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Susitna-Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
Title:
Study of fish distribution and abundance in the upper Susitna River, Study
plan Section 9.5 : Final study plan SuWa 200
Author(s) – Personal:
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Alaska Energy Authority
AEA-identified category, if specified:
Final study plan
AEA-identified series, if specified:
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
Published for:
Date or date range of report:
Volume and/or Part numbers:
Study plan Section 9.5
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Document type:
Pagination:
44 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)
Study of Fish Distribution and Abundance in the
Upper Susitna River
Study Plan Section 9.5
Final Study Plan
Alaska Energy Authority
August 2013
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9.5. Study of Fish Distribution and Abundance in the Upper Susitna
River
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 Study of Fish
Distribution and Abundance in the Upper Susitna River, Section 9.5. RSP Section 9.5 focuses on
describing the current fish assemblage including spatial and temporal distribution, and relative
abundance by species and life stages in the Susitna River upstream of the proposed Watana Dam.
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 Susitna River Fish Distribution
and Abundance Implementation Plan (FDA IP) 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 FDA IP 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 9.5 was one of the 13 approved with modifications. In
its April 1 SPD, FERC recommended the following:
Tributary Sampling Lengths
- We recommend that the sampling unit lengths for the seven accessible tributaries and four
tributaries with unknown accessibility that would be subject to the GRTS sampling design, as
specified in section 5.2 of the Implementation Plan, include the entire classified mesohabitat
for those units less than 200 meters, 400 meters, or 800 meters in length (as proposed based
on basin area) or sampling units of these lengths, whichever is smaller, rather than the
proposed 40-meter subsample.
Mainstem Sampling Lengths
- We recommend that sampling unit lengths for all main channel and side channel habitat
units be equal to 20 times the wetted channel width of the habitat unit, the entire length of the
habitat unit, or 500 meters, whichever is less.
- We recommend that sampling unit lengths for all slough macrohabitats encompass the
entire length of the slough, a distance equal to 20 times the wetted channel width of the
slough, or 200 meters, whichever is less. We also recommend that slough sampling be
initiated at the downstream end of the slough.
- We recommend that, to the extent possible based on site-specific field conditions, AEA
sample all main channel and side channel macrohabitat units with boat electrofishing
methods.
- We recommend that AEA’s proposed tributary mouth sampling unit lengths include the
backwater area within the tributary, if present, and extend a distance 200 meters
downstream of the tributary mouth/confluence with the mainstem.
Sample Timing
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- We recommend that the proposed summer sampling events be conducted in mid-July, and
again in either late August or early September.
Catch Per Unit Effort Metrics
- We recommend that calculation of CPUE from electrofishing data be based only on the first
pass, as requested by NMFS and FWS.
- We recommend that minnow traps be soaked for 24 hours and placed within locations most
likely to capture fish (e.g., low-velocity habitat in close proximity to cover).
Outmigrant Trap Locations
- We recommend that AEA install and operate one additional outmigrant trap in the
mainstem Susitna River, downstream of the mouth of Kosina Creek near the proposed dam
site. The actual location should be selected after consultation with the TWG.
Resident Fish Radio Telemetry Tagging
- To the extent possible given the constraints of field sampling conditions, we recommend
that AEA target its fish sampling to meet the following specific objectives: (1) a minimum of
10 tags per species be allocated for tagging adult grayling and rainbow trout of sufficient
size for spawning at tributary mouths during the spring sampling event; (2) a minimum of 10
tags should be allocated for tagging adult Dolly Varden of sufficient size for spawning at
tributary mouths during a late summer or early fall sampling event; (3) a minimum of 10 tags
should be allocated for tagging adult whitefish prior to spawning in early September; and (4)
a minimum of 10 tags should be allocated for tagging burbot in the early fall prior to fall or
winter spawning migrations.
In accordance with the April 1 SPD, AEA has adopted the FERC requested modifications in the
FDA IP and this Final Study Plan. The Susitna River Fish Distribution and Abundance
Implementation Plan has similarly been updated with FERC staff recommendations from the
April 1, 2013 Study Plan Determination and provides further detail.
9.5.1. General Description of the Proposed Study
This study is focused on describing the current fish assemblage including spatial and temporal
distribution, and relative abundance by species and life stage in the Susitna River upstream of the
proposed Watana Dam. Fishery resources in the upper sections of the Susitna River basin
consist of a variety of salmonid and non-salmonid resident fish (Table 9.5-1). With one known
exception (i.e., Chinook salmon), existing information indicates that anadromous fish are
restricted to the mainstem Susitna River and tributaries downstream of Devils Canyon near RM
150 due to their apparent inability to pass several steep rapids. In addition to investigating the
resident salmonid and non-salmonid fishes present in this part of the river, this study will also
investigate the distribution and abundance of any anadromous fish above the proposed Watana
Dam site. Chinook salmon have been observed in relatively low numbers above Devils Canyon
(maximum peak count of 46 adult Chinook salmon during 1984; Thompson et al. 1986).
The physical habitat modeling efforts proposed in the Fish and Aquatics Instream Flow Study
(Section 8.5) require information on the distribution and periodicity of different life stages for
the fish species of interest. Not all life stages of the target fish species may be present
throughout the Upper Susitna River, and seasonal differences may occur in their use of some
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habitats. For example, some fish that use tributary streams during the open-water period may
overwinter in mainstem habitats.
This study is designed to provide baseline biological information regarding periodicity and
habitat suitability for the Instream Flow Modeling Study (see Section 8.5). Results of this study
will include key life history information about fish species in the Upper Susitna River, which
will provide inputs for the Study of Fish Barriers in the Middle and Upper Susitna River and
Susitna Tributaries (Section 9.12) and the Study of Fish Passage Feasibility at Watana Dam
(Section 9.11).
Study Goals and Objectives
The overarching goal of this study is to characterize the current distribution, relative abundance,
run timing, and life history of resident and non-salmon anadromous species (e.g., Dolly Varden,
humpback whitefish, round whitefish, Arctic grayling, northern pike, and Pacific lamprey), and
freshwater rearing life stages of anadromous fish (fry and juveniles) in the Susitna River above
the proposed dam site (RM 184). Specific objectives include the following:
1. Describe the seasonal distribution, relative abundance (as determined by catch per unit
effort [CPUE], fish density, and counts), and fish-habitat associations of resident fishes,
juvenile anadromous salmonids, and the freshwater life stages of non-salmon
anadromous species.
2. Describe seasonal movements of juvenile salmonids and selected fish species such as
rainbow trout, Dolly Varden, humpback whitefish, round whitefish, northern pike, Pacific
lamprey, Arctic grayling and burbot within the hydrologic zone of influence upstream of
the Project.
a. Document the timing of downstream movement and catch using out-migrant
traps.
b. Describe seasonal movements using biotelemetry (passive integrated transponders
[PIT] and radio-tags).
c. Describe juvenile Chinook salmon movements.
3. Characterize the seasonal age class structure, growth, and condition of juvenile
anadromous and resident fish by habitat type.
4. Determine whether Dolly Varden and humpback whitefish residing in the Upper River
exhibit anadromous or resident life histories.
5. Determine baseline metal concentrations in fish tissues for resident fish species in the
mainstem Susitna River (see Section 5.5 Water Quality and Section 5.7, Mercury
Assessment and Potential for Bioaccumulation Study).
6. Document the seasonal distribution, relative abundance, and habitat associations of
invasive species (northern pike).
7. Collect tissue samples to support the Genetic Baseline Study for Selected Fish Species
(Section 9.14).
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9.5.2. Existing Information and Need for Additional Information
Information regarding resident species, non-salmon anadromous species, and the freshwater
rearing life stages of anadromous salmon was collected during studies in connection with Alaska
Power Authority’s (APA’s) proposed Susitna Hydroelectric Project in the 1980s. Existing
information includes the spatial and temporal distribution of fish species and their relative
abundance. The Pre-Application Document (PAD) (AEA 2011a) and Aquatic Resources Data
Gap Analysis (ARDGA; AEA 2011b) summarized this existing information and also identified
data gaps for resident and rearing anadromous fish.
A total of nine anadromous and resident fish species have been documented inhabiting the
Susitna River drainage upstream of Devils Canyon (Table 9.5-1). Chinook salmon use of the
Upper Susitna River was first documented during the 1980s studies; this is the only anadromous
fish documented to pass the rapids at Devils Canyon. Resident species that have been identified
in all three segments of the Susitna River include Arctic grayling, Dolly Varden, humpback
whitefish, round whitefish, burbot, longnose sucker, and sculpin (Schmidt et al. 1985;
Buckwalter 2011). To varying degrees, the relative abundance and distribution of these species
were determined during the early 1980s studies. For most species, the dominant age classes and
sex ratios were also determined, and movements, spawning habitats, and overwintering habitats
were identified for certain species.
One species that has not been documented in the Susitna River, but may occur in the upper
Susitna drainage, is lake trout. Lake trout have been observed in Sally Lake and Deadman Lake
of the upper Susitna watershed (Delaney et al. 1981a) but have not been observed in the
mainstem Susitna or tributary streams. Pacific lamprey have been observed in the Chuit River
(Nemeth et al. 2010), which also drains into Cook Inlet. Northern pike is an introduced species
that has been observed in the Lower and Middle River (Rutz 1999). Although it is considered
unlikely that Pacific lamprey and northern pike are present in the Upper Susitna River, this study
will be helpful for evaluating these species’ distributions.
In the proposed impoundment zone, Arctic grayling are believed to be the most abundant fish
species (Delaney et al. 1981a; Sautner and Stratton 1983) and were documented spawning in
tributary pools. In tributaries, juvenile grayling were found in side channels, side sloughs, and
pool margins and in the mainstem at tributary mouths and clear water sloughs during early
summer. Dolly Varden populations in the Upper Susitna River are apparently small but widely
distributed. Burbot in the Upper Susitna River were documented in mainstem habitats with
backwater-eddies and gravel substrate. The abundance of longnose suckers in the Upper Susitna
River was less than downstream of Devils Canyon. Specific information needs relative to fish
distribution and abundance in the Upper Susitna River that were identified in the ARDGA (AEA
2011b) include the following:
• Population estimates of adult Arctic grayling and Dolly Varden in select tributaries
within the proposed impoundment zone.
• The migration timing of Arctic grayling spawning in the proposed impoundment zone,
the relative abundance and distribution of Dolly Varden, lake trout, and juvenile Chinook
salmon in the impoundment zone.
• Physical habitat characteristics used by round whitefish, longnose sucker, and burbot
within the impoundment zone.
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Little is known about the density and distribution of juvenile salmon in the Susitna River
upstream of Devils Canyon (RM 150) and the proposed dam site at RM 184. All five species of
Pacific salmon were captured in the Lower and Middle Susitna River during the 1980s licensing
studies. Coho, chum, sockeye, and pink salmon have not been observed upstream of the Devils
Canyon rapids. Chinook salmon are the only anadromous species known to occur in the Upper
Susitna River and tributaries although the information on the extent of their distribution is
limited. In 1984, Chinook spawning was documented upstream of Devils Canyon but
downstream of the proposed dam site at Chinook Creek (RM 156.8), and Fog Creek (RM 176.7)
(ADF&G 1985). More recent sampling has documented adults in Fog and Tsusena Creeks (RM
181.3) and upstream of the proposed dam site in Kosina Creek (RM 201). Juvenile Chinook
salmon have been documented recently upstream of Devils Canyon in Fog Creek, and upstream
of the proposed dam site in Kosina Creek, and in the Oshetna River (RM 225) (Buckwalter
2011). Historic data indicate that Susitna River Chinook salmon spawn exclusively in tributary
streams (Thompson et al. 1986;Barrett et al.1983; Barrett 1974, 1985) and that nearly all
Chinook salmon juveniles in this system out-migrate to the ocean as age-1+ fish, and very few
exit the system as fry.
Existing fish and aquatic resource information appears insufficient to address the following
issues that were identified in the PAD (AEA 2011a):
• 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.
• F3: Potential effect of Watana Dam on fish movement.
Site-specific knowledge of the distribution, timing, and abundance of fish likely to occupy the
proposed Watana Reservoir primarily depends on the results of surveys conducted by the Alaska
Department of Fish and Game (ADF&G) during the early 1980s using multiple sampling
methods (AEA 2011a). The existing information can provide a starting point for understanding
the distribution and abundance of anadromous and resident freshwater fishes in the Susitna River
and the functional relationship with the habitat types present. However, any significant
differences in the patterns in abundance and distribution observed during the 1980s compared to
current conditions need to be determined.
In addition to providing baseline information about aquatic resources in the proposed Project
area, aspects of this study are designed to complement and support other fish and aquatic studies.
9.5.3. Study Area
The study area encompasses the mainstem Susitna River from the proposed Watana Dam site
(RM 184) upstream to the Oshetna River confluence (RM 233.4) (Figure 9.5-1). The Upper
Susitna River is delineated by the location of the proposed Watana Dam because effects of the
Project are anticipated to be different upstream and downstream of the proposed dam. The
mainstem Susitna River and its tributaries upstream of the proposed dam will be within the
impoundment zone and subject to Project operations that affect daily, seasonal, and annual
changes in pool elevation plus the effects of initial reservoir filling. Tributary surveys upstream
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of the proposed Watana Dam are further delineated by the 3,000-foot elevation contour, which is
based on the known extent of juvenile Chinook salmon distribution. Some study components,
such as resident fish life-history studies and juvenile Chinook salmon distribution sampling, may
extend beyond the core area.
9.5.4. Study Methods
This study will employ a variety of field methods to build upon the existing information related
to the distribution and abundance of fish species in the Upper Susitna River. The following
sections provide brief descriptions of study site selection, sampling frequency, the approach, and
suite of methods that will be used to accomplish each objective of this study. This study was
initiated in 2012 and will continue over the next two years to survey as much habitat as possible.
Refined and detailed study methods are presented in the Fish Distribution and Abundance
Implementation Plan (FDA IP). The refinements in the IP are intended to support the methods
described below and would in fact supersede any methods detail provided below.
Fish Distribution and Abundance Sampling Plan
Some details of the sampling scheme have been provided for planning purposes; however, a final
sampling scheme has been developed as part of the detailed FDA IP, for Sections 9.5 and 9.6.
The Susitna River Fish Distribution and Abundance Implementation Plan has similarly been
updated with FERC staff recommendations from the April 1, 2013 Study Plan Determination.
FDA IP development includes (1) a summary of relevant fisheries and an overview of the life
history needs for fish species known to occur in the Susitna River to guide site selection and
sampling protocols, (2) a review of the preliminary results of habitat characterization and
mapping efforts (Section 9.9), (3) a description of site selection and sampling protocols, (4)
development of field data collection forms, (5) development of database templates that comply
with 2012 AEA QA/QC procedures, and (6) FERC’s requested modifications included in the
April 1 SPD. The FDA IP includes the level of detail sufficient to instruct field crews in data
collection efforts. In addition, the plan includes protocols and a guide to the decision-making
process in the form of a chart or decision tree that will be used in the field, specific sampling
locations, details about the choice and use of sampling techniques and apparatuses, and a list of
field equipment needed. The implementation plan addresses how sampling events will be
randomized to evaluate precision by habitat and gear type. The implementation plan helps
ensure that fish collection efforts occur in a consistent and repeatable fashion across field crews
and river segments. Proposed sampling methods by objective are presented below and in Table
9.5-2. Brief descriptions of each sampling technique are provided in Section 9.5.4.4.
9.5.4.1. Study Site Selection
The Upper Susitna River will represent an area where the mainstem river will be inundated and
tributaries will be partially altered. As a result, the sampling effort will be tailored to collect
necessary information to document fish assemblages, distribution, and abundance generally
within the mainstem river and more intensely within the tributary habitat inundated up to an
elevation of 3,000 feet.
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A nested stratified sampling scheme will be used to select study sites to cover the range of
habitat type. The habitat classification hierarchy, as described in Section 9.9.5.4.1 of the Habitat
Classification Study, will be composed of five levels representing (1) major hydraulic segment;
(2) geomorphic reach; (3) mainstem habitat type; (4) main channel mesohabitat; and (5) edge
habitat (Table 9.9-4, Nested and tiered habitat mapping units and categories).
Level 1 will generally identify the Lower River (RM 28-98), Middle River (RM 98-184), and
Upper River (RM 184-233) from each other. The mainstem Susitna River and its tributaries
upstream of the proposed dam will be within the impoundment zone and subject to Project
operations that affect daily, seasonal, and annual changes in pool elevation plus the effects of
initial reservoir filling. In contrast, the mainstem downstream of the Project will be subject to
the effects of flow modification from Project operations, which will diminish below the Three
Rivers Confluence.
Level 2 will identify unique reaches established from the channel’s geomorphic characteristics
(established from the Geomorphology Study [Section 6.0]). The Geomorphic Study Team will
delineate the Lower, Middle, and Upper River segments into large-scale geomorphic river
reaches with relatively homogeneous landform characteristics, including at generally decreasing
scales: geology, hydrology (inflow from major tributaries), slope, channel planform, braiding or
sinuosity index (where relevant), entrenchment ratio, channel width, and substrate size.
Stratification of the river into relatively homogeneous segments will facilitate relatively unbiased
extrapolation of sampled site data within the individual segments because sources of variability
associated with large-scale features will be reduced.
Level 3 classifies the mainstem habitat into main channel, off-channel, and tributary habitat
using an approach similar to the 1980s historical habitat mapping definitions (ADF&G 1983).
The main channel includes five mainstem habitat types, whereas the off-channel habitat will be
categorized into four types (Table 9.9-4). The 1980s classification of riverine habitats of the
Susitna River included six major mainstem habitat categories consisting of main channel, side
channel, side slough, upland slough, tributaries, and tributary mouths (ADF&G 1984). These
mainstem habitat categories will be maintained in the 2012 classification system, but they are
further categorized into main channel, off-channel, and tributary. These will be expanded to
include five types of main channel (main channel, split main channel, multiple split main
channel, side channel, and tributary), and four types of off-channel (slide slough, upland slough,
backwater, and beaver complex) (Table 9.9-4).
Level 4 will further delineate Level 3 main channel and tributary habitats into mesohabitat types
(pool, riffle, glide, and cascade) (Table 9.9-4). However, off-channel habitat will remain at
Level 3 (side slough, upland slough, backwater, and beaver complex).
The presence, 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.
Thus, fish sampling in the Upper River will necessarily vary with habitat and will not be
stratified equally among geomorphic reaches (Level 2). Stratification will occur across
geomorphic reaches as much as possible but will be dictated by the distribution of habitat types
present within each reach. For example, based on preliminary geomorphic reach delineation, we
would expect to find multiple split main channel habitats in reaches UR1 and UR6 but not in the
more confined and incised reaches UR2 through UR5. In order to ensure that representative
habitats are sampled along the Upper River, six replicate sampling sites will be selected within
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each Level 3 habitat type for fish distribution sampling (27 sites). In addition, one replicate of
each Level 4 main channel habitat nested within each Level 3 habitat will be selected for relative
abundance sampling (Figure 9.5-2).
Habitat mapping in the tributaries will be completed differently than in the mainstem river due to
the lack of complete aerial imagery, relatively smaller channel size, steep gradient, and limited
on the ground accessibility for direct mapping. Because of this general inaccessibility, very
rugged terrain, and mostly non-wadeable stream channels, near census mapping (100 percent
coverage) is challenging and in some cases unsafe or impossible. For these reasons, only
tributaries mapped by the Characterization and Mapping of Aquatic Habitats Study (Section 9.9;
Table 9.9-2) will be selected for fish distribution and abundance sampling. Up to 18 tributary
streams will be targeted for sampling during 2013 and 2014. All tributaries in which Chinook
salmon juveniles or adults were observed within or at the mouth of a tributary during 2012, or
during previous surveys by Buckwalter (2011) (i.e., Fog Creek, Kosina Creek, Tsusena Creek,
Oshetna River), will be sampled. Of the remaining tributaries that are suitable for sampling
(Table 9.9-2), efforts will be directed towards streams that are not already identified as
supporting anadromous fishes in the ADF&G Anadromous Waters Catalog (AWC). Selected
study sites will comprise a target of 25 percent of the mapped habitats in each tributary; this
target will vary with access considerations. All known Chinook salmon-bearing tributaries will
be sampled up to the 3,000-foot elevation contour, which is based on the known extent of
Chinook salmon distribution.
Site selection includes first completing the geomorphic reach delineation and habitat mapping
tasks. 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.
9.5.4.2. Sampling Frequency
Sampling frequency will vary among sites based on specific objectives. Generally, fish
distribution and abundance sampling will occur seasonally during the ice-free period in mid-July,
and again in either late August or early September. Additional effort, up to bi-weekly sampling,
will be required immediately following ice-out in an attempt to capture critical juvenile Chinook
salmon out-migration from natal tributaries to rearing habitats.
9.5.4.3. Fish Sampling Approach
The initial task of this study will consist of a focused literature review to guide selection of
appropriate sampling methods by species and habitat type, sampling event timing, and sampling
event frequency. Anticipated products from the literature review include the following:
• A synthesis of existing information on life history, spatial and temporal distribution, and
relative abundance by species and life stage.
• A review of sampling strategies, methods, and procedures used in the 1980s fish studies.
• Preparation of periodicity charts for each species within the study area (timing of adult
migration, holding, and spawning; timing of incubation, rearing, and out-migration).
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• A summary of mainstem Susitna River habitat utilization for each species, by riverine
habitat type (main channel, side channel, side slough, upland slough, tributary mouth,
tributary).
• A summary of existing age, size, and genetics information.
• A summary of distribution of invasive species, such as northern pike.
Knowledge of behavior and life history of the target species is essential for effective survey
design. Selected fish sampling techniques will vary based on habitat characteristics, season, and
species/ life history of interest. Timing of surveys depends on the objectives of the study and the
behavior of the target fish species. Since life stage-specific information is desirable, timing of
the survey must match the use of the surveyed habitat by that life stage.
9.5.4.3.1. Objective 1: Fish Distribution, Relative Abundance, and Habitat Associations
Two general approaches to fish sampling will be used. The first is focused on gathering data on
general fish distribution (presence/absence). This sampling involves a single pass with
appropriate gear types. To the extent possible, the selected transects will be standardized and the
methods will be repeated during each sampling event at a specific site to evaluate temporal
changes in fish distribution. The second sampling approach is to gather data on relative
abundance as determined by CPUE and density; complementary data on fish size, age, and
condition factor will also be collected. The selected transects and fish capture methods (i.e.,
number of passes, amount of soak time) will be standardized such that they are repeatable on
subsequent sampling occasions. This approach will also emphasize the identification of foraging
and spawning habitats.
Long daylight hours during the summer may reduce the difference between day and night
sampling effectiveness. The periods of twilight are important sampling periods. Sampling
schedules will encompass daylight, twilight, and evening periods.
Task A: Fish Distribution Surveys
Fish distribution surveys will include seasonal sampling events during the ice-free seasons.
Methods will be selected based on species, life stage, and water conditions. Snorkeling and
electrofishing are preferred methods for juvenile fishes in clear water areas where velocities are
safe for moving about in the creek. The use of minnow traps, beach seines, set nets, and fyke
nets will be employed as alternatives in deeper waters and habitats with limited access, low
visibility, and/or high velocities. For larger/adult fishes, gillnets, seines, trotlines, hoop traps,
and angling will be used.
Survey methods will likely vary for the different study areas in the Upper Susitna River.
Whereas snorkeling, minnow trapping, backpack electrofishing, and beach seines may be
applicable to sloughs and other slow-moving waters, it is anticipated that gillnetting, boat
electrofishing, hoop traps, and trot lines may be more applicable to the mainstem. The decisions
about what methods to apply will be made by field crews after initial site selection in
coordination with Fish Distribution and Abundance Study Lead and the Fish Program Lead and
in accordance with state and federal fish sampling permit requirements.
Task B: Relative Abundance
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Relative abundance surveys will include seasonal multi-pass sampling events during the ice-free
seasons. As mentioned above, methods will be selected based on species, life stage, and water
conditions. All methods will be conducted consistent with generating estimates of CPUE that are
meaningful and facilitate comparison of counts or densities of fish over space and time. This
includes calibration and quality control of methods and documentation of conditions that affect
sampling efficiency—such as visibility, water temperature, and conductivity—to ensure that a
consistent level of effort is applied over the sampling unit.
Task C: Fish-Habitat Associations
In conjunction with Tasks 1 and 2, data will be collected for fish distribution and abundance by
habitat type. This task includes an analysis of fish presence, distribution, and density by
mesohabitat type by season. The information on fish habitat use will help identify species and
life stages potentially vulnerable to Project effects.
9.5.4.3.2. Objective 2: Seasonal Movements
Task A: Document the timing of downstream movement and catch for all fish species using
out-migrant traps.
Understanding the timing of migration from natal tributaries to the mainstem Susitna River and
from the Upper Susitna River to the proposed dam site (RM 184) is important for assessing the
potential effects of the proposed Project. Out-migrant traps (rotary screw traps and inclined
plane traps) are useful for determining the timing of downstream migrating juvenile salmonids
and resident fish.
A maximum of two out-migrant traps will be deployed. In addition to collection of data on
migratory timing, size at migration, and growth, out-migrant traps will also serve as a platform
for tagging juvenile fish (Objective 2, Task C), recapturing previously tagged fish, collecting fish
for stomach contents analysis in support of the River Productivity Study (Section 9.8), and
collecting tissue samples (Objective 7) to support the Genetic Baseline Study for Selected Fish
Species (Section 9.14).
Task B: Describe seasonal movements using biotelemetry.
Biotelemetry techniques will include radio telemetry and PIT technology. PIT tags will be
surgically implanted in small fish >60 mm to monitor movement and growth; radio transmitters
will be surgically implanted in adult fish of sufficient body size of selected species distributed
temporally and longitudinally in the Upper River.
PIT tag antenna arrays with automated data logging will be used at selected side channels and
tributary mouths to detect movement of tagged fish into or out of the site. Recaptured fish will
provide information on the distance and time travelled since the fish was last handled and
changes in length (growth).
Radio-tagged fish will be tracked with monthly aerial surveys and by boat, in conjunction with
the Salmon Escapement Study (Section 9.7) to describe seasonal movements of selected fish
species with emphasis on identifying spawning and overwintering habitats within the hydrologic
zone of influence upstream of the Project.
Up to 30 radio transmitters will be implanted in selected species including Arctic grayling, Dolly
Varden, burbot, round whitefish, humpback whitefish, and northern pike if present (Objective 6).
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A PIT tag will be implanted into up to 1,000 fish of these species per PIT tag array that are in
close proximity to an array and approximately 60 mm and larger.
Task C: Describe juvenile Chinook salmon movements.
Juvenile Chinook salmon movement within the Upper River will be described using out-migrant
traps and biotelemetry methods outlined in Objective 2, Tasks A and B. This study proposes to
implant PIT tags in all juvenile Chinook salmon >60 mm in length to document seasonal
movement within the Upper River using antenna arrays placed in tributary mouths, sloughs, and
side channels and on out-migrant traps to recapture fish. Because of the low number of adult
Chinook salmon tracked to the Upper River with radio-tags in 2012, all juvenile Chinook salmon
of taggable size need to be tagged to obtain a sufficient sample size. Out-migrant traps will be
used to document juvenile Chinook salmon migratory timing and size at migration from natal
tributaries to the Upper River and out-migration from the Upper River to below the proposed
dam site (RM 184). The data on juvenile Chinook salmon movement patterns and timing will
support the Study of Fish Passage Feasibility at Watana Dam (Section 9.11).
9.5.4.3.3. Objective 3: Characterize the seasonal age class structure, growth, and
condition of juvenile anadromous and resident fish by habitat type.
In conjunction with Objectives 1 and 2, all captured fish will be identified to species, measured
to the nearest millimeter (mm) fork length, and weighed to the nearest gram. Length frequency
data by species will be compared to length-at-age data in the literature to infer age classes.
Recaptured PIT-tagged fish (Objective 2, Task B) will provide information on changes in length
and weight (growth). Recorded parameters in each habitat unit will include number of fish by
species and life stage, fork length, global positioning system (GPS) location of sampling area,
time of sampling, weather conditions, water temperature, water transparency, behavior, and
location and distribution of observations.
9.5.4.3.4. Objective 4: Determine whether Dolly Varden and humpback whitefish residing in
the Upper River exhibit anadromous or resident life histories.
Otoliths will be collected from Dolly Varden and humpback whitefish greater than 200 mm (7.8
inches) in length to test for marine-derived elements indicative of an anadromous life history
pattern. It is assumed that larger fish are more likely to have exhibited anadromy and therefore
otolith collection is proposed only from fish greater than 200 mm in length. A target of 30 fish
of each species during 2013 and 2014 will be collected (60 fish of each species total).
9.5.4.3.5. Objective 5: Determine baseline metal and mercury concentrations in fish tissues
for resident fish species in the mainstem Susitna River.
Tissue or whole fish samples will also be collected in the mainstem Susitna River for assessment
of metals (see Section 5.5.4.7, Baseline Metal Levels in Fish Tissue) and mercury (see Section
5.7.4.2.6, Mercury Assessment and Potential for Bioaccumulation Study) concentrations. Target
fish species for baseline metals testing include: Dolly Varden, Arctic grayling, whitefish species,
long nose sucker, lake trout, burbot, and resident rainbow trout. Target fish species for mercury
sampling include: Dolly Varden, arctic grayling, stickleback, long nose sucker, whitefish species,
lake trout, burbot, and resident rainbow trout.
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9.5.4.3.6. Objective 6: Document the seasonal distribution, relative abundance, and habitat
associations of invasive species (northern pike).
Northern pike were likely established in the Susitna River drainage in the 1950s through a series
of illegal introductions (Rutz 1999). The proliferation of this predatory species is of concern
owing to its effect on salmonids and other species such as stickleback. At this time, northern
pike have not been documented in the Upper River, so no targeted collection effort for pike will
be made. However, the presence/absence and habitat associations of northern pike and other
invasive fish species will be documented as a component of all fish capture and observation
sampling events associated with Objectives 1 and 2.
9.5.4.3.7. Objective 7: Collect tissue samples from juvenile salmon and all resident and non-
salmon anadromous fish.
In support of the Genetic Baseline Study for Selected Fish Species (Section 9.14), fish tissues
will be collected opportunistically in conjunction with all fish capture events. The target number
of samples, species of interest, and protocols are outlined in Section 9.14. Tissue samples
include an axillary process from all adult salmon, caudal fin clips from fish >60 mm, and whole
fish <60 mm.
9.5.4.4. Fish Sampling Techniques
A combination of gillnetting, electrofishing, angling, trot lines, minnow traps, snorkeling, out-
migrant trapping, beach seines, fyke nets, hoop nets, dual-frequency identification sonar
(DIDSON), and underwater video camera techniques will be used to sample or observe fish in
the Upper River, and moving in and out of selected sloughs and tributaries draining to the
Susitna River. Several assumptions are associated with the use of the proposed methods:
• If it can be conducted safely, snorkeling, electrofishing, and gillnetting will require
nighttime sampling in clear-water areas to increase the efficacy of fish capture or
observation.
• Gillnetting is likely the most effective means of capturing fish in open-water areas of the
main Susitna River channel.
• All fish sampling and handling techniques described within this study will be conducted
under state and federal biological collection permits. Limitations on the use of some
methods during particular time periods or locations may affect the ability to make
statistical comparisons among spatial and temporal strata.
• Fish sampling techniques provide imperfect estimates of habitat use and relative fish
abundance. Use and comparison of multiple sampling methods provides the opportunity
to identify potential biases, highlight strengths and weaknesses of each method, and
ultimately improve estimates of fish distribution and relative abundance.
• Sampling in the reservoir inundation zone will be scaled based on elevation and Chinook
salmon distribution. More intensive surveys will be conducted in tributaries to be
inundated up to an elevation of 2,200 feet. Sampling from 2,200 feet to 3,000 feet
elevation will be focused on Chinook salmon. If Chinook salmon are located, sub-
sampling will continue upstream to the upper extent of suitable Chinook salmon habitat.
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9.5.4.4.1. Gillnet Sampling
Variable mesh gillnets (7.5-foot-deep panels with 1-inch to 2.5-inch stretched mesh) will be
deployed. In open water and at sites with high water velocity, gillnets will be deployed as drift
nets, while in slow water sloughs, gillnets will be deployed as set (fixed) nets. The location of
each gillnet set will be mapped using hand-held GPS units and marked on high-resolution aerial
photographs. The length, number of panels, and mesh of the gillnets will be consistent with nets
used by ADF&G to sample the river in the 1980s (ADF&G 1982, 1983, 1984). To reduce
variability among sites, soak times for drift gillnets will be standardized; all nets will be retrieved
a maximum of 30 minutes after the set is completed. The following formula will be used to
determine drifting time:
T = ([(set time + retrieval time)/2] + soak time)
9.5.4.4.2. Electrofishing
Boat-mounted, barge, or backpack electrofishing surveys will be conducted using standardized
transects. Boat-mounted electrofishing is the most effective means of capturing fish in shallow
areas (<10 feet deep) near stream banks and within larger side channels. Barge-mounted
electrofishing is effective in areas that are wadeable, but have relatively large areas to cover and
are too shallow or otherwise inaccessible to a boat-mounted system. Backpack electrofishing is
effective in wadeable areas that are relatively narrow. The effectiveness of barge and backpack
electrofishing systems can be enhanced through the use of block nets. Electrofishing methods
will follow NMFS (2000) Guidelines for Electrofishing Waters Containing Salmonids Listed
Under the Endangered Species Act. CPUE will be calculated based only on the first pass.
Sites will be selected carefully, because electrofishing may have limited success in swift, turbid,
or low conductivity waters. Suspended materials in turbid water can affect conductivity, which
may result in harmful effects on fish, especially larger fish due to a larger body surface in contact
with the electrical field. Sudden changes in turbidity can create zones of higher amperage, which
can be fatal to young-of-year fish as well as larger fish. Electrofishing in swift current is
problematic, with fish being swept away before they can be netted. Similarly, turbidity increases
losses from samples. Electrofishing will be discontinued immediately in a sampling reach if
large salmonids or resident fish are encountered.
Selection of the appropriate electrofishing system will be made as part of site selection, which
will include a site reconnaissance. In all cases, the electrofishing unit will be operated and
configured with settings consistent with guidelines established by Smith Root. The location of
each electrofishing transect will be mapped using hand-held GPS units and marked on high-
resolution aerial photographs. To the extent possible, the selected electrofishing system and
transects will be standardized and the methods will be repeated during each sampling period at a
specific site to evaluate temporal changes in fish distribution. Habitat measurements will be
collected at each site using the characterization methods identified in Section 9.9. Any changes
will be noted between sample periods. The electrofishing start and stop times and water
conductivity will be recorded. Where safety concerns can be adequately addressed,
electrofishing will also be conducted after sunset in clear water areas; otherwise, electrofishing
surveys will be conducted during daylight hours.
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9.5.4.4.3. Angling
Angling with hook and line can also be an effective way to collect fish samples depending on the
target species. During field trips organized for other sampling methods, hook-and-line angling
will be conducted on an opportunistic basis using artificial lures or flies with single barbless
hooks. The primary objective of hook-and-line sampling will be to capture subject fish for
tagging (e.g., northern pike) and to determine presence/absence; a secondary objective will be to
evaluate seasonal fish distribution. Because it is labor and time intensive, angling is best used as
an alternative method if other more effective means of sampling are not available. Angling can
also be used in conjunction with other methods, particularly if information is required on the
presence and size of adult fish.
9.5.4.4.4. Trot Lines
Trot lines can be an effective method for capturing burbot, rainbow trout, Dolly Varden,
grayling, and whitefish. Trotlines are typically a long line with a multitude of baited hooks and
are typically anchored at both ends and set in the water for a period of time. Trot line sampling
was one of the more frequently used methods during the 1980s and was the primary method for
capturing burbot; however, trot lines are generally lethal. Trot lines will consist of 14 to 21 feet
of seine twine with six leaders and hooks lowered to the river bottom. Trot lines will be checked
and rebaited after 24 hours and pulled after 48 hours. Hooks will be baited with salmon eggs,
herring, or whitefish. Salmon eggs are usually effective for salmonids, whereas herring or
whitefish are effective for burbot. Trot line construction and deployment will follow the
techniques used during the 1980s studies as described by ADF&G (1982). As per ADF&G Fish
Resource Permit stipulations, all salmon eggs used as bait will be commercially sterilized or
disinfected with a 10-minute soak in a 1/100 Betadyne solution prior to use.
9.5.4.4.5. Minnow Traps
Minnow traps baited with salmon eggs are an effective method for passive capture of juvenile
salmonids in pools and slow-moving water (Bryant 2000). In reaches where both electrofishing
and snorkeling would be ineffective due to stream conditions such as deep, fast water, baited
minnow traps will be used as an alternative to determine fish presence. During the 1980s,
minnow traps were the primary method used for capturing sculpin, lamprey, and threespine
stickleback. Minnow traps also captured rainbow trout and Arctic grayling. Minnow traps will
be baited with salmon roe, placed within locations most likely to capture fish (e.g., low-velocity
habitat in close proximity to cover) and will be allowed to soak for 24 hours. Minnow traps will
be deployed at densities of 1-2 traps for every 10-meters of habitat unit length, depending on
width and habitat complexity. All fish captured will be identified to species, measured, and
released alive near the point of capture. As per ADF&G Fish Resource Permit stipulations, all
salmon eggs used as bait will be commercially sterilized or disinfected with a 10-minute soak in
a 1/100 Betadyne solution prior to use.
9.5.4.4.6. Snorkel Surveys
This survey technique is most commonly used for juvenile salmonid populations, but can also be
used to assess other species groups. Generally, snorkeling works well for detecting presence or
absence of most species. Limits occur when water is turbid or deep due to the inability to see the
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fish, or the water is too swift to safely survey (Dolloff et al. 1993, 1996). To get relative
abundance estimates, a closed population is needed within a single habitat unit, and block nets
will be used to prevent fish from leaving the unit (Hillman et al. 1992).
In stream channels with a width of less than 4 m, the survey will be conducted by a single
snorkeler viewing and counting fish on both sides of the channel, alternating from left to right
counts. In stream channels with a width greater than 4 m, the surveys will be conducted by two
snorkelers working side by side and moving upstream in tandem, with each individual counting
fish on one side of the channel. The counts from all snorkelers are then summed for the total
count for the reach sampled. This expansion estimate assumes that counts are accurate and that
snorkelers are not counting the same fish twice (Thurow 1994). Data will be recorded following
completion of the survey. Survey reaches will be snorkeled starting at the downstream end and
working upstream.
Snorkel surveys will also be used in combination with other techniques to estimate relative
abundance. This use of snorkel surveys provides a calibration factor for the counting efficiency
of snorkel surveys compared to other methods such as electrofishing and seining (Dolloff et al.
1996).
For most of the snorkel surveys in this study, two experienced biologists will snorkel along
standardized transects in clear water areas during both day and night during each field survey
effort. Snorkelers will visually identify and record the number of observed fish by size and
species. The location of each snorkel survey transect will be mapped using hand-held GPS units
and marked on high-resolution aerial photographs.
9.5.4.4.7. Fyke/Hoop Nets
Fyke or hoop nets will be deployed to collect fish in sloughs and side channels with moderate
water velocity (< 3 feet per second). After a satisfactory location has been identified at each site,
the same location will be used during each subsequent collection period. The nets will be
operated continuously for up to two days. Each fyke net will be configured with two wings to
guide the majority of water and fish to the net mouth. The fyke nets will have 1/8-inch mesh, 1-
foot diameter hoops, and up to 4 hoops. Where possible, the guide nets will be configured to
maintain a narrow open channel along one bank. Where the channel size or configuration does
not allow an open channel to be maintained, the area below the fyke net will be checked
regularly to assess whether fish are blocked and cannot pass upstream. A live car will be located
at the downstream end of the fyke net throat to hold captured fish until they can be processed.
The fyke net wings and live car will be checked daily to clear debris and to ensure that captured
fish do not become injured. The location of the fyke net sets will be mapped using a hand-held
GPS unit and marked on high-resolution aerial photographs.
9.5.4.4.8. Hoop Traps
Commercially available hoop traps have been used successfully by ADF&G on the Tanana River
as a non-lethal method to capture burbot for tagging studies (Evenson 1993; Stuby and Evenson
1998). Two sizes of traps have been used. Small and large hoop traps are 3.05 meters (m) and
3.66 m long, respectively. The small hoop trap has seven 6.35-mm steel hoops with diameters
tapered from 0.61 m at the entrance to 0.46 m at the cod end. The large trap has inside diameters
tapering from 91 to 69 centimeters (cm) with throat diameters of 36 cm. Each trap has a double
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throat that narrows to an opening 10 cm in diameter. All netting is knotted nylon woven into 25-
mm bar mesh. Each trap is kept stretched open with two sections of PVC pipe spreader bars
attached by snap clips to the end hoops. Bernard et al. (1991) provides an account of the efficacy
of the small and large traps.
Hoop traps will be deployed in mainstem areas of lower velocity to capture burbot from late
August through early October for radio-tagging (Objectives 1 and 2). Soak times will generally
be overnight, but not more than 12 hours (M. Evenson pers comm 2012). All burbot captured
will be measured and released. Up to 10 radio tags will be surgically implanted in burbot
spatially distributed throughout the Upper Susitna River.
9.5.4.4.9. Beach Seine
Beach seines are an effective method to capture fish in a wide variety of habitats and are most
effective in shallow water areas free of large woody debris and snags such as boulders. Seining
allows the sampling of relatively large areas in short periods of time as well as the capture and
release of fish without significant stress or harm. Repetitive seining over time with standardized
net sizes and standardized deployment in relatively similar habitat can be an effective way to
quantify the relative abundance of certain species over time and space, especially for small
juvenile migrating salmon (Hayes et al. 1996). Beach seines will be 5 feet in depth and 40 feet
in length, 1/4-inch mesh (net body) with a 1/8-inch net bag; however, the actual length of seine
used will depend on the site conditions. Low water conditions may be sampled using a shorter
and shallower beach seine; as long as the area sampled is noted and the net is deep enough to fill
the water column, then comparisons can be made. The location fished will be mapped using
hand-held GPS units and marked on high-resolution aerial photographs. The area swept will be
noted. Repetitive seining over time with standardized nets and soak times in relatively similar
habitats can be an effective way to quantify the relative abundance of certain species over time
and space, especially for small juvenile migrating salmon. To the extent possible, the same area
will be fished during each sampling event; net sizes and soak times will be standardized.
9.5.4.4.10. Out-Migrant Trap
Rotary screw traps are useful for determining the timing of emigration by downstream migrating
juvenile salmonids and resident fish (Objective 2). Out-migrant traps will be installed in a
maximum of three sites: one site located near the proposed Watana Dam, one site near a tributary
mouth, and one site in the mainstem Susitna River, downstream of the mouth of Kosina Creek
near the proposed dam site. The location will occur with input from the Fish and Aquatic TWG
and will be based on the physical conditions at the selected sites and logistics for deploying,
retrieving, and maintaining the traps. Flow conditions permitting, traps will be fished on a cycle
of 48 hours on, 72 hours off throughout the ice-free period. Each trap will be checked at least
twice per day.
9.5.4.4.11. Fish Handling
Field crews will record the date, start and stop times, and level of effort for all sampling events,
as well as water temperature and dissolved oxygen at sampling locations. All captured fish will
be identified to species. Up to 100 individuals per species per life stage per season will be
measured to the nearest mm fork length, and in Focus Areas up to 30 fish per species per site will
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be measured on a monthly basis. Sampling supplies will be prepared before sampling begins.
For example, the date, location, habitat type, and gear type recorded in log book, beginning fish
number in proper sequence, daily sample objective by gear type, and an adequate live box and
clean area should be available. To increase efficiency, fish should be sampled in order in groups
of 10, and the sample routine followed in a stepwise manner: (1) identify species and life stage,
(2) measure lengths, (3) remove tissue samples for genetic analysis, and (4) cut all dead fish for
accurate sex identification. Care will be taken to collect all data with a consistent routine and to
record data neatly and legibly.
For methods in which fish are observed, but not captured (i.e., snorkeling, DIDSON, and
underwater video), an attempt will be made to identify all fish to species. For snorkeling, fork
length of fish observed will be estimated within 40-mm bin sizes. If present, observations of
poor fish condition, lesions, external tumors, or other abnormalities will be noted. When more
than 30 fish of a similar size class and species are collected at one time, the total number will be
recorded and a subset of the sample will be measured to describe size classes for each species.
All juvenile salmon, rainbow trout, Arctic grayling, Dolly Varden, burbot, and whitefish greater
than 60 mm in length will be scanned for PIT tags using a portable tag reader. A PIT tag will be
implanted into a sub-sample of fish of these species that do not have tags and are approximately
60 mm and larger. Because Chinook salmon are of particular interest and in low abundance, all
captured juvenile Chinook salmon of taggable size will receive tags. For selected species, up to
1,000 fish per species per PIT tag array will be tagged based on proximity to PIT arrays. Target
species are Dolly Varden, humpback whitefish, round whitefish, northern pike, Arctic grayling,
and burbot. Radio transmitters will be surgically implanted in up to 30 adult fish of sufficient
body size of each species and distributed temporally and longitudinally in the Upper River.
In support of the bioenergetics modeling (Objective 5, Section 9.8.4.5.1), fish species targeted
for dietary analysis will include juvenile Chinook and coho salmon, juvenile and adult rainbow
trout. Of these species Chinook salmon and rainbow trout may be encountered in the Upper
River. A total of five fish per species/age class per sampling site collection will be sampled for
fish stomach contents, using non-lethal methods (described in Section 9.8.4.7). All fish will
have fork length and weight recorded with the stomach sample. In addition, scales will be
collected from the preferred area of the fish, below and posterior to the dorsal fin, for age and
growth analysis. At two selected sample collection locations (one each in Upper and Middle
River), punch samples of muscle tissue will be obtained from each fish for use in the stable
isotope analysis (Section 9.8.4.5.2).
Otoliths will be collected from Dolly Varden and humpback whitefish greater than 200 mm (7.8
inches) in length to test for marine-derived elements indicative of an anadromous life history
pattern (Objective 4). It is assumed that larger fish are more likely to have exhibited anadromy
and therefore it is proposed to collect otoliths only from fish greater than 200 mm. A target of 30
fish of each species during 2013 and 2014 will be collected (60 fish of each species total).
Tissue, fillets, and/or liver (burbot only) samples will also be collected in the mainstem Susitna
River for assessment of metals concentrations (Objective 5) (see Section 5.5.4.7 Water Quality
and Section 5.7.4.2.6, Mercury Assessment and Potential for Bioaccumulation Study). Target
fish species in the vicinity of the Watana Reservoir will be Dolly Varden, Arctic grayling,
stickleback, whitefish species, burbot, longnose sucker, and resident rainbow trout. If possible,
fillets will be sampled from seven adult individuals from each species. Larger, older fish tend to
have higher mercury concentrations; these fish will therefore be targeted with a desired sample
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size of seven per species. Body size targeted for collection will represent the non-anadromous
phase of each species’ life cycle. For stickleback, whole fish samples will need to be used.
Collection times for fish samples will occur in late August and early September.
Tissue samples will be collected opportunistically in conjunction with all fish capture methods
from selected resident and non-salmon fish to support the Genetic Baseline Study (Objective 7;
Section 9.14). Tissue samples will include an axillary process from all adult salmon, caudal fin
clips from fish >60 mm, and whole fish <60 mm. The target number of samples, species of
interest, and protocols are outlined in Section 9.14.
9.5.4.4.12. Remote Fish Telemetry
Remote telemetry techniques will include radio telemetry and PIT tags. Both of these methods
are intended to provide detailed information from relatively few individual fish. PIT tags will be
surgically implanted in small fish >60 mm; radio transmitters will be surgically implanted in
adult fish of sufficient body size of selected species distributed temporally and longitudinally in
the Upper River. The target species to radio-tag include Dolly Varden, humpback whitefish,
round whitefish, northern pike, Arctic grayling, rainbow trout, lake trout, longnose sucker, and
burbot. Radio-tracking provides information on fine and large spatial scales related to location,
speed of movement, and habitat utilization by surveying large areas and relocating tagged
individuals during aerial, boat, and foot surveys. PIT tags can be used to document relatively
localized movements of fish as well as growth information from tagged individuals across
seasons and years. However, the “re-sighting” of PIT-tagged fish is limited to the sites where
antenna arrays are placed. To determine movement in and out of side sloughs or tributaries
requires that tagged fish pass within several feet of an antenna array, thereby limiting its use to
sufficiently small water bodies. To characterize growth rates, fish must be recaptured, checked
for a tag, and measured.
Radio Telemetry
The primary function of the telemetry component is to track tagged fish spatially and temporally
with a combination of fixed station receivers and mobile tracking. Time/date stamped, coded
radio signals from tags implanted in fish will be recorded by fixed station or mobile positioning.
All telemetry gear (tags and receivers) across both studies will be provided by ATS, Inc.
(Advanced Telemetry Systems, www.atstrack.com).
The types of behavior to be characterized include the following:
• Arrival and departure timing at specific locations/positions
• Direction of travel
• Residence time at specific locations/positions
• Travel time between locations/positions
• Identification of migratory, holding, and spawning time and locations/positions
• Movement patterns in and between habitats in relation to water conditions (e.g.,
discharge, temperature, turbidity)
Locating radio-tagged fish will be achieved by fixed receiver stations and mobile surveys (aerial,
boat, and foot). Fixed stations will largely be those used for the Salmon Escapement Study
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(Section 9.7), of which, only one is slated for installation in the Upper River at the Kosina Creek
confluence (RM 206.8). Up to three additional fixed stations may be established at strategic
locations with input from the Fish and Aquatic TWG. These stations will be serviced in
conjunction with the Salmon Escapement Study during the July through October period, but will
be extended to begin on June 1 to track resident fish. Fixed stations will be downloaded as
power supplies necessitate and up to twice monthly during the salmon spawning period
(approximately July through October). The Salmon Escapement Study will provide
approximately weekly aerial survey coverage of the study area (approximately July through
October). At other times of the year, the frequency of aerial surveys will be monthly and during
critical species-specific time periods (e.g., burbot spawning), bi-weekly. Using the guidance of
fixed-station and aerial survey data on the known positions of tagged fish, specific locations of
any concentrations of tagged fish that are suspected to be spawning will be visited to obtain
individual fish positions. Foot and boat surveys will be conducted approximately July through
October as part of the Salmon Escapement Study (Section 9.7). Spatial and temporal allocation
of survey effort will be finalized based on the actual locations and number of each species of fish
tagged.
The fundamental reason for using radio telemetry as a method to characterize resident and non-
salmonid anadromous species is that it can provide useful information to address the overarching
goal of the study and several of its objectives. In particular, radio telemetry can provide data on
seasonal distribution and movement of the target fish throughout the range of potential habitats.
Relocation data from the radio telemetry component of this study will be used to characterize the
timing of use and degree of movements among macrohabitats and over periods during which the
radio-tags remain active (potentially two or three seasons for large fish). This objective may be
achieved by the use of long-life tags (e.g., greater than one year) and shorter life tags (e.g., three-
month tags) applied to appropriate-sized fish over time. In general, successful radio telemetry
studies use a tag weight to fish weight guideline of 3 percent (with a common range of 2 to 5
percent depending on the species). The range in size encountered for a particular species may be
broad enough to warrant the use of different-sized tags with different operational life
specifications. Actual tag life will be determined by the appropriate tag for the size of the fish
available for tagging.
In this regard, the range in weights for the seven target species to be radio-tagged was estimated.
Fish weights and the respective target weight of radio-tags (Table 9.5-3) were calculated using
existing or derived length–weight relationships for Alaska fish (Figure 9.5-3), and length
frequency distributions for Susitna River fish. This analysis illustrates that there is a relatively
broad range of potential tag weights (0.5 grams [g] to 81 g) that are necessary to tag each species
over the potential range in fish size. Further, it is evident that some species will require tags with
a relatively short (30 to 200 days) operational period (tag life).
The broad range in tag weight complicates the scope of the task in terms of technological
feasibility. In general, there is a preference for using coded tags because it allows the unique
identification of a hundred tags on a single frequency. Conversely, standard tags (not coded)
require a single frequency for each tagged fish to allow unique identification. The radio
telemetry industry provides a variety of equipment to match research needs, but there are always
trade-offs in terms of tracking performance and cost between different systems. This plan
intends to capitalize on the use of the existing telemetry platform (ATS telemetry equipment) to
sufficiently monitor the target species, but directly constrains the potential options for tagging
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and monitoring. More specifically, the smallest ATS coded tag weighs 6 g and therefore
precludes application to all the species at the lower portion of their most frequently occurring
size range (Table 9.5-3). For example, if fish need to weigh a minimum of 200 g to be tagged,
then Dolly Varden would be tagged only at its largest samples, and burbot would be tagged
almost across its entire adult size range (Table 9.5-3) based on their respective length–frequency
distributions.
The use of non-coded tags on the smaller adult fish would require the use of many frequencies
(e.g., 50 to 150) and an entirely separate array of receivers. Overall, tagging fish weighing less
than 200 g would be expensive and logistically inefficient. The only viable option to cover the
entire range of fish sizes would be to use alternative vendors’ radio telemetry receivers and tags
that use coded technology through the entire range of tag sizes (e.g., Lotek Wireless).
Tags will be surgically implanted in up to 30 fish of sufficient body size of each species
distributed temporally and longitudinally in the Upper River. These fish will be captured during
sampling events targeting adult fish and with directed effort using a variety of methods. The
final spatial and temporal allocation of tags will be determined after 2012 study results are
available (i.e., preliminary fish abundance and distribution). To the extent possible, tags will be
allocated as follows: (1) a minimum of 10 tags per species will be allocated for tagging adult
grayling and rainbow trout of sufficient size for spawning at tributary mouths during the spring
sampling event; (2) a minimum of 10 tags will be allocated for tagging adult Dolly Varden of
sufficient size for spawning at tributary mouths during at late summer of early fall sampling
event; (3) a minimum of 10 tags will be allocated for tagging adult whitefish prior to spawning in
early September; and (4) a minimum of 10 tags will be allocated for tagging burbot in the early
fall prior to fall or winter spawning migrations. The tag’s signal pulse duration and frequency,
and, where appropriate, the transmit duty cycle, will be a function of the life history of the fish
and configured to maximize battery life and optimize the data collection. Larger tags can
accommodate the greatest battery life and therefore will be used when fish are large enough, but
smaller, shorter life tags will be used across the range of adult body sizes.
PIT Tag Antenna Arrays
As described above, fish of appropriate size from target species will be implanted with a PIT
tagged for mark-recapture studies. Half-duplex PIT tags either 12 mm in length or 23 mm in
length will be used, depending on the size of the fish to be implanted. Each PIT tag has a unique
code that allows identification of individuals. Recaptured fish will provide information on the
distance and time travelled since the fish was last handled and changes in fish length and weight.
PIT tag antenna arrays with automated data logging will be deployed at up to six selected side
channel, slough, and tributary mouths to detect movement of tagged fish into or out of the site
with particular focus on juvenile Chinook salmon. With input from the Fish and Aquatic TWG,
site selection for antenna arrays will be based on habitats and tributaries identified as suitable
habitat for juvenile Chinook salmon. A variety of antenna types may be used including hoop
antennas, swim-over antennas, single rectangle (swim-through) antennas, or multiplexed
rectangle antennas to determine the directionality of movement. Antennas will be deployed
shortly after ice-out in 2013. Data loggers will be downloaded every two to four weeks
depending on the need to replace batteries and on reliability of logging systems. Power to the
antennas will be supplemented with solar panels.
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All juvenile Chinook salmon 60 mm or greater in length will be PIT-tagged. For selected
species, up to 1,000 fish per species per PIT tag array will be tagged based on proximity to PIT
arrays. Target species are Dolly Varden, humpback whitefish, round whitefish, northern pike,
Arctic grayling, and burbot.
9.5.4.4.13. DIDSON and Video Cameras
DIDSON and video cameras are proposed to survey selected sloughs and side channels. The
deployment techniques will follow those described by Mueller et al. (2006). Mueller et al.
(2006) found that DIDSON cameras were useful for counting and measuring fish up to 52.5 feet
(16 meters) from the camera and were effective in turbid waters. In contrast, they found that
video cameras were only effective in clear water areas with turbidity of less than four
nephelometric turbidity units (NTU). However, Mueller et al. (2006) noted that identifying
species and observing habitat conditions were more effective with video cameras than DIDSON
cameras.
DIDSON is a high-resolution imaging sonar that provides video-type images over a 29-degree
field of view and can thus be used to observe fish behavior associated with spawning, i.e.,
dynamic behavior that cannot be identified on the static side-scan sonar images. To obtain high-
quality images of adult salmon, the maximum range will be limited to 15 meters (49 feet).
Within this field of view, evidence of spawning behavior, e.g., redd digging, chasing, spawning,
will be clearly identifiable. Furthermore, on DIDSON images fish can be classified by size
category, e.g., <40 centimeters, 40 – 70 centimeters, >70 centimeters (<5 inches, 25-44 inches,
>44 inches, respectively). Although this is not sufficient for definitive species identification, it
will allow recognition of smaller resident fish, medium-sized adult salmon, and large Chinook
salmon.
Underwater video imaging can record images in real-time over short time intervals and can
provide information on fish species presence/absence in the immediate vicinity. Video systems
can also be configured to record images for longer periods of time using time lapse or motion
triggered recorders. Although water clarity and lighting can limit the effectiveness of video
sampling, a distinct advantage of video over DIDSON is the ability to clearly identify fish
species. In clear water under optimal lighting, video can capture a much larger coverage area
than DIDSON (Mueller et al. 2006). Video is often combined with a white or infrared (IR) light
source especially under ice and in low light northern latitudes; however, lighting may affect fish
behavior. Since nighttime surveys will be required to identify possible diurnal changes in fish
behavior and habitat use, the video system will be fitted with IR light in the form of light
emitting diodes that will surround the lens of the camera. Muller et al. (2006) reported that most
fish are unaffected by IR lights operated at longer wavelengths because it falls beyond their
spectral range. In addition, the video system will be equipped with a digital video recorder for
reviewing and archiving footage of fish observations.
9.5.5. Consistency with Generally Accepted Scientific Practices
This study plan was developed by fisheries scientists in collaboration with the Fish and Aquatic
TWG and draws upon a variety of methods including many that have been published in peer-
reviewed scientific journals. As such, the methods chosen to accomplish this effort are consistent
with standard techniques used throughout the fisheries scientific community. However,
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logistical and safety constraints inherent in fish sampling in a large river in northern latitudes
also play a role in selecting appropriate methodologies. In addition, some survey methods may
not be used in the mainstem river immediately upstream of Devils Canyon to avoid any risk of
being swept into the canyon. During the 1980s studies, no surveys were conducted on the
mainstem river from RM 150 to RM 189.0, except for spawning surveys conducted by
helicopter.
9.5.6. Schedule
Initial data collection efforts for this multi-year study began in the summer/fall of 2012 and will
commence after the FERC study plan determination in early 2013 and continue through October
2014. The schedule allows for two complete open water study seasons. The proposed schedule
(Table 9.5-6) for completion of the Study of Fish Distribution and Abundance in the Upper
Susitna River is as follows:
• Initial collection efforts (Chinook salmon spawning surveys and fish trapping targeting
juvenile Chinook salmon) in Upper River tributary streams – July to October 2012
• File a supplemental memorandum with the FERC reporting interim 2012 collection
results – First quarter 2013
• Development of Implementation Plan and selection of study sites – January to March
2013
• Open water fieldwork – May to October 2013 and May to October 2014
• Reporting of interim results – September 2013 and 2014
• Quality control check of geospatially-referenced relational database – December 2013
and 2014
• Data analysis – October to December 2013 and October to December 2014
• Initial and Revised Study Reports on 2013 and 2014 activities – anticipated to be filed
during the first quarter of 2014 and 2015, one and two years, respectively, after the FERC
Study Plan Determination (February 2013)
9.5.7. Relationship with Other Studies
Over the study implementation phase, an iterative process of information exchange will take
place between interrelated studies that depend upon one another for specimen collection or data.
As studies collect and synthesize data, findings will be disseminated to interdependent studies.
In addition to providing baseline information about aquatic resources in the Project area, aspects
of this study are designed to complement and support other fish and aquatic studies (Figure 9.5-
10). Fish collections in the Upper River will identify species that could colonize the future
reservoir site (Section 9.10) and help validate fish periodicity, habitat associations, and selection
of target species for reach-specific analyses for the Fish and Aquatics Instream Flow Study
(Section 8.5). Patterns of distribution and abundance from traditional sampling methods will
help validate and complement information from radio telemetry, fishwheel, and sonar
observations of salmon in the Salmon Escapement Study (Section 9.7). The Salmon Escapement
Study will provide fixed receiver and aerial tracking of fish radio-tagged in this study. Fish
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movement, habitat association, and growth data will provide inputs for bioenergetics and trophic
analysis modeling for the River Productivity Study (Section 9.8). Additionally, targeted species
will be sampled for fish stomach contents in support of the bioenergetics modeling component.
Fish distribution and abundance will complement information about harvest rates and effort
expended by commercial, sport, and subsistence fisheries to support the Fish Harvest Study
(Section 9.15). Fish collections and observations in conjunction with aquatic habitat
characterization will aid in the development of fish and habitat associations for the
Characterization and Mapping of Aquatic Habitats Study (Section 9.9). Fish collections will
provide data on fish use in sloughs and tributaries with seasonal flow-related or permanent fish
barriers for the Study of Fish Passage Barriers in the Middle and Upper Susitna River and
Susitna Tributaries (Section 9.12) and will provide information for the Study of Fish Passage
Feasibility at Watana Dam (Section 9.11). Fish tissue sample collections will support the
Genetics Baseline Study for Selected Fish Species (Section 9.14) and the Mercury Assessment
and Potential for Bioaccumulation Study (Section 5.7).
9.5.8. Level of Effort and Cost
Initial data collection efforts for this multi-year study began in the summer/fall 2012 and will
commence after the FERC study plan determination in early 2013 and continue until March
2015. Sampling will be conducted according to a stratified scheme designed to cover a range of
habitat types with a minimum of three replicates each. The level of effort at each sample site and
sampling frequency will vary based on tasks and objectives. Selection of sampling sites will be
influenced by the results of the Characterization and Mapping of Aquatic Habitats Study
(Section 9.9) and tributary habitat mapping and fish sampling conducted by AEA during 2012,
which may indicate that some tributaries are unsuitable for sampling because of safety issues or
passage barriers.
The number and size of sample sites and sampling frequency require a large-scale field effort
and subsequent data compilation, as well as quality assurance/quality control (QA/QC) and
analysis efforts. Generally:
• Sampling will be conducted seasonally during the ice-free period in all study sites.
• Sampling will be conducted more frequently immediately following break-up to
document seasonal movement patterns of juvenile Chinook salmon from natal tributaries
to rearing habitats.
• Fish capture and observation methods may include snorkeling, seining, gillnetting,
minnow trapping, angling, trot lines, and out-migrant traps depending on stream
conditions such as depth, flow, and turbidity, target species, and life stage.
• Field crews will consist of two to four individuals, depending on sampling method used.
• Sampling in remote areas requires helicopter, fixed-wing airplane, and boat support.
• Radio-tracking of tagged fish includes 12 aerial surveys, and foot and boat surveys as
necessary.
The estimated cost for implementing the Study of Fish Distribution and Abundance in the Upper
Susitna River is $2,500,000.
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9.5.9. Literature Cited
ADF&G (Alaska Department of Fish and Game). 1982. Aquatic Studies Procedures Manual:
Phase I. Su-Hydro Aquatic Studies Program. Anchorage, Alaska. 111 pp.
ADF&G. 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.
ADF&G. 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.
ADF&G. 1985. Adult salmon investigations, May-October 1984. ADF&G Susitna Hydro
Aquatic Studies Report No. 6 Susitna Hydro Document No. 2748. Anchorage, Alaska.
AEA (Alaska Energy Authority). 2011a. Pre-application Document (PAD): Susitna-Watana
Hydroelectric Project FERC Project No. 14241. December 2011. Prepared for the Federal
Energy Regulatory Commission, Washington, D.C.
AEA. 2011b. Aquatic Resources Gap Analysis. Prepared by HDR, Inc., Anchorage. 107
pp.Barrett, B. M. 1985. Adult Salmon Investigations, May - October 1984. Alaska
Department of Fish and Game, Susitna Hydro Aquatic Studies, Anchorage, Alaska. 528
pp.
Barrett, B. M., F. M. Thompson, S. Wick, and S. Krueger. 1983. Adult Anadromous Fish
Studies, 1982. Alaska Department of Fish and Game, Susitna Hydro Aquatic Studies,
Anchorage, Alaska. 275 pp.
Bernard, D. R., G. A. Pearse, and R. H. Conrad. 1991. Hoop traps as a means to capture burbot.
North American Journal of Fisheries Management 11:91-104.
Bryant, M. D. 2000. Estimating Fish Populations by Removal Methods with Minnow Traps in
Southeast Alaska Streams. North American Journal of Fisheries Management 20:923-
930, 2000.
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.
Delaney, K., D. Crawford, L. Dugan, S. Hale, K. Kuntz, B. Marshall, J. Mauney, J. Quinn, K.
Roth, P. Suchanek, R. Sundet, and M. Stratton. 1981a. Resident Fish Investigation on
the Upper Susitna River. Alaska Department of Fish and Game, Anchorage, AK. 157
pp.
Dolloff, C.A., D.G. Hankin, G.H Reeves. 1993. Basinwide estimation of habitat and fish
populations in streams. USDA Forest Service General Technical Report SE-GTR-83. 25
p.
Dolloff, A., J. Kershner, R. Thurow. 1996. Underwater Observation. Pp. 533-554 In Fisheries
Techniques, Murphy and Willis (eds), American Fisheries Society, Bethesda Maryland,
732 p.
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Evenson, M. J. 1993. Seasonal movements of radio-implanted burbot in the Tanana River
Drainage. Alaska Department of Fish and Game Fishery Data Series No. 93-47,
Fairbanks, AK. 35 pp.
Hayes, D. B., C. P. Ferreri, and W. W. Taylor. 1996. Active fish capture methods. Pages 193–
220 In B. R. Murphy and D. W. Willis, editors. Fisheries techniques. American Fisheries
Society, Bethesda, Maryland.
Hillman, T. W., J. W. Mullan, J. S. Griffith. 1992. Accuracy of underwater counts of juvenile
chinook salmon, coho salmon, and steelhead. North American Journal of Fisheries
Management. 12:598-603.
Mueller, R.P., R.S. Brown, H. Hop, and L. Moulton. 2006. Video and acoustic camera
techniques for studying fish under ice: a review and comparison. (16):213-226. Nemeth,
M.J., A. M. Baker, B. C. Williams, S. W. Raborn, J. T. Priest, and S. T. Crawford. 2010.
Movement and abundance of freshwater fish in the Chuit River, Alaska, May through
July, 2009. Annual report prepared by LGL Alaska Research Associates, Inc.,
Anchorage, Alaska for PacRim Coal, L.P. 86 pp.
NMFS. 2000. Guidelines for electrofishing waters containing salmonids listed under the
Endangered Species Act. 5 pp.
Rutz, D.S. 1999. Movements, food availability and stomach contents of Northern Pike in
selected Susitna River drainages, 1996-1997. Alaska Department of Fish and Game
Fishery Data Series No. 99-5. Anchorage, Alaska. 78 pp.
Sautner, J., and M. Stratton. 1983. Upper Susitna River Impoundment Studies 1982. Alaska
Department of Fish and Game. Anchorage, Alaska. 220 pp.
Schmidt, D.C., S.S. Hale, and D.L. Crawford. 1985. Resident and juvenile anadromous fish
investigations (May - October 1984). Alaska Department of Fish and Game, Anchorage,
Alaska. 483 pp.
Stuby, L. and M. J. Evenson. 1998. Burbot research in rivers of the Tanana River Drainage,
1998. Alaska Department of Fish and Game Fishery Data Series No. 99-36, Fairbanks,
AK. 66 pp.
Thompson, F. M., S. Wick, and B. Stratton. 1986. Report No 13, Volume I, Adult Salmon
Investigations: May - October 1985. Alaska Department of Fish and Game, APA
Document No 3412, Anchorage, Alaska. 173 pp.
Thurow, R.F. 1994. Underwater methods for study of salmonids in the Intermountain West. U.S.
Dept of Agriculture, Forest Service, Intermountain Research Station. General Technical
Report INT-GTR-307. Odgen, Utah. 28 p.
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9.5.10. Tables
Table 9.5-1. Summary of life history, known Susitna River usage of fish species within the Upper Susitna River
Segment (compiled from Delaney et al. 1981).
Common Name Scientific Name Life Historya Susitna Usageb Distributionc
Arctic grayling Thymallus arcticus F O, R, P Low, Mid, Up
Burbot Lota lota F O, R, P Low, Mid, Up
Chinook salmon Oncorhynchus tshawytscha A M2, R Low, Mid, Up
Dolly Varden Salvelinus malma A,F O, P Low, Mid, Up
Humpback whitefishd Coregonus pidschian A,F O, R, P Low, Mid, Up
Lake trout Salvelinus namaycush F U U
Longnose sucker Catostomus catostomus F R, P Low, Mid, Up
Round whitefish Prosopium cylindraceum F O, M2, P Low, Mid, Up
Sculpine Cottid M1, F P Low, Mid, Up
a A = anadromous, F = freshwater, M1 = marine
b O = overwintering, P = present, R = rearing, S = spawning, U = unknown, M2 = migration
c Low = Lower River, Mid = Middle River, Up = Upper River, U = unknown
d Whitefish species that were not identifiable to species by physical characteristics in the field were called humpback by
default. This group may have contained Lake (Coregonus clupeaformis), or Alaska (Coregonus nelsonii) whitefish.
e Sculpin species generally were not differentiated in the field. This group may have included Slimy (Cottus cognatus),
Prickly (Cottus asper), Coastal range (Cottus aleuticus), and Pacific staghorn (Leptocottus armatus).
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Table 9.5-2. Proposed methods by objective, task, species, and life stage.
Obj Task
Species/
Life stage Study Sites Proposed Methods by Season
1A Distribution Juvenile salmon,
non-salmon
anadromous,
resident
Representative
habitat types • Single pass sampling
• Selection of methods will be site-specific, species-specific, and life-stage-specific.
• For juvenile and small fish sampling, electrofishing, snorkeling, seining, fyke nets,
angling, DIDSON and video camera where feasible and appropriate.
• For adults, directed efforts with seines, gillnets, trot lines, and angling.
• To the extent possible, the selected transects will be standardized and the methods
will be repeated during each sampling period at a specific site to evaluate temporal
changes in fish distribution.
• Additional info from radio telemetry studies (Objective #2).
1B Relative abundance Juvenile salmon,
non-salmon
anadromous,
resident
Representative
habitat types • Multi-pass sampling
• To the extent possible, the selected transects will be standardized and the methods
will be repeated during each sampling period at a specific site to evaluate temporal
changes in fish distribution.
• Snorkeling, beach seine, electrofishing, fyke nets, gillnet, minnow traps, fishwheels,
out-migrant traps, etc.
1C Fish habitat associations Juvenile salmon,
non-salmon
anadromous,
resident
Representative
habitat types • Analysis of data collected under Objective 1: Distribution. Combination of fish
presence, distribution, and density by mesohabitat type by season.
2A Timing of downstream
movement and catch using
out-migrant traps
All species;
juveniles
At selected out-
migrant trap &
PIT tag array
sites
• Out-migrant Traps: Maximum of 2. One near the proposed dam site; one near the
mouth of a known Chinook salmon spawning tributary.
• Combine with fyke net sampling to identify key site-specific differences.
• Sampling in mainstem off-channel habitats downstream of tributaries with fyke nets,
seines, and out-migrant traps
2B Describe seasonal
movements using
biotelemetry (PIT and radio-
tags)
All species PIT arrays sites
River-wide aerial
tracking surveys
• PIT tags: tags opportunistically implanted from a variety of capture methods in Focus
Areas. Antenna arrays in up to 6 sites at selected side channel, side slough, tributary
mouth, and upland sloughs in the Upper River.
• Radio-tags surgically implanted in up to 30 fish of sufficient body size of each species
distributed temporally & longitudinally.
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Obj Task
Species/
Life stage Study Sites Proposed Methods by Season
2C Describe juvenile Chinook
salmon movements
Juvenile Chinook
salmon
Representative
habitat types • PIT tag arrays at tributary mouths, sloughs, and side channels (Obj 2B)
• Outmigrant trap in known Chinook spawning tributary
• DIDSON or underwater video to monitor movement into or out of specific habitats
• Monthly measurements of fish size/ growth
5 Document age structure,
growth, and condition by
season
Juvenile
anadromous and
resident fish
All study sites for
Obj 1B
• Stock biology measurements – length from captured fish up to 100 individuals per
season per species per life stage .
• Emphasis placed on juvenile Chinook salmon.
6 Seasonal presence/absence
and habitat associations of
invasive species
Northern pike All study sites • Same methods as #1 and #2 above.
• The presence/absence of northern pike and other invasive fish species will be
documented in all samples
• Additional direct efforts with angling as necessary
7 Collect tissue samples to
support the Genetic Baseline
Study
All All study sites in
which fish are
handled
• Opportunistic collections in conjunction with all capture methods listed above.
• Tissue samples include axillary process from all adult salmon, caudal fin clips from
fish >60 mm, and whole fish <60 mm.
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Table 9.5-3. Upper River tributaries selected for fish distribution and abundance sampling.
Tributary
Susitna River Mainstem
PRM
Listed in AWC
Catalog
Stream Access-
ibility
Average Wetted Width1
(m)
Drainage Basin Area
(km2)
Average Channel Width2
(m)
GRTS Sampling Unit Size
(m)
Oshetna River 235.1 yes yes 17 1424.5 34 800
Black River NA no yes 14 NA NA 400
Goose Creek 232.8 yes yes 10 269.1 12 200
Jay Creek 20 no no 8 160.1 14 DIR
Kosina Creek 209.1 yes partial 33 1036.5 45 800
Tsisi Creek NA no yes 58 NA NA 400
Unnamed Tributary 206.3 no unknown NA <80.3 NA 200
Unnamed Tributary 204.5 no unknown NA <80.3 NA 200
Unnamed Tributary 197.7 no unknown NA <80.3 NA 200
Watana Creek 196.9 yes partial 11 452.7 16 400
Watana Creek Tributary NA no yes NA NA 13 200
Unnamed Tributary 194.8 no unknown NA 321.2 NA 400
Deadman Creek 184.9 no no 32 453.5 27 DIR
Notes:
1 Data taken from HDR (unpublished 2012 data).
2 Data taken from Saunter and Stratton (1983).
NA = data not available or applicable
DIR = tributary subject to direct rather than statistical sampling due to accessibility issues.
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Table 9.5-4. GRTS Based Sampling Target by Upper River Tributary.
Tributary
Susitna River
Historic River Mile
Chinook Salmon
Presence Documented
Percent Sampling by Length
Number of Population
Sample Units
Number of Distribution Samples1
Number of Abundance Samples
Oshetna River 235.1 yes 25 52 8 5
Black River NA no 25 24 3 3
Goose Creek 232.8 yes 25 81 12 8
Kosina Creek 209.1 yes 25 24 3 3
Tsisi Creek NA no 25 23 3 3
Unnamed Tributary 206.3 no 15 29 1 3
Unnamed Tributary 204.5 no 15 21 0 3
Unnamed Tributary 197.7 no 15 41 2 4
Watana Creek 196.9 yes 25 60 9 6
Watana Creek
Tributary
NA no 25 67 10 7
Unnamed Tributary 194.8 no 15 32 2 3
Total -- -- -- 454 53 48
Notes:
1 These are single-pass samples without block nets; abundance samples will also be used for distribution
(101 total samples).
Table 9.5-5. Length and weight of fish species to be radio-tagged and respective target radio-tag weights.
All sizes Most likely to be caught
Species Length (mm) Weight (g)
Fish
Length (mm)
Est.
Weight Min (g)
Est.
Weight Max (g)
Tag Weight
of Min (3%)
Tag Weight
of Max (3%)
Fish length
(mm) @ 200 g weight
Arctic grayling 36–444 <1–830 120–420 18 705 0.5 21.2 270
Dolly Varden 30–470 <1–1,007 130–300 20 256 0.6 7.7 277
Round whitefish 23–469 <1–1,035 150–390 23 553 0.7 16.6 287
Rainbow trout 27–612 <1–3,327 180–480 96 1635 2.9 49.1 232
Humpback whitefish 30–510 <1–1,544 210–450 180 1141 5.4 34.2 219
Burbot 26–791 <1–3,532 300–510 186 931 5.6 27.9 307
Northern pike 83–713 5–2707 200-700 62 2700 1.9 81.0 296
Lake Trout U U U U U TBD TBD TBD
Longnose Sucker U U U U U TBD TBD TBD
Notes:
U = Unknown size distribution.
FINAL STUDY PLAN STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE UPPER SUSITNA RIVER 9.8
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-32 July 2013
Table 9.5–6. Schedule for implementation of the Fish Distribution and Abundance in the Upper Susitna River.
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
Initial Studies and Technical Memo •
Study Site Selection
Develop and File Implementation Plan ♦
Fish Sampling --------
Data Entry
Preliminary Data Analysis
Initial Study Report Δ
Final Data Analysis
Updated Study Report ▲
Legend:
Planned Activity
----- Follow-up activity (as needed)
• Technical Memorandum
♦ Implementation Plan
Δ Initial Study Report
▲ Updated Study Report
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 33 March 2013
9.5.11. Figures
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 34 March 2013
Figure 9.5-1. Fish distribution and abundance study area.
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 35 March 2013
Figure 9.5-2. Locations of 20 tributaries upstream of Devils Canyon selected for sampling.
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 36 March 2013
Figure 9.5-3. GRTS sample locations selected for the Oshetna River. Each black circle represents the downstream edge
of an 800m sample unit.
2060000 2065000 2070000 2075000 2080000306000030800003100000312000031400003160000
EastingNorthingDistribution
Relative Abundance
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 37 March 2013
Figure 9.5-4. GRTS sample locations selected for Goose Creek. Each black circle represents the downstream edge of a
200- meter sample unit.
2055000 2060000 2065000 20700003135000314500031550003165000
EastingNorthingDistribution
Relative Abundance
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 38 March 2013
Figure 9.5-5. GRTS sample locations selected for the Kosina River. Each black circle represents the downstream edge of
an accessible 800-meter sample unit.
1964000 1966000 1968000 1970000 1972000 1974000 1976000313000031400003150000316000031700003180000
EastingNorthingDistribution
Relative Abundance
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-39 July 2013
Figure 9.5-6. Map showing sample locations in the Oshetna River, Black River and Goose Creek. Dots represent location of sampled
reaches of length 800 meters (Oshetna River), 400 meters (Black River) or 200 meters (Goose Creek).
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-40 July 2013
Figure 9.5-7. Map showing sample locations in Kosina and Tsisi creeks. Dots represent locations of 800 meters (Kosina Creek) or 400 meters (Tsisi Creek) sampling
units.
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-41 July 2013
Figure 9.5-8. Fish distribution and abundance sampling transects in the Upper Susitna River.
FISH DISTRIBUTION AND ABUNDANCE IMPLEMENTATION PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9-42 July 2013
Figure 9.5–9. Existing or derived length–weight relationships for fish species to be radio-tagged.
0
200
400
600
800
1000
1200
1400
1600
1800
2000
0 100 200 300 400 500 600Weight (g)Length (mm)
RBTR DLVD
PIKE BRBT
RDWF HBWF
GRAY
FINAL STUDY PLAN
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FERC Project No. 14241 Page 43 July 2013
Figure 9.5-10. Flow chart showing study interdependencies for the Fish Distribution and Abundance Study in the Upper River.
FINAL STUDY PLAN
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 44 July 2013