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Susitna-Watana Hydroelectric Project Document
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Title:
Characterization and mapping of aquatic habitats, Study plan Section 9.9 :
Final study plan SuWa 200
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Alaska Energy Authority
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Final study plan
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Susitna-Watana Hydroelectric Project document number 200
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[Anchorage : Alaska Energy Authority, 2013]
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July 2013
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Study plan Section 9.9
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43 p.
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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)
Characterization and Mapping of Aquatic Habitats
Study Plan Section 9.9
Final Study Plan
Alaska Energy Authority
August 2013
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9.9. Characterization and Mapping of Aquatic Habitats
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 Characterization and
Mapping of Aquatic Habitats, Section 9.9. RSP Section 9.9 focuses on describing the aquatic
habitats of the Susitna River using a specific hierarchical and nested classification system based
on historic and current data.
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. 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 9.9 was one of the 13 approved with modifications. In its
April 1 SPD, FERC recommended the following:
Edge Habitat
- We recommend that AEA remove the level 5 calculation of edge habitat from the habitat
classification system.
Backwater and Beaver Dam Habitats
- We recommend changing the classification of backwater, beaver complex, and clearwater
plume habitats from level 3 (mainstem habitat) to level 4 (mainstem and tributary
mesohabitats).
Classification of Upper River Tributaries
- We recommend that AEA consult with the TWG and file no later than June 30, 2012, the
following information to quantify small and low-order tributaries in the Upper River study
area:
1) A detailed description of the specific methods to be used for selecting a representative
sample of small and low-order Upper River tributaries for aquatic habitat mapping.
2) Documentation of consultation with the TWG, including how its comments were
addressed.
Habitat Mapping at Multiple Flows
- We recommend modifying the study plan to have AEA identify and give specific
consideration to backwater habitats, as defined by the agencies (i.e., the confluence of off-
channel habitats with main channel habitats), as a unique habitat feature and ensure a
representative subsample of these locations when selecting transect locations for one-
dimensional or two-dimensional aquatic habitat modeling within Middle River and Lower
River instream flow study sites.
Classification of Middle and Lower River Tributaries
- We recommend modifying the study plan to have AEA classify Middle River tributary
reaches within the zone of hydrologic influence into geomorphic reaches based on tributary
basin drainage area and stream gradient to provide a general understanding of the relative
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potential value to fish and aquatic resources, and report on these attributes in the initial and
updated study reports.
Habitat Mapping and Ground-Truthing
- We recommend that AEA provide a detailed description of methods and results of 2012 and
2013 habitat mapping in the initial study report, including a complete set of photographic
base maps delineating macrohabitats (level 3) and mesohabitats (level 4) for all mapped
locations.
In accordance with the April 1 SPD, AEA has adopted the FERC requested modifications. On
July 18, 2013, AEA filed the Characterization and Mapping of Aquatic Habitats Technical
Memorandum with FERC. Information in the Technical Memorandum supersedes relevant
details within this Final Study Plan.
9.9.1. General Description of the Proposed Study
This study plan describes a Susitna River-specific hierarchical and nested classification system
developed with input from the Fish and Aquatics Technical Workgroup (TWG). The
classification system as proposed includes modifications based on “lessons learned” during
implementation of initial ground surveys in 2012, evolving needs of other dependent studies,
completion of the aerial video in 2012, and inclusion of licensing participants’ comments and
FERC recommendations on the Proposed Study Plan.
The Susitna River habitat classification system has four main mapping components that
correspond to river segments and water bodies within those sections. The four components are:
1) the mainstem Susitna River from the Oshetna River confluence (approximately RM 233)
downstream to the Chulitna River confluence (approximately RM 98); 2) Upper River and
Middle River tributaries up to the upper limit of the zone of hydrologic influence (ZHI); 3) lakes
that are within the proposed reservoir inundation zone and 4) the lower River from RM 98 to the
upper end of tidal influence (approximately RM 28). The first three mapping components will
delineate and map habitats to a mesohabitat level, Level 4 (Table 9.9-5). However, because of
the very large size and channel complexity of the Lower River (Figure 9.9 -18) it is impractical to
map the Lower River Segment beyond Level 3 (Mainstem Habitat Type). Furthermore, results
from the 2012 video imagery indicate that the Lower River appears to contain only two out of
five mesohabitat types (glides and riffles). The low gradient and aggraded gravel bed of the
Lower River is generally not conducive to the formation of other mesohabitat types, such as
pools or runs, although they likely are present in very low numbers. Thus the need to delineate
habitat to this finer scale is not necessary in the Lower River.
The Susitna River habitat classification system combines the historic approach (ADF&G 1983a)
to mainstem habitat classification and a modified version of the mesohabitat classification
system from the USFS Aquatic Habitat Surveys Protocol (USFS 2001). This hybrid
classification system will describe habitats that are defined by the unique hydrolog y of this river
system, yet are significant to the day-to-day function and behavior of fish and aquatic organisms.
This study will be valuable for gathering baseline habitat data that can be used along with other
data being gathered (e.g., fish distribution and abundance, water surface elevation and discharge
relationships, instream flow modeling, flow routing) to assess potential impacts associated with
proposed Project operations.
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9.9.2. Study Goals and Objectives
Construction and operation of the Project will modify the aquatic habitat in the area inundated by
the Project reservoir and has the potential to alter aquatic habitats in the mainstem channel of the
Susitna River downstream from the Project dam, including along channel margins, at tributary
confluences, at the inlets and outlets to side channel sloughs, and off-channel water bodies in the
zone of hydrologic influence. The goal of this study is to characterize and map all aquatic
habitats with the potential to be altered and/or lost as the result of reservoir filling, hydropower
operations, and associated changes in flow, water surface elevation, sediment regime, and
temperature. Study objectives for collecting baseline data vary depending on the nature of the
potential Project effects and where in the study area the effects may occur. Study methods will,
therefore, also vary within the study area. Objectives are described below according to the
following breakdown.
Upper River Tributaries and Lakes:
a. Characterize and map Upper River tributary and lake habitat for the purpose of
evaluating the potential loss or gain in available fluvial habitat that may result from
dam emplacement and inundation by the reservoir.
b. Characterize and map Upper River tributary and lake habitat for the purposes of
informing other studies including Fish Distribution and Abundance in the Upper
River (Section 9.5) and River Productivity (Section 9.8).
Susitna Mainstem: Objectives for the mainstem Susitna River vary depending on the river
segment.
a. Characterize and map the Upper River mainstem upstream from the Watana dam site
to the confluence with the Oshetna River:
i. To provide baseline data for the purpose of evaluating the potential loss
or gain in accessible available fluvial habitat that may result from dam
emplacement and inundation by the reservoir.
ii. To inform other studies including Fish Distribution and Abundance in
the Upper River (Section 9.5), River Productivity (Section 9.8), and
Future Watana Reservoir Fish Community and Risk of Entrainment
(Section 9.10).
b. Characterize and map the Middle River mainstem from the Chulitna River confluence
to the proposed Watana Dam site, including tributaries within the zone of hydrologic
influence (ZHI1):
i. To provide baseline data for the purpose of evaluating the potential loss
or gain in accessible available fluvial habitat that may result from flow
regulation below the proposed Watana Dam.
1 The ZHI (zone of hydrologic influence) is defined as the approximated section of tributary extending from the Susitna River’s
modeled water’s edge at a 1.5 year flow return interval downstream to the tributary’s confluence with the Susitna River at a base
flow.
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ii. To inform other studies including Fish Distribution and Abundance in
the Middle and Lower River (Section 9.6), River Productivity (Section
9.8), and Instream Flow (Section 8.5).
c. Characterize and map the Lower River mainstem from the upper limit of tidal
influence to the Three Rivers Confluence:
i. To provide baseline data for the purpose of evaluating the potential loss or
gain in available fluvial habitat that may result from flow regulation below the
proposed Watana Dam.
ii. To inform other studies including Fish Distribution and Abundance in the
Middle and Lower River (Section 9.6), River Productivity (Section 9.8), and
Instream Flow (Section 8.5).
9.9.3. Existing Information and Need for Additional Information
During the 1980s study efforts, habitat characterization and mapping in the Middle River
mainstem were conducted at a relatively coarse scale; mainstem habitat types that were
representative of distinct functional hydrology and channel morphology were identified. Under
this system, the Susitna River was classified into seven mainstem habitat types: mainstem
channel, side channel, side slough, upland slough, tributary mouth, tributary, and lakes, defined
by source water and hydrologic connectivity (Trihey 1982; ADF&G 1983a). For example, side
channels were described as side channels that carried less than 10 percent of the mainstem flow,
whereas sloughs were identified as having a water source derived from some combination of
groundwater, tributaries, and/or local runoff. Upland sloughs, unlike side sloughs, were those that
were disconnected from mainstem flows at their heads. These seven mainstem habitat types were
mapped in the Middle River based on aerial photography and were given individual alpha-
numeric identifiers such as “Slough 22” (ADF&G 1983a). Subsequent sampling of fish
populations and collection of water quality and habitat suitability data were conducted in subsets
of the mapped habitats. Additional habitat characterization and mapping efforts developed during
the 1980s defined unique categories of river habitat based on clear or turbid water conditions
under specific flows, in combination with presence or absence of open water leads during winter
(Steward and Trihey 1984 ) or hydrologic zones (ADF&G 1983a, 1983b). The habitat categories
were focused on main channel and side channel habitats in intensively studied areas in an attempt
to scale the information up to the entire Middle Susitna River Segment for simulating the
relationship between habitat and flow.
Very little habitat information has been collected in the Upper Susitna River. In the early 2000s,
the Alaska Department of Fish and Game (ADF&G) conducted sampling in the Upper Susitna
River sub-basin as part of its Alaska Freshwater Fish Inventory (AFFI) program (Buckwalter
2011a). These surveys were focused on documenting fish presence and collecting reach-level
habitat data in medium and large tributary drainages (Buckwalter 2011b). The AFFI habitat
studies were conducted at a scale that is not necessarily informative for understanding impacts to
fish use or productivity. Because the upper river surveys were focused on fish inventory, they
applied a dispersed sampling design that covered 60 streams; however, habitat data were collected
at only one transect per stream. The scale of these historic data collection efforts limits their
applicability for evaluating fish-habitat relationships and the potential for changes in fish habitat
use throughout the Susitna River as a result of hydropower facility development and operation.
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To augment the historic habitat data, this study will characterize and map aquatic habitat at finer
scales than did the 1980s studies, including to the mesohabitat level in the main channel and
tributaries. Mapping of off-channel habitats will include refinements to the typing of off-channel
habitats and typing and habitat metric sub-sampling in sloughs.
Characterization and mapping of mesohabitats is important in assessing potential impacts to fish
populations because it is at this level that fish selectively use different habitats (Hardy and Addley
2001) to support different life stages and life functions. A full complement of mesohabitat types
is required to sustain multiple life stages, support a diverse fish community, and furthermore, the
distribution of these habitats throughout the river will influence fish distributions. Fine-scale
habitat attributes, such as those found at the mesohabitat level, are thought to be particularly
relevant to aquatic organisms. Organisms interact with their environment at different scales
depending on their size and mobility (Parasiewicz 2007), both of which change with growth and
development. Parasiewicz (2007) further suggested that mesohabitats are habitats within which
an organism can be observed for a significant portion of its daily routine, similar to functional
habitat discussed by Kemp et al. (1999). For this study, information will be collected to support
the development of habitat descriptions at more ecologically significant scales by considering
several attributes that are biologically important to fishes (Harper et al. 1992; Maddock 1999).
The higher-scale mainstem habitat classifications used in the 1980s will be retained to allow for
some level of comparison over time.
In addition to considering the scale of habitat classification, it is also important to consider the
use of an objective classification approach that not only captures existing site-specific
characteristics, but also can be used for comparisons across space and time. Mesohabitat
assessments based on river morphology and ecologically significant habitat attributes should be
consistent and reproducible. The USFS Aquatic Habitat Surveys Protocol (USFS 2001) is an
example of a standardized protocol that was developed in Alaska to facilitate creation of a
regional stream habitat database as well as one that allows for aggregation of habitat data at
multiple scales. The USFS 2001 protocol is integrated into the habitat mapping study design
described in this study.
Sources of existing information that will directly support habitat mapping are outlined in Table
9.9-1.
Existing fish, habitat, and aquatic resource information appears insufficient to address the
following issues that were identified in the PAD (AEA 2011b).
F1: Effect of change from riverine to reservoir lacustrine habitats resulting from Project
development on aquatic habitats, fish distribution, composition, and abundance, including
primary and secondary productivity.
F2: Potential effect of fluctuating reservoir surface elevations on fish access and
movement between the reservoir and its tributaries and habitats.
F4: Effect of Project operations on flow regimes, sediment transport, temperature, and
water quality that result in changes to seasonal availability and quality of aquatic habitats,
including primary and secondary productivity. The effect of Project-induced changes
include stream flow, stream ice processes, and channel morphology (streambed
coarsening) on anadromous fish spawning and incubation habitat availability and
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suitability in the mainstem and side channels and sloughs in the Middle River above and
below Devils Canyon.
F7: Influence of Project-induced changes to mainstem water surface elevations from July
through September on adult salmon access to upland sloughs, side sloughs, and side
channels.
F9: The degree to which Project operations affect flow regimes, sediment transport,
temperature, and water quality that result in changes to seasonal availability and quality
of aquatic habitats, including primary and secondary productivity.
The information collected during this study will be essential to understanding fish habitat
distribution and will provide information relevant to addressing the five potential fisheries issues
listed above.
9.9.4. Study Area
The study area encompasses the mainstem Susitna River from the Oshetna River confluence at
approximately RM 233 downstream to the upper extent of tidal influence at approximately RM
28. As described above, the mainstem study area is further divided according to
geomorphic/hydrologic river segments; the Upper River, Middle River, and Lower River (see
Figure 9.5-1). The study area also encompasses tributaries in the Upper River (RM 180 to 233)
and Middle River segments (RM 98 to 18). The study area for tributaries is described as follows.
Note that the study area for selected tributaries in the Upper River has been modified in
accordance with the Characterization and Mapping of Aquatic Habitats Technical Memorandum
that was reviewed by the agencies and filed with FERC on June 30, 2013.
Upper River: For selected streams in watersheds known to support Chinook salmon, the
habitat mapping study area extends up to 3,000 feet elevation, unless a permanent
impassable barrier exists between 2,200 and 3,000 feet elevation. If a barrier exists
within this range surveys will stop at the barrier. In watersheds not known to support
Chinook salmon, the habitat mapping study area will terminate at 2,200 feet elevation
regardless of the presence of a barrier below this elevation.
Middle River:
o For selected streams above Devils Canyon known to support Chinook salmon, the
study area extends up to 3,000 feet elevation or the first impassable barrier,
whichever is less.
o For all other selected tributaries in the Middle River the study area extends from
the confluence with the mainstem up to the upper limit of the zone of hydrologic
influence.
9.9.5. Study Methods
9.9.5.1. Overview
Given the linear extent and remoteness of the river, an approach that combines analysis of aerial
imagery with ground-based collection of habitat data will be used. This combination of methods
will allow for maximizing coverage of river habitats in concert with efficient collection of
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detailed data at selected habitats. Furthermore, the habitat characterization methods can be
tailored to accommodate variations in channel size and overall stream length. Habitat data
collected in this study will utilize the Susitna-Watana Hydroelectric Project habitat classification
system that was developed during 2012 study design and planning process and standard
protocols outlined in the USFS Aquatic Habitat Surveys Protocol (USFS 2001). The USFS
protocol will be subject to minor modifications regarding parameter data collection to allow for
site specific characterization, for example maximum depth will not be collected in deep
mainstem channel habitats.
Because of the major differences in channel morphology and hydrology between tributaries and
the mainstem river and because Project effects are different in different geomorphic segments of
the river, habitat mapping methods are differentiated within the study area as follows.
Tributaries
o Tributaries in the Upper River
o Tributary segments in the Middle River
Mainstem
o Upper River mainstem
o Middle River mainstem
o Lower River mainstem
9.9.5.2. Overview of Aerial Video for Habitat Mapping
Low altitude aerial video can be an excellent tool when mapping mesohabitats over long
distances in remote and challenging topography. Low altitude aerial video combined with
ground sub-sampling for habitat mapping studies has been used in numerous FERC hydro
project relicensings in Washington, California, Texas, and North and South Carolina. When shot
with a professional high definition (HD) camera from a helicopter at a slow speed (15 to 40 mph,
depending on stream size), low height (75-300 feet), under good lighting conditions, good water
clarity, and a fairly open canopy, the video provides an up-close and panoramic view of all the
stream’s features. To maximize the quality of the video, it is shot in an upstream direction from
the right rear of a helicopter with its cabin door removed. A narrator/navigator is posit ioned in
the left front next to the pilot. From this low elevation, the viewer can clearly discern
mesohabitat types, channel character, dominant substrate classes, woody debris, and riparian
vegetation. Figure 9.9-1 is a screen capture from an aerial video of an Upper Susitna River
tributary.
Aerial video collected in early September 2012 (before the mid September flood) included the 12
primary and 4 secondary2 tributaries above Devils Canyon (Table 9.9-2), the Upper River
mainstem, and the Middle River mainstem. While glare and swirling winds were a problem on a
few tributaries, conditions were excellent overall. In addition, test video was shot of the Lower
River between RM 65 and RM 81 to determine the practical and technical application of aerial
2 For the purpose of this Final Study Plan a tributary that confluences directly with the Susitna River is referred to as
a primary tributary. A tributary that confluences with a primary tributary is referred to as a secondary tributary and
a tributary that confluences with a secondary tributary is referred to as a tertiary tributary.
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video for habitat characterization in the wide and highly braided Lower River. Use of video in
the Lower River is discussed further in Section 9.9.5.4.3. The final video product will include
live narration, on-screen continuous global positioning system (GPS) position, rivermile to the
tenth of a mile, and running time to the tenth of a second.
The digital video file is playable using standard media player software, such as VLC, which
supports many useful player controls including screen capture and can be downloaded as
freeware at http://www.videolan.org/vlc/download-windows.html. Digital video files will be
made available to licensing participants through AEA.
9.9.5.3. Upper and Middle River Tributary Habitat Mapping above Devils Canyon
Upper River and Middle River tributaries above Devils Canyon will be mapped using results of
the AEA 2012 low-altitude aerial video and in-river habitat ground survey sub-sampling. Low
altitude video surveys will only be used to type mesohabitats where they are clearly visible;
otherwise, ground based surveys will be conducted. Whether aerial video is also used to
describe other habitat variables, such as woody debris or dominant substrate size, will be
determined on a stream-by-stream basis and once such application is determined necessary and
valid. Aerial video will not be used to directly estimate channel dimensions.
9.9.5.3.1. Application of Aerial Video for Mapping Upper and Middle River Tributaries above
Devils Canyon
Habitat in the 12 primary tributaries and 4 secondary tributaries (Table 9.9-2) will be typed to the
mesohabitat level shown in Table 9.9-3 using a video sampling method. Tributaries that are not
conducive to aerial video mapping, such as those with obscured view of the river due to riparian
vegetation, will be mapped using ground methods only. The need and method for mapping
tributaries of a lower stream order than those listed in Table 9.9-2 will be determined with input
from the TWG prior to the 2013 field season. Smaller tributaries may not support fish and as
such may not require mapping. Alternatively, if they are mapped, it may be that they are sub-
sampled or a representative subset of tributaries could be selected by a randomized method.
In response to the FERC April 1 SPD and consultation with the TWG, AEA will habitat map an
additional 19 small primary and secondary tributaries in the Upper River that are not conducive
to aerial video mapping. Refer to section 9.9.5.3.2.3 below and the attached Technical
Memorandum for more information regarding selection and mapping methods for smaller non-
videotaped tributaries.
In video sampling, first a string is stretched horizontally across the computer monitor at about the
center. The video is then played from the beginning at normal or slow speed and paused at a
predetermined time interval. When paused, the mesohabitat type that is directly crossed by the
line is classified and entered into an Excel spreadsheet with the corresponding running time, e.g.
00hrs:12mins:3secs_riffle. A time interval between 3 and 5 seconds, depending on the stream
width and mesohabitat length, e.g., geomorphic reaches with short habitat units may have 3-
second intervals, while reaches with long habitat units may have 5-second intervals. For
example, at an average speed of 18 mph and a recommended 3-second interval for tributaries, a
sample is taken approximately every 80 feet or 66 samples per mile. Most of the of the video
taped tributaries (Kosina, Watana, Deadman, etc.) are over 10 miles long, which would result in
over 600 mesohabitat samples in each tributary under that time interval.
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A library of aerial video screen captures (mesohabitat type-index) will be built that includes
several variants of each mesohabitat type (Figure 9.9-3 through Figure 9.9-16). The video
“mapper” will constantly refer to the library of image captures to ensure accuracy and
consistency in mesohabitat typing. Ideally the type-index images would be ground-verified prior
to use in the video mapping. However, ground sub-sampling of all tributaries will not be
completed until 2013. Therefore, for some streams, the completed video frequency analysis will
need to be reviewed and checked against ground mapping later in 2013 and revised if needed.
Given the low altitude perspective and clarity of the video, most mesohabitat types will be easily
and accurately classifiable without ground verification.
The primary result of the video mapping is a mesohabitat frequency of 100 percent of the
tributary study area. This frequency analysis can also be subdivided by geomorphic reach.
Histograms and tables of mesohabitat type frequency will be produced. The metadata can also
be used for other studies such as selection of random mesohabitat units for fish population
surveys.
The method proposed above is a random sampling and replicable method. It is random for
several reasons: a) the speed of the helicopter is changing by a few tenths to a few miles per hour
several times per minute; b) because the camera is hand-held and the altitude of the helicopter is
constantly changing the angle of the lens relative to the ground is constantly changing; c) the
height above the ground is constantly changing by a few to tens of feet; and, d) the sequence and
lengths of mesohabitat types is highly variable in mountain streams. All these factors contribute
to a constantly varying ground distance between sample points, even though the sample time
interval is constant. The video sampling method has also been tested for “replicability”, as
described below.
To be certain mesohabitat typing using video is a reliable tool and the results are replicable, an
analysis of the replicability of results was conducted recently in a California hydroelectric
project relicensing. To check the general replicability of the habitat type identification, an
independent reviewer conducted video mapping of randomly selected ground-verified segments
representing 20 percent or more of three PHABSIM reaches. Because ground-truthing is an
essential component of video mapping, the independent reviewer had also participated in the
habitat mapping ground surveys, but not on the test stream segment. The three PHABSIM
reaches selected represented a variety of channel and habitat types: wide, open canopy; variable
gradient and canopy coverage; and a smaller, higher-gradient channel. The test concluded that
the aerial video habitat mapping method is a reliable tool and that differences between replicates
would be minimal; therefore, differences between one investigator and another would be
minimal, as long as the investigators were involved with the ground mapping and were given
clear definitions and type-index images of the various mesohabitat types. An added value of the
video record is the ability to check a habitat typing call with another researcher, if in doubt.
Within each geomorphic reach, habitats will be typed to the mesohabitat level according to a
nested hierarchical classification system developed in part with input from the Fish and Aquatic
TWG (Table 9.9-4). Note that the mesohabitat categories have been nested and expanded to
accommodate the high diversity of habitat types found in the tributaries during 2012 video and
ground surveys.
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9.9.5.3.2. Ground Mapping Upper and Middle River Tributaries above Devils Canyon
Because of the general inaccessibility, very rugged terrain, and mostly non -wadeable stream
channels, near census mapping (100 percent coverage) would be very challenging and in some
cases unsafe or impossible. For this reason AEA proposes to map habitat in 16 Upper and
Middle Susitna River tributaries (Table 9.9-2) using a combination of video, as described above,
and on-the-ground sub-sampling described below. Ground mapping will be done at a low to
moderate flow that is relatively near in discharge as the flow during the aerial video. In other
words, at a flow that will allow similar habitat type calls for the two methods. AEA, in
collaboration with the TWG, will determine how many and which smaller independent
tributaries, and how many and which smaller tributaries to the primary tributaries need to be
mapped. Refer to section 9.9.5.3.2.3 below and the attached Technical Memorandum for more
information regarding selection and mapping methods for smaller non-videotaped tributaries.
Geomorphic Reach Delineation 9.9.5.3.2.1.
Using desk-top tools including IFSAR topographic contour data, U.S. Geological Survey
(USGS) topographic maps, aerial video, and information from reconnaissance flights, tributaries
will first be segmented into geomorphic reaches where the channel is relatively homogeneous in
stream gradient, confinement, and hydrology. Major breaks in each of these parameters will
constitute a geomorphic/hydrologic reach boundary. Hydrologic reach breaks will be established
at tributaries that appear to contribute more than approximately 10 percent of total flow to the
parent tributary. A segment boundary will not be placed where downstream channel
characteristics are primarily controlled by bedrock rather than fluvial processes. Bedrock
channels are generally insensitive to short-term changes in sediment supply or discharge. Only a
persistent decrease in discharge and/or an increase in sediment supply sufficient to convert the
channel to an alluvial morphology would significantly alter fluvial bedrock channels
(Montgomery and Buffington 1993). For this reason, flow accretion will only be used as a factor
for segmentation at locations where channel characteristic below the contribution point are
controlled by fluvial processes.
Ground Mapping in Videotaped Streams 9.9.5.3.2.2.
Within each geomorphic reach type, continuous habitat surveys will be conducted over a
distance equivalent to at least 20 channel widths with the goal of sampling at least five units of
each of the primary mesohabitat types occurring in the geomorphic reach. Primary is defined as
mesohabitat types with a frequency in the geomorphic reach type of greater than 10 percent.
Survey distance will be extended, either contiguously or at another location in the geomorphic
reach, until the requisite number of replicates is obtained. If accessible by foot or helicopter, e.g.
not in the bottom of a gorge, habitats with a frequency lower than 10 percent also will be
surveyed, but data will be collected on five replicates or fewer.
Because helicopter landing zones in the uplands near the tributaries are extremely limited, a
randomized approach for selecting mapping sections is impractical. A high percentage of
randomly selected sites would likely not be accessible, and, when one was accessible, in -channel
accessibility over a distance of 20 or more channel widths would likely also be a problem.
Instead, sub-sample sites within each geomorphic reach will be selected based first on access to
the site by helicopter and foot and second on the availability of multiple and varied mesohabitat
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types within safe and reasonable hiking/wading access. The concept of segmenting the stream
into geomorphic reaches assumes that mesohabitat types within the segment are generally
similar.
Channel metrics to be sub-sampled on the ground will be collected using a modified U.S.
Department of Agriculture, Forest Service (USFS) Tier I and Tier III stream habitat survey
protocol (2001). Note that some of the variables listed in the USFS protocol assume the stream
being surveyed is wadeable.
Ground survey crews in 2012 were not able to effectivel y or safely collect some of the Tier I or
Tier III variables that were proposed for collection in the PSP. In many of the primary tributaries
in the Upper Susitna, habitat variables that involved crossing the streams were very difficult to
collect given the difficult wading conditions in most reaches. Flows, even during late summer
seasonal lows, were too fast and deep to negotiate at most points along the streams. Wading
factors were typically above 8-9 (product of depth x velocity) over predominantly boulder
substrate. Depths of 2.5 – 3 feet in combination with velocities of 3 to 4 feet per second around
boulder substrates were very common in the Upper Susitna tributaries. Crossings with lesser
wading factors were few and far between. As a result, some variables that were included for
collection in the PSP have either been eliminated or the collection method or frequency of
collection has been modified in this RSP.
Aquatic habitat surveys will be conducted by two-person survey crews. Each survey crew will
consist of a fish biologist and qualified fisheries technician. Survey sections will begin at a
predetermined location based on the survey section selection process described above and will
progress in an upstream direction. If a permanent impassable barrier is encountered below the
2,200-foot elevation point, the barriers will be documented and surveys will continue upstream
to the survey end. If a permanent impassable barrier is encountered above the 2,200-foot
elevation point ground sub-sampling surveys will not be conducted beyond that point.
In stream sections with complex channel morphology (e.g., three or more parallel channels), the
primary and one secondary channel will be designated and will be fully mapped. The remaining
secondary channels will be identified and typed using the aerial video. In a highly complex
channel type (Figure 9.9-16) the unit will be more characterized than mapped, e.g. length, width,
number, type of sub-channels, and the general mesohabitat type present.
Habitat data will be recorded on the stream survey field data form. Separate stream survey data
sheet(s) will be completed for each geomorphic reach. Habitat parameters to be measured for
this component of the study are described in Section 9.9.5.3.2.4 and 9.9.5.3.2.5.
Ground Mapping of Smaller Tributaries within the Upper River Inundation Zone 9.9.5.3.2.3.
Most small tributaries in the Upper River inundation zone are obscured from overhead view due
to a closed canopy of riparian vegetation. For this reason, small tributaries in the Upper River
inundation zone can only be mapped using ground survey methods.
AEA will ground map 4 small unnamed tributaries in the Upper River that are also being
sampled for fish distribution and abundance (Table 9.9.2). As described in the Attached
Technical Memorandum, AEA will also ground map an additional 10 smaller primary tributaries
and 5 secondary/tertiary tributaries in the Upper River inundation zone that are not being
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sampled for fish distribution and abundance. The total number of small primary and secondary
tributaries to be ground mapped only (without video) in the Upper River inundation zone is 19.
Ground-map-only tributaries will be segmented into geomorphic reaches using the approach
described above in Section 9.9.5.3.2.1.
Within each geomorphic reach type, habitat surveys will be conducted over a distance equivalent
to 20 channel widths. Depending on access to and along the stream, the 20 channel width
section may be a continuous section or broken up into 2 or more accessible lengths. Because
most of the small tributaries in the inundation zone are heavily forested, access by helicopter or
cross-country to any point along the stream will be problematic. Therefore, the starting and
ending points of habitat mapping survey sections will largely depend on access. Most small and
shorter streams will be accessed by helicopter to a landing zone along the Susitna River near the
mouth of the tributary. In the lower geomorphic reach, surveyors will begin the 20 channel
width mapping section just upstream of the ordinary high water line of the mainstem. Upstream
geomorphic reaches will be mapped only if safe and reasonable access by helicopter is available.
Whether a landing is safe will be determined by the helicopter pilot. Whether access is
reasonable will be determined by the field crew lead and will depend primarily on the distance
and difficulty of cross country travel from the helicopter landing zone to the stream section to be
mapped. Conditions preventing access will be documented when access is not attempted.
Mapping methods and protocols for small tributaries will be the same as those for larger
tributaries, as described in this section.
Tier I Data Collection 9.9.5.3.2.4.
The following habitat metrics will be collected for each geomorphic reach:
Geomorphic reach type (confined, similar gradient, similar hydrology)
Channel type (primarily single thread, primarily split, primarily braid, or combination
with estimated percent of each type)
Measured bankfull width
Measured or estimated bankfull maximum depth
Measured gradient
Estimated dominant substrate composition
GPS location of channel measurements
Note that incision depth was eliminated at Tier I because collection generally requires crossing
the stream.
Tier III Data Collection 9.9.5.3.2.5.
The following habitat metrics will be collected for each mesohabitat unit.
Habitat unit type
Measured unit length
Measured average wetted width (three measurements per unit)
If pool, estimated or measured maximum depth
If pool, estimated or measured pool crest depth
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Estimated average maximum depth of unit
Measured width of unit
Woody debris count in unit
Estimated percent substrate composition in unit
Estimated percent undercut, each bank in unit
Estimated percent erosion, each bank in unit
Estimated percent riparian vegetation cover in unit
Dominant riparian vegetation type for each unit
Estimated percent instream cover in unit
Photograph of each unit
GPS location of each unit
Habitat units within the survey section will be sequentially numbered as they are encountered
during each survey, and data will be recorded for each habitat unit. Data collected for all habit at
units will include the unit length, the mesohabitat type according to Table 9.9-3, three
measurements of wetted width from which an average wetted width will be calculated, percent
substrate composition, percent eroding bank on each side of the channel, percent undercut bank
on each side of the channel, dominant riparian vegetation type, cover type, and cover percent.
Additional data will be recorded for pool habitat units. The maximum pool depth and depth at
the pool tail crest will be measured to the nearest 0.1 foot, whenever possible. These data will be
used to calculate residual pool depth. The structural feature responsible for forming the pool will
be identified (e.g., boulder, undercut bank, large or small wood).
Split channels are defined as separate flow paths located within the bankfull channel and
separated from each other by gravel bars that are barren or support only annual vegetation.
When split flow is encountered, each split will be surveyed and the proportion of flow conveyed
by the split will be estimated, recorded, and used to classify each channel as primary (majority of
the flow) or secondary (minority of the flow). Habitat units in the split that convey the most
flow will be designated primary units and will continue to be numbered sequentially as part of
the main channel survey. Where more than two split channels exist, only the primary and
secondary splits will be numbered. The data form will note the total number of split channels.
Side channels are defined as features with a fluvial-sorted mineral bed that are separated from
the main channel by an island that is at least as long as the main channel bankfull width and that
supports permanent vegetation. At a minimum, the inlet and outlet of each side channel will be
documented by collecting a GPS waypoint and taking a photograph looking upstream from the
outlet and downstream from the inlet. The side channel will be identified as entering from the
left or right bank (looking downstream) and classified as wet or dry. Habitat data will be
collected in wetted side channels according to the methodology described above. Where more
than two side channels exist, only the primary and secondary channels will be numbered. The
data form will note the total number of split channels.
Relative flow levels on the day of the survey will be estimated according to the following:
Dry
Puddled: Series of isolated pools connected by surface trickle or subsurface flow.
Low Flow: Surface water flowing across 50 to 75 percent of the active channel surface.
Consider general indications of low flow conditions.
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Moderate Flow: Surface water flowing across 75 to 90 percent of the active channel
surface.
High Flow: Stream flowing completely across active channel surface but not at bankfull.
Bankfull Flow: Stream flowing at the upper level of the active channel bank.
Flood Flow: Stream flowing over banks onto low terraces or floodplain.
In addition, Susitna River mean daily discharge will be obtained from the nearest downstream
USGS stream gauge and entered onto each day’s survey forms.
Special Habitat Features
Special habitat features include tributary channels, seeps and springs that contribute groundwater
to the mainstem, and temporary (e.g., subsurface flow) or permanent barriers to upstream fish
migration. A separate data sheet will be maintained for each reach listing the type, location, and
a description of special habitat features.
For features classified as stream barriers, the following information will be recorded in the
comments section. Only cursory information will be collected under the Habitat Mapping study
as most of the following barrier data is being collected under the Fish Passage Barrier Study Plan
(Section 9.12).
Barrier type (beaver dam, debris dam, vertical falls, chute/cascade, boulder, other)
Temporal nature (ephemeral or permanent)
Maximum height of falls or biggest single step if cascading
Maximum depth of plunge pool
Chute/cascade gradient and length
Length of feature.
A GPS waypoint and a photograph will be taken of each special feature. Additional photographs
will be taken of representative channel conditions throughout each reach. The photo number,
waypoint, date, and associated habitat unit or feature number will be recorded for each
photograph.
9.9.5.4. Mainstem Habitat Mapping
The mainstem Susitna River from the Oshetna River to the upper extent of tidal influence
includes approximately 200 miles of river and many times more than that distance when the
lengths of side channels, braided channels, and sloughs, are included. An approach that includes
the use of aerial imagery and collection of ground-based habitat data is required given the linear
extent of this large river, its channel complexity, and its remoteness. This combination of
methods will allow for maximizing coverage of river habitats in concert with ground sub -
sampling at selected habitat areas. Furthermore, this combination allows habitat characterization
and mapping methods to be tailored to accommodate different study objectives, different
mapping tools available, and different methods, depending on the specific river segment.
9.9.5.4.1. Upper River Mainstem
The Upper River will be mapped using hierarchically-nested habitat typing adapted to feasible
identification levels based on the use of aerial still imagery, LiDAR, and aerial videography. A
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linear network will be created in GIS by drawing lines through the middle of the stream channel
as viewed by aerial imagery or LiDAR. The reference imagery was collected at river flows
generally ranging from 10,000 to 12,000 cfs, which will be considered a representative mid-flow
to conduct mapping. Divided channels will have multiple lines representing that stream section.
Main channel and off-channel habitat will be delineated. The length of the lines will be based on
mesohabitat classification for the main channel and macrohabitat classification for off-channel
habitat. Each individual vector line will have a length and a hierarchical-tiered habitat
classification organized in "Levels".
The habitat classification hierarchy will be composed of four levels representing (1) major
hydraulic segment; (2) geomorphic reach; (3) mainstem habitat type; and, (4) main channel
mesohabitat (Table 9.9-5). Level 1 will generally identify the Upper, Middle, and Lower River
from each other. Level 2 will identify one of six unique reaches established from the channel’s
geomorphic characteristics (established from the Geomorphology Mapping Study). Level 3 will
classify the mainstem habitat type of main, off-channel, and tributary habitat using an approach
similar to the 1980s historical habitat mapping definitions (ADF&G 1983a). All off-channel
habitats will be classified to Level 3 and all main channel habitat will be identified to Level 4
mesohabitat type (i.e., riffle, pool, run, etc.).
A series of tables and figures were created to illustrate the habitat mapping approach and also the
analyses that will be conducted from the data. Figure 9.9-17 shows an example of how habitat
will be visually mapped from a GIS layer. An example of the raw database is shown in Table
9.9-6. The GIS database will create a hierarchical table that will be used to summarize the
proportion of habitat by mapped unit of length (Tables 9.9-7 and 9.9-8). The tiered approach
will allow for summaries at all five levels to support resource study planning. The table will also
provide individual identification of all unique habitat types. This information will be important
to understand how to best represent the Upper River.
Several controls will be established to ensure that the habitat mapping effort is both precise and
accurate. Habitat typing will be conducted by no more than two GIS technicians to ensure typed
habitat is consistent. Examples of specific aerial images of habitat as related to the levels will be
created. These examples will be reviewed and confirmed by the technical lead and provide a
voucher reference to help identify habitat types. Also, all typed data will be identified as having
clear or turbid water to better identify slough habitat and correct any habitat typing errors. Final
habitat typing will be reviewed by the technical lead to ensure consistency and accurate habitat
mapping.
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In addition to the remote mapping, on-the-ground truthing and refinement will occur. In 2013, a
subset of off-channel and main channel habitat units will be ground-mapped and will include
metrics described for tributaries, e.g., depth, width, wood, cover, etc., as appropriate, for off-
channel and main channel habitats. Five to ten main channel mesohabitat units and five to ten
off-channel habitat units of each type will be randomly selected for sub-sampling. If there is
fewer than the selected number, all units of that habitat type all will be sub-sampled.
9.9.5.4.2. Middle River Mainstem
The Middle River mainstem will be mapped in similar fashion to the Upper River mainstem.
The hierarchical tiered classification system will be implemented to identify habitat from aerial
still imagery, LiDAR, and aerial videography. The Middle River habitat data will also be used
by the Instream Flow study to establish habitat complexity and frequency. All habitat segments
will be identified using a mid-channel line, which will provide habitat length; however, off-
channel slough habitat will be drawn separately in an area (polygon) in the Middle River to
identify the size of each slough and better characterize slough diversity for Instream Flow Study
needs. Area mapping will be reported separately from the linear database.
On-the-ground habitat mapping (one hundred percent in Focus Areas) will identify backwater
habitat as a unique habitat feature and will give special consideration to such features that meet
the FWS and NMFS definition of backwater habitats3. This information will be used in the
instream flow study to specifically include these habitat types in Middle River Focus Area 2D
modeling.
The ten Focus Areas under consideration for modeling include a large number and diversity of
side channels, side sloughs, upland sloughs, and tributary mouths, that in sum, would be
representative of potential backwater habitats at off-channel and tributary mouths in the Middle
River.
As described in RSP 8.5, the 2-D model will utilize a variable mesh (also referred to as flexible
mesh) to model all off-channel and tributary confluences where backwater habitats are generally
formed. 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).
As in the Upper River segment, in addition to the remote mapping, on -the-ground truthing and
refinement will occur in the Middle River segment. In 2013, a subset of off-channel and main
channel habitat units will be ground-mapped and will include metrics described for tributaries,
e.g., depth, width, wood, cover, etc., as appropriate. Separate from Focus Area, 5 to 10 main
channel mesohabitat units and 5 to 10 off-channel habitat units or each type will be randomly
selected for sub-sampling. If there is fewer than the selected number of units of a habitat type,
then all will be sub-sampled. Main channel and off-channel habitats in Focus Sites will be 100
percent mapped to the mesohabitat level. Ground mapping will include metrics described for
tributaries, e.g., depth, width, wood, cover, etc., as appropriate, for off-channel and main channel
3 NMFS and FWS define backwater (i.e., mainstem and side channel backwater pools) as “Slo w water habitats that
form due to mainstem backwater up [to] abandon or active side channels separated from the mid channel by a visible
current shear line. Water depth and velocity controlled by mainstem water surface elevation. Water physical and
chemical characteristics reflect those of the dominant mainstem flow, however, the reduction in surface slope could
increase sediment and organic matter deposition.” In addition, NMFS and FWS have a separate definition for
“tributary mouth backwater” habitats.
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habitats. Mesohabitat metrics of surveyed sloughs will be directly extrapolated to non-surveyed
sloughs of like type, i.e., slough or upland slough.
As defined for the Susitna-Watana licensing studies, the mainstem includes tributaries segments
within the zone of hydrologic influence (ZHI). AEA proposes to habitat map the zone of
hydrologic influence of 20 named and unnamed tributaries in the Middle River (Table 9.9-
4). Nine tributaries occur within Focus Areas and 11 are located outside of Focus Areas. These
20 tributaries were selected based on their known fish use and based on their range of stream size
and drainage basin area. Tributary segments in the Middle River mainstem that are within the
zone of hydrologic influence will be mapped according to the methods described above for
tributaries.
AEA will classify Middle River tributary reaches within the zone of hydrologic influence into
geomorphic reaches based on tributary basin drainage area and stream gradient to provide a
general understanding of the relative potential value to fish and aquatic resources, and report on
these attributes in the initial and updated study reports.
9.9.5.4.3. Lower River Mainstem
Because of the very large size and channel complexity of the Lower River (Figure 9.9-18) it is
impractical to map the entire river segment beyond Level 3 (Mainstem Habitat Type). Of the
five mesohabitat types in Level 4, the Lower River appears to primarily differentiate into only
glides and riffles. The low gradient and aggraded gravel bed of the Lower River is generally not
conducive to the formation of other mesohabitat types, such as pools or runs, although they are
likely present in very low numbers.
Whether the Lower River is mapped to Level 3 depends on the extent of mapping to be
conducted under the Geomorphic Mapping Study, which will use existing LiDAR and aerial
imagery from the Matanuska-Susitna Borough LiDAR and Imagery Project.
In early September 2012, AEA conducted a test to determine the possible application of aerial
video for habitat mapping the Lower River. A one-mile wide segment was selected between RM
65 and RM 81. The test section was flown at three different heights above ground (AG). The
number of parallel flight paths necessary to cover the river width at the three different elevations
was as follows: one path at 2,650 feet AG; two paths at 1,700 feet AG; and four paths at 400 feet
AG. The test showed that a height of 400 feet or lower with three to five paths in a mile-wide
section would be necessary to visually differentiate mesohabitat types of riffle, glide, pool, or
run, if they did occur. Further, several parallel paths would be extremely difficult to track even
with GPS and would be very difficult to follow in the video.
In summary, this study will rely on the Geomorphic Mapping Study to map the Lower River to
Level 3. Development of mapping methods beyond Level 3 will wait until results of the 2012
interim studies, particularly the hydrologic study, are reviewed and analyzed. The habitat
characterization objectives for the Lower River will then be more clearly identified and defined.
9.9.5.5. Lake Mapping
Lakes in the Upper River basin within the potential zone of reservoir inundation will be located,
mapped, and identified in the Project GIS database. Mapping will include elevation, surface
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area, perimeter, maximum depth, presence of surface water connection to the Susitna River, and
other relevant limnology information on a lake-by-lake basis.
There are 12 lakes currently known to be within the zone of reservoir inundation, according to
the National Hydrography Database (NHD). These are shown by number in Figure 9.9-19
9.9.5.6. Study Coordination and Updates
Multiple studies will be collecting field data in 2013 to better refine habitat mapping
databases. Instream flow studies (Section 8.5) will be conducting extensive physical and
biological studies in 2013. Also, the Geomorphology studies (Sections 6.5 and 6.6) will be area
mapping Focus Areas in 2013 that could provide more refined area habitat units, where
available. All relevant collected data from other studies will be reviewed and assessed to
determine if updating or modifying the habitat mapping database with the additional information
will be beneficial and supportive to the overall study goals.
9.9.6. Consistency with Generally Accepted Scientific Practices
Studies to map and characterize aquatic habitats are commonly conducted during water resource
development projects, including for hydroelectric projects as part of FERC licensing. Field
studies will use protocols developed in consultation with agency representatives and modified
from standard federal protocols developed for use in Alaska (USFS 2001) and will be consistent
with the instream flow analysis. Remote mapping will utilize protocols similar to those
performed at other hydroelectric projects.
9.9.7. Schedule
Habitat mapping ground surveys began in 2012 and will continue through 2013 with follow-up
work in 2014 (Table 9.9-9). Aerial video data collection was conducted during the first two
weeks of September 2012. Although not expected, any follow-up video work will occur in 2013.
Habitat characterization of the Upper and Middle rivers began in 2012 and will continue into
2013. The Initial Study Report (ISR) and Updated Study Report (USR) will be filed in February
2014 and February 2015, respectively. Updates on study progress will be presented at Technical
Workgroup meetings, to be held quarterly during 2013 and 2014.
9.9.8. Relationship with Other Studies
In addition to providing baseline information about aquatic resources in the Project area, aspects
of the Characterization and Mapping of Aquatic Habitats Study are designed to complement and
support other AEA studies (Figure 9.9-19). In addition to a review of background information
that will aid in study planning and design, five study components will provide the necessary
precursor or input information. Inputs from the Geomorphology Study (Section 6.5), Aerial
Video Study, GIS Mapping and Aerial Imagery, Fish Distribution and Abundance in the Upper
(Section 9.5) and Middle and Lower Susitna River (Section 9.6) will aid in the physical and
biological delineation and mapping of habitat. The characterization of aquatic habitat will then
provide useful output or feedback to understanding five AEA studies. The mapping of aquatic
habitat will aid in understanding the behavior, movements, and spatial use of fish in the Fish
Distribution and Abundance in the Upper (Section 9.5) and Middle and Lower Susitna River
(Section 9.6). Habitat characterization will help in understanding the potential Project effects of
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the flow regime in the Instream Flow Study (Section 8). The characterization of aquatic habitat
will allow for the identification of habitat affected by the Project reservoir and this may affect the
future reservoir fish community (Section 9.10). Finally, the River Productivity Study (9.8) will
use the habitat mapping for identification of study site selection and quantification of habitat
types for interpolation.
9.9.9. Level of Effort and Cost
The total estimated cost of the study for 2013 and 2014 is $1,000,000 including remote mapping,
field surveys, data analysis, and technical report preparation.
9.9.10. Literature Cited
ADF&G (Alaska Department of Fish and Game). 1983a. Su Hydro draft basic data report,
volume 4, part 1. ADF&G Su Hydro Aquatic Studies Program, Anchorage, Alaska.
ADF&G. 1983b. Resident and juvenile anadromous fish studies on the Susitna River below
Devil Canyon, 1982. Susitna Hydro Aquatic Studies. Phase II Basic Data Report. Volume
3. Prepared for Alaska Power Authority, Anchorage, Alaska.
ADF&G (Alaska Department of Fish and Game). 2012. Anadromous Waters Catalog.
http://www.sf.adfg.state.ak.us/SARR/AWC/index.cfm. Accessed December 2012.
AEA (Alaska Energy Authority). 2011b. Pre-application Document: Susitna-Watana
Hydroelectric Project FERC Project No. 14241. December 2011. Prepared for the Federal
Energy Regulatory Commission, Washington, DC.
AEA. 2013. Susitna River Fish Distribution and Abundance Implementation Plan: Susitna-
Watana Hydroelectric Project FERC Project No. 14241. March 31, 2013.
Buckwalter, J.D. 2011a. Synopsis of ADF&G’s Upper Susitna Drainage Fish Inventory, August
2011. November 22, 2011. ADF&G Division of Sport Fish, Anchorage, AK. 173 pp.
Buckwalter, J.D. 2011b. Station Reports. August 2001. ADF&G Division of Sport Fish,
Anchorage, AK. 146 pp.
FERC (Federal Energy Regulator y Commission). Office of Energy Projects. 2013. April 01,
2013 Study Plan Determination for the Susitna-Watana Hydroelectric Project No 14241-
000. Federal Energy Regulatory Commission.
Hardy, TB and R.C. Addley. 2001. Vertical integration of spatial and hydraulic data for
improved habitat modeling using geographic information systems. In Hydroecology:
Linking hydrology and aquatic ecology. Proceedings of the Birmingham, United
Kingdom Workshop, Acreman M.C. (ed.). July 1999. IAHS Publication No. 266, 65–75.
Harper, D.M., C.D. Smith, and P.J. Barham. 1992. Habitats as the building blocks for river
conservation assessment. In River Conservation and Management, Boon P.J., Calow, P.,
Petts, G.E. (eds). John Wiley: Chichester; 311–319.
Kemp, J.L., D.M. Harper, and G.A. Crosa. 1999. Use of ‘functional habitats’ to link ecology
with morphology and hydrology in river rehabilitation. Aquatic Conservation: Marine
and Freshwater Ecosystem 9(1): 159–178.
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Maddock, I. 1999. The importance of physical habitat assessment for evaluating river health.
Freshwater Biology 41: 373-391.
Montgomery, David, R. and John M. Buffington. 1993. Channel-reach morphology in mountain
drainage basins. Geological Society of America Bulletin 1997:109. No. 5:596:611.
Moore, K. M. S., K. K. Jones, and J. M. Dambacher. 2006. Aquatic Inventories Project: Methods
for Stream Habitat Surveys. Oregon Department of Fish and Wildlife, Corvallis, Oregon.
Parasiewicz, P. 2007. The MesoHABSIM model revisited. River Research and Application 23:
893-903.
Steward, C.R., and E.W. Trihey. 1984. Draft. Fish habitat and instream flow relationships in the
middle reach of the Susitna River: an extrapolation methodology. Alaska. Susitna
Hydroelectric Project Doc. No. 378. 20 pp.
Trihey, E. W. 1982. Preliminary assessment of access by spawning salmon to side slough habitat
above Talkeetna. Susitna Hydroelectric Project Doc. No. 134. 24 pp.
Trihey, E.W. 1984. Response of aquatic habitat surface areas to mainstem discharges in the
Talkeetna to Devil Canyon reach of the Susitna River. Alaska. Susitna Hydroelectric
Project Doc. No. 1693.15 pp.
USFS (U.S. Forest Service). 2001. Chapter 20 – Fish and Aquatic Stream Habitat Survey. FSH
2090-Aquatic Habitat Management Handbook (R-10 Amendment 2090.21-2001-1).
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9.9.11. Tables
Table 9.9-1. Primary sources of existing information supporting the aquatic habitat study.
River Segment or Tributaries Existing Information Available for Habitat Mapping
Upper River tributaries IFSAR 20-foot contour topographic data
Low altitude aerial video
Upper River mainstem
IFSAR 20-foot contour topographic data
Low altitude aerial video
Matanuska-Susitna Borough LiDAR and Imagery
River cross-sectional profiles of depth and velocity
2012 geomorphic mapping of channel types
Middle River mainstem
IFSAR 20-foot contour topographic data
Low altitude aerial video
Matanuska-Susitna Borough LiDAR and Imagery
River cross-sectional profiles of depth and velocity
2012 geomorphic mapping of channel types
1980s geomorphic mapping of channel types
Lower River mainstem
IFSAR 20-foot contour topographic data
Matanuska-Susitna Borough LiDAR and Imagery
River cross-sectional profiles of depth and velocity
2012 partial geomorphic mapping of channel types
1 IFSAR. Interferometric synthetic aperture radar is a radar technique used in geodesy and remote sensing
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Table 9.9-2. Tributaries in the Upper River proposed for habitat mapping also proposed for fish distribution and abundance sampling.
Primary
Tributary
Secondary
Tributary
Geomorphic
Reach
Project
River
Mile
Approximate
Total Stream
Length
Approximate
Drainage
Area Mi.
Approximate
Elevation and
River Mile of
Anadromous
Barrier
Habitat Mapping
Study Area1
Documented
Chinook in
Watershed
Mapping Method
Species Known to be Present in Tributary or Plume2 Chinook Dolly Varden Lake Trout Arctic Grayling Round Whitefish Humpback Whitefish Whitefish spp. Salmonid spp. Burbot Longnose Sucker Slimy Sculpin Sculpin spp. Rainbow Trout Sampled [NO FISH} Oshetna River – LB UR 3 235.1 55.6 550 None PRM 0.0 to 3.000 ft Yes Aerial and Ground X X X X X X X X
Black River - LB UR 3 12.7 (LB) NI NI None PRM 0.0 to 3,000 ft Yes Aerial and Ground
Goose Creek – LB UR 3 232.8 25.2 103.9 None PRM 0.0 to 2,200 ft NI Aerial and Ground X X X X X
Jay Creek - RB UR 4 211.0 19.6 61.8 None PRM 0.0 to 2,200 ft NI Aerial and Ground X X X X X X X X
Kosina Creek - LB UR 4 209.1 39.5 400.2 None PRM 0.0 to 3,000 ft Yes Aerial and Ground X X X X X X X X X
Tsisi Creek1 - LB UR 4 7.4 (LB) NI NI None PRM 0.0 to 3,000 ft Yes Aerial and Ground
Unnamed Tributary - LB UR 5 206.3 7.43 <31 None PRM 0.0 to 2,200 ft NI Ground only X X
Unnamed Tributary - LB UR 5 204.3 6.2 <31 Possible – PRM 0.5 PRM 0.0 to 2,200 ft NI Ground only X X X
Unnamed Tributary - LB UR 6 197.7 5.4 <31 PRM 1.3 PRM 0.0 to 2,200 ft NI Ground only X X X X
Watana Creek - RB UR 6 196.9 26.9 174.8 None PRM 0.0 to 3,000 Yes Aerial and Ground X3 X X X X X X X X
Watana Tributary - RB UR 6 8.7 (RB) UNI NI None PRM 0.0 to 3,000 ft Yes Aerial and Ground
Unnamed Tributary - RB UR 6 194.8 7.1 124 None PRM 0.0 to 2,200 ft NI Ground only X X X X X X X
Deadman Creek - RB UR 6 189.4 41.9 175.1 ≈1,700 ft - PRM 0.4 PRM 0.0 to 3,000 ft NI Aerial and Ground X X X X X
Tsusena Creek - RB MR 2 184.6 30.7 145.3 ≈1,700 ft – PRM 3.8 PRM 0.0 to barrier Yes Aerial and Ground X X X X X X X X
Unnamed Tributary - RB MR 2 184.0 10.4 <31 ≈1700 ft – PRM 1.8 PRM 0.0 to barrier NI Aerial and Ground X X X X X X X
Fog Creek - LB MR 2 179.3 27.8 147.2 None PRM 0.0 to 3,000 ft Yes Aerial and Ground X X X X X X X X X
Fog Tributary3 - LB MR 2 5.2 (LB) NI NI None PRM 7.3 to 3,000 ft Yes Aerial and Ground X
Devil Creek - RB MR 4 164.8 15.8 74.8 ≈1,400 – PRM 2.2 PRM 0.0 to barrier NI Aerial and Ground X X X X
Chinook Creek - LB MR 4 160.5 10.6 24.7 None PRM 0.0 to 3,000 ft Yes Aerial and Ground X X
Cheechako Creek - LB MR 4 155.9 10.7 36.4 ≈1,500 – PRM 2.5 PRM 0.0 to barrier Yes Aerial and Ground X X X X
1/ Upper extent of habitat mapping study area will extend to 3,000 feet for streams in watersheds known to support Chinook salmon. Othrerwise the survey will terminate at 2,200 feet or confirmed Chinook barrier, whichever is lower.
2/ Fish species presence based on historical and current surveys.
3/ Juvenile Chinook found in watershed during AEA 2013 fish distribution and abundance sampling.
NI: No information available at this time.
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Table 9.9-3. Upper River tributary mesohabitat types and descriptions.
Channel Type
(# of channels)
Hydraulic
Type
Mesohabitat
Type Definition
Single (1)
Split (2)
Channel
Complex (3 or >
channels)
Fast Water
Falls
Steep near vertical drop in water surface elevation greater than
approximately 5 feet over a permanent feature, generally
bedrock.
Cascade
A fast water habitat with turbulent flow; many hydraulic jumps,
strong chutes, and eddies and between 30-80 percent white
water. High gradient; usually greater than 4 percent slope. Much
of the exposed substrate composed of boulders organized into
clusters, partial bars, or step-pool sequences. 1
Chute
An area where most of the flow is constricted to a channel much
narrower than the average channel width. Laterally concentrated
flow is generally created by a channel impingement or a laterally
asymmetric bathymetric profile. Flow is fast and turbulent.
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 percent
slope, occasionally 7.0-8.0 percent. 1
Boulder Riffle
Same flow and gradient as Riffle but with numerous boulders
that can create sub-unit sized pools or pocket water created by
scour.
Riffle
A fast water habitat with turbulent, shallow flow over submerged
or partially submerged gravel and cobble substrates. Generally
broad, uniform cross-section.1 Low gradient; usually 0.5-2.0
percent slope, rarely up to 6 percent.
Run/Glide
A habitat area with minimal surface turbulence with generally
uniform depth that is greater than the maximum substrate size.1
Velocities are on border of fast and slow water. Gradients are
approximately 0 to less than 2 percent. Generally deeper than
riffles with few major flow obstructions and low habitat
complexity.1
Slow Water
Pool
A slow water habitat with a flat surface slope and low water
velocity that is deeper than the average channel depth.
Substrate is highly variable. 1
Pool subtypes
Straight Scour Pool: Formed by mid-channel scour. Generally
with a broad scour hole and symmetrical cross-section.1
Plunge Pool: Formed by scour below a complete or nearly
complete channel obstruction (logs, boulders, or bedrock). Pool
must be Substrate is highly variable. Frequently, but not always,
shorter than the active channel width.1
Lateral Scour Pool: Formed by flow impinging against one
stream bank or partial obstruction (logs, root wad, or bedrock).
Asymmetrical cross-section. Includes corner pools in
meandering lowland or valley bottom streams.1
Backwater Pool: Found along channel margins; created by
eddies around obstructions such as boulders, root wads, or
woody debris. Part of active channel at most flows; scoured at
high flow. Substrate typically sand, gravel, and cobble. Generally
not as long as the full channel width. 1
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Channel Type
(# of channels)
Hydraulic
Type
Mesohabitat
Type Definition
Beaver Pond Water impounded by the creation of a beaver dam. Maybe within
main, side, or off-channel habitats. 1
Single (1)
Split (2)
Channel Complex
(3 or > channels)
Alcove
An off-channel habitat that is laterally displaced from the general
bounds of the active channel and formed during extreme flow
events or by beaver activity; not scoured during typical high
flows. Substrate is typically sand and organic matter. Generally
not as long as the full channel width. An alcove is differentiated
from a backwater being more protected and not scoured at high
flows whereas a backwater is part of the active channel and is
scoured at high flows 1
Off-channel Percolation
channel
A slough characterized by groundwater percolation through
the floodplain that comes from main stream channel. Upstream
surface connection to active channel cut off due to accumulation
of sediment/debris at the upstream end. Upstream surface water
connection to the active channel present only during high flows.
3 Adapted from Moore et al. 2006.
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Table 9.9-4. Named and unnamed tributaries in the Middle River below Devils Canyon selected for ground habitat mapping within the zone of hydroelectric influence.
Project
Rivemile
(PRM)
Tributary Name Geomorphic
Reach
Focus
Area
Intensive
Study in
Focus
Area
Mesohabitat
Map and
Survey for
Potential
Barriers in ZHI
Documented
in
Anadromous
Waters
Catalog
Historical
Data
Available
Proposed for
FDA Fish
Sampling in
2013
Approximate
Length of
ZHI1 (mi)
Approximate
Drainage Area
(mi2)
152.3 Portage Creek MR-5 FA151 X X X Yes 0.19 178.6
148.3 Jack Long Creek MR-6 X X X Yes 0.03 NI
144.6 Unnamed MR-6 FA144 X NI Yes 0.01 NI
142.1 Indian River MR-6 FA141 X X X Yes 0.14 86.2
140.1 Gold Creek MR-6 X X X Yes 0.15 23.7
134.3 Fourth of July
Creek
MR-6 X X X Yes 0.12 NI
134.1 Sherman Creek MR-6 X X X Yes 0.02 NI
128.1 Skull Creek MR-6 FA128 X X X Yes 0.04 NI
127.3 Fifth of July Creek MR-6 X X X Yes 0.01 NI
124.4 Deadhorse Creek MR-6 X X X Yes 0.18 6.5
121.4 Little Portage
Creek
MR-7 X X X Yes 0.12 2.4
120.2 McKenzie Creek MR-7 X X X Yes 0.02 2.3
119.7 Lower McKenzie
Creek
MR-7 X X Yes 0.16 NI
117.2 Lane Creek MR-7 X X X Yes 0.11 10.4
115.4 Unnamed MR-7 FA115 X NI Yes 0.12 NI
115.0 Gash Creek MR-7 FA 113 X X X Yes 0.01 NI
114.9 Slash Creek MR-7 FA 113 X X X Yes 0.02 NI
113.7 Unnamed MR7 FA 113 X NI No NI NI
110.5 Chase Creek MR-7 X X X Yes 0.17 NI
105.1 Whiskers Creek MR-8 FA104 X X X Yes 0.33 17.2
NI: No information available at this time.
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Table 9.9-5. Nested and tiered habitat mapping units and categories.
Level Unit Category Definitions
1 Major Hydrologic Segment Upper, Middle, Lower River
Defined Segment Breaks
Upper River – RM 184 – 248 (habitat mapping will only extend up to mainstem RM 233 and
will include the Oshetna River.
Middle River - RM 98 - 184
Lower River - RM 0 – 98
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 three 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 (also referred to as macrohabitat):
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
Tributary Habitat:
Tributary mesohabitats within the hydrologic zone of influence will be typed using the
classification system described in Table 9.9-3, above.
4 Main Channel, Off-channel,
and Tributary Mesohabitat
Main Channel
Pool – slow water habitat with minimal turbulence and deeper due to a strong hydraulic control.
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Level Unit Category Definitions
Glide – An area with generally uniform depth and flow with no surface turbulence. Low
gradient; 0-1 percent 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 percent to less than 2
percent. 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 percent 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 percent slope.5
Clearwater Plume – Discharge from a tributary that forms a pronounced area of clearwater, in
contrast to the turbid water of the main channel, along the main channel shoreline. The length,
breadth, and depth of the clearwater plume depend on the relative discharge between the
tributary and the main channel, their relative turbidity, and on mixing conditions along the
shoreline. A clear water plume will be mapped as if it were a separate mesohabitat type.
Off-channel:
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. A backwater will be mapped
as if it were a separate mesohabitat type.
Beaver Complex – Complex ponded water body created by beaver dams. A beaver dam
will be mapped as if it were a separate mesohabitat type.
1For 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.
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2 All habitat within this designation will receive an additional designation within the database of whether water was clear or turbid.
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 (1983a).
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 9.9-6. Example of raw data from mapping displayed in Figure 9.9-17.
Map
ID Level 1 Level 2 Level 3 Level 4 Turbid Unit Length
1 Middle MR-71 Main Channel Glide Yes 2,819
2 Middle MR-7 Main Channel Glide Yes 2,339
3 Middle MR-7 Side Channel Run Yes 2,101
4 Middle MR-7 Main Channel Glide Yes 1,503
5 Middle MR-7 Side Slough Side Slough No 824
6 Middle MR-7 Side Channel Run Yes 978
7 Middle MR-7 Side Channel Glide Yes 1,356
8 Middle MR-7 Main Channel Riffle Yes 954
1 MR-7 represents Middle Reach 7 of the geomorphic reaches
Table 9.9-7. Example data summarizing percent composition of unique habitat types.
Level 1 Level 2 Level 3 Level 4 Segment
Count
Total Length
(feet El.) % of MR-7
Middle MR-71
Main Channel Glide 3 6,661 51.7%
Riffle 1 954 7.4%
Side Channel Glide 1 1,356 10.5%
Run 2 3,079 23.9%
Side Slough Side Slough 1 824 6.4%
Total 8 12,874 100.0%
1 MR-7 represents Middle Reach 7 of the geomorphic reaches
Table 9.9-8. Example data summarizing length and percent composition of general habitat units by main channel and
off-channel habitat.
Main Channel
Mesohabitat
Total Length
(feet El.) Percent Off-Channel Habitat Total Length
(feet El.) Percent
Glide 8,017 66.5% Main Channel 7,615 59.2%
Riffle 954 7.9% Side Channel 4,435 34.4%
Run 3,079 25.6% Side Slough 824 6.4%
Total 12,050 100.0% Total 12,874 100.0%
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Table 9.9-9. Schedule for implementation of the Habitat Characterization and Mapping Study.
Activity
2012 2013 2014 2015
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
Data Collection
Initial Study Report Δ
Follow up Data Collection
Updated Study Report ▲
Legend:
Planned Activity
----- Follow-up activity (as needed)
Δ Initial Study Report
▲ Updated Study Report
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9.9.12. Figures
Figure 9.9-1. Video frame capture of a tributary mid-channel scour pool in a confined channel with boulder and cobble
substrate and no stream wood visible.
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Figure 9.9-2. Locations of 20 tributaries upstream of Devils Canyon selected for habitat mapping and fish distributio n and abundance sampling.
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Figure 9.9-3. Aerial video tributary habitat mapping type-index – Falls.
Figure 9.9-4. Aerial video tributary habitat mapping type-index – Cascade.
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Figure 9.9-5. Aerial video tributary habitat mapping type-index – Chute.
Figure 9.9-6. Aerial video tributary habitat mapping type-index- Rapid.
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Figure 9.9-7. Aerial video tributary habitat mapping type-index – Run.
Figure 9.9-8. Aerial video tributary habitat mapping type-index - Boulder Riffle.
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Figure 9.9-9. Aerial video tributary habitat mapping type-index - Cobble/Gravel Riffle - Split Channel.
Figure 9.9-10. Aerial video tributary habitat mapping type-index – Glide.
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Figure 9.9-11. Aerial video tributary habitat mapping type-index - Mid Channel Scour Pool.
Figure 9.9-12. Aerial video tributary habitat mapping type-index - Lateral Scour Pool - Braided Channel.
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Figure 9.9-13. Aerial video tributary habitat mapping type-index – Alcove – Special Habitat Feature.
Figure 9.9-14. Aerial video tributary habitat mapping type-index – Beaver Complex – Special Habitat Feature.
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Figure 9.9-15. Aerial video tributary habitat mapping type-index - Unclassified - Boulder Riffle?
Figure 9.9-16. Aerial video tributary habitat mapping type-index - Unclassified – Braided Channel?
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Figure 9.9-17. Example of mapping using the tiered habitat classification system in GIS.
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Figure 9.9-18. Aerial video capture of the Lower River mainstem.
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Figure 9.9-19. Lakes located in Upper River inundation zone proposed for habitat mapping.
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Figure 9.9-20. Interdependencies for Characterization and Mapping of Aquatic Habitats.