloughs, upland
sloughs, and backwater areas), and tributary habitats are used by adult salmonids for migration
and spawning, though main channel and off-channel habitats are of principal importance with
regard to instream flow studies because these areas are most influenced by Susitna River stream
flow fluctuations. Knowledge of the timing of salmonid spawning and associated migrations will
help identify the periods during which fish populations may be affected by changes in Susitna
River stream flow. In addition, the behavior of spawning salmonids, such as colonization rates of
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new spawning areas and redd residence time by spawners, is an important aspect of this life
history stage and will help guide instream flow studies in the Susitna River.
Pacific salmon species are known to utilize Middle and Lower Susitna River habitats for
migration and spawning between RM 206.8 and Cook Inlet (RM 0.0) (Jennings 1985; Thompson
et al. 1986; Buckwalter 2011). During upstream spawning migrations, all Pacific salmon species
utilize the mainstem Susitna River to access spawning areas located in main channel, off-
channel, and/or tributary habitats of the Middle and Lower Susitna River. For spawning in the
Middle Susitna River, adult sockeye, chum, and pink salmon utilized main channel and off-
channel habitats during the 1980s, while Chinook and coho salmon typically spawned in
tributary habitats not influenced by Susitna River stream flow conditions (see Section 8.5.2.1.2)
(Jennings 1985; Barrett et al. 1985; Thompson et al. 1986). In the Lower Susitna, the primary
spawning areas for chum and pink salmon occurred in main channel and off-channel habitats,
while Chinook, coho, and sockeye salmon generally used tributaries for spawning (Barrett et al.
1983; Barrett et al. 1985; Thompson et al. 1986).
The timing of salmon spawning migrations in the Susitna River during the 1980s began in late
May and continued through September, though specific timing of movement differed by species
(see Section 8.5.2.1.7). In the Middle and Lower Susitna River, salmon species that utilized main
channel and off-channel habitat for spawning typically spawned from late July through early
October (see Section 8.5.2.1.7) (Jennings 1985; Barrett et al. 1985; Thompson et al. 1986). The
period of salmon egg incubation occurred from the onset of spawning through the end of fry
emergence, which was estimated to begin in late January and continue through April and/or May
(see Section 8.5.2.1.7) (Bigler and Levesque 1985; Jennings 1985; Stratton 1986; Vining et al.
1985). Among habitats utilized by spawning salmon, side channel and side slough habitats were
observed to be most vulnerable to dewatering and/or freezing as a result of fluctuations in
Susitna River discharge (Vining et al. 1985).
8.5.2.5. Study Area Selection
In general, the Susitna River was divided in the 1980s studies into segments, sub-reaches, and
study sites based on hydrology, channel morphology, tributary input, macro- and mesohabitat
features, and fish use. At the broadest scale, the Susitna River was divided into three reaches
following the historic river mile convention used at the time:
1. Upper river – Representing that portion of the watershed above the proposed Devils
Canyon Dam site at RM 152.
2. Middle river – Extending approximately 53.5 miles from RM 152 downstream through
Devils Canyon to the Three Rivers Confluence at RM 98.5.
3. Lower river – Extending 98.5 miles downstream from the Three Rivers Confluence to
Cook Inlet (RM 0).
These three breaks formed the first order level of stratification in the 1980s studies.
A second level of stratification was designated based on classifying riverine-related habitats of
the Susitna River into six macro-habitat categories consisting of mainstem, side channel, side
slough, upland slough, tributaries, and tributary mouths (Estes and Vincent-Lang 1984). The
distribution and frequency of these habitats varied longitudinally within the river depending in
large part on its confinement by adjoining floodplain areas, size, and gradient. The habitat types
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were described by ADF&G with respect to mainstem flow influence in the Susitna Hydroelectric
Aquatic Studies Procedures Manual (ADF&G 1984) as follows, with additional clarification
added here where considered appropriate:
• Mainstem habitat consists of those portions of the Susitna River that normally
convey stream flow throughout the year. Both single and multiple channel reaches are
included in this habitat category. Groundwater and tributary inflows appear to be
inconsequential contributors to the overall characteristics of mainstem habitat.
Mainstem habitat is typically characterized by high water velocities and well-armored
streambeds. Substrates generally consist of boulder- and cobble-size materials with
interstitial spaces filled with a grout-like mixture of small gravels and glacial sands.
Suspended sediment concentrations and turbidity are high during summer due to the
influence of glacial meltwater. Stream flows recede in early fall and the mainstem
clears appreciably in October. An ice cover forms on the river in late November or
December.
• Side channel habitat consists of those portions of the Susitna River that normally
convey stream flow during the open-water season but become appreciably dewatered
during periods of low flow. Side channel habitat may exist either in well-defined
overflow channels, or in poorly defined water courses flowing through partially
submerged gravel bars and islands along the margins of the mainstem river. Side
channel streambed elevations are typically lower than the mean monthly water
surface elevations of the mainstem Susitna River observed during June, July, and
August. Side channel habitats are characterized by shallower depths, lower velocities,
and smaller streambed materials than the adjacent habitat of the mainstem river.
• “Side” slough habitat is located in spring- or tributary-fed overflow channels
between the edge of the floodplain and the mainstem and side channels of the Susitna
River and is usually separated from the mainstem and side channels by well-vegetated
bars. An exposed alluvial berm often separates the head of the slough from mainstem
or side channel flows. The controlling streambed/stream bank elevations at the
upstream end of the side sloughs are slightly less than the water surface elevations of
the mean monthly flows of the mainstem Susitna River observed for June, July, and
August. At intermediate- and low-flow periods, the side sloughs convey clear water
from small tributaries and/or upwelling groundwater (Estes et al. 1981). These clear
water inflows are essential contributors to the existence of this habitat type. The water
surface elevation of the Susitna River generally causes a backwater to extend well up
into the slough from its lower end (Estes et al. 1981). Even though this substantial
backwater exists, the sloughs function hydraulically very much like small stream
systems and several hundred feet of the slough channel often conveys water
independent of mainstem backwater effects. At high flows the water surface elevation
of the mainstem river is sufficient to overtop the upper end of the slough (Estes et al.
1981). Surface water temperatures in the side sloughs during summer months are
principally a function of air temperature, solar radiation, and the temperature of the
local runoff.
• “Upland” slough habitat differs from the side slough habitat in that the upstream
end of the slough is not interconnected with the surface waters of the mainstem
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Susitna River or its side channels at less than bankfull flows. The upstream end can
be vegetated with mature trees, although a morphologic signature of a converging
inlet and gravel levee closure can still be discerned. These sloughs are characterized
by the presence of beaver dams and an accumulation of silt covering the substrate
resulting from the absence of mainstem scouring flows. They are not truly “upland”
in the geomorphic sense, but the use of this nomenclature in the 1980s studies reflects
the observation that the understanding of floodplain and channel forming processes
was in the early stage in fisheries, where some variation in interpretation existed over
what constituted a floodplain versus an upland terrace (e.g., see Williams 1978).
Essentially, the main distinguishing characteristic between a “side” slough and an
“upland” slough was the level of high flow at which each was engaged.
• Tributary habitat consists of the full complement of hydraulic and morphologic
conditions that occur in the tributaries. Their seasonal stream flow, sediment, and
thermal regimes reflect the integration of the hydrology, geology, and climate of the
tributary drainage. The physical attributes of tributary habitat are not dependent on
mainstem conditions.
• Tributary mouth habitat extends from the uppermost point in the tributary
influenced by mainstem Susitna River or slough backwater effects to the downstream
extent of the tributary plume that extends into the mainstem Susitna River or slough
(Estes et al. 1981).
A schematic of these types of habitats as applied in the 1980s studies is depicted in Figure 8.5-3.
These categories were also used by Trihey and Associates in its instream flow modeling studies
(Aaserude et al. 1985). Beginning in the 1983 open-water studies, however, a fundamental
change was made in how side sloughs and side channels were identified during field studies
(Dugan et al. 1984). During 1981 and 1982, side sloughs and side channels were distinguished
primarily on their morphology. Side sloughs included an unvegetated berm at the head of the
slough and were rarely overtopped. In contrast, a side channel conveyed mainstream flow during
most of the year. During 1983 and following years, if a berm was overtopped and a channel
conveyed mainstem flows it was characterized as a side channel. If the berm was not overtopped
it was characterized as a side slough. Consequently, during the latter years of the 1980s Fish and
Aquatic Program an area may have been characterized as a side channel during periods of high
flows and a side slough during periods of lower flows.
Specific sites chosen for completion of the various studies by ADF&G between 1981 and 1985
varied from year to year and study to study. In general, sampling was relatively broad during
1981 and 1982, and more focused during 1983 to 1985. The 1981 Aquatic Habitat Studies were
focused on ‘Fishery Habitat’ evaluations and ‘Selected Habitat’ evaluations (Estes et al. 1981).
The Fishery Habitat evaluations collected point information on observed fish habitat use and
general habitat evaluations (water quality, hydrology, and mapping). The Selected Habitat
evaluations collected water quality, discharge, and mapping information at selected sloughs
between Talkeetna and Devils Canyon.
A total of 5 river reaches were delineated and 8 to 13 representative study sites were selected in
each, without consideration of proportional sampling or optimal allocation (e.g., see Cochran
1977). These included the following:
• Yentna Reach (Cook Inlet to Little Willow Creek; RM 0.0–50.5): 13 sites
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• Sunshine Reach (Rustic Wilderness to Parks Highway Bridge; RM 58.1–83.5): 10
sites
• Talkeetna Reach (Parks Highway Bridge to Curry; RM 83.5–120.7): 11 sites
• Gold Creek Reach (Curry to Portage Creek; RM 120.7–148.8): 12 sites
• Impoundment Reach (Devils Canyon to Denali Highway; RM 151–281): 8 tributaries
With few exceptions, the sites sampled for aquatic habitat studies were the same as those
sampled under resident and juvenile anadromous fish studies in 1981 and 1982. Selection of
specific sampling sites was apparently not based upon a statistical sampling design. Instead, sites
were considered representative of each reach, and were based effectively on where fish were
found. This basis was carried forward in subsequent years. For example, in 1982, habitat
information was collected where spawning fish were located within the mainstem Susitna River
downstream of Devils Canyon (tributary/mainstem confluence areas and sloughs were not
sampled). Only spawning sites for chum salmon were observed in the mainstem, which led to the
identification of eight mainstem spawning locations between Lane Creek (RM 113.6) to Devils
Canyon.
In addition, 17 Designated Fish Habitat (DFH) sites were chosen in 1982 based upon four criteria
(Estes and Schmidt 1983; ADF&G 1983):
1. Areas that will be affected by changes in discharge of the mainstem Susitna.
2. Sites identified from previous studies to have significant populations of resident and
juvenile anadromous species.
3. Access to areas will not create severe logistics problems and limit the overall scope of the
studies.
4. Sites selected represent a cross-section of critical areas available to resident and juvenile
anadromous fish of the Susitna River.
Five of the DFH sites were located downstream of Talkeetna from RM 88.4 to 73.1 and twelve
were located in the reach from Portage Creek (RM 148.8) to Whiskers Creek (RM 101.2).
During 1983 and 1984, studies became focused on collecting specific data needed to develop
three types of instream flow models: Resident and Juvenile Habitat (RJHAB) models, Instream
Flow Group (IFG) models, and Direct Input Habitat (DIHAB) models developed by Trihey and
Associates (Hilliard et al. 1985). As before, sites were selected based on where fish were found.
During 1983, 32 sites (11 tributaries, 3 upland sloughs, 8 side slough/channel, 6 side channel, 4
side slough) were sampled in the reach from Talkeetna to Devils Canyon for fish distribution,
and 13 sites were modeled by ADF&G with either the RJHAB (2 upland sloughs, 2 side channel/
sloughs, 1 side slough, 1 side channel) approach or IFG approach (3 side slough/channels, 1 side
slough, 3 side channels). The 13 modeled sites were chosen based upon observations of large
numbers of spawning salmon or concentrations of juvenile salmon during 1981 and 1982 studies
(Dugan et al. 1984). They were also selected as being representative of the habitat types present
between the Chulitna River and Devils Canyon likely to be affected by changes in mainstem
flow from the proposed project (Dugan et al. 1984; Marshall et al. 1984).
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Sampling in 1984 focused on main channel margins, side channels, side sloughs, and tributary
mouth habitats in the middle and lower river segments between RM 147.1 and 35.2. During
1984, crews sampled three types of study sites:
• RJHAB sites (16 sites)
• IFG sites (6 sites)
• DIHAB sites (14 sites)
• Opportunistic sites (31 sites)
Opportunistic sites were sampled only once to expand the understanding of juvenile and resident
fish distribution (Suchanek et al. 1985).
Instream flow modeling of spawning habitat was conducted for chum and sockeye salmon at
mainstem margin, side channel, upland slough, and side slough habitat types. Modeled sites were
considered to represent the range of spawning conditions for sloughs and side channels present in
the mainstem between the Chulitna River and Devils Canyon. In addition, instream flow studies
were performed to describe juvenile Chinook habitat-flow responses within mainstem margins,
side channels, side sloughs, and upland sloughs of the middle river. The modeling studies relied
effectively on the habitat classification, and manipulations thereof, for stratifying and
extrapolating model results from sampled sites to larger study reaches (Steward et al. 1985;
Ashton and Klinger-Kingsley 1985; and Klinger-Kingsley et al. 1985). The overall approach
proposed for the extrapolation process was described in Aaserude et al. (1985) and consisted of
methods for both single thread and multiple thread portions of the river. However, project
funding was curtailed in 1985 and the approach was never implemented.
8.5.2.6. HSC
An important element of these studies was the collection of microhabitat data of various species
and life stages of fish reflective of a suite of different parameters influenced by, or potentially
influenced by, flow. These included water depth, water velocity, substrate, upwelling occurrence,
and turbidity.
A more detailed synthesis of pertinent information will be completed as part of the IFS and
supplemented by analysis of aquatic-related information conducted as part of the Fish and
Aquatics Study (see Section 9.0). As part of this synthesis, information will be compiled and
reviewed related to instream flow regimes implemented at other large hydropower projects, with
a special emphasis on projects developed in arctic and sub-arctic environments.
An extensive set of Habitat Suitability Criteria were developed as part of the 1980s instream
flow studies. These criteria were developed using a combination of site-specific data collected
through fish sampling and literature sources, and through refinement based on the professional
judgment of project biologists. Table 8.5-1 summarizes the species and life stages for which
HSC were developed during the 1980s efforts. Also described are the various habitat parameters
for which curves describing HSC were developed (e.g., depth).
HSC for rearing juvenile salmon were developed for the habitat parameters of depth, velocity,
and cover used by juvenile Chinook, coho, sockeye, and chum salmon (Suchanek et al. 1984b).
These HSC were developed based on field data collected at representative tributary, slough, and
side channel sites between the Chulitna River confluence and Devils Canyon (Middle Susitna
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River) and were considered to be specific to this reach. Fish observations were obtained by beach
seining (turbid water) or electrofishing (clear water) systematically established 300-square-foot
cells with relatively uniform physical habitat (within cells) that captured the overall variability of
site habitat conditions (across cells). Fish observations were then related to depth, velocity, and
cover conditions characterized by each cell and collectively used to develop HSC for these
parameters. In addition, if differences in habitat utilization were apparent at varying turbidity
levels, separate HSC were developed for turbid vs. clear water conditions for those species with
sufficient sample sizes (i.e., juvenile Chinook). An example of HSC developed through this
effort is shown in Figure 8.5-4. A subsequent effort used similar methods to verify the
applicability of these juvenile salmon rearing HSC curves for the lower river downstream of the
Chulitna River confluence (Suchanek et al. 1985). Findings from this effort resulted in some
modifications to HSC for use in the Lower River, particularly for water depth.
Spawning HSC for chum and sockeye salmon were developed from redd observations in sloughs
and side channels of the middle Susitna River (Vincent-Lang et al. 1984b). Data collection sites
were concentrated in areas used for hydraulic simulation modeling to maximize the concomitant
collection of utilization and availability data necessary for the evaluation of preference. HSC for
chum salmon were modified using limited preference data; however, preference could not be
incorporated for sockeye salmon. HSC for depth, velocity, and substrate were developed from
this effort. Additionally, modified HSC were developed for substrate that reflected the presence
or absence of upwelling. A related study also examined chum salmon spawning habitat
utilization in select tributary mouths of the middle Susitna River and found that the range of
utilized depths, velocities, and substrates was generally comparable to redds in sloughs in side
channels (Sandone et al. 1984). Spawning habitat utilization for Chinook, coho, and pink salmon
was evaluated in tributaries of the middle Susitna River (Vincent-Lang et al. 1984a). Sufficient
data were collected to develop depth, velocity, and substrate HSC curves for Chinook salmon.
However, observations for spawning coho and pink salmon were insufficient to develop HSC.
Instead, spawning HSC for these two species were based solely on literature data and modified
using qualitative field observations.
HSC for resident fish species were developed based on data collected through electrofishing,
beach seining, and hook-and-line sampling in tributary mouths, tributaries, and sloughs of the
middle Susitna River (Suchanek et al. 1984a). Cover and velocity HSC were developed for adult
rainbow trout, arctic grayling, round whitefish, and longnose sucker. HSC for cover were
developed separately for turbid vs. clear water conditions. A single depth HSC was developed
for all of these species combined. Only round whitefish were collected in sufficient numbers to
develop separate HSC for juveniles.
8.5.2.7. Winter Studies
Winter instream flow conditions are a critical component of fish habitat, particularly with respect
to egg incubation and juvenile rearing. Intergravel flow and groundwater upwelling are critical
for egg incubation and emergent fry survival, while depth, velocity, and temperature of surface
flow are important habitat characteristics for juvenile and adult fish. Project operations will
likely result in substantially higher flows during the winter period, which may influence the
quality and quantity of existing rearing and holding habitats for juvenile and adult fish and may
affect the extent and degree of intergravel flow or lateral exchange between mainstem and off-
channel habitats, which can consequently alter subsurface water temperatures critical for
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salmonid egg incubation and fry survival. Winter studies conducted in the Susitna River during
the 1980s were primarily focused on relationships between salmon egg incubation and discharge,
water quality and temperature, and fish movement and habitat utilization.
Success of salmon egg incubation during winter is dependent on discharge conditions in addition
to water quality and temperature. During winter studies conducted during 1983–1984 in the
middle Susitna River, redd dewatering and freezing were observed to be primary sources of
chum salmon egg mortality as discharge levels declined after the fall spawn period through
winter (Vining et al. 1985). During the study, chum salmon eggs located in side channel habitats
were most susceptible to mortality, while eggs located in side slough habitats that were less
affected by main channel stream flow and influenced by groundwater upwelling were less prone
to freezing and dewatering (Vining et al. 1985). Similar results were observed during a
concurrent study on the lower Susitna (Bigler and Levesque 1985). Groundwater upwelling can
provide a thermal buffer for incubating eggs from climatic changes and colder surface stream
flow and aid egg development in terms of increasing intergravel water exchange, replenishment
of dissolved oxygen, and removal of metabolic wastes (Vining et al. 1985; Burgner 1991). Based
on the results of the 1983–1984 study, Vining et al. (1985) observed that the amount of spawning
habitat available in fall does not necessarily predict the amount of egg incubation habitat and
recommended that future analyses of effective spawning habitat area account for seasonal
changes in Susitna River discharge (Vining et al. 1985). In addition, Vining et al. (1985) also
noted that future project operations could cause higher Susitna River winter discharges and that
the effect of such changes on redd dewatering and/or freezing might depend on whether
temperatures of Project outflows were higher or lower than existing stream temperatures.
The rate of salmonid egg incubation is a function of water temperature because egg development
occurs more quickly in warmer winter temperatures and slower in colder thermal regimes, with
mortality occurring at the point of freezing (Burgner 1991). In the Susitna River during the
1980s, intergravel water temperatures were observed to vary among habitat types, such that
intergravel water temperatures in tributary and main channel areas were strongly affected by
surface water and were near freezing during winter, while temperatures in side sloughs were
more stable as a result of groundwater influence (Figure 8.5-5) (Hoffman et al. 1983; Seagren
and Wilkey 1985; Vining et al. 1985). In side channel areas, intergravel temperature was highly
variable and was most dependent on-site-specific conditions that controlled the relative influence
of groundwater and surface water sources (Vining et al. 1985). Vining et al. (1985) recorded
faster development times among salmon eggs fertilized on the same date and artificially planted
in Susitna River side channel and side slough habitats fed by groundwater upwelling relative to
main channel areas with no groundwater influence. Similarly, the development times of chum
and sockeye salmon eggs in laboratory conditions that reflected winter temperature regimes from
main channel and side slough Susitna River habitats were faster in warmer side slough water
temperature regimes influenced by groundwater upwelling (Wangaard and Burger 1983). Water
quality conditions at salmon spawning sites during winter varied between surface and intergravel
water and according to the relative influence of groundwater (Hoffman et al. 1983; Vining et al.
1985). Vining et al. (1985) observed that the difference between intergravel and surface water
dissolved oxygen levels was greatest for slough habitat and least for tributary and mainstem
habitats, while differences were intermediate in side channel habitats. In terms of salmon egg
incubation, dissolved oxygen levels in the Susitna River were generally above recommended
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values (7.19 mg/L; Alderdice and Velsen 1978) and low levels of dissolved oxygen were most
likely ameliorated by the presence of upwelling water (Vining et al. 1985).
Substrate was characterized among salmon spawning areas in main channel, side channel, and
slough habitats in the Susitna River during winter 1983–1984 (Vining et al. 1985). Vining et al.
1985 observed that slough habitats had the highest level of fines, followed by side channel,
tributary, and mainstem habitats, though fine sediment compositions in substrates sampled
directly from redds were typically lower than in the surrounding habitat. Percent composition of
fine substrates among sampled slough habitats in the middle Susitna indicated greater than 35
percent fines; however, the percent of fine substrate at redd locations among slough samples did
not exceed 16 percent in five of the six sites evaluated (Vining et al. 1985). Bigler and Levesque
(1985) similarly concluded that substrate was not a limiting factor to embryo development.
Little information is available about winter habitat use by juvenile salmon in the Susitna River.
Surveys during the winter of 1980 to 1981 by Delaney et al. (1981c) found that the majority of
juvenile Chinook salmon captured between Cook Inlet and Devils Canyon occurred at slough
and mainstem Susitna River sites. The majority of juvenile coho salmon captured between Cook
Inlet and Talkeetna during winter occurred at tributary mouth sites, whereas between Talkeetna
and Devils Canyon, winter occurrence was greater at slough sites. Stratton (1986) studied
overwinter habitat use by Chinook and coho salmon at four locations (Indian River, Slough 9A,
Slough 10, and Slough 22) from October 1985 to April 1986. Findings suggested that coho
salmon preferred areas with greater depth and cover consisting of debris, vegetation, and
undercut banks, and beaver dams and ponds in particular. Chinook salmon preferred shallower,
slightly higher velocity and cover consisting of rocks and boulders. Bigler and Levesque (1985)
captured Chinook salmon juveniles using fyke nets at several side channels in the Lower Susitna
River Trapper side channel in April and May, suggesting these side channels were being utilized
as overwintering habitat.
8.5.2.8. Periodicity
Fish periodicity analyses will describe the temporal and spatial utilization of mainstem and
tributary habitats in the Susitna River by individual fish species and life stages and will be
essential to evaluate potential effects of Susitna River stream flow fluctuations on fish
communities. Fish spawning and egg incubation are critical life history stages that are
particularly sensitive to fluctuations in stream flow. Moreover, rearing and holding conditions in
main channel and off-channel habitats in the Susitna River that are utilized by juvenile and adult
fish can be transformed in response to Susitna River discharge. During 2013–2014 instream flow
studies, periodicity analyses will be used to inform selection of study areas and guide habitat-
specific modeling and spatial and temporal habitat analyses.
Periodicity of fish habitat use in the middle and lower Susitna River during the 1980s was
developed based on data collected during fish distribution and abundance studies. Salmon
species in particular were studied intensively during the 1980s to identify the distribution,
abundance of each life stage, and species that used available aquatic habitats in the Susitna
River. Periods of peak and off-peak habitat use by salmon in the Susitna River during the 1980s
were developed by species and life stage based on juvenile and adult salmon distribution and
abundance investigations conducted primarily during 1981–1985 (Table 8.5-2) (see Fish and
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Aquatics, Section 9.0). Other anadromous and freshwater resident fish species were studied,
primarily to identify spawn locations and timing of seasonal movement patterns.
Adult salmon species (Chinook, sockeye, chum, coho, and pink) migrate upstream from marine
areas into the Susitna River beginning in late May and continue through September, though
specific timing of movement differs by species (Table 8.5-2). Salmon spawning timing in the
Middle and Lower Susitna River typically occurs from late July through early October in
tributary, main channel, and off-channel habitats (Jennings 1985; Barrett et al. 1985; Thompson
et al. 1986). During the 1980s studies, Chinook and coho salmon spawned almost exclusively in
tributary habitats that were not directly influenced by Susitna River stream flow, whereas
sockeye, chum, and pink utilized habitats that were hydrologically connected to main channel
stream flows (Jennings 1985; Barrett et al. 1985; Thompson et al. 1986). Subsequent to the
spawn period, salmon egg incubation in the Susitna River occurred from July through the end of
fry emergence in April and May during the following spring (Table 8.5-2) (Bigler and Levesque
1985; Jennings 1985; Vining et al. 1985). Among habitats utilized by spawning salmon, side
channel and side slough marginal habitats were observed to be most vulnerable to dewatering
and/or freezing as a result of fluctuations in Susitna River discharge (Vining et al. 1985).
Juvenile salmon exhibit a range of life history patterns in the Susitna River. Chum and pink
salmon typically emigrate from riverine areas to the ocean soon after emerging from the gravel
or within the first several months (Table 8.5-2) (Jennings 1985). Most Chinook, coho, and
sockeye salmon utilize Susitna River nursery habitats for at least one year prior to emigrating to
marine areas (Table 8.5-2) (Jennings 1985). During the period of residence in the Susitna River,
salmon fry were observed to use a wide range of habitats during 1980s studies (Dugan et al.
1984). Salmon fry and juveniles were typically most abundant in off-channel areas, though
habitat utilization appeared to vary seasonally and by ontogenetic stage (Dugan et al. 1984;
Stratton 1986). The timing of salmon emigration to estuarine and marine areas typically occurs
over a long period in the spring and early summer in the Susitna River, from March through
early August (Table 8.5-2) (Jennings 1985; Roth and Stratton 1985; Roth et al. 1986).
For resident and non-salmonid fish, the timing and distribution of juvenile and adult fish,
location and periodicity of adult spawning, and descriptions of seasonal movements patterns
were described in association with fish distribution and abundance studies during 1981–1985
(see Fish and Aquatics, Section 9.0). Studies during the 1980s were conducted in the lower,
middle, and upper Susitna River and included rainbow trout, Arctic grayling, burbot, round
whitefish, humpback whitefish, longnose sucker, Bering cisco, and Dolly Varden.
8.5.2.9. Instream Flow Methods and Models
Instream flow studies conducted during the 1980s focused on the middle and lower Susitna River
downstream of Devils Canyon. Studies during the 1980s evaluated changes in fish habitat
relative to changes in mainstem Susitna River stream flow using hydraulic and/or habitat
modeling and habitat mapping techniques. Modeling and mapping efforts were performed during
1983 and 1984 at 20 sites in the lower Susitna River between RM 35 and RM 92 and at 36 sites
in the middle Susitna River between RM 101 and RM 148 (Table 8.5-3). Fish habitat availability
was modeled over a range of Susitna River discharges using the following habitat models: IFIM
HABTAT, Direct Input Habitat (DIHAB), and Resident Juvenile Habitat (RJHAB). The IFIM
HABTAT model was used in conjunction with Instream Flow Group (IFG) hydraulic models,
whereas no hydraulic modeling was completed in association with DIHAB or RJHAB models.
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Two-dimensional mapping was also used to quantify available habitat at tributary mouths in the
middle river and was done independently of IFG hydraulic modeling. Habitat model selection
was based on-site-specific channel and hydrologic characteristics, the desired resolution of
microhabitat simulation, and the field logistics associated with each method.
Instream flow sites during the 1980s were primarily located in side channel, side slough, and
upland slough habitats with relatively few sites in tributary mouths and mainstem channel
margins. The IFIM HABTAT model was used in conjunction with IFG hydraulic models at sites
characterized by steady or uniform flow conditions and rigid stream channels and where stream
flow was assumed to be the primary determinant of fish habitat quality (Trihey 1979; Hilliard et
al. 1985). In the middle and lower Susitna River, IFG models were applied in side channel and
slough habitats (Hilliard et al. 1985). The IFG and HABTAT models were used to model
changes in juvenile and adult fish habitats at 6 sites in the lower river in 1983 and at 15 sites in
the middle river during 1983 and 1984 (Vincent-Lang 1984b; Hilliard et al. 1985) (Table 8.5-3).
At each site, water depth and velocity data were measured at multiple cross-sections at multiple
Susitna River stream flows to model hydraulic conditions at the site over a range of flows.
Modeled stream flow data were used in conjunction with channel geometry and substrate data
from the site to model changes in usable fish habitat area over the modeled flow range. Examples
of IFG site locations in various side channel habitats in the Middle Susitna River are depicted in
Figure 8.5-6 and Figure 8.5-7.
The DIHAB model was created for areas where steady, gradually varied flow did not exist
(Hilliard et al. 1985). During the 1980s, DIHAB models were used at chum spawning sites
characterized by spatially variable hydraulic conditions or near zero water velocities; such
conditions were incompatible with IFG hydraulic models (Hilliard et al. 1985). The DIHAB
models were used to evaluate changes in adult chum spawning habitat at 14 sites located on
mainstem margins and side channel habitats in the middle river in 1984 (Table 8.5-3). In addition
to water depth and velocity and substrate data, the presence of upwelling was incorporated into
DIHAB models as a binary variable (i.e., present, not present). DIHAB models used hydraulic
and channel geometry data to estimate changes to habitat area over the range of measured stream
flows, but did not incorporate hydraulic models. An example DIHAB site location in side
channel habitat is shown in Figure 8.5-7.
The RJHAB habitat model was a simplified means of estimating changes in fish habitat without
using hydraulic models. RJHAB modeling was applied at 22 side channel, tributary mouth, side
slough, and upland slough sites in 1983 and 1984 in the middle and lower river (Table 8.5-3)
(Marshall et al. 1984; Quane et al. 1985; Suchanek et al. 1985). At each RJHAB site, multiple
cross-sections were established and divided into shoreline and mid-channel cells (Figure 8.5-8).
Depth, velocity, and instream and overhead cover data measured in shoreline and mid-channel
cells at a range of Susitna River stream flows were assumed to be representative of the usable
fish habitat at each cross-section and for the site (Marshall et al. 1984). An example of an
RJHAB site location in Whiskers Creek side slough is shown in Figure 8.5-7.
Habitat mapping was conducted at tributary mouths in the middle river in 1983 to characterize
changes in spawning habitat independent of hydraulic modeling. The two tributary mouth sites
measured in 1983 were considered to be representative of the 14 major tributary confluences in
the middle river (Table 8.5-3) (Sandone et al. 1984). At habitat mapping sites, depth, velocity,
and substrate habitat parameters were measured across multiple transects at four separate Susitna
River stream flows. These data were used to create two-dimensional parameter-specific maps
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delineating the area of suitable chum spawning habitat. The three separate parameter-specific
maps were overlaid to identify the composite area of habitat suitability that was available at each
measured flow level (Sandone et al. 1984).
The output provided by IFIM HABTAT, DIHAB, and RJHAB habitat models was generally
similar to that supplied by the habitat mapping method used at tributary mouths. Each method
characterized changes in fish habitat by relating the amounts of wetted surface area and area
usable for juvenile and adult fish to Susitna River discharge. The amount of wetted surface area
at modeling sites invariably increased with rising stream flows; however, the relationship
between the amount of habitat area suitable for juvenile and adult fish use was often not directly
correlated with Susitna River discharge. Suitable depth, velocity, substrate, and/or cover habitat
was defined for each life stage of anadromous and resident fish species in the form of HSC.
Species and life stage-specific HSC provided a basis for evaluating the amount of usable habitat
at observed and simulated stream flow levels for each habitat model.
Results from intensively studied modeling sites were extrapolated to non-modeled habitats
throughout the Susitna River based on characterization of aquatic habitats over a range of stream
flow levels and classification of habitats into discrete groups. In 1984, 172 specific areas of the
middle river, including modeled and non-modeled areas, were characterized in terms of the
hydrology, hydraulics, and channel morphology at the site using aerial photography recorded at
various stream flow levels and site-specific data (Aaserude et al. 1985; Klinger-Kingsley et al.
1985). Based on hydrological, hydraulic, and morphological site characteristics, specific areas
were stratified into 10 representative habitat groups, which served as the basis for extrapolation
of modeled results to non-modeled sites (Aaserude et al. 1985; Steward et al. 1985). The
relationship between usable fish habitat area to changes in Susitna River stream flow was
evaluated at the micro-habitat scale at individual modeling sites and these results were
summarized to create a composite habitat-discharge relationship for all habitats within the same
group (Aaserude et al. 1985; Steward et al. 1985). To address variability in structural habitat
characteristics (i.e., fish cover type, substrate size and embeddedness, channel geometry and
streamside vegetation) among individual areas within representative groups, structural habitat
indices were developed (Aaserude et al. 1985). Extrapolation of habitat availability results from
modeled sites to non-modeled sites with an adjustment for differences in structural habitat
(Aaserude et al. 1985).
8.5.2.10. Need for Additional Information
The 1980s reports and information serve as a valuable resource and reference point from which
to view conditions in the Susitna River as they existed in the early 1980s. The information also
provides details on fish species distribution and abundance and riverine processes as they were
operating at that time and includes distinct habitat-flow response relationships that were defined
for different habitat types and different locations. However, additional information needs to be
collected to provide a contemporary understanding of the baseline conditions existing in the
Susitna River, and among other things test hypotheses regarding the validity of the 1980s
habitat-flow response relationships. In addition, the configuration and proposed operations of the
Project are different from the previously proposed project and must be evaluated within the
context of the existing environmental setting. This includes consideration of potential load-
following effects on important aquatic and riparian habitats downstream of the proposed Watana
Dam site (including both the Middle River and Lower River segments, as appropriate). Potential
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effects of proposed Project operations on aquatic habitats and biota and potential benefits and
impacts of alternative operational scenarios have not been quantitatively analyzed. The aquatic
habitat-specific models will provide an integrated assessment of the effects of Project operations
on biological resources and riverine processes. These models will provide an analytical
framework for assessing alternative operational scenarios and quantitative metrics that will
provide the basis for the environmental assessment and aid in comparing alternatives that may
lead to refinements in proposed Project operations.
8.5.3. Study Area
During the 1980s studies, the Susitna River was characterized into three segments extending
above and below the two proposed dam sites. After researching potential Project configurations,
AEA is proposing a single dam configuration at the Watana Dam site at RM 184. The proposed
study characterizes the Susitna River as three segments (Figure 8.5-9). The Upper River Segment
represents that portion of the watershed above the Watana Dam site at RM 184, the Middle River
Segment extends from RM 184 downstream to the Three Rivers Confluence at RM 98.5, and the
Lower River Segment extends from the Three Rivers Confluence to Cook Inlet (RM 0). Potential
Project effects to the Upper River Segment above the Watana Dam site are addressed in Section
9.0, Fish and Aquatics; Section 10.0, Wildlife; Section 11.0, Botanical; and other studies.
Potential Project effects to the Upper River Segment will not be addressed in the IFS (see
Section 8.5). The study area of the IFS includes the two lower segments of the river: the Middle
River Segment and the Lower River Segment.
The Middle River Segment encompasses approximately 85 miles between the proposed Watana
Dam site (at RM 184) and the Three Rivers Confluence, located at RM 98.5. The river flows
from Watana Canyon into Devils Canyon, the narrowest and steepest gradient reach on the
Susitna River. In Devils Canyon, constriction creates extreme hydraulic conditions including
deep plunge pools, drops, and high velocities. The Devils Canyon rapids appear to present a
partial barrier to the migration of anadromous fish, hindering upstream passage at some flow
conditions; only a few adult Chinook salmon have been observed upstream of Devils Canyon.
Downstream of Devils Canyon, the Middle Susitna River widens but remains essentially a single
channel with stable islands, occasional side channels, and sloughs.
The Lower River Segment consists of an approximate 98-mile section between the Three Rivers
Confluence and Cook Inlet (RM 0). An abrupt change in channel form occurs where the Chulitna
River joins the Susitna River near the town of Talkeetna. The Chulitna River drains a smaller
area than the Middle River Segment at the confluence, but drains higher elevations (including
Denali and Mount Foraker) and many glaciers. The annual flow of the Chulitna River is
approximately the same as the Susitna River at the confluence, though the Chulitna contributes
much more sediment than the Susitna River. For several miles downstream of the Three Rivers
Confluence, the Susitna River becomes braided, characterized by unstable, shifting gravel bars
and shallow subchannels. For the remainder of its course to Cook Inlet, the Susitna River
alternates between single channel, braided, and meandering plan forms with multiple side
channels and sloughs. Major tributaries drain the western Talkeetna Mountains (the Talkeetna
River, Montana Creek, Willow Creek, Kashwitna River), the Susitna lowlands (Deshka River),
and the Alaska Range (Yentna River). The Yentna River is the largest tributary in the Lower
River Segment, supplying about 40 percent of the mean annual flow at the mouth.
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Although both Middle and Lower River segments are under consideration as part of this IFS, the
majority of detailed study elements described in this RSP are concentrated within the Middle
River Segment. This is because Project operations related to load-following and variable flow
regulation will likely have the greatest potential effects on this segment of the river. These
effects tend to attenuate in a downstream direction as channel morphologies change, and flows
change due to tributary inflow and flow accretion. The diversity of habitat types and the
information from previous and current studies that indicate substantial fish use of a number of
slough and side channel complexes within this segment, also support the need to develop a
strong understanding of habitat–flow response relationships in this segment.
Determining how far downstream Project operational effects will extend will depend in part on
the results of the Open-water Flow Routing Model (see Section 8.5.4.3), which is scheduled to
be completed in Q1 2013 as well as results of the operations model (see Section 8.5.4.3.2). The
results of the Open-water Flow Routing Model completed in Q1 2013 will be used to determine
whether and the extent to which Project operations related to load-following as well as seasonal
flow changes occur within a section of the Lower River Segment that includes all of Geomorphic
Reach LR-1 and a portion of LR-2 (down to RM 75). Thus, an initial assessment of the
downstream extent of Project effects will be developed in Q1 2013 with review and input of the
TWG. This assessment will include a review of information developed during the 1980s studies
and study efforts initiated in 2012, such as sediment transport (see Section 6.5), habitat mapping
(see Sections 6.5 and 9.9), operations modeling (see Section 8.5.4.2.2), and the Mainstem Open-
water Flow Routing Model (see Section 8.5.4.3). The assessment and the following criteria will
be used to evaluate the need to extend studies into the Lower River Segment and if studies are
needed, will identify which geomorphic reaches require instream flow analysis in 2013. The
criteria include: 1) Magnitude of daily stage change due to load-following operations relative to
the range of variability for a given location and time under existing conditions (i.e., unregulated
flows); 2) Magnitude of monthly and seasonal stage change under Project operations relative to
the range of variability under unregulated flow conditions; 3) Changes in surface area (as
estimated from relationships derived from LiDAR and comparative evaluations of habitat unit
area depicted in aerial digital imagery under different flow conditions) due to Project operations;
4) Anticipated changes in flow and stage to Lower River off-channel habitats; 5) Anticipated
Project effects resulting from changes in flow, stage and surface area on habitat use and function,
and fish distribution (based on historical and current information concerning fish distribution and
use) by geomorphic reaches in the Lower River Segment; and 6) Initial assessment of potential
changes in channel morphology of the Lower River (see Section 6.5.4.6) based on Project-related
changes to hydrology and sediment supply in the Lower River. Results of the 2013 studies will
then be used to determine the extent to which Lower River Segment studies should be adjusted in
2014.
8.5.4. Study Methods
Evaluation of potential Project effects to Middle and Lower river habitats will consist of the
following components (these components will be refined based on TWG review and input):
• IFS Analytical Framework (see Section 8.5.4.1)
• River Stratification and Study Area Selection (see Section 8.5.4.2)
• Hydraulic Routing (see Section 8.5.4.3)
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• Hydrologic Data Analysis (see Section 8.5.4.4)
• Habitat Suitability Criteria Development (see Section 8.5.4.5)
• Habitat-Specific Model Development (see Section 8.5.4.6)
• Temporal and Spatial Habitat Analyses (see Section 8.5.4.7)
• Instream Flow Study Integration (see Section 8.5.4.8)
Details concerning each of these components including proposed methodologies and resulting
work products are provided below.
8.5.4.1. IFS Analytical Framework
The Instream Flow Study is designed to characterize the existing, unregulated flow regime and
the relationship of instream flow to riparian and aquatic habitats under alternative operational
scenarios. The instream flow framework is designed to integrate riverine processes, including
geomorphology, ice processes, water quality, and groundwater-surface water interactions to
quantify changes in indicators used to measure the integrity of aquatic resources. Figure 8.5-10
depicts the analytical framework of the IFS that will be used to evaluate unregulated flows and
alternative operational scenarios under average, wet, dry, warm, and cold hydrological
conditions. The overall framework includes analytical steps that are consistent with those
described in the Instream Flow Incremental Methodology (IFIM) (Stalnaker et al. 1995), which
will be used as a guide for completing the instream flow evaluation for the Project.
The proposed Project will alter stream flow and sediment and large woody debris (LWD)
transport downstream of the proposed dam site. These stressors will affect channel morphology
and the quantity, quality, and timing of downstream habitats. The IFS framework will be used to
assess Project effects on downstream habitats under existing channel conditions, and will also
provide for the evaluation of alternative operational scenarios under estimated future channel
conditions. Changes in flow, ice processes, and sediment and LWD transport may cause channel
degradation, avulsion, and other channel changes and may contribute to changes in the
distribution and abundance of various habitat units (see page 2 of Figure 8.5-10). Integration of
the Geomorphology Study (see Section 6.0) and other riverine process studies will allow future
channel change to be evaluated at future time steps within the expected term of the license.
These time steps will be determined in consultation with the TWG after initial geomorphology
investigations provide insight into the magnitude and rate of downstream channel change.
Figure 8.5-10 depicts the analytical framework of the IFS commencing with the Reservoir
Operations Model (ROM) that will be used to generate Project flow releases under alternative
operational scenarios. The ROM (see Section 8.5.4.3.2) will provide input data to the mainstem
open-water flow routing model (see Section 8.5.4.3.1) and Ice Processes Model (see Section 7.6)
that will be used to predict hourly flow and water surface elevations at multiple downstream
locations, taking into account accretion and flow attenuation. Coincident with the development
of the open-water flow routing model, a series of biological and riverine process studies will be
completed to supplement the information collected in the 1980s, as necessary, to assess the
temporal and spatial relationships between riverine and biological functions. These analyses will
result in development of a series of flow-sensitive models that will quantify Project effects on
indicators for each aquatic and riparian resource.
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Resource and process effects will be location- and habitat-specific (e.g., responses are expected
to be different in off-channel sloughs versus main channel versus split channel versus tributary
delta versus riparian habitats), but there will also be a cumulative analysis that translates effects
throughout the Susitna River. The IFS framework provides for the analysis of indicators that
estimate flow-habitat response patterns for different species and life stages of fish and other
aquatic biota. These models represent core tools that will be used for assessing changes in
aquatic habitats under alternative operational scenarios. Additionally, a fish passage analysis (see
Section 9.12) will be used to develop the relationship between main channel flow and
connectivity with side channel and off-channel areas. Data collection and modeling for the Fish
Passage Study will be coordinated with the Instream Flow, Fish and Aquatics (see Section 9.0),
and Geomorphology (see Section 6.0) studies to ensure identification of potential fish passage
barriers and hydraulic control points (see Figure 8.5-1).
Alternative operational scenarios will likely affect habitats and riverine processes on both a
spatial and temporal scale. The habitat and process models will therefore be spatially discrete
(e.g., by Focus Area, reach, and segment) and yet able to be integrated to allow for a holistic
evaluation by alternative operational scenario. This will allow for an Integrated Resource
Analysis (IRA) of multiple resources for each operational scenario and provides feedback,
leading to potential modifications of alternative operational scenarios (see Section 8.5.4.8).
The IFS framework (Figure 8.5-10) represents a measurement-oriented approach to assessing the
relationship of hydrologic and geomorphic variables to the biological and ecological resources of
concern. Stressors associated with Project effects include changes in the volume, timing, and
quality of instream flow, and changes in ice processes and sediment and large woody debris
transport. The effects of these stressors on resources of concern will be evaluated using
indicators that measure changes in habitat suitability, quality, and accessibility. Reference
conditions establish the range of variation for each indicator and are defined by analysis of
unregulated flows under average, wet, and dry hydrologic conditions and warm and cold Pacific
decadal oscillation phases. Project effects under alternative operational scenarios are defined as
departures from the reference conditions. The IFS framework provides the tools to identify
operational scenarios that balance resource interests and quantify any loss of aquatic resources
and their habitats that result from Project operations.
As part of the analytical framework, an Instream Flow Study–Technical Workgroup (IFS-TWG)
has been formed consisting of technical representatives from the TWG. The IFS-TWG will
provide input into specific study design elements pertaining to the IFS including selection of
study areas, selection of methods and models, selection of HSC criteria, review and evaluation of
hydrology and habitat-flow modeling results, and review of Project operations/habitat modeling
results. For example, a TWG meeting occurred on September 14, 2012, and focused on the study
area selection process. Additional TWG meetings are expected to occur on a regular basis
through development of the License Application.
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8.5.4.2. River Stratification and Study Area Selection
8.5.4.2.1. Proposed Methodology
8.5.4.2.1.1. River Stratification
The fundamental question in stratifying the river system for the 2012–2014 studies is as follows:
How many levels of stratification are necessary for each study focus before study areas should be
selected? Effects to physical processes and aquatic resources will be resource type-, location-,
and habitat-specific. For example, at the site scale level, responses of fish habitat to changes in
flow are expected to be different in side sloughs versus mainstem versus side channel versus
tributary delta versus riparian habitats. At a broader scale, e.g., segment, it is plausible that
effects to the same mainstem habitat types will differ depending on location in the river network,
not only at the Project footprint scale listed above, but also between geomorphic reaches. In
addition, there will be a cumulative effect running down the length of the Susitna River below
the dam. Different Project operations will likely affect different habitats and processes
differently, both spatially and temporally. The habitat and process models will therefore need to
be spatially discrete, at potentially the site/area level, mainstem habitat type level, and segment
levels, and yet able to be integrated to allow for a holistic evaluation of each alternative
operational scenario.
As noted in Section 8.5.3, the study area consists of two segments of the river:
• Middle River Segment – Susitna River from Watana Dam site to confluence of Chulitna
and Talkeetna rivers (Three Rivers Confluence) (RM 184 to RM 98.5)
• Lower River Segment – Susitna River extending below Talkeetna River to mouth (RM
98.5 to RM 0)
The Middle River Segment represents the section of river below the Project dam that is projected
to experience the greatest effects of flow regulation caused by Project operations. Within this
reach, the river flows from Watana Canyon into Devils Canyon, the narrowest and steepest
gradient reach on the Susitna River. The Devils Canyon constriction creates extreme hydraulic
conditions including deep plunge pools, drops, and high velocities. Downstream of Devils
Canyon, the Susitna River widens but remains essentially a single main channel with stable
islands, numerous side channels, and sloughs.
The Lower River Segment receives inflow from three other large river systems. An abrupt, large-
scale change in channel form occurs where the Chulitna and Talkeetna rivers join the Susitna
River near the town of Talkeetna. The annual flow of the Chulitna River is approximately the
same as the Susitna River at the confluence, though the Chulitna contributes much more
sediment than the Susitna. The Talkeetna River also supplies substantial flow rates and sediment
volumes. Farther downriver, the Susitna River becomes notably more braided, characterized by
unstable, shifting gravel bars and shallow subchannels. The Yentna River is a large tributary to
the Lower Susitna River and supplies about 40 percent of the mean annual flow at the mouth.
Geomorphic analysis of both the Middle River and Lower River segments confirmed the distinct
variations in geomorphic attributes (e.g., channel gradient, confinement, channel planform types,
and others) (see Section 6.5). That analysis resulted in a further refinement of the classification
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into eight geomorphic reaches in the Middle River Segment (Figure 8.5-11) and six geomorphic
reaches in the Lower River Segment (Figure 8.5-12).
Further refinements to the stratification system being applied to the Susitna River have been
made since the PSP as a result of discussions during the August, September, and October 2012
TWG meetings and two interdisciplinary team meetings that were focused on study area
selection and habitat mapping. Although the major divisions associated with the Middle and
Lower segments have been retained, these are now incorporated into a more refined hierarchical
stratification system that scales from relatively broad to more narrowly defined categories as
follows:
Segment → Geomorphic Reach → Mainstem Habitat Type →
Main Channel Mesohabitat Types → Edge Habitat Types
The highest level category is termed Segment and refers to the Middle River Segment and the
Lower River Segment. The Geomorphic Reach level is next and consists of the eight categories
(MR-1 through MR-8) for the Middle River Segment and six categories (LR-1 through LR-4) for
the Lower River Segment (see Section 6.5.4.1.2.2 and Table 8.5-4). The geomorphic reach
breaks were based in part on the following five factors: 1) Planform type (single channel,
island/side channel, braided); 2) Confinement (approximate extent of floodplain, off-channel
features); 3) Gradient; 4) Bed material / geology; and 5) Major river confluences. This level is
followed by Mainstem Habitat Types, which capture the same general categories applied
during the 1980s studies but includes additional sub-categories to provide a more refined
delineation of habitat features (Table 8.5-5). Major categories and sub-categories under this level
include Main Channel Habitats consisting of Main Channel, Split Main Channel, Braided Main
Channel, Side Channel, and Off-channel Habitats that include Side Slough, Upland Slough,
Backwater and Beaver Complexes; and Tributary Habitats that consist of the segment of the
tributary influenced by mainstem flow. The next level in the hierarchy is Main Channel and
Tributary Mesohabitats, which classifies habitats into categories of Cascades, Riffle, Pool,
Run, and Glide. The mesohabitat level of classification is currently limited to the main channel
and tributary mouths for which the ability to delineate these features is possible via aerial
imagery and videography. Mesohabitat mapping in side channel and slough habitat types will
require ground surveys. The last level in the classification is Edge Habitat and is intended to
provide an estimate of the length of shoreline in contact with water within each habitat unit. The
amount of edge habitat within a given habitat unit will provide an index of habitat complexity,
i.e., more complex areas that consist of islands, side channels, etc. will contain more edge habitat
than uniform, single channel areas. These stratification levels are described in Table 8.5-5 with
further information provided in both the Geomorphic Study Plan (see Section 6.5.4.1.2.2) and the
Habitat Characterization Study Plan (see Section 9.9).
The fundamental goal of stratification is to define segments/reaches with effectively similar
characteristics where, ideally, repeated replicate sampling would result in parameter estimates
with similar statistical distributions. The stratification/classification system described above is
designed to provide sufficient partitioning of sources of variation that can be evaluated through
focused study efforts that target each of the habitat types, and from which inferences concerning
habitat–flow responses in unmeasured sites can be drawn.
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8.5.4.2.1.2. Selection of Study Areas/Study Sites
The selection of study areas or study sites represents an important aspect of instream flow study
development inasmuch as the sites or areas studied are those that will ultimately be used for
evaluating Project effects. It is therefore fundamentally important that the logic and rationale for
the selection of such areas be clearly articulated, understood, and agreed to by agencies and
licensing participants.
In general (as noted by Bovee 1982), there are three characteristic approaches to instream flow
studies that pertain to site selection that have been considered for application in the Project.
These are described below.
Representative Sites – where professional judgment or numerically and/or qualitatively derived
criteria are relied on to select one or more sites/areas that are considered representative of the
stratum or larger river. Representative sites typically contain all habitat types of importance. In
general, the representative site approach can be applied fairly readily to simple, single thread
channel reaches, where the attributes that are measured are extrapolated linearly based on stream
length or area. In this case, the goal of stratification will be to identify river segments that are
relatively homogenous in terms of mesohabitat mixes, and the methods used for stratification
tend to be classification-based using logical or heuristic rules. This approach typically requires
completing some form of mapping up front, and using the results to select sites that encompass
the range of habitat conditions desired. The number of replicate sites can be identified via power
analysis, although this ideally requires a priori knowledge of the statistical variance associated
with a measurable quantity. In the absence of such knowledge, a distribution may be assumed
(e.g., standard normal, Student’s t statistic, other).
- Applicability to the Susitna–Watana Project: Yes, but will require results of more
detailed habitat mapping that will be completed in Q1 2013 to determine
representativeness of study areas.
Critical Sites – where available knowledge indicates that either (i) a sizable fraction of the target
fish population relies on a specific location, (ii) a particular habitat type(s) is (are) highly
important biologically, or (iii) where a particular habitat type is well known to be influenced by
flow changes in a characteristic way, and the decision is made to focus on those areas. For
example, in the case of the Susitna River, historical fish studies repeatedly showed the
importance of certain side slough, upland slough, and side channel areas for spawning and
juvenile rearing. Critical sites or areas are typically selected assuming that project effects to other
areas are secondary in terms of implications to fish population structure, health, and size. This
assumption can only really be tested if other sites are identified that are similar looking but were
not deemed critical, and sampling is performed on those sites as well to confirm the critical
nature of the sites that were identified as such.
- Applicability to the Susitna–Watana Project: Yes, especially with respect to selection of
side channel/side slough/upland slough complexes that have been shown to be influenced
by main channel flows and that are biologically important.
Randomly Located Sites – where sites, areas, or measurement locations are selected randomly
from each defined stratum or habitat type, and replicate sites or cross-sections are sampled to
estimate variance (e.g., Williams, 1996; Payne et al. 2004). Site selection based on random
sampling tends to involve statistical multivariate grouping or stratification approaches, such as
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cluster analysis or ordination techniques. In this case, initial groundwork is necessary to identify
relevant variables suitable for grouping, and then the data need to be collected or derived to
describe those variables spatially. The approach is the least subject to potential for bias, because
it relies on distinct rules and algorithms. However, this approach becomes increasingly difficult
to apply in site selection when the sites become more complex, such as is the case on the Susitna
River. In addition, the number of sites will be contingent on the variability within the universal
data set: the greater the number of clusters, the greater the potential number of sites. Strict
random sampling is therefore not likely applicable for evaluating off-channel habitats and
sloughs where the morphology of multiple channels varies substantially and in complex ways
within and across sites.
- Applicability to the Susitna–Watana Project: Yes, but more appropriate with respect to
main channel mesohabitat sampling (i.e., riffle, run, glide, pool) or selection of mainstem
habitat types for HSC sampling (see Section 8.5.4.5).
These approaches were reviewed at a recent TWG meeting (September 11, 2012) and the
proposed process and criteria used for the selection of study areas/sites presented.
Focus Areas
During the September 11, 2012, TWG meeting, the concept of “intensive study areas” was
introduced and discussed. Such areas represent specific sections of the river that will be
investigated across resource disciplines that will provide for an overall understanding of
interrelationships of river flow dynamics on the physical, chemical, and biological factors that
influence fish habitat.
The concept represents a combination of all three of the methods described above, inasmuch as
(1) the areas would contain habitat types representative of other areas; (2) the areas would
include certain habitat types repeatedly used by fish and therefore can be considered “critical
areas”; and (3) sampling of certain habitat features or mesohabitat types within the areas would
be best approached via random sampling.
A total of 10 intensive study areas (hereafter referred to as Focus Areas [Focus Areas]), were
presented and discussed with the TWG and are proposed in this RSP for detailed study within the
Middle River Segment. Locations of the Focus Areas are depicted in Figure 8.5-11. The Focus
Areas are intended to serve as specific geographic areas of the river that will be the subject of
intensive investigation by multiple resource disciplines including Fish and Aquatics Instream
Flow, Riparian Instream Flow (see Section 8.6), Groundwater (see Section 7.5), Geomorphology
(see Section 6.0), Ice Processes (see Section 7.6), and Water Quality (see Section 5.0). The
Focus Areas were selected during an inter-disciplinary resource meeting that involved a
systematic review of aerial imagery within each of the Geomorphic Reaches (MR-1 through
MR-8) for the entire Middle Segment of the river. Focus Areas were selected within Geomorphic
Reach MR-1 (one Focus Area), Geomorphic Reach MR-2 (two Focus Areas), Geomorphic
Reach MR-5 (one Focus Area), Geomorphic Reach MR-6 (four Focus Areas), Geomorphic
Reach MR-7 (one Focus Area), and Geomorphic Reach MR-8 (one Focus Area). Focus Areas
were not selected for Geomorphic Reaches MR-3 or MR-4 due to safety considerations related to
Devils Canyon. MR-3 is a relatively short (3.5-mile) steep (17 ft/mi.) reach located just upstream
from the Devils Canyon reach. The reach is confined within a relatively narrow canyon.
Although flow routing transects were initially considered for this reach, any attempt to sample it
was abandoned once field teams were on the ground and realized it could not be safely
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measured. Of particular concern were the swift currents within the reach and the lack of any
margin of safety for recovering someone before they would be swept into Devils Canyon. MR-3
consists primarily of single-thread main channel habitat with two areas with split-main channel
islands. No major tributaries enter the reach and it is likely that any anadromous salmonids
(Chinook) that make it through Devils Canyon simply pass through MR-3. The main channel
portions of the reach are similar to those in MR-2 and MR-1. The Devils Canyon Reach (MR-4)
is non-navigable and cannot, under any flow condition, be safely surveyed.
The areas selected were those deemed representative of the major features in the geomorphic
reach and included mainstem habitat types of known biological significance (i.e., where fish
have been observed based on previous and/or contemporary studies), as well as some locations
(e.g., Slough 17) where previous sampling revealed few/no fish. The Focus Areas include
representative side channels, side sloughs, upland sloughs, and tributary mouths.
Three of the Focus Areas in Geomorphic Reach MR-6 and one in Geomorphic Reach MR-8
contain specific habitat types that were found, during the 1980s studies, to be consistently used
by salmon for spawning and/or rearing. These areas included Slough 21, Slough 11, and Skull
Creek in Geomorphic Reach MR-6 and Whiskers Slough in Geomorphic Reach MR-8. Overall,
92 percent of the sockeye, 70 percent of the chum, and 44 percent of the slough-spawning pink
salmon were found in just these four sloughs. By definition, these areas represent “critical areas”
and were included in the Focus Areas to allow some comparisons with the 1980s data. Although
other portions of these same Focus Areas were not studied during the 1980s, these areas will be
studied as part of the RSP. The upper three Focus Areas (one in Geomorphic Reach MR-1 and
two in Geomorphic Reach MR-2) were selected based on their representativeness of the
respective geomorphic reaches and the inclusion of a mix of side channel and slough habitat
types. However, there is no existing fish information on these areas because they were not
sampled in the 1980s. Nominally, the Focus Areas range in length from 0.5 mile to 1.9 miles.
Details of each of the Focus Areas including their identification number, common name,
description, geomorphic reach assignment, location (RM), length, habitat types included in the
Focus Area, fish use and types of instream flow studies conducted in the 1980s, and the rationale
for selection, are presented in Table 8.5-6; schematic photos of each of the areas are depicted in
Figure 8.5-13 through Figure 8.5-22. A similar process will be applied to the Lower Segment of
the river in December 2012 but will focus on the upper portions of that segment that will be most
susceptible to flow modification.
These 10 areas have been selected for planning purposes but will be evaluated further for their
representativeness of other areas based on results of habitat mapping that will be completed at
the end of 2012. The results of this evaluation will be discussed with the TWG and refinements
in Focus Area selection made prior to commencement of the 2013 studies. The initial set of study
areas will be developed in consultation with the TWG by February/March of 2013 to enable
detailed field studies to occur. The data and information collected in 2013 from this study and
other related investigations (e.g., fish distribution – Section 9.5; radio-tagging – Section 9.7;
habitat characterization – Section 9.9; and others) will be reviewed, and necessary refinements to
existing sites made or new sites added to the studies completed in 2014. This adaptive
management approach to site selection will allow for shifts in study focus to other areas, should
results of 2013 studies reveal their biological importance and sensitivity to flow modifications.
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It should be noted that the criteria applied in the selection of the Focus Areas incorporated (or
will incorporate) elements from all three of the above mentioned selection methods and
considered the following:
• All major habitat types (main channel, side channel, side slough, upland slough,
tributary delta) will be sampled within each geomorphic reach.
• At least one (and up to three) Focus Area(s) per geomorphic reach (excepting
geomorphic reaches associated with Devils Canyon – MR-3 and MR-4) will be
studied that is/are representative of other areas.
• A replicate sampling strategy will be used for measuring habitat types within each
Focus Area, which may include a random selection process of mesohabitat types.
• Areas that are known (based on existing and contemporary data) to be biologically
important for salmon spawning/rearing in mainstem and off-channel habitats will be
sampled (i.e., critical areas).
• Areas for which little or no fish use has been documented or for which information on
fish use is lacking will also be sampled.
Sites Outside of the Focus Areas
In addition to the identified Focus Areas, a total of 80 cross-sectional transects in the Middle
River Segment and 8 transects in the Lower River Segment have been established and flow data
collected to support development of the open-water flow routing model (see Section 8.5.4.3 and
Table 8.5-7). These transects were primarily located across single thread sections of the river;
however, some do extend across more complex sections. In most cases, two to three sets of flow
measurements have been made at each transect. The resulting data sets can be used, at a
minimum, for evaluating velocity-depth distributions across the channel that can be related to
biologically relevant criteria associated with various life stage requirements (e.g., spawning,
adult holding, juvenile rearing). In many cases (pending review of the cross-sectional data), it
should be possible to develop actual habitat-flow relationships following a 1-D PHABSIM type
analysis (see Section 8.5.4.6). The cross-sectional transects represent an important dataset that
can be used to characterize habitat-flow response characteristics of the main channel of the
Susitna River. These types of data were never collected during the 1980s studies and no main
channel habitat-flow relationships were developed. Importantly, once the main channel habitat
mapping is completed (see Section 9.9), the transect locations will be assigned to specific
mesohabitat types (e.g., riffle, run, glide, pool) that could be randomly selected for analysis.
These additional transects may also be useful for extrapolating results/relationships from
measured to unmeasured sites (see Section 8.5.4.7). Supplemental main channel transects will be
established as needed to more fully characterize main channel habitats, either as part of the Focus
Area analysis or at separate locations associated with specific mesohabitat types. The need for
and exact number of the supplemental transects will be determined based on results of the habitat
mapping.
8.5.4.2.2. Work Products
A detailed description of the rationale and methods used in the selection of study areas and study
sites will be provided in the Instream Flow Study Report. Information provided will include the
following:
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• Maps and orthophotos depicting geomorphic reach breaks and highlighting locations of
Focus Areas as well as locations of all Open Water Flow Routing Model cross-sections.
• Aerial photos of each of the Focus Areas depicting upper and lower boundaries and
highlighting the different habitat types contained within each Focus Area.
• Results of mainstem habitat mapping presented in both tabular and graphical formats that
present the relative proportions of habitat features contained in the Focus Areas within a
given geomorphic reach relative to those features contained in the entire geomorphic
reach.
• Ground-based, geo-referenced, and labeled digital images of each of the Focus Areas to
include specific habitat types and features within each Focus Area.
• Detailed narrative describing the study area selection process leading to the selection of
Focus Areas. This will include stratification procedures, site/area criteria development
and application, as well as results of any statistical analysis including both perspective
and retrospective power analysis used for determining sample size.
8.5.4.3. Hydraulic Routing and Operations Modeling
Project operations will likely store water during the snowmelt season (May through August) and
release it during the winter (October through April; AEA 2011). This would alter the seasonal
hydrology in the Susitna River downstream from the dam, resulting in lower flows from May
through August and higher flows from October through April. In addition to these seasonal
changes, the Project may be operated in a load-following mode. Daily load-following operations
will typically release higher volumes of water during peak-load hours, and lower volumes of
water during off-peak hours. Flow fluctuations that originate at the powerhouse will travel
downstream and attenuate, or dampen, as they travel downstream. The waves created by load-
following operations will affect the aquatic habitat of the Susitna River downstream from the
powerhouse, especially along the margins of the river alternately wetted and dewatered (the
varial zone).
8.5.4.3.1. Proposed Methodology
To analyze the impacts of alternative Project operational scenarios on habitats downstream of the
Watana Dam site, an open-water flow routing model will be used to translate the effects of
changes in flow associated with Project operations to downstream Susitna River locations; the
open-water flow routing model will be extended downstream until the flow fluctuations are
within the range of the without-Project natural variation and conditions.
Steady-state flow models assume that velocity or flow at a given location remains constant.
Unsteady flow models are used when flows change rapidly and the consideration of time is an
additional variable. One-dimensional unsteady flow hydraulic models are commonly used to
route flow and stage fluctuations through rivers and reservoirs. Examples of public-domain
computer models used to perform these types of processes include FEQ (USGS 1997),
FLDWAV (U.S. National Weather Service 1998), UNET (U.S. Army Corps of Engineers 2001),
and HEC-RAS (U.S. Army Corps of Engineers 2010a, 2010b, and 2010c). The HEC-RAS model
has proven to be very robust under mixed flow conditions (subcritical and supercritical), as will
be expected in the Susitna River. The HEC-RAS model also has the capability of automatically
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varying Manning’s “n” with stage through the use of the equivalent roughness option. Another
feature of HEC-RAS is the capability of varying Manning’s “n” on a seasonal basis. The robust
performance and flexibility of HEC-RAS make this model an appropriate choice for routing
stage fluctuations downstream from the proposed Project dam under open-water conditions (i.e.,
summer, ice-free). Under winter ice-covered conditions, the CRISSP1D (Comprehensive River
Ice Simulation System Project) model or the River1D model could be used to route unsteady
flows downstream through the Susitna River. CRISSP1D is a one-dimensional unsteady flow
model that can be used to analyze water temperature, thermal ice transport processes, and ice
cover break-up (Chen et al. 2006). Likewise, River1D, developed by the University of Alberta, is
an alternate one-dimensional unsteady flow model that could be used to analyze ice processes.
The seasonal timing of the transition from the HEC-RAS model to the Ice Processes Model and
vice versa will vary from year-to-year and will depend on seasonal climate conditions. The Ice
Processes Model and how it will be used to model flow in the Susitna River is described in
Section 7.6. This section, 8.5.4.3, concentrates on how the HEC-RAS model will be developed
and calibrated for the mainstem open-water period.
The foundation of the IFS analyses rests with the development of the Susitna River Mainstem
Flow Routing Models (MFRM) (HEC-RAS, Ice Processes Model) that will provide hourly flow
and water surface elevation data at numerous locations longitudinally distributed throughout the
length of the river extending from RM 184 downstream to RM 75 (about 23 miles downstream
from the confluence with the Chulitna River). Two different flow routing models will be
developed: an open-water model (HEC-RAS) and a winter model to route flows under ice-
covered conditions. The HEC-RAS routing model will initially be developed based on river
cross-sections and on gaging stations on the Susitna River that were established and measured in
2012 as part of the IFS program. A list of the river cross-sections that were surveyed is provided
in Table 8.5-7. A total of 88 cross-sections were surveyed in 2012 (16 between the proposed dam
site and Devils Canyon, 59 between Devils Canyon and the Three Rivers Confluence, and 13
downstream from the Three Rivers Confluence). The table shows the preliminary river mile of
each section, the date of measurement, the measured discharge, and reference discharge from the
USGS Susitna River at Gold Creek. Both sets of discharge values are currently preliminary and
in the review process. The cross-sections were measured during three field trips intended to
capture high-flow (28,000 cfs), medium-flow (16,000 cfs), and low-flow (8,000 cfs) conditions
corresponding to the USGS gage station at Gold Creek (No 15292000). The first two trips were
successful at capturing high-flow and medium-flow conditions during late June-early July and
August, respectively. However, the low-flow trip that began on September 14 was interrupted by
a 25-year flood event that required evacuation of the field team on September 20. Work resumed
on September 29, but was suspended on October 6 when a second late fall storm resulted in
unseasonably high flows. A final attempt commenced on October 15, but abundant river ice and
slush pans precluded accurate flow measurements.
At each river cross-section, ground surface and water surface elevations were surveyed using
Real Time Kinematic (RTK) GPS instrumentation. River bathymetry and flow velocities were
measured using an Acoustic Doppler Current Profiler (ADCP) system consisting of a Sontek M9
equipped with RTK GPS positioning. Water surface slopes were also measured at each section.
Photographs of each section were also taken and vegetation descriptions were also developed.
Examples of some of the river cross-sections that were surveyed in 2012 are shown in Figure
8.5-23. At RM 170 (between the proposed dam site and Devils Canyon), the channel had a single
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thread with a width of about 600 feet. At RM 75 (downstream from the Three Rivers
Confluence), the channel was multi-threaded with a total width of about 1 mile.
At each river cross-section, a minimum of four passes across the channel width were used to
measure the flow in accordance with U.S. Geological Survey (USGS) standards. An example of
the output from one of the passes is shown in Figure 8.5-24 for RM 170 on June 21, 2012. While
maximum velocities in the 10 to 15 feet per second (fps) range were recorded, the cross-sectional
average velocity was 8.0 fps.
A total of 13 gaging stations were established on the Susitna River in 2012 at the locations listed
in Table 8.5-8. These stations were set up to measure stage in real time every 15 minutes. The
stations will be maintained in 2013–2014. Data recorded at these stations will be used to
calibrate flow pulse arrival time in the open-water flow routing model, based on measured
diurnal glacial melt pulses and rainstorm-generated flood peaks.
The hourly flow records from USGS gaging stations on the Susitna River will also be utilized to
help develop the HEC-RAS routing model. Depending on the initial results of the flow routing
models, it may be necessary to add additional transects to improve the performance of the
models between RM 75 and RM 184, and to possibly extend the models farther downstream past
RM 75. Additional transects between RM 75 and RM 184 will be added if calibration of certain
sections of the river proves problematic without supplementing the HEC-RAS model with
additional intermediate cross-sections.
Results of the draft open-water flow routing model will be available in Q1 2013. These initial
results will be used to assess the magnitude, timing, and frequency of hourly flow and stage
changes associated with proposed load-following operations during ice-free periods. Project
operations will likely include storing water during the snowmelt season (May through August)
and releasing it during the winter (October through April) (AEA 2011). This would reduce flows
downstream of the dam site from May through August and increase flows October through April.
During Q1 2013, results of the draft open-water flow routing model will also be used to evaluate
downstream changes in flow and stage associated with reduced Project flow releases during the
open-water portions of the reservoir refill period. Because the results of the Ice Processes Model
will not be available prior to the start of the 2013 summer field season, the downstream extent of
Project effects on flow and stage during the winter will be assessed by routing winter flow
releases identified by the operations model (see Section 8.5.4.3.2) downstream using the open-
water flow routing model. Although stage and flow projections during the winter will not be
robust, they will provide sufficient information on downstream flow and stage effects to support
early 2013 decisions regarding the need to extend resource studies into the Lower River
Segment. Should extension of an open-water flow routing model downstream of RM 75 be
needed to address data needs of riverine process and habitat modeling studies, the additional
channel and hydraulic data can be collected in Q3 2013.
During the development and calibration of the HEC-RAS model, the drainage areas of ungaged
tributaries will be quantified and used to help estimate accretion flows to the Susitna River
between locations where flows are measured. The flow estimates developed for ungaged
tributaries will be refined based on flows measured in those tributaries in 2013 and 2014.
The gaging stations initially installed in 2012 will be maintained through 2013 and 2014 to help
calibrate and validate the flow routing models and provide data supporting other studies. The
gaging stations will be used to monitor stage and flow under summer ice-free conditions and to
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monitor water pressure under winter ice-covered conditions. The stations record additional
measurements including water temperature and camera images of the river conditions (summer
and winter). Continuous measurement of water pressures during the 2012–2013 and the 2013–14
winter periods under ice-covered conditions will produce information different from open-water
conditions. During partial ice cover, the pressure levels measured by the pressure transducers are
affected by flow velocities, ice-cover roughness characteristics, and other factors such as
entrained ice in the water column. The pressure-head data are important for understanding
groundwater/surface water interactions.
Periodic winter discharge measurements (January and March) will be completed at selected
gaging stations in the winter, in coordination with USGS winter measurement programs, and will
provide valuable information for understanding hydraulic conditions in the river during a season
when groundwater plays a more prominent role in aquatic habitat functions. Winter flow
measurements will also be used to help develop the Ice Processes Model and supporting analysis
(see Section 7.6).
Once developed and calibrated, the HEC-RAS model can be provided a time history of flow
releases from the dam and it will predict the flow and stage history at each of the downstream
cross-sections. These predicted flow and stage responses can then be evaluated at multiple levels
to assess the impacts to aquatic habitat.
Output from the flow routing models will provide the fundamental input data to a suite of
habitat-specific and riverine process-specific models that will be used to describe how the
existing flow regime relates to and has influenced various resource elements (e.g., salmonid
spawning and rearing habitats and the accessibility to these habitats in the mainstem, side
channels, sloughs, and tributary deltas; invertebrate habitat; sediment transport processes; ice
dynamics; large woody debris (LWD); the health and composition of the riparian zone). These
same models will likewise be used to evaluate resource responses to alternative Project
operational scenarios, again via output from the routing models, including various baseload and
load-following alternatives, as appropriate. As an unsteady flow model, the routing models will
be capable of providing flow and water surface elevation information at each location on an
hourly basis and therefore Project effects on flow can be evaluated on multiple time steps
(hourly, daily, and monthly) as necessary to evaluate different resource elements.
The study objective for the flow routing data collection effort is to provide input, calibration, and
verification data for a river flow routing model extending from the proposed dam site to RM 75.
Specific objectives are as follows:
• Survey cross-sections to define channel topography and hydraulic controls between RM
75 and RM 184, excluding Devils Canyon (for safety reasons).
• Measure stage and discharge at each cross-section during high and low flows, with the
potential addition of an intermediate flow measurement.
• Measure the water surface slope during discharge measurements, and document the
substrate type, groundcover, habitat type, and woody debris in the flood-prone area for
the purposes of developing roughness estimates.
• Install and operate 13 water-level recording stations within the mainstem Susitna River.
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The HEC-RAS routing model will rely upon existing Susitna River hydrology as well as on
output from the ROM.
8.5.4.3.2. Operations Model
The U.S. Army Corps of Engineers, Hydrologic Engineering Center (HEC) reservoir system
simulation model HEC-ResSim (USACE 2007) Version 3.0 will be used to develop the reservoir
outflows used in the Instream Flow Study. HEC-ResSim is a general-purpose, sequential stream
flow routing model. The model is free and in the public domain. HEC-ResSim includes a
graphical user interface, and graphics and reporting facilities. HEC’s Data Storage System
(HEC-DSS) is used for storage and retrieval of input and output time-series data.
Essential HEC-ResSim capabilities applicable to Watana Reservoir are summarized in this
section. The model time increment of operation, which is an input variable, will be hourly.
Reservoir operations are driven by a set of operating rules. Refinements are achieved through
iterative model runs. HEC-ResSim incorporates a reservoir water balance such that inflow minus
outflow, minus losses such as evaporation, equals the change in reservoir storage for the time
period.
Although the HEC-ResSim program contains river channel routing capabilities, the more
detailed hydraulic channel routing capabilities of HEC-RAS will be used in the Instream Flow
Study for river channel flow routing downstream from Watana Dam. Therefore, a description of
HEC-ResSim river channel flow routing capabilities has not been included. Where specific data
values are provided herein for the dam, reservoir, and operating parameters, it must be
understood that all values are preliminary and subject to change as studies progress.
8.5.4.3.2.1. Hydrology
Required model input data includes long-term reservoir inflow time-series data. For Watana
Dam, the reservoir inflows will be a continuous 61-year record of daily flows for Water Years
1950 through 2010. The U.S. Geological Survey (USGS) provided the basis for the continuous
long-term daily flows with a Susitna River watershed record extension study (Curran 2012). Two
of the USGS gages included in the record extension study were Susitna River at Gold Creek
(USGS gage 15292000) that has a drainage area of 6,160 square miles, and Susitna River near
Cantwell (USGS gage 15291500) that has a drainage area of 4,140 square miles. Watana Dam
has a drainage area of 5,180 square miles, about half-way between these two USGS gages.
Inflows to Watana Reservoir were based on proportioning the USGS flows based on drainage
area.
Providing environmental flows at the Gold Creek USGS gage is a primary reservoir operating
criterion. With Watana Dam, a majority of the flow tributary to the Gold Creek USGS gage will
be regulated, but significant natural inflows between Watana Dam and Gold Creek must also be
included. To accomplish this, a 61-year daily record was constructed from the Gold Creek USGS
gage flows minus the calculated Watana Reservoir inflows and used as time-series natural inflow
data for input to the model.
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8.5.4.3.2.2. Reservoir Operations
The basic reservoir input data includes a table of values for elevation (feet), reservoir storage
(acre-feet), and water surface area (acres), and a table of values for release capacities based on
elevation including the spillway, valves, and the turbines. Release capabilities can be broken
down by individual valve or spillway bay.
Releases from the reservoir in the HEC-ResSim model are based on zones, defined by reservoir
water surface elevations, and a reservoir operating scheme. The initially defined zones in the
model configuration were an Inactive zone up to 1,850 feet in elevation, a Conservation zone up
to 2,050 feet in elevation, a Flood Control zone up to 2,064 feet in elevation and a Spillway
Operation zone that extended to the top of the dam crest at 2,075 feet in elevation. It is possible
to create additional user-defined zones in HEC-ResSim. The operating scheme in HEC-ResSim
is defined by adding rules to the zones, with the exception of the Inactive zone from which
releases cannot occur. A rule represents the goals and constraints upon the releases. The reservoir
operating scheme, called an operations set, controls releases from the various reservoir outlets,
and therefore, the downstream discharge resulting from the Project. The rules within each zone
are prioritized to control the actual releases from the reservoir outlets. The allocation of releases
from the outlets can also be specified.
The highest priority rules in the Conservation zone would be the minimum and maximum flow
requirements at Gold Creek (USGS gage No. 15292000), which was initially used as a
downstream control point for releases from the reservoir based on studies from the 1980s. The
initial environmental flow requirements from Case E-VI in the 1985 FERC License Application
Amendment were used, with the exception of the flow requirements from October 29 to May 5,
which were updated to reflect an increase from 2,000 cfs to 3,000 cfs. A sequential release
allocation for the reservoir outlets was also added in order to increase the flow, as necessary,
through the powerhouse when the flow to meet the hourly Watana load was less than the
minimum release required from the reservoir to meet flow requirements at Gold Creek.
Hydropower operations in the Conservation zone form the other primary reservoir release rule.
The Flood Control zone used the same operating rules as the Conservation zone and included a
release rule for the low-level fixed-cone outlet valves. The Spillway Operation zone included a
release rule for operation of the gated spillway.
8.5.4.3.2.3. Hydropower Operations
Basic hydropower input data includes installed capacity and unit efficiencies as a constant or as a
function of flow, reservoir elevation, or operating head. A tailwater rating table, hydraulic losses
as a constant or a function of flow, turbine hydraulic capacities, and an allowance for station use
are also included as input data.
Hydropower rules specify the minimum releases needed from a reservoir’s powerhouse to meet a
power generation requirement and schedule. The hydropower rules available in the model
specify the generation requirement as a function of time of year (month, week, or day with
hourly load factors), power guide curve, or as an external time-series dataset of the load. The
release from the powerhouse, which is a function of the plant’s generating efficiency, the
hydraulic head, and the required energy can also be specified based on limits to the rate of
change of flow through the powerhouse and downstream flow requirements, which in turn affect
the energy generation.
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The initial Watana powerhouse hydropower rule was to specify time-series energy generation
requirements for each hour of the year (8,760 values). The required generation values were based
on the Watana powerhouse generating a specified part of the total Railbelt energy demand. As
studies progress, the hourly time-series generation requirements at Watana are expected to be
based on studies that integrate the Watana generation capabilities into the Railbelt system. The
hourly load data for Watana would then be based on the total projected load for the Project
considering the capability of other Railbelt Utilities loads and resources in the region. Factors
such as outages of other Railbelt generating units could then be incorporated in the generation
requirements at Watana Dam.
8.5.4.3.2.4. Model Output
HEC-ResSim can provide results for many parameters such as the simulated reservoir elevation
and powerhouse generation. Data can be plotted or output in standard or user-customized reports.
Only one parameter, total reservoir outflow, must be provided from HEC-ResSim for input to the
HEC-RAS model. Total reservoir outflow is the summation of all outlets including the
powerhouse, spillway, and the fixed-cone outlets. The extent of data to be provided is yet to be
determined, but it could include hourly outflow for all 61 years of operation (over 500,000
values). The outflows could also be provided on a daily average flow basis if needed.
8.5.4.3.3. Work Products
Work products for open-water flow routing will consist of a calibrated executable model and a
draft and final report. Specific work products will include the following:
• A detailed description of the methods used to develop the routing model.
• Map displaying the location of all mainstem transects used as part of open-water flow
routing modeling.
• Data used in the modeling effort including topographic, bathymetric, and digital terrain
model data, USGS flow records, and water surface elevations.
• Plot of channel cross-section profiles for all transects used as part of the modeling.
• Details of model calibration including calibration period, observed and simulated water
surface elevations, Manning’s roughness values, and tabular listing of calibration results.
These work products will be compiled and presented in the open-water flow routing component
of the Initial Study Report (ISR) and Updated Study Report (USR).
8.5.4.4. Hydrologic Data Analysis
The assessment of hydrology data will include a summary of seasonal and long-term hydrologic
characteristics for the river including daily, monthly, and annual summaries, exceedance
summaries, and recurrence intervals of small and large floods. The recent record extension
analysis performed by USGS (Curran 2012) will be used to develop the synthetic period of
record (POR) flows for the past 61 years at selected tributaries. The hydrologic data collection at
tributaries will provide data required for the simulation of flows at hourly intervals required for
evaluating potential Project effects.
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8.5.4.4.1. Proposed Methodology
8.5.4.4.1.1. Hydrologic Data Collection
As part of the 2013–2014 IFS, hydrologic data collection will include stage and discharge
measurements, cross-sectional and areal bathymetric surveys, velocity mapping, and roughness
determinations. The IFS will also incorporate hydrologic data collected by other studies,
including water quality (see Section 5.0), water temperature, and ice process data (see Section
7.6).
Stage and discharge measurements were performed in 2012 at 88 cross-sections between RM 75
and RM 184. Twelve of these cross-sections are located at or near gaging stations operated by
USGS or AEA. Stage and discharge measurements were also performed at inactive USGS
gaging stations in the Lower River (Susitna River at Susitna Station [ESS20], RM 20) and in the
upper basin (Susitna River near Cantwell [ESS80], RM 224) (see Table 8.5-8 for gaging station
naming convention). Gaging equipment was re-installed at these locations, as well as at two tidal
monitoring stations in the Susitna delta. Water level, water temperature, camera images, and
meteorological data from these stations are shared online via an internal project website.
Depending on results of the 2012 open-water flow routing model and analysis from other studies,
additional cross-sections will be surveyed in 2013 and 2014. The geomorphology studies (see
Sections 6.5 and 6.6) will require 50 to 100 additional cross-sections for the development of the
1-D sediment transport model and other geomorphologic analysis. The location for these sections
and the field data collection will closely coordinate with the Geomorphology Discipline Lead
and relevant study staff. These cross-sections should satisfy most of the additional cross-sections
needed for the open-water flow routing model. Sections of the river that demonstrate changes in
cross-section profiles seasonally, or event-based (floods), may require additional cross-section
measurements during each summer season. Stage and discharge measurements will be used to
calibrate the flow routing models, and to develop or confirm ratings for new and existing gaging
stations.
Instantaneous stage measurements will be performed using either RTK GPS methods or optical
levels, using benchmarks and geodetic control points that are part of the Project control network.
The 2012 river cross-section field program established that the RTK survey method allowed for
the greatest number of cross-sections to be surveyed each day and helped maintain safety
objectives. In addition, the RTK data quality parameters and time stamp information contained in
the field controller database files ensured the accuracy of the water level measurements and
eliminated the possibility for transformation of numbers by the field crews. The GPS Project
survey-control (CP) network (horizontal and vertical) will be evaluated each spring. Vertical
datum will be verified and any missing benchmarks due to bank erosion or other issues replaced
if needed. Additional CP surveys will be conducted to support Focus Areas and other studies
from the Lower River Segment to the Upper River Segment, as needed. RTK survey control
points will be placed at final Focus Areas to provide study field teams with horizontal and
vertical control networks designed to allow efficient ground surveying with RTK, optical levels,
or other conventional survey methods.
A standard operating procedure (SOP) guide will be established to provide uniform survey
methods and data reporting standards. This will include the use of Focus Area survey control
networks (horizontal and vertical) by the various field study teams working in these areas. The
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SOP will include the appropriate reporting of RTK survey methods and data. All surveying
information will be provided in data sets applicable to existing or developing relational or spatial
databases.
While conducting field surveys for new or existing survey control points in study Focus Areas,
additional survey control points will be established to verify the accuracy of Project Light
Detection and Ranging (LiDAR) information. The field plans for collecting the LiDAR
validation data will be coordinated with the study teams depending on this data and the Project
Geographic Information System (GIS) technical group. Existing RTK river cross-section survey
control points will be relabeled in the spring of 2013 to reflect final Project River Mile (PRM)
designations.
During 2012, a number of 1980s cross-section and survey-control points were found and
surveyed to current horizontal and vertical datum standards. Additional survey control points
will be reviewed from any newly found 1980s information. The potential 1980s information will
be evaluated for follow-up field surveying. An evaluation will be made on how to project the
1980s project survey-control datum (horizontal and vertical) to current Project standards.
Any new AEA gaging or water level stations will have RTK or CP surveys established as well as
temporary benchmarks (TBMs) to allow efficient optical level-loop surveys. Project survey
control will be maintained, or established if needed, at USGS gaging stations on the Susitna
River within the Project study area, and at key tributaries. The offsets from USGS local datum to
Project elevation datum will be maintained to provide USGS to Project vertical datum
conversion standards. These conversions are critical to using the USGS gage water levels in all
relevant Project hydrology modeling and studies.
Together with water temperature and meteorological data, continuous stage measurements will
be recorded at AEA gaging stations with a minimum of 15-minute intervals and made available
to studies via the near-real-time reporting data network. Continuous stage measurements are
made using vented pressure transducers accurate to within about 0.02 feet. The gaging stations
will require periodic elevation surveys, either performed by RTK surveying or by optical level-
loop survey methods. The elevations surveys will be conducted during discharge measurements,
changes or repositioning of pressure transducers, and before and after major hydrologic events
such as fall freeze-up and spring break-up. The data collection stations will be operated
throughout the year to support both summer (open-water) and winter (ice covered) study needs
for the IFS and other studies. Table 8.5-9 shows a listing of the current 2012 stations in the near-
real-time reporting data network.
Maintaining a constant stage record during river freeze-up and spring break-up is a challenge.
River ice jams and ice jam break-ups will result in some minor losses of stage data. In the early
winter, when ice conditions become more stable and safe for field crews to operate on the ice,
pressure transducers and water temperature sensors will be added at gaging stations to provide
the Ice Processes Study team (see Section 7.6) with winter pressure (water pressures under ice,
water levels in ice-free or partial ice cover reaches) and water temperature measurements.
Sensors lost during spring break-up will be replaced as soon as it is safe and practical to install
new pressure transducers. All data are recorded on Campbell Scientific CR1000 data loggers,
with internal memory backup. AEA gaging stations also have data archived through hourly data
retrievals over the radio telemetry network. This approach will help ensure that no data are lost
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from icing conditions except for the narrow period when pressure transducers are damaged at a
gaging station and new sensors have not yet been installed.
Additional gaging stations will be added at selected tributaries to help provide additional
hydrologic analysis for hydrologic and fisheries studies. These tributaries will include Fog
Creek, Portage Creek, and Indian River. These gaging stations will be installed in spring 2013 to
help measure the spring snowmelt peaks. The stations will use the same Metadata standards as
the existing AEA gaging stations and will report similar data. Additional stations may be added
to the near-time-reporting network as warranted by study activities and analysis needs and
deadlines. Additional gaging stations may be added on additional tributaries based on the
drainage area evaluations being performed by UAF-GINA.
During open-water conditions, mainstem discharge measurements will be performed using
acoustic Doppler current profilers (ADCPs) following current USGS guidance (Mueller and
Wagner 2009). Due to their shallow depths, tributary inflows will usually be measured using
conventional current meter methods (Rantz et al. 1982). Winter mainstem flows will be
measured using a combination of current meter and ADCP methods. The winter gaging program
will be coordinated with USGS so that the measurements from both programs occur at the same
general time period. The current schedule is to conduct winter measurements in January and
March of 2013 and 2014. The winter discharge measurement will occur at the AEA gaging
stations from ESS80 downstream to ESS20 (Table 8.5-8). Winter discharge measurement will
not be collected at ESS10 and ESS15. These discharge measurements will help assess gaining
and losing river reaches during winter conditions. This effort will be coordinated with Ice
Processes (see Section 7.6) so that measurements also have direct applications to the ice
processes analysis and model development efforts. The winter and summer discharge
measurement events will likely involve multiple teams to allow collection of data under a shorter
period so flow conditions can be more similar for comparisons between gaging stations in the
network.
In accordance with current USGS guidance (Mueller 2012), all discharge measurements will
include sufficient quality assurance data to rate the measurements as Excellent, Good, Fair, or
Poor, corresponding to categories of uncertainty ranging from 0 to over 8 percent.
During 2012, cross-sectional bathymetric surveys were performed as part of discharge
measurements completed using the Sontek M9 ADCP. The Sontek M9 is equipped with a 0.5-
megahertz (MHz) vertical-beam depth sounder and RTK GPS positioning. A minimum of four
transects were completed at each cross-section, and results were used to prepare a digital
elevation model of the streambed. Together with shore-based RTK GPS surveys, the digital
elevation model was used to develop cross-sections for use in the open-water flow routing
model.
Additional cross-sections will be needed for geomorphology modeling, flow routing, and other
IFS models. Depending on the need for concurrent flow data, the cross-sections will be surveyed
using either ADCPs or single-beam depth sounders. In either case, bathymetric data will be
referenced to the Project geodetic control network using RTK GPS survey methods.
Roughness determinations will be made by solving Manning’s equation using field
measurements of discharge and water-surface slope. Each cross-section will have vegetation
descriptions and photographs (upstream, downstream, into bank, opposite bank) above ordinary
high water elevations. The distance away from shoreline for cross-section surveys is determined
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in the field by the Lead Field Hydrologist. These results will be compared against visual
estimates based on handbook values.
8.5.4.4.1.1.1. Hydrologic Data Real-time Reporting Network Operations
Project hydrologic studies include river-flow routing models (see Section 8.5) ice,
geomorphology (see Section 6.6) and water quality (see Section 5.6) models and several studies
to look at the potential effects of the Project and how to minimize them. In order to accurately
simulate unsteady flows, the studies require a series of gaging (water level and discharge), water
level, and meteorological stations. These stations are connected through a radio telemetry system
using spread-spectrum radio communication and a network of base stations. The purpose of the
radio telemetry system is to provide a number of key Project objectives, described below.
Safety
• Real-time access to data can reduce field hours associated with data retrieval; in some
cases this reduces trips per year, or time on-site for each trip.
• Providing real-time access to field weather conditions for travel logistics such as
helicopters or small aircraft. The data reporting network was used for supporting
helicopter logistics and inclement weather evaluations.
Data Quality
• Real-time access to data can allow easier and more cost effective data monitoring;
thus, field-related problems (e.g., ice jam floods, bears, lightning strikes) can be
detected quickly, and site conditions better understood before going in the field, all of
which reduces data loss.
• Real-time data access minimizes data loss by enabling timely response to problems
caught when they occur, rather than their discovery during a site visit. By providing
information on a specific problem, proper equipment replacements and tools can be
brought along for the site visit, ensuring that the problem will be corrected without
necessitating an additional trip.
• Real-time retrieval of data also allows off-site data storage, so if a site is severely
damaged, there is no data loss, even if there is a complete failure of data acquisition
equipment. Data are preserved both on the data servers and the data loggers to
provide redundant data security.
• Study teams have access to data for ongoing data quality control (QC) before going
into the field, so teams can better address potential sensor or programming issues and
proactively plan for field repairs. Two-way communications allow programming
updates and modifications to be accomplished without expensive site visits.
Deadlines
• Real-time access allows field staff access to data 24/7, so data QC, reduction, and
analysis applications can be accomplished between field trips. This also benefits the
effectiveness of field trips by allowing a better understanding of field conditions
before going in the field. QC checks and graphs can be set up, tested, and adjusted
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early in the Project in an unhurried manner. QC can be up-to-date when it is time to
create reports.
Data network management includes maintaining network Metadata standards. This results in
sharing of common data-acquisition equipment, and allows savings for backup equipment to help
support the various station types in the network. Network management also includes the
coordination of network operation and maintenance activities; bulk procurement of network
station supplies; setup of water level, gaging, repeater, and base stations; and coordinated
reporting for the stations in the network linked together with the radio telemetry data
communication system.
The data network installed in 2012 established the following equipment standards:
• Campbell Scientific CR1000 data control/acquisition loggers, extended temperature
rating
• Campbell Scientific RF450 Spread-Spectrum Radios for data transmissions
• Campbell Scientific CS450 vented pressure transducers for water stage and
temperature (at transducer location)
• GWS-YSI Cold -Range air temperature sensors
• Campbell Scientific CC5MPX lower power, cold weather digital cameras with lens
heaters for supporting winter operations
• HC2S3-L Rotronic air temperature, relative humidity sensor
• Campbell Scientific CS109 temperature sensors for general water level and soil
temperatures
• 12-volt solar power systems for all stations
Data network operations also include data retrieval and online reporting for water level and
gaging stations, repeater stations, base stations, meteorological stations, and associated co-
located meteorological sensors. Internal information reporting is currently available on an
internal website/wiki and includes network status and diagnostics information (Figure 8.5-25).
Data reporting includes current conditions pages for each station (Figure 8.5-26), basic station
information pages, and near-real-time graphs for selected sensors (such as air temperature,
relative humidity, water level over sensor, water temperature, and station diagnostics
information). Data plots are set up to display in 7- and 14-day periods, as well as 2-, 4-, 6-, and
12-month graphs. Short-period graphs are updated hourly, while long-period graphs (1 month or
longer) are updated every three hours. Cameras will be maintained at gaging stations and
selected repeater stations. Low and high resolution cameras image are taken hourly. The low
resolution images are transferred to the CR1000 data logger and transmitted with other station
data and reported hourly, and displayed online internally in 24-hour sequences. The high
resolution camera images are stored locally on the camera on camera internal memory cards and
downloaded during regular station visits. All camera images collected are accessible through the
online image interface.
The radio telemetry remote collection of data from gaging and meteorological stations is
supported by a series of repeater stations. Some data collection stations (gaging or
meteorological) also serve as repeater stations. Additional repeater stations may be installed in
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2013 and 2014 as the data network changes to meet various study needs. Typically repeater
stations will be visited once a year for annual maintenance, or as needed for station problems
from issues such as bear damage or extreme weather events.
8.5.4.4.1.2. Hydrologic Data Analyses
The hydrologic period of record for the Project has been established for the 61-year period
extending from Water Years 1950 through 2011 (October 1, 1949 to September 30, 2011).
Historically, flows have been measured by USGS in the Susitna basin at various locations and
over different time periods. USGS gaging stations on the Susitna River are listed in Table 8.5-10,
and USGS gaging stations on tributaries of the Susitna River are listed in Table 8.5-11.
The periods of record of measured flows at each of the sites listed in Table 8.5-10 and Table
8.5-11 were extended to cover the 61-year period (Water Years 1950 through 2011) by
synthesizing the missing daily flow records to fill in the gaps. This work was performed by
USGS (Curran 2012). The 61-year period of record at the sites listed in Table 8.5-10 and Table
8.5-11 will establish a baseline hydrologic condition from which to assess Project effects.
Potential alterations to this baseline condition will be assessed as part of the Glacier and Runoff
Changes Study (see Section 7.7). These evaluations will be performed with the WaSiM-ETH
model (Water Balance Simulation Model). The WaSiM-ETH model accounts for
evapotranspiration, snow accumulation, snow and glacier melt, interception, infiltration, soil
water storage, and runoff, such as surface, interflow, and baseflow. The model will be calibrated
to match conditions observed from 1960 through 2010, and used to forecast conditions out to the
year 2100. The proposed extent of the WaSiM-ETH model is the Susitna River basin upstream
from the proposed dam site.
Hydrologic data analyses will include post-processing of discharge data, correction of pressure
transducer records and conversions to station gage height records, rating curve development,
stream flow computations, and cross-section and bathymetric data post-processing.
Discharge data post-processing will include the elements described in Mueller (2012) for ADCP
measurements. A similar procedure will be used for current meter data, resulting in data
qualification as Excellent, Good, Fair, or Poor.
Pressure transducer records will be corrected using instantaneous stage measurements and
hydrologic data correction software such as Aquarius Workstation. The software maintains a
record of all corrections used in the computation of hourly and daily stream flow data. Other data
from the gaging, water level, and repeater stations will have monthly quality assurance
evaluations performed as well as a shorter timer check made to identify problems with station or
sensor operations.
Rating curves for new gaging stations will be developed using rating development software such
as the Aquarius Rating Development Toolbox. Stream flow computations will be performed
using hydrologic data management software such as Aquarius Workstation.
Bathymetric data will be post-processed using hydrographic data processing software (e.g.,
HyPack) to obtain a digital terrain model. The digital terrain model can be used to develop cross-
sections or as input for 2-D hydraulic and other instream flow models. ADCP files will be post-
processed using velocity mapping software (e.g., VMS) to develop cross-sectional or plan-view
velocity maps for calibration of hydraulic models.
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Data analysis will include the development of daily and hourly inflow routing to Focus Areas
from the Susitna open-water flow routing modeling and analysis for selected tributaries. Analysis
will also include calculations of hydrologic data statistics for the Susitna River and selected
tributaries.
Five representative years will be selected that represent wet, average, and dry conditions, and
warm and cold Pacific decadal oscillation phases so that Project effects for various project
alternatives can be evaluated under a range of climatic and hydrologic conditions. In addition, a
multi-year continuous flow record will be evaluated to identify year-to-year variations
independent of average, wet, or dry conditions. The specific representative years and the duration
of the continuous flow record will be selected by AEA in consultation with the TWG in Q3 2013
(Table 8.5-14).
8.5.4.4.1.3. Indicators of Hydrologic Alteration and Environmental Flow Components
The assessment of hydrology data will include a summary of seasonal and short-term and long-
term hydrologic characteristics for the river including daily, monthly, and annual summaries, and
exceedance summaries and recurrence intervals of small and large floods. The analysis will
utilize the Indicators of Hydrologic Alteration (IHA) and Range of Variability models developed
by The Nature Conservancy (TNC 2009) for computing baseline hydrologic characteristics. The
IHA models are components of an analytical software package designed to assess the impacts of
a project on unregulated hydrologic conditions (TNC 2009). These analyses are based on
hydrologic statistics defined in Table 8.5-12, and Environmental Flow Components (EFC)
defined in Table 8.5-13.
The traditional approach developed by The Nature Conservancy utilizes average daily flows to
compute parameters that may be categorized in five general groups of statistics:
1. Magnitude of annual extremes (1-, 3-, 7-, 30-, and 90-day maximum and minimum
flows)
2. Timing of annual extremes (Julian date of 1-day maximum and minimum)
3. Magnitude of monthly conditions (variability of monthly means over analysis period)
4. Frequency and duration of high and low flow pulses (defined by annual exceedance
flows)
5. Rate and frequency of changes in daily flows
The environmental flow components listed in Table 8.5-13 are divided into five parameter
groups: (1) monthly low flows; (2) extreme low flows; (3) high flow pulses; (4) small floods; and
(5) large floods.
The hydrologic statistics described in Table 8.5-12 and Table 8.5-13 will be reviewed in
consultation with the TWG to identify those parameters that are ecologically relevant to Susitna
River resources. Pre- and post-Project hydrologic conditions will be assessed by performing
IHA/EFC evaluations in the Susitna River at one or more locations downstream from the
proposed dam site. The period of assessment will be based on the 61-year duration from Water
Years 1950 through 2010 (October 1, 1949 to September 30, 2010). Daily flows will be used to
perform these assessments in accordance with standard IHA/EFC statistics; however,
modifications to the standard list of statistics are envisioned to address alternative operational
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scenarios. In addition to the analyses using daily flow records, modifications to the analysis
package will be developed in collaboration with the TWG to utilize hourly data instead of daily
data to evaluate flow components specific to the evaluation of hydropower load-following
operations:
• Minimum, maximum, and mean within-day flow hydrograph
• Hourly rate of stage change for various event types (load-following operations; diurnal
meltwater fluctuations)
• Monthly and seasonal frequency of stage change rates
• Reservoir pool levels (annual and monthly extremes; daily stage change)
The aquatic resources working group for the Baker River Hydroelectric Project (FERC No.
2150) used a similar process to evaluate effects of load-following operations on the Skagit River,
Washington. To compare baseline and alternative operational scenarios they evaluated standard
IHA/EFC parameters using daily flow records, modified flow parameters in response to project-
specific applications (e.g., 2-day minimum), and developed additional statistics based on hourly
flow records (Hilgert et al. 2008).
For the Susitna-Watana Project, an acceptable range of variation in IHA/EFC indicator condition
will be identified by evaluating existing, unregulated flows over individual Water Years selected
to represent average, wet, and dry hydrologic conditions and warm and cold Pacific decadal
oscillation phases. In addition, the available continuous flow record will be evaluated to identify
year-to-year variations independent of average, wet, or dry conditions. The selection of
representative hydrologic conditions and the duration of the continuous flow record will be
developed in consultation with the TWG in Q4 2013 (Table 8.5-14).
The IHA/EFC-type statistics represent one tool to evaluate comparisons between existing,
unregulated flow conditions and alternative operational scenarios. The U.S. Army Corps of
Engineers HEC-EFM (Ecosystem Functions Model) program
(http://www.hec.usace.army.mil/software/hec-efm/index.html) is another planning tool that aids
in analyzing ecosystem responses to changes in flow. The strength of the HEC-EFM is that it can
evaluate project-specific functional relationships developed from expert knowledge, it links
ecology with established hydrologic, hydraulic, and GIS tools, and it can be applied quickly and
inexpensively. The merits of these planning tools will be discussed with the TWG in Q3 2013,
and if HEC-EFM is deemed preferable by the TWG, it will be used to support the evaluation of
potential Project effects on resources of concern.
The IHA/EFC analysis or the HEC-EFM program, depending on TWG preference, are planning
tools that are part of the IFS Analytical Framework. The IFS Analytical Framework (see Section
8.5.4.1) is designed to integrate study and model results of riverine processes and to assess
relationships between riverine and biological functions. One objective of the IFS modeling
efforts is to extrapolate measured conditions to non-modeled conditions both spatially and
temporally. This allows data collected over the study period to be used to evaluate Project effects
over the range of environmental conditions that occur naturally. The results of the hydrologic
analyses, combined with the results of the habitat modeling efforts, provide guidance when
identifying potential modifications to operational rules to minimize harmful Project effects on
downstream resources.
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In consultation with the TWG, the IHA/EFC or HEC-EFM programs will be used to evaluate
existing conditions and alternative operational scenarios for the Susitna-Watana Project. Select
hydrologic parameters, considered to be ecologically relevant to Susitna River resources, will be
developed in consultation with the TWG in Q3 2013, and initial results and potential
modification reviewed by the TWG in Q1 2014 (Table 8.5-14).
8.5.4.4.2. Work Products
The hydrologic data analysis component will include the following work products:
• Period of Record (POR) data files from gaging stations, including gage height
calculations of hourly and daily discharge, and rating curve summaries.
• Cross-section profiles and roughness calculations, and measured water surface elevations.
• POR data files from gaging stations for air and water temperature, and camera image data
sets for stations with camera systems installed.
• Project GPS Survey Control Network (horizontal and vertical) Annual Reports.
• Tabular summaries of selected IHA-type and general hydrologic statistics.
• Summary charts to provide visual comparisons of selected hydrologic statistics to
facilitate discussion of the effect of modeled future operational scenarios on the without-
Project hydrologic regime.
Interim results of the IHA-type analyses will be presented in the ISR, and final results presented
in the USR in Q1 2015 (Table 8.5-14).
8.5.4.5. Habitat Suitability Criteria Development
Habitat Suitability Criteria and index curves have been utilized by natural resources scientists for
over two decades to assess the effects of habitat changes on biota. The abbreviation "HSI" is
used in this document to refer to either Habitat Suitability Index (HSI) models or Habitat
Suitability Criteria (HSC) curves, depending on the context. HSI models provide a quantitative
relationship between numerous environmental variables and habitat suitability. An HSI model
describes how well each habitat variable individually and collectively meets the habitat
requirements of the target species and life stage, under the structure of Habitat Evaluation
Procedures (USFWS 1980). Alternatively, HSC are designed for use in the Instream Flow
Incremental Methodology to quantify changes in habitat under various flow regimes (Bovee et
al. 1998). HSC describes the instream suitability of habitat variables related only to stream
hydraulics and channel structure. Both HSC and HSI models are scaled to produce an index
between 0 (unsuitable habitat) and 1 (optimal habitat). Both models are hypotheses of species-
habitat relationships and are intended to provide indicators of habitat change, not to directly
quantify or predict the abundance of target organisms. For the Susitna-Watana Hydroelectric
Project aquatic habitat studies, both HSC (i.e., depth, velocity, and substrate/cover) and HSI
(e.g., turbidity, colonization rate, dewatering mortality) models will be used to analyze the
effects of alternative operational scenarios.
For the mainstem aquatic habitat model, HSC/HSI curves for some species (e.g., benthic
macroinvertebrates, benthic algae, fry) will also need to be developed to describe the response of
aquatic organisms to relatively short-term flow fluctuations (i.e., ramping). Methods for
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development of HSC/HSI for benthic macroinvertebrate and algal habitats are described in the
River Productivity Study (see Section 9.8), but in general include the collection of velocity,
depth, and substrate composition data during benthic macroinvertebrate and algae sampling.
Development of HSC/HSI curves for fish is described in the following section.
8.5.4.5.1. HSC/HSI Proposed Methodology
The fish community in the Susitna River is dominated by anadromous and non-anadromous
salmonids, although numerous non-salmonid species are also present (Table 8.5-15).
Development of HSC will involve the following steps: (1) selection of target species and life
stages, (2) development of draft HSC curves using existing information, (3) collection of site-
specific HSC data, (4) development of habitat utilization frequency histograms/preference curves
from the collected data, (5) determination of the variability/uncertainty around the HSC curves,
and (6) finalization of the HSC curves in collaboration with the TWG. Each of these steps will be
described in the following sections.
8.5.4.5.1.1. Habitat Suitability Criteria (HSC)
HSC curves represent an assumed functional relationship between an independent variable, such
as depth, velocity, substrate, groundwater upwelling, turbidity, etc., and the response of a species
life stage to a gradient of the independent variable (suitability). In traditional instream flow
studies, HSC curves for depth, velocity, substrate, and/or cover are combined in a multiplicative
fashion to rate the suitability of discrete areas of a stream for use by a species and life stage of
interest. HSC curves translate hydraulic and channel characteristics into measures of overall
habitat suitability in the form of weighted usable area (WUA). Depending on the extent of data
available, HSC curves can be developed from the literature, or from physical and hydraulic
measurements made in the field in areas used by the species and life stages of interest (Bovee
1986). HSC curves for the Project will be based on information consisting of the following (in
order of preference): (1) new site-specific data collected for selected target species and life stages
(seasonally if possible [e.g., winter]); (2) existing site-specific data collected from the Susitna
River during the 1980s studies; (3) site-specific data collected from other similar Alaska river
systems; and (4) professional opinion (roundtable or Delphi) of local resource specialists that are
familiar with habitat use by the species and life stages of interest for this study.
8.5.4.5.1.1.1. Select Target Species and Life Stages
For planning purposes, target species are assumed to include Chinook, coho, chum, and sockeye
salmon; rainbow trout; arctic grayling; Dolly Varden; burbot; longnose sucker; humpback
whitefish; and round whitefish. The target species are generally considered the most sensitive to
habitat loss through manipulation of flows in the Susitna River. Other species and life stages will
be considered in collaboration with the TWG (Table 8.5-15). A draft list of target species and life
stages will be presented to the TWG during a meeting to be held in Q1 2013. The final list of
species and life stages to be included in the HSC/HSI development process will be developed
during a subsequent TWG meeting to be held just prior to field activities in Q2 2013.
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8.5.4.5.1.1.2. Develop Draft HSC Curves
The initial determination of mainstem, microhabitats used by the target fish species in the
Susitna River will rely heavily on information obtained as part of the 1980s assessments, in
particular, the Instream Flow Relationships Report (Trihey & Associates and Entrix 1985 a, b)
and a four-volume series on the aquatic habitat and instream flow assessment (Hilliard et al.
1985; Klinger-Kingsley et al. 1985; Stewart et al. 1985; Aaserude et al. 1985). This information
will be synthesized and compared to findings of other studies and data gaps will be identified.
Comparisons will be made to an available set of library-based HSC curve sets including a data
set of over 1,300 recently obtained field microhabitat observations for most of the same species
found in the Susitna. Study gaps will be identified and plans to fill the gaps integrated into the
2013–2014 HSC sampling plan. The existing HSC curve sets developed during the 1980s will be
compared with more contemporary curve sets developed for similar river systems. In addition,
the HSC data collected in 2012 will be compared with existing curve sets to see if patterns of use
are similar. Several different methods will be evaluated for updating the 1980s HSC curve sets
including the following: Enveloping, Habitat Guilds, bootstrapping, roundtable/expert opinion,
and statistical approaches as noted by Ahmadi-Nedushan et al. (2006). To the extent available,
habitat suitability information will address fish responses to changes in depth, velocity, substrate,
cover, groundwater upwelling, and turbidity. A summary of the 1980s data sets available and
reviewed to date is presented in Table 8.5-1. The draft HSC curve will be presented in the
HSC/Periodicity TM scheduled for completion Q4 2012, and will be reviewed during a Q1 2013
TWG meeting (Table 8.5-14).
8.5.4.5.1.1.3. HSC Study Area Selection
The distribution and number of HSC study areas for the 2013 and 2014 data collection will be
based on a stratified random sampling approach, based on the hierarchical classification system
described in Section 8.5.4.2.1.1 as well as several other attributes. This will include levels based
on river segment, geomorphic reach (see Section 6.0), and mainstem habitat composition (see
Section 6.8.4.1) (Table 8.5-5), as well as relative fish use, number of instream flow Focus Areas,
mesohabitat composition (see Section 9.9), and site-specific attributes including the presence of
groundwater upwelling, water clarity (turbid vs. clear water areas), and safety concerns.
A stratified random sampling scheme will be used to select study areas to cover the range of
habitat types. The mainstem Susitna River and its tributaries downstream of the proposed dam
will be subjected to Project operations that will affect flow levels on an hourly, daily, seasonal,
and annual timeframe. It is assumed that the effects of Project operations on mainstem and
tributary habitats will diminish below the Three Rivers Confluence. The mainstem Susitna River
and its tributaries upstream of the proposed dam will be within the proposed impoundment zone
and therefore are not included as part of the instream flow sampling effort. Hence, sample sites
will be stratified and randomly selected from within the Middle River Segment (RM 98-RM 184)
and Lower River Segment (RM 77¬RM 98) of the Susitna River.
A second level of stratification will be based on geomorphic reaches as described in Section
8.5.3 and in more detail in Section 6.5) (Table 8.5-4). The Lower and Middle River segments
have been delineated into large-scale geomorphic river reaches with relatively homogeneous
landform characteristics, including at generally decreasing scales: geology, hydrology (inflow
from major tributaries), slope, channel form, braiding or sinuosity index (where relevant),
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entrenchment ratio, channel width, and substrate size (Figure 8.5-11 and Figure 8.5-12). Reach
stratification facilitates a relatively unbiased extrapolation of sampled site data within the
individual reaches because sources of variability associated with large-scale features will be
reduced.
The third level of stratification that will be employed is based on a modified 1980s classification
of river types. Major categories and sub-categories under this level include Main Channel
Habitats consisting of Main Channel, Split Main Channel, Braided Main Channel, Side Channel,
and Off-channel Habitats that include Side Slough, Upland Slough, Backwater and Beaver
Complexes; and Tributary Habitats that consist of the segment of the tributary influenced by
mainstem flow. Each of these main channel and off-channel habitat types will be identified and
mapped based on the use of aerial imagery, LiDAR, and aerial videography (see Section 6.8.4.1).
The distribution and frequency of these habitats vary longitudinally within the river depending in
large part on its confinement by adjoining floodplain areas, size, and gradient.
The Geomorphic Study Team will complete the delineation of mainstem habitat units for the
Middle River Segment before the end of Q4 2012. Once the mainstem habitat areas are mapped,
a minimum of three replicates will be randomly selected from each of the mainstem habitat types
(or bins) that are represented within each of the geomorphic reaches.
Applying the stratification system discussed above, the proposed HSC sampling effort for the
Lower River Segment (RM 77 – RM 97) will include three replicates of each mainstem channel
type for a maximum of 24 sample sites. Similarly, in the Middle River Segment, three sites of
each habitat type will be randomly selected from within each of the seven geomorphic reaches
(excludes Reach MR-4 due to safety issues) for a maximum of 168 potential sampling locations,
including sites within the Focus Areas. For each of the Middle River Segment sampling sites, a
special effort will be made to ensure that HSC sampling occurs within each of the main channel
mesohabitat types present. The proposed number and distribution of 2013 HSC sampling sites
will be presented to the TWG during the Q2 2013 meeting (Table 8.5-14).
Site selection includes completing the geomorphic reach delineation and habitat mapping tasks
first. In addition to technical considerations, access and safety will be key non-technical
attributes for site selection for all studies. This, too, influenced site selection in the 1980s studies,
and will certainly influence site selection in the present studies.
Finally, winter sites will be selected based on information gathered from winter 2012–2013 pilot
studies at Whiskers Slough and Skull Creek (Figure 8.5-27). At a minimum, attempts will be
made to complete winter sampling at all Focus Areas located downstream of Devils Canyon.
Winter sampling upstream of Devils Canyon will be dependent on access/safety issues. The
farthest upstream sites will need to be accessed by air travel; sites closer to Talkeetna may be
accessed by snow machine. Safety and access are important considerations for the selection of
these sites. Sampling methodologies including, but not limited to, under-ice use of Dual
Frequency Identification Sonar (DIDSON) and video cameras will be tested in 2012–2013.
8.5.4.5.1.1.4. Collect Site-Specific Habitat Suitability Information
Collection of site-specific habitat suitability information was initiated in the Susitna River during
a pilot effort in 2012 and will continue during 2013–2014. The primary goals of the 2012 pilot
effort were to evaluate various sampling techniques, assess logistical aspects of site access, and
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begin collection of site-specific habitat suitability data for target species. Information gathered
during the 2012 sampling effort was used to guide development of 2013–2014 study methods.
The 2012 pilot effort consisted of three separate sampling events completed during July 17–19,
August 21–23, and September 17–19. During 2012, site-specific habitat data were collected at 22
Middle River Segment sites located in tributary, tributary mouth, main channel, side channel,
side slough, and upland slough sites between RM 178.0 and RM 101.4 (Table 8.5-16). In the
Lower River Segment, 11 sites were sampled in tributary, tributary mouth, side channel and side
slough habitats between RM 95.4 and RM 77.0 (Table 8.5-16). Site-specific observations were
obtained using visual means in clear water areas during snorkel surveys and pedestrian surveys
of spawning grounds, and using beach seine methods in turbid areas. Specific locations of
juvenile fish located during snorkel surveys were identified using colored weights, while fish
position was transmitted verbally from the snorkeler to the data recorder. Seine sampling was
performed in turbid areas of uniform depth and velocity and micro-habitat data were recorded at
a representative location within the seined area. Micro-habitat and biological data recorded
during the 2012 sampling effort consisted of the following datum:
• Site location (aerial photographs and/or GPS)
• Mesohabitat type
• Fish species
• Assumed life stage (adult, juvenile, or fry)
• Total fish length (mm) for juvenile fish and/or life stage for adult fish
• Number of fish observed
• Water depth (nearest 0.1 ft) at juvenile observations using a top setting rod
• Water depth at upstream end of the redd (nearest 0.1 ft) for adult spawning observations
• Position in water column of juvenile fish (distance from the bottom)
• Focal point and mean column velocity (feet per second to nearest 0.05 fps) measured
using a calibrated Swoffer current meter
• Substrate size (dominant, sub-dominant, percent dominant) characterized in accordance
with a Wentworth grain size scale modified to reflect English units (Table 8.5-17)
• Proximity to habitat structure/cover features (juvenile observations): boulder (> 10 inch
diameter), large wood debris (> 4 inch diameter, > 10 feet long), aquatic vegetation,
undercut bank, overhanging vegetation (< 3.3 ft of water surface), and water depth (> 3.3
ft depth)
• Relevant comments pertaining to fish cover associations and/or behavioral characteristics
• Presence of groundwater upwelling (changes in water clarity, temperature, or visible
upwelling)
• Water turbidity (Hach 2100P portable turbidity meter)
• Redd dimensions (length and width in feet to nearest 0.1 ft)
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A total of 252 observations of site-specific habitat use were recorded during 2012 in the Middle
and Lower segments (Table 8.5-16). Habitat measurements were obtained for juvenile and/or
adult stages of Chinook, sockeye, coho, chum, and pink salmon; rainbow trout; Arctic grayling;
and longnose sucker.
For 2013–2014 studies, site-specific habitat suitability information will be collected for target
species using HSC-focused field surveys to locate and measure micro-habitat use by spawning
and rearing (adult and juvenile) life stages. Proposed sampling methods include biotelemetry,
pedestrian, snorkel, and seining. Two other possible methods, DIDSON sonar and electrofishing,
are being explored for use in detecting habitat use in turbid water conditions. Selected methods
will vary based on habitat characteristics, season, and species/life history of interest. Selected
methods are subject to ADF&G Fishery Resource Collection Permit requirements. Additionally,
winter surveys will utilize underwater video during clear water periods to identify under-ice and
open-water habitat use by rearing life stages. Depending on safety concerns, it has been proposed
to conduct both daytime and nighttime surveys during winter sampling to determine any
differences in habitat use.
For development of site-specific HSC curves, habitat use information (water depth, velocity,
substrate type, upwelling, turbidity, and cover) will be collected at the location of each identified
target fish and life stage.
As part of the 2013 studies, AEA will test the feasibility of measuring vertical hydraulic gradient
as a site-specific microhabitat variable using field measurements, and if determined feasible and
effective at describing upwelling and downwelling, AEA will incorporate the methods into the
site-specific HSC development process. The results of the feasibility test will be summarized in
the Initial Study Report.
If possible, a minimum of 100 habitat use observations will be collected for each target species
life stage. However, the actual number of measurements targeted for each species and life stage
will be based on a statistical analysis that considers variability and uncertainty (Bootstrapping).
While information will be collected on all species and life stages encountered, the locations,
timing, and methods of sampling efforts may target key species and life stages identified in
consultation with the TWG during Q1 of 2013. A description of each of the proposed sampling
methods is presented below.
8.5.4.5.1.1.5. Spawning/Redd Surveys
The timing and location of spawning/redd surveys will be based in part on the periodicity data
developed in a previous step (see Section 8.5.4.5.1.2) as well as from information obtained
during radio telemetry surveys conducted as part of fisheries studies. This information will be
used to help identify sampling timing and areas with the highest concentration of spawning
activity for the five salmon species (sockeye, coho, Chinook, pink, and chum salmon). A
proposed schedule for 2013 and 2014 spawning/redd surveys is presented in Table 8.5-14.
Although several different methods may be used to identify the presence of spawning fish
(biotelemetry, pedestrian survey, or DIDSON sonar), once an actively spawning fish or newly
constructed redd is identified, each of the following measurements will be made:
• Location of sample area on high-resolution aerial photographs and/or GPS location for
individual or groups of measurements
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• Species of fish occupying the redd or responsible for construction
• Redd dimensions (length and width in feet to nearest 0.1 ft)
• Water depth at upstream end of the redd (nearest 0.1 ft), using a top setting rod
• Mean water column velocity (feet per second to nearest 0.05 fps), using a Price AA
current meter
• Substrate size (dominant, sub-dominant, and percent dominant) characterized in
accordance with a Wentworth grain size scale modified to reflect English units (Table
8.5-17)
• Water temperature (to nearest 0.1 degree Celsius)
• Dissolved oxygen, using a hand-held probe
• Indications of the presence of groundwater upwelling (changes in water clarity,
temperature, or visible upwelling)
• Turbidity (using a portable turbidity meter) for each group of redds or in mainstem
habitat areas with relatively large concentrations of spawning fish (this information to be
used for comparison to measurements made during the 1980s survey)
The accuracy of water velocity meters and water quality probes and meters will be assessed prior
to each field effort and, if possible, concurrently with field data collection. Price AA current
meter accuracy will be tested prior to use by performing a spin test and meter performance will
be evaluated continuously during field measurements by monitoring bucket wheel rotation
(USGS 1999). For each spin test, the meter bucket wheel should spin freely for a minimum of
two minutes, though optimum spin time is more than four minutes (USGS 1999). Results of all
Price AA meter spin tests will be recorded in a current meter accuracy test log. Accuracy of
hand-held temperature probes will be tested prior to field use in controlled water baths using a
National Institute of Standards and Technology thermometer as a control (Dunham et al. 2005).
Dissolved oxygen probe accuracy will be tested using known 0 percent oxygen (sodium sulfite)
and 100 percent oxygen (water-saturated air) solutions. Turbidity meters will be checked for
accuracy prior to each use using multiple turbidity standards that encompass a wide range of
turbidity values (< 0.1 NTU – 800 NTU). All data will be recorded on waterproof data sheets to
ensure consistent data collection between surveys.
8.5.4.5.1.1.6. Juvenile and Resident Rearing
To ensure the identification of habitat use by adult (resident species) and juvenile rearing
species, a combination of survey methods will be employed including snorkel surveys,
beach/stick seining, underwater video, and if permitted, electrofishing. Seining and electrofishing
techniques will predominately be used in turbid water areas (main channel, side channels, side
sloughs) where underwater visibility is limited (generally greater than 4 nephelometric turbidity
units [NTU]). The surveys will be conducted by a team of two or three fish biologists with
extensive experience in salmonid species identification. A proposed schedule for 2013 and 2014
adult and juvenile rearing surveys is presented in Table 8.5-14. A general description of each of
the proposed sampling methods is presented below.
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Snorkel Survey/Fish Observations 8.5.4.5.1.1.6.1
Prior to each survey, a Secchi disk reading will be taken to determine the visibility corridor for
sampling. For this, a Secchi disk will be held underwater by the data recorder, and a tape
measure extended by the snorkeler from the Secchi disk outward to a point where the disk is no
longer clearly visible. As a general rule, when visibility conditions are less than four feet, no
underwater sampling will occur. Water temperature will also be recorded at the beginning of
each survey.
To ensure accurate estimation of fish size underwater, the snorkelers will calibrate their sight to a
ruler prior to beginning each survey. Rulers and objects of known length (e.g., fingers, marks on
diving gloves) will be used during the survey to maintain accuracy in the estimation of fish
length. Starting at the lower/downstream point within a study area, the snorkelers will proceed in
an upstream direction making observations of all microhabitat types within their line of sight.
When two divers are working together, both sides of the clear water slough or side channel will
be covered, with the midpoint of the water body serving as the delineation point of coverage for
each diver. When only a single diver is conducting the survey, the diver will survey one or both
sides of the channel, depending on the range of microhabitats present. When a fish is observed
the snorkeler will verbally transmit the following information to the data recorder:
• Location of sample site or area on high-resolution aerial photographs and/or GPS location
for individual or groups of measurements
• Fish species
• Assumed life stage (adult, juvenile, or fry)
• Total fish length (mm)
• Number of fish observed
• Mesohabitat type
• Water depth (nearest 0.1 ft) using a top setting rod
• Location in water column (distance from the bottom)
• Focal point and mean column velocity (feet per second to nearest 0.05 fps) measured
using a Price AA current meter
• Substrate size (dominant, sub-dominant, and percent dominant) characterized in
accordance with a Wentworth grain size scale modified to reflect English units (Table
8.5-17)
• Proximity/affinity to habitat structure/cover features (e.g., boulder, wood debris, aquatic
vegetation, undercut bank, and overhanging vegetation)
• Relevant comments pertaining to cover associations and/or behavioral characteristics of
the fish observed
All data will be recorded on waterproof data sheets to ensure consistent data collection between
surveys. Accuracy of instruments used in association with snorkel observations will be tested as
described for equipment used in spawning observations (see Section 8.5.4.5.1.1.5).
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Only fish holding over a fixed position will be included in the microhabitat survey. Moving fish
will not be enumerated in order to minimize inaccurate habitat measurements, and to prevent
double-counting of fish.
Pole/Beach Seining 8.5.4.5.1.1.6.2
Pole seining will be used in turbid water areas of all mainstem habitat types that cannot be
sampled with underwater techniques due to visibility limitations. Pole seines used for this effort
will be 4 feet in depth and 40 feet in length, 3/16-inch mesh (net body) with a 1/8-inch mesh net
bag. The pole seine is operated with one person on each pole and the net is worked through the
sample area in an upstream direction. A bag is kept in the middle of the net to collect fish as they
are directed into the net by the wings. The operators must work carefully to ensure that the lead
line is kept on the bottom to prevent the fish from escaping from under the net and to keep the
bag expanded as they work the net upstream.
An attempt should be made to sample fish from relatively small areas of approximately 5 meters
by 5 meters with consistent depths, velocities, and substrates; however, exact size and
dimensions will sometimes change to facilitate sampling larger areas of relatively uniform
habitat when fish densities are low. The field crew should measure and record the area sampled
by the seine in order to express the number of fish captured per unit area.
Once captured, fish will be identified to species, counted, and released in close proximity to the
capture site. For each area sampled, data collection will be similar to that collected during
snorkel surveys with the exception of fish distance from the bottom and focal velocity. Because
no direct observation of the position of the fish in the water column can be made in turbid water,
fish position and focal velocity will not be recorded; a single depth and velocity measurement
will be recorded at a location with representative characteristics of the area seined. Additionally,
surveyors will need to rely on feeling the channel bottom with their hands and feet to
characterize substrate composition. All data will be recorded on waterproof data sheets. Digital
photographs will be taken of representative habitat types where fish of different species and size
classes are observed.
Electrofishing 8.5.4.5.1.1.6.3
If electrofishing is permitted in turbid water areas of the Middle and Lower River segments,
barge or backpack electrofishing surveys maybe used to capture fish and determine micro-habitat
use. Barge-mounted electrofishing is effective in areas that are wadeable, but have relatively
large areas to cover. Backpack electrofishing is effective in wadeable areas that are relatively
narrow and shallow. The effectiveness of barge and backpack electrofishing systems can be
enhanced through the use of block nets. In all cases the electrofishing unit will be operated and
configured with settings consistent with guidelines established by ADF&G. The location of each
electrofishing area will be mapped using hand-held GPS units and marked on high-resolution
aerial photographs.
Selection of the appropriate electrofishing system will be made as part of site selection. To the
extent possible, the selected electrofishing system will be standardized and the methods will be
repeated during each sampling period at a specific site to evaluate temporal changes in fish
habitat use. HSC measurements will be collected at each site using the methods described in the
Pole/Beach Seining section above. Where safety concerns can be adequately addressed,
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electrofishing may also be conducted after sunset in clear water areas; otherwise, electrofishing
surveys will be conducted during daylight hours.
8.5.4.5.1.1.7. Habitat Utilization Frequency Histogram/HSC Curve Development
Histograms (i.e., bar charts) will be developed for each of the habitat parameters (e.g., depth,
velocity, substrate, cover, groundwater use, etc.) using the site-specific field observations. The
histogram developed using field observations will be compared to the draft HSC curves and
literature-based HSC curves. Prior to calculation of the HSC curves, the habitat data from each
stream will be organized by species and life stage, entered into commercially available
spreadsheets, and subsequently checked for data entry accuracy. Frequency distributions will
then be generated for mean velocity, depth, and substrate type for each species and then
normalized. Histogram plots of depth and mean column velocity utilization will be developed
using bin sizes defined by using the Stuges (1926) formula:
R/(1+3.322Log(n))
Where R is the range of values and n is the total number of observations. The frequency of the
field observations will then be converted into HSC curves by scaling the distribution between 0
and 1 (utilization values divided by the maximum value observed). The resulting curves will be
inspected and visually adjusted, in part to smooth-out sharp breakpoints, and in the case of depth,
extend the range of the curve to reflect a non-limiting condition.
For comparative purposes, HSC curves for each species and life stage will first be developed
using pooled data from all sampling areas and time periods, and then (depending on available
data) separate curves will be developed based on stream-specific data (i.e., geomorphic reach,
mainstem habitat type, clear vs. turbid water, and upwelling areas) and winter vs. summertime
sampling efforts. Thus, for certain species and life stages, four or five separate HSC curves may
be generated.
8.5.4.5.1.1.8. Bootstrap Analysis for HSC Curve Development
For data sets with less than the target number of observations (n ≥100), bootstrap analysis will be
used to assess the variability and confidence intervals around each of the data sets used to
develop the HSC curves. Bootstrapping is a data-based simulation method for assigning
measures of accuracy to statistical estimates and can be used to produce inferences such as
confidence intervals (Efron and Tibshirani 1993). This method is especially useful when the
sample size is insufficient for straightforward statistical inference. Bootstrapping provides a way
to account for the distortions that may be caused by a specific sample that may not be fully
representative of a population.
To complete the analysis, a group of individual observations (e.g., depth, velocity measurement
for a particular species and life stage) will be resampled with replacement up to the number of
the original data set. Each sample involves the following steps:
4. A vector of length equal to the observed data set (N) is created.
5. The vector is filled with the N random samples (with replacement) from the observed
data set.
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6. The observations are then grouped into bins for velocity and depth— bin sizes will be
driven by the desire to group a minimum of 25 observations within each velocity and
depth bin.
7. The bin counts will be normalized so that the HSC value for the bin with the maximum
count equals 1.0.
The resulting bootstrap samples represent 1,000 possible HSC curves that might be generated
from empirical data assuming random chance in observing fish. Using the resulting curve sets,
confidence intervals can then be derived from the resulting HSC curves.
8.5.4.5.1.2. Habitat Suitability Index (HSI)
Additionally, criteria will be developed related to juvenile fish stranding and trapping in the
varial zone (e.g., the size, species, and periodicity of susceptible fish, recolonization rates,
critical streambed gradient, cover factor, periodicity of cover factor, isolation elevations
with/without cover, and minimum size of trapping areas). These criteria are described in more
detail in subsequent sections.
8.5.4.5.1.2.1. Winter Habitat Use Sampling
Susitna River overwintering habitats are critical to juvenile and adult fish species. Susitna River
stream flows are typically lowest during the winter period and, with the exception of open-water
leads associated with groundwater upwelling, the river is largely covered in surface ice.
Although some winter studies were conducted in the Susitna River during the 1980s, information
related to salmon egg development and juvenile and adult fish behavior and habitat utilization
during winter is limited (see Section 8.5.2.1.6) (Vining et al. 1985; Stratton 1986; Sundet 1986).
Project operations will likely result in substantially higher stream flow levels during the winter
period, and will likely influence the quality and quantity of existing habitat for salmon egg
incubation, and juvenile and adult fish rearing and holding. To understand potential effects of
Project operations during winter, it will be important to evaluate the relationship between
intergravel flow characteristics in different habitat types (e.g., side channels, side sloughs, upland
sloughs) and main channel surface flow and to identify winter habitat use and behavior of
juvenile and adult fish species. Observations of site-specific habitat utilization and diurnal
behavior of juvenile and adult fish behavior will provide important support to HSC and HSI
development and habitat modeling efforts for the 2013–2014 Instream Flow Study.
Winter habitat use and intergravel water quality monitoring studies will be initiated during a
2012–2013 pilot effort and will be continued during winter 2013–2014. The winter 2012–2013
pilot study will be comprised of three components: 1) intergravel temperature, dissolved oxygen,
and water level monitoring; 2) fish behavior and habitat use observations; and 3) winter fish
capture. The pilot study will evaluate the feasibility of using different instruments, methods, and
approaches for winter data collection in preparation for a more developed effort during the
winter 2013–2014 study period. The 2012–2013 pilot study will also provide preliminary data
and information regarding intergravel temperature and water quality conditions, site-specific fish
habitat use and behavior and species richness and size class composition among sampled
habitats. These studies will be coordinated with the study leads for fish, geomorphology,
groundwater, and ice processes.
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The 2012–2013 pilot study will be conducted at two areas in the Middle River Segment that
contain a diversity of habitat types with groundwater influence, have documented fish utilization,
and are accessible to and from Talkeetna during winter. The tentative areas for the 2012–2013
pilot study are habitat complexes near Whiskers Slough (RM 104.8–106.0) and Skull Creek (RM
128.1–129.7), which are also proposed Focus Areas that will be used across resource disciplines
(Figure 8.5-28 and Figure 8.5-29). Within each proposed study area, potential sampling locations
have been identified; however, adjustments to each location may be made depending on field
conditions and site selection processes described below (Figure 8.5-28 and Figure 8.5-29). The
initial work on the 2012–2013 pilot study will consist of a focused review of literature from
1980s studies and more recent research to identify potential methods for each component of
2012–2013 pilot studies.
For the 2012–2013 study component focused on intergravel temperature, dissolved oxygen, and
water level monitoring, sites will be selected using a stratified random sampling approach. The
Whiskers Slough and Skull Creek study areas will be stratified by habitat type (Beaver complex,
backwater, side slough, upland slough, tributary mouth, main channel) and areas in which
salmon were observed spawning in 2012. A total of 8–12 monitoring sites will be randomly
selected among strata. Depending on individual site characteristics, temperature monitoring
devices will be installed at locations of 1) groundwater upwelling, 2) bank seepage and lateral
flow from mainstem, 3) mixing between upwelling and bank seepage, 4) no apparent intergravel
discharge, fish spawning, and 5) main channel Susitna River flow.
Intergravel temperature will be measured at each monitoring site and surface temperature probes
will be co-located at a subset of the monitoring sites to allow for surface and intergravel
comparisons. For intergravel temperature measurement, Hobo Tidbit temperature probes will be
deployed at three separate gravel depths (5 cm, 20 cm, and 35 cm) corresponding to observed
burial depth ranges of chum and sockeye eggs (Bigler and Levesque 1985; DeVries 1997).
Probes will be attached to stainless steel cable and inserted into the gravel using a steel
installation device (e.g., Nawa and Frissell 1993; Zimmerman and Finn 2012). Dissolved oxygen
(DO) will be measured in conjunction with intergravel temperature at one location at each of the
two study areas. The DO sensors (HOBO logger with optical sensor) will likewise be inserted
into the gravel to a depth of approximately 20 centimeters using a stainless steel cable. Stage
response of surface stream flow and subsurface groundwater to fluctuations in Susitna River
main channel stage will be assessed using pressure transducers (Solinst level loggers), deployed
in side channel, side slough, and main channel areas, and piezometers deployed subsurface in
adjacent floodplain areas. The final number and location of monitoring sites will vary depending
on site conditions and safety concerns (Figure 8.5-28 and Figure 8.5-29). Temperature, DO, and
stage recording equipment will be deployed in January 2013 following the chum and sockeye
salmon spawning period; a subset of temperature loggers and DO loggers will be retrieved prior
to ice break-up in April 2012, while remaining temperature and water level recorders will remain
at deployment sites through June 2013 to record temperature and water stage patterns through the
period of ice break-up. Data from the above-gravel loggers (temperature and stage recorders)
will be downloaded on a monthly basis and will occur concurrently with times specified as part
of the fish observation study. Accuracy of temperature, DO, and water level loggers will be
tested prior to deployment using techniques described in Section 8.5.4.5.1.1.5.
Specific tasks for the intergravel temperature, dissolved oxygen, and water level monitoring
component of the 2012–2013 pilot study are as follows:
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• Monitor intergravel temperature at representative habitats and at 2012 salmon spawning
sites at varying gravel depths to encompass salmonid egg burial depths during winter and
early spring (January – June); retrieve a subset of loggers prior to ice break-up (April).
• Record surface water temperature at a subset of sites to allow comparison between
surface and intergravel temperature.
• Monitor intergravel DO at one monitoring site in each study area.
• Evaluate the potential relationships between water temperature among monitoring sites in
off-channel and main channel habitats and Susitna River stage.
• Compare water level (stage) response in off-channel and floodplain areas relative to
Susitna River main channel stage.
• Evaluate available data related to species-specific thermal tolerances of salmonid egg
incubation and fry emergence.
• Develop recommendations for intergravel temperature monitoring in 2013–2014 studies.
The 2012–2013 winter study component focused on observations of fish behavior will use
underwater video cameras and DIDSON sonar to monitor fish communities during day and night
conditions. Observational studies will be conducted at five to six sites in slough and side channel
habitats of the Whiskers Slough and Skull Creek study areas during February – April 2013
(Figure 8.5-28 and Figure 8.5-29). Observation sites will be monitored with an underwater
camera on a monthly basis during the sampling period, at randomly selected times during day
and night. The DIDSON sonar will be utilized in turbid conditions (>4 NTU) and
opportunistically during clear water conditions to gauge the applicability of DIDSON technology
for monitoring fish behavior and habitat utilization. Each method will be used in ice-covered and
open-water conditions. For ice-covered areas, the video camera or DIDSON unit will be lowered
through auger holes drilled through the ice to make 360-degree surveys. Mueller et al. (2006)
found that DIDSON cameras were effective in turbid waters for counting and measuring fish up
to 52.5 feet from the camera. Mueller et al. (2006) found that video cameras were only effective
in clear water areas with turbidity less than 4 NTU, but that video was more effective at
identifying species and observing habitat conditions than DIDSON cameras. In addition to fish
observations, video cameras will also be used to characterize winter habitat attributes such as the
presence of anchor ice, hanging dams, and substrate type.
In addition to fish observations, measurements of site-specific habitat characteristics (velocity,
water depth, substrate, cover, etc.) will be measured at observed fish locations using HSC
sampling methods (see Section 8.5.4.5.1.1). Water velocity and depth measurements will be
made either through the ice (ice holes) or in open-water leads using a topset wading rod and
Price AA meter. HSC measurements will only be collected at those fish observation points where
positive fish species identification and estimates of total length can be made. Instantaneous
measurements of water temperature and dissolved oxygen will be recorded using hand-held
probes to describe water quality conditions in the area of fish observations.
Specific tasks for fish behavior observation and habitat use component of the 2012–2013 pilot
study are as follows:
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• Utilize underwater cameras and DIDSON sonar to record juvenile and adult fish behavior
during day and night conditions to identify potential diurnal patterns in habitat utilization
during February – April 2013.
• Obtain measurements of site-specific habitat utilization data for juvenile and adult fish
species in support of HSC and HSI development.
• Develop recommendations for 2013–2014 winter fish behavior observation studies.
The results of the 2012–2013 pilot winter study will be used to develop the sampling methods for
the 2013–2014 winter studies and will be finalized and distributed to TWG participants by Q3
2013. Proposed study methods for 2013–2014 winter fish distribution studies will be completed
during Q3 2013 following analysis of data collected during 2012–2013.
8.5.4.5.1.2.2. Stranding and Trapping
Fluctuations in river flow will cause portions of the channel along the margins to alternate
between wet and dry conditions, an area referred to as the varial zone. Flow fluctuations can be
the result of precipitation falling as rain or the result of snowmelt and glacial meltwater, but the
frequency, timing, and magnitude of flow fluctuations will change under proposed Project
operations. In addition to altering the availability of suitable habitat, flow fluctuations associated
with Project operations have the potential to cause strand or trap of fish and other aquatic
organisms on dewatered portions of the channel bed. While the physical and hydraulic processes
associated with stranding and trapping are related, aquatic organisms have different responses to
stranding and trapping. Stranding occurs where fish become beached on dewatered streambed
areas as water levels recede and is generally associated with shoreline areas having low gradient
and/or dewatered areas having sufficient cover to attract fish (Figure 8.5-30). Trapping occurs
where fish in channel depressions become isolated from flowing water as water levels recede and
are subjected to stress or mortality from predation, reduced dissolved oxygen, water temperature
fluctuations, or subsequent stranding if trapping areas drain.
The incidence and severity of stranding and trapping effects will be influenced by a suite of
biological and hydrological/geomorphological factors. Stranding susceptibility varies with fish
size, time of day, and season.
Based on a review of studies conducted in Washington State, Washington Department of Fish
and Wildlife (Hunter 1992) concluded that salmonid fry smaller than 50 mm in length are most
susceptible to stranding.
The following excerpts and synopses support Hunter’s (1992) hypothesis that salmonid fry
smaller than about 50 mm in length are more vulnerable to direct impacts from ramping events
than larger fish.
Source River Location Comment
Bauersfeld 1977 Columbia River, Washington Reporting on stranding of trout, Chinook, coho, and
chum salmon, Bauersfeld noted that 86 percent of all
stranded fish were between 30 and 50 mm. The majority
of fish stranded (78 percent) were Chinook salmon.
Bauersfeld 1978 Cowlitz River, Washington “A size comparison of Chinook stranded . . .versus fish
available . . . shows that stranding was size selective,
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impacting the small (35 to 45 mm) recently emerged fry,
even though larger fish were present.”
Olson 1990 Sultan River, Washington “Susceptibility to stranding was particularly evident for
salmon fry less than 50 mm long and for steelhead less
than 40 mm long.” All Chinook salmon fry observed
(n=44) during downramping trials were 48 mm or less
and all but one coho fry were less than 46 mm (n = 12).
All steelhead fry stranded were less than 40 mm in
length.
R.W. Beck 1989 Skagit River, Washington “Once [steelhead] fry size increased above 4.0 cm,
vulnerability decreased rapidly ... Above a fry size of
4.0 cm the percentage of the main-channel population is
always found to be much greater than the associated
stranded fry of corresponding size.” R.W. Beck and
Assoc. reported that the mean size of Chinook fry
stranded was 4.3 cm. Ninety-nine percent of Chinook
fry stranded were less than 50 mm.
Stober et al. 1982 Skagit River, Washington “The 1992 observations indicate that while the fry may
be present in the nearshore area, they appear to be less
susceptible to stranding once they reach a length of
about 40 mm.”
Related to this, size (or life stage) periodicity will dictate the seasonal timing during which
vulnerable size classes may be present in the varial zone. Stranding and trapping susceptibility
may also vary by species based on differences in periodicity, as well as species-specific habitat
preferences and behavior. Recolonization rates, or how quickly organisms return once a
dewatered area is rewetted, will also influence cumulative susceptibility to stranding and
trapping.
Hydrological/geomorphological factors also affect stranding and trapping rates. Streambed areas
with low gradient represent the greatest risk to stranding. Bauersfeld (1978) reported that
stranding occurred primarily on bars with less than 4 percent gradient; other studies also reported
high incidence of juvenile salmonids stranding on bars with low gradient slope (Hilgert and
Madsen 1998; R.W. Beck 1989).
The density of juvenile salmonids may be higher in the vicinity of woody debris and emergent or
submergent macrophytes, which contributes to a higher incidence of stranding should those areas
become dewatered. At existing hydroelectric projects, site-specific trapping and stranding criteria
can be developed through experimental manipulation of flow conditions through project
operations. The current pre-Project conditions of the Susitna River preclude this approach. Thus,
stranding and trapping criteria for the Susitna River will need to be determined based on a
combination of observations under natural flow variations as well as literature-based information
derived from other regulated systems where stranding and trapping studies have been conducted.
The general susceptibility of target species and life stages to stranding and trapping will initially
be identified based on their life stage periodicity, length frequency, habitat utilization,
distribution, and abundance in the Middle and Lower segments, as determined by fish
distribution studies (see Section 9.6) and the downstream extent of Project effects. This
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information will then be used to identify areas for potential field investigations of stranding and
trapping. Under existing, unregulated conditions, the frequency, magnitude, and rate of water
level fluctuations in the Susitna River will be less than the rate of change associated with load-
following operations at existing hydroelectric projects. However, flow reductions under
unregulated flows in the Susitna River have the potential to cause stranding and trapping of
aquatic organisms. Field surveys of potential stranding and trapping areas will be conducted
immediately following flow reduction events. Immediately following such an event, a field crew
will conduct a survey of potential stranding and trapping areas following field protocols to be
developed in consultation with the TWG. Field surveys will follow a stratified random sampling
strategy at potential stranding areas to estimate the number, size, and species of fish stranded or
trapped. Field surveys will be conducted at potential stranding and trapping areas on an
opportunistic basis following up to three flow reduction events during 2013 and up to three flow
reduction events during 2014. The goal of these surveys will be to provide a relative indication
of those species, life stages, and sizes susceptible to stranding and trapping to corroborate
literature-derived criteria. In addition, the mechanisms through which each stranding or trapping
occurs will be identified (e.g., streambed gradient, emergent vegetation, etc.) and reviewed to
ensure that subsequent modeling efforts accurately reflect the relevant processes. The risks of
fish stranding and trapping will be assessed through the development of models developed to
evaluate each process separately. While stranding and trapping are both related to reductions in
water surface elevations, the specific mechanisms through which they occur are different,
requiring discrete models for each process. Time step increments, used to calculate stage
changes, will be identified during calibration of the mainstem open-water flow routing model in
Q4 2012 (see Section 8.5.4.3). Depending on the initial calibration results, time steps as short as
three minutes may be needed to match predicted to measured stage changes in the open-water
flow routing model. In 2014, the calibrated open-water flow routing model will be used to
evaluate the effects of Project operations on stranding and trapping using one-hour time steps
unless the TWG determines that shorter time steps are needed to evaluate specific fisheries
resources. Each model will incorporate relevant criteria, developed as described above, and
provide indices to quantify the extent of stranding/trapping for individual events. The stranding
index will reflect the area of potential stranding and is conceptually depicted as follows, where
SI = stranding index, AS = stranding area in square feet, and CS = cover factor for stranding:
SI = AS * CS
The trapping index will reflect the area of potential trapping and is conceptually depicted as
follows, where TI = trapping index, AT = trapping area (square feet), TT(D) = duration of
trapping factor, and CT = cover factor:
TI = AT * TT(D) * CT
These indices will then be considered in relation to the monthly frequency of potential
stranding/trapping events for a given Project operational scenario such as the example provided
in Table 8.5-18.
8.5.4.5.1.2.3. River Productivity
Development of HSC/HSI for macroinvertebrates and algae will follow a similar general
approach, which includes a literature search for available information, conducting field studies to
supplement literature-based information and to provide site-specific data, and use of a panel of
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TWG participants to finalize the HSC/HSI curves. A complete presentation of the development
of the HSC/HSI for macroinvertebrates and algae is provided in Section 9.8. A summary of the
methods for developing HSC/HSI for both macroinvertebrates and algae is presented below.
Literature-based draft HSC/HSI curves will be developed for benthic macroinvertebrate and
algae communities. Potential sources of information include the Internet, university libraries,
peer-reviewed periodicals, and government and industry technical reports. Special emphasis will
be given to the existing 1980s study (Hansen and Richards 1985) for applicable information and
methodology. Because benthic macroinvertebrate and algae communities are comprised of
numerous taxa, the HSC/HSI curves will be developed for commonly used benthic metrics or
guilds (e.g., functional feeding groups, taxa habits, habitat preference, diversity, biomass, or
dominant taxa) selected to summarize and describe the communities.
Macroinvertebrate sampling will be stratified by reach and mainstem habitat type defined in the
Project-specific habitat classification scheme (mainstem, tributary confluences, side channels,
and sloughs). To accomplish this objective, sampling will occur at six stations, each with three
sites (one mainstem site and two off-channel sites associated with the mainstem site), for a total
of 18 sites. Measurements of depth, mean water column velocity, and substrate composition will
be taken concurrently with benthic macroinvertebrate sampling at the sample location for use in
HSC/HSI development in the instream flow studies (see Section 9.8.4.2). Efforts will be made to
locate sampling stations at Focus Areas established by the Instream Flow Study team (see
Section 8.5) in an attempt to correlate macroinvertebrate data with additional environmental data
(flow, substrates, temperature, water quality, riparian habitat, etc.) for statistical analyses, and
HSC/HSI development. Station and site locations will be determined during Q1 2013.
For use in the mainstem aquatic habitat model, HSC/HSI curves will also need to be developed
to describe the response of aquatic organisms to cyclic inundation and dewatering of varial zone
areas (see Section 8.5.4.6.1.6). For instance, algae (algae growing on substrates) will colonize a
site if it contains suitable depth, velocity, and substrate, but colonization may not occur until the
area has been inundated for a period of time. Conversely, the effects of dewatering of the site on
algae production will depend on the duration of dewatering and conditions at the time of the
dewatering (see Section 9.8.4.9).
Next, a histogram (i.e., bar chart) will be developed for each of the habitat parameters (e.g.,
depth, velocity, substrate, frequency of dewatering) using site-specific field observations. The
histogram developed using field observations from 2013 will then be compared to the literature-
based HSI curve to validate applicability of the literature-based HSI curve for aquatic habitat
modeling. This stage will be conducted by Q3 2014.
8.5.4.5.1.3. Periodicity
A species and life stage periodicity table will be developed applicable to the different segments
of the Susitna River. Information presented in the 1980s reports will be used to generate a draft
periodicity table that will be included in the HSC/Periodicity TM scheduled for completion in
December 2012. Specifically, the TM will summarize fish habitat utilization in terms of
periodicity of use among main channel and off-channel macro-habitats in the Upper, Middle and
Lower Susitna River based on relevant literature from the 1980s studies. Periodicity and macro-
habitat use will be described by species and life stage (e.g., migration, spawning, incubation,
emergence, rearing) for target species. An example of the draft periodicity table for Chinook
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salmon is presented in Table 8.5-2. Periodicity information for target fish species will be
obtained from 1980s study results; if necessary, information from other literature sources
representing similar regions and fish populations (e.g., Morrow 1980, etc.) and TWG members
will be used. Updates and/or revisions to the draft periodicity table will be completed in
cooperation with the TWG during proposed meetings to be held in the Q1 2013 and Q4 2014
(Table 8.5-14). The final periodicity table will be developed following the 2014 field season and
will incorporate the findings of the 2012, 2013, and 2014 fisheries studies (Table 8.5-14).
Climatic and hydrologic patterns are important considerations in determining salmon distribution
and abundance. Large-scale climatic changes (e.g., Pacific Decadal Oscillation) affect regional
weather conditions that subsequently influence hydrologic conditions (Hartmann and Wendler
2005). Changes in river hydrology can influence the stability and persistence of aquatic habitats
and can determine fish distribution and abundance (Connor and Pflug 2004). Long-term adult
salmon escapement data will be examined to identify relationships between temporal patterns in
environmental conditions and salmon distribution, abundance, and migration. Analyses of flow-
dependent biological cues, such as possible relationships between climatic, hydrologic, and fish
habitat indices and salmon abundance and migration timing, will be based on available long-term
datasets for Deshka River Chinook salmon and Yentna River sockeye salmon. Other Susitna
River basin long-term data sets pertaining to salmon migration timing and abundance will be
included if available. Implementation details will be developed in consultation with the TWG in
Q2 2013, initial study results discussed with the TWG in Q4 2013, and reported in the ISR in Q1
2014 (Table 8.5-14).
8.5.4.5.2. Work Products
The HSC/HSI Development Study component will include the following work products:
• Draft HSC curves based on information collected during the 1980s studies of the Susitna
River and other regional data sources. Data gaps will also be identified as part of this
effort.
• Map displaying the number and distribution of HSC sampling locations based on a
stratified random sampling approach.
• Summary of site-specific HSC curve data collected for the target fish species and life
stages as a function of depth, velocity, and substrate.
• Histogram plots displaying results of site-specific data collection.
• Results of bootstrap analysis used to assess variability and confidence intervals around
each of the HSC curves developed from site-specific data.
• HSI curves developed from site-specific data to describe the response of aquatic
organisms to groundwater upwelling, turbidity, colonization rates, winter habitat use, and
stranding and trapping criteria.
• Analysis of potential relationships between climatic, hydrologic, and fish habitat indices
and salmon abundance and migration timing in the Deshka and Yentna rivers.
These work products and other results of the HSC/HSI analyses will be compiled and presented
in initial and updated study reports. With the Initial Study Report, AEA will file a detailed
description of the methods that will be used for evaluating fish abundance measures (e.g.,
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number of individuals by species and age class) relative to specific microhabitat variable
measurements where sampling overlaps, to determine whether a relationship between a specific
microhabitat variable and fish abundance is evident. The results of that analysis will be
presented in the Q1 2014 TWG meeting. If the results of the initial comparisons indicate strong
relationships may exist between a specific microhabitat parameter and fish abundance for a
target species and life stage, expanded sampling may be necessary in 2014 to investigate these
microhabitat relationships further. AEA will include in the results of the evaluation any
proposals to develop HSC curves for any of the 8 additional parameters as part of the 2014 study
season.
8.5.4.6. Habitat-Specific Model Development
This study component develops the core structures of the aquatic habitat-specific models.
Development of these models will require careful evaluation of existing data and information as
well as focused discussions with technical representatives from the TWG. These models will rely
in part on information and technical analyses performed in other study components as a basis for
developing model structures (e.g., Habitat Mapping; other riverine process studies). Physical
habitat models are often used to evaluate alternative instream flow regimes in rivers (e.g., the
Physical Habitat Simulation [PHABSIM] modeling approach developed by USGS; Bovee 1998;
Waddle 2001). Methods available for assessing instream flow needs vary greatly in the issues
addressed, their intended use, their underlying assumptions, and the intensity (and cost) of the
effort required for the application. Many techniques have been used, ranging from those
designed for localized site or specific applications to those with more general utility. The
summary review reports of Wesche and Rechard (1980), Stalnaker and Arnette (1976), EA
Engineering, Science and Technology (1986); the proceedings of the Symposium on Instream
Flow Needs (Orsborn and Allman eds. 1976); Electric Power Research Institute (2000); and
more recently the Instream Flow Council (Annear et al. 2004) provide more detailed information
on specific methods. The methods proposed in the IFS include a combination of approaches that
vary depending on habitat types (e.g., mainstem, side channel, slough, etc.) and the biological
importance of those types, as well as the particular instream flow issue (e.g., connectivity/fish
passage into the habitats, provision of suitable habitat conditions in the habitats, etc.).
8.5.4.6.1. Proposed Methodology
Development of the models will involve completion of a series of tasks as noted below.
• Transect/Study Segment Selection – In coordination with the TWG and riverine process
study leads, use the results of the Characterization of Aquatic Habitats (see Section 9.9)
component to select transects/study segments within each of the selected habitat types
identified in the Susitna River to describe habitat conditions based on channel
morphology and major habitat features. Additional habitat transects/segments will be
selected to describe distinct habitat features such as groundwater areas, spawning and
rearing habitats, overwintering habitats, distinct tributary mouths/deltas, and potential
areas vulnerable to fish trapping/stranding. The transects used for defining the open-water
flow routing model will also be integrated into this analysis.
• TWG Site Reconnaissance – Conduct a site reconnaissance with personnel from
agencies, Alaska Native entities, and other TWG members to review river reaches, select
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proposed Focus Areas and potential transect/study segment locations, and discuss options
for model development. This reconnaissance trip has been scheduled for early-mid
September and will encompass a three- to four-day effort. The first day will be an office-
based meeting during which specific methods will be reviewed and their applicability to
addressing specific questions will be discussed, and the field itinerary reviewed. This will
be followed by a one- to two-day field reconnaissance of representative habitat types
including but not limited to mainstem channel, side channels, side sloughs, and upland
sloughs. Stops will be made at each of these habitat types and assessment methods will be
discussed, with the goal of reaching consensus on which methods will be applied for
evaluating flow-habitat relationships. Participants will reconvene in the office on the final
day of the trip to discuss observations and reach agreement on assessment methods.
• Model Selection: Field Surveys and Data Collection – Once study areas and
transects/study segments have been identified, detailed field surveys will begin. These
will be tailored based on habitat types to be measured and the selected models to be used.
It is likely this will involve a combination of 1-D and 2-D modeling approaches as well
as application of empirically-based methods such as the RJHAB model applied in the
1980s studies (Hale et al. 1984). The RJHAB model was used to assess/model the effects
of flow alterations on juvenile fish habitat for off-channel areas. At this time, it is
anticipated that two-dimensional modeling will be applied to one or more representative
reaches in the Middle River Segment. For this, a multi-stepped approach will be used so
that after each field data collection effort, topographic data will be projected via computer
analysis to identify locations requiring the collection of more data points. Table 8.5-19
provides a listing of potential models/methods that will be considered as part of the IFS.
The most appropriate methods for selected study areas will be determined via careful
review of site conditions and the underlying questions needing to be addressed. Methods
selection will be done as a collaborative process within the IFS-TWG.
Regardless of specific method, field surveys will involve measurement of water velocities, water
depths, water surface elevations, bottom profiles/topography, substrate characteristics, and other
relevant data (e.g., upwelling, water temperature) under different flow conditions. One of the
tasks for 2012 is to evaluate and determine specific flow targets for these field surveys.
8.5.4.6.1.1. Habitat Model Selection
Identifying and quantifying the predicted changes in aquatic habitat in the Middle and Lower
segments of the Susitna River under the proposed Project operational scenarios will require the
use of several different hydraulic and biological models. Each of the models proposed for use has
been selected to assist in the evaluation of the physical, and biological effects of the proposed
Project.
The mainstem aquatic habitat model integrates hydraulic modeling, channel bathymetry, and
biological information on the distribution, timing, abundance, and suitability of habitat to
estimate metrics (such as varial zone area and frequency of inundation and dewatering) that will
be used to compare the effects of the proposed operational scenarios. The following section
provides an overview of the habitat and hydraulic models proposed as part of the evaluation of
Project-related effects including boundary conditions transects, 2-Dimensional (2-D) modeling,
single transect PHABSIM, stranding and trapping, and fish passage/connectivity.
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8.5.4.6.1.1.1. Boundary Condition Transects
The upstream and downstream boundaries as well as the lateral extents of the Focus Areas have
been chosen so that appropriate boundary conditions can be established for the hydraulic and bed
evolution modeling. Considerations included encompassing potential inflow and outflow points
to preserve the mass balance and minimize difficulties and assumptions associated with inflow
points. Potential upstream connections for side channels, side sloughs, and upland sloughs were
also identified and included in the modeling domain. The upstream and downstream limits on the
main channel were identified to either provide relatively uniform flow conditions or sufficient
distance upstream and downstream from areas of interest so that flow conditions in the area of
interest are not significantly affected by the flow directions at the boundary.
Water levels measured during the cross-section and bathymetric surveys for each boundary
condition transect will be used to assist in calibrating the 2-D models for each Focus Area. In
addition to water surface elevations, the depths and velocities measured at the boundary transects
will be used to assist with hydraulic modeling for the single transect PHABSIM sites.
8.5.4.6.1.1.2. 2-D Modeling
Determining the relationship between river flow and the physical and hydraulic characteristics of
a river system as dynamic as the Susitna River is a complex undertaking that requires
considerable investigation and coordination. This is especially true for assessing project-related
impacts to small, local-scale channel areas containing unique morphology and habitat features
(e.g., fish spawning, groundwater upwelling, stranding and trapping, fish passage/connectivity).
To assist with this effort, 2-D hydraulic modeling will be used to evaluate the detailed hydraulic
characteristics of the Susitna River on smaller, more local scales where it is necessary to consider
the more complex flow patterns to understand and quantify project effects under various Project
operation scenarios. The 2-D model will be applied to specific Focus Areas that are
representative of important habitat conditions and the various channel classification types. These
sites will be chosen in coordination with the TWG and the Fish and Aquatics Instream Flow,
Riparian Instream Flow, Ice Processes, and Fish studies to facilitate maximum integration of
available information between the studies (see Section 8.5.4.2). A detailed discussion of the 2-D
modeling is presented in Section 6.6.
Selection of the appropriate mesh size for the 2-D bed evolution mode is dictated by several
factors including the size and complexity of the site feature(s); the desired resolution of output
information such as water surface elevation, velocity, depth, and bed material gradation; and any
limitations on the maximum number of elements that the model can simulate.
One approach to reduce the trade-offs between model complexity and physical limitations of the
2-D model is to utilize a variable mesh (also referred to as flexible mesh). A variable mesh
allows a finer mesh to be used in areas where either the information desired or the condition
being modeled requires higher spatial resolution (RSP 6.6.4). The 2-D models being considered
for this study are formulated with a flexible mesh, allowing the size of the model element to be
varied. Figure 8.5-31 provides examples of a relatively coarse and relatively fine mesh applied to
the potential Focus Area at Whiskers Slough in the Middle River Segment.
Examples of areas that may require finer mesh sizes include sloughs, smaller side channels,
spawning areas, stranding and trapping areas, hydraulic control features, and tributary mouths.
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Areas where lower spatial resolution may be appropriate include main channel, floodplains, and
large side channels. In the areas of higher resolution, the mesh size will be on the order of several
feet to 25 feet. In areas where lower spatial resolution is appropriate, the mesh size may be in the
range of 25 to 100 feet (RSP 6.6.4).
At some Focus Areas, two model meshes may need to be developed. One mesh would be for
executing the bed evolution model, which requires orders of magnitude more time to execute
than the 2-D model without the moveable bed options running. The other mesh would be
associated with a fixed bed representation of the site that would be used to output the hydraulic
conditions at a finer resolution for development of aquatic habitat indices.
8.5.4.6.1.1.3. Single Transect PHABSIM
Another model that will be considered for evaluating Project-related effects on fish habitats is the
single transect Physical Habitat Simulation (PHABSIM) modeling. The PHABSIM model
(Milhous et al. 1981) will be applied to some or all of the open-water flow routing model
transects to develop relationships between main channel flow and habitat for the spawning and
rearing life stages of the target fish species. Supplemental main channel transects will be
established as needed to more fully characterize main channel habitats, either as part of the Focus
Area analysis or at separate locations associated with specific habitat types. The need for and
exact number of the supplemental transects will be determined based on results of the habitat
mapping (see Section 9.9) that will be completed in Q1 2013. PHABSIM-based models will also
be applied to selected habitat types within the Focus Areas where 2-D modeling is not warranted.
PHABSIM is part of an analytical framework for addressing flow management issues called the
Instream Flow Incremental Methodology (IFIM) (Bovee et al. 1998). PHABSIM is used to
predict physical habitat changes associated with flow alterations by describing the flow-
dependent characteristics of physical habitat in light of selected biological responses of target
species and life stages. The stream hydraulic component predicts depths and water velocities at
specific locations on a cross-section of a stream. Field measurements of depth, velocity, substrate
material, and cover at specific sampling points on a cross-section or transect are taken at
different flows. Hydraulic measurements, such as water surface elevations, are also collected
during the field survey. These data are used to calibrate the hydraulic models, which are then
used to calculate depths and velocities at flows different from those measured. The habitat
component weights each stream cell using indices (HSC/HSI) that assign a relative value
between 0 and 1 for each habitat attribute, indicating how suitable that attribute is for the life
stage under consideration. In the last step of the habitat component, the hydraulic estimates of
depth and velocity at different flow levels are combined with the suitability values for those
attributes to weight the area of each cell at the simulated flows. The weighted values for all cells
are summed – thus the term weighted usable area (WUA).
8.5.4.6.1.1.4. Stranding and Trapping
The purpose of this analysis is to develop indices that provide a relative quantification between
proposed Project operational scenarios and the potential for stranding and trapping of aquatic
organisms. More specifically, the effort is targeted to evaluating the stranding and trapping
potential for juvenile fish. Stranding involves the beaching of fish as the water level recedes and
is typically associated with low gradient (<4 percent) shoreline areas or cover conditions that
result in fish remaining in an area as it is dewatered. Mortality occurs in stranding as fish are left
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beached on the dewatered shoreline. Trapping is the retention of fish in pools formed by
depressions as the water level recedes. Stress and potential mortality to trapped fish occur from
several mechanisms including temperature fluctuations, reduction in dissolved oxygen,
predation, and stranding as the water in the pool infiltrates into the substrate. Both the stranding
and trapping analyses utilize results of hourly water surface elevation determinations from the
Mainstem Open-water Flow Routing Model to track water level fluctuations and calculate
numerical indices representing the potential for stranding and the potential for trapping of
aquatic organisms.
Indices for predicting stranding and trapping are based on equations that relate physical
characteristics of the stranding and trapping areas to the potential for stranding and trapping to
occur. The information for the physical site characteristics is derived from the bathymetry and
mapping through the application of GIS. The hourly water surface elevations provide the basis
for identifying when a stranding or trapping site becomes dewatered or disconnected from the
mainstem channel as well as the duration. A detailed description of the criteria and methods for
identifying potential stranding and trapping areas is presented in Sections 8.5.4.5.1.2.2 and
8.5.4.6.1.6.
8.5.4.6.1.1.5. Breaching Flows
The breaching or topping of off-channel habitat features by mainstem river flows not only affects
the quantity of water within these features but water quality (turbidity and temperature) and
habitat quality as well. During the 1980s study of the Susitna River, researchers reported that
although breaching flows typically increase the availability of juvenile rearing habitat in small
off-channel areas, as mainstem discharge increases the quality of rearing habitat declines as
velocities in nearshore areas increase (Schmidt et al. 1985). A similar finding was reported for
the effect of water turbidity. Although some turbidity did increase off-channel use by juvenile
Chinook salmon, high turbidity resulting from mainstem flows topping reduced juvenile fish use
(Steward et al. 1985). Vining et al. 1985, reported that the winter topping of cold mainstem river
water into off-channel habitats was the most significant factor contributing to high levels of
embryo mortality in habitats used for chum salmon incubation in the Middle River Segment.
Determining the relationship between mainstem river flow and overtopping or breaching of
sensitive off-channel features will allow for the assessment of potential impacts of proposed
winter Project operation scenarios.
8.5.4.6.1.1.6. Fish Passage/Connectivity
Several environmental variables may affect fish passage and connectivity with sloughs and side
channels and tributary deltas. In general, at a given passage area the water conditions (primarily
depth) interact with conditions of the channel (length and uniformity, substrate size) to
characterize the passage conditions that a particular fish encounters when attempting to migrate
into, within, and out of a slough, side channel, or tributary delta. The likelihood of a particular
fish successfully navigating through a difficult passage reach will depend on the environmental
conditions as well as the individual capabilities and condition of the fish.
Depth passage in sloughs, upland sloughs, side channels, and at tributary delta mouths will be
assessed following the methods of Sautner et al. (1984a) that focus on salmon passage in sloughs
and side channels. Two-dimensional modeling, not available in the 1980s, will also be applied.
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Although salmon passage remains a key concern, the passage methods are generally applicable
to other species where depth passage criteria are known or can be developed. The main goal of
the fish passage and off-channel connectivity is to evaluate the potential creation of fish passage
barriers within existing habitats (tributaries, sloughs, side channels, off-channel habitats) related
to future flow conditions and water surface elevations.
8.5.4.6.1.2. Physical and Hydraulic Data Collection
As part of the 2013–2014 IFS, physical and hydrologic data collection will include hydraulic
boundary conditions, stage and discharge measurements, cross-sectional and areal bathymetric
surveys, velocity mapping, and roughness (channel substrate) determinations. The IFS will also
incorporate hydrologic data collected by other studies, including water quality (see Section 5.0),
water temperature, and ice processes data (see Section 7.6). A summary of the data collection
effort for each of these study components is provided below.
8.5.4.6.1.2.1. Boundary Conditions Transect
Much of the data collection performed in this task will be shared with and used by other studies
including Fluvial Geomorphology (see Section 6.6), Riparian Instream Flow (see Section 8.6),
Groundwater (see Section 7.5), and Ice Processes (see Section 7.6) studies. The majority of this
data collection effort is to be conducted during the 2013 field season and will be used to support
development of single transect PHABSIM and 2-D modeling efforts. The primary field data to
be collected at each of the boundary a condition transects will include the following:
• Cross-section survey to define channel topography and hydraulic controls at the
upstream- and downstream-most portion of each Focus Area using RTK GPS
instrumentation.
• Velocity and discharge measurements collected using an Acoustic Doppler Current
Profiler (ADCP) system consisting of a Sontek M9 equipped with RTK GPS positioning
to generate the necessary discharge and velocity distribution data. Price AA current meter
to be used for all velocity measurements for areas where the ADCP cannot be used.
• Measurement of the water surface elevation during discharge measurements, and
documentation of the substrate type, groundcover, habitat type, and woody debris in the
flood-prone area for the purposes of developing roughness estimates.
• Measurement of stage and discharge during high and low flows, with the potential
addition of an intermediate flow measurement.
Data collected at each of the boundary condition transects will be used to compute the energy
slope, velocity, depth, and other hydraulic variables at each cross-section in the Focus Areas and
to provide boundary conditions for localized 2-D models.
8.5.4.6.1.2.2. Bathymetry
Within the Focus Areas, bathymetric surveys will be required for 2-D hydraulic and other IFS
models. Cross-sectional bathymetric surveys will be performed as part of discharge
measurements completed in 2012 and 2013 using the Sontek M9 ADCP and vertical-beam depth
sounder and RTK GPS positioning systems. The results of these surveys will be used to prepare
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a digital elevation model of the streambed. Together with shore-based RTK GPS surveys, the
digital elevation model will also be used to develop cross-sections for use in the open-water flow
routing model.
It is anticipated that both multi-beam and single-beam sonar systems will be needed to complete
the bathymetric surveys in deep and shallow water areas. As a result, single-beam sonar surveys
will be conducted along pre-planned survey lines throughout each Focus Area. The planned
survey lines will be developed using recent imagery and hydrographic data acquisition software
(e.g., HyPack). The density of survey lines will be commensurate with the minimum model grid
spacing needed for 2-D hydraulic or other IFS models.
In several of the Focus Areas, water depths and velocities will preclude boat surveys throughout
the entire wetted area. Areas of shallow, fast water may require land-based surveying during low
water conditions using RTK GPS methods.
Roughness determinations will be made by solving Manning’s equation using field
measurements of discharge and water surface slope. These results will be compared against
visual estimates based on handbook values. Bathymetric data will be post-processed using
hydrographic data processing software (e.g., HyPack) to obtain a digital terrain model. The
digital terrain model can be used to develop cross-sections or as input for 2-D hydraulic and
other instream flow models. ADCP files will be post-processed using velocity mapping software
(e.g., VMS) to develop cross-sectional or plan-view velocity maps for calibration of hydraulic
models.
8.5.4.6.1.2.3. Fish Passage/Connectivity/Breaching Flows
The physical and hydraulic data collection process used to evaluate potential fish passage, off-
channel connectivity, and breaching flows will include but not be limited to the following:
• Identifying fish species to be included in the Fish Passage Barriers Study (see Section
9.12).
• Defining the passage criteria for the identified fish species.
• Defining potential fish passage barriers and hydraulic connectivity points within each of
the Focus Area to be sampled.
• Conducting field data collection.
• Coordinating with other interdependent studies.
• Evaluating potential effects of altered river flows on fish access to off-channel habitats
and breaching flows.
Data collection for determining potential for fish passage and off-channel connectivity will
involve establishing cross-sectional and water surface elevation transects at one or more
locations to represent the shallowest conditions (hydraulic control feature) fish may encounter
while moving upstream. The basic criteria for defining and modeling fish passage and
connectivity to off-channel areas for this study will be water depth as it relates to mainstem flow
level. Depth criteria will establish the minimum water depth and the maximum distance (at the
minimum depth) through which a fish can successfully pass. Depth requirements for successful
passage increase with an increase in the length of passage. Depth criteria will be used to assess
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access into, within, and out of side channels and sloughs. The ability of fish to enter or exit
slough and side channel habitats from the mainstem Susitna River and access spawning or
rearing areas within these habitats is primarily a function of water depth and the length of a reach
when the water is shallow (Sautner et al. 1984a).
Stage (water surface elevation) and discharge will be monitored at a minimum of one fish
passage/connectivity site within each of the Focus Areas. Monitoring of stage and discharge will
assist in determining the influence that mainstem river flow has on hydraulic characteristics of
off-channel habitats and fish passage potential. To monitor changes in stage resulting from
changes in mainstem flow, pressure transducers (Solinst level loggers) will be deployed at the
upper and lower ends of selected side channel and slough habitats and in adjoining areas of the
main channel Susitna River. The stage and discharge data will be used to develop a stage vs.
flow rating curve for use in modeling or predicting the depth across the control feature to aid in
determining the mainstem flow required to maintain minimum fish passage depth, off-channel
connectivity, and breaching flows.
As noted in Section 9.12, there are 12 major tributaries with names, approximately 50 unnamed
tributaries, and approximately 50 sloughs located within the Middle River Segment. Passage
evaluation studies in the Middle River Segment will therefore begin in 2013 within each of the
Focus Areas that support spawning habitats and center on the associated tributary mouths, side
channels, and side sloughs. This will include Focus Area-173, Focus Area-171, Focus Area-151,
Focus Area-144, Focus Area-141, Focus Area-138, Focus Area-128, and Focus Area-104 (Table
8.5-6) and with those tributaries and sloughs that will be physically characterized by the ISF and
geomorphic study teams. In 2014, barrier surveys will be expanded to include select tributaries,
meaning those determined to have fish present based on historic and 2013 data. Surveys will
extend from the mouth to the upper extent of Project hydrologic influence. The upper limit of
hydrologic influence will be determined from supporting studies including the open-water flow
routing model and the geomorphic mapping, among others.
8.5.4.6.1.2.4. Focus Area Depth, Velocity, and Substrate Characterization for Single
Transect PHABSIM Modeling
The collection of physical and hydraulic measurements at each of the Focus Area single transect
sampling sites will be completed following the procedures for PHABSIM studies outlined by
Bovee and Milhous (1978), Bovee (1982), and Trihey and Wegner (1981). The establishment of
1-D PHABSIM transects will be completed as follows:
• Locations of Transects –Transect positions will be recorded using a hand-held GPS unit
and mapped in a field book and on low elevation aerial photographs. The position of each
transect will be temporarily established using wooden stakes pounded solidly into the
ground.
• Establishment of Site Benchmark – A semi-permanent benchmark will be established at
each transect. All survey measurements, including water surface and bed elevations, will
be referenced to this benchmark. Each benchmark (large boulder or rebar) will be placed
above the floodplain of the river and marked with fluorescent flagging for high visibility.
The elevation of each transect benchmark will be tied to elevation markers established as
part of the open-water flow routing modeling (see Section 7.0, Hydrology-Related
Resources).
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• Installation of Head Pins – Head pins (rebar) will be installed on the side of the side
channel or off-channel area near the starting point of each transect. These head pins serve
as a secondary vertical reference point for water surface and bed elevation measurements
collected across the stream channel. Differences between transect benchmark and head
pin elevations will be used as a quality control check for surveying accuracy. The head
pins are also intended to serve as a backup benchmark in case the transect benchmark is
disturbed.
• Establishment of Working Pins – Working pins (wooden stakes) will be established on
either end of a transect. These working pins will be positioned in such a way that the line
connecting these points is perpendicular to the main flow of the side channel or off-
channel area. A surveying tape or incremented Kevlar line will be stretched across the
channel and connected to these points during the collection of instream flow data. The
survey tape will be tied to the working pin at the same position (e.g., 2 ft on the tape)
during each sampling so that velocities can be measured at the same positions across the
transect.
• Survey of Benchmark Elevations and Completion of Level Loop – Following the
installation of the benchmarks at each transect, a level loop survey will be completed to
establish benchmark elevation in relationship to elevation markers established during the
open-water flow routing model data collection effort (see Section 7.0). The elevation data
will be obtained using an Auto Level and stadia rod (0.01 ft accuracy). The level loop
will be considered accurate if closed to within 0.02 ft of the initial benchmark elevation.
Water surface elevations will be measured at the right bank, mid-channel, and left bank of each
transect under all of the specified “calibration” discharges. Velocity profiles will then be
obtained across each transect at the same tape positions under each of the “calibration” flow
measurements.
Data will be collected at established intervals across each transect following the protocols
recommended by USGS. The following data were collected at each measurement point
(verticals) across each transect:
• Water Depth (measured to nearest 0.1 ft) – Depths will be measured using a top setting
rod. Measured water depths are not used during the hydraulic modeling process because
the IFG4 model calculates depths by subtracting bed elevations from water surface
elevations. Depth measurements, however, can provide a useful quality control check of
water surface elevations at each calibration flow.
• Mean Column Water Velocity (measured to nearest 0.1 fps) – Velocities will be
measured using a spin-tested Price AA velocity meter i; velocities will be measured at
6/10ths depth in the water column for depths less than 2.5 feet, and 2/10ths and 8/10ths
depth in the water column for depths greater than 2.5 feet.
• Substrate (dominant and sub-dominant) – Substrate types will be recorded at each
transect vertical under clear water conditions. Substrate size (dominant, sub-dominant,
and percent dominant) will be characterized in accordance with a modified Wentworth
grain size scale.
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8.5.4.6.1.3. Hydraulic Model Calibration
8.5.4.6.1.3.1. River Corridor Stage vs. Discharge
Susitna River mainstem flow routing models (HEC-ResSim; HEC-RAS; CRISSP1D; and/or
other routing models) will provide hourly flow and water surface elevation data at numerous
locations longitudinally distributed throughout the length of the river extending downstream
from RM 184. Two different flow routing models will be developed: an open-water model
(HEC-RAS) and Ice Processes Model to route flows under ice-covered conditions (CRISSP1D).
Output from the flow routing models will provide the fundamental input data to a suite of
habitat-specific and riverine process models that will be used to describe how the existing flow
regime relates to and has influenced various resource elements (e.g., salmonid spawning and
rearing habitats, invertebrate habitat, sediment transport processes, ice dynamics, large woody
debris [LWD], and the composition and structure of riparian floodplain vegetation). These same
models will likewise be used to evaluate fish habitat responses to alternative Project operational
scenarios. As an unsteady flow model, the open-water flow routing model will be capable of
providing flow and water surface elevations on an hourly basis and therefore Project effects on
flow can be evaluated on multiple time steps (hourly, daily, monthly) as necessary to evaluate
different resource elements. During the development and calibration of the HEC-RAS model, the
drainage areas of ungaged tributaries will be quantified and used to help estimate accretion flows
to the Susitna River between locations where flows are measured. The flow estimates developed
for ungaged tributaries will be refined based on flows measured in those tributaries in 2013 and
2014.
8.5.4.6.1.3.2. Focus Area Stage vs. Discharge
Calibration and validation of the stage vs. discharge relationships developed for cross-sections
within each of the Focus Areas will follow a stepwise process. First, the hydraulic components of
the models will be calibrated by adjusting roughness and loss coefficients to achieve reasonable
agreement between measured and modeled water surface elevations, and between measured and
modeled velocities. Discharges along the study reach will be obtained from the three USGS
gages. These gages will also provide a continuous record of stages and water surface elevations
at the gage locations. These data will be supplemented with stage data from at least 10 pressure-
transducer type water level loggers that have been or will be installed as part of various studies
being conducted in the Middle and Lower River segments. Water levels measured during the
cross-section and bathymetric surveys will also be used to calibrate the models. In addition to
water surface elevations, the depths and velocities predicted by the 2-D model should be
compared with measured data from ADCP measurements at the Focus Areas. Depending on the
range of conditions and spatial coverage of the depth and velocity data from the Fish and
Aquatics Instream Flow Study, additional data may be needed for calibration specifically for this
study. Specific calibration criteria will be established for both the 1-D and 2-D models during the
model selection phase. The 2-D water surface elevations will also be compared against water
surface elevations generated by the 1-D model and the open-water flow routing model to ensure
that the models are producing consistent results.
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8.5.4.6.1.3.3. Focus Area Depth, Velocity, and Substrate
Analysis of the physical and hydraulic data collected at each of the Focus Area 1-D sampling
sites will include several steps for the development, calibration, and use of the hydraulic
modeling output. Hydraulic and habitat simulation modeling will be conducted using the latest
version of the PHABSIM computer software (Milhous et al. 1989). The 1-D hydraulic model
calibration process will be completed in accordance with the following steps:
1. Raw field data will be entered into Excel spreadsheets, reviewed, and reduced into a form
ready for creation of hydraulic data decks. Any data entry errors will be identified, noted
in a copy of the review sheet, and corrected. These computer spreadsheets will then be
used to generate data input files for the PHABSIM 1-D hydraulic simulation program,
IFG4.
2. Stage versus discharge relationships will be developed using one or more hydraulic
simulation procedures. Depending upon the hydraulic characteristics of a given transect,
a stage-discharge relationship will be developed using one of three methods: a log-log
regression method (rating curve developed using the IFG4 program), a channel geometry
and roughness method (rating curve developed using the Manning’s Equation-based
program MANSQ), or a step-backwater method (rating curve developed using the
program WSP).
3. Velocities across each transect will be calibrated to provide a realistic distribution of
mean column velocities across the river channel for the entire range of flows employed in
the habitat simulations.
Stage and discharge measurements were performed in 2012 at 88 cross-sections between RM 76
and RM 184. Twelve of these cross-sections are located at or near gaging stations operated by
USGS or AEA. Stage and discharge measurements were also performed at inactive USGS
gaging stations in the Lower River Segment (Susitna River at Susitna Station [ESS20], RM 20)
and in the upper basin (Susitna River near Cantwell [ESS80], RM 224). Gaging equipment was
re-installed at these locations, as well as at two tidal monitoring stations in the Susitna delta.
Water level, water temperature, camera images, and meteorological data from these stations are
shared online via an internal project website.
Depending on results of the 2012 open-water flow routing model and analysis from other studies,
additional cross-sections may be surveyed in 2013 and 2014. Sections of the river that have
stable cross-sections will likely not require additional cross-section measurements. Sections of
the river that demonstrate changes in cross-section profiles seasonally or event-based (floods)
may require additional cross-section measurements. Stage and discharge measurements will be
used to calibrate the open-water flow routing models, and to develop or confirm ratings for new
and existing gaging stations.
8.5.4.6.1.4. Weighted Usable Area Habitat Metrics
The methods proposed in the IFS include a combination of approaches depending on habitat
types (e.g., mainstem, side channel, slough, etc.) and the biological importance of those types, as
well as the particular instream flow issue (e.g., connectivity/fish passage into the habitats,
provision of suitable habitat conditions in the habitats, etc.). During the 1980s studies, methods
were designed to focus on both mainstem and off-channel habitats, although mainstem analysis
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was generally limited to nearshore areas. PHABSIM-based 1-D models, juvenile salmon rearing
habitat models, fish passage models, and others were employed and will be considered as part of
the IFS plan. As part of the 2013–2014 study efforts, more rigorous approaches and intensive
analyses will be applied to habitats determined as representing especially important habitats for
salmonid production. This will include both 1-D and 2-D hydraulic modeling that can be linked
to habitat-based models.
As part of the Geomorphology Modeling Study (see Section 6.6), several 2-D models are being
considered including the Bureau of Reclamation’s SRH2-D, USACE’s Adaptive Hydraulics
ADH, the USGS’s MD_SWMS suite, DHI’s MIKE 21, and the suite of River2D models (see
Section 6.6 for a description of various 2-D model attributes and references). The River2D model
is a two-dimensional, depth-averaged finite-element hydrodynamic model developed at the
University of Alberta and is capable of simulating complex, transcritical flow conditions.
River2D also has the capability to assess fish habitat using the PHABSIM weighted usable area
approach (Bovee 1982). Habitat suitability indices are input to the model and integrated with the
hydraulic output to compute a weighted useable area at each node in the model domain. While
evaluation of habitat indices is directly incorporated into the River2D suite of models, other 2-D
models are also complementary to habitat evaluations. Selection of potential 2-D models for fish
and aquatics evaluations will be coordinated with other pertinent studies and the TWG in Q1
2013 and revisited in Q1 2014.
The models noted above will be used to translate changes in water surface elevation/flow at each
of the measured transects/study segments into changes in depth, velocity, substrate, cover, and
other potential habitat (e.g., turbidity, upwelling). Linking this information with HSC/HSI curves
will allow for translation of changes in hydraulic conditions resulting from Project operations
into indices of habitat suitability. This will allow for the quantification of habitat areas
containing suitable habitat indices for target species and life stages of interest for baseline
conditions and alternative operational scenarios.
In response to the effect of potential load-following operations, habitat modeling using weighted
usable area indices may need to be developed using both daily and hourly time steps. Evaluating
the effects of changes in habitat conditions on an hourly basis may require additional habitat-
specific models such as effective habitat and varial zone modeling.
8.5.4.6.1.5. Effective Spawning/Incubation Habitat Analyses
Operation of the Project has the potential to influence the quantity and quality of spawning
habitat by altering stream flow in the main channel and off-channel areas of the Susitna River.
While changes in physical conditions (i.e., depth, velocity, and substrate) will determine the
suitability of habitat for salmon spawning, the subsequent survival of eggs and alevins can be
influenced by a different suite of flow-related processes. The eggs of Pacific salmon are laid in
nests, or egg pockets, dug by the female in the gravel of the streambed. The female then covers
the egg pockets with several inches of gravel by vigorous body and tail movements. Eggs within
the spawning site (redd) incubate through the winter and depending on water temperature, hatch
in late winter through spring, then remain within the redd as alevin until emergence. Mortality
during the incubation period, which includes the egg and alevin stages, is generally high and can
be caused by scour associated with flood flows or dewatering and freezing during low flow
conditions. The location of redds within the river channel may have a major influence on redd
survival. If redds are constructed toward the center of the channel when mainstem flows are low,
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redds may be scoured by winter flood events. If redds are constructed along the channel margins
or in off-channel areas when mainstem flows are high, redds are at risk of dewatering or freezing
when flows drop during the winter incubation season. In the Susitna River, as elsewhere,
upwelling areas provide stable intergravel conditions and warmer temperatures during the winter
incubation period, providing some protection from dewatering or freezing.
Flow changes can influence the prevalence of groundwater upwelling, which in turn can affect
the rate of survival and development for eggs and alevins. In the Susitna River, Vining et al.
(1985) suggested that upwelling is the single most important feature in maintaining the integrity
of incubation in slough habitat as well as localized areas in side channel habitats. Upwelling and
intergravel flow also play an important role in determining the water quality at redd sites,
particularly with respect to temperature and dissolved oxygen concentrations. Winter increases in
mainstem flow or stage may affect upwelling by:
• Decreasing the rate of groundwater upwelling from the adjacent floodplain.
• Diluting relatively warm, stable, upwelling habitats when side channels are breached by
mainstem flow.
• Changing the rate of intergravel flows associated with hydraulic gradients between main
channel and off-channel habitats.
The risks posed by flow-related processes on salmonid redds and egg/alevin incubation will be
assessed by developing an effective spawning/incubation model that incorporates separate but
integrated analyses for each process. The spawning/incubation model will be based on
identifying potential use of discrete channel areas (cells) by spawning salmonids on an hourly
basis. Use of each cell by spawning fish will be assumed to occur if the minimum water depth is
suitable and velocity and substrate suitability indices are within an acceptable range defined by
HSC/HSI. Species-specific HSC/HSI information used to identify potential use of a cell by
spawning fish will be developed as described in Section 8.5.4.5. If suitable spawning conditions
exist, that cell will then be tracked on an hourly time step from the initiating time step through
emergence to predict whether eggs and alevin within that cell were subject to interrupted
upwelling, dewatering, scour, freezing, or unsuitable water quality (e.g., Figure 8.5-32).
This process will be repeated for each hour of the potential spawning period based on the
periodicities shown in Table 8.5-2. If sufficient site-specific periodicity information is available,
each hour can be weighted depending on whether it occurs during the peak or off-peak of the
spawning period. If hydraulic conditions during the spawning season were considered suitable
for spawning in a particular cell during the initiating time step, and conditions remained suitable
for egg viability every hour through emergence, then the cell area at the initiating time step
would be considered effective spawning/incubation habitat. This process is repeated for each cell
within the habitat unit containing suitable spawning habitat at time step 1, and the entire process
repeated for each time step through the end of incubation. The resulting areas will then be
summed to determine the cumulative total effective spawning/incubation area for the habitat unit
under existing conditions and alternative operational scenario for each hydrologic year under
consideration. The duration of spawning to emergence will be calculated for each target species
based on temperature units within the intergravel environment. Shorter incubation periods would
be expected with warmer water temperatures and longer incubation periods would be expected
with colder water temperatures. The incubation period will be divided into an egg phase and an
alevin phase. After salmon eggs hatch, they remain within the gravel environment as alevins,
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maturing while they absorb their yolk sac. During this post-hatching but pre-emergence period,
the alevins are particularly susceptible to dewatering. Assumptions regarding the start, peak, and
end of spawning, and duration of egg incubation and alevin life stage, will be developed from
previous studies of the Susitna River, meetings with the TWG (Q1 2013), and validated through
site-specific biological surveys conducted as part of the licensing effort.
To assess the vulnerability of eggs and alevin to flow-related processes, losses due to dewatering,
freezing, or water quality, will be tracked based on the continued presence of upwelling within
the cell area. If a cell is exposed to factors that cause mortality, the cell is lost for that initiating
hour. If a loss occurs, cell accounting is re-started if the next hour time step is within the
potential spawning period. Cumulative spawning activity within each cell will be accounted for
on an hourly basis for each target species, using the hourly flow hydrograph determined from the
open-water flow routing model.
As shown in Figure 8.5-32, the model will first consider whether upwelling has been reduced
during a given time step. During winter low flows, the aquifer discharges relatively warm
groundwater from the floodplain into off-channel habitats via upwelling and provides a stable
environment for incubation. Increased winter flows can alter the hydraulic gradient of the
floodplain, changing the direction of groundwater flow and affecting the prevalence of
upwelling. Reduced upwelling may not lead to direct mortality of eggs and alevin. However, the
resulting colder water temperatures would prolong the period of incubation, thereby potentially
increasing the risk of dewatering, scour, or freezing events. Reduced upwelling could also
increase the risk of dewatering or freezing by eliminating sustained flows of warmer water to the
redd. Reduced upwelling could also affect dissolved oxygen concentrations within a redd by
altering intergravel flow. Some redds may be constructed in areas of upwelling that originate
from the hydraulic gradient between main channel and off-channel habitats. Depending on
intergravel transit time, this upwelling may mimic the temperature of main channel open-water
flow, or may reflect the temperature of the aquifer. Higher main channel river stages may
increase this type of upwelling, having either a positive or negative effect on redds depending on
the nature of the upwelling. A pilot study is proposed for 2012–2013 to monitor intergravel water
temperature and dissolved oxygen levels in off-channel habitats with and without the presence of
groundwater upwelling (see Section 8.5.2.1.6). Results of this study will be used to investigate
the relationship between mainstem river flow and intergravel water quality conditions.
Persistent upwelling would presumably be mutually exclusive with dewatering, scouring flows,
freezing, or unsuitable water quality. However, as described above, it is assumed that the quality
(i.e., temperature, dissolved oxygen) and quantity of groundwater upwelling for incubation will
be influenced by mainstem flow and stage. Criteria will be developed such that a reduction of
upwelling would include any adverse change in water quality below a critical level even if
upwelling persisted. The analysis for upwelling will rely on the results of groundwater modeling
to predict whether upwelling is reduced for a given cell and time step. If upwelling is not
reduced, the area represented by that cell would be carried forward through subsequent time
steps. If upwelling persists through emergence, that cell would be tallied as part of the
cumulative effective spawning/incubation habitat. If, however, upwelling is reduced at any point
during the incubation period, the potential for dewatering, scour, freezing, or unsuitable water
quality will be considered.
In a worst case scenario, it could be assumed that all eggs or alevin will be lost if the surface
substrate in the cell became scoured, the cell became dewatered or frozen, or water quality fell
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below critical levels. This assumption is probably overly conservative for several of the potential
impact parameters. For example, salmon eggs can survive short periods of dewatering provided
that the eggs remain damp (Becker et al. 1983), whereas once intergravel temperature reaches
freezing or below, it is assumed that 100 percent mortality occurs. Therefore, separate criteria
will need to be defined to assess the degree to which the spawning area is no longer effective
(i.e., percent of spawning area rather than a binary result) depending on the severity of the
impact. The final criteria for assessing the degree of impact will be developed in collaboration
with the TWG during Q1 2013.
All of the analyses associated with the effective spawning/incubation model will be performed at
each of the Focus Areas with suitable spawning habitat. The results of the effective
spawning/incubation analysis will be a reach-averaged area calculated by weighting the effective
spawning area derived for each Focus Area by the proportion of Focus Area within the
geomorphic reach (see Section 8.5.4.7). The results are calculated in terms of weighted area
(similar to PHABSIM results) and do not represent actual area dimensions. The results cannot be
used to calculate numbers of emergent fry but instead provide habitat indicators that will be used
to conduct comparative analyses of alternative operating scenarios under various hydrologic
conditions.
8.5.4.6.1.6. Varial Zone Modeling
Fluctuations in flow will cause shallow portions of the river channel to alternate between wet and
dry conditions; this area of alternating wet and dry is referred to as the varial zone (Figure
8.5-33). Flow reductions along the channel margins can cause stranding and trapping of juvenile
fish and benthic macroinvertebrates within the varial zone. Repeated dewatering of the varial
zone can result in reduced macroinvertebrate and algae density, diversity, and growth (Fisher and
LaVoy 1972; Dos Santos et al. 1988).
Analyses of Project effects on the downstream varial zone can be quantified as the frequency,
magnitude, and timing of downramping events exceeding specified downramping rates; the
frequency, number, and timing of downramping events that occur following varying periods of
inundation; and the frequency, timing, and magnitude of potential stranding and trapping of
aquatic organisms.
The proposed load-following operations of the Project will affect hourly flow fluctuations
downstream of the Watana Dam site. Based on analyses of studies of the effects of hydropower
load-following operations in Washington State, it is generally assumed that faster rates of water
surface elevation reduction are correlated to an increased risk of stranding of aquatic organisms
(Hunter 1992). Salmonid fry are particularly susceptible to stranding and the daily and seasonal
timing of downramping events will influence the potential risk to aquatic organisms.
The goal of the downramping analysis will be to quantify the frequency, magnitude, and timing
of downramping rates by downramping event by geomorphic reach downstream of the Watana
Dam site. The objectives of this analysis will be to quantify reach-averaged downramping events
by rate under existing conditions and under alternative operating scenarios for selected
hydrologic years. Using the results of the mainstem flow routing models, a post-processing
routine will be used to identify those specific hourly time periods when the water surface
elevations are decreasing (i.e., downramping). For those time periods, the hourly reduction in
water surface elevation will then be computed and expressed in units of inches per hour. A
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frequency analysis will be conducted on the hourly downramping hours by downramping event
by geomorphic reach. The frequency analysis will determine the number of downramping events
exceeding selected numeric categories. These categories will be selected in collaboration with
the TWG, but for planning purposes, the following categories are proposed:
• Greater than 0 but less than 1 inch per hour
• Greater than 1 but less than 2 inches per hour
• Greater than 2 but less than 4 inches per hour
• Greater than 8 inches per hour
• Exceeding downramping guidelines developed by Hunter (1992) (Table 8.5-20)
The number of events where downramping rates exceed these categories will be tabulated by
month and by annual total under existing conditions and for alternative operating scenarios.
The frequency, number, and timing of downramping events that occur following varying periods
of inundation will be quantified to evaluate the effects of downramping events on organisms
exhibiting a range of colonization rates. This varial zone analysis can be conducted by total
Focus Area or can be conducted by discrete habitat types within a Focus Area (e.g., main
channel, side channel, sloughs) using an hourly time step integrated over a specified period that
considers antecedent fluctuations in water surface elevations.
The selection of time periods to define the upper and lower extent of the varial zone for the
Project will be coordinated with the TWG. However, for planning purposes, three time scales are
being considered: 12 hours, 7 days, and 30 days. A 12-hour time series may provide an
indication of the effects of water level changes on aquatic biota that rapidly colonize a previously
dewatered area. Salmonid fry and some benthic macroinvertebrates may rapidly recolonize or
occupy a previously dewatered area when they are moving downstream from upstream areas
during out-migration or as a result of displacement from upstream areas. A 7-day time series may
be used as an indicator of the risk of dewatering due to hourly and daily changes in load-
following operations, such as weekday versus weekend generation. Some aquatic organisms may
require several days to colonize an area (algae), or the density of organisms may increase rapidly
over the first several days of access to a previously dewatered area. A 30-day time series can be
used as an indicator of the risk of dewatering associated with weekly to monthly changes in flow
patterns, such as changes in minimum flow requirements or seasonal runoff. A complex
assemblage of benthic macroinvertebrates may require weeks to months to become established
along channel margins. Information on the rate of colonization, dewatering mortalities, and
conditions supporting suitable habitats for organisms of interest will be developed as part of the
HSC/HSI study component. Figure 8.5-34 illustrates the concept of a varial zone analyses under
antecedent flow conditions.
8.5.4.6.1.6.1. Fish Stranding and Trapping
Though stranding and trapping are related processes, there are differences that require two
separate analyses for the effects. Both analyses develop indices that represent the potential effect
of reductions in water levels during downramping events on fish and other aquatic organisms.
Stranding involves the beaching of fish as the water levels recede and is typically associated with
low gradient shoreline areas or cover conditions that attract fish to areas where dewatering
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occurs. Mortality occurs when stranded fish are beached on dewatered portions of the channel
bed. As water levels recede, some fish may become trapped in channel depressions or pools.
Although trapped fish may survive for short periods of time, the potential for mortality increases
based on factors including temperature fluctuations, reduction in dissolved oxygen, predation,
and stranding as the water in the pool infiltrates the substrate.
The approach to the stranding and trapping analyses is similar to other analyses involving the
evaluation of the effects of water surface elevation fluctuations in the varial zone. Stranding and
trapping indices utilize results of the mainstem flow routing models to determine the water
surface elevations on an hourly basis within Focus Areas. Stage fluctuations are applied within
Focus Areas using the digital terrain models to quantify the frequency, timing, and magnitude of
stranding events under existing conditions and alternative operational scenarios. The results of
the mainstem flow routing models and the digital terrain models are also combined to quantify
the frequency, timing, and duration of trapping events for discrete channel features within Focus
Areas. The stranding and trapping analyses determine evaluation indices based on each water
level fluctuation cycle.
The stranding and trapping analyses track the period of dewatering (stranding) or the period of
disconnection (trapping). Fish are assumed to return to potential stranding and trapping areas
shortly after the water surface elevation rises to once again inundate/connect the side channel
areas. Stranding and trapping indices are not treated as values that are summed on an hourly
basis; instead, stranding and trapping are viewed as a series of events, and part of the index
expression includes this frequency of events. Therefore, the results are computed at the end of an
event based on the duration of the event, and then results are summed over the series of events.
Downramping rates will be determined as part of the stranding analyses including the
exceedance of specific numeric categories ranging from 1 inch per hour to over 8 inches per
hour. For trapping analyses, ramping rates will not be directly incorporated as a factor in the
calculation of the indices. Strong relationships between ramping rate and incidence of trapping
are not consistently demonstrated in previous studies (Hunter 1992; Higgins and Bradford 1996;
R.W. Beck and Associates 1989). The results of both stranding and trapping evaluation
indicators can be quantified under existing conditions and alternative operational scenarios for
selected hydrologic conditions.
The indices for stranding and trapping are based on equations that relate physical characteristics
of the stranding and trapping sites to the potential for stranding and trapping to occur. The
information for the physical site characteristics will be derived from the bathymetry and mapping
through the application of GIS. The index equations have physical factors related to site area,
depth, and cover conditions. The observations and data collected during the stranding and
trapping field surveys will assist in developing the ratings for several of these factors (see
Section 8.5.4.5).
For planning purposes, potential stranding areas are defined as areas with a bed slope of 4
percent or less, excluding depression areas that are included in the trapping area analysis.
Stranding areas are also defined as areas with features, such as emergent vegetation found
alongside slough margins, which are observed to contribute to an increased risk of stranding
regardless of bed slope based on the results of site-specific surveys. Specific stranding zones are
defined at elevation intervals to allow for tracking of dewatering of stranding areas as the water
surface elevation rises and falls. Stranding areas are also defined as contiguous areas of 1,000
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square feet or greater. The potential presence of fish in a stranding site is assumed to be directly
proportional to the size of the stranding area.
The resulting equation for stranding is:
SI = AS * CS
Where:
SI = stranding index
AS = stranding area in square feet
CS = cover factor for stranding
The stranding index (SI) is calculated once for each stranding event. It is assumed that the 1-hour
time interval of the modeling is sufficient to cause mortality for fish stranded for this length of
time. It was also assumed that once the stranding area is again inundated, it reaches its full
potential for stranding; that is, the fish population is replenished.
For planning purposes, the equation for quantifying evaluation indicators for trapping has been
formulated as:
TI = A T * TT(D) * CT
Where:
TI = trapping index
AT = trapping area (square feet)
TT(D) = duration of trapping factor
CT = cover factor representing the influence of emergent vegetation and other cover
The factors AT and CT represent the risk that fish will be trapped in the pool. The larger these
factors, the higher the potential for trapping fish in the pool. TT(D) represents the potential for
mortality of fish trapped in a pool once it becomes isolated from the mainstem; it is the ratio of
fish mortalities to total fish trapped. The trapping factors are not species-specific. The results of
the trapping index calculations require review of fish periodicity to determine whether species of
interest and associated life stages susceptible to trapping are present during a particular period.
The trapping index (TI) is calculated once per trapping event and contains factors that describe
the likelihood that fish will be trapped in the pool when the pool becomes disconnected from the
mainstem flow. The TI is calculated for each individual trapping depression. Each pool has an
effective elevation assigned to its outlet, which allows for determination of trapping duration
based on application of the hourly elevations available from the open-water flow routing model.
It is only necessary to calculate the index at the end of the event, not at intermediate points. It is
assumed that once the trapping area is reconnected, it reaches its full potential for trapping within
the one hour that elapses before the next time interval. This assumption represents a 100 percent
recolonization within one hour. These and other details of the stranding and trapping analyses
will be developed in collaboration with the TWG during Q2 2013 and reviewed in Q2 2014.
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8.5.4.6.1.6.2. River Productivity
The production of freshwater fishes in a given habitat is constrained both by the suitability of the
abiotic environment and by the availability of food resources (Wipfli and Baxter 2010). Algae
are an important base component in the lotic food web, being responsible for the majority of
photosynthesis in a river or stream and serving as an important food source to many benthic
macroinvertebrates (see Section 9.8). In turn, benthic macroinvertebrates are an essential
component in the processes of an aquatic ecosystem due to their position as consumers at the
intermediate trophic level of lotic food webs. The significant functional roles that
macroinvertebrates and algae play in food webs and energy flow in the freshwater ecosystem
make these communities important elements in the study of a stream’s ecology.
The operations of the proposed Project would likely affect the abundance and distribution of
algae and benthic macroinvertebrate populations, which could ultimately affect fish growth and
productivity in the system. The degree of impact on the benthic communities and fish resulting
from hydropower operations will necessarily vary depending on the magnitude, frequency,
duration, and timing of river flows. The overall goal of the River Productivity Study is to collect
baseline data to assist in evaluating the effects of Project-induced changes in flow and the
interrelated environmental factors (temperature, substrate, water quality) upon the benthic
macroinvertebrate and algal communities in the Susitna River (see Section 9.8).
Both benthic macroinvertebrate and algal communities are groups of organisms that spend most
or all of their lives in the channel substrate. These groups of organisms respond to inundation
and dewatering of the river channel resulting from fluctuations in water surface elevation caused
by Project operations, as well as variation in river flow. To assess the relative impact or change
in the quality and quantity of available habitat and colonization rates for both of these groups of
organisms, HSC/HSIs representing the influence of habitat quality and the duration of inundation
and dewatering will be developed. The HSC/HSI will provide depth, velocity, substrate, cover,
colonization, and dewatering criteria for both algae and benthic macroinvertebrates. The
HSC/HSI results will be used in the aquatic habitat and varial zone modeling to translate
physical characteristics present for different Project operations scenarios to indices of the amount
and distribution of potential habitat that is suitable for the selected communities, and the duration
of inundation and dewatering of varial zone areas.
The various indices of Project effects on mainstem aquatic habitats will be summarized and
tabulated to allow ready comparison of the effects of an existing operations scenario to
alternative operational scenarios. It is anticipated that the varial zone analysis will be used as a
primary indicator of the effects of operational scenarios on algae and macroinvertebrates in the
mainstem Susitna River. Analyses of usable habitat area will be developed for each guild or
metric, but the results may be of primary interest in identifying the spatial distribution of
potential habitats. Each indicator of environmental effect will be tallied separately, and the
relative importance of the effects of Project operations on various aquatic resources may be
determined independently by interested parties.
8.5.4.6.1.7. Fish Passage/Off-channel Connectivity
The extent to which mainstem flows dictate connectivity to off-channel habitats will be
evaluated via development of models that consider the depth, velocity, and substrate
requirements of adult salmon upstream migrations as well as juvenile downstream movements.
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This analysis will be initiated in 2013 in the Middle River Segment within each of the Focus
Areas that support spawning habitats and center on the associated tributary mouths, side
channels, and side sloughs. This will include Focus Area-173, Focus Area-171, Focus Area-151,
Focus Area-144, Focus Area-141, Focus Area-138, Focus Area-128, and Focus Area-104 (Table
8.5-6). In 2014, barrier surveys may be expanded to include both additional locations within the
Middle River Segment that, based on results from fish distribution (see Section 9.5) and
escapement studies (see Section 9.7), indicate are used for spawning, and that based on
geomorphic analysis (see Section 6.5) would be susceptible to flow changes resulting from
Project operations, as well as locations in the Lower River Segment. To the extent applicable, the
analysis will utilize information and modeling results developed during the 1980s studies, but
will also collect and analyze entirely new data as a means to test the results of the earlier studies,
as well as to apply new technologies in making this evaluation (e.g., possible application of 2-D
modeling).
8.5.4.6.2. Work Products
The hydraulic and habitat modeling study components will include the following work products:
• Map displaying hydraulic and habitat sampling areas for each Focus Area including
boundary condition transects, 2-D modeling areas, single transect PHABSIM transects,
stranding and trapping areas, fish passage/connectivity, and breaching flow hydraulic
control features.
• Electronic copies of all physical and hydraulic field data collected at each Focus Area
including field notes, photographs, site maps, and datasheets.
• Hydraulic modeling calibration results including cross-sectional profiles, stage vs.
discharge relationships, velocity calibrations, 2-D grid (coarse and fine), PHABSIM
hydraulic models, and digital terrain modeling.
• Results of flow vs. habitat relationship modeling for each target species and life stage for
both single transect and 2-D PHABSIM.
• Results of downramping analysis summarized by month and annually for each hourly
change rate in water surface elevation for each habitat transect.
• HSC/HSI curves for macroinvertebrates and algae related to suitability of water velocity
and depth, substrate preference, and colonization rates.
• Results of varial zone modeling including effective spawning/incubation area, stranding
and trapping analysis, and river productivity for each Focus Area.
• Tabular summary for comparison of the results of habitat modeling for each of the
proposed Project operations scenarios.
These work products and other results of the hydraulic and habitat modeling will be compiled
and presented in initial and updated study reports.
8.5.4.7. Temporal and Spatial Habitat Analyses
The IFS will result in the collection of data and development of different types of habitat-flow
relationships from spatially distinct locations within each of the Focus Areas, and from selected
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cross-sectional transects outside of the Focus Areas that contain a variety of habitat types. Types
of relationships will include but not be limited to those founded on PHABSIM that depict WUA
or habitat versus flow by species and life stage; effective habitat versus discharge relationships
that define how spawning and incubation areas respond to flow changes; varial zone analysis that
quantifies areas of stranding and trapping relative to flow change; and groundwater-surface water
flow relationships relative to upwelling and spawning habitats. Additional components that will
factor into the habitat – flow relationships will include those associated with breaching flows,
upwelling, water temperature, and turbidity. These relationships will be part of the analytical
framework and conceptual models that will be used in evaluating the operational effects of the
Project (see Section 8.5.4.8) on different habitats. This will require both a temporal analysis that
focuses on how the various habitat response variables change with flow over biologically
important time periods (i.e., periodicity), and a spatial analysis that can be used not only for
evaluating specific relationships on a site/transect specific or Focus Area basis, but also for
expanding or extrapolating results from measured to unmeasured habitats within the river. This
latter analysis is needed in order to assess system-wide Project effects.
8.5.4.7.1. Proposed Methodology
8.5.4.7.1.1. Temporal Analysis
Temporal analysis will involve the integration of hydrology, Project operations, the Mainstem
Open-water Flow Routing Model, and the various habitat-flow response models to project
spatially explicit habitat changes over time. Several analytical tools will be utilized for
evaluating Project effects on a temporal basis. This will include development and completion of
habitat-time series that represent habitat amounts resulting from flow conditions occurring over
different time steps (e.g., daily, weekly, monthly), as well as separate analysis that address
effects of rapidly changing flows (e.g., hourly) on habitat availability and suitability.
The Mainstem Open-water Flow Routing Model and habitat models will be used to process
output from the Project operations model. This will be done for different operating scenarios,
hydrologic time periods (e.g., ice free periods: spring, summer, fall; ice-covered period: winter
[will rely on Ice Processes Model – Section 7.6]), Water Year types (wet, dry, normal), and
biologically sensitive periods (e.g., migration, spawning, incubation, rearing) and will allow for
the quantification of Project operation effects on the following:
• Habitat areas (for each habitat type – main channel, side channel, slough, etc.) by species
and life stage; this will also allow for an evaluation of the effects of breaching flows on
these respective habitat areas and biologically sensitive periods (e.g., breaching flows in
side channels during egg incubation period resulting in temperature change).
• Varial zone area (i.e., the area that may become periodically dewatered due to Project
operations, subjecting fish to potential stranding and trapping and resulting in reduced
potential invertebrate production).
• Effective spawning areas for fish species of interest (i.e., spawning sites that remain
wetted through egg incubation and hatching).
• Other riverine processes that will be the focus of the Geomorphology (see Sections 6.5
and 6.6), Water Quality Modeling (see Section 5.6), and Ice Processes (see Section 7.6)
studies including mobilization and transport of sediments, channel form and function,
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water temperature regime, and ice formation and decay timing. The IFS studies will be
closely linked with these studies and will incorporate various model outputs in providing
a comprehensive evaluation of instream flow-related effects on fish and aquatic biota and
habitats.
As an example, using the habitat versus flow relationships (based on HSC and HSI metrics
described in Sections 8.5.4.5.1.1 and 8.5.4.5.1.2) developed within the different Focus Areas and
at selected cross-sections, an evaluation of habitat change over time can be completed using
habitat time series analysis. The basic premise of a habitat time series analysis is that the
physical habitat in a stream at any given time can be calculated from the stream flow using the
equation:
HA(t) = WUA{Q(t)}
where WUA = physical habitat versus flow relationship for a given species and life
stage;
Q(t) = stream flow at time t; and
HA(t) = habitat area for time t.
The basic steps to calculating a habitat time series are illustrated in Figure 8.5-35, where the
habitat versus flow relationship (WUA) is integrated with the daily flow records to derive habitat
availability over time. In this form, time series analysis provides a method for assessing the
relative impacts from changes in the flow regime resulting from different operational scenarios.
The results of the time series analysis can be compared under baseline (unregulated) conditions
with one or more Project Operational Scenarios. This type of analysis will be done for each
biologically relevant period (e.g., adult migration and holding, spawning, incubation, juvenile
rearing, and others) for a given species and life stage, and for different Water Year types (e.g.,
wet, normal, dry). Consideration will also be given to identifying year types that reflect cold,
normal, and above average air temperatures. The analysis will include development of habitat-
duration curves that depict habitat exceedances based on the hydrologic record.
Other types of temporal analysis have been previously described in this RSP (see Section
8.5.4.6.1.5 – Effective Spawning Habitat Analyses; and Section 8.5.4.6.1.6 – Varial Zone
Modeling). These analyses will be coordinated with other resource studies that will evaluate
among other things, temporal changes in physical habitats (e.g., changes in channel form,
substrate composition, embeddedness (spawning gravel quality and quantity) etc.) (see RSP
Geomorphology – Sections 6.5 and 6.6), and temporal changes in water quality characteristics
(temperature – effects on growth and incubation, turbidity, etc.) (see RSP Water Quality
Modeling– Section 5.6). The final approach and details concerning the methods that will be used
for conducting the temporal analysis, including the time steps (hourly, daily, monthly, etc.),
indicator parameters (spawning period, incubation, substrate composition, water temperature,
and other biologically relevant indicators), and Project operational scenarios will be worked out
in consultation with the TWG in Q4 2013.
8.5.4.7.1.2. Spatial Analysis
How the data and habitat-flow relationships collected and developed from one location relate to
other unmeasured locations is the focus of the spatial analysis. This analysis is crucial to
providing an overall understanding of how Project operations may affect habitats and riverine
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processes on a system-wide basis and will feed directly into the Integrated Resource Analysis
(see Section 8.5.4.8). This analysis will be completed in Q2 through Q4 2014 after all data are
collected and respective models have been developed. Just like the temporal analysis, the final
procedure(s) for completing spatial analysis will be developed collaboratively with the TWG and
with input from other resource disciplines.
Completion of spatial analyses of the Susitna River will be challenging given its length, widely
variable size (width), diverse geomorphologies, and complex habitat types. This variability is
readily apparent in the Middle River Segment and becomes even more pronounced in the Lower
River Segment with the addition of flow from the Talkeetna and Chulitna rivers and resulting
expanded floodplain. This will require the development of an approach that considers the
distinctiveness of the different habitat types within a given area and at the same time the
similarity of these habitat types to other areas. Development of habitat – flow relationships for
specific habitat types (e.g., side channel, side slough) and mesohabitat types (riffle, run, pool,
etc.) from one area should then, with appropriate adjustment for dimensional differences and
other distinguishing factors, be expandable to unmeasured areas containing similar
characteristics.
A substantial effort was already advanced toward development of a spatial habitat analysis
approach as part of the 1980s studies (Aaserude et al. 1985; Klinger-Kingsley et al. 1985;
Steward et al. 1985). Inspection of those studies indicates that although the tools and
computational techniques that were applied may be outdated, the general principles and precepts
that served to guide development of the approach remain sound today. As a result, they provide a
good starting point from which to build a more contemporary approach founded on new
sampling technologies and more sophisticated models that will provide for a more robust spatial
analysis, including procedures for extrapolation of habitat-flow relationships from measured to
unmeasured areas.
Importantly, the 1980s studies made a clear distinction regarding extrapolation approaches that
are suited for single thread channel versus those for multi-thread channels. Aaserude et al. (1985)
correctly noted that for single thread channels, it is appropriate and is routinely done today to
utilize extrapolation procedures that are based on proportional lengths of mesohabitat types that
are identified as part of a habitat mapping exercise. This approach was originally fostered by
Morhardt et al. (1983) and has remained in use since. Indeed, this approach, or some
modification thereof, will be utilized for extrapolating PHABSIM-based habitat–flow
relationships derived from main channel mesohabitat specific transects (e.g., riffle, run, pool,
etc.) as identified from the Characterization of Aquatic Habitats Study (see Section 9.9) to
unmeasured mesohabitats within a given geomorphic reach. This will be done in a series of steps
that include the following:
• Completion of habitat mapping (see Section 9.9) that will delineate main channel
mesohabitats into categories of cascades, riffle, pool, run, and glide as described in
Section 8.5.4.2.1.1.
• Determination of percentages of each mesohabitat type within each geomorphic reach.
• Assignment of existing transects (those already established as input to the open-water
flow routing model (see Section 8.5.4.3) and new main channel transects established
either as part of the detailed Focus Area studies (see Section 8.5.4.6.1.2) or added to
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capture a specific main channel habitat not represented by the existing transects to a
specific mesohabitat category.
• Weight each of the transects within a given geomorphic reach based on the percentages
of mesohabitats represented in the reach (e.g., in a reach that is 30 percent riffle with 6
riffle transects; each transect would be assigned a weighting factor of 5 percent (30
percent/6) of the total reach length).
• Apply additional transect weighting based on location to account for tributary and
accretion flow.
• Derive habitat-flow relationships (by species and life stage) for a given geomorphic reach
based on transect specific habitat-flow relationships by mesohabitat type weighted by the
percentages of the reach (based on lineal distance) containing each mesohabitat type (as
determined from habitat mapping).
This latter step will then result in a composited habitat-flow relationship that considers all
mesohabitat types within a given geomorphic reach. Further compositing of relationships for all
geomorphic reaches (with consideration for flow accretion, etc.) will allow for the derivation of
habitat-flow relationships (by species and life stage) for the entire segment of the main channel
Susitna River. Coupled with the open-water flow routing model, these relationships can then be
used to evaluate how main channel habitats may vary under different operational scenarios and
will provide one of the tools necessary for completing the spatial analysis. It should be noted that
due to sampling and modeling limitations, main channel mesohabitat mapping was not
completed in the 1980s studies nor was there any development of main channel habitat-flow
response relationships.
A different approach will be needed for multi-thread channels because they contain multiple
habitat types (e.g., side channel, side slough, upland slough, etc.) within which each may contain
multiple mesohabitat types (e.g., riffle, run, pool, etc.). In addition, flows within some of the
habitat types may be governed by groundwater-surface water interactions that cannot be modeled
directly by PHABSIM. The framework for evaluating multi-channel habitats described in
Aaserude et al. (1985) provides a logical construct for achieving this and as noted above, is the
starting point for the current Instream Flow Study. Unlike the approach for a single thread
channel where a reasonable assumption is that habitat-flow response relationships will generally
be similar among mesohabitat types, the diversity of habitats within a multi-thread channel
means that habitat-flow responses are dynamic and highly variable. In addition, multi-thread
channels are spatially discontinuous and disconnected so that it is not possible to extrapolate
entire multi-channel units to others. As noted by Aaserude et al. (1985), the braided river
environment is too dynamic and variable for the development of quantitative relationships
between discharge and physical habitat variables such as depth, velocity, and channel structure
on a river corridor-wide basis for use in extrapolation. Instead, an approach for evaluating habitat
is needed that focuses on portions of the river corridor but then relates the findings of those
portions to other areas of similar character.
The method presented by Aaserude et al. (1985) was based on the provision of two separate
databases, the first containing habitat-flow response relationships for the full range of habitat and
mesohabitat types found within selected portions of the river, the second an expansive database
consisting of aerial imagery and targeted measurements of a select number of habitat response
variables from essentially all of the habitat types found within the primary multi-threaded
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channels in the Middle River Segment. Input to the first database was provided largely by a
number of site-specific studies that included application of PHABSIM (IFG), DIHAB, and
RJHAB models to define habitat-flow response relationships in different habitat types, as well as
surveys to determine breaching flows. However, the “one size fits all” concept that may be valid
for expansion of mesohabitat types does not apply to the multi-thread network of channels in the
Susitna River. Consequently, further stratification of the habitat types (side channel, side slough,
upland slough, etc.) was needed and resulted in the designation of 10 “representative groups”
that provided a sub-level of categorization to the habitat types (Steward et al. 1985; Aaserude et
al. 1985). These 10 groups consisted of “identifiable combinations of flow – related attributes”
(Steward et al. 1985) that were deemed readily distinguishable and included the following:
• Group I – Predominantly upland sloughs. Areas are highly stable due to persistence of
non-breached conditions. Area hydraulics characterized by pooled clear water with
velocities frequently near 0 fps and depths > 1 ft. Pools commonly connected by short
riffles with velocities < 1 fps and depths < 0.5 ft.
• Group II – Side sloughs that are characterized by relatively high breaching flows
(>19,500 cfs), clear water caused by upwelling groundwater and large channel length to
width ratios (> 15:1).
• Group III – Areas with intermediate breaching flows and relatively broad channel
sections. These areas consist of side channels which transform into side sloughs at
mainstem discharges ranging from 8,200 to 16,000 cfs. These areas are distinguishable
from Group II by lower breaching flows and smaller length to width ratios. Upwelling
water is present.
• Group IV – Side channels that are breached at low flows and possess intermediate mean
velocities (2–5 fps) at a mainstem discharge of approximately 10,000 cfs.
• Group V – Mainstem and side shoal areas that transform to clear water side sloughs as
mainstem flows recede. Transformations generally occur at moderate to high breaching
flows.
• Group VI – Similar to Group V. Sites within this group are primarily overflow channels
that parallel the adjacent mainstem, usually separated by sparsely vegetated gravel bar.
Upwelling may or may not be present. Habitat transformations within this group are
variable in type and timing.
• Group VII – Side channels that breach at variable yet fairly low mainstem discharges and
exhibit characteristic riffle/pool sequence. Pools are frequently large backwater areas
near the mouth of the sites.
• Group VIII – Area that dewater at relatively high flows. Flow direction at the head of the
channels tends to deviate sharply (> 30 degrees) from the adjacent mainstem.
• Group IX – Secondary mainstem channels that are similar to the primary mainstem
channels in habitat character, but distinguished as being smaller and conveying a lesser
proportion of the total discharge. Areas within this group have low breaching discharges
and are frequently similar in size to large side channels, but have characteristic mainstem
features, such as relatively swift velocities (> 5fps) and coarser substrate.
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• Group X – Large mainstem shoals and margins of mainstem channels that show signs of
upwelling.
Another element of the method described by Aaserude et al. (1985) that was used as part of the
representative group designation was its consideration of habitat transformation wherein
mainstem areas may functionally transition from side channels to side sloughs and ultimately
become dewatered as flows recede. A total of 11 habitat transformation categories were defined
and considered when comparing flow conditions; these included comparative categories of clear
vs. turbid water, upwelling present vs. absent, and distinct vs. indistinct side channel formation.
Model development from which to base habitat-flow response relationships within each of the
groups relied upon the site-specific models applied at different study areas. In addition to
traditional metrics of weighted usable area (WUA), a number of other metrics were derived that
included Wetted Surface Area (WSA), Gross Habitat Area (GHA), a Habitat Availability Index
(HAI), a Habitat Distribution Index (HDI), and a Habitat Quality Index (HQI). These
relationships were then applied to un-modeled areas assigned to different “representative groups”
taking into account two important distinguishing characteristics—structural habitat quality and
breaching flow. Structural habitat quality was evaluated for each site based on field data that
considered cover type, percent cover, dominant substrate size, substrate embeddedness, channel
geometry, and riparian vegetation. From this, a Structural Habitat Index (SHI) was computed for
each un-modeled area. Breaching flows were likewise determined for each unmeasured area.
These two elements were then used as adjustment factors for defining the derived non-modeled
habitat – flow response relationship; this process is conceptually shown in Figure 8.5-36. Once
relationships were derived from un-modeled areas, it was then possible to integrate results into
an overall assessment of habitat-flow responses within each representative group; these were
presented in Steward et al. (1985). The next step in the process would have been to conduct a
system-wide (at least for the Middle River Segment) evaluation of habitat-flow responses that
would have aggregated the responses into a system-wide habitat-flow response relationship.
However, this step was never completed as part of the 1980s studies.
Review and inspection of Aaserude et al. (1985), Steward et al. (1985), and Klinger and Trihey
(1984) clearly indicate that the challenges of model extrapolation from measured to unmeasured
areas had received substantial attention and had resulted in a carefully designed and logical
approach for application on the Middle River Segment of the Susitna River. This same approach
will serve as the starting point for consideration of the spatial analysis that will be completed for
multi-channel areas as part of the 2013–2014 Instream Flow Study. However, even though some
of the same steps may be applicable for the current studies (e.g., habitat mapping, use of aerial
imagery, field data collection, derivation of certain habitat-flow response relationships), the
analytical tools that are available (e.g., 2-D modeling, LiDAR, digital orthophotos and
videography, Forward Looking Infrared [FLIR], GIS, Real Time Kinematic [RTK]-GPS surveys,
etc.) and that will be used are much more sophisticated and will result in a more detailed and
robust assessment. Moreover, the analysis will also rely on inputs from other inter-related
resource studies, including, in particular Geomorphology (see Sections 6.5 and 6.6),
Groundwater (see Section 7.5), Water Quality (see Sections 5.5 and 5.6), and Characterization of
Aquatic Habitats (see Section 9.9) (Figure 8.5-1). The Focus Areas identified in this RSP (see
Section 8.5.4.2) were purposely selected based, in part, on the diversity of habitat types they
contained and their representativeness of other areas in the river. The inter-related resource
studies that will be completed at each of these areas will provide a strong base of information,
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data, and flow-sensitive models that can be used, with proper adjustment, for expanding results
to un-measured areas.
However, as noted in Section 8.5.2.2, the 1980s project assumed a two-dam scenario, with the
lower dam serving as a re-regulating structure to smooth out load-following effects from the
upper dam. Thus, the flow changes assumed to occur in the Middle and Lower River segments
were more focused on shifts in the seasonal/monthly timing and magnitude of flows rather than
on daily flow fluctuations. The extrapolation methods were therefore narrowly focused on being
able to evaluate those effects as they occurred at different locations of the river. The spatial
analysis for the Susitna-Watana Project will need to consider both those types of effects as well
as the daily flow fluctuations associated with load-following. Methods for expanding the results
of the varial zone modeling (see Section 8.5.4.6.1.6) and effective habitat modeling (see Section
8.5.4.6.1.5) will therefore need to be developed and integrated into the extrapolation process.
In addition, decisions regarding whether and the extent to which detailed studies will be
extended into the Lower River Segment will be discussed pending results of the open-water flow
routing modeling in Q2 2013. If needed, these studies would be scheduled to occur commencing
in Q3 2013 and extend into Q3 2014. Temporal and spatial analytical techniques applicable to
the Lower River Segment would be developed in Q4 2014.
8.5.4.7.1.3. Finalization of Analytical Methods
The results of the temporal and spatial analyses will include tabular listings of habitat indicator
values under existing and alternative flow regimes. Model results will be developed for
representative hydrologic conditions and a multi-year, continuous hydrologic record to evaluate
annual variations in indicator values. The availability of indicator values over a multi-year record
will support sensitivity analyses of the habitat indicators used to evaluate proposed reservoir
operations. Sensitivity analyses of individual components of the habitat modeling efforts are a
standard technique in model construction, calibration, and assessment and are envisioned as
implicit steps in the IFS. For instance, selection of draft HSC/HSI (Section 8.5.4.5.1.1.2) will be
subject to sensitivity analyses to identify those inputs where additional data may be required to
improve model output, or where the use of available values leads to uncertainty in model
outputs. Integrating the level of uncertainty in the various model components will provide the
TWG with an overall understanding of the robustness of individual habitat indicators. Analysis
of habitat indicators over a multi-year record will identify the sensitivity of indicators to
hydrologic conditions and the level of certainty associated with decisions regarding alternative
instream flow regimes. The design of the sensitivity analyses for habitat indicators will be
developed by AEA and reviewed in consultation with the TWG in Q4 2013 and implemented in
Q3 through Q4 2014 (Table 8.5-14).
It will be important to reach consensus with licensing participants and the TWG on the final
methods that will be applied for both the temporal and spatial analysis. These methods will be
reviewed and discussed during one or more TWG meetings that will occur in Q3 2013. Based on
input and comments from the TWG, the method will be finalized and described in the Initial
Study Report prepared in Q1 2014. Application of the method will occur in Q4 2014 and be
included as part of the Instream Flow Study Integration (see Section 8.5.4.8).
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8.5.4.7.2. Work Products
Results of the temporal and spatial analysis will be provided in tabular and graphical formats and
described in a detailed report. This will include a summarization of the various indices of Project
effects on aquatic habitats to allow ready comparison of the effects of alternative operational
scenarios.
Work products associated with the analysis will include but not be limited to the following:
• Tabular listing of habitat quantities under different flows at different times by species and
life stage.
• Time series plots depicting habitats over time by species and life stage under unregulated
conditions and under different operational scenarios; separate time series will be
developed for different Water Year types.
• Habitat – duration curves based on time series analysis.
• Development of extrapolation methods and the application of those methods that will
provide an estimate of system-wide effects of Project operations on various habitat
indices for both single thread and multiple thread channels.
• Preparation of sections within the Initial Study Report that describe temporal and spatial
analytical methods.
8.5.4.8. Instream Flow Study Integration
8.5.4.8.1. Proposed Methodology
Construction and operation of the proposed Project will change downstream flow conditions on
an hourly, daily, and seasonal basis. Load-following operations will increase the frequency,
timing, and magnitude of hourly and daily flow fluctuations, and increased flow releases during
winter months will be followed by decreased flow releases as the reservoir refills. The effects of
such flow changes will vary depending on the operational rules guiding power generation. The
suite of Project operational rules governing hourly, daily, and seasonal dam releases are termed
operational scenarios. Scenarios developed to benefit one specific resource may have a
detrimental effect on another resource. For instance, maintaining high flow releases during the
spring salmon smolt out-migration period may delay reservoir refill and could affect Project
releases for late summer coho rearing. An operational scenario designed to benefit one resource,
such as cottonwood germination, may have an unintended detrimental effect on another resource.
Constraints on Project flow releases to benefit one natural resource may affect the ability of AEA
to meet its energy needs. Identifying an operational scenario that satisfies the interests of all
parties requires an evaluation of multiple resource benefits and risks.
Tools to inform the evaluation of flow scenarios have been developed in support of other water
control decisions. A Decision Support System (DSS) was developed to support the evaluation of
alternative flow regimes on resources of the Black Canyon of the Gunnison National Park (Auble
et al. 2009). The DSS developed by Auble was intended to provide decision-makers with the
tools to manage large data sets of simulated flow alternatives and evaluate the relative
desirability of those alternatives with respect to natural resources. The intent was not to evaluate
alternatives, but to provide a tool for informing the evaluation of alternatives. The basic approach
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was to array differences among alternative flow regimes by calculating values of indicator
variables representing different habitat characteristics or processes of the riverine ecosystem.
Auble noted that the scientific understanding and quantitative relations between flow and the
physical and biological responses of riverine systems are complex and may be imperfectly
represented by the indicators. Disagreement about the relative importance or weighting of
multiple resource concerns can delay or derail the decision-making process. Ideally, a DSS
requires a balance between simplification of assumptions to reduce complexity and
oversimplification that does not reflect the constituent variables and calculations. Auble
produced a set of indicators grouped into several areas of natural resources concerns. The
indicators were replicable calculations that reflected conditions or processes within each area of
concern. Alternatives were compared directly in terms of these indicators, each of which could
be individually understood and challenged in terms of the assumptions involved in the
calculations. Different users could make different decisions using this system because they might
weight the importance of multiple indicators differently or value different aspects of the system.
Thus, the goal of the DSS was not to make a decision, but rather to reduce the complexity of
information and focus attention on trade-offs involved in the decision.
The Yakima River DSS (Bovee et al. 2008) was designed to quantify and display the
consequences of alternative water management scenarios to provide water releases for fish,
agriculture, and municipal water supply. Output of the Yakima River DSS consisted of a series
of conditionally formatted scoring tables that compiled changes in evaluation indicators.
Increases in the values of selected indicators were reflected in a color-coded scoring matrix to
provide decision-makers with a quick visual assessment of the overall results of an operating
scenario. The scoring matrix required that evaluation indicators used to describe resources be
rated as comparative values. A variety of weighting strategies were provided during the decision-
making process to reflect the relative importance of different indicators.
In support of relicensing decisions for the Baker River Hydroelectric Project, FERC No. 2150, a
DSS-style matrix was developed to evaluate multiple resource concerns under alternative
operational scenarios (Hilgert et al. 2008). The focus of the operations and aquatic habitat
analyses was to identify a mode of operation that would protect aquatic resources while meeting
multiple licensing participant interests. Aquatic habitat analyses were run concurrent with
analyses of economic, flood control, and other resources. Various licensing participants
championed different approaches to the relationships between minimum and maximum flow
releases, minimum and maximum reservoir pool levels, and downramping rates. Through study
and analysis, some scenarios were proven infeasible and abandoned, others were modified, and
others were dissected and recombined with other approaches. Alternative operational scenarios
were evaluated using a matrix that presented indicators of resource concerns without applying
comparative weighting factors. Collaboration among licensing participants gradually led to
consensus on a preferred flow management plan that contributed led to a Settlement Agreement.
Evaluation of Project effects on Susitna River resources will require inventive modeling
approaches that integrate aquatic habitat modeling with evaluation of riverine processes such as
groundwater-surface water interactions, water quality, and ice processes. The number of reaches,
habitat types, target species and life stages, and resource-specific models will result in large data
sets for multiple resources that will be difficult to comprehend when evaluating alternative
operational scenarios. A DSS-type process will be needed to evaluate the benefit and potential
impacts of alternative operational scenarios. For illustration purposes, an example matrix was
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developed (Table 8.5-21) to display a range of potential indicator variables including the
following:
• Power
• Hydrologic
• Reservoir
• Ramping rates
• Stranding and trapping
• Salmon spawning and incubation
• Salmon rearing
• Other fish species
• Riparian
• Recreation
• Other aquatic conditions
As habitat-specific models are developed, they will be used to evaluate existing conditions and
the effects of alternative operational scenarios for multiple resources and riverine processes. A
Project operations model (see Section 8.5.4.3.2) will be used to simulate Project inflow, outflow,
power generation, and reservoir pool levels for alternative operational scenarios under a range of
hydrologic years. The operations model will be used to quantify revenue from power generation
based on operational constraints selected for each alternative scenario. Types of constraints may
include maximum and minimum instream flow releases, ramping rates, and reservoir levels.
These constraints may be varied within a hydrologic year according to schedules specified for
each alternative. Operations model output may include simulated reservoir elevations, turbine,
spill, and total outflow, as well as hourly stream flow immediately below the powerhouse.
Output from the operations model will be used as input for the downstream habitat models.
Hourly flows immediately below the powerhouse will be routed downstream using the mainstem
open-water flow routing models (see Section 8.5.4.3) and Ice Processes Model (see Section 7.6).
Each habitat and riverine processes model can be used to develop large data sets of hourly
habitat conditions. The DSS-type process will be used to focus attention on those attributes that
the TWG believes are highest priority in evaluating the relative desirability of alternative
scenarios with respect to natural resources. Evaluation indicators selected for a DSS-type matrix
represent a preliminary analysis to identify the most promising scenarios. When discussion of
alternatives focuses on only a few remaining scenarios, those final scenarios will be evaluated
using the larger data set of habitat indicators to ensure that environmental effects are consistent
with the initial analyses.
The selection of indicator variables will be developed in collaboration with the TWG. For
planning purposes, it is assumed that values for each evaluation indicator will be developed and
presented for a range of alternative operational scenarios without rating or comparative
weighting of various resources. Although incorporating a relative weighting system similar to the
Yakima River DSS (Bovee et al. 2008) would simplify the evaluation process, reaching
consensus on weighting factors may divert attention from understanding and discussing the
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merits of constituent variables. Table 8.5-21 represents one option to present Project decision-
makers with information on the effects of alternative operational scenarios on resource values.
Development of a DSS-type process, and supporting software to efficiently process data
analyses, will be initiated in collaboration with the TWG after the initial results of the various
habitat modeling efforts are available in 2014 (Table 8.5-14). The intent is to prepare the DSS-
type evaluation process by Q1 2015 to assist scenario evaluations in support of the License
Application.
8.5.4.8.2. Work Products
Work efforts in support of Instream Flow Study integration will be described in the ISR and USR
(Table 8.5-14) to be prepared at the end of each year of study. A DSS-type program will
developed in collaboration with the TWG to support decision-makers with the evaluation of
alternative operational scenarios. Specific work products for the study integration efforts will
consist of the following:
• Summary of any study integration efforts in 2013 to be included in the ISR
• Summary of study integration efforts in 2014 to be included in the USR
• DSS-type matrix with supporting documentation
8.5.5. Consistency with Generally Accepted Scientific Practice
The proposed IFS, including methodologies for data collection, analysis, modeling, field
schedules, and study durations, is consistent with generally accepted practice in the scientific
community. The study plans were collaboratively developed with technical experts representing
the applicant, state and federal resource agencies, Alaska Native entities, non-government
organizations, and the public. Many of these technical experts have experience in multiple FERC
licensing and relicensing proceedings. The IFS is consistent with common approaches used for
other FERC proceedings and the IFS references specific protocols and survey methodologies, as
appropriate.
8.5.6. Schedule
The schedule for completing all components of the Mainstem Aquatic Habitat Model is provided
in Table 8.5-14. The TWG will have opportunities for study coordination through regularly
scheduled meetings, reports, and, as needed, technical subcommittee meetings. Initial and
Updated Study Reports will be issued in December 2013 and 2014, respectively. Preparation of
reports is planned at the end of 2013 and 2014 for each of the study components. Workgroup
meetings are planned to occur on at least a quarterly basis, and workgroup subcommittees will
meet or have teleconferences as needed.
8.5.7. Level of Effort and Cost
Based on a review of study costs associated with similar efforts conducted at other hydropower
projects, and in recognition of the size of the Project and logistical challenges and costs
associated with the remoteness of the site, study costs associated with the Instream Flow Study
are expected to be approximately $5,000,000 to $6,000,000. Estimated study costs are subject to
review and revision as additional details are developed.
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Portions of this study will be conducted in conjunction with water resource, geomorphology,
water quality, operational modeling, and fisheries and aquatic resource studies; however, specific
costs of those studies will be reflected in those individual study plans.
8.5.8. Literature Cited
Aaserude, R.G., J. Thiele, and D. Trudgen. 1985. Characterization of aquatic habitats in the
Talkeetna to Devil Canyon segment of the Susitna River, Alaska. Prepared for Alaska
Power Authority by Trihey and UAF (Trihey Associates and University of Alaska
Fairbanks), Anchorage, Alaska. 144 pp. APA Document 2919.
ADF&G (Alaska Department of Fish and Game). 1983. Aquatic Studies Procedures Manual:
Phase II - Final Draft 1982-1983. Alaska Department of Fish and Game. Su-Hydro
Aquatic Studies Program. Anchorage, Alaska. 257 pp. APA Document 938.
ADF&G (Alaska Department of Fish and Game). 1984. ADF&G Su Hydro Aquatic Studies May
1983 - June 1984 Procedures Manual Final Draft. Alaska Department of Fish and Game.
Su-Hydro Aquatic Studies Program. Anchorage, Alaska. APA Documents 885 and 886.
AEA (Alaska Energy Authority). 2011. Pre-Application Document. Susitna-Watana
Hydroelectric Project FERC Project No. 14241. Alaska Energy Authority, Anchorage,
Alaska.
Ahmadi-Nedushan, B., St-Hilaire, A., Bérubé, M., Robichaud, E., Thiémonge, N. & Bobée, B.
2006. A review of statistical methods for the evaluation of aquatic habitat suitability for
instream flow assessment. River Research and Applications 22, 503-523.
Alderdice, D.F., and F.P.J. Velsen. 1978. Relation between temperature and incubation time for
eggs of Chinook salmon (Oncorhynchus tshawytscha). Journal of the Fisheries Research
Board of Canada 35:69-75.
Annear, T., I. Chisholm, H. Beecher, A. Locke and 12 other authors. 2004. Instream flows for
riverine resource stewardship, revised edition. Instream Flow Council, Cheyenne, WY.
268 pp.
Ashton, W.S., and S.A. Klinger-Kingsley. 1985. Response of Aquatic Habitat Surface Areas to
Mainstem Discharge in the Yentna to Talkeetna Reach of the Susitna River. Final Report
to Alaska Power Authority by R&M Consultants, Inc., and Trihey and Associates,
Anchorage, Alaska. 201 pp. APA Document 2774.
Auble, G.T., Wondzell, M., and Talbert, C. 2009. Decision support system for evaluation of
Gunnison River flow regimes with respect to resources of the Black Canyon of the
Gunnison National Park: U.S. Geological Survey Open-File Report 2009–1126, 24 p.
B. Efron & R.J. Tibshirani (1993): An introduction to the bootstrap. Chapman & Hall, New
York.
Barrett, B., M., F. M. Thompson, and S. N. Wick. 1985. Adult salmon investigations. Susitna
Hydro Aquatic Studies Report No. 6. Prepared for the Alaska Power Authority. Alaska
Department of Fish and Game. 528 pp. APA Document 2748.
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Barrett, B.M., F.M. Thompson, S. Wick, and S. Krueger. 1983. Adult Anadromous Fish Studies,
1982. Phase II data report, Volume 2. Prepared for the Alaska Power Authority. Alaska
Department of Fish and Game. 275 pp. APA Document 588.
Bauersfeld, K. 1977. Effects of peaking (stranding) of Columbia River dams on juvenile
anadromous fishes below the Dalles Dam, 1974 and 1975. Washington Department of
Fisheries, Technical Report 31. 111 pp.
Bauersfeld, K. 1978. Stranding of juvenile salmon by flow reductions at Mayfield Dam on the
Cowlitz River 1976. Washington Department of Fisheries Technical Report No. 36.
Prepared for the City of Tacoma, Department of Public Utilities. 36 pp.
Becker, C. D., Neitzel, D. A., & Abernethy, C. S. (1983). Effects of dewatering on Chinook
salmon redds: tolerance of four development phases to one-time dewatering. North
American Journal of Fisheries Management, 3(4), 373-382.
Bigler, J., and K. Levesque. 1985. Lower Susitna River Preliminary Chum Salmon Spawning
Habitat Assessment. Alaska Department of Fish and Game, Susitna Hydro Aquatic
Studies. 140 pp. APA Document 3504.
Bovee, K. D. 1982. A guide to stream habitat analysis using the Instream Flow Incremental
Methodology. Instream Flow Paper No. 12. Washington DC: U.S. Fish and Wildlife
Service (FWS/OBS-82/26).
Bovee, K. D. 1986. Development and evaluation of habitat suitability criteria for use in the
instream flow incremental methodology. Washington DC: U.S. Fish and Wildlife Service
(Biological Report 86[7]). 235pp.
Bovee, K. D., B. L. Lamb, J. M. Bartholow, C. B. Stalnaker, J. Taylor, and J. Henriksen. 1998.
Stream habitat analysis using the instream flow incremental methodology. U.S.
Geological Survey, Biological Resources Discipline Information and Technology Report
USGS/BRD-1998-0004. viii + 131 pp.
Bovee, K.D., and R. Milhous. 1978. Hydraulic Simulation in Instream Flow Studies: Theory and
Techniques. Instream Flow Information Paper No. 5. Cooperative Instream Flow Service
Group, US Fish and Wildlife Service, Ft. Collins, Colorado. 156 pp.
Bovee, K.D., Waddle, T.J., Talbert, C. Hatten, J.R., and Batt, T.R. 2008. Development and
Application of a Decision Support System for Water Management Investigations in the
Upper Yakima River, Washington: U.S. Geological Survey Open-File Report 2008-1251,
289 p.
Buckwalter, J.D. 2011. Synopsis of ADF&G's Upper Susitna Drainage Fish Inventory, August
2011. Alaska Department of Fish and Game, Division of Sport Fish, Anchorage, Alaska.
27 pp.
Burgner, R.L. 1991. Life history of sockeye salmon (Oncorhynchus nerka). Pages 1-118 in C.
Groot and L. Margolis, eds., Pacific Salmon Life Histories. UBC Press, Vancouver.
C.C. Estes and D.S. Vincent-Lang. 1984. Aquatic Habitat and Instream Flow Investigations
(May–October, 1983). Prepared by Susitna Hydro Aquatic Studies, Alaska Department of
Fish & Game. Prepared for Alaska Power Authority, Anchorage, Alaska. APA
Documents 1930, 1931, 1932, 1933, 1934, 1935, 1936, 1937, 1938.
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Chen, F. Shen, H.T., and Jayasundara, N. 2006. A One-Dimensional Comprehensive River Ice
Model, Proceedings of the 18th IAHR International Symposium on Ice, Sapporo, Japan.
Cochran, W. G. 1977. Sampling techniques (3rd ed.). New York: John Wiley & Sons
Connor, E. & Pflug, D. 2004. Changes in the distribution and density of pink, chum, and
Chinook salmon spawning in the upper Skagit River in response to flow management
measures. North American Journal of Fisheries Management, 24(3), 835-852.
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8.5.9. Tables
Table 8.5-1. Summary of HSC curves developed during 1980s Susitna Studies.
Species Life Stage Depth Velocity Substrate Upwelling Cover Turbidity4
Coho Juvenile 1
Chinook Spawning
Juvenile 1
Sockeye Spawning
Juvenile 1
Chum Spawning 3
Juvenile 1
Pink Spawning 3
Rainbow Trout Spawning
Dolly Varden Adult 2
Arctic Grayling Adult 2
Humpback Whitefish Juvenile
Round Whitefish Adult 2
Longnose Sucker Adult 2
Burbot Adult
Notes:
1, 2 Depth curves for multiple species combined
3 Integrated with substrate suitability
4 Separate curves developed for clear vs. turbid water for one or more parameters
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Table 8.5-2. Periodicity of Pacific salmon habitat utilization in the Middle Segment (RM 184-98.5) of the Susitna River by species and life history stage. Shaded areas indicate timing of
utilization and dark gray areas represent peak use.
Species Life Stage Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Chinook
Salmon
Adult Migration
Spawning
Incubation
Fry Emergence
Rearing (0+)
Rearing (1+)
Juvenile Migration (0+)
Juvenile Migration (1+)
Chum
Salmon
Adult Migration
Spawning
Incubation
Fry Emergence
Rearing (0+)
Juvenile Migration (0+)
Coho
Salmon
Adult Migration
Spawning
Incubation
Fry Emergence
Rearing (0+)
Rearing (1+)
Rearing (2+)
Juvenile Migration (0+)
Juvenile Migration (1+)
Juvenile Migration (2+)
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Species Life Stage Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
Sockeye
Salmon1
Adult Migration1
Spawning1
Incubation
Fry Emergence
Rearing (0+)
Rearing (1+)
Juvenile Migration (0+)
Juvenile Migration (1+)
Pink
Salmon2
Adult Migration
Spawning
Incubation
Fry Emergence
Juvenile Migration (0+)
1 Early-run and late-run sockeye salmon exhibit distinct timing of adult migration and spawning, and utilize separate areas for spawning. Periodicity presented here represent that of late-run sockeye, as
early-run sockeye do not utilize the Middle Susitna River.
2 No rearing period for age 0+ pink salmon is identified because this species migrates to the estuary soon after emergence.
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Table 8.5-3. Instream flow sites and habitat modeling methods used during the 1980s in the Middle and Lower Susitna
River (Marshall et al. 1984; Sandone et al. 1984; Vincent-Lang et al. 1984; Hilliard et al. 1985; Suchanek et al. 1985).
River
Mile Site Name
Susitna
Segment Habitat Type Site Type
No. of
Transects
Year(s)
Measured
35.2 Hooligan Side Channel Lower Side Channel RJHAB 5 1984
36.2 Eagles Nest Side Channel Lower Side Channel RJHAB 4 1984
36.3 Kroto Slough Head Lower Side Slough RJHAB 5 1984
39.0 Rolly Creek Mouth Lower Tributary Mouth RJHAB 6 1984
42.9 Bear Bait Side Channel Lower Side Channel RJHAB 5 1984
44.4 Last Chance Creek Side Channel Lower Side Channel RJHAB 6 1984
59.5 Rustic Wilderness Side Channel Lower Side Channel RJHAB 5 1984
63.0 Caswell Creek Lower Tributary Mouth RJHAB 8 1984
63.2 Island Side Channel Lower Side Channel IFG-4, RJHAB 9 1984
74.4 Mainstem West Bank Lower Side Slough IFG-4 7 1984
74.8 Goose 2 Side Channel Lower Side Channel RJHAB 6 1984
75.3 Circular Side Channel Lower Side Channel IFG-4 6 1984
79.8 Sauna side channel Lower Side Channel IFG-4 4 1984
84.5 Sucker side channel Lower Side Channel RJHAB 6 1984
86.3 Beaver Dam side channel Lower Side Channel RJHAB 5 1984
86.3 Beaver Dam Slough Lower Side Slough RJHAB 5 1984
86.9 Sunset side channel Lower Side Channel IFG-4 7 1984
87.0 Sunrise side channel Lower Side Channel RJHAB 7 1984
88.4 Birch Slough Lower Side Slough RJHAB 8 1984
91.6 Trapper Creek side channel Lower Side Channel IFG-4, RJHAB 5 1984
101.2 101.2 R, Whiskers East Middle Side Channel IFG-4 9 1984
101.4 Whiskers Slough Middle Side Slough RJHAB 8 1983
101.5 101.5 L, Whiskers West Middle Side Channel IFG-2 5 1984
101.7 101.7 L Middle Side Channel DIHAB 4 1984
105.8 105.8 L Middle Mainstem DIHAB 4 1984
107.6 Slough 5 Middle Upland Slough RJHAB 9 1983
112.5 Slough 6A Middle Upland Slough RJHAB 8 1983
112.6 112.6 L, Side Channel 6A Middle Side Channel IFG-2 9 1984
113.6 Lane Creek mouth Middle Tributary Mouth
Habitat
Mapping 7 1983
113.7 Slough 8 Middle Side Slough RJHAB 5 1983
114.1 114.1 R Middle Side Channel DIHAB 3 1984
115.0 115.0 R Middle Side Channel DIHAB 4 1984
118.9 118.9 L Middle Mainstem DIHAB 3 1984
119.1 119.1 L Middle Mainstem DIHAB 3 1984
119.2 119.2 R, Little Rock side channel Middle Side Channel IFG-2 5 1984
125.2 125.2 R Middle Side Channel DIHAB 2 1984
125.3 Skull Creek Middle Side Slough IFG-4 11 1983
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River
Mile Site Name
Susitna
Segment Habitat Type Site Type
No. of
Transects
Year(s)
Measured
128.8 Slough 9 Middle Side Slough IFG-4 10 1983
130.2 130.2 R Middle Side Channel DIHAB 3 1984
131.1 4th of July Creek mouth Middle Tributary Mouth
Habitat
Mapping 8 1983
131.3 131.3 L Middle Side Channel DIHAB 4 1984
131.7 131.7 L Middle Side Channel IFG-4 7 1984
132.6 132.6 L, Side channel 10A Middle Side Channel IFG-4, RJHAB 9 1983-84
133.8 133.8 R Middle Mainstem DIHAB 3 1984
133.8 Side channel 10 Middle Side Channel IFG-4 4 1983
134.9 Lower Side channel 11 Middle Side Channel IFG-2 6 1983
136.0 136.0 L, Slough 14 Middle Side Channel IFG-4 6 1984
136.3 Upper Side channel 11 Middle Side Channel IFG-4 4 1983
137.5 137.5 R Middle Side Channel DIHAB 3 1984
138.7 138.7 L Middle Mainstem DIHAB 3 1984
139.0 139.0 L Middle Mainstem DIHAB 4 1984
139.4 139.4 L Middle Side Channel DIHAB 3 1984
141.2 Side channel 21 Middle Side Channel IFG-4 5 1983
141.8 Slough 21 Middle Side Slough IFG-4 5 1983
144.4 Slough 22 Middle Side Slough RJHAB 8 1983
147.1 147.1 L, Fat Canoe SC Middle Side Channel IFG-2 6 1984
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Table 8.5-4. Geomorphic reach designations for the Upper River (UR) Segment, Middle River (MR) Segment, and Lower
River (LR) Segment of the Susitna River as described in Section 6.5.4.1.2.2.
Reach Designation Upstream Limit RM) Downstream Limit (RM)
Reach Classifi-cation Slope (ft/mi) Lateral Constraints
Upper River Segment (UR)
UR-1 260 248 SC2 N/A Quaternary Basin Fill
UR-2 248 233 SC1 N/A Quaternary Basin Fill
UR-3 233 223 SC1 N/A Quaternary Basin Fill
UR-4 223 206 SC2 N/A Granodiorite
UR-5 206 201 SC1 N/A Quaternary Basin Fill
UR-6 201 184 SC2 N/A Quaternary Basin Fill
Middle River Segment (MR)
MR-1 184 182 SC2 9 Gneiss
MR-2 182 166.5 SC2 10 Quaternary Basin Fill
MR-3 166.5 163 SC2 17 Granites
MR-4 163 150 SC1 30 Granites
MR-5 150 145 SC2 12 Moraine and Turbidites
MR-6 145 119 SC3 10 Moraines
MR-7 119 104 SC2 8 Moraines
MR-8 104 98.5 MC1/SC2 8 Holocene Lacustrine and Alluvial Terrace
deposits
Lower River Segment (LR)
LR-1 98.5 84 MC1 5 Upper Pleistocene Outwash, Moraine and
Lacustrine deposits
LR-2 84 61 MC1 5 Upper Pleistocene Outwash, Moraine and
Lacustrine deposits
LR-3 61 40.5 MC3 4 Glaciolacustrine and Moraine deposits
LR-4 40.5 28 MC3 2 Glaciolacustrine and Moraine deposits
LR-5 28 20 SC2 2 Glaciolacustrine and Moraine deposits
LR-6 20 0 MC4 1.4 Glaciolacustrine and Holocene Estuarine deposits
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Table 8.5-5. Nested and tiered habitat mapping units, categories, and definitions.
Level Unit Category Definitions
1 Major Hydrologic Segment Upper, Middle, Lower River
Defined Segment Breaks
Upper River - RM184-248 (habitat mapping will only extend up to mainstem RM 233 and will
include the Oshetna River.
Middle River - RM 98.5-184
Lower River - RM 0-98.5
2 Geomorphic Reach
Upper River Segment Geomorphic
Reaches 1-6
Middle River Segment Geomorphic
Reaches 1-8
Lower River Segment1 Geomorphic
Reaches 1-6
Geomorphic reaches that uniquely divide the Major Hydrologic Segments based on geomorphic
characteristics.
3 Mainstem Habitat
Main Channel Habitat
Off-Channel Habitat Types2
Tributary Habitat
Main Channel Habitat:
Main Channel – Single dominant main channel.
Split Main Channel –Three or fewer distributed dominant channels.
Multiple Split Main Channel – Greater than 3 distributed dominant channels.
Side Channel – Channel that is turbid and connected to the active main channel but
represents non-dominant proportion of flow3. Tributary Mouth - Clear water areas that exist where tributaries flow into Susitna River main
channel or side channel habitats (upstream Tributary habitat will be mapped as a separate
effort).
Off-Channel Habitat: Side Slough: Overflow channel contained in the floodplain, but disconnected from the main
channel. Has clear water.3,4
Upland Slough: Similar to a side slough, but contains a vegetated bar at the head that is rarely
overtopped by mainstem flow. Has clear water.3,4
Backwater: Found along channel margins and generally within the influence of the active main
channel with no independent source of inflow. Water is not clear.
Beaver Complex – Complex ponded water body created by beaver dams.
Tributary Habitat:
Tributaries will be mapped to the upper limit of Susitna River hydrological influence.
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Level Unit Category Definitions
4 Main Channel and Tributary Main Channel and Tributary
Mesohabitat
Main Channel Mesohabitat
Pool – slow water habitat with minimal turbulence and deeper due to a strong hydraulic control.
Glide – An area with generally uniform depth and flow with no surface turbulence. Low
gradient; 0-1% slope. Glides may have some small scour areas but are distinguished from
pools by their overall homogeneity and lack of structure. Generally deeper than riffles with few
major flow obstructions and low habitat complexity.5
Run – A habitat area with minimal surface turbulence over or around protruding boulders with
generally uniform depth that is generally greater than the maximum substrate size. 5 Velocities
are on border of fast and slow water. Gradients are approximately 0.5% to less than 2%.
Generally deeper than riffles with few major flow obstructions and low habitat complexity.5
Riffle – A fast water habitat with turbulent, shallow flow over submerged or partially submerged
gravel and cobble substrates. Generally broad, uniform cross-section.
Low gradient; usually 0.5-2.0% slope.5
Rapid - Swift, turbulent flow including small chutes and some hydraulic jumps swirling around
boulders. Exposed substrate composed of individual boulders, boulder clusters, and partial
bars. Lower gradient and less dense concentration of boulders and white water than Cascade.
Moderate gradient; usually 2.0-4.0% slope.5
Tributary Mesohabitat:
Tributary mesohabitats within the hydrologic zone of influence will be typed using the
classification system described in Table 9.9-3, above.
5 Edge Habitat Length of Shoreline Habitat Calculation- will be determined by doubling the length of the mapped habitat unit.
Notes:
1. For the purposes of this RSP, classification of the Lower River segment will stop at Level 2. A classification system for the Lower River segment is still in development pending
determination of Project effects in the Lower River.
2. All habitat within this designation will receive an additional designation of whether water was clear or turbid within the database.
3. The terms Side Channel, Slough, and Upland Slough are similar but not necessarily synonymous with the terms for macrohabitat type as applied by Trihey (1982) and ADF&G (1983).
4. All slough habitat will have an associated area created during the mapping process to better classify size. A sub-sample of side sloughs and upland sloughs will be mapped to the mesohabitat
level using the tributary habitat classifications system shown in Table 9.9-3
5. Adapted from Moore et al. 2006.
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Table 8.5-6. Locations, descriptions and selection rationale of proposed Focus Areas for detailed study in the Middle River Segment of the Susitna River. Focus Area identification numbers (e.g., Focus Area 184) represent the truncated Project River Mile (PRM) at the downstream
end of each Focus Area.
Focus Area ID Common Name Description Geomorphic Reach
Location (PRM)
Area
Length (mi)
Habitat Types Present
Fish use in 1980s Instream Flow Studies in 1980s
Rationale for Selection Main Channel, Single Main Channel, Split Side Channel Tributary Mouth Side Slough Upland Slough Beaver Complex Upstream Downstream Spawning Rearing IFG DIHAB RJHAB Focus
Area-
184
Watana Dam
Area approximately 1.4
miles downstream of dam
site
MR-1 185.7 184.7 1.0 X X X N/A N/A N/A N/A N/A Focus Area-184 length comprises 50% of MR-1 reach length (2 miles long) and contains split
main channel and side channel habitat present in this reach.
Focus
Area-
173
Stephan Lake,
Complex
Channel
Wide channel near
Stephan Lake with
complex of side channels
MR-2 175.4 173.6 1.8 X X X X N/A N/A N/A N/A N/A
Focus Area-173 contains a complex of main channel and off-channel habitats within wide
floodplain. Represents greatest channel complexity within MR-2. Reach MR-2 is 15.5 miles long
and channel is generally straight with few side channels and moderate floodplain width (2-3 main
channel widths).
Focus
Area-
171
Stephan Lake,
Simple Channel
Area with single side
channel and vegetated
island near Stephan Lake
MR-2 173.0 171.6 1.4 X X X N/A N/A N/A N/A N/A
The single main channel with wide bars, single side channel and moderate floodplain channel
width in Focus Area-171 are characteristic of MR-2. Reach MR-2 channel morphology is generally
straight with few side channels and moderate floodplain width (2-3 main channel widths).
Focus
Area-
151
Portage Creek Single channel area at
Portage Creek confluence MR-5 152.3 151.8 0.5 X X X X
Focus Area-151 is a single main channel and thus representative of the confined Reach MR-5.
Portage Creek is a primary tributary of the Middle Segment and the confluence supports high fish
use.
Focus
Area-
144
Side Channel
21
Side channel and side
slough complex
approximately 2.3 miles
upstream Indian River
MR-6 145.7 144.4 1.3 X X X X X X X X X
Focus Area-144 contains a wide range of main channel and off-channel habitats, which are
common features of Reach MR-6. Side Channel 21 is a primary salmon spawning area. Reach
MR-6 is 26 miles long (30% of Middle Segment length) and is characterized by a wide floodplain
and complex channel morphology with frequent channel splits and side channels.
Focus
Area-
141
Indian River
Area covering Indian River
and upstream channel
complex
MR-6 143.4 141.8 1.6 X X X X X X X X X
Focus Area-141 includes the Indian River confluence, which is a primary Middle Susitna River
tributary, and a range of main channel and off-channel habitats. Channel and habitat types
present in Focus Area-141 are typical of complex Reach MR-6. High fish use of the Indian River
mouth has been documented and DIHAB modeling was performed in main channel areas.
Focus
Area-
138
Gold Creek
Channel complex including
Side Channel 11 and
Slough 11
MR-6 140.0 138.7 1.3 X X X X X X X X X
The Focus Area-138 primary feature is a complex of side channel, side slough and upland slough
habitats, each of which support high adult and juvenile fish use. Complex channel structure of
Focus Area-138 is characteristic of Reach MR-6. IFG modeling was performed in side channel
habitats.
Focus
Area-
128
Skull Creek
Complex
Channel complex including
Slough 8A and Skull Creek
side channel
MR-6 129.7 128.1 1.6 X X X X X X X X X
Focus Area-128 consists of side channel, side slough and tributary confluence habitat features
that are characteristic of the braided MR-6 reach. Side channel and side slough habitats support
high juvenile and adult fish use and habitat modeling was completed in side channel and side
slough habitats.
Focus
Area-
115
Lane Creek
Area 0.6 miles downstream
of Lane Creek, including
Upland Slough 6A
MR-7 116.5 115.3 1.2 X X X X X X X X
Focus Area-115 contains side channel and upland slough habitats that are representative of MR-
7. Reach MR-7 is a narrow reach with few braided channel habitats. Upland Slough 6A is a
primary habitat for juvenile fish and habitat modeling was done in side channel and upland slough
areas.
Focus
Area-
104
Whiskers
Slough Whiskers Slough Complex MR-8 106.0 104.8 1.2 X X X X X X X X X X X
Focus Area-104 contains diverse range of habitat, which is characteristic of the braided,
unconfined Reach MR-8. Focus Area-104 habitats support juvenile and adult fish use and a range
of habitat modeling methods were used in side channel and side slough areas.
Focus
Area-
TBD
TBD Lower Susitna River (TBD) TBD TBD TBD TBD TBD TBD TBD
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Table 8.5-7. Partial list of river cross-sections, and flow and water surface elevations measured in 2012 on the Susitna
River between River Miles 75 and 184. The list does not include additional measurements in late September/October.
Those measurements had not been processed at the time this study plan was prepared.
River
Mile2
High Q Trip Medium Q Trip Low Q Trip
Date Q, cfs3 Gold Ck4 Date Q, cfs3 Gold Ck4 Date Q, cfs3 Gold Ck4
184.1 6/17/12 27,698 32,800 8/6/12 14,707 19,300 9/15/12 7,838 10,800
183.4 6/18/12 24,493 32,200 8/6/12 14,419 19,300 9/15/12 7,630 10,800
182.8 6/18/12 25,389 32,300 8/6/12 stage only5 9/15/12 stage only5
182.6 6/19/12 26,676 34,400 8/6/12 stage only5 9/15/12 stage only5
182.2 6/19/12 27,619 35,500 8/6/12 14,239 19,100 9/15/12 7,714 11,000
181.7 6/19/12 27,886 35,500 8/7/12 14,775 18,300 9/15/12 8,353 11,100
180.3 6/20/12 29,426 36,300 8/7/12 14,183 18,200 9/15/12 8,310 11,300
179.8 6/20/12 29,128 36,400 8/7/12 stage only5 9/15/12 stage only5
178.9 6/20/12 29,645 36,200 8/7/12 14,705 18,200 9/15/12 8,689 11,500
176.8 6/21/12 30,866 37,500 8/7/12 14,345 18,100 9/14/12 8,361 10,100
176.1 6/16/12 29,756 36,900 8/7/12 14,799 18,000 9/14/12 8,738 10,000
173.9 6/21/12 31,240 37,500 8/8/12 14,559 17,300 9/16/12 10,768 16,500
172.0 6/21/12 31,163 37,300 8/8/12 stage only5 9/16/12 stage only5
170.0 6/21/12 30,571 37,000 8/8/12 stage only5 9/16/12 11,082 17,200
167.0 6/22/12 31,121 36,700 8/8/12 14,568 17,200 9/16/12 11,137 17,600
164.5 6/22/12 32,265 36,700 8/8/12 14,655 17,300 9/17/12 14,619 20,200
150.2 6/25/12 32,162 35,900 8/10/12 14,588 16,800
149.5 6/26/12 30,487 35,800 8/10/12 stage only5
148.7 6/26/12 30,036 36,000 8/10/12 15,351 16,800 9/29/12 18,488 20,000
147.6 6/25/12 33,180 36,400 8/10/12 stage only5
144.8 6/26/12 32,114 35,600 8/10/12 14,941 16,600
143.2 6/27/12 31,030 34,400 8/12/12 stage only5
142.3 6/27/12 31,396 34,500 8/12/12 17,354 18,100 9/29/12 18,131 19,800
142.1 6/27/12 31,868 34,800 8/12/12 stage only5
141.5 6/27/12 31,949 35,100 8/12/12 stage only5
140.8 6/27/12 31,121 35,000 8/12/12 stage only5
140.2 6/28/12 30,330 32,900 8/12/12 17,006 18,100
139.4 6/28/12 29,492 32,900 8/12/12 stage only5
138.9 6/28/12 29,753 33,200 8/12/12 16,798 18,100 9/29/12 18,301 19,800
138.5 6/28/12 30,583 33,200 8/12/12 16,803 18,000
138.2 6/28/12 30,555 33,300 8/12/12 stage only5
136.7 6/29/12 30,378 32,300 8/13/12 16,350 17,800 9/30/12 17,619 17,800
136.4 6/29/12 29,071 32,200 8/13/12 stage only5
135.7 6/30/12 28,039 31,000 8/13/12 16,449 17,700
135.4 6/30/12 28,230 31,000 8/13/12 16,344 17,700
134.7 6/30/12 28,203 31,000 8/13/12 stage only5
134.3 6/30/12 27,893 31,000 8/13/12 16,409 17,600 9/30/12 17,382 17,700
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River
Mile2
High Q Trip Medium Q Trip Low Q Trip
Date Q, cfs3 Gold Ck4 Date Q, cfs3 Gold Ck4 Date Q, cfs3 Gold Ck4
133.3 7/1/12 26,756 30,000 8/13/12 stage only5
132.9 7/1/12 26,943 30,000 8/13/12 stage only5
131.8 7/1/12 26,526 29,700 8/13/12 15,627 17,400
131.2 7/2/12 25,463 28,000 8/13/12 stage only5 10/1/12 15,568 15,500
130.9 7/2/12 26,166 27,900 8/14/12 16,491 17,400
130.5 7/2/12 25,715 28,000 8/14/12 16,275 17,300
130.0 7/2/12 25,678 27,900 8/14/12 stage only5
129.4 7/2/12 25,046 27,800 8/14/12 16,039 17,300
128.1 7/3/12 28,628 31,200 8/14/12 stage only5
126.6 7/3/12 28,243 30,900 8/14/12 16,330 17,300
124.4 7/4/12 26,748 30,000 8/15/12 15,926 17,600
123.3 7/4/12 27,608 29,900 8/15/12 16,078 17,600 10/1/12 15,582 15,400
122.6 7/5/12 27,248 28,800 8/15/12 stage only5
121.8 7/5/12 26,427 28,500 8/15/12 stage only5
120.7 7/5/12 26,132 27,900 8/15/12 16,161 17,600 10/1/12 15,582 15,300
120.3 7/6/12 23,875 24,700 8/15/12 stage only5
119.3 7/6/12 23,331 24,100 8/15/12 stage only5
119.2 7/6/12 22,890 24,000 8/15/12 16,287 17,600
117.2 7/6/12 22,687 23,400 8/15/12 stage only5
116.4 7/7/12 20,715 21,600 8/16/12 16,005 17,600 10/3/12 13,998 13,500
115.0 7/7/12 20,656 21,600 8/16/12 stage only5
114.0 7/7/12 20,747 21,100 8/16/12 stage only5
113.0 7/7/12 20,665 21,000 8/16/12 16,136 17,600 10/3/12 14,323 13,400
112.7 7/8/12 23,766 28,600 8/16/12 stage only5
112.2 7/8/12 25,006 28,900 8/16/12 stage only5
111.8 7/8/12 25,958 29,100 8/16/12 stage only5
110.9 7/8/12 25,860 29,100 8/16/12 stage only5
110.0 7/9/12 28,329 31,900 8/16/12 16,311 17,500 10/3/12 13,476 13,400
108.4 7/9/12 28,296 31,900 8/17/12 stage only5
106.7 7/9/12 28,825 31,800 8/17/12 15,254 18,000 10/3/12 14,172 13,400
104.8 8/17/12 16,394 17,900
103.0 7/9/12 28,409 31,600 8/18/12 15,508 16,300 10/4/12 14,558 13,700
102.4 8/18/12 15,278 16,100
101.5 8/18/12 15,362 16,000
101.0 8/18/12 15,377 16,000
100.4 8/19/12 15,345 16,400
99.8 7/10/12 26,635 26,900 8/19/12 stage only5
99.6 10/4/12 14,575 13,700
95.0 7/11/12 46,499 22,600 8/20/12 40,623 16,600 10/5/12 39,065 13,800
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River
Mile2
High Q Trip Medium Q Trip Low Q Trip
Date Q, cfs3 Gold Ck4 Date Q, cfs3 Gold Ck4 Date Q, cfs3 Gold Ck4
94.0 7/11/12 45,118 21,800 8/20/12 40,261 17,400
87.7 8/21/12 46,330 18,500
86.9 7/12/12 44,469 20,100 8/21/12 46,197 18,500
84.6 8/22/12 41,697 18,200
83.0 7/12/12 42,550 19,700 8/22/12 stage only5
82.0 7/13/12 41,895 18,800 8/22/12 stage only5
81.2 8/22/12 40,468 17,600
80.0 8/23/12 36,933 16,100
79.0 7/13/12 41,975 18,700 8/23/12 stage only5
78.0 8/23/12 37,947 15,800
76.0 8/24/12 36,503 16,200
1 Data are provisional pending final review and approval
2 Approximate river mile to be superseded by new river mile system
3 Provisional measured flow at cross-section location
4 Provisional online flow data for USGS gaging station no. 15292000 (Susitna River at Gold Creek)
5 Only stage was measured at these cross-sections.
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Table 8.5-8. Summary of gaging stations established on Susitna River in 2012.
Gaging Station Approximate River Mile Segment
Susitna River near Cantwell (ESS80) 223.2 Upper Susitna River
Susitna River below Deadman Creek (ESS70) 184.0 Middle Susitna River (above Devils
Canyon) Susitna River below Fog Creek (ESS65) 173.9
Susitna River above Devil Creek (ESS60) 164.3
Susitna River above Portage Creek (ESS55) 148.6
Middle Susitna River (below Devils
Canyon)
Susitna River at Curry (ESS50) 120.7
Susitna River below Lane Creek (ESS45) 113.0
Susitna River above Whiskers Creek (ESS40) 103.3
Susitna River at Chulitna River (ESS35) 98.1
Susitna River below Twister Creek (ESS30) 95.9
Lower Susitna River Susitna River at Susitna Station (ESS20) 25.7
Susitna River near Dinglishna Hill (ESS15) 19.9
Susitna River below Flat Horn Lake (ESS10) 13.7
Notes:
1. ESS = AEA Susitna River Surface-Water Station.
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Table 8.5-9. Susitna Real-Time Reporting Network Stations.
Site Name Short Name Parameters
Upper Segment AEA Gaging Stations
15291500 Susitna River Near Cantwell ESS80 discharge, water level, water and air temperature, camera
Middle Segment AEA Gaging Stations
Susitna River Below Deadman Creek ESS70 discharge, water level, water and air temperature, camera
Susitna River Below Fog Creek ESS65 discharge, water level, water and air temperature, camera
Susitna River Above Devil Creek ESS60 discharge, water level, water and air temperature, camera
Susitna River Below Portage Creek ESS55 discharge, water level, water and air temperature, camera
Susitna River at Curry ESS50 discharge, water level, water and air temperature, camera
Susitna River Below Lane Creek ESS45 discharge, water level, water and air temperature, camera
Susitna River Above Whiskers Creek ESS40 discharge, water level, water and air temperature, camera
Susitna River at Chulitna River ESS35 discharge, water level, water and air temperature, camera
Susitna River Below Twister Creek ESS30 discharge, water level, water and air temperature, camera
Lower Segment AEA Gaging Stations
15294350 Susitna River at Susitna Station ESS20 discharge, water level, water and air temperature, camera
Susitna River Near Dinglishna Hill ESS15 water level, water and air temperature, camera
Susitna River Below Flat Horn Lake ESS10 water level, water and air temperature, camera
Repeater Stations
Mount Susitna Near Granite Creek ESR1 air temperature
Repeater, East of ESM1, First Potential
Site ESR2 air temperature
Repeater, Dam Site to Glacial Repeater ESR3 air temperature
Curry Ridge near McKenzie Creek
Repeater ESR4 air temperature
Curry Pt. To State Park Repeater ESR5 air temperature, camera
State Park over Devils Canyon Repeater ESR6 air temperature, camera
Portage Creek Repeater ESR7 air temperature
ESR2 to ESS80, ESM2 link ESR8 air temperature
Base Stations
Talkeetna Base Station ESB2 N/A
Notes:
1. ESS = AEA Susitna River Surface-Water Station.
2. ESR = AEA Susitna River Repeater Station
3. ESB = AEA Susitna River Base Station
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Table 8.5-10. Period of record of flows measured by the USGS on the Susitna River.
Gage Number Site Approximate River Mile
Drainage Area (mi2) Latitude Longitude
Elevation (ft, NGVD 29) Period of Record of Measured Flows
15291000 Susitna River near
Denali 290.6 950 63.10389 147.51583 2,440 27 years: 1957-1976;
1978-1986
15291500 Susitna River near
Cantwell 223.2 4,140 62.69861 147.54500 1,900 17 years: 1961-1972;
1980-1986
15292000 Susitna River at
Gold Creek 136.6 6,160 62.76778 149.69111 677 57 years: 1949-1996;
2001-2011
15292780 Susitna River at
Sunshine 83.9 11,100 62.17833 150.17500 270 5 years: 1981-1986
15294350 Susitna River at
Susitna Station 25.8 19,400 61.54472 150.51250 40 19 years: 1974-1993
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Table 8.5-11. Period of record of flows measured by the USGS on tributaries of the Susitna River.
Gage Number Site
Approximate River Mile in Susitna
River at Confluence
Drainage
Area (mi2) Latitude Longitude
Elevation
(ft, NGVD 29) Period of Record of Measured Flows
15291200 Maclaren River near
Paxson 259.7 280 63.11944 146.52917 2,866 28 years: 1958-1986
15292400 Chulitna River near
Talkeetna 98.0 2,570 62.55861 150.23389 520 20 years: 1958-1972;
1980-1986
15292700 Talkeetna River
near Talkeetna 97.0 1,996 62.34694 150.01694 400 47 years: 1964-2011
15294005 Willow Creek Near
Willow 48.4 166 61.78083 149.88444 350 25 years: 1978-1993;
2001-2011
15294345 Yentna River near
Susitna Station 27.6 6,180 61.69861 150.65056 80 6 years: 1980-1986
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Table 8.5-12. List of 33 Index of Hydrologic Alteration (IHA) parameters (The Nature Conservancy 2009).
IHA Parameter
Group Hydrologic Parameters Ecosystem Influences
1. Magnitude of
monthly water
conditions
Mean or median value for each
calendar month
_________________________
Subtotal 12 parameters
• Habitat availability for aquatic organisms
• Soil moisture availability for plants
• Availability of water for terrestrial animals
• Availability of food/cover for forbearing mammals
• Reliability of water supplies for terrestrial animals
• Access by predators to nesting sites
• Influences water temperature, oxygen levels, photosynthesis in water
column
2. Magnitude
and duration
of annual
extreme water
conditions
Annual minima, 1-day mean
Annual minima, 3-day means
Annual minima, 7-day means
Annual minima, 30-day means
Annual minima, 90-day Means
Annual maxima, 1-day mean
Annual maxima, 3-day means
Annual maxima, 7-day means
Annual maxima, 30-day means
Annual maxima, 90-day means
Number of zero-flow days
Base flow: 7-day minimum flow/mean
flow for year
_________________________
Subtotal 12 parameters
• Balance of competitive, ruderal, and stress-tolerant organisms
• Creation of sites for plant colonization
• Structuring of aquatic ecosystems by abiotic vs. biotic factors
• Structuring of river channel morphology and physical habitat conditions
• Soil moisture stress in plants
• Dehydration in animals
• Anaerobic stress in plants
• Volume of nutrient exchanges between rivers and floodplains
• Duration of stressful conditions such as low oxygen and concentrated
chemicals in aquatic environments
• Distribution of plant communities in lakes, ponds, floodplains
• Duration of high flows for waste disposal, aeration of spawning beds in
channel sediments
3. Timing of
annual
extreme water
conditions
Julian date of each annual 1-day
maximum
Julian date of each annual 1-day
minimum
_________________________
Subtotal 2 parameters
• Compatibility with life cycles of organisms
• Predictability/avoidability of stress for organisms
• Access to special habitats during reproduction or to avoid predation
• Spawning cues for migratory fish
• Evolution of life history strategies, behavioral mechanisms
4. Frequency
and duration
of high and
low pulses
Number of low pulses within each
Water Year
Mean or median duration of low
pulses (days)
Number of high pulses within each
Water Year
Mean or median duration of high
pulses (days)
_________________________
Subtotal 4 parameters
• Frequency and magnitude of soil moisture stress for plants
• Frequency and duration of anaerobic stress for plants
• Availability of floodplain habitats for aquatic organisms
• Nutrient and organic matter exchanges between river and floodplain
• Soil mineral availability
• Access for waterbirds to feeding, resting, reproduction sites
• Influences bedload transport, channel sediment textures, and duration of
substrate disturbance (high pulses)
5. Rate and
frequency of
water
condition
changes
Rise rates: Mean or median of all
positive differences between
consecutive daily values
Fall rates: Mean or median of all
negative differences between
consecutive daily values
Number of hydrologic reversals
_________________________
Subtotal 3 parameters
_________________________
Grand total 33parameters
• Drought stress on plants (falling levels)
• Entrapment of organisms on islands, floodplains (rising levels)
• Desiccation stress on low-mobility streamedge (varial zone) organisms
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Table 8.5-13. List of 34 Environmental Flow Component (EFC) parameters (The Nature Conservancy 2009).
EFC Type Hydrologic Parameters Ecosystem Influences
1. Monthly
low flows
Mean or median values of low flows during each
calendar month
__________________________
Subtotal 12 parameters
• Provide adequate habitat for aquatic organisms
• Maintain suitable water temperatures, dissolved oxygen, and water
chemistry
• Maintain water table levels in floodplain, soil moisture for plants
• Provide drinking water for terrestrial animals
• Keep fish and amphibian eggs suspended
• Enable fish to move to feeding and spawning areas
• Support hyporheic organisms (living in saturated sediments)
2. Extreme
low flows
Frequency of extreme low flows during each
Water Year or season
Mean or median values of extreme low flow
event:
• Duration (days)
• Peak flow (minimum flow during event)
• Timing (Julian date of peak flow)
__________________________
Subtotal 4 parameters
• Enable recruitment of certain floodplain plant species
• Purge invasive, introduced species from aquatic and riparian
communities
• Concentrate prey into limited areas to benefit predators
3. High flow
pulses
Frequency of high flow pulses during each Water
Year or season
Mean or median values of high flow pulse event:
• Duration (days)
• Peak flow (maximum flow during event)
• Timing (Julian date of peak flow)
• Rise and fall rates
__________________________
Subtotal 6 parameters
• Shape physical character of river channel, including pools, riffles
• Determine size of streambed substrates (sand, gravel, cobble)
• Prevent riparian vegetation from encroaching into channel
• Restore normal water quality conditions after prolonged low flows,
flushing away waste products and pollutants
• Aerate eggs in spawning gravels, prevent siltation
4. Small
floods
Frequency of small floods during each Water
Year or season
Mean or median values of small flood event:
• Duration (days)
• Peak flow (maximum flow during event)
• Timing (Julian date of peak flow)
• Rise and fall rates
__________________________
Subtotal 6 parameters
Applies to small and large floods:
• Provide migration and spawning cues for fish
• Trigger new phase in life cycle (i.e., insects)
• Enable fish to spawn in floodplain, provide nursery area for juvenile
fish
• Provide new feeding opportunities for fish, waterfowl
• Recharge floodplain water table
• Maintain diversity in floodplain forest types through prolonged
inundation (i.e., different plant species have different tolerances)
• Control distribution and abundance of plants on floodplain
• Deposit nutrients on floodplain
5. Large
floods
Frequency of large floods during each Water
Year or season
Mean or median values of large flood event:
• Duration (days)
• Peak flow (maximum flow during event)
• Timing (Julian date of peak flow)
• Rise and fall rates
__________________________
Subtotal 6 parameters
__________________________
Grand total 34 parameters
Applies to small and large floods:
• Maintain balance of species in aquatic and riparian communities
• Create sites for recruitment of colonizing plants
• Shape physical habitats of floodplain
• Deposit gravel and cobbles in spawning areas
• Flush organic materials (food) and woody debris (habitat structures)
into channel
• Purge invasive, introduced species from aquatic and riparian
communities
• Disburse seeds and fruits of riparian plants
• Drive lateral movement of river channel, forming new habitats
(secondary channels, oxbow lakes)
• Provide plant seedlings with prolonged access to soil moisture
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Table 8.5-14. Schedule for implementation of the Fish and Aquatics Instream Flow Study.
Activity 2012 2013 2014 2015
Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2
8.5.2 Existing Information and Need for Additional Information Δ ▲
8.5.4.2 River Stratification and Study Area Selection
Compile aquatic habitat (RSP Sec 9.09) and geomorphology (see
Section 6.8.4) characterization study results --- --------- ---
Identify proposed Focus Areas
Refine Focus Areas and identify supplementary areas if needed for any
underrepresented habitats --- -------- ----
TWG confirmation of study areas --- ---
Review available data and modify or add Focus Areas and
supplementary sampling areas Δ
TWG review of proposed area weighting factors to extrapolate modeled
to non-modeled areas -- ------- --
TWG meeting on area weighting -------- ▲
8.5.4.3 Hydraulic Flow Routing
Review 2012 transect data RM 184 to 75
Develop draft mainstem (open-water) flow routing model
Model verification using stage recorder data ------- ---
Identify need for additional data
Distribute draft mainstem (open-water) routing model to TWG for review
Collect additional channel and hydraulic data as needed
Refine draft mainstem (open-water) flow routing model Δ
Use draft model to support IFS, water quality, geomorphology, and
fisheries 2013-2014 study efforts
Refine mainstem (open-water) routing model using 2013 and 2014 data
Distribute final mainstem (open-water) routing model to TWG for review ▲
Use final mainstem (open-water) routing model for scenario evaluations
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Activity 2012 2013 2014 2015
Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2
8.5.4.4 Hydrologic Data Analysis
Obtain existing daily flow records from USGS
Obtain basin area calculations from GINA-UAF
Calculate estimated trib accretion flows
TWG review of hydrologic record of daily flow
TWG review of representative years for modeling Δ
Collect 15-min stage records from mainstem, tribs and Focus Areas
Develop hourly flow record for Focus Areas / other mainstem locations
Develop hourly inflow for select tributaries
Develop list of potential and recommended IHA-type parameters
TWG review of selected IHA-type parameters
Examine 2014 stage data and refine hydrologic record to support
scenario evaluations
TWG meeting to review complete hydrologic record ▲
Use hydrologic record for scenario evaluations
8.5.4.5 Habitat Suitability Criteria Development
Use 1980s Susitna data and other existing HSC curves to develop draft
species / life stage HSC curves for the Lower and Middle Susitna River
Propose target HSC species, life stages, substrate and cover
TWG meeting on HSC/HSI and data collection study details ---- -
Conduct HSC/HSI summer surveys (snorkel, seining, electrofishing)
Conduct fish HSC/HSI winter surveys (underwater camera,
electrofishing) ----- -----
Conduct aquatic biota stranding and trapping surveys ----- -------
Coordinate and review adult/spawning HSC data collected by Fish and
Aquatic biotelemetry (see Section 9.06) ------- -- ------- --
Distribute preliminary findings of winter surveys to TWG
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Activity 2012 2013 2014 2015
Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2
Distribute preliminary results of HSC/HSI surveys and changes to draft
HSC/HSI ---- --Δ
TWG meeting on species and life stage HSC/HSI --- --- --- --- ▲
Periodicity
Review draft species and life stage periodicity data developed under
Fish Distribution and Abundance (see Section 9.06) ------ -------
Identify specific HSC/HSI periodicity data needs --------- ------- ---
Distribute HSC/HSI periodicity to TWG ---- Δ -------
TWG meeting on HSC/HSI periodicity used to model scenarios ▲
Review and discuss implementation details of flow-dependent
biological cue study
Distribute initial study results to TWG
Report on flow-dependent biological cues Δ
8.5.4.6 Habitat-Specific Model Development
Habitat Model Selection
Propose habitat models for Focus Areas and supplemental area --- -
TWG review and meeting on habitat model selection Δ-- ------
Physical and Hydraulic Data Collection
Collect data for digital terrain model -----
Collect x-section and stage:discharge data at Focus Areas and
supplemental areas --- ------- ---
Collect substrate/cover data at Focus Areas and supplemental areas ----- --
Provide summaries of data collection efforts Δ ▲
Hydraulic Model Calibration ▲
Aquatic Habitat Modeling Δ --------- ------- -- ▲
8.5.4.7 Temporal and Spatial Habitat Analyses ▲
Develop proposed methods for completing temporal and spatial
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Activity 2012 2013 2014 2015
Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2 Q 3 Q 4 Q 1 Q 2
analyses
Review and discuss temporal and spatial analytical methods with TWG
Distribute temporal and spatial analyses to TWG Δ
Apply temporal and spatial analytical methods ▲
Develop proposed methods for overall sensitivity analyses of habitat
indicators
Review methods for sensitivity and analyses with TWG Δ
Conduct overall sensitivity analyses of modeling outputs ▲
8.5.4.8 Instream Flow Study Integration ▲
Reporting Δ ▲
Integrated Resource Analyses
Legend:
Planned Activity
------ Follow up activity (as needed)
Δ Initial Study Report
▲ Updated Study Report
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Table 8.5-15. Common names, scientific names, life history strategies, and habitat use of fish species within the Lower,
Middle, and Upper Susitna River, based on sampling during the 1980s (from HDR 2011).
Common Name Scientific Name Life History Susitna Usage
Arctic grayling Thymallus arcticus F O, R, P
Dolly Varden Salvelinus malma A,F O, P
Humpback whitefish Coregonus pidschian A,F O, R, P
Round whitefish Prosopium cylindraceum F O, M2, P
Burbot Lota lota F O, R, P
Longnose sucker Catostomus catostomus F R, P
Sculpin Cottid spp. M1, F P
Eulachon Thaleichthys pacificus A M2, S
Bering cisco Coregonus laurettae A M2, S
Threespine stickleback Gasterosteus aculeatus A,F M2, S, R, P
Arctic lamprey Lethenteron japonicum A,F O, M2, R, P
Chinook salmon Oncorhynchus tshawytscha A M2, R
Coho salmon Oncorhynchus kisutch A M2, S, R
Chum salmon Oncorhynchus keta A M2, S
Pink salmon Oncorhynchus gorbuscha A M2
Sockeye salmon Oncorhynchus nerka A M2, S
Rainbow trout Oncorhynchus mykiss F O, M2, P
Northern pike Esox lucius F P
Lake trout Salvelinus namaycush F U
Pacific lamprey Lampetra tridentata A,F U
Alaska blackfish Dallia pectoralis F U
Notes:
A = anadromous
M1 = marine
F = freshwater
O=overwintering
R=rearing
P=present
M2 = migration
S=spawning
U=unknown
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Table 8.5-16. Site-specific habitat suitability measurements recorded during 2012 at Middle and Lower Susitna River
sampling sites, by fish life stage.
Susitna River
Segment
River
Mile Site Name Habitat Type
Fish Life
Stage
Number of
Observations
Middle 178.3 178.3R Side Channel Fry 6
Juvenile 4
Adult 5
Middle 176.6 Fog Creek mouth Tributary Mouth Fry 4
Adult 1
Middle 174.2 174.2L Mainstem N/A 0
Middle 144.4 Slough 22 Side Slough Fry 5
Adult 1
Middle 141.8 Slough 21 Side Slough N/A 0
Middle 141.2 Side Channel 21 Side Channel Fry 9
Adult 7
Middle 138.6 Indian River Mouth Tributary Mouth Fry 11
Adult 8
Middle 135.6 Slough 11 Side Slough Adult 8
Middle 133.9 Slough 10 Upland Slough N/A 0
Middle 133.7 Slough 9A Side Slough Adult 19
Middle 131.2 Unnamed Side Channel Side Channel Adult 11
Middle 131.1 4th of July Creek Mouth Tributary Mouth Fry 3
Adult 8
Middle 128.8 Slough 9 Side Slough Adult 15
Middle 125.3 Skull Creek Side Slough Adult 26
Middle 122.5 Slough 8B Side Slough N/A 0
Middle 121.0 Tulips Creek mouth Tributary Mouth N/A 0
Middle 115.0 115.0R Side Channel Fry 2
Middle 113.7 Slough 8 Side Slough Fry 4
Juvenile 1
Middle 113.6 Lane Cr Mouth Tributary Mouth Fry 2
Adult 1
Middle 112.5 Slough 6A Upland Slough Fry 15
Middle 101.4 Whiskers Slough Side Slough Fry 13
Adult 3
Middle 101.4 Whiskers Creek Mouth Tributary Mouth Fry 12
Lower 95.4 Cache Creek slough Side Slough Fry 6
Juvenile 1
Lower 95.4 Unnamed Side Channel Side Channel Fry 4
Juvenile 1
Lower 93.5 Unnamed Side Channel Side Channel Fry 4
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Susitna River
Segment
River
Mile Site Name Habitat Type
Fish Life
Stage
Number of
Observations
Juvenile 1
Lower 91.6 Trapper Creek Side Channel Side Channel Fry 12
Juvenile 4
Lower 91.5 Trapper Creek Tributary Mouth Fry 4
Lower 91.5 Birch Slough Side Slough Fry 2
89.2 Birch Slough Side Slough Fry 1
Lower 85.2 Sunshine Creek Side Channel Side Channel Fry 13
Juvenile 3
Lower 85.1 Sunshine Creek Tributary Mouth Fry 18
Lower 83.1 Rabideux Creek Tributary Mouth N/A 0
Lower 77.0 Montana Creek Tributary Mouth Adult 7
Side Channel Adult 10
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Table 8.5-17. Proposed substrate classification system for use in development of HSC/HSI curves for the Susitna-Watana
Project (adapted from Wentworth 1922).
Substrate Code Substrate Type Size (Decimal Inches) Size (mm)
1 Silt, Clay, or Organic <0.01 <0.1
2 Sand 0.01-0.10 0.1-2.0
3 Small Gravel 0.10-0.30 2.0-8.0
4 Medium Gravel 0.30-1.25 8.0-32
5 Large Gravel 1.25-2.50 32-64
6 Small Cobble 2.50-5.0 64-128
7 Large Cobble 5.0-10.0 128-256
8 Boulder >10.0 >256
9 Bedrock
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Table 8.5-18. Example of table that will be developed as part of the stranding and trapping analyses to illustrate the frequency of potential stranding and trapping events
by month for a given Project operational scenario.
Existing Condition Operating Scenario 1 Operating Scenario 2
Evaluation Indicator JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP OCT NOV DEC >1"/hour
>2"/hour
>4"/hour
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Table 8.5-19. Assessment of physical and biological processes and potential habitat modeling techniques.
Physical and Biological Processes
Habitat Types
Mainstem Side Channel Slough Tributary Mouths
Spawning PHAB/VZM PHAB PHAB/HabMap PHAB/RFR
Incubation RFR/VZM PHAB PHAB/HabMap PHAB/RFR
Juvenile Rearing PHAB/RFR PHAB PHAB/HabMap PHAB/RFR
Adult Holding RFR RFR PHAB/HabMap PHAB/RFR
Macroinvertebrates VZM/WP VZM/WP PHAB/HabMap/WP N/A
Standing/Trapping VZM VZM VZM/WP VZM/WP
Upwelling/Downwelling FLIR HabMap/FLIR HabMap/FLIR HabMap/FLIR
Temperature WQ WQ WQ WQ
Ice Formation IceProcesses/WQ/RFR IceProcesses/WQ/RFR HabMap/Open leads N/A
Notes:
1. PHAB-Physical Habitat Simulation Modeling (1-D, 2-D, and empirical); VZM-Effective Spawning and Incubation/Varial Zone
Modeling; RFR-River Flow Routing Modeling; FLIR – Forward-looking Infrared Imaging; HabMap-Surface Area Mapping; WQ-
Water Quality Modeling; WP-Wetted Perimeter Modeling.
Table 8.5-20. Seasonal daylight and night downramping guidelines (Hunter 1992).
Season Daylight Rates* Night Rates
February 16 to June 15 (salmon fry) No Ramping 2 inches/hour
June 16 to October 31 (steelhead and trout fry) 1 inch/hour 1 inch/hour
November 1 to February 15 2 inches/hour 2 inches/hour
Notes:
1. * Daylight is defined as 1 hour before sunrise to 1 hour after sunset.
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Table 8.5-21. Conceptual Comparison of Multiple Resource Indicators of the Effects of Alternative Operational Scenarios
for the Susitna-Watana Hydroelectric Project. Indicators to be coordinated with resource-specific working groups.
(Indicators provided for illustration purposes only)
Existing
Conditions (EC-01)
Scenario 1
(Ver. 1/20/15) (OS-01)
Scenario 2
(Ver. 02/14/15) (OS-02)
Scenario 3
(Ver. 02/14/15) (OS-03) Run Description Average monthly MIF(cfs)
Max generation Nov-Mar (cfs)
Min generation Nov-Mar (cfs)
Max generation Apr-Oct (cfs)
Min generation Apr-Oct (cfs)
Ramping Rates
Evaluation Indicators Power Weighted average generation Nov-Mar (MWh)
Weighted average generation Apr-Oct (MWh)
Weighted annual dependable capacity (MWh) Hydrologic Max 1-day flow (cfs) wet / avg /dry wet / avg / dry wet / avg / dry wet / avg / dry wet / avg / dry
Min 2-day low, Nov-Mar (cfs)
Min 2-day low Jul-May as % of 2-day max Jul-Sep
Freshets (Apr-Jun) [Qc]>1.5*[QC-1+QC-2+QC-3]/3
Water Particle Travel Time, 25% exceedance, Apr-
Jun
Other IHA statistics Reservoir Average reservoir volume (KAF) wet / avg /dry
wet / avg / dry wet / avg / dry wet / avg / dry
Min 2-day reservoir volume (KAF)
Weighted annual euphotic zone (KAF)
Other Biological/recreation indicators Ramping Weighted avg annual total, Middle Susitna, reach-
averaged (ra) downramping events >1-inch pr
hour
Weighted average annual total, Middle Susitna,
reach-averaged downramping events > 2-inch per
hour
Weighted average annual total, Middle Susitna,
reach-averaged downramping events > 4-inches per
hour
Varial Zone Median annual, MS, reach-averaged (ra) channel
width-ft
Total varial zone, MS, 12-hr/12-hr, ra, median
annual channel width-ft
Total varial zone, MS, 12-hr/7-day, ra, median
annual channel width-ft
Total varial zone, MS, 12-hr/30-day, ra, median
annual channel width-ft
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Evaluation Indicators
(Indicators provided for illustration purposes only)
Existing Conditions (EC-01)
Scenario 1 (Ver. 1/20/15) (OS-01)
Scenario 2 (Ver. 02/14/15) (OS-02)
Scenario 3 (Ver. 02/14/15) (OS-03) Potential Salmon Habitat Chum spawning habitat, Devils Canyon to Three
Rivers Confluence (DCto3R) reach-averaged(ra),
gross channel width, (ft)
Chum effective spawning/incubation, DCto3R-
reach-averaged (ra), channel width accounting for
dewatering, groundwater/surface water interactions,
water quality effects, net width (ft)
Coho effective spawning/incubation, DCto3R-ra, net
width, (ft)
Sockeye effective spawning and incubation,
DCto3R-ra, slough/side channel, net width (ft)
Pink effective spawning/incubation, DCto3R-ra,
slough/side channel, net width (ft)
Coho juvenile habitat, open-water, DCto3R-ra,
channel width (ft)
Coho juvenile habitat, ice-period, DCto3R-ra,
channel width (ft)
Chinook juvenile habitat, ice-period, DCto3R-ra,
slough/side channel width (ft) Other Fish Grayling average minimum spawning, Watana Dam
to Devils Canyon (DtoDC), reach averaged WUA,
(ft2)
Northern pike effective spawning and incubation,
DCto3R-reach averaged slough/side channel net
width (ft)
Riparian Wet meadow area, reach averaged, DC to3R, post-
licensing yrs 10-20 (acres)
Scrub thickets, reach averaged, DC to 3R, post-
licensing yrs 10-20 (acres)
Floodplain plant community colonization area, reach
averaged, DC to 3R, post-licensing yrs 10-20
(acres)
Other riparian indicators Recreation Devils Canyon to 3R, tour boat accessible, May to
Sep (days)
Three Rivers to Sunshine, days channel exceeds
minimum boating depth, May to Sep
Devils Canyon to 3 R, upstream extent of January
ice cover for snow machine travel
Other recreation/access indicators Other Aquatics Other potential indicators of Project effects such as:
▫ minimum slough area,
▫ percent of river length mobilized-D25
▫ downstream extent of ice-free zone,
▫ 30-day wetted euphotic streambed,
▫ other reaches, seasons, life stages, mesohabitats
to be determined in consultation with TWG
Notes:
1. Average of five select years weighted by likelihood of occurrence (Dry Year* 0.077, Somewhat Dry Year* 0.231, Average Year *
0.462, Somewhat Wet Year * 0.115, Wet Year*0.115) (values are for illustration purposes only)
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8.5.10. Figures
Figure 8.5-1. Study interdependencies for Fish and Aquatics Instream Flow Study.
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Figure 8.5-2. Relative amounts of habitat types in different areas of the Susitna River at seven mainstem discharges. Source: Klinger-Kingsley et al. (1985).
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Figure 8.5-3. Habitat types identified in the middle reach of the Susitna River during the 1980s studies (adapted from
ADF&G 1983; Trihey 1982).
Figure 8.5-4. Example HSC curves for rearing juvenile Chinook salmon in the Middle Susitna River developed during the
1980s instream flow studies. Source: Suchanek et al. 1984b.
SideSlough
Upland
Slough
Tributary TributaryMouth
Lake
HyporheicZone
Side Channel
MainstemChannel
0.0
0.2
0.4
0.6
0.8
1.0
0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 4.0Suitability
Velocity (ft/s)
Chinook Juvenile
Susitna River (Turbid)
Susitna River (Clear)
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Figure 8.5-5. Mean daily intergravel and surface water temperature data from a spawning site in Skull Creek. Source:
Trihey (1982).
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Figure 8.5-6. Locations of instream flow transects and model types applied during the 1980s Su-Hydro studies in lower and upper Side Channel 11 and in Slough 11,
located near Gold Creek. Breaching flows based on those studies are also depicted for various side channel and side slough habitats.
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Figure 8.5-7. Locations of instream flow transects and model types applied during the 1980s Su-Hydro studies in the Whiskers Slough complex. Breaching flows based
on those studies are also depicted for various side channel and side slough habitats.
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Figure 8.5-8. Transects and shoreline and mid-channel sampling cells associated with RJHAB modeling (Marshall et al.
1984).
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Figure 8.5-9. Map depicting the Upper, Middle and Lower Segments of the Susitna River potentially influenced by the Susitna-Watana Hydroelectric Project.
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Dam/Reservoir Operations
Model (8.5.4.3.2)
Unregulated and Alternative
Operational Scenarios
Mainstem Flow Routing
HEC-RESSim, HEC-RAS
(7.6, 8.5.4.3)
Accretion
Attenuation
Celerity
Hourly Q, WSE by River Mile
Hydrology (8.5.4.4)
Representative Water Years
Seasonal Storage & Release
Hourly Dam Releases
Flood Flows
Reach (6.5) /
Habitat Type (9.9) / Focus
Area Selection (F, G, WQ,
WR, B, W)
Riverine Processes
Geomorphology (6.0)
•Sediment Transport
•Future Channel Changes
Ice Processes (7.6)
Large Woody Debris (LWD) (6.6)
Groundwater (7.5)
Water Quality / Temperature (5.0,
7.5, 8.5)
Biological Information
Periodicity (9.6, 8.5.4.5)
Distribution (9.6, 9.12,8.5.4.5)
Abundance (9.6)
Seasonal Habitat Utilization (9.6,
8.5.4.5)
HSC/HSI(8.5.4.5, 9.6)
Riparian (8.6, 11.0)
Main Channel /
Split Channels (8.5)
Riverine Processes
Habitat Modeling
Fish Passage (9.12)
Habitat Specific Models
(8.5.4.6) (see next page)
Habitat vs. Flow (1D / 2D)
Connectivity and Passage (9.12)
Effective Spawning/Incubation
Riparian Vegetation
Varial Zone (12-hr, 7-day, 30-day)
Stranding
Trapping
Tributary Deltas
(6.6, 8.5)
Riverine Processes
Habitat Modeling
Fish Passage (9.12)
Riparian (8.6)
Riverine Processes
Vegetation Modeling
Off-channel Sloughs (8.5)
Riverine Processes
Backwater/Overtopping
Habitat Specific Modeling
Fish Passage (9.12)
Hourly / Daily / Monthly
Habitat by Unregulated and
Alternative Operational
Scenarios
Integrated Resource Analysis (8.5.4.8)
Fish Habitat (F)
Water Quality (WQ)
Geomorphology (G)
Riparian (B)
Wildlife (W)
Cultural (C)
Recreation (R)
Aesthetics (A)
Project Economics
Subsistence (S)
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Figure 8.5-10. Conceptual framework for the Susitna-Watana Instream Flow Study depicting integration of habitat
specific models and riverine processes to support integrated resource analyses; and integration of riverine processes to
develop fish and aquatic habitat specific models.
Existing
Channel Conditions
Unregulated Flows
(Representative Water Years)
Habitat Specific Models (8.5.4.6)
Fish and Aquatic Indicators
Habitat (WUA) vs. Flow (2-D/1-D)
Breaching flows (connectivity)
Fish Passage (9.12)
Effective Spawning/Incubation
Winter rearing
Varial Zone Analyses (12-hr, 7-day, 30-day)
Stranding
Trapping
Geomorphology Modeling (Reach Scale) (6.0)
•Aggradation ▪Degradation
•Channel Change ▪Turbidity
•Habitat Unit Distribution and Abundance
Time Step 1
Channel Conditions
Time Step 2
Channel Conditions
Alternative Operational Scenarios (8.5.4.3.2)
(Representative Water Years) (8.5.4.4.1.1.2
Water Quality (5.0)
Reach Scale
•Surface Water Temp
•Dissolved Oxygen
•Metals
•Nutrients
Focus Area
•Surface Water Temp
•Intergravel Water Quality
Ice Processes (7.6)
Reach Scale
•Ice Cover
•Ice Dam Formation
•Winter Flow Routing
Focus Area
•Habitat Unit Water Level
•Breaching Flows
•Ice Dam Formation
Groundwater/Surface
Water Interactions (7.5)
Reach Scale
•Geohydrologic Processes
•Regional Aquifers
Focus Area
•Upwelling
•Downwelling
•Intergravel Water Quality
Geomorphology (6.0)
Reach Scale
•Aggradation
•Degradation
•Channel Change
•Turbidity
•Habitat Unit Change
Focus Area
•Scour and Fill
•Large Woody Debris
•Habitat Unit Change
Inputs
Flows at Dam Site (RSP 7.7)
Accretion (RSP 8.5)
Mainstem Physical/Hydraulics (RSP 7.5, 8.5)
Mainstem Open-water Flow Routing (RSP 8.5)
Mainstem Ice Process Flow Routing (RSP 7.6)
Reach-Scale Habitat Distribution (RSP 9.9)
Reach-Scale Fish Distribution (RSP 9.6)
Fish Distribution by Habitat Type (RSP 9.6)
Sediment (RSP 6.5)
Large Woody Debris (RSP 6.5)
Focus Area Physical/Hydraulics(RSP 8.5)
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Figure 8.5-11. Map of the Middle Segment of the Susitna River depicting the eight Geomorphic Reaches and locations of proposed Focus Areas. No Focus Areas are
proposed for in MR-3 and MR-4 due to safety issues related to sampling within or proximal to Devils Canyon.
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Figure 8.5-12. Map of the Lower Segment of the Susitna River depicting the six Geomorphic Reaches. Focus Areas have not been identified in this segment but will be
considered pending results of open-water flow routing modeling.
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Figure 8.5-13. Map showing Focus Area 184 that begins at Project River Mile 184.7 and extends upstream to PRM 185.7. The Focus Area is located about 1.4 miles
downstream of the proposed Watana Dam site near Tsusena Creek.
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Figure 8.5-14. Map showing Focus Area 173 beginning at Project River Mile 173.6 and extends upstream to PRM 175.4. This Focus Area is near Stephan Lake and
consists of main channel and a side channel complex.
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Figure 8.5-15. Map showing Focus Area 171 beginning at Project River Mile 171.6 and extends upstream to PRM 173. This Focus Area is near Stephan Lake and
consists of main channel and a single side channel with vegetated island.
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Figure 8.5-16. Map showing Focus Area 151 beginning at Project River Mile 151.8 and extends upstream to PRM 152.3. This single main channel Focus Area is at the
Portage Creek confluence.
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Figure 8.5-17. Map showing Focus Area 144 beginning at Project River Mile 144.4 and extends upstream to PRM 145.7. This Focus Area is located about 2.3 miles
upstream of Indian River and includes Side Channel 21 and Slough 21.
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Figure 8.5-18. Map showing Focus Area 141 beginning at Project River Mile 141.8 and extends upstream to PRM 143.4. This Focus Area includes the Indian River
confluence and a range of main channel and off-channel habitats.
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Figure 8.5-19. Map showing Focus Area 138 beginning at Project River Mile 138.7 and extends upstream to PRM 140. This Focus Area is near Gold Creek and consists
of a complex of side channel, side slough and upland slough habitats including Upper Side Channel 11 and Slough 11.
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Figure 8.5-20. Map showing Focus Area 128 beginning at Project River Mile 128.1 and extends upstream to PRM 129.7. This Focus Area consists of side channel, side
slough and tributary confluence habitat features including Skull Creek.
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Figure 8.5-21. Map showing Focus Area 115 beginning at Project River Mile 115.3 and extends upstream to PRM 116.5. This Focus Area is located about 0.6 miles
downstream of Lane Creek and consists of side channel and upland slough habitats including Slough 6A.
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Figure 8.5-22. Map showing Focus Area 104 beginning at Project River Mile 104.8 and extends upstream to PRM 106. This Focus Area covers the diverse range of
habitats in the Whiskers Slough complex.
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Figure 8.5-23. Examples of cross-sections established on the Susitna River in 2012 at River Miles 170 and 76.
Figure 8.5-24. Output from ADCP from one pass across the Susitna River at River Mile 170 on June 21, 2012.
Station (feet)
0 500Elevation(feet, NAVD 88)1300
1320
Station (feet)
0 1000 2000 3000 4000 5000Elevation(feet, NAVD 88)200
220
240
260
River Mile 170.0, June 21, 2012
Q = 31,000 cfs
Average V = 8.0 fps
Average D = 6.9 ft
River Mile 76.0, August 24, 2012
Q = 36,900 cfs
Average V = 4.9 fps
Average D = 6.5 ft
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Figure 8.5-25. Susitna Network Stations Diagnostics Screen. Data fields are color coded to allow quick scans for evaluating station conditions. Email and text
messaging are used to communicate warning conditions and non-reporting stations.
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Figure 8.5-26. Typical AEA gaging station current conditions reporting page.
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Figure 8.5-27. Geomorphic Reaches and winter habitat use sampling areas in the Middle Susitna River Segment.
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Figure 8.5-28. Location of proposed winter fish habitat use sampling sites at Whiskers Slough in the Middle Susitna River Segment.
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Figure 8.5-29. Location of proposed winter fish habitat use sampling sites at the Skull Creek Complex in the Middle Susitna River Segment.
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Figure 8.5-30. Cross-sectional conceptual diagram illustrating stranding and trapping areas.
Trapping Area Stranding Area:
gradient < critical value
Stranding Area:
gradient < critical value
and cover present
Streambed
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Figure 8.5-31. Conceptual layout of 2-D coarse and fine mesh modeling within the proposed Whiskers Slough Focus Area.
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Figure 8.5-32. Conceptual diagram depicting the Effective Spawning/Incubation Model.
Potential spawning
cell at time step TX
(suitable D, V, & substrate)
Upwelling
present at
TX+1
Potential spawning cell
at time step TX+1
Cell
dewatered
at TX+1
Cell scoured
at TX+1
Cell frozen
at TX+1
Cell water
quality unsuitable
at TX+1
* If subsequent time step is still within the spawning period and the cell still meets criteria for the duration of incubation period, effective habitat for
this cell would be weighted according to the duration of the remaining spawning period.
Assess cell conditions
at TX+1 based on
mainstem flow/stage
Cell does not count towards
effective habitat. Restart
cell accounting for next time
step unless spawning period
complete.*
Cell area initiating at TX contributes to total
effective spawning/incubation within habitat
unit. Process repeated for each cell area within
habitat unit at TX and each hour time step of
spawning period.
Yes
Yes
Yes
Yes
No
No
No
No
Upwelling
decreased
at TX+1
Yes
No
Yes
No
Incubation
period complete
at TX+2,3,4…
Assess cell conditions
at TX+2,3,4…based on
mainstem flow/stage
No
Yes
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Figure 8.5-33. Conceptual framework of the varial zone model.
Dry Zone
Maximum stage during previous 12 hours
Minimum stage during previous 7 days
Varial Zone
Continuously Wetted
Zone
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Figure 8.5-34. Illustration of 12-hour/12-hour, 12-hour/7-day, and 12-hour/30-day varial zones modeling scenarios
assuming single transect analyses (adapted from Hilgert et al. 2008).
Flow (cfs)4000
6000
800010000
20000
40000
30-Day Minimum
7-Day Minimum
12-Hour Minimum
12-Hour Maximum
10/1/1994 11/1/1994 Wetted Width (feet)300
400
500
600
700 12-Hour Maximum
12-Hour Minimum
7-Day Minimum
30-Day Minimum
80
85
90
95
100 12-Hour/12-Hour
Varial Zone
X Data
0 200 400 600Stage (feet)80
85
90
95
100 12-Hour/7-Day
Varial Zone
Station (feet)
0 200 400 600
80
85
90
95
100
Transect 5
12-Hour/30-Day
Varial Zone
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Figure 8.5-35. Example time series analysis.
Oct Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sep Oct Total Habitat Area (acres)0
10
20
30
40
50
60
70
80
Average Year
Baseline Unregulated
0
2000
4000
6000
8000
J F M A M J J A S O N D
MonthFlow (cfs)Monthly Flow Time Series
0
20000
40000
60000
0 2000 4000 6000 8000
Flow (cfs)WUA (ft2/1000ft)Flow/Habitat Relationship
Steelhead Spawning
Habitat Time Series
Baseline -------Scenario 1
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Figure 8.5-36. Conceptual figures illustrating procedure used for deriving non-modeled specific area (sa) Habitat
Availability Index curve using a modeled curve, as applied during the 1980s Su-Hydro Studies (see Steward et al. 1985;
Aaserude et al. 1985). The procedure included lateral shifts (upper figure) due to adjustments from differences in
breaching flows (Qms Qsa) as well as vertical shifts (middle figure) proportional to structural habitat indices
(SHIsa/SHIms) to account for differences in structural habitat quality. The lower figure shows final hypothetical
modeled and non-modeled specific area curves.
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