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Susitna-Watana Hydroelectric Project Document
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Title:
Study of fish distribution and abundance in the upper Susitna River, Study
plan Section 9.5 : Initial study report
SuWa 207
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Prepared by R2 Resource Consultants, Inc.
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Draft initial study report
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Series (ARLIS-assigned report number):
Susitna-Watana Hydroelectric Project document number 207
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Published by:
[Anchorage : Alaska Energy Authority, 2014]
Date published:
February 2014
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Alaska Energy Authority
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Study plan Section 9.5
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Draft
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217 p. in various pagings
(including appendices)
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Notes:
The following parts of Section 9.5 appear in separate files: Main report ; Appendices.
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
Initial Study Report
Prepared for
Alaska Energy Authority
Prepared by
R2 Resource Consultants, Inc.
February 2014 Draft
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page i February 2014 Draft
TABLE OF CONTENTS
1. Introduction ....................................................................................................................... 1
2. Study Objectives................................................................................................................ 3
3. Study Area ......................................................................................................................... 4
4. Methods .............................................................................................................................. 4
4.1. Study Site Selection .......................................................................................... 4
4.1.1. Early Life History Sites .................................................................. 5
4.1.2. Fish Distribution and Abundance Sampling Sites .......................... 5
4.1.3. Rotary Screw Trap Sites ................................................................. 8
4.1.4. PIT Interrogation Antenna Sites ..................................................... 8
4.1.5. Fixed Radio Telemetry Sites ........................................................... 9
4.1.6. Variances from the Study Plan ....................................................... 9
4.2. Sampling Frequency ....................................................................................... 11
4.2.1. Variances from the Study Plan ..................................................... 11
4.3. Fish Sampling Approach................................................................................. 11
4.4. Objective 1: Fish Distribution, Relative Abundance, and Habitat
Associations .................................................................................................... 12
4.4.1. Task A: Fish Distribution Surveys ................................................ 12
4.4.2. Task B: Relative Abundance ........................................................ 13
4.4.3. Task C: Fish-Habitat Associations................................................ 14
4.4.4. Variances from Study Plan ........................................................... 14
4.5. Objective 2: Seasonal Movements .................................................................. 16
4.5.1. Task A: Document the timing of downstream movement and
catch for all fish species using out-migrant traps. ......................... 16
4.5.2. Task B: Describe seasonal movements using biotelemetry. ......... 16
4.5.3. Task C: Describe juvenile Chinook salmon movements. ............. 17
4.5.4. Variances from Study Plan ........................................................... 17
4.6. Objective 3: Early Life History...................................................................... 19
4.6.1. Determine movement patterns and timing of juvenile salmonids
from spawning to rearing habitats................................................. 19
4.6.2. Variances from Study Plan ........................................................... 19
4.7. Objective 4: Characterize the seasonal age class structure, growth, and
condition of juvenile anadromous and resident fish by habitat type. ............. 20
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page ii February 2014 Draft
4.7.1. Variances from Study Plan ........................................................... 21
4.8. Objective 5: Determine whether Dolly Varden and humpback whitefish
residing in the Upper River exhibit anadromous or resident life histories. .... 21
4.9. Objective 6: Determine baseline metal and mercury concentrations in fish
tissues for resident fish species in the mainstem Susitna River. ..................... 22
4.9.1. Variances from Study Plan ........................................................... 22
4.10. Objective 7: Document the seasonal distribution, relative abundance, and
habitat associations of invasive species (northern pike). ................................ 22
4.11. Objective 8: Collect tissue samples from juvenile salmon and resident and
non-salmon anadromous fish. ......................................................................... 22
4.12. Fish Sampling Techniques .............................................................................. 23
4.12.1. Gillnets .......................................................................................... 23
4.12.2. Electrofishing ................................................................................ 24
4.12.3. Angling ......................................................................................... 25
4.12.4. Trot Lines ...................................................................................... 25
4.12.5. Minnow Traps ............................................................................... 25
4.12.6. Snorkel Surveys ............................................................................ 26
4.12.7. Fyke/Hoop Nets ............................................................................ 27
4.12.8. Hoop Traps.................................................................................... 27
4.12.9. Beach Seine ................................................................................... 27
4.12.10. Rotary Screw Trap ........................................................................ 28
4.12.11. Fish Handling ................................................................................ 28
4.12.12. Remote Fish Telemetry ................................................................. 29
5. Results .............................................................................................................................. 31
5.1. Objective 1: Fish Distribution, Relative Abundance, and Habitat
Associations .................................................................................................... 31
5.1.1. Task A: Fish Distribution.............................................................. 31
5.1.2. Task B: Relative Abundance ........................................................ 36
5.1.3. Task C: Habitat Associations ........................................................ 38
5.2. Objective 2: Seasonal Movements .................................................................. 39
5.2.1. Task A: Document the timing of downstream movement and
catch for all fish species using out-migrant traps. ......................... 39
5.2.2. Task B: Describe seasonal movements using biotelemetry .......... 40
5.2.3. Task C: Describe juvenile Chinook salmon movements. ............. 45
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page iii February 2014 Draft
5.3. Objective 3: Early Life History...................................................................... 45
5.4. Objective 4: Characterize the seasonal age class structure, growth, and
condition of juvenile anadromous and resident fish by habitat type. ............. 45
5.4.1. Growth by Habitat Type ............................................................... 45
5.4.2. Condition Factor by Habitat Type ................................................ 46
5.5. Objective 5: Determine whether Dolly Varden and humpback whitefish
residing in the Upper River exhibit anadromous or resident life histories. .... 46
5.6. Objective 6: Determine baseline metal and mercury concentrations in fish
tissues for resident fish species in the mainstem Susitna River. ..................... 47
5.7. Objective 7: Document the seasonal distribution, relative abundance, and
habitat associations of invasive species (northern pike). ................................ 47
5.8. Objective 8: Collect tissue samples from juvenile salmon and all resident
and non-salmon anadromous fish. .................................................................. 47
6. Discussion......................................................................................................................... 47
6.1. Fish Distribution, Relative Abundance and Habitat Associations .................. 48
6.2. Seasonal Movements ...................................................................................... 49
6.3. Early Life History ........................................................................................... 50
6.4. Seasonal size-class structure, growth and condition ....................................... 51
6.5. Anadromous life-histories ............................................................................... 51
6.6. Baseline metals and mercury .......................................................................... 52
6.7. Invasive Species .............................................................................................. 52
6.8. Tissue Collection ............................................................................................ 52
7. Literature Cited .............................................................................................................. 54
8. Tables ............................................................................................................................... 57
9. Figures .............................................................................................................................. 91
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page iv February 2014 Draft
LIST OF TABLES
Table 2-1. Study objectives for the Study of Fish Distribution and Abundance in the Upper
Susitna River from the Revised Study Plan. ................................................................................. 58
Table 4.1-1. Tributaries selected for fish distribution and abundance sampling in the Upper
Susitna River in 2013. ................................................................................................................... 60
Table 4.1-2. Sampling Effort for GRTS and direct sampling tributaries, 2013. ........................... 61
Table 4.1-3. Upper Susitna River tributary habitat classification and mesohabitat sampling, 2013
....................................................................................................................................................... 62
Table 4.1-4. Sample effort for mainstem transects in the Upper River, 2013. ............................. 65
Table 4.2-1. Salmon early life history sampling summary, 2013. ................................................ 66
Table 4.2-2. Antenna orientation for fixed-station receiver locations in the Upper Susitna River,
2013............................................................................................................................................... 66
Table 4.2-3. Monitoring efficiency (percent operational) of fixed-station receivers in the Susitna
River drainage in 2013, by week. ................................................................................................. 67
Table 4.2-4. Summary of aerial surveys of radio-tagged fish in the Upper Susitna River, 2013.
Data are currently preliminary through 9/9. ................................................................................. 68
Table 4.5-1. Length and weight of fish species tagged for biotelemetry studies in the Upper
Susitna River, 2013. ...................................................................................................................... 69
Table 4.5-2. Radio tag allocation by season Upper Susitna River, 2013 ...................................... 70
Table 4.7-1. Summary of size-at-life stage index used to classify Susitna River species, 2013. . 71
Table 4.7-2. Summary of fish with length and weight measurements collected in the Upper,
Middle and, Lower Susitna River by hydrologic segment, 2013. ................................................ 72
Table 4.7-3. Sample sizes of juvenile Chinook salmon and Arctic grayling included in the
condition factor analysis by mainstem geomorphic reach and tributary ...................................... 73
Table 4.8-1. Summary of otolith collection for Dolly Varden in 2013. ....................................... 74
Table 4.9-1. Summary of tissue collection for baseline metal and mercury concentration
evaluation, 2013. ........................................................................................................................... 75
Table 4.11-1. Summary of tissue collection for genetic baseline development, 2013. ................ 77
Table 5.1-1. Fish Distribution in the Upper Susitna River 2012 & 2013 and select historical
records. .......................................................................................................................................... 78
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page v February 2014 Draft
Table 5.1-2. Upper Susitna fish observations, 2013. .................................................................... 79
Table 5.1-3. Fish distribution and abundance (transect, GRTS, and direct sample) sampling total
observations for each gear type by species and life stage, 2013. .................................................. 80
Table 5.2-1. Upper Susitna River rotary screw trap catch by species and life stage, 2013. ......... 81
Table 5.2-2. Movement and survival of Arctic grayling during 2 week periods, by tagging group,
Upper Susitna River, 2013. ........................................................................................................... 82
Table 5.2-3. Movement and survival of longnose sucker during 2 week periods, by tagging
group, Upper Susitna River, 2013. ................................................................................................ 83
Table 5.2-4. Number of fish in the Upper Susitna River implanted with PIT tags, detected by
stationary antennas, and recaptured during subsequent sampling events, by species, 2013. ....... 86
Table 5.2-5. Number of individual fish detected and total number of detectionsa by species at
Upper River PIT antenna stations at Kosina Creek and the Oshetna River in 2013. ................... 86
Table 5.2-6. Arctic grayling movement between macrohabitat types in the Upper River in 2013
based on a comparison of initial tagging events versus subsequent recapture or detection at PIT
antennas......................................................................................................................................... 87
Table 5.3-1. Early life history sampling catch by location and gear type, 2013. ......................... 88
Table 5.4-1. Number PIT-tagged recaptured PIT-tagged juvenile Chinook salmon and Arctic
grayling available for growth analysis for the Upper Susitna River, 2013. .................................. 89
Table 5.4-3. Condition factor of juvenile Chinook salmon by tributary, Upper Susitna River,
2013............................................................................................................................................... 89
Table 5.4-4. Condition factor of Arctic grayling by macrohabitat type and tributary, Upper
Susitna River, 2013. ...................................................................................................................... 90
LIST OF FIGURES
Figure 3-1. Upper Susitna River fish distribution and abundance study area. ............................. 92
Figure 4.1-1. Salmon Early Life History sampling sites in the Upper Susitna River basin,
2013. ...................................................................................................................................... 93
Figure 4.1-2. Locations of 13 tributaries upstream of the proposed Watana Dam location
selected for sampling up to the 3,000 ft contour, 2013. ....................................................... 94
Figure 4.1-3. GRTS fish distribution and abundance sampling targets and field sampling
locations (including oversamples) in Unnamed Tributary 194.8, Watana Creek, Watana
Creek Tributary, and Unnamed Tributary 197.7, 2013......................................................... 95
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page vi February 2014 Draft
Figure 4.1-4. GRTS fish distribution and abundance sampling targets and field sampling
locations (including oversamples) in Unnamed Tributary 204.3, Unnamed
Tributary 206.3, Kosina Creek, and Tsisi Creek, 2013......................................................... 96
Figure 4.1-5. GRTS fish distribution and abundance sampling targets and field sampling
locations (including oversamples) in Goose Creek, the Oshetna River, and the Black
River, 2013. ........................................................................................................................... 97
Figure 4.1-6. Fish distribution and abundance transect sampling locations in the Upper
Susitna River, 2013. .............................................................................................................. 98
Figure 4.1-7. Out-migrant (rotary screw) trap, PIT tag array, and radio fixed receiver
locations in the Upper Susitna River Study Area, 2013. ...................................................... 99
Figure 4.2-1. Summary of PIT tag interrogation system operation in the Upper Susitna
River, 2013. Black indicates continuous operation; gray indicates partial or
interrupted operation. .......................................................................................................... 100
Figure 4.2-2. Screw trap operation in the Upper Susitna River, 2013. ....................................... 101
Figure 4.5-1. Summary of PIT tagging effort in the vicinity of the Oshetna River, 2013. ......... 102
Figure 4.5-2. Summary of PIT tagging effort in the vicinity of Kosina Creek, 2013. ................ 103
Figure 4.5-3. Illustration of swim over Oshetna River PIT tag interrogation antenna
orientation positioning at high (top) and low flow (bottom), 2013. ................................... 104
Figure 4.5-4. Swim through PIT tag interrogation antenna on Kosina Creek side channel at
RM 0.2, 2013. ..................................................................................................................... 105
Figure 4.7-1. Condition factor by size (fork length mm) for juvenile Chinook salmon (top)
and Arctic Grayling (bottom) for Lower, Middle, and Upper Susitna River, 2013............ 106
Figure 5.4-1. Box-and-whisker plot of juvenile Chinook salmon condition factor in Upper
River Tributaries and the mainstem Susitna River (UR-6). ................................................ 109
Figure 5.4-2. Box-and-whisker plot of Arctic Grayling condition factor in Upper River
Tributaries (Trib) various mainstem Susitna River macrohabitats. MC=main channel,
SMC=split main channel, SC=side channel, SS=side slough, US=upland slough, CWP=
clear water plume (special mesohabitat type). .................................................................... 109
APPENDICES
Appendix A: Distribution of Fish Radio-Tagged in the Upper Susitna River, 2013
Appendix B: Fish Distribution Maps for the Upper Susitna River 2012 and 2013
Appendix C: Seasonal Fish Distribution, Upper Susitna River 2012 and 2013
Appendix D: Upper River Fish Observations and Relative Abundance, 2013
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page vii February 2014 Draft
LIST OF ACRONYMS, ABBREVIATIONS, AND DEFINITIONS
Abbreviation Definition
ADF&G Alaska Department of Fish and Game
AEA Alaska Energy Authority
APA Alaska Power Authority
AWC Anadromous Waters Catalog
CIRWG Cook Inlet Regional Working Group
CPUE catch per unit effort
ELH early life history
FDA Fish Distribution and Abundance
FERC Federal Energy Regulatory Commission
FL fork length
FWS Fish and Wildlife Service
GIS Geographic Information System
GPP Gas-Powered Pulsator
GPS global positioning system
ILP Integrated Licensing Process
IP Implementation Plan
ISR Initial Study Report
JOA Juvenile/Adult
JUV juvenile
MC main channel
N/A Not applicable
NMFS National Marine Fisheries Service
PIT passive integrated transponders
PRM Project River Mile
Project Susitna-Watana Hydroelectric Project
RM River mile
RSP Revised Study Plan
RST rotary screw traps
SPD study plan determination
TWG Technical Workgroup
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page viii February 2014 Draft
EXECUTIVE SUMMARY
Study of Fish Distribution and Abundance in the Upper Susitna River 9.5
Purpose The goal of this study is to characterize the current distribution, relative
abundance, run timing, and life history of resident and non-salmon
anadromous fish species as well as freshwater rearing life stages of
anadromous salmonids in the Upper Susitna River. Seven specific
objectives have been developed for this study and include multiple tasks.
Data collected as part of this study will be used to provide a baseline
characterization of fish assemblages in the Susitna River, to identify and
evaluate potential Project-induced effects on fish assemblages, and inform
development of any necessary protection, mitigation, and enhancement
measures.
Status Data collection is complete for the first year of this multiyear study. Initial
database quality assurance and quality control was completed to compile
preliminary summary statistics and preliminary data analysis for the Initial
Study Report. Database quality assurance and quality control, data
analysis, and coordination with interdependent studies is an ongoing
iterative process. A second study year of data collection is planned.
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page ix February 2014 Draft
Study of Fish Distribution and Abundance in the Upper Susitna River 9.5
Study Components Major study components include the following eight objectives:
• Objective 1: Describe the seasonal distribution, relative abundance,
and fish habitat associations of juvenile anadromous salmonids,
non-salmonid anadromous fishes and resident fishes.
• Objective 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.
• Objective 3: Describe early life history, timing, and movements of
anadromous salmonids.
• Objective 4: Characterize the seasonal age class structure, growth,
and condition of juvenile anadromous and resident fish by habitat
type.
• Objective 5: Determine whether Dolly Varden and humpback
whitefish residing in the Upper River exhibit anadromous or
resident life histories.
• Objective 6: Determine baseline metal concentrations in fish tissues
for resident fish species in the mainstem Susitna River (see ISR
Studies 5.5 and 5.7).
• Objective 7: Document the seasonal distribution, relative
abundance, and habitat associations of invasive species (northern
pike).
• Objective 8: Collect tissue samples to support the Genetic Baseline
Study for Selected Fish Species (ISR Study 9.14).
2013 Variances AEA implemented the methods as described in the Study Plan with the
exception of the following variances. The significance of these variances
is discussed within the ISR.
• the addition of an early life history study objective (Objective 3
above; Section 4.6.2);
• adjustments to rotary screw trap, PIT array, radio telemetry fixed
receiver, and fish distribution and abundance sampling locations
(Section 4.1.6);
• adjustments to the number of fixed receiver locations (Section
4.1.6.4);
• adjustments to the timing of fish distribution and sampling efforts
(Section 4.2.1);
• adjustments to sample unit lengths (Section 4.1.6.1.1);
• adjustments to gear type applications (e.g., numbers of passes, soak
times, minnow trap densities; Section 4.4.4.1);
• refinements to estimating the detection efficiency of PIT tag
interrogation systems (Section 4.5.4.1);
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page x February 2014 Draft
Study of Fish Distribution and Abundance in the Upper Susitna River 9.5
• adjustments to the timing of radio-tag implementation and aerial
survey methods for tracking resident fish (Sections 4.5.4.2 and
4.5.4.3);
• utilizing size instead of age to evaluate habitat associations of
juvenile anadromous and resident fish (Section 4.7.1); and
• adjustments to the timing of fish tissue sample collection for metals
and mercury analysis (Section 4.9.1).
Steps to Complete
the Study
[As explained in the cover letter to this draft ISR, AEA’s plan for
completing this study will be included in the final ISR filed with FERC on
June 3, 2014.]
Highlighted
Results and
Achievements
In 2013, nine fish species were captured in the Upper Susitna River,
including juvenile Chinook salmon, which were not found during 2012
studies. Over 12,600 fish were observed during three seasonal surveys at
over 150 sites representative of 12 tributaries and approximately 47 miles
of the Susitna River. Similar to previous studies by ADF&G, juvenile
Chinook salmon were rare. They were documented in the Oshetna River
and Kosina Creek, and for the first time, in the Black River. Arctic
grayling and sculpin were the most widely distributed and abundant
species. Watana Creek was notable for relatively high abundance of Dolly
Varden and Arctic grayling. No northern pike were observed in the Upper
River. Over 1,300 fish were tagged for biotelemetry studies of fish
movement. Sampling in 2013 met all first-year study goals and objectives.
]
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 1 February 2014 Draft
1. INTRODUCTION
On December 14, 2012, Alaska Energy Authority (AEA) filed its Revised Study Plan (RSP) with
the Federal Energy Regulatory Commission (FERC or Commission) for the Susitna-Watana
Project (FERC Project No. 14241), 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 stage 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 comment 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.
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IN THE UPPER SUSITNA RIVER (9.5)
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FERC Project No. 14241 Page 2 February 2014 Draft
- 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
- 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 the Final Study Plan.
Following the first study season, FERC’s regulations for the Integrated Licensing Process (ILP)
require AEA to “prepare and file with the Commission an initial study report describing its
overall progress in implementing the study plan and schedule and the data collected, including an
explanation of any variance from the study plan and schedule.” (18 CFR 5.15(c)(1)) This Initial
Study Report on the Fish Distribution and Abundance in the Upper Susitna River Study has been
prepared in accordance with FERC’s ILP regulations and details AEA’s status in implementing
the study, as set forth in the FERC-approved RSP and as modified by FERC’s April 1 SPD and
FDA IP TM (collectively referred to herein as the “Study Plan”).
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 3 February 2014 Draft
2. STUDY OBJECTIVES
As established in RSP Section 9.5.1., 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 rotary screw
traps.
b. Describe seasonal movements using biotelemetry (passive integrated transponders
[PIT] and radio-tags).
c. Describe juvenile Chinook salmon movements.
3) Describe early life history of anadromous salmonids. Determine movement patterns and
timing of juvenile salmonids from spawning to rearing habitats. (Note that this objective
was not part of the Study Plan; it was added during implementation.)
4) Characterize the seasonal age class structure, growth, and condition of juvenile
anadromous and resident fish by habitat type.
5) Determine whether Dolly Varden and humpback whitefish residing in the Upper River
exhibit anadromous or resident life histories.
6) Determine baseline metal concentrations in fish tissues for resident fish species in the
mainstem Susitna River (see RSP Section 5.5 Water Quality and Section 5.7, Mercury
Assessment and Potential for Bioaccumulation Study).
7) Document the seasonal distribution, relative abundance, and habitat associations of
invasive species (lake trout and northern pike).
8) Collect tissue samples to support the Genetic Baseline Study for Selected Fish Species
(RSP Section 9.14).
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3. STUDY AREA
As established by RSP Section 9.5.3, the study area encompasses the mainstem Susitna River
and its tributaries from the proposed Watana Dam site (PRM 187.1) upstream to an including
the Oshetna River (PRM 235.1) (Figure 3-1). 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 of the proposed Watana Dam are
further delineated by the 3,000-ft 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.
4. METHODS
This study employed a variety of field methods to build on the existing information related to the
distribution and abundance of fish species in the Upper Susitna River consistent with the Study
Plan except for specific variances as described below. The following sections provide brief
descriptions of study site selection, sampling frequency, the approach, and suite of methods that
were used to accomplish each objective of this study. This study was initiated in 2012 and will
continue in the next year of study to meet study objectives.
Fish Distribution and Abundance Sampling Plan
A final sampling scheme was developed as part of the detailed Fish Distribution and Abundance
Implementation Plan (IP), for ISR Studies 9.5 and 9.6. The IP included (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 in 2012 (Study 9.9), (3) a description of
site selection and sampling protocols, (4) development of field data collection forms, (5)
development of database templates that complied with 2012 AEA QA/QC procedures, and (6)
the FERC requested modifications included in the April 1 SPD. The IP included the level of
detail sufficient to instruct field crews in data collection efforts. In addition, the plan included
protocols and a guide to the decision-making process in the form of a chart that was used in the
field, specific sampling locations, details regarding the choice and use of sampling techniques
and apparatuses, and a list of field equipment needed. The Implementation Plan addressed the
random selection of sampling locations. The Implementation Plan outlined measures to ensure
that fish collection efforts occurred in a consistent and repeatable fashion across field crews and
river segments. Sampling methods by objective are presented below and in Table 2-1. Brief
descriptions of each sampling technique are provided in Section 4.12.
4.1. Study Site Selection
AEA implemented site selection as described in the Study Plan with the exception of variances
explained below (Section 4.1.6). The Upper Susitna River includes the area where the mainstem
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river will be inundated and tributaries will be partially altered. The sampling effort was tailored
to collect information to document fish assemblages, distribution, and abundance generally
within the mainstem river and more intensely within the tributary habitat to be inundated up to an
elevation of 3,000 ft, which was based on the known upper extent of juvenile Chinook salmon
distribution.
4.1.1. Early Life History Sites
Early life history (ELH) sampling was added to Upper River fish distribution sampling. The
focus was to locate juvenile Chinook salmon in Upper River tributaries in June. A secondary
objective was to investigate the outlet area of two lakes for the presence of juvenile sockeye
salmon. Sites were selected in the field to represent geomorphic reaches within select tributaries
based on the following criteria: 1) proximity to previously identified Chinook habitats; 2)
proximity to lakes with potential sockeye spawning habitat; 3) helicopter access; 4) landowner
permission; 5) suitable habitat for effective backpack electrofishing; and 6) accessibility and
proximity to other mesohabitat types. A total of 41 mesohabitat units were sampled within 21
sites during the first sampling event (Figure 4.1-1).
A second sampling event was conducted in late June to replicate the first event by visiting the
same locations and sampling the same mesohabitat units. However, substantially lower water
made replication difficult and several macrohabitat units were replaced with similar nearby units
during the second event. A total of 43 mesohabitat units were sampled within 20 sites during the
second sampling event. .
4.1.2. Fish Distribution and Abundance Sampling Sites
4.1.2.1. Tributaries
All known Chinook salmon-bearing tributaries and other tributaries that are not currently listed
in ADF&G’s Anadromous Waters Catalog (AWC) in the Upper River, upstream of the proposed
dam site (PRM 187.1) were incorporated into the site selection process for fish distribution and
abundance sampling (ADF&G 2012). Initially 13 Upper River tributary streams were selected
for sampling based on: AWC catalog listings, drainage basin, historical sampling efforts, and the
potential for impact or inundation from the proposed Project (Figure 4.1-2). These tributaries
were screened for sampling accessibility based on stream gradient, channel morphology (i.e.,
confined canyon), mesohabitat type (e.g. rapid and cascade) and physical access. The screening
resulted in seven tributaries known to be accessible or to have substantial lengths of accessible
reaches, two tributaries that were largely inaccessible, and four tributaries where access was
unknown (Table 4.1-1).
The accessible portion of each selected tributary up to the 3,000-ft (914 m) elevation contour was
divided into units of equal length based on channel width and drainage basin area. Large
tributary streams with drainage basins greater than 1,000 km2 (386 mi2) and with channel widths
of 35 to 45 m (115-148 ft) were assigned 800 m (2,625 ft) sampling units. Tributaries with
drainage areas ranging from 300 to 1,000 km2 (115 to 386 mi2) and with channel widths of 15 to
35 m (49 to 115 ft) were assigned 400 m (1,312 ft) sampling units. Tributaries draining less than
300 km2 (115 mi2) and with channel widths of 5 to 15 m (16 to 49 ft) were assigned 200 m (656
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ft) units. Sampling unit lengths for each of the selected tributaries are shown in Table 4.1-1.
Within each tributary, the target for total length sampled was up to 25 percent of the length of the
accessible portion of the tributary from the mouth upstream to the location of 3,000 ft (914 m)
elevation contour. This target was dependent upon documentation of Chinook salmon presence
in the tributary watershed (Table 4.1-2). In tributaries without Chinook salmon present the target
for total sample length was 15 percent..
The seven accessible or partially accessible tributaries and the four tributaries where access
conditions were unknown were subjected to a statistical sampling design. A generalized random
tessellation stratified (GRTS) sampling method was used to select study units within each
tributary (Stevens and Olsen 2004). Specifically, the grts routine in package spsurvey (Kincaid
and Olsen 2012) for R (R Core Team 2012) was used to generate the GRTS samples. This
sampling method is a compromise between random and systematic sampling that allows random
ordering of population units with spatial balance. Using the GRTS samples, oversampling (e.g.,
selecting 10 samples but planning to use only the first 3) is allowed; thus, when units were
determined to be inaccessible in the field, the next unit on the randomized list was used while
maintaining spatial balance in the final sample set.
For each selected tributary, the sample size was based on the targeted percent coverage of the
accessible population for distribution sampling (Table 4.1-1) and 10 percent coverage for
abundance sampling. For example, if there were 100 population units on a given tributary, 25
were selected for distribution sampling, and the first 10 of these would also be used for relative
abundance sampling. There was a minimum sample size of three units for abundance sampling
in each tributary. The remaining population units (75 percent) were termed oversample sites and
retained as back-up sample sites in the event that a site was unable to be sampled.
Oversamples were used a total of 13 times in cases when the initially selected site occurred on
private lands that could not be accessed, when no landing zones were available near the site, or
when site conditions were unsafe for sampling. Twenty out of the 101 sample sites selected
were not sampled in 2013 because of a lack of suitable landing zone and no available oversample
site as all proximate oversample sites had been previously selected. These included Unnamed
Tributary 197.7 (6 Sites) and Unnamed Tributary 204.3 (3 Sites), Unnamed Tributary 206.3 (4
Sites), Unnamed Tributary 206.3 (3 Sites) and Watana Creek (4 Sites).
Within each GRTS study unit, one unit of each available mesohabitat type was randomly
selected for sampling. Study units evaluated for mesohabitats were 200 m (656 ft), 400 m (1,312
ft), or 800 m (2625 ft) in length (as proposed based on basin area). Sampling units within study
GRTS units were either the complete mesohabitat unit length or 200 m (656 ft) per mesohabitat
type per site, whichever was shorter.
After video and field reconnaissance, a total of 81 Upper River tributary sites were selected and
sampled using the GRTS selection method (Table 4.1-2). This included 44 and 37 sites where
distribution and relative abundance sampling took place respectively. The 81 sampling sites
were further delineated into 151 mesohabitat units (e.g. pool, riffle, glide) for gear selection and
fish habitat association purposes (Table 4.1-2). A target of three and a minimum of two gear
types were used for sampling each mesohabitat unit to capture a variety of fish species, sizes, and
life stages. Maps showing the final sample locations are provided for Watana Creek, Watana
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Creek Tributary, Unnamed Tributary 197.7, and Unnamed Tributary 194.8 (Figure 4.1-3);
Unnamed Tributary 204.3, Unnamed Tributary 206.3, Kosina Creek, and Tsisi Creek (Figure
4.1-4); and the Oshetna River, Black River and Goose Creek (Figure 4.1-5).
A direct sampling methodology was implemented on the two tributary streams (Jay and
Deadman Creeks) with minimal to moderate access and limited feasible sampling areas (Table
4.1-2; Figure 4.1-2). Following reconnaissance, an average of two days of sampling effort was
conducted in Jay Creek; Deadman Creek could not be accessed (Table 4.1-3). Two locations
were sampled in Jay Creek (Table 4.1-3), representing differences in elevation or other habitat
features. Effort at each sampling unit was considered complete when the field lead judged that
the unit was sufficiently represented or that additional sampling effort would not provide
additional information.
4.1.2.2. Mainstem
Fish distribution and relative abundance sampling in the Upper Susitna River mainstem was
conducted from the proposed dam site (PRM 187.1) upstream to the Oshetna River confluence
(PRM 235.1). This survey area included Geomorphic Reaches UR-3 (PRM 234.5-224.9), UR-4
(PRM 224.9-208.1), UR-5 (PRM 208.1-203.4), and UR-6 (PRM 203.4-187.1). Due to channel
morphology in the Upper River and corresponding limitations of habitat mapping therein, a
systematic transect approach was adopted whereby fish sampling sites were selected within
habitat units encountered along transects. Using a random start for the Upper River study area,
20 transects were equally spaced every 3.9 km (2.4 mi) (Figure 4.1-6). Following ground-level
reconnaissance, 4 of the 20 transects were not sampled due to land access and safety issues
(Table 4.1-4).
Some Upper River transects spanned multiple habitat types (e.g., main channel, side channel,
upland slough, and side slough). When multiple habitat types were encountered, one habitat unit
of each type was selected along each transect. When multiple habitat units of the same type were
present, units were randomized and one was selected for sampling. One transect per geomorphic
reach was selected for relative abundance sampling, for a total of four relative abundance
transects. The remaining transects were sampled for distribution only (e.g., no block nets, single
pass sampling).
Main and side channel habitats were sampled with boat electrofishing whenever site conditions
and permit stipulations allowed (conductivity, visibility, and absence of adult salmonids). The
sampling length for all mainstem habitat units sampled using boat electrofishing was equal to 20
times the wetted channel width of the habitat unit, the entire length of the habitat unit, or 500 m
(1,640 ft), whichever was less. When site conditions did not allow for boat electrofishing, 200 m
(328 ft) were sampled using wadeable sampling techniques parallel to the bank. The sampling
unit length for all upland and side slough habitat units was 20 times the wetted channel width of
the habitat unit, the entire length of the habitat unit, or 200 m (656 ft), whichever was less. If the
randomly selected habitat unit was totally inaccessible to field crews, then a second randomly
selected habitat unit was sampled.
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4.1.3. Rotary Screw Trap Sites
Final site selection for Upper River rotary screw traps used the following criteria: 1) a position
downstream of documented Chinook salmon; 2) landowner permission to access; 3) accessibility
by helicopter; 4) a minimum depth of 1.25 m (4.1 ft) during low flow periods; and 5) consistent
laminar flow with velocities in the range of 0.6 to 2 m/s (2 to 6.6 ft/s). Site reconnaissance
included review of aerial videography from summer 2012, a pre-bank-ice break-up site visit to a
short list of locations on May 24, and a final pre-installation site visit on June 7. For the Oshetna
River, a location just upstream of the confluence with the Susitna River (PRM 235.1) at Oshetna
RM 0.1 was selected (Figure 4.1-7). This location is downstream of the only documented
observation of juvenile Chinook in the Oshetna basin at a side channel near Oshetna RM 1.7
(Buckwalter 2011). A second rotary screw trap site was selected on Kosina Creek near RM 2.2.
This location was downstream of the Tsisi and Kosina Creeks confluence where Chinook salmon
spawning has been documented upstream (HDR 2013).
4.1.4. PIT Interrogation Antenna Sites
PIT tag antenna interrogation sites were determined using the following criteria: 1) a location
downstream of documented Chinook salmon, 2) landowner permission to access, 3) helicopter
accessibility, 4) a maximum depth of around 0.5 m (1.64 ft), and 5) lower velocity areas where
installation and maintenance could be done safely under a range of flow conditions.
In the Oshetna River, site selection focused on locations as near to the Susitna River confluence
as possible. A side channel near RM 1.9 along the left bank (facing downstream) was initially
selected that could be monitored across its full width and in which Buckwalter (2011) had
documented juvenile Chinook salmon. However, water levels dropped upon returning to this
location and the continued reductions in flow expected through the summer would limit fish use
of this feature. Instead, a site at the head of a side channel along the left bank near Oshetna RM
4.5 was chosen. A 60-ft antenna was installed on June 19, 2013 at the head of the side channel
and then rotated out into the main channel as side channel flow decreased during the season
(Figure 4.1-7).
The area of Kosina Creek near the Tsisi Creek confluence was generally high energy with
abundant boulder substrates, which can confound the effective installation of an antenna. During
the reconnaissance survey, areas where an antenna would capture a substantial portion of the
channel had water depths and velocities that precluded wading and antenna installation. The
lower portion of Tsisi Creek was also investigated but had the same limitations. Areas of Kosina
Creek upstream of the Tsisi Creek confluence were found to have a lower gradient more suitable
for antenna installation. However, the channel was substantially broader (greater than 300 ft)
and an antenna along the channel margin here could only cover an inconsequential portion of the
channel with minimal detection efficiency. Sites lower in Kosina Creek were investigated and
the side channels near the Susitna River confluence were found to have conditions more suitable
for antenna installation. Full coverage of a side channel increased detection probabilities by
confining fish movements within a closed channel. Likewise, installing an antenna lower in the
tributary (RM 0.2) increased the number of fish moving past the antenna to or from the Susitna
River. A 5 x 1.5 m (16 x 4.9 ft) swim-though type antenna was installed in a Kosina side channel
on June 18, 2013. This location and antenna style were selected for robust operation over a
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range of flow conditions downstream of documented Chinook spawning location (Link et al.
2013).
4.1.5. Fixed Radio Telemetry Sites
Three fixed radio telemetry stations were installed in the Upper Susitna River. Stations at the
mouths of Kosina Creek (PRM 209.1) and the Oshetna River (PRM 235.1) monitored the
movement of radio-tagged fish in the mainstem Susitna River as well as in their respective
tributaries. The Deadman station (PRM 191.2) was located on the north bank of the Susitna
River between Deadman and Watana creeks and monitored the movement of fish in the
mainstem of the Susitna River (Figure 4.1-7).
4.1.6. Variances from the Study Plan
4.1.6.1. Fish Distribution and Abundance Sites
4.1.6.1.1. Sampling Unit Length
Fish distribution and abundance sampling units were sampled at lengths of 500 m (0.3 mi) when
boat electrofishing was feasible as recommended the in April 1, 2013 Study Plan Determination
and outlined in the Implementation Plan (IP Section 5.4). However, the level of effort required to
effectively cover and gather a representative sample in long units, using other techniques
including backpack electrofishing, snorkeling, minnow trapping, and seining, was deemed
incompatible with the seasonal sampling goals and the number of sites targeted for sampling
given the remoteness of the sampling locations. Therefore, when boat electrofishing was not
feasible, sampling units were shortened to either the complete mesohabitat unit or 200 m (656 ft)
per mesohabitat type per site, whichever was shorter.
4.1.6.1.2. Site Access Issues
The lower reaches of tributaries of the Upper Susitna River are typified by high gradient,
confined canyons, with dense vegetation. These conditions, particularly in the smaller tributaries,
limited helicopter access. Other factors that influenced sampling locations included dangerous
sampling conditions (high water, high wind, and icy conditions) and dry target sites.
Land ownership and accessibility influenced fish sampling in discrete areas of the Upper River.
Upper River tributary sites on Cook Inlet Regional Working Group (CIRWG) land were
restricted from access; this included an area from the proposed dam site (PRM 187.1) to PRM
198.7 (right bank) and 204.9 (left bank) and directly impacted sampling Unnamed Tributaries
197.7 and 204.5.
Prior to sampling in July, the 121 target sites (101 GRTS selected tributary sites: IP Section
4.4.1; 20 Upper River mainstem transects: IP 4.4.2) and 2 direct sample tributaries were visited
and assessed for safety. Following the reconnaissance visit, 13 target GRTS sites deemed not
conducive to sampling were replaced, consistent with GRTS protocol. Sampling took place at 81
GRTS selected tributary sites, 1 direct sample tributary, and 16 Upper River mainstem transects
for a total of 97 target sites. Of the 33 GRTS tributary sites that were not sampled or replaced
with oversamples; 24 (73 percent) had no safe landing zone in the vicinity, 7 (21 percent) were
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located on CIRWG land where access was not permitted, and 2 (6 percent) were deemed to have
dangerous sampling conditions. During each seasonal sampling event, two days of sampling
effort were applied to Jay Creek, the accessible direct sampling tributary. Deadman Creek could
not be sampled due to CIRWG land in the lower reaches and a lack of safe landing zones in
upper reaches. A total of 16 Upper River mainstem transects were sampled; three transects were
deemed to be unsafe for sampling efforts due to swift water and boulder gardens in constricted
canyons and one transect could not be accessed for sampling due to CIRWG land extending to
the water’s edge.
4.1.6.2. Rotary Screw Traps
The inability to access areas above ordinary high water mark along CIRWG land restricted the
placement of rotary screw traps (IP Section 5.7.1) and fixed radio receivers (IP Section 5.8.2.1)
in the Upper River to locations on State of Alaska or Federal land. A third rotary screw trap
could not be cited near the proposed dam site as recommend in the April 1, FERC SPD (B-134).
Rotary screw traps were fished near the mouths of the only two known Upper River tributaries
that support Chinook salmon, Kosina Creek and the Oshetna River.
4.1.6.3. PIT tag interrogation system
The IP proposed that two stationary PIT tag interrogation systems would be installed in
tributaries to the Upper River mainstem, specifically in the Oshetna River near its confluence
with the Susitna River and in Kosina Creek at the confluence with Tsisi Creek. A
reconnaissance survey was conducted on June 11, 2013 to determine the feasibility of installing
PIT antennas at these two sites and to identify alternative sites if necessary. The mainstem
channels of both the Oshetna River and Kosina Creek were found to be too wide, typically
greater than 61 m (200 ft) for installing antennas that would span the entire channel. Thus,
alternate sites were investigated where channel margin or side channel antennas would be
feasible and the likelihood of detecting tagged fish moving past the site would be maximized
given the size constraints of PIT antenna technology.
4.1.6.4. Radio Telemetry Fixed Receivers
Section 5.8.2.1 of the Implementation Plan included information on proposed fixed-station
receiver sites for the Salmon Escapement Study will be operated at ten strategic locations in the
Middle and Upper River including: Lane Creek Station (PRM 116.7), Gateway (PRM 130.1),
Fourth of July Creek (PRM 134.3), Indian River (PRM 142.1), Slough 21 (Approximately PRM
144), Portage Creek (PRM 152.3), Cheechako Station (RM 152.4), the Chinook Creek
confluence (PRM 160.5), Devils Station (PRM 166.9, located upstream of the Devils Creek
confluence), and the Kosina Creek confluence (PRM 209.2). The locations for the eight
proposed resident fish stations are included in Figure 5.6-1 and include: Montana Creek
confluence (PRM 80.1), Whiskers Creek confluence (PRM 105.1), Indian River confluence
(PRM 142.1), Portage Creek confluence (PRM 152.3), Fog Creek confluence (PRM 179.3),
Watana dam site (PRM 187.1), Watana Creek confluence (PRM 196.9), and Oshetna River
confluence (PRM 235.1). However, the lack of access to Cook Inlet Region Village Corporation
land necessitated a number of changes from the Study Plan in regard to the quantity and location
of telemetry fixed stations in the Upper River during 2013. Fixed stations planned for the
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Watana Dam Site and the mouth of Watana Creek were not installed due to the lack of land
access. To gather radio tag detections in this area, a fixed receiver was installed on the bluff on
the north side of the Susitna River between Deadman and Watana creeks.
4.2. Sampling Frequency
Sampling frequency varied among sites based on study objectives. Generally, sampling occurred
seasonally during the ice-free period. Breakup in 2013 was unusually late across Southcentral
and Interior Alaska. Sustained record-cold weather in April and May prevented substantial
snowmelt or ice decay until late May, several weeks after breakup is typically over in the region
(ISR Study 7.6). Ice breakup activity was concentrated between May 25 and May 29 and the
Susitna River at Gold Creek was above flood stage from May 28 to June 4, 2013. Bi-weekly
early life history sampling was initiated shortly after ice-out out and continued through June in
an attempt to capture critical juvenile Chinook salmon out-migration from natal tributaries to
rearing habitats (Table 4.2-1). Fish distribution and abundance sampling was conducted in three
seasonal blocks in 2013: July 13 to August 11, August 12 to September 9, and September 10 to
October 4. PIT tag interrogation antennas were installed on June 18 and 19, 2013 in the Oshetna
River and Kosina Creek and were operated nearly continuously until October 8 (Figure 4.2-1).
Installation of rotary screw traps took place between June 12 and14 at Kosina Creek (RM 2.2)
and on June 14 at the Oshetna River (RM 0.1). Rotary screw traps were then operated on a 48-
hours-on/72-hours-off schedule until the rivers began to freeze up and the traps were removed on
October 3 and October 9, 2013 (Figure 4.2-2). Stationary radio receivers were installed at the
Deadman Creek, Kosina Creek, and Oshetna River sites between June 29 and July 2 (Table 4.2-
2). Fixed radio telemetry monitoring efficiency was tested on a weekly basis (Table 4.2-3).
Aerial surveys were conducted approximately weekly between July 2 and October 7 (Table 4.2-
4) and continued monthly thereafter. The monthly schedule is planned to continue through April
2014.
4.2.1. Variances from the Study Plan
The applicant accepted and followed the FERC recommendation of sampling in mid-July and
late August/early September and added an additional fall sampling effort in late September/early
October. Additional sampling for early life history was also added in June.
4.3. Fish Sampling Approach
The initial task of this study, included in the Implementation Plan, consisted of a focused
literature review to guide selection of appropriate sampling methods. Products from the
literature review included 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.
• 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.
The fish sampling techniques selected depended on habitat characteristics, season, and the
species or life history of interest. A summary of relevant existing fish and aquatic habitat
information collected in the Susitna River study area was provided in the Implementation Plan.
The literature review focused on five study topics: (1) resident and juvenile fish distribution and
abundance in the Upper Susitna River (1980s and 2012); (2) adult salmon escapement and
distribution (1980s and 2012); (3) salmon and trout incubation and emergence (1980s); (4)
aquatic habitat delineation (2012); and (5) open-water flow routing modeling (2012). Although
an abundance of data had been collected, the 1980s information summarized was selected
primarily to guide site selection and sampling techniques for the Study of Fish Distribution and
Abundance in the Upper River.
4.4. Objective 1: Fish Distribution, Relative Abundance, and Habitat
Associations
AEA implemented the methods as described in the Study Plan with the exception of variances
explained below (Section 4.4.4). Two general approaches to fish sampling were used. The first
focused on gathering data on general fish distribution (presence). This sampling involved a
single pass with appropriate gear types without using block nets. To the extent possible,
transects were standardized and the methods were repeated during each sampling event to
evaluate temporal changes in fish distribution. The second sampling approach was to gather data
on relative abundance as determined by CPUE and density; complementary data on fish size,
age, and condition factor were also collected. The transects and fish capture methods (e.g.,
number of passes, amount of soak time, use of block nets when feasible) were standardized such
that they were repeatable on subsequent sampling occasions. This approach also emphasized the
identification of foraging and spawning habitats.
4.4.1. Task A: Fish Distribution Surveys
4.4.1.1. Field Methods
Fish distribution surveys included seasonal sampling events during the ice-free seasons.
Methods were selected based on target species, life stages, and water conditions. Snorkeling and
electrofishing were preferred methods for juvenile fishes in clear water areas where velocities
were safe. Minnow traps, beach seines, set nets, and fyke nets were employed as alternatives in
deeper waters and in habitats with limited access, low visibility, or high velocities. For larger
fishes, gillnets, seines, trotlines, hoop traps, and angling were used. Whereas snorkeling,
minnow trapping, backpack electrofishing, and beach seines were applicable to sloughs and other
slow-moving waters, gillnetting, boat electrofishing, hoop traps, and trot lines were more
applicable to the mainstem. The decisions about what methods to apply were made by field
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crews based on Appendix 3 of the Fish Distribution Abundance Implementation Plan (Gear
Selection) 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.
4.4.1.2. Analytical Methods
For the purposes of describing juvenile salmon and resident fish distribution in the Upper River,
locations where species were documented during the various study components of this study
were pooled with other available information from 2012 and 2013 AEA fish studies. The list of
data sources included: early life history sampling, rotary screw trapping, fish distribution and
abundance sampling, PIT array detections, resident fish radio-telemetry detections, directed fish
sampling efforts for interrelated studies, genetics sampling efforts (ISR Study 9.14), and
metal/mercury sampling efforts (ISR Study 5.5). The 2013 data for fish distribution was pooled
with 2012 fish distribution data (HDR 2013).
To describe seasonal distribution, fish collections were then assigned the following seasons:
Salmon Early Life History (June 4 to June 30), Early Summer (July 1 to August 10), Late
Summer (August 11 to September 9), and Fall (September 10 to October 7).
4.4.2. Task B: Relative Abundance
4.4.2.1. Field Methods
Relative abundance surveys included seasonal sampling events during the ice-free season. As
described above, methods were selected based on target species, life stage, and water conditions.
All methods were conducted with a level of effort consistent with generating estimates of CPUE
that facilitated comparison of counts or densities of fish over space and time. This included
calibration and quality control of methods and documentation of conditions that affected
sampling efficiency, such as visibility, water temperature, and conductivity, to ensure that
consistent effort was applied within and among sampling units and events.
4.4.2.2. Analytical Methods
Sites identified as distribution sampling and relative abundance sampling were combined for
estimates of CPUE because multiple pass sampling was not employed for relative abundance.
This resulted in a larger overall sample size for estimating relative abundance. The approach
used to estimate CPUE was generally similar among the three types of relative abundance
protocols in the Upper River (i.e., GRTS tributaries, direct-sampling tributaries, and mainstem
transects). For GRTS tributary sampling, CPUE was calculated specific to each mesohabitat
type present within a given GRTS segment and then averaged among segments to derive a
representative CPUE value for each mesohabitat type within each GRTS tributary. Estimates
derived for direct sampling tributaries were obtained in the same fashion, except estimates were
averaged across direct sample sites, instead of GRTS segments, for each tributary. Mainstem
CPUE estimates were derived for each mesohabitat type within a macrohabitat unit and then
averaged among macrohabitat units within each mainstem geomorphic reach. Although the
sampling design for the Upper River mainstem did not distinguish between various main channel
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types (i.e., main channel, split main channel, and multiple split main channel), average CPUE
estimates for the main channel macrohabitat types have been generated at this finer level of
classification. When sampling within a GRTS segment, a direct sampling site, or a mainstem
macrohabitat site included multiple mesohabitat units of the same type (e.g., two distinct pools),
catch and effort were summed at the mesohabitat level prior to averaging. In all cases, estimates
were derived specific to the each of the three Fish Distribution and Abundance sampling events
(i.e., early summer, late summer, and fall).
Although CPUE estimates were derived in a similar manner across the three types of relative
abundance sampling in the Upper River study area, it is important to note that these study
components had different study designs and utilized different site selection processes. Therefore,
caution should be used when making quantitative comparisons among areas where different
protocols were used. Tributaries sampled in the Upper River study area were non-randomly
selected and thus should not be used to draw inferences about other Upper River tributaries.
Furthermore, unlike the GRTS sampling design, direct sampling sites were not randomly
selected with a tributary, and therefore, the relevance of the averaged CPUE estimates to the
unsampled portions of a direct sample tributary is unknown.
Gear-specific CPUE estimates were derived for each species, as well as Pacific salmonid life
stages. For the purposes of this draft ISR, the four gear types used to determine CPUE included:
backpack electrofishing, boat electrofishing, seining, and snorkeling. For backpack and boat
electrofishing, CPUE was estimated as the number of fish captured per hour of electrofishing
pulse time. Snorkeling and seining CPUE estimates were standardized as the number of fish
captured or observed per 1,000 m2 sampled. Additional details regarding CPUE calculations and
associated gear-specific sample sizes can be found in Appendix D.
4.4.3. Task C: Fish-Habitat Associations
In conjunction with Tasks A and B, data was collected for fish distribution and abundance by
macro and mesohabitat type.
4.4.4. Variances from Study Plan
4.4.4.1. Sampling Approach
In the Revised Study Plan (Section 9.5.4.3.1), the applicant proposed that relative abundance
sampling would include multiple pass sampling when electrofishing, snorkeling, and minnow
trapping were employed. However due to ADF&G permit stipulations limiting electrofishing
efforts to one pass, the April 1 FERC SPD recommendation that minnow traps be set for 24
hours, and the extensive level of effort involved in three pass snorkeling 200 m (656 ft) sampling
units, multiple pass sampling for relative abundance was abandoned.
Study teams experimented with comparing three-pass depletion minnow trapping to 24-hour sets
for relative abundance sampling during the July sampling event and found the level of effort
required to return to sites to check and re-bait traps impeded the progress of sampling.
Ultimately the FERC recommendation of 24-hour or overnight soaks was adopted.
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The FERC Study Plan Determination recommended placing minnow traps at a density of 20
traps per 200 m (656 ft) of habitat sampled and placing traps strategically in places most likely to
catch fish. However, due to limited helicopter capacity and the need to carry many gear types, it
was not feasible to transport the volume of minnow traps required to meet the FERC SPD
trapping density; on average this would have required each crew to carry approximately 60 traps.
Instead, one to fifteen (generally 2 to 6, median =3) minnow traps were placed in each
mesohabitat appropriate for minnow trapping in areas most likely to catch fish. Because of the
high gradient nature of the Upper Susitna River the most common mesohabitats (boulder riffle
and riffle) were only marginally suitable for minnow trapping in pocketwater. The lower density
of minnow trapping in the Upper River study may impact AEA’s ability to meet the stated fish
relative abundance study objectives for fish species generally susceptible to this gear type.
However, because multiple gear types were used at each site, it is anticipated that another type
may be used for analysis, in which case, low density minnow trapping would not impact AEA’s
ability to meet the study objectives.
Block nets were not used in Upper River sampling because habitats were not appropriate for use.
The lack of block netting may result in some fish being disturbed and moving between
mesohabitats during sampling; however this is not anticipated to impact AEA’s ability to meet
the stated study objective for fish habitat associations.
To streamline sampling, after initial sampling with varying soak times for different gear types,
fyke net and hoop trap soak times were adjusted to a sampling regime that matched that of
minnow trapping: a 24-hour overnight soak. Standardization of fyke net and hoop trap soak
times to an overnight soak is common practice and did not impact AEA’s ability to meet the
stated study objective.
In Appendix 3 of the Implementation Plan, Protocol for Site-Specific Gear Type Selection, AEA
recommended that three or more sampling techniques be used at each site, but a minimum of two
sampling techniques were to be attempted per habitat (or mesohabitat) type. However, during
implementation there were times (approximately 4 percent of mesohabitats) when only one
sampling technique was used in a habitat (or mesohabitat) unit. This occurred in habitats that
were not conducive to multiple sampling techniques (e.g. very shallow, high velocity riffles
were only backpack electrofished). The decision to use applicable methods was made in the
field based on site conditions while using the Gear Selection Appendix as a guide. This meant
that sampling techniques were not forced into habitat where they would not be effective (e.g.,
placing baited minnow traps where the velocity was too high). This adjustment did not
compromise AEA’s ability to meet study objectives.
4.4.4.2. Use of sonar
Although sonar was used as part of the escapement study, DIDSON and video cameras were not
employed as techniques for sampling juvenile anadromous or resident fish in the Upper River
during ice-free sampling period as proposed in the RSP (Section 9.5.4.4). Underwater video was
used occasionally during snorkel surveys to document and corroborate species identification.
The lack of sonar as a fish sampling technique did not impact AEA’s ability to meet the stated
study objective.
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4.5. Objective 2: Seasonal Movements
AEA implemented the methods for Objective 2 as described in the Study Plan with the exception of
the variances explained in Section 4.5.4.
4.5.1. Task A: Document the timing of downstream movement and catch for all
fish species using out-migrant traps.
As described in Section 4.1.3 and Section 4.2, two rotary screw traps were deployed in the Upper
River study area shortly after ice break-up. In addition to collecting data on migratory timing,
size-at-migration, and growth, rotary screw traps also served as a source of juvenile fish to PIT
tag (Objective 2, Task B), a way to recapture previously PIT-tagged fish, collect fish for radio
tagging (Objective 2, Task B), collect fish for stomach contents analysis in support of the River
Productivity Study (ISR Study 9.8), and collect tissue samples (Objectives 4,5 & 7) to support
other studies including the Genetic Baseline Study for Selected Fish Species (ISR Study 9.14).
4.5.2. Task B: Describe seasonal movements using biotelemetry.
Biotelemetry techniques included radio telemetry and Passive Integrated Transponder (PIT)
technology. Half duplex PIT tags (12 and 23 mm [0.5 to 0.9 in]) were surgically implanted in
fish greater than 60 mm (2.4 in) to monitor movement and growth. Fish for PIT tagging were
captured opportunistically during fish distribution and abundance sampling, targeted sampling
for juvenile Chinook salmon, and with rotary screw traps.
PIT Tagging in the Upper River was focused in proximity to array antennas and included the
Oshetna, Black, Goose, Jay, and Kosina drainages as well as the mainstem Susitna between
PRMs 200 and 235.1 (Figures 4.5-1 and 4.5-2). Target species for PIT tagging included juvenile
anadromous salmon, Arctic grayling, Arctic lamprey, burbot, Dolly Varden, northern pike,
rainbow trout, humpback whitefish, and round whitefish. Of these species juvenile Chinook
salmon, Arctic grayling, burbot, Dolly Varden, humpback whitefish, and round whitefish were
present and PIT tagged in the Upper River Study area (Table 4.5-1). Because many species are
rare or present in low abundance in the Upper River, progress towards PIT tagging goals was
below the maximum target of 1,000 tagged fish of each species per array for all species except
Arctic grayling. Recaptured fish provided information on the time and distance travelled since
the fish was last handled and growth. PIT tag antenna arrays with automated data logging were
installed and operated on a side channel of Kosina Creek RM 0.2 and a side/partial main channel
of the Oshetna River RM 4.5 (Figures 4.5-3 and 4.5-4).
For radio telemetry, AEA targeted Arctic grayling, burbot, Dolly Varden, lake trout, longnose
sucker, rainbow trout, humpback whitefish, round whitefish, and northern pike when present
(Table 5.4-2). Several target species were rare or absent from the Upper River study area
including humpback whitefish, lake trout, rainbow trout and northern pike. One juvenile lake
trout and 12 humpback whitefish were captured during FDA sampling. Most of the humpback
whitefish of taggable size were captured during installation and testing of the Oshetna rotary
screw trap in June before tag implantation had begun. Of the remaining species that were more
common in the study area, the tagging goal (30) for Arctic grayling was exceeded (57); numbers
for round whitefish were over halfway towards the goal (18), while burbot (7) and longnose
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suckers (10) were difficult to acquire for tagging (Table 4.5-2). Radio transmitters were
surgically implanted in adult fish of sufficient body size distributed temporally and
longitudinally in the Upper River to monitor movement patterns (Table 4.5-1). Radio-tagged fish
were tracked from July through October 7, 2013 with weekly aerial surveys in conjunction with
the Salmon Escapement Study (ISR Study 9.7) to describe seasonal movements within the
hydrologic zone of influence upstream of the Project (Table 4.2-4). Aerial surveys were
partitioned into mainstem Susitna and tributary zones (ISR Study 9.6, Appendix B, Figure B20).
4.5.3. Task C: Describe juvenile Chinook salmon movements.
Juvenile Chinook salmon movement within the Upper River was described using the rotary
screw traps and biotelemetry methods outlined in Objective 2, Tasks A and B. All juvenile
Chinook salmon greater than 60 mm (2.4 in) in length were evaluated for PIT tagging. Fish
deemed to be taggable based on size and condition were implanted with a PIT tag to document
seasonal movement using antenna arrays placed in tributary mouths and side channels and rotary
screw traps. Rotary screw traps were also used to document juvenile Chinook salmon migratory
timing and size-at-migration from natal tributaries.
4.5.4. Variances from Study Plan
4.5.4.1. Evaluation of PIT tag interrogation system Detection Efficiencies
The IP (Section 5.6.2) proposed that the detection efficiency of PIT tag interrogation systems be
determined using indirect methods as described by Connolly et al. (2008). This approach relies
on the detection of fish at multiple locations (i.e., antennas located upstream and downstream) to
identify missed detections of fish passing a given antenna. However, the limited availability of
appropriate sites for antenna installation in 2013 precluded this approach because antenna sites
could not be arranged in a longitudinal series; instead antennas were installed at a single site
within a given tributary or slough. Handheld detections of fish upstream or downstream of a
given PIT tag antenna during initial tagging and following recapture by rotary screw trap,
electrofishing, or other methods provided some indication of the detection efficiency of each
antenna. Whether the number of such recaptures was adequate to estimate detection efficiencies
will be determined during analysis during the next year of study and presented in the Updated
Study Report (USR).
As an alternative approach for estimating detection efficiency, AEA measured the read range of
each antenna for each tag size. This information, combined with the antenna dimensions, water
depth over the antenna (for a swim-over configuration), and wetted channel width was used to
estimate the percentage of the channel’s cross-sectional area in which a tag would be detected.
This information was routinely recorded during site visits to download data. This approach did
not account for behavioral factors that could influence detection, such as fish position relative to
the channel bottom or margins, or swimming speed relative to the antenna. Nonetheless, this
approach offered a means of quantifying the probability of a fish being detected as it moved past
an antenna.
In addition, detection efficiencies were evaluated by drifting neutrally buoyant test tags past an
antenna and calculating the percentage of tags that were detected. Again, this approach did not
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account for behavioral factors that would influence detection, but it did offer an additional means
of estimating the probability of detection. This effort occurred during site visits to demobilize
and winterize antennas in October 2013.
4.5.4.2. Radio Tagging Targets
The following FERC recommendation (B-135) was not adopted by AEA:
“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.”
The FERC-recommended approach targets fish when they will potentially be at a phase of their
life history (pre-spawning development) when they are more energetically taxed (as a result of
limited food availability during the winter months) and potentially more sensitive to the stresses
associated with handling. In particular, rainbow trout and Arctic grayling spawn in the early
spring, and allocate the majority of their pre-winter energetic gain toward development of
gametes. They have limited energy reserves remaining for metabolic processes in the spring.
Further, sexually maturing fish have less space in their abdominal cavity due to enlarged sex
organs; there is less room for insertion of a tag and there is a higher chance of internal injuries
during the surgical procedure. Surgically tagging these species in close temporal proximity to
their spawning migration (e.g., “immediately prior”) may have too high a metabolic cost and a
higher risk for injury that could increase post-tagging mortality relative to fish tagged outside
this life history phase. The average tag life, in days, for rainbow trout and Arctic grayling tags is
450, 652, and 901 for the smallest to the largest tags, respectively. AEA recommended that the
primary period for tagging these fish be the summer or fall; the time when they are at an
energetic maximum and likely to be most resilient to the stresses associated with handling. The
available tag life should allow data to be collected the following year on spawning migrations
and spawning habitat destinations. Tagging the identified species during the specified periods
was done based on the surgeon’s discretion.
4.5.4.3. Aerial Surveys
Section 5.8.2.2 of the Implementation Plan stated that the proposed frequency of aerial surveys
would provide a means of focusing a higher-resolution and time-intensive tracking effort on
identifying exact locations of spawning and holding fish. To do this, the most recent observed
river locations (to the nearest 1 km [0.62 mi]) of all fish “at large” would be made available to
the aerial survey team. During the survey, the location of all detected fish would be compared to
the last seen location from previous surveys to ascertain whether its position had changed by
more than 2 km (1.25 mi). When tagged fish were within 2 km of their last observed location,
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the helicopter would circle at a lower altitude to pinpoint the fish location to mainstem, side
channel, or slough habitats.
Survey methods for radio-tagged resident fish were modified from the Implementation Plan to
accommodate the high number of frequencies that needed to be scanned for salmon and resident
fish. Resident tag frequencies were programmed into a receiver and scanned automatically. No
manual tracking, directed searching, or identification of habitat type was conducted during the
period when adult salmon were being tracked. Resident tag frequencies were tracked manually
during the period when adult salmon tags were not present. Specific aerial survey methods were
not identified in the RSP, but were described in Section 5.8.2.2 of the Implementation Plan. The
variance in aerial telemetry survey method may not have had a negative effect on meeting the
stated objectives of the study because geographic positions of the tags could be related to digital
habitat classifications made by other studies in AEA’s program. However, the lack of directed
effort at pinpointing tag locations (accuracy less 100 yd for some resident fish tags) may make
habitat use inferences less accurate if habitat delineations were much smaller than the resolution
of the tag positions.
4.6. Objective 3: Early Life History
AEA implemented the methods for Objective 3 as described in the Study Plan with the exception of
the variance explained in Section 4.6.2.
4.6.1. Determine movement patterns and timing of juvenile salmonids from
spawning to rearing habitats.
Earl y life history (ELH) sampling described fish distribution in Upper River tributaries with a
focus on locating juvenile Chinook salmon during the early open water season. There was also a
secondary objective to investigate the outlet area of two lakes for the presence of juvenile
sockeye salmon. Sites were selected in the field in accordance with the methods outlined in
Section 4.1.1. The target sample length was 100 m (328 ft) of each mesohabitat type accessible
at each site. Sampling methods included electrofishing, fyke nets, and downstream migrant traps
(Objective 2, Task A). Two sampling events took place in June as described in Section 4.2.
During the first event, 41 mesohabitat units within 21 sites were sampled (Figure 4.1-1). Over
3,600 m (2.2 mi) of stream were electrofished and 12 fyke net days were completed. During the
second event, a total of 43 mesohabitat units were sampled within 20 sites. Just over 3,500 m
(2.2 mi) of stream were electrofished and 12 fyke net days were completed. Rotary screw trap
sampling continued throughout the open water season. Biotelemetry could not be used for this
task because juvenile salmonids were too small to tag at this life stage.
4.6.2. Variances from Study Plan
Unlike the RSP for the Study of Fish Distribution and Abundance in the Middle and Lower
Susitna River (Study 9.6), the Upper River Study Plan and Fish Distribution and Abundance
Implementation Plan did not include an objective for Upper River salmon early life history
sampling (Section 9.5.5). When AEA adopted the FERC recommendation of seasonal sampling
in mid-July and late August/early September in the Upper River additional locations were added
to gather information during the period from ice break-up to July. Because the data from the
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1980s showed the bulk of Chinook salmon moving out of Middle River rearing habitat by mid-
July, AEA was concerned the same outmigration timing could occur in the Upper River and thus,
tributary sampling starting in mid-July might miss a large component of rearing juvenile
Chinook salmon. Thus, AEA added two directed sampling events to survey habitats where early
life stages of juvenile salmon might be expected to be rearing based on 2012 known spawning
distributions as well as incidental reports of salmon spawning activity from ADF&G.
4.7. Objective 4: Characterize the seasonal age class structure,
growth, and condition of juvenile anadromous and resident fish
by habitat type.
AEA implemented the methods for Objective 4 as described in the Study Plan with the exception of
the variances explained in Section 4.7.1. In conjunction with Objectives 1 and 2, captured fish
were identified to species and classified to life stage or smolt index when possible. A summary
of fish length-at-maturation for the region was used as a basis for assigning life stages (Table
4.7.1). Each time a gear was used for sampling, a random sample of 25 individuals per species,
life stage, and site were measured for fork length (FL) in millimeters and measured in grams.
For species without a forked tail (e.g., sculpin and burbot), total length was measured laterally
along the mid-line from the anterior edge of the snout to the posterior edge of the tail. The total
sample size of fishes measured for length and weight in 2013 is presented in (Table 4.7-2).
Species were classified by life stage (Table 4.7-1) and when sample sizes were sufficient natural
breaks in length-frequency were used to further refine size bins. Recaptured PIT-tagged fish
(Objective 2, Task B) provided growth rate information. Parameters recorded in each habitat
unit included the number of fish by species and life stage, fork length, weight, global positioning
system (GPS) location of sampling unit, time of sampling, weather conditions, water
temperature, water transparency, behavior, and the location and distribution of observations.
For the ISR, condition factors were compared by habitat for Chinook salmon and Arctic grayling
only. Prior to analysis of fish condition by habitat type, outliers that might skew comparisons
were identified and removed. A log-log regression on length vs. weight for all measured fish
within a species was fitted, including fish captured in migrant traps. The Grubbs test (Grubbs,
1950, Lukasz, 2011) was then used for sequentially identifying outliers in the residuals from
these regressions. The experiment-wise error for the outlier removal for each species was
maintained at 0.05 by using alpha of 0.05 divided by the total number of outliers for each
sequential test. The resulting condition factors were also evaluated to ensure there were no
obvious differences among size or age classes of fish before combining. Fish condition, or
wellbeing, was estimated using Fulton’s condition factor where the coefficient of condition, K-
FL was derived from the formula: K-FL = W x 105/L3, where K-FL = condition factor by fork
length, W = weight of fish in grams, and L = fork length of fish (mm) (Fulton 1902, Fulton
1904). Specific growth rates were estimated as SGR= 100*(ln(L2) –ln(L1))/(d2 - d1), where L2
= mean length on day (d) 2 and L1 = mean length on day (d) 1, and (d2 - d1) is the number of
days between measurements. When all data were combined, fish condition factors were
relatively stable across life stages, although estimates for fry were more variable and perhaps
higher for Arctic grayling (Figure 4.7-1). Therefore, life stages were combined for the habitat
anal ysis, but fry (less than 50mm [2 in] for Chinook; less than 60mm [2.4 in] for Arctic grayling)
were not included. The total sample sizes of fish included in the condition factor analysis by
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Geomorphic Reach or Tributary are included in Table 4.7-3. Note that fish from distribution and
abundance sampling (Objective 1, Section 4.4), and ELH studies (Objective 3, Section 4.6) were
included in this analysis.
4.7.1. Variances from Study Plan
4.7.1.1. Collection of Lengths and Weights
The Implementation Study Plan stated that each time sampling gear was checked, a random
sample of 25 individuals per species, life stage, and site would be measured for fork length (FL)
and weighed (IP Section 5.1.5). However, the FERC SPD mistakenly interpreted AEA’s study
plan as proposing to measure and weigh all fish and no modifications were recommended (SPD
p. B-130). Due to ADF&G fish collection permit restrictions on fish handling; only the first 25
individuals of each species were weighed and measured during each check of a rotary screw trap.
The sample size of 25 measurements per species per life stage per site is consistent with
collecting the data necessary to evaluate length frequency distributions and condition factor for
fish by species, gear type and macrohabitat and thus, will be sufficient to meet the study
objective.
4.7.1.2. Age Assignment
As an initial step towards assigning age-classes to the 2013 fish collections, a literature review
was conducted compiling information collected in the Susitna Basin during the 1980s
hydropower licensing efforts and relevant studies from Alaska. The literature review revealed
substantial individual variability in growth and overlap in size-at-age classes, particularly for fish
two years of age and older. The review also found considerable variability in growth and size-at-
age from different locations or regions within the basin adding further ambiguity to the task of
assigning age to size. AEA determined that ages could not be assigned with certainty to Susitna
River fishes based on length. The objective of documenting the seasonal age class structure of
juvenile anadromous and resident fish by habitat type (RSP Section 9.6.4.3.5) was therefore
replaced with seasonal size structure by habitat type. Evaluating habitat associations by size
instead of age will continue to meet the objective of documenting the seasonal life stage use,
growth and condition of species associations with habitat types.
4.8. Objective 5: Determine whether Dolly Varden and humpback
whitefish residing in the Upper River exhibit anadromous or
resident life histories.
AEA implemented the methods for Objective 5 as described in the Study Plan with no variances.
Dolly Varden and humpback whitefish greater than 200 mm (7.9 in) in length were targeted for
otolith collection to test for marine-derived elements indicative of an anadromous life history
pattern. AEA assumed that larger fish were more likely to have exhibited anadromy and
therefore otoliths were collected from fish greater than 200 mm (7.9 in) in length. Thirty fish of
each species were targeted for collection during 2013 with an additional 30 proposed for the next
year of study (60 fish of each species total). A total of 28 adult Dolly Varden were collected in
the Upper River in 2013. Adult humpback whitefish were extremely scarce in the Upper River
and none were collected (Table 4.8-1). Analysis will be conducted during the next study year.
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4.9. Objective 6: Determine baseline metal and mercury
concentrations in fish tissues for resident fish species in the
mainstem Susitna River.
AEA implemented the methods for Objective 6 as described in the Study Plan with the exception of
the variance explained in Section 4.9.1. Tissue or whole fish samples were collected in the
reservoir inundation zone for assessment of metals (ISR Study 5.5, Baseline Metal Levels in Fish
Tissue) and mercury concentrations (ISR Study 5.7, Mercury Assessment and Potential for
Bioaccumulation Study). Target fish species for baseline metals testing included: Arctic
grayling, burbot, Dolly Varden, longnose sucker, lake trout, rainbow trout, and whitefish species.
Targets for mercury sampling included seven adult individuals of the following species: Arctic
grayling, burbot, Dolly Varden, long nose sucker, sculpin, stickleback, lake trout, rainbow trout,
humpback whitefish, and round whitefish (Table 4.9-1).
4.9.1. Variances from Study Plan
In an effort to obtain target samples sizes, collection of fish for mercury analysis occurred from
June to September as opposed to the August and September window proposed in the Study Plan
(RSP 5.7.4.2.6). Target sample sizes were not obtained for some species including: burbot,
stickleback, rainbow trout, and humpback whitefish because either species were not captured or
because fish of sufficient body size were rare. Two lake trout were collected from Sally Lake in
2012 but additional lake trout could not be collected from Sally Lake in 2013 due to land access
restrictions. Seven lake trout were collected from Deadman Lake, within the watershed but
outside of the inundation zone. None of these variances should reduce AEA’s ability to
determine baseline metal and mercury concentrations in fish tissues for resident fish species; it
was anticipated prior to the field season that flexibility over time and space would be needed to
achieve target fish collections.
4.10. Objective 7: Document the seasonal distribution, relative
abundance, and habitat associations of invasive species
(northern pike).
AEA implemented the methods for Objective 7 as described in the Study Plan with no variances.
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 the negative effect of northern pike 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 was made. However, the presence and habitat associations of northern
pike have been documented as a component of all fish capture and observation sampling events
associated with Objectives 1 and 2.
4.11. Objective 8: Collect tissue samples from juvenile salmon and
resident and non-salmon anadromous fish.
AEA implemented the methods for Objective 8 as described in the Study Plan with no variances. In
support of the Genetic Baseline Study for Selected Fish Species (ISR Study 9.14), fish tissues
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were collected opportunistically in conjunction with all fish capture events. The target species,
number of samples, and protocols are outlined in the ISR for Study 9.14. Tissue samples
included an axillary process from all adult salmon, caudal fin clips or mucus swabs from fish
greater than 60 mm (2.4 in), and whole fish less than 60 mm (2.4 in). Genetics samples were
collected from juvenile and adult Chinook salmon, Arctic grayling, burbot, Dolly Varden,
longnose sucker, sculpin, humpback whitefish and round whitefish (Table 4.11-1). A total of
717 tissue samples were collected during the Fish Distribution and Abundance sampling in the
Upper River Study Area; 195 samples were collected from the Susitna River and 522 samples in
tributaries (Table 4.11-1).
4.12. Fish Sampling Techniques
A combination of gillnetting, electrofishing, angling, trot lines, minnow trapping, snorkeling,
rotary screw trapping, beach seining, fyke netting, and hoop trapping was used to meet the eight
study objectives discussed above. Brief descriptions of how these field methods were
implemented across field teams and study sites is presented below. Several assumptions were
associated with the use of these methods:
• Boat electrofishing and gillnetting were 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 were conducted
under state and federal biological collection permits. Limitations on the use of some
methods during particular time periods or locations may have affected the ability to make
statistical comparisons among spatial and temporal strata.
• Fish sampling techniques provided imperfect estimates of habitat use and relative fish
abundance. Use and comparison of multiple sampling methods provided 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 tributaries within the reservoir inundation zone was scaled based on
elevation and Chinook salmon distribution. Sampling was conducted to 3,000 ft in
elevation, the upper known extent of Chinook salmon distribution.
4.12.1. Gillnets
Variable mesh gillnets (7.5-ft-deep panels with 1-in to 2.5-in stretched mesh) were deployed in
appropriate habitats. In open water and at sites with high water velocity, gillnets were deployed
as drift nets, while in slow water sloughs, gillnets were deployed as set (fixed) nets. The location
of each gillnet set was mapped using hand-held GPS units and marked on high-resolution aerial
photographs. To reduce variability among sites, soak times for drift gillnets were standardized;
all nets were retrieved a maximum of 30 minutes after the set was completed. The following
formula was used to determine drifting time:
T = ([(set time + retrieval time)/2] + soak time)
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4.12.2. Electrofishing
4.12.2.1. Backpack Electrofishing
All backpack electrofishing procedures followed NMFS (2000) Guidelines for Electrofishing
Waters Containing Salmonids Listed Under the Endangered Species Act. Personnel operating
electrofishing units were trained and certified as per ADF&G permit requirements.
A Smith-Root LR-24 backpack electrofishing unit was operated by a trained field crew leader
who was assisted by one or two people with dipnets. Each backpack unit was fitted with a
standard Smith-Root cathode and a single anode pole with a steel ring. Electrofishing was often
paired with snorkel surveys, where snorkel surveys were conducted first as a reconnaissance to
make sure there were no large salmonids in the area. Single-pass fish distribution electrofishing
surveys were conducted through the selected study reach moving in an upstream direction.
Block nets were used for relative abundance sampling when sites conditions allowed.
Depending on stream width, an additional crew leader sometimes operated a second
electrofishing unit. All stunned fish were captured with dipnets away from the electric field and
held in buckets for later processing.
An ADF&G-generated table that recommends target voltage settings for juvenile salmonid
sampling in cold water was used as a reference at the onset of sampling (Buckwalter 2011).
Backpack electrofisher settings were determined in the field based on water quality conditions,
professional judgment, and the overall goal of minimizing impacts to fish health (Temple and
Pearsons 2007). Prior to electrofishing, ambient water chemistry was recorded including
conductivity (microSiemens), turbidity (nephelometric turbidity units [NTU]), and surface water
temperature (°C) with a digital meter at the downstream end of sampling site to determine initial
backpack electrofishing unit settings. In all cases, the electrofishing unit was operated and
configured with settings consistent with guidelines established by the manufacturer (Smith-Root
2009), ADF&G (Buckwalter 2011) and NMFS (2000). The location of each electrofishing unit
was mapped using hand-held GPS units and marked on high-resolution aerial photographs. Start
and stop times were recorded to quantify sampling effort between surveys. Habitat
measurements were collected at each study site location. All captured fish were identified to
species, measured for length, and returned to the stream unharmed. For each sample unit, fish
capture data and sampling effort (e.g., electrofishing ‘power on’ recorded in seconds) was
documented separately so that CPUE could be calculated.
4.12.2.2. Boat Electrofishing
In study site locations that were too deep or too swift to safely operate a backpack electrofishing
unit, boat-based electrofishing was used as a fish sampling technique. Boat-based electrofishing
was conducted while drifting in a downstream direction by an experienced three- or four-person
field crew. One person operated the boat, while the field crew leader operated the electrofishing
unit and one or two netters captured stunned fish. In the remote Upper River, an inflatable
cataraft with a collapsible aluminum frame was used. The boat was outfitted with either a
Smith-Root 2.5 Gas-Powered Pulsator (GPP) electrofisher powered by a smaller generator for
use in low-conductivity waters or a 5 GPP electrofisher for use in higher-conductivity waters.
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As standard practice, low frequency pulse settings were selected initially to avoid exposing fish
to more harmful higher pulse frequencies.
Boat electrofisher settings were determined in the field based on water quality conditions,
professional judgment, and the overall goal of minimizing impacts to fish health (Temple and
Pearsons 2007). Prior to electrofishing, ambient water chemistry was recorded including
conductivity (microSiemens), turbidity (NTU), and surface water temperature (°C) with a digital
meter at the downstream end of sampling site to help determine initial unit settings (Temple and
Pearsons 2007). In all cases, the electrofishing unit was operated and configured with settings
consistent with guidelines established by the manufacturer and ADF&G (Buckwalter 2011). The
field team recorded a GPS location at the upstream start of each stream or sample segment prior
to moving downstream to sample. Start and stop times were recorded to quantify sampling effort
between surveys. Habitat measurements were also collected at each study site location. All
captured fish were identified to species, measured for length, and returned to the stream
unharmed. For each sample unit, fish capture data and sampling effort (e.g., electrofishing
‘power on’ recorded in seconds) was documented separately so that CPUE could be calculated.
Electrofishing surveys were only conducted during daylight hours due to safety concerns.
4.12.3. Angling
Angling with hook and line was an effective way to collect fish samples for select target species
under certain conditions. During field trips organized for other sampling methods, hook-and-line
angling was conducted on an opportunistic basis using artificial lures or flies with single barbless
hooks. The primary objective of hook-and-line sampling was to capture fish for radio and PIT
tagging and to determine presence; a secondary objective was to evaluate seasonal fish
distribution. Because it was labor and time intensive, angling was best used as an alternative
method if other more effective means of sampling were not available. Angling was also used in
conjunction with other methods, particularly if information on the presence and size of adult fish
was required.
4.12.4. Trot Lines
Trot lines consisted of a long line with a multitude of baited hooks and were typically anchored
at both ends and set in the water for a period of time. Trot lines consisted of 14 to 21 ft of seine
twine with six leaders and hooks lowered to the river bottom. Trot lines were checked and re-
baited after 24 hours and pulled after 48 hours. Hooks were baited with salmon eggs, herring, or
whitefish. Trot line construction and deployment followed 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 were commercially sterilized or disinfected with a 10-minute soak in a
1/100 Betadyne solution prior to use.
4.12.5. Minnow Traps
Both wire and fabric collapsible minnow traps were used in 2013. The wired two-piece minnow
traps were 16.5 in long, with a 9 in diameter, and had an 1-in opening. The collapsible traps had
a length of 18 in and a width of 10 in. The openings of the collapsible trap were 2.5 in in
diameter. Minnow traps were baited with commercially processed salmon roe. As per ADF&G
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Fish Resource Permit stipulations, all salmon eggs used as bait were commercially sterilized or
disinfected with a 10-minute soak in a 1/100 Betadyne. After roe was sterilized, 1 Tbsp of roe
was measured out and placed in a 1-oz plastic Whirl-Pak bag (Fort Atkinson, WI, USA). Filled
plastic bags were perforated using a fork or utility knife before bait was placed inside the trap.
One to two minnow traps were deployed for every 10 m (33 ft) sampled depending on the habitat
unit size and complexity. The unit was divided into quadrants and the number of traps was
equally distributed among quadrants. Traps were placed in the low velocity areas with cover that
were most likely to contain fish. Traps were placed on the stream bottom, parallel to the current.
To prevent loss, each trap was anchored to the stream bank by a tether line and flagged. Baited
and set minnow traps were soaked overnight for 18 to 24 hours. After each soak period,
captured fish were measured and identified to species. Fish were held in a live well and released
unharmed to the same site where they were originally captured.
4.12.6. Snorkel Surveys
Single-pass snorkel surveys (Dolloff et al. 1993) were conducted by a two-person field crew
trained in snorkel survey methods and fish species identification. Climatological and
hydrological conditions, such as air and water temperatures, cloud cover, and water
clarity/visibility, were documented before beginning a survey and snorkeling was only conducted
if conditions were adequate based on Appendix 3 of the Implementation Plan. Snorkelers used a
plastic salmonid silhouette with parr marks to evaluate visibility as the horizontal underwater
distance at which the parr marks were visible. As the snorkeler approached the model, the
distance at which the parr marks on the silhouette became visible was measured. Similarly,
during retreat, the distance at which the parr marks were no longer visible was measured, and
visibility was calculated as the average of these two distances (Thurow 1994). Habitat units
were snorkeled by starting at the downstream end of the sample area and working upstream
unless water velocity precluded upstream movement. Snorkeled distance depended on the length
of the habitat unit being sampled.
Snorkel surveys consisted of a single snorkeler. Observations were collected by counting fish on
both sides of the stream channel while alternating from left to right counts. Snorkelers visually
identified and counted all species encountered and fish counts were grouped by species and size-
class-bins estimated in 20 mm (0.8 in) increment bins (e.g., 1-20 millimeters, 21-40 millimeters,
etc.). Snorkel observations were called out to a non-snorkeling team member and recorded. For
most of the snorkel surveys in this study, one experienced biologist was the designated snorkeler,
while a field technician acted as a recorder. A hand-held GPS unit was used to record the
downstream and upstream extent of the area surveyed and the location was marked on high-
resolution aerial photographs.
To facilitate comparison of relative abundance estimates from snorkel surveys with estimates
from other sampling methods (e.g., minnow trapping or electrofishing), block nets were used to
ensure a closed population within a single habitat unit and prevent fish from leaving or entering
the unit (Hillman et al. 1992). The survey length and average wetted width of the sample area
were recorded to facilitate estimation of relative fish abundance.
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4.12.7. Fyke/Hoop Nets
In general, a fyke net consists of a large hoop net with wings that act as funnels to direct fish into
the network of hoops. A hoop net has a similar set up, but lacks wings for directing fish into the
net. Fyke/hoop nets were deployed to collect fish in tributaries, sloughs, and side channels with
moderate water velocity (i.e., less than 3 ft per second). After a satisfactory location was
identified at each site, the same location was used during subsequent collection periods. The
fyke nets were approximately 40 ft long and consisted of two rectangular steel frames (3 ft wide
by 2.5 ft high), and four steel hoops, all covered by 0.25-in delta stretch mesh nylon netting. A
26 ft long by 4.1 ft deep leader net made of 0.33-in delta stretch nylon netting was sometimes
attached to a center bar of the first rectangular frame (net mouth). The second rectangular frame
had two 4-in wide by 28-in high openings, one on each side of the frame’s center bar. The four
hoops followed the second frame. The throats, 4-6 in diameter, were located between the second
and third hoops. The net ended in a cod end bag 8 ft long with an 8-in opening at the end, which
was tied shut while the net was fishing. Each fyke/hoop net was configured with two wings, set
perpendicular to the shore, to guide the majority of water and fish to the net mouth. Where
possible, the guide nets were configured to maintain a narrow open channel along one bank.
Where the channel size or configuration did not allow an open channel to be maintained, the area
below the fyke/hoop net was checked regularly to assess whether fish were blocked and unable
to pass upstream. A live car was located at the downstream end of the fyke/hoop net throat to
hold captured fish until they were processed. The fyke/hoop net wings and live car were
checked at least once per day while fishing, to record and measure captured fish. The location of
the fyke/hoop net sets were mapped using a hand-held GPS unit and marked on high-resolution
aerial photographs. Fyke nets were set overnight for 18 to 24-hours.
4.12.8. Hoop Traps
Hoop traps are essentially a hoop net that is baited with fish or salmon roe to attract fish into the
net (Larson 2000). Hoop traps can also be known as fyke traps if they include the wings to help
funnel fish into the trap (Larson 2000). Hoop traps had between 4 to 7 hoops. Smaller traps
consisted of four 0.25-in steel hoops with diameters tapered from 3 ft at the entrance to 2.25 ft at
the cod end. Larger traps consisted of seven 0.25-in thick steel hoops inside with diameters that
tapered from 2 ft at the entrance to 1.5 ft at the cod end. Both the four- and seven-hooped traps
had two necks inside and were made up of 0.25-in diameter knotless delta mesh. Each trap was
kept stretched open with two sections of PVC pipe spreader bars attached by snap clips to the
end hoops. Hoop traps were generally set overnight for 18 to 24-hours.
4.12.9. Beach Seine
Seining methodology was dependent on habitat type and the target species. Typically, speed and
coordination were essential parts of successful seining. The size and swiftness of the target fish
influenced both the length of the seine used and the speed at which it was deployed and
retrieved. In wadeable systems, smaller nets were used and deployed by hand with one end of
the net anchored to the shore and the other end extended out from shore and then looped around
to encircle the fish as the ends were pulled in against the beach or gravel bar. Once all fish were
withdrawn from the net, the net was cleaned of all leaf litter, sticks, rocks, and other debris,
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checked for damage, and reloaded for the next set. Damage to seines was repaired following
instructions in Gebhards (in Murphy and Willis 1996).
Seine nets of various sizes were available for use that ranged from 14 to 120 ft long, 3 to 6 ft
wide, and had mesh diameters that ranged from 0.125 to 1 in. The largest and smallest available
nets were 120ꞌx5ꞌ x0.5" mesh and 14ꞌx6ꞌx0.125" mesh, respectively. With this range in net sizes
a large variety of fishes and habitats were sampled; because the area sampled was noted, the net
size was noted, and the nets were deep enough to fill the water column, comparisons could be
made. The location of beach seining was recorded using a hand-held GPS unit, in addition to
being marked on high-resolution aerial photographs. The area seined was delineated using
fiberglass measuring tapes or a marked wading rod.
4.12.10. Rotary Screw Trap
Rotary screw traps were useful for determining the timing of emigration by downstream
migrating juvenile salmonids and resident fish (Objective 2). In the Upper River, the Oshetna
River near the confluence with the Susitna River (PRM 235.1) and Kosina Creek (PRM 209.1)
near RM 2.2 were selected as locations where hydrologic conditions were suitable and
logistically favorable for the deployment of rotary screw traps (Figure 4.1-7). Flow conditions
permitting, traps were fished on a cycle of 48 hours (two days and nights) on, 72 hours off
throughout the ice-free period. Each trap was checked at least daily when fishing (Figure 4.2-2).
When checked, fish were removed from the live-boxes for processing using dip and minnow
nets. To reduce fish losses from the live-box, fish refuge structures, flow deflectors, and debris
separators were sometimes installed to dissipate water velocities and reduce predation. Before
fish were removed from the live-box, floating and large submerged debris was removed.
Once removed from the live-box, fish were sorted by species and size class and placed in 5-
gallon buckets with supplemental aeration or a holding pen situated in flowing water. For
juvenile anadromous salmonids a life stage index was be used for grouping life stage classes
(alevin, fry/parr/smolt). Standard fish handling procedures were followed (Section 4.12.11).
Any additional processing and data collection (e.g., tissue sampling, PIT tagging) was also
performed if applicable to the species, life stage, and site location. Fish were held until fully
recovered, and the time and water temperature (°C) at release was recorded.
4.12.11. Fish Handling
Special care was taken to ensure that all fish were handled properly and that unintended
mortalities were minimized. In general, fish were kept in cool, well-oxygenated water, and the
amount of time spent away from the river environment was minimized to the extent possible.
Strategies to minimize fish stress and mortality included the following:
1. Minimizing handling to that necessary to meet Project objectives.
2. Minimizing the time fish were held.
3. Minimizing the time fish were held in anesthetic.
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4. Starting with low concentrations of anesthetic and then increasing as necessary. Fish
were anesthetized only to the point at which they could be handled easily without strain.
5. Removing smaller or more sensitive fish from anesthetic first, followed by larger, less
sensitive species.
6. Holding fish in fresh or flow-through river water during examination.
7. Using wet transfers.
8. Monitoring water temperatures and dissolved oxygen concentrations in closed systems
regularly and adjusting as necessary.
Field crews recorded 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 or observed
fish were identified to species and life stage when possible. For juvenile anadromous salmonids,
a life stage index was used for grouping life stages (e.g., alevin, fry/parr/smolt). When possible,
resident fishes were grouped as young-of-year (0+), juvenile (typically age 1+ and 2+), and adult
(typically age 3+). Each time a gear was sampled, a random sample of 25 individuals per
species, life stage, and site were measured for fork length (FL) in mm and weighed (grams). For
species without a forked tail (e.g., sculpin and burbot), length was measured laterally along the
mid-line from the anterior edge of the snout to the posterior edge of the tail. The remaining fish
of each species and age class were then enumerated.
For methods in which fish were observed but not captured (e.g., snorkeling), an attempt was
made to identify all fish to species. For snorkeling, fork lengths of observed fishes were
estimated to 20-mm bins of sizes. If present, observations of poor fish condition, lesions,
external tumors, or other abnormalities were noted. All juvenile salmon, Arctic grayling, burbot,
Dolly Varden, rainbow trout, and whitefish greater than 60 mm (2.4 in.) in length were scanned
for PIT tags using a portable tag reader and a PIT tag was implanted in untagged fish. Because
Chinook salmon were of particular interest and in low abundance, all suitable juvenile Chinook
salmon of taggable size received PIT tags. Radio tags were surgically implanted in targeted fish
as described in Section 4.12.13.
4.12.12. Remote Fish Telemetry
Remote telemetry techniques included radio telemetry and PIT tags. Both of these methods were
intended to provide detailed information from relatively few individual fish. PIT tags were
surgically implanted in small fish greater than 60 mm (2.4 in); radio transmitters were 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 included Arctic grayling,
burbot, Dolly Varden, longnose sucker, northern pike, lake trout, rainbow trout, humpback
whitefish, and round whitefish. Radio-tracking provided information on fine and coarse spatial
scales related to location, speed of movement, and habitat use by surveying large areas and
relocating tagged individuals during aerial surveys. PIT tags were 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 was limited to the sites where
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antenna arrays were placed. Determining movement in and out of side sloughs or tributaries
required that tagged fish pass within several feet of an antenna array, thereby limiting array use
to sufficiently small water bodies. To characterize growth rates, recaptured fishes were
measured.
4.12.12.1. Radio Telemetry
The primary function of the telemetry component was 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 were recorded by fixed station or
mobile positioning. All telemetry gear (tags and receivers) across both studies was 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
• 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 was achieved by fixed receiver stations and mobile surveys (aerial,
boat, and foot). Three telemetry fixed stations were installed in the Upper Susitna River.
Stations at the mouths of Kosina Creek (PRM 209) and the Oshetna River (PRM 235) monitored
the movement of radio-tagged fish in the mainstem Susitna as well as in their respective
tributaries. The Deadman station (PRM 191) was located north of the Susitna River between
Deadman and Watana creeks and monitored the movement of fish in the mainstem of the Susitna
River (Figure 4.1-7). These stations were serviced in conjunction with the Salmon Escapement
Study during the July through October period. The Kosina Creek station was extended to track
resident fish into the winter. Fixed stations were downloaded weekly during the salmon
spawning period (approximately July through October). The Salmon Escapement Study
provided approximately weekly aerial survey coverage of the study area (approximately July
through October). At other times of the year, the frequency of aerial surveys was reduced to
every third week. Spatial and temporal allocation of survey effort was finalized based on the
actual locations and number of each species of fish tagged.
Relocation data from the radio telemetry component of this study was 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 years for large fish). This objective is being
achieved with 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). Actual tag life was determined by the appropriate tag
for the size of the fish available for tagging.
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This study intended to capitalize on the use of the existing telemetry platform (ATS telemetry
equipment) to sufficiently monitor target species, but that directly constrained the potential
options for tagging and monitoring. More specifically, the smallest ATS coded tag weighed 6 g
(0.2 oz) which precluded its application to all the species at the lower portion of their most
frequently occurring size range (Table 4-2).
Tags were surgically implanted in fish of sufficient body size, distributed temporally and
longitudinally in the Upper River with a goal of 30 per-species. These fish were captured during
sampling events targeting adult fish and with directed effort using a variety of methods. The
tag’s signal pulse duration and frequency, and, where appropriate, the transmit duty cycle, was a
function of the life history of the fish and configured to maximize battery life and optimize the
data collection. Larger tags accommodated the greatest battery life and therefore were used
when fish were large enough, but smaller, shorter life tags were used across the range of adult
body sizes.
4.12.12.2. PIT Tag Antenna Arrays
As described above, fish of appropriate size from target species were implanted with a PIT tag
for mark-recapture studies. Half-duplex PIT tags, either 12 mm (0.5 in) in length or 23 mm (0.9
in) in length, were used depending on the size of the fish to be implanted. Each PIT tag had a
unique code that allowed identification of individuals.
PIT tag antenna arrays with automated data logging were deployed at two 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 (Figure 4.1-7). With input from the Fish and
Aquatic TWG, site selection for antenna arrays was based on habitats and tributaries identified as
suitable habitat for juvenile Chinook salmon. Antennas were deployed shortly after ice-out in
2013. Each PIT tag interrogation system consisted of a power source, data logger, antenna, and
tuning capacitor. A solar panel and controller was used to power the reader and charge the
battery bank. Data loggers were downloaded every two to four weeks depending on the need to
replace batteries and on reliability of logging systems.
5. RESULTS
5.1. Objective 1: Fish Distribution, Relative Abundance, and Habitat
Associations
5.1.1. Task A: Fish Distribution
Table 5.1-1 describes the species distribution within the Upper River study area, including the
mainstem Susitna River geomorphic reaches (UR-3, UR-4, UR-5, and UR-6), tributaries, and
lakes, as documented during 2012 and 2013 field studies. Additionally, the table incorporates
historic fish distribution information from ADF&G (1981 & 1984), Sautner and Stratton 1983,
1984) and Buckwalter (2011). Fish distribution maps based on 2012 and 2013 fish observations
are presented in Appendix B (Figures B1 through B8). Tables C1 through C9 in Appendix C
further describe the distribution of these species with respect to four seasonal sampling events
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defined as spring Early Life History (ELH) sampling (June 4 to June 30), early summer (July 1
to August 10), late summer (August 11 to September 9), and fall (September 10 to October 7).
Although these sampling events are based on 2013 sampling protocols, observations made
during 2012 field studies have also been grouped into these seasonally defined events. For
Chinook salmon, the tables, figures, and discussion below focus only on the juvenile life stage;
accounts of adult Pacific salmon in the Upper Susitna River are provided in ISR Study 9.7.
Nine fish species are known to inhabit the Upper Susitna River study area. These include one
anadromous species (Chinook salmon) and eight resident species (Arctic grayling, burbot, Dolly
Varden, lake trout, longnose sucker, sculpin, humpback whitefish, and round whitefish ) (Sautner
and Stratton 1983; Buckwalter 2011; HDR 2013; Table 5.1-1). During field surveys sculpin
were not always identified to the species level; therefore, they are reported herein as sculpin spp.
When sculpin were identified to species, identifications included only slimy sculpin. Each of
these nine species was documented in the Upper River study area in 2012 (HDR 2013) and 2013.
With the exception of lake trout and humpback whitefish, each species was also documented
between Devils Canyon and the proposed Watana Dam site (Table 5.1-1), and all species except
for lake trout have been documented downstream of Devils Canyon (ISR Study 9.6).
Generally, distribution patterns among species varied, particularly with regard to differences
between the mainstem Susitna River and tributary habitats. Only Arctic grayling and sculpin
were widely distributed in both the mainstem river and its tributaries (Table 5.1-1; Figures B2
and B6). Burbot, longnose sucker, and round whitefish were also widespread in the Susitna
River, but their distribution within tributaries was limited primarily to larger streams such as
Kosina Creek and the Oshetna River (Figure B3; Figure B5; Figure B8). Other species (e.g.,
juvenile Chinook salmon and humpback whitefish) were observed at a few mainstem locations,
and humpback whitefish observations within tributaries were also limited (Figure B1; Figure
B7). Dolly Varden were found exclusively in tributary streams, and lake trout were found
primarily in lakes although they were observed at a single tributary location (Figures B4 and B3).
Additional information regarding the spatial and seasonal distribution of each of the nine
documented species is provided in the subsections that follow. Data developed in support of the
ISR is available for download at http://gis.suhydro.org/reports/isr
(ISR_9_5_FDAUP_FishObservations).
5.1.1.1. Chinook salmon
Juvenile Chinook salmon were documented in Kosina Creek, the Oshetna River, and the Black
River, a tributary of the Oshetna River (Table 5.1-1; Figure B1). All three of the streams where
juvenile Chinook salmon were documented were sampled during each of the four seasonal
events defined above (Table C1). During the spring event, juveniles were observed only in the
Black River. During the other sampling events, they were documented in each of these three
streams with the exception of the Oshetna River during late summer.
5.1.1.2. Arctic grayling
Within the Upper Susitna River, Arctic grayling were distributed throughout the mainstem river
(PRM 187.1 to 235.1), in 15 of the 20 tributaries surveyed, and in 3 lakes (Table 5.1-1; Figure
B2). The 15 streams included Deadman Creek, Unnamed Tributary 194.8, Watana Creek, 3
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unnamed Watana Creek tributaries, Unnamed Tributary 197.7, Unnamed Tributary 203.4,
Kosina Creek, 2 Kosina Creek tributaries (Tsisi and Gilbert creeks), Jay Creek, Goose Creek, the
Oshetna River, and 1 Oshetna River tributary (the Black River). Lake observations occurred in
an unnamed lake in the Deadman Basin, Sally Lake in the Watana Basin, and Tsisi Lake in the
Kosina Basin. Upstream of the study area, Arctic grayling were also documented in the Susitna
River and in the lower reach of Clearwater Creek (PRM 266.6), thus extending their distribution
from the Oshetna River to Clearwater Creek.
The distribution of Arctic grayling was largely consistent among sampling seasons (Table C2).
Arctic grayling were present in the Susitna River during the early summer, late summer, and fall
sampling events. Four of the streams in which Arctic grayling were observed (Kosina Creek,
Tsisi Creek, the Oshetna River, and the Black River) were sampled during all four seasonal
events; within these streams, Arctic grayling were present during all four events. Similarly, they
were consistently found in 3 of the 5 streams that were sampled during early summer, late
summer, and fall (Watana, Jay, and Goose creeks). In the other two streams that were sampled
across multiple events, Arctic grayling were detected only during early summer in Unnamed
Tributary 194.8 and only during late summer in an unnamed tributary to Watana Creek. In Tsisi
Lake, which was the only lake sampled across multiple events, Arctic grayling were observed
only during the spring event.
5.1.1.3. Burbot
Within the Upper Susitna River (PRM 187.1-235.1), burbot were present throughout the
mainstem river and in four streams: Kosina and Jay creeks, and the Oshetna and Black rivers
(Table 5.1-1, Figure B3). Within Kosina and Jay creeks, burbot were observed in only in the
lower stream reaches. In the Oshetna River, burbot observations extended upstream to its
confluence with the Black River and then continued in the Black River to the upstream sampling
extent.
On a seasonal basis, the distribution of burbot was largely consistent in the Susitna, Oshetna, and
Black rivers, whereas observations in Kosina and Jay creeks were limited to only certain events
(Table C3). In the Susitna, Oshetna, and Black, burbot were observed during all events with the
exception of the spring event in the Susitna River. In Kosina Creek, which was sampled during
all four events, burbot observations occurred only during the spring period. Jay Creek was
sampled during early summer, late summer, and fall, yet burbot were documented only during
the late summer and fall. In Kosina and Jay creeks, where burbot were observed only in the
lower stream reaches, it is plausible that burbot are moving into the creeks on a seasonal basis,
whereas their use of larger riverine habitats, such as the Susitna, Oshetna, and Black rivers, is
more consistent across seasons.
5.1.1.4. Dolly Varden
As mentioned above, Dolly Varden were observed exclusively in tributary habitats. Six
tributaries supported Dolly Varden including: Unnamed Tributary 194.8, Watana Creek, 1
unnamed Watana Creek tributary, Unnamed Tributary 198.4, Kosina Creek, and Jay Creek
(Table 5.1-1; Figure B4).
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There was little seasonal variation in the presence of Dolly Varden (Table C4). Among the
streams that were sampled across multiple events and that supported Dolly Varden, Dolly
Varden were observed in all cases with the exception of early summer in Kosina Creek.
5.1.1.5. Lake Trout
Three of the five lakes that were sampled in the Upper Susitna River supported lake trout (Table
5.1-1; Figure B3). These lakes included Deadman Lake in the Deadman Basin, an unnamed lake
also in the Deadman Basin, and Sally Lake in the Watana Basin. No lake trout were observed in
a small unnamed lake near PRM 205.9 or in Tsisi Lake in the Kosina Basin. Within riverine
habitats, there was a single juvenile lake trout observation made in an unnamed tributary to
Watana Creek draining Big Lake.
The one stream in which lake trout were observed was sampled during the early summer, late
summer, and fall events, yet the only observation of lake trout occurred during fall sampling
(Table C5). With this single observation, and the fact that each of the three lakes supporting lake
trout were sampled during only a single sampling season, there is insufficient data to characterize
seasonal distribution patterns for lake trout in the Upper Susitna River study area. However, it
should be noted that lake trout are typically associated with lacustrine habitats; thus the specimen
collected likely originated in Sally Lake or Big Lake (Figure B3).
5.1.1.6. Longnose Sucker
Longnose suckers were distributed throughout the mainstem Susitna River and a few tributary
streams (Table 5.1-1; Figure B5). Within the Upper Susitna River study area, they were
observed in geomorphic reaches UR-6, UR-5, UR-4, and UR-3, and in five tributaries: Watana,
Kosina, and Goose creeks, and the Oshetna and Black rivers. Upstream of the study area,
longnose suckers were also documented in the Susitna River and the lower reach of the Tyone
River (PRM 247.3), thus extending their distribution from the Oshetna River to the Tyone River.
Seasonal distribution patterns in the Upper River study area tended to vary by stream (Table C6).
Longnose suckers were consistently observed across all four sampling events in the Susitna and
Oshetna rivers. Among the tributary streams that supported longnose suckers and that were
sampled during each event, detections occurred only during the spring and fall events in Kosina
Creek and only during late summer in the Black River. In Watana and Goose creeks, which
were sampled during all events except spring, longnose suckers were observed during early
summer in both creeks and during late summer in Goose Creek.
5.1.1.7. Sculpin
Sculpin were widely distributed throughout the Upper Susitna River study area (Table 5.1-1;
Figure B6). They were present in the mainstem river from PRM 187.1 to 235.1, in 18 of the 20
tributaries surveyed, and in one lake. The 18 streams included Deadman Creek, Unnamed
Tributary 194.8, Watana Creek, 4 unnamed Watana Creek tributaries, Unnamed Tributary 197.7,
Unnamed Tributary 203.4, Unnamed Tributary 206.3, Kosina Creek, 3 Kosina Creek tributaries
(Tsisi and Gilbert creeks, and one unnamed tributary), Jay Creek, Goose Creek, the Oshetna
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River, and 1 Oshetna River tributary (the Black River). The single lake that supported sculpin
was Sally Lake, located in the Watana Basin.
The distribution of sculpin within the study area varied little among seasons (Table C7). Among
the streams that supported sculpin and were sampled across multiple seasons, the only events in
which sculpin were not detected were: the spring event in the Susitna River, and early summer
and fall events in one of the unnamed Watana Creek tributaries.
5.1.1.8. Humpback whitefish
Of the eight riverine species documented in the Upper Susitna River study area, humpback
whitefish were the least commonly observed (Table 5.1-1; Figure B7). Observations in the
mainstem Susitna River were limited to a single location in UR-6. Humpback whitefish were
also observed at a few locations in Kosina Creek and the Oshetna River. Based on observations
of unidentified whitefish, it is possible that humpback whitefish were also present in Tsisi Creek
(Table 5.1-1).
The distribution of humpback whitefish appears to have varied seasonally in the mainstem river
and in Kosina Creek, but was more consistent in the Oshetna River (Table C8). In UR-6 and
Kosina Creek, humpback whitefish were detected only during fall. In the Oshetna River,
presence was documented during the spring event and during early and late summer. However,
these seasonal patterns should be viewed with caution due to the relatively few humpback
whitefish observations in the study area.
5.1.1.9. Round whitefish
Round whitefish were documented in the mainstem Susitna River from PRM 187.1 to 235.1 and
in seven streams within four tributary basins (Table 5.1-1; Figure B8). Streams that supported
round whitefish were: Watana Creek, an unnamed Watana Creek tributary, Kosina Creek, Tsisi
Creek in the Kosina Basin, Goose Creek, the Oshetna River, and the Black River within the
Oshetna Basin. All occurrences of unidentified whitefish were in tributaries with confirmed
round whitefish presence (Table 5.1-1).
Patterns of seasonal distribution were evident in both mainstem and tributary habitats (Table C9).
In the mainstem Susitna River, round whitefish were not observed during the spring event, yet as
time progressed, their occurrence in each of the mainstem geomorphic reaches became more
common. In early summer, they were observed only in UR-6; in late summer, they were
observed in UR-6, UR-4, and UR-3; and in the fall, they were detected in all four of the UR
reaches within the study area (UR-6, UR-5, UR-4, and UR-3). In tributaries, the seasonal
distribution was opposite of that seen in the mainstem, although some tributaries supported round
whitefish throughout all sampling periods. For example, in early summer, round whitefish were
detected in all seven streams, yet during late summer and fall, they were detected in five and
three of the seven streams, respectively. The streams in which round whitefish were consistently
found across the early summer, late summer, and fall sampling events included Kosina and
Goose creeks and the Oshetna River. Round whitefish were also observed in two of four streams
that were sampled during the spring event (i.e., Kosina Creek and the Oshetna River).
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5.1.2. Task B: Relative Abundance
During 2013 all Upper River fish sampling, a total of 12,700 fish were captured or observed
(Table 5.1-2). Backpack electrofishing and snorkeling accounted for 84 percent of the total catch
(Table 5.1-2). Table 5.1-3 lists total fish counts for relative abundance sampling for all three
sampling events for each gear type by species and life stage. Fish counts including all sampling
and relative abundance as determined by catch-per-unit-effort (CPUE) analysis are presented
below. CPUE was calculated to be species and gear specific using catch data from distribution
and abundance sampling as described in Section 4.4.2.1 and was averaged across mesohabitats
within a macrohabitat for discussing relative abundance. Summaries of CPUE in the Upper
River are presented in Appendix D. Data developed in support of the ISR is available for
download at http://gis.suhydro.org/reports/isr (ISR_9_5_FDAUP_FishObservations, and
ISR_9_5_FDAUP_FishCPUEData).
5.1.2.1. Juvenile Chinook Salmon
During 2013, 281 juvenile Chinook salmon were observed during all sampling in the Upper
River (Table 5.1-2). Averaged CPUE for juvenile Chinook salmon was variable across sampling
locations and methods (Tables D19 and D20). In tributaries, CPUE ranged from 0 at 95 percent
of the mesohabitats to 80 fish per 1000 m2 in Kosina Creek run habitat (Table D19). No juvenile
Chinook were captured in the mainstem Susitna during the 196 distribution and abundance
samples. The three highest estimates of CPUE were from sites in spawning tributaries (Kosina
Creek and the Black River). In general Upper River CPUE averages for juvenile Chinook
salmon were similar in magnitude to estimates of CPUE for Middle and Lower River sites. For
the tributary sites where juvenile Chinook salmon were present, CPUE data indicated that
backpack electrofishing and snorkeling were effective capture techniques for juvenile Chinook
salmon (Table D14). Averaged CPUE estimates for juvenile Chinook salmon during Upper
River fish distribution and abundance sampling are displayed in Tables D19 and D20.
5.1.2.2. Arctic Grayling
Arctic grayling was the second most abundant species in the 2013 Upper River fish sampling
with 4,869 Arctic grayling observed during all sampling (Table 5.1-2). Averaged CPUE for
Arctic grayling was highly variable across sampling locations and methods with 59 percent of
sites containing Arctic grayling (Table D14). In tributaries, CPUE averages ranged from 0 to
1,500 fish per 1000 m2 in Goose Creek riffle habitat (Table D24). In the mainstem Susitna,
CPUE averages ranged from 0 to 77.7 fish per hour in UR-3 riffle habitat (Table D21). The
CPUE averages for Arctic grayling were greater in tributaries than in the mainstem and also were
an order of magnitude greater than estimates of average CPUE estimated from Middle and
Lower River sites. For the tributary sites where Arctic Grayling were present, CPUE data
indicates that snorkeling and backpack electrofishing were effective capture techniques. For the
mainstem sites where Arctic Grayling were present, CPUE data indicated that backpack
electrofishing, boat electrofishing, and seining were effective capture techniques (Table D14).
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5.1.2.3. Burbot
During 2013, 129 burbot were observed during all sampling (Table 5.1-2). Averaged CPUE for
burbot was low to moderate across sampling locations and methods with burbot observed at 10
percent of sampling sites (Table D14). In tributaries, average CPUE estimates ranged from 0 to
a maximum of 17.1 fish per hour in Jay Creek pool habitat (Table D25). In the mainstem
Susitna, average CPUE ranged from 0 to 11.7 fish per hour in UR-3 riffle habitat (Table D26).
The CPUE averages for burbot were similar in tributaries and mainstem macrohabitat and were
similar to average CPUE from Middle and Lower River sites. For the main channel
mesohabitats, CPUE data indicated that backpack and boat electrofishing were effective capture
techniques for burbot (Table D14).
5.1.2.4. Dolly Varden
During 2013, 778 were observed during all sampling (Table 5.1-2). Averaged CPUE for Dolly
Varden was calculated only in tributaries (Table D14) and was variable across mesohabitats.
Averaged CPUE estimates ranged from 0 at 88 percent of the mesohabitats to 191 fish per 1000
m2 in Watana Creek pool habitat (Table D29). The CPUE averages for Dolly Varden were
similar to averaged CPUE from Middle River mesohabitats. The CPUE data indicate that
snorkeling and backpack electrofishing were effective capture techniques for Dolly Varden
(Table D14).
5.1.2.5. Lamprey
No lamprey were observed during Upper River fish distribution and abundance sampling.
5.1.2.6. Longnose Sucker
During 2013, 336 longnose sucker were observed during all sampling (Table 5.1-2). Averaged
CPUE for longnose sucker generally was low across sampling locations and was zero for 93
percent of sampling sites (Table D14). Moderate average CPUEs were observed in pool and
riffle habitat in a UR-6 side channel (Table D30 and D32). In tributaries, CPUE averages ranged
from 0 to 5.3 fish per 1000 m2 in Unnamed Tributary 194.8 run habitat (Table D33). In the
mainstem Susitna, longnose sucker CPUE ranged from 0 to 47.2 fish per 1000 m2 in UR-6 riffle
habitat (Table D32). The CPUE averages for longnose sucker were similar in Upper River
tributaries and mainstem macrohabitats and generally were similar to the averaged CPUE from
Middle and Lower River mesohabitats; however, occasionally higher average CPUEs were
evident in Middle and Lower river habitats (ISR Study 9.6). For both tributary and mainstem
mesohabitats, CPUE data indicated that backpack and boat electrofishing, seining, and
snorkeling all were effective capture techniques for longnose sucker (Table D14).
5.1.2.7. Sculpin
Sculpin was the most abundant species group in the Upper River with 5,944 sculpin observed
during all 2013 fish sampling (Table 5.1-2). Averaged CPUE was highly variable across
sampling locations and methods with no sculpin observed at 22 percent of sites (Table D14). In
tributaries, CPUE averages ranged from 0 to 210.9 fish per hour in Black River pool habitat
(Table D34). In the mainstem Susitna, CPUE averages ranged from 0 to 59.2 fish per hour in
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UR-4 clearwater plume habitat (Table D34). The CPUEs for sculpin were greater in tributaries
than in the mainstem and generally were similar to CPUEs estimated from Middle and Lower
River mesohabitats. For the sites where sculpin were present, CPUE data indicated that
backpack electrofishing, snorkeling, and seining were effective capture techniques (Table D14).
5.1.2.8. Lake trout
Only one lake trout was observed during Upper River fish distribution and abundance sampling
in 2013 (Table 5.1-3).
5.1.2.9. Humpback Whitefish
No humpback whitefish were observed during Upper River fish distribution and abundance
sampling in 2013 (Table 5.1-3).
5.1.2.10. Round Whitefish
During 2013, there were 280 round whitefish observed during all 2013 sampling (Table 5.1-2).
Averaged CPUE for round whitefish was low to moderate across sampling locations and
methods with 0 CPUE at 88 percent of sampling sites (Table D14). In tributaries, CPUE
averages ranged from 0 to 11.5 fish per 1000 m2 and 11.5 fish per hour in Goose Creek run and
pool habitat, respectively (Tables D39 and D42). In the mainstem Susitna, CPUE averages
ranged from 0 to 40.8 fish per hour in UR-3 run habitat (Table D39). The CPUE averages for
longnose sucker generally were lower in Upper River tributaries than in mainstem macrohabitats.
The averaged CPUEs for Upper River tributaries generally were similar to the averaged CPUE
from Middle and Lower River mesohabitats (ISR Study 9.6). For both tributary and mainstem
mesohabitats, CPUE data indicated that backpack and boat electrofishing, seining, and
snorkeling all were effective capture techniques for longnose sucker (Table D14).
5.1.3. Task C: Habitat Associations
Fish observation data were used to provide a preliminary look at fish-habitat associations in the
Upper River because 2013 data QA/QC and analysis is ongoing. Combining counts from all data
sources, a total of 12,700 fish observations were made in 12 Upper River tributaries and the
mainstem Susitna River (Table 5.1-2). The highest total counts of fish were obtained in the
Oshetna River, largely driven by high numbers of sculpin documented during distribution and
relative abundance sampling (Table D11) and Arctic grayling captured in the Oshetna rotary
screw trap (Table 5.2-1). In general, more fish were observed in tributaries than in the mainstem
reaches.
To begin to understand species-specific patterns in habitat use, species counts are presented by
mesohabitat unit and sampling event in Appendix D (Tables D2 to D13). The following general
patterns are evident from this early data.
• Juvenile Chinook salmon were found in tributary habitats during all three sampling
events. They were documented in fast water habitats only, e.g. boulder rifle and run
habitats.
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• Arctic grayling were observed in a variety of habitats in tributaries, the main channel
Susitna River and off-channel Susitna River. Arctic graying counts were higher and
more frequent in fast water mesohabitat types, e.g. boulder riffles, riffles, runs, and
glides.
• Burbot observations by mesohabitat were low overall, on the order of an individual fish
observed in all fast water habitats and an occasional pool or percolation channel.
• Dolly Varden were observed only in tributaries. They were found in fast and slow
mesohabitats including rapids, boulder riffles, riffles, runs, glides, pools, and percolation
channels.
• One juvenile lake trout was found during fish distribution and abundance sampling. This
fish was found in a riffle in a tributary to Watana Creek, 7.5 km (4.7 mi) downstream of
Big Lake and 16 km (10 mi) upstream from Sally Lake.
• Longnose sucker were found in a variety of habitats in tributaries as well as main channel
and off-channel habitats in the Susitna River. Longnose sucker were observed in boulder
riffles, riffles, runs and pools.
• Sculpin were found in tributaries as well as main channel and off-channel habitats in the
Susitna River. They were found in all fast water habitat types, pools, percolation
channels, and in a beaver pond.
• Very few humpback whitefish were observed in the Upper River. These few fish were
found in riffles in the Oshetna River and Kosina Creek and in a run in the Susitna River.
• Round whitefish were observed frequently in tributaries and in the main channel of the
Susitna River. They were found predominantly in fast water mesohabitats including
rapids, boulder riffles, riffles, and runs but were also observed in pools.
Data developed in support of the ISR is available for download at
http://gis.suhydro.org/reports/isr (ISR_9_5_FDAUP_FishObservations).
5.2. Objective 2: Seasonal Movements
5.2.1. Task A: Document the timing of downstream movement and catch for all
fish species using out-migrant traps.
Rotary screw traps (RST) operated in Kosina Creek (PRM 209.1) and the Oshetna River (PRM
235.1) were used to document seasonal fish movements of anadromous salmon and resident fish
species out of these Upper River tributaries between mid-June and early October. During this
period, the Kosina Creek trap caught 153 total fish while the Oshetna River trap caught 1,001
total fish (Table 5.2-1). The Kosina Creek trap caught one anadromous fish, a juvenile Chinook
salmon, and six species of resident fish including Arctic grayling, Dolly Varden, longnose
sucker, sculpin, humpback whitefish, and round whitefish. The Oshetna trap also caught seven
total fish species, including juvenile Chinook salmon, Arctic grayling, burbot, longnose sucker,
sculpin, humpback whitefish, and round whitefish. Data developed in support of the ISR is
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available for download at http://gis.suhydro.org/reports/isr(ISR_9_5_FDAUP_Fish
Observations).
The Kosina Creek rotary screw trap catch was comprised primarily of juvenile Arctic grayling
(Figure 5.2-1). Minimal fish movement was documented during spring sampling; catch
consisted of only one adult Arctic grayling. Catch of Arctic grayling increased slightly during
early summer and included both Arctic grayling and Chinook salmon smolts. A pulse of nine
juvenile Chinook salmon smolts and one adult was documented between August 8 and 18, 2013.
More resident fish were caught during the mid-summer season including: Arctic grayling, Dolly
Varden, sculpin, and round whitefish and undifferentiated whitefish. Capture of Arctic grayling
continued during fall when other species included small numbers of longnose sucker, sculpin,
humpback whitefish, round whitefish and undifferentiated whitefish. One late-season Chinook
salmon parr was documented on September 27, 2013.
In the Oshetna River rotary screw trap, spring sampling documented high numbers of fish shortly
after the trap was installed (Figure 5.2-2). Catch was comprised mostly of Arctic grayling and
adult longnose sucker but also included, burbot, juvenile longnose sucker, sculpin, and
humpback, round, and undifferentiated whitefish. Catch dropped off and few fish were captured
during early July, most of which were Arctic grayling. During the early summer season, catches
peaked, remained relatively high, and consisted primarily of juvenile Arctic grayling, along with
lower numbers of adult Arctic grayling, adult and juvenile longnose sucker, all life stages of
sculpin, undifferentiated whitefish and occasional humpback and round whitefish. One Chinook
salmon smolt was also captured in late July. As the mid-summer season arrived, catches of
Arctic grayling decreased slightly but remained relatively steady. Other resident fish species
were caught more frequently including longnose sucker, sculpin and unidentified and round
whitefish. A final large pulse of fish occurred during the transition from mid-summer to fall.
Arctic grayling numbers remained high, and an increase in catches of all life stages of juvenile
longnose sucker and round whitefish was also observed. Other species caught during this final
period included burbot, sculpin, undifferentiated whitefish, and round whitefish.
5.2.2. Task B: Describe seasonal movements using biotelemetry
The radio telemetry results below include reporting from fish tagged in July and August and
tracked through the end of August 2013.
5.2.2.1. Radio Telemetry
Data developed in support of the ISR is available for download at
http://gis.suhydro.org/reports/isr (ISR_9_5_FDAUP_RadioTelemetry).
5.2.2.1.1. Tagging Locations
Arctic grayling
Arctic grayling were primarily radio-tagged where clearwater tributaries entered the Susitna
River (Table 5.2-2 and Figures A1, A2, A3). These locations offered good numbers of fish for
tagging, did not have land access issues, and most were within the regular flight paths for aerial
surveys. Tags were released at Deadman (7), Watana (3), Kosina (8) and Goose (3) creeks in the
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Project inundation zone. Additional Arctic grayling were tagged in the Oshetna River (8) and
Clearwater Creek (2), outside of the inundation zone, to observe if fish in those locations entered
the inundation zone during their yearly migrations. Thirty-two tags were released in Arctic
grayling during the reporting period ending 30 August. An additional 25 Arctic grayling were
tagged in September (Table 4.5-2).
Burbot
Seven burbot were tagged in September 2013, after the reporting period ending August 30.
Longnose sucker
Longnose sucker were captured with a fyke net and radio-tagged at one location on the Tyone
River (Table 5.2-3 and Figures A4, A5, A6). This site is outside the Project inundation zone. A
total of five tags were released in longnose sucker in the reporting period ending August 30,
2013. An additional 5 longnose sucker were tagged in September.
Round Whitefish
Eighteen round whitefish were tagged in September 2013, after the reporting period ending
August 30.
5.2.2.1.2. Timing of tags released
The majority of the Arctic grayling tags (31 of 57) and half of the longnose sucker tags (5 of 10)
were released between July 15 and 31 during the first radio-tagging effort in the Upper River
(Table 4.5-2). Difficulty procuring fish of sufficient size from standard operations forced the
crew to angle for the majority of the fish. Catches from angling were limited to Arctic grayling.
The second field stint, which occurred during late August, was stopped after a day and half due
to high water conditions and produced one radio-tagged Arctic grayling (Table 4.5-2). Tagging
continued more successfully in September, and included burbot and round whitefish.
5.2.2.1.3. Movements
Arctic grayling
Arctic grayling displayed a variety of migratory patterns after being radio-tagged. Most fish,
such as 9089 (Figure A7), 9102 (Figure A8), and 9108 (Figure A9) moved downstream from
where they were tagged and were observed at other stream mouths. From its tagging site at the
mouth of Deadman Creek, Fish 9089’s migration included traveling over five miles downstream
in the mainstem, to below Tsusena Creek, as well as trips of over one half mile up two
tributaries. Fish 9102 traveled 12 mi downriver, from its tagging location at Kosina Creek, to
Watana Creek before moving over one half mile up the tributary. After being tagged at Kosina
Creek, Fish 9108 remained at Kosina Creek for a couple of weeks before migrating 50 mi
downriver to Chinook Creek. Some of the fish that moved downriver stayed in the mainstem
while others moved into tributaries. Other fish stayed at the creek mouth where they were
tagged (Fish 9107, Figure A10) or migrated between the mainstem and tributary near where they
were tagged. During the reporting period, Fish 9107 was never observed more than 1.5 mi from
its tagging location at the mouth of Kosina Creek. There was little upstream movement observed
through August 31. As all of the fish were tagged in areas that would not be considered
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migratory corridors and were tracked for less than two months, it is not surprising that there were
few large scale movements observed. Some Arctic grayling tagged in the Upper River migrated
past the Watana Dam site and into the Middle River.
Longnose sucker
Longnose sucker primarily moved downstream after being tagged (Fish 9123, Figure A11),
although in a couple cases this may have been due to a fish dying and drifting downriver (Fish
9120). Fish 9123 migration took it almost 100 mi downriver from its tagging site in the Tyone
River to the mouth of Portage Creek where it remained through the conclusion of the reporting
period. A single longnose sucker was not observed downstream from where it was tagged (Fish
9119). Multiple longnose sucker tagged in the Upper River migrated downstream past the
Watana Dam site and into the Middle River.
5.2.2.1.4. Identification of foraging and spawning locations
Arctic grayling
Arctic grayling tagged in the Upper River were observed at a number of possible foraging areas
in the Upper and Middle River. Radio-tagged fish primarily spent time at the mouths of
clearwater streams but also moved into some tributaries for portions of the summer. Arctic
grayling were not spawning during the reporting period.
Longnose sucker
A single longnose sucker held at a possible foraging location at the mouth of Portage Creek.
Other longnose sucker in this study were not observed holding in a single location for multiple
surveys or with other radio-tagged longnose sucker at the same location. Longnose sucker were
not spawning during the reporting period.
5.2.2.1.5. Tag life
All tags released through August 31 had enough battery life to broadcast a signal past August 31
(end of reporting period). According to the manufacturer, the earliest date the battery life of a
tag may stop it from broadcasting a signal is October 29. In total, seven tags could lose power
starting the last days of October and through the first week of November.
5.2.2.1.6. Post-Tagging Survival
Arctic grayling
Initial survival from radio tagging was high with only two of the 31 Arctic grayling tagged from
July 15 to 31 dying by August 15 (Table 5.2-2). Mortalities increased during the second half of
August and at the end of the reporting period when 8 of the 32 (25 percent) Arctic grayling tags
were in mortality mode. The tag groups with the highest mortalities at the end of August were
fish tagged at the mouth of Kosina Creek and at Goose Creek, with two of eight (25 percent) and
two of three (67 percent) dying, respectively.
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Longnose sucker
Of the five longnose sucker radio-tagged in the Upper River, three (60 percent) were still alive at
the end of the reporting period ending August 30, 2013 (Table 5.2-2).
5.2.2.2. PIT Tagging
A total of 1,224 PIT tags were implanted in eight fish species in the Upper River (Table 5.2-4).
Arctic grayling were the most frequently tagged species (n=913), followed by Dolly Varden
(n=109), round whitefish (n=98), and burbot (n=31). Only 22 Chinook salmon were tagged and
none of these were subsequently detected or recaptured. Smaller numbers of PIT tags were
applied to undifferentiated whitefish (21), longnose sucker (20), humpback whitefish (9), and
lake trout (1) (Table 5.2-4).
Of the fish implanted with PIT tags and released, 3 percent (n=42) were subsequently observed
in the Upper River, either via detection at stationary PIT antennas or recapture during later
sampling (Table 5.2-4). These fish constitute the dataset of PIT-tagged individuals for which
movement information can be discerned. Arctic grayling (n=35) comprised most of the fish
observed subsequent to tagging, while a small number of tagged round whitefish (n=3), Dolly
Varden (n=2), burbot (n=1), and longnose sucker (n=1) were also observed. Three additional
Dolly Varden were recaptured, however, implant records (i.e., date and location of release) for
these fish were not available. The Oshetna River antenna array detected more individuals (24)
with a higher number of detections (28.876) than the Kosina Creek array (10 individuals and 171
detections; Table 5.2-5). Details regarding movements or recapture of PIT-tagged fish are
presented by species. Data developed in support of the ISR is available for download at
http://gis.suhydro.org/reports/isr (ISR_9_5_FDAUP_PITTagData).
5.2.2.2.1. Arctic grayling
Of the 35 Arctic grayling that were observed subsequent to tagging, nine were documented
moving between streams; the majority (n=26) were detected or recaptured exclusively in the
same stream in which they were tagged. One juvenile (180 mm [7 in]) was tagged and released
at the Oshetna River rotary screw trap (RM 0.1, upstream of PRM 235.1) on June 16 and
detected eight days later on June 24 at the Kosina Creek PIT antenna (RM 0.2, upstream of PRM
209.1), having covered a distance of roughly 26 mainstem river miles. The remaining eight
Arctic grayling observed moving between streams were all classified as juvenile/adult. One of
these fish (190 mm [7.5 in]) was tagged in Goose Creek (upstream of PRM 232.8) on August 17
and detected 18 days later on September 4 at the Oshetna River PIT antenna (RM 4.5). Another
juvenile/adult (190 mm [7.5 in]) was captured and tagged in the Susitna River mainstem (PRM
209) on August 4 and detected three days later at the nearby Kosina Creek PIT antenna.
The remaining seven juvenile/adult Arctic grayling that exhibited inter-stream movements (mean
length 272 mm [10.7 in]) were all tagged and released at the Oshetna River rotary screw trap and
subsequently detected at the Kosina Creek PIT antenna, covering a distance of roughly 26
mainstem river miles. The average interval between release at the Oshetna River rotary screw
trap and detection in Kosina Creek was 40 days (range 6-79 days). All of these fish were
released from the Oshetna River over a six-day period (June 15-20), while their detections in
Kosina Creek spanned from June 21 to September 2.
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Of the 27 Arctic grayling that were observed exclusively in the stream in which they were
tagged, the majority (19) were tagged in the Oshetna River and detected at the Oshetna River
PIT antenna. For this subset of fish, the average time between a fish’s tagging event and its final
antenna detection was 23 days (range 0-104 days).
Arctic grayling were the only species in the Upper River that was detected or recaptured in
sufficient numbers to offer a comparison of different macrohabitats used by individual fish. For
each macrohabitat type in which fish were tagged, Table 5.2-6 displays the corresponding
number of fish detected or recaptured by macrohabitat type. Movements were documented
between split, single, and complex tributary channels as well as between complex tributary and
split main channels. It should be noted that the majority of these fish were tagged at rotary screw
traps and subsequently observed at PIT antennas, each of which were situated in a fixed
macrohabitat type. Only three Arctic grayling were observed subsequent to tagging at sites other
than a rotary screw trap or PIT antenna. Thus, a comparison of movements is largely limited to
the macrohabitat types in which the two rotary screw traps and two PIT antennas were located in
the Upper River.
5.2.2.2.2. Burbot
One burbot (355 mm [14 in]) initially captured at the Oshetna River rotary screw trap (RM 0.1)
and tagged on June 15 was detected 27 days later roughly 4.4 river miles upstream at the Oshetna
River PIT antenna (RM 4.5) on July 12.
5.2.2.2.3. Dolly Varden
Two recaptured Dolly Varden were found in the same tributaries in which they were initially
captured. One juvenile/adult (85 mm [3.3 in]) was tagged in Watana Creek on July 31 and
recaptured 29 days later on August 29. The other juvenile/adult (113 mm [4.4 in]) was tagged in
Jay Creek on August 9 and recaptured 53 days later on October 1.
5.2.2.2.4. Longnose sucker
One juvenile longnose sucker (177 mm [7 in]) was captured in a Susitna River side channel near
PRM 202.7 on August 6 and recaptured at the same site 14 days later on August 20.
5.2.2.2.5. Humpback Whitefish
While not detected or recaptured in the Upper River, one juvenile humpback whitefish (225 [8.9
in]) tagged at the Oshetna River rotary screw trap (PRM 235) on June 21 was recaptured 16 days
later on July 7 at the Curry Station rotary screw trap (PRM 124), having covered a distance of
roughly 111 river miles. This fish was then detected 27 days later on August 3 near PRM 104 at
the Whiskers Slough PIT antenna.
5.2.2.2.6. Round Whitefish
Each of the three round whitefish observed subsequent to tagging were initially captured in the
Oshetna River. After being tagged and released at the Oshetna River rotary screw trap (RM 0.1)
on July 30, one juvenile/adult (237 mm [9.3 in]) was detected 9 days later on August 8 at the
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Kosina Creek PIT antenna (RM 0.2), having covered a distance of roughly 26 mainstem river
miles. One juvenile (147 mm [5.8 in]) tagged in the Oshetna River on September 12 was
detected at the Oshetna River PIT antenna on 15 separate days between September 16 and
October 6. One juvenile/adult (285 mm [11.2 in]) was tagged in the Oshetna River on
September 12 and detected on the same day at the Oshetna River PIT antenna as well as seven
days later on September 19.
5.2.3. Task C: Describe juvenile Chinook salmon movements.
Although 22 juvenile Chinook salmon were PIT tagged in the Upper River study area, none of
these fish were subsequently detected. Thus, descriptions of juvenile Chinook salmon
movements in the Upper River are currently based solely on information from rotary screw trap
data, as described in Section 5.2.1.
5.3. Objective 3: Early Life History
Juvenile Chinook salmon in the Upper River were documented on June 29, 2013 in two locations
on the Black River, a tributary to the Oshetna River. Six total Chinook salmon fry (fork lengths
38 to 39 mm) were captured by backpack electrofishing in riffle habitats in a complex, braided
channel (Table 5.3-1). The two locations, situated in close proximity, were located 2.9 km (1.8
mi) upstream of the confluence with the Oshetna, suggesting that these young-of-the-year fish
are likely the offspring of adults that spawned in the Black River in 2012. Low catch during the
spring precluded the evaluation of movement of juvenile salmon from spawning rearing habitats
in the Upper River. Data developed in support of the ISR is available for download at
http://gis.suhydro.org/reports/isr (ISR_9_5_FDAUP_FishObservations).
5.4. Objective 4: Characterize the seasonal age class structure,
growth, and condition of juvenile anadromous and resident fish
by habitat type.
Total sample sizes of fish measured for length and weight, by hydrologic segment, are presented
in Table 4.7-2. A summary of fish size, growth and condition factor by habitat types is discussed
in the subsections below:
5.4.1. Growth by Habitat Type
The number of recaptured PIT-tagged fish used in the growth analysis for the Upper Susitna
River is presented in Table 5.4-1. No juvenile Chinook salmon and six Arctic grayling were
recaptured. Fish recaptures less than seven days in duration were eliminated from the growth
analysis. The tally of fish with seven or more days in duration between recapture events resulted
in a sample size of only one adult Arctic grayling. The site-specific growth rate for this fish is
described below. Data developed in support of the ISR is available for download at
http://gis.suhydro.org/reports/isr (ISR_9_5_FDAUP_PITTagData).
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5.4.1.1. Arctic Grayling
One adult Arctic grayling was recaptured in the Upper Susitna River at Watana Creek within the
single-channel tributary habitat type. This fish grew at a rate of 0.11 mm/day for a specific
growth rate (SGR) of 0.03 percent of its length per day. No comparisons with seasons, fish
sizes, or habitat types could be made for Arctic grayling in the Upper River.
5.4.2. Condition Factor by Habitat Type
A summary of the condition factors by habitat type is described for the pilot species below. Data
developed in support of the ISR is available for download at http://gis.suhydro.org/reports/isr
(ISR_9_5_FDAUP_FishCondFactors).
5.4.2.1. Chinook Salmon
5.4.2.1.1. Juveniles
In the Upper River, 90 juvenile Chinook salmon met the criteria for this analysis. All juvenile
Chinook were captured in tributaries including: Kosina Creek, the Black River, and the Oshetna
River. Condition factors were similar for Chinook salmon from all three tributaries (Figure
5.4-1); however, only Kosina Creek fish had mean and median condition factors greater than
one.
5.4.2.2. Arctic Grayling
5.4.2.2.1. Juvenile / Adult
In the Upper River, 1,049 Arctic grayling met the analysis criteria (Table 4.7-3). Most of these
fish (83 percent) were collected from tributaries including the Black and Oshetna rivers, as well
as Goose, Watana, Kosina, and Tsisi creeks. Nevertheless, the numbers captured in the
mainstem Susitna River in various habitat types were sufficient for analysis. The condition
factors for these fish are summarized in Table 5.4-4. There were no differences in Arctic
grayling condition factors among habitat types (Figure 5.4-2).
5.5. Objective 5: Determine whether Dolly Varden and humpback
whitefish residing in the Upper River exhibit anadromous or
resident life histories.
Dolly Varden and humpback whitefish greater than 200 mm (7.9 inches) in length were targeted
for otolith collection to test for marine-derived elements indicative of an anadromous life history
pattern. Laboratory testing for the presence of marine derived nutrients is not complete at this
time and no results are available for this report.
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5.6. Objective 6: Determine baseline metal and mercury
concentrations in fish tissues for resident fish species in the
mainstem Susitna River.
Tissue or whole fish samples were collected in the reservoir inundation zone for assessment of
metals and mercury in support of the Baseline Water Quality Study and the Mercury Assessment
and Potential for Bioaccumulation Study (ISR Studies 5.5 and 5.7, respectively). The results of
baseline sampling for metals, total mercury, and methylmercury (MeHg) concentrations in fish
tissue samples are summarized in Section 5.6 and discussed in Section 6.2.3 of the
bioaccumulation study (ISR Study 5.7).
5.7. Objective 7: Document the seasonal distribution, relative
abundance, and habitat associations of invasive species
(northern pike).
Northern pike were not previously documented in the Upper River, so no targeted collection
efforts for pike were made. No northern pike have been collected in the Upper River fish
sampling events conducted by AEA to date (Tables 4.5-1, 4.8-1, 4.9-1 and 4.11-1). Data
developed in support of the ISR is available for download at http://gis.suhydro.org/reports/isr
(ISR_9_5_FDAUP_FishObservations).
5.8. Objective 8: Collect tissue samples from juvenile salmon and
all resident and non-salmon anadromous fish.
Fish tissues were collected opportunistically in conjunction with all fish capture events in
support of the Fish Genetic Baseline Study (ISR Study 9.14). Analysis of these samples is
reported in that study’s ISR.
6. DISCUSSION
The study of Fish Distribution and Abundance in the Upper Susitna River is ongoing. As
indicated in Section 4, tasks associated with each of the eight study objectives were initiated in
2013. To address interannual variation and expand upon the current data set, additional work
will continue in the next study year (see Section 7.1).
Summary information specific to the status of each of the study objectives is provided in the
sections that follow. The discussions include: an overview of interdependencies with other ISR
studies, the current status of ISR studies that support the specific objectives of the Study of Fish
Distribution and Abundance in the Upper Susitna River, a summary of key findings in 2013, and
an assessment of the adequacy of the data collected in 2013 to meet the study objectives. Where
applicable, a comparison between 2013 results and previously collected data in the Upper River
study area is also provided.
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6.1. Fish Distribution, Relative Abundance and Habitat Associations
Three ISR studies support Objective 1 of the Study of Fish Distribution and Abundance in the
Upper Susitna River: the Geomorphology Study (Study 6.5), Characterization and Mapping of
Aquatic Habitats Study (Study 9.9), and the Study of Fish Passage Barriers in the Middle and
Upper Susitna River and Susitna Tributaries (Study 9.12). These studies were initiated in 2012
and study results have been used to inform the site selection process for Fish Distribution and
Abundance studies in the Upper Susitna River study area. Study variances for these studies are
not anticipated to affect the successful completion of the Study of Fish Distribution and
Abundance in the Upper Susitna River. As fish distribution and abundance data analysis
continues, the Characterization and Mapping of Aquatic Habitats Study (ISR Study 9.9) provides
information relevant to fish-habitat associations in the Upper Susitna River.
Work completed under Objective 1 supports five other ISR studies. Fish collections in the Upper
River are being used to: 1) identify species that could colonize the future reservoir site (ISR
Study 9.10); 2) provide data on fish barriers for the Study of Fish Passage Barriers in the Middle
and Upper Susitna River and Susitna Tributaries (ISR Study 9.12) and 3) fish movements for the
Study of Fish Passage Feasibility at Watana Dam (ISR Study 9.11. In addition, patterns of
distribution and abundance from standardized sampling methods will complement information
from opportunistic sampling conducted for radio telemetry, fishwheel, and sonar observations of
as part of the Salmon Escapement Study (ISR Study 9.7). Fish distribution and abundance is
also being used to provide distribution and relative abundance information relevant to the Fish
Harvest Study (ISR Study 9.15).
During the 2013 study year, nine fish species were documented in the Upper Susitna River study
area: Chinook salmon, Arctic grayling, burbot, Dolly Varden, lake trout, longnose sucker,
sculpin, humpback whitefish, and round whitefish (Table 5.1.1-1). Each of these species was
also documented within the study area during studies conducted in the 1980s (ADF&G 1981;
ADF&G 1983a; ADF&G 1984) and during 2012 field efforts (HDR 2013).
Distribution patterns varied among species particularly with respect to the use of mainstem
Susitna River habitat versus use of tributaries. The most widely distributed species were Arctic
grayling and sculpin, which occupied both mainstem and tributary habitats. Some species, such
as burbot, longnose sucker, and round whitefish, were most commonly found in the mainstem
Susitna River and in larger tributaries. Dolly Varden were found exclusively in tributary
habitats. Species with the fewest observations and most constricted distributions were juvenile
Chinook salmon, humpback whitefish, and lake trout.
Overall, the relative abundance of juvenile Chinook salmon in the Upper River was low;
however, high abundances were observed in localized areas. During 2013sampling efforts, 281
juvenile Chinook salmon observations were made; these occurred in Kosina Creek and the
Oshetna and Black rivers (Table 5.1-2). Estimated CPUE values were zero in 95 percent of
mesohabitats (Table D15). Exceptions were observed in Kosina Creek and the Black River
where CPUE was moderate. Juvenile chinook salmon were most commonly associated with fast
water habitats.
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Arctic grayling and sculpin were the most abundant and widely distributed species found in the
Upper River study area, occurring in 59 percent and 78 percent of sites respectively. As
determined by CPUE, Dolly Varden was abundant in specific tributaries and all other species
had low to moderate abundance in Upper River sites. Although gear-specific CPUE was
frequently zero for other species, comparisons across species for each gear provide confidence
that fishes were captured when present.
Estimates of relative abundance and a description of habitat associations for in the Upper River
were not available from the 1980s studies. Thus, no comparisons between 2013 findings and
historic data were made for these components of Objective 1.
Work completed in 2013 is on-track for meeting Objective 1. Work will continue in the next
year of study in order to obtain additional data in support of this task.
6.2. Seasonal Movements
Objective 2 of the Study of Fish Distribution and Abundance in the Upper Susitna River is
supported by the Salmon Escapement Study (Study 9.7). The Salmon Escapement Study
provides movement data for target species and life stages via fixed receiver and aerial tracking of
radio-tagged fish. The study is ongoing, and variances in 2013 are not anticipated to affect the
successful completion of the Study of Fish Distribution and Abundance in the Upper Susitna
River.
Work completed under Objective 2 of the Study of Fish Distribution and Abundance in the
Upper Susitna River supports three other ISR studies. Information on fish movement patterns in
the Upper River will be used to support the Study of Fish Passage Barriers in the Middle and
Upper Susitna River and Susitna Tributaries (Study 9.12), the Study of Fish Passage Feasibility
at Watana Dam (ISR Study 9.11), and the Future Watana Reservoir Fish Community and Risk of
Entrainment Study (Study 9.10).
In 2013, information about seasonal patterns of fish movement in the Upper River was obtained
via downstream migrant trapping and biotelemetry surveys. The downstream migrant traps,
which were located in Kosina Creek and the Oshetna River, resulted in 153 and 1,001 fish
captures, respectively. During trap operation in 2013, eight species were captured in the traps:
Chinook salmon, Arctic grayling, burbot, Dolly Varden, longnose sucker, sculpin, humpback
whitefish, and round whitefish. Each of these species was captured in both the Kosina and
Oshetna traps with the exception of burbot, which was captured only in the Oshetna River, and
Dolly Varden, which was captured only in Kosina Creek. Biotelemetry surveys utilized PIT and
radio tags to track the movement of the seven species: Chinook salmon, Arctic grayling, burbot,
Dolly Varden, longnose sucker, humpback whitefish, and round whitefish.
Pulses in the numbers of fish captured at the downstream migrant traps can be used to infer
movement patterns for individual species. This was particularly the case for Arctic grayling,
which was the most abundant species captured in both the Kosina and Oshetna traps. Pulses in
catch indicate downstream movement of grayling during early-, mid- and late-summer sampling
periods, suggesting a relatively constant low level of movement out of the Oshetna and into the
mainstem Susitna. Similar patterns in seasonal movement were observed for other resident fish
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species including longnose sucker, humpback whitefish, and round whitefish. Occasional
catches of other resident species in traps included Dolly Varden, burbot, and sculpin; but were
too low to infer any patterns about seasonal movements. For juvenile Chinook salmon, a single
smolt was captured at the Oshetna trap in late July, and a pulse of nine smolts was observed at
the Kosina trap in early to mid-August. A single Chinook salmon parr was caught late season,.
Interbasin movements were evident from recaptures of radio-tagged and PIT-tagged Arctic
grayling and humpback whitefish. Within the Upper River study area, inter-stream migration
distances up to approximately 26 miles were observed, as some Arctic grayling PIT-tagged in the
Oshetna River and Goose Creek were subsequently detected in Kosina Creek and the Oshetna
River respectively. More extensive inter-basin movements were also observed from radio
telemetry surveys; radio-tagged Arctic grayling tagged in the Upper River migrated downstream
past the proposed Watana Dam site and travelled as far as 50 miles downstream to Chinook
Creek. Finally, one humpback whitefish that was PIT tagged in the Oshetna River was
subsequently recaptured twice in the Middle River, first in the Curry rotary screw trap and again
by the Whiskers Creek PIT array.
During the 1980s studies, seasonal movement studies were not conducted in the Upper River.
Thus, no historic data are available for comparison with the results of Objective 2.
Work completed in 2013 is on-track for meeting Objective 2. However, small sample sizes for
some species may limit the ability to draw conclusions regarding species-specific seasonal
movement patterns. Downstream migrant trapping and biotelemetry efforts will continue in the
next year of study in order to increase sample sizes and obtain additional information on fish
movement patterns and timing.
6.3. Early Life History
Objective 3 of the Study of Fish Distribution and Abundance in the Upper Susitna River is not
dependent on other ISR studies.
Five fish species were captured during the spring, Early Life History sampling in the Upper
River including: Chinook salmon, Arctic grayling, Dolly Varden, humpback whitefish, and
round whitefish. For Chinook salmon, which is the only Pacific salmon species known to occur
in the Upper River, observations occurred in late June in the Black River approximately 2.9 km
(1.8 mi) upstream of its confluence with the Oshetna River.
Early life history was not originally proposed as a component of the Upper River Study but was
added during the 2013 study season to specifically target juvenile anadromous salmon during the
timeframe from ice break up to June 30. Thus, even with low numbers of juvenile Chinook
salmon observed in the Upper River, work completed in 2013 will supplement the Middle River
data collection toward Objective 3. This spring sampling effort will continue in the next study
year to collect more information on juvenile salmonids movement patterns and timing of
movement from spawning to rearing habitats.
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6.4. Seasonal size-class structure, growth and condition
Objective 4 of the Study of Fish Distribution and Abundance in the Upper Susitna River is not
interrelated with other ISR studies.
To meet Objective 4, over 5,000 paired length-weight measurements were obtained from
individual fish representing nine species: Chinook salmon, Arctic grayling, burbot, Dolly
Varden, lake trout, longnose sucker, sculpin, humpback whitefish, and round whitefish. For the
two species reported on within this ISR (i.e., Chinook salmon and Arctic grayling), 123 and
1,652 paired measurements were obtained, respectively.
Arctic grayling growth analysis was limited to data available for a single adult Arctic grayling
that was PIT-tagged and subsequently recaptured and measured. The growth rate of this fish was
0.11 mm/day and had a specific growth rate of 0.03 percent of its length per day. There is
currently insufficient data to compare growth rates among seasons, fish size, or habitat types.
Arctic grayling condition factors were largely consistent among mainstem Susitna River and
tributary macrohabitat types. This could reflect that food resources are not limiting or that the
species is high mobile and opportunistically moving to habitats with resources. Condition
factors of Arctic grayling observed in the Upper River were consistent with those from the
Middle/Lower River.
Condition factors calculated for Upper River juvenile Chinook salmon were greatest in Kosina
Creek compared to other locations. Although sample sizes are relatively small and the study is
ongoing, Kosina Creek may provide better juvenile rearing habitats than other locations in the
Upper River. Condition factors in Kosina Creek were consistent with those observed in the
Middle/Lower Study Area while the condition factor of juvenile Chinook salmon from the
Oshetna and Black Rivers were on average the lowest found in the Upper/Middle/Lower Susitna
Basin.
During the 1980s studies growth rates and condition factors were not determined in the Upper
River study area. Thus, no historic data is available for comparison with the results of Objective
4.
Work completed in 2013 is on-track for meeting Objective 4. However, sample sizes for growth
analyses are currently limited and preclude growth rate comparisons among seasons, fish size,
and habitats. Work will continue in the next study year to increase sample sizes for the size-
class, growth, and condition factor analyses.
6.5. Anadromous life-histories
Objective 5 of the Study of Fish Distribution and Abundance in the Upper Susitna River is not
dependent on used to support other ISR studies. Results of this study objective will be used to
directly address the study objective and the question of whether anadromous forms of Dolly
Varden or Humpback Whitefish migrate up through Devils Canyon and are present above the
proposed Watana Dam location.
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Twenty-eight otolith samples were collected from adult Dolly Varden during the fish distribution
surveys in the Upper River in 2013. No samples were obtained from humpback whitefish, due to
the scarcity of adults in the Upper River. Results from laboratory testing for the presence of
marine derived nutrients are not available at this time.
Work completed in 2013 is on-track for meeting Objective 5. Work will continue in the next
year of study to meet the established target sample sizes.
6.6. Baseline metals and mercury
Objective 6 of the Study of Fish Distribution and Abundance in the Upper Susitna River is not
dependent on other ISR studies. However, fish tissue sample collections are being used to
support the Baseline Metal Levels in Fish Tissue (Study 5.5) and Mercury Assessment and
Potential for Bioaccumulation (Study 5.7) studies. During fish distribution and abundance
sampling in the Upper River in 2013, 66 tissue samples representing eight species were collected
for metals and mercury analysis. Samples were collected from Arctic grayling, burbot, Dolly
Varden, longnose sucker, sculpin, lake trout, humpback whitefish, and round whitefish. Results
are presented and discussed in ISR Study 5.5 and ISR Study 5.7.
Work completed in 2013 is on-track for meeting Objective 6. Work will continue in the next
year of study to meet the established target sample sizes.
6.7. Invasive Species
Objective 7 of the Study of Fish Distribution and Abundance in the Upper Susitna River is not
dependent on other ISR studies. If documented, the presence of invasive species would be used
to identify species that could colonize the future reservoir site (Study 9.10).
No non-native fish species were documented in the Upper River study area. Work completed in
2013 is on-track for meeting Objective 7. The presence of a single invasive lake trout individual
was documented in an unnamed tributary of Watana Creek midway between two lake habitats.
Observation of invasive and non-native species will continue to be documented during surveys
conducted in the next study year.
6.8. Tissue Collection
Objective 8 of the Study of Fish Distribution and Abundance in the Upper Susitna River is not
dependent on other ISR studies. However, fish tissue sample collections are being used to
support the Genetics Baseline Study for Selected Fish Species (Study 9.14). During fish
distribution and abundance sampling in the Upper River in 2013, 717 tissue samples representing
eight species were collected for genetics analysis. Samples were collected from juvenile and
adult Chinook salmon, Arctic grayling, burbot, Dolly Varden, longnose sucker, sculpin,
humpback whitefish, and round whitefish. Results are presented and discussed in ISR Study
9.14.
Work completed in 2013 is on-track for meeting Objective 8. Work will continue in the next
year of study to meet the established target sample sizes.
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7. LITERATURE CITED
Adams, F.J. 1999. Status of rainbow trout in tributaries of the upper King Salmon River,
Becharof National Wildlife Refuge, Alaska, 1990-92. U.S. Fish and Wildlife Service,
Alaska Fisheries Technical Report Number 53, King Salmon, Alaska.
Alaska Department of Fish and Game (ADF&G). 1981. Subtask 7.10 Phase 1 Final Draft Report
Resident Fish Investigation on the Upper Susitna River. Anchorage, Alaska.
ADF&G. 1982. Aquatic Studies Procedures Manual: Phase I. Prepared by Alaska Department of
Fish and Game, Su-Hydro Aquatic Studies Program. Prepared for Alaska Power
Authority, Anchorage, Alaska. pp 111.
ADF&G. 1984. Susitna Hydro aquatic studies report No. 1. ADF&G, Susitna Hydro Aquatic Studies
Report Series, Susitna Hydro Document No. 1450, Anchorage, Alaska.
ADF&G. 2012. Alaska Fish Resource Monitor, Anadromous Waters. Accessed November 2012.
Alaska Department of Fish and Game, Anchorage, Alaska.
Alaska Energy Authority (AEA). 2012. Revised Study Plan: Susitna-Watana Hydroelectric
Project FERC Project No. 14241. December 2012. Prepared for the Federal Energy
Regulatory Commission by the Alaska Energy Authority, Anchorage, Alaska.
http://www.susitna-watanahydro.org/study-plan.AEA, 2013a. 2012. Adult Salmon
Distribution and Habitat Utilization Study. Susitna-Watana Hydroelectric Project (FERC
No. 14241. Prepared by LGL Alaska for Alaska Energy Authority, March 2013.
Buckwalter, J.D. 2011. Synopsis of ADF&G’s Upper Susitna Drainage Fish Inventory, August
2011. November 22, 2011. ADF&G Division of Sport Fish, Anchorage, AK. 173 pp.
Buckwalter, J. D., J. M. Kirsch, and D. J. Reed. 2012. Fish inventory and anadromous cataloging in
the upper Koyukuk River and Chandalar River basins, 2010. Alaska Department of Fish and
Game, Fishery Data Series No. 12-22, Anchorage.
Burr, 1993. Maturity of lake trout from eleven lakes in Alaska. Northwest Science, Vol 67, No.
2, 1993.
Docker, M. F. 2009. A review of the evolution of nonparasitism in lampreys and an update of the
paired species concept. Pages 71-114 in L. R. Brown, S. D. Chase, M. G. Mesa, R. J.
Beamish, and P. B. Moyle, editors. Biology, management, and conservation of lampreys
in North America, American Fisheries Society Symposium 72. American Fisheries
Society, Bethesda, MD.
Dolloff, C.A., D.G. Hankin, and G.H Reeves. 1993. Basinwide Estimation of Habitat and Fish
Populations in Streams. USDA Forest Service General Technical Report SE-GTR-83. pp 25.
Fulton, T. W. 1902. The rate of growth of fishes. 20th Annual Report of the Fishery Board of
Scotland 1902 (3):326-446.
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
IN THE UPPER SUSITNA RIVER (9.5)
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Fulton, T. W. 1904. The rate of growth of fishes. 22nd Annual Report of the Fishery Board of
Scotland 1904 (3):141-241.
Grubbs, F.E. 1950. Sample criteria for testing outlying observations. Ann. Math. Stat. 21, 1, 27-
58.
HDR. 2013. 2012 Upper Susitna River Fish Distribution and Habitat Study: Fish Distribution
Report. Susitna-Watana Hydroelectric Project (FERC No. 14241) Prepared by HDR for
Alaska Energy Authority, April 2013.
Heard, W. R. 1966. Observations on lampreys in the Naknek River System of Southwest
Alaska.Copeia 1966(2):332-339.
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.
Kincaid, T. M. and A.R. Olsen. 2012. spsurvey: Spatial Survey Design and Analysis. R package
version 2.3. US Environmental Protection Agency.
Larson, L. 2000. Fishery Data Series No. 00-20. A Trap Efficiency Study for Dolly Varden in Kenai
Lake, 1998. Alaska Department of Fish and Game. Soldotna, Alaska. pp 8.
Link, M.R., B. Nass, J.J. Smith, D. Robichuad, S. Burril, K. English, S. Crawford, J.T. Priest,
and M.J. Nemeth. 2013. Draft Report: Adult salmon distribution and habitat utilization
study. LGL Alaska Research Associates, Inc. Draft Report prepared for Alaska Energy
Authority, January 2013.
Lukasz K. 2011. Outliers: Tests for outliers. R package version 0.14. http://CRAN.R-
project.org/package=outliers.
Murphy, B.R., and D.W. Willis, editors. 1996. Fisheries Techniques, 2nd edition. American Fisheries
Society, Bethesda, Maryland.
National Marine Fisheries Service (NMFS). 2000. Guidelines for Electrofishing Waters Containing
Salmonids Listed Under the Endangered Species Act.
Russell, R. 1977. Rainbow trout life history studies, in the lower Talarik Creek-Kvichak
Drainage. Alaska Department of Fish and Game, Completion Report, D-J Study G -II-E,
Juneau, AK.
Rutz, D. (1999). Movements, food availability and stomach contents of Northern Pike in selected
Susitna River drainages, 1996-1997. Alaska Department of Fish and Game, Division of
Sport Fish, Research and Technical Services.
Sautner, J., and M. Stratton. 1983. Upper Susitna River Impoundment Studies 1982. Alaska
Department of Fish and Game. Anchorage, Alaska. 220 pp.
Smith-Root, Inc. 2009. User’s Manual LR-24 Backpack Electrofisher. Vancouver, WA. 58 pp.
INITIAL STUDY REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE
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Stevens, D. L., Jr. and A. R. Olsen (2004). "Spatially-balanced sampling of natural resources."
Journal of American Statistical Association 99(465): 262-278.
Temple, G.M., and T.N. Pearsons. 2007. Electrofishing: Backpack and Drift Boat. In Salmonid Field
Protocols Handbook: Techniques for Assessing Status and Trends in Salmon and Trout
Populations. State of the Salmon. Portland, Oregon. pp 95-132.
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. pp 28.
Vladykov, V. D., and E. Kott. 1978. A new nonparasitic species of the holarctic lamprey genus
Lethenteron Creaser and Hubbs, 1922 (Petromyzontidae) from northwestern North
America with notes on other species of the same genus. University of Alaska, Fairbanks,
AK.
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8. TABLES
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Table 2-1. Study objectives for the Study of Fish Distribution and Abundance in the Upper Susitna River from the Revised Study Plan. Note that the Revised
Study Plan was succeeded by the Final Susitna River Fish Distribution and Abundance Implementation Plan (March 2013).
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, gill nets, 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, fish wheels,
rotary screw 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
• Rotary Screw 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 lateral 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. Antenna arrays 2
sites at selected side channel, side slough, tributary mouth, or 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.
2C Describe juvenile
Chinook salmon
movements
Juvenile Chinook
salmon
Representative habitat
types • PIT tag arrays at tributary mouths, sloughs, and side channels (Obj 2B)
• Rotary screw trap in known Chinook spawning tributaries
• Monthly measurements of fish size/ growth
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Obj Task
Species/
Life stage Study Sites Proposed Methods by Season
3A Describe emergence
timing of salmonids
Juvenile salmonids Select Tributary
Habitat • Bi-weekly sampling from breakup to July 1 using fyke nets, seines, electrofishing and
minnow traps in salmon spawning areas within Focus Areas.
3B Determine movement
patterns and timing of
juvenile salmonids
from spawning to
rearing habitats
Juvenile salmonids Select Tributary
Habitat • Focus on timing of emergence and movement of newly emergent fish from spawning to
rearing areas
4 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.
5 Seasonal
presence/absence and
habitat associations of
invasive species
Northern pike All study sites • Same methods as #1 and #2 above.
• The presence of northern pike and other invasive fish species will be documented in all
samples
• Additional direct efforts with angling as necessary
6 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 4.1-1. Tributaries selected for fish distribution and abundance sampling in the Upper Susitna River in 2013.
Tributary
Susitna
River
Mainstem
PRM
Listed
in AWC
Catalog
Stream
Accessibility
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
Proposed Reservoir Inundation Zone PRM 232.5
Jay Creek 211.0 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 189.4 no no 32 453.5 27 DIR
Proposed Dam Site PRM 187.1
Notes:
1 Data taken from AEA (unpublished 2012 data).
2 Data taken from Saunter and Stratton (1983).
DIR = tributary subject to direct rather than statistical sampling due to accessibility issues.
NA = data not available or applicable
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Table 4.1-2. Sampling Effort for GRTS and direct sampling tributaries, 2013.
Tributary
Susitna
River Project
River Mile
Chinook
Salmon
Presence
Documented
Percent Sampling by
Length
Number of GRTS
Population
Sample Units
Target Number of
Distribution
Samples
Number of Distribution
Sites
Sampled1
Target
Number of
Abundance
Samples
Number of Abundance
Site Sampled
Number of Mesohabitat
Units
Sampled
GRTS Sampled Tribs
Oshetna River 235.1 yes 25 52 8 8 5 5 27
Black River NA no 25 24 3 3 3 3 12
Goose Creek 232.8 yes 25 81 12 12 8 8 40
Proposed Reservoir Inundation Zone PRM 187.1-232.5
Kosina Creek 209.1 yes 25 24 3 3 3 3 10
Tsisi Creek NA no 25 23 3 3 3 3 10
Unnamed Tributary4 206.3 no 15 29 1 0 3 0 0
Unnamed Tributary3 204.5 no 15 21 0 0 3 0 0
Unnamed Tributary3 197.7 no 15 41 2 0 4 0 0
Watana Creek 196.9 yes 25 60 9 9 6 6 30
Watana Creek
Tributary2 NA no 25 67 10 6 7 7 18
Unnamed Tributary3 194.8 no 15 32 2 0 3 2 4
Total -- -- -- 454 53 44 48 37 151
Direct Sample Tribs
Jay Creek 211 no NA NA NA 2 NA NA 8
Deadman Creek3 189.4 no NA NA NA 0 NA NA 0
Total -- -- -- -- -- 2 -- -- 8
Grand Total -- -- -- -- -- 46 -- 37 159
Notes:
1 These are single-pass samples without block nets; abundance samples will also be used for distribution (81 total samples)
2 Not all sites sampled due to lack of safe landing zones
3 Not sampled die to private land ownership lower reaches and lack of landing zones in upper reaches. Two days of sampling effort applied each season.
4 Only 1 landing zone present, stream conditions deemed unsafe to sample
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Table 4.1-3. Upper Susitna River tributary habitat classification and mesohabitat sampling, 2013
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Table 4.1-4. Sample effort for mainstem transects in the Upper River, 2013.
Transect ID PRM Sampled Sample Type Main Channel Side Channel Side Slough Tributary Mouth/Plume Total
Proposed Dam Site PRM 187.1
1 188.3 No Distribution 0 0 0 0 0
2 190.7 Yes Distribution 1 0 0 0 1
3 193.1 Yes Distribution 1 0 0 0 1
4 195.5 Yes Distribution 1 0 1 0 2
5 197.9 Yes Distribution 1 0 0 0 1
6 200.3 Yes Distribution 1 1 0 0 2
7 202.7 Yes Relative Abundance 1 1 0 0 2
8 205.1 Yes Relative Abundance 1 0 0 0 1
9 207.5 Yes Distribution 1 0 0 0 1
10 209.9 Yes Distribution 1 0 0 0 1
11 212.3 Yes Distribution 1 0 0 1 2
12 214.7 Yes Distribution 1 0 0 0 1
13 217.1 Yes Relative Abundance 1 0 0 1 2
14 219.5 Yes Distribution 1 0 0 1 2
15 221.9 No Distribution 0 0 0 0 0
Proposed Reservoir Inundation Zone at Low Pool 222.5
16 224.3 Yes Distribution 1 0 0 0 1
17 226.7 No Distribution 0 0 0 0 0
18 229.1 No Distribution 0 0 0 0 0
19 231.5 Yes Relative Abundance 1 0 0 0 1
Proposed Reservoir Inundation Zone at Maximum Pool 232.5
20 233.9 Yes Distribution 1 0 0 0 1
Total 16 1 1 3 22
Notes:
* Dangerous sampling conditions including swift bouldery habitats.
** Dangerous sampling conditions and no location to stop the raft for sampling purposes.
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Table 4.2-1. Salmon early life history sampling summary, 2013.
Event 1 Event 2
Start date End date Start date End date
6/4/13 6/12/13 6/23/13 6/29/13
Tributary Number of sites Number of sites
Oshetna River 8 8
Black River 2 2
Kosina Creek 6 7
Tsisi Creek 2 2
Tsisi Lake 1 1 ns
Tsisi Lake 2 1 ns
Susitna River 1 1
Total 21 20
ns = not sampled
Table 4.2-2. Antenna orientation for fixed-station receiver locations in the Upper Susitna River, 2013.
Station PRM Installation Date Status
Antenna Orientation
Rational Antenna 1 Antenna 2 Antenna 3
Oshetna
River 235.1 29-Jun Installed Down Susitna
River
Up Susitna
River
Up
Oshetna
River
Large accessible
tributary within
impoundment zone
Proposed Reservoir Inundation Zone PRM 232.5
Kosina
Creek 209.1 30-Jun Installed Down Susitna
River
Up Susitna
River
Up Kosina
Creek
Salmon spawning
stream
Deadman 191.2 2-Jul Installed in place
of Watana Dam
Site
Down Susitna
River
Up Susitna
River
Monitor fish movement
between the Middle
and Upper rivers
Watana
Dam Site 188.0 N/A Not installed due
to land access
Down Susitna
River
Up Susitna
River
Monitor fish moving
past the proposed dam
site
Proposed Dam Site 187.1
Watana
Creek 169.9 N/A Not installed due
to land access
Down Susitna
River
Up Susitna
River
Up
Watana
Creek
Large accessible
tributary within
impoundment zone
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Table 4.2-3. Monitoring efficiency (percent operational) of fixed-station receivers in the Susitna River drainage in
2013, by week. Percentages were calculated as the number of hours of recorded receiver activity divided
by the number of hours in the week; "-" = 'not deployed'. Receivers were considered active in a given
hour if at least one fish detection, beacon hit, or noise event was recorded during the hour. Data are
currently preliminary through 9/9. Shading indicates incomplete data series.
Week Deadman Creek Kosina Creek Oshetna River
6/2 - 6/8 - - -
6/9 - 6/15 - - -
6/16 - 6/22 - - -
6/23 - 6/29 - - 0%
6/30 - 7/6 57% 86% 0%
7/7 - 7/13 100% 100% 20%
7/14 - 7/20 100% 100% 100%
7/21 - 7/27 100% 100% 100%
7/28 - 8/3 100% 51% 100%
8/4 - 8/10 100% 0% 100%
8/11 - 8/17 100% 17% 100%
8/18 - 8/24 24% 0% 23%
8/25 - 8/31 0% 0% 0%
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Table 4.2-4. Summary of aerial surveys of radio-tagged fish in the Upper Susitna River, 2013. Data are currently preliminary through 9/9.
Zone Number 201 203 205 207 212 215 222 225 232 235
Waterbody Susitna River
Deadman
Creek PRM
189.4
Susitna River
Unnamed
Tributary
PRM 194.8
Watana
Creek
PRM
196.9
Susitna River Kosina
Creek
PRM
209.1
Susitna River Oshetna
River
PRM
235.1
Susitna River
Begin Dam Site PRM
187.1
Deadman Creek
PRM 189.4
Wantana Creek
PRM 196.9
Kosina Creek
PRM 209.1
Above Oshetna
River PRM 235.1
End Deadman Creek
PRM 189.4
Watana Creek PRM
196.9
Kosina Creek PRM
209.1
Oshetna River
PRM 235.1
7-2 H H 7-6 H H H H 7-7 H H 7-12 H H H H 7-15 H 7-18 H H H 7-19 H H H H 7-20 H H H H H H
7-21 H H
7-22 H H
7-23 H
7-24 H
7-25 H
7-26 H H H H
7-27 H H
7-28 H H
7-29 H
7-30 H
7-31 H H H H H H H
8-1 H H H H H 8-6 H H H H H H H H H
8-13 H H H H H H H H H 8-19 H H H H H H H H H 8-26 H H H H H H H H H H=Helicopter Survey
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Table 4.5-1. Length and weight of fish species tagged for biotelemetry studies in the Upper Susitna River, 2013.
Species Lifestage Tag Type N
Median Length
(mm)
Length Range
(mm)
Chinook salmon Juvenile PIT 22 74 61-95
Arctic grayling Adult PIT 76 347 330-430
Arctic grayling Juvenile PIT 408 136 55-189
Arctic grayling Juvenile-or-adult PIT 429 248 190-328
Arctic grayling Juvenile-or-adult Radio 57 317 241-410
Burbot Adult PIT 2 597 590-603
Burbot Juvenile PIT 15 198 161-270
Burbot Juvenile-or-adult PIT 14 338 281-495
Burbot Juvenile-or-adult Radio 7 528 405-655
Dolly Varden Juvenile PIT 2 78 74-81
Dolly Varden Juvenile-or-adult PIT 107 149 85-238
Lake trout Juvenile PIT 1 114 -
Longnose sucker Adult PIT 1 370 -
Longnose sucker Juvenile PIT 2 171 164-177
Longnose sucker Juvenile-or-adult PIT 17 223 188-340
Longnose sucker Juvenile/adult Radio 10 374 281-412
Whitefish, humpback Juvenile PIT 5 249 152-268
Whitefish, humpback Juvenile-or-adult PIT 4 299 280-355
Whitefish, round Adult PIT 14 329 320-403
Whitefish, round Juvenile PIT 37 155 84-198
Whitefish, round Juvenile-or-adult PIT 47 260 199-310
Whitefish, round Juvenile/adult Radio 18 322 280-412
Whitefish, undifferentiated Juvenile PIT 4 108 80-168
Whitefish, undifferentiated Juvenile-or-adult PIT 17 270 215-320
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Table 4.5-2. Radio tag allocation by season Upper Susitna River, 2013
Species
Upper Susitna
May/June July August Sept Total Live b
Arctic grayling 0 (0a) 31 (10) 1 (10) 25 (10) 57 (30) 28
Burbot 0 (10) 0 (10) 0 (10) 7 (10a) 7 (30) 2
Dolly Varden 0 (10) 0 (10) 0 (10a) 0 (0) 0 (30) 0
Longnose sucker 0 (10) 5 (10) 0 (10) 5 (10) 10 (30) 2
Northern pike 0 (10) 0 (10) 0 (10) 0 (10) 0 (30) 0
Lake trout 0 (10) 0 (10) 0 (10) 0 (10) 0 (30) 0
Rainbow trout 0 (0a) 0 (10) 0 (10) 0 (10) 0 (30) 0
Humpback whitefish 0 (10) 0 (10) 0 (10a) 0 (0) 0 (30) 0
Round whitefish 0 (10) 0 (10) 0 (10a) 18 (0) 18 (30) 9
Format: tags applied (target number of tags).
a FERC recommended tagging (n≥10) periods. Tagging during spawning periods conducted at the discretion of the
surgeon as based on fish condition. b Live tags as of aerial survey on January 29, 2014. Data subject to ongoing evaluation of tag status.
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Table 4.7-1. Summary of size-at-life stage index used to classify Susitna River species, 2013.
Species Life stage Source Juvenile Juvenile-or-adult Adult
Alaska blackfish <42 42–113 >113 Buckwalter et al. (2012)
Arctic grayling <190 190–328 >328 Buckwalter et al. (2012)
Arctic lamprey <125 125-219 >219 Heard 1966; Docker 2009; Vladykov and Kott 1978
Bering cisco Not Applicable
burbot <280 280–498 >498 Buckwalter et al. (2012)
Dolly Varden <83 >83 - Buckwalter et al. (2012)
eulachon Not Applicable
longnose sucker <188 188–348 >348 Buckwalter et al. (2012)
northern pike <330 330–448 >448 Buckwalter et al. (2012)
sculpin (slimy) <51 51–68 >68 Buckwalter et al. (2012)
threespine stickleback <40 40-70 >70 ADFG 1981
lake trout <300 300-430 430 Burr 1993
rainbow trout <200 200-325 >325 Russell 1977, Adams 1999
humpback whitefish <280 280–363 >363 Buckwalter et al. (2012)
round whitefish <199 199–318 >318 Buckwalter et al. (2012)
Whitefish,
undifferentiated <199 199-363 >363
Chinook salmon alevin, fry, parr, smolt index
chum salmon alevin, fry, parr, smolt index
coho salmon alevin, fry, parr, smolt index
pink salmon alevin, fry, parr, smolt index
sockeye salmon alevin, fry, parr, smolt index
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Table 4.7-2. Summary of fish with length and weight measurements collected in the Upper, Middle and, Lower
Susitna River by hydrologic segment, 2013.
Species
Hydrologic Segment
Lower River Middle River Upper River Total
Chum salmon 60 56 116
Chinook salmon 672 1,366 123 2,161
Coho salmon 487 2,820 3,307
Pink salmon 7 39 46
Sockeye salmon 253 199 452
Pacifc salmon, undifferentiated 44 77 121
Arctic grayling 38 889 1,652 2,579
Burbot 152 280 85 517
Dolly Varden 13 167 299 479
Lamprey 123 19 142
Longnose sucker 661 560 126 1,347
Northern pike 44 44
Salmonid, undifferentiated 4 1 5
Sculpin 679 2,129 2,596 5,404
Stickleback, ninespine 140 140
Stickleback, threespine 884 457 1,341
Stickleback, undifferentiated 3 48 51
Trout, lake 1 1
Trout, rainbow 142 349 491
Whitefish, Bering cisco 2 2
Whitefish, round 108 472 173 753
Whitefish, humpback 8 102 8 118
Whitefish, undifferentiated 52 317 20 389
Grand Total 4,572 10,350 5,084 20,006
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Table 4.7-3. Sample sizes of juvenile Chinook salmon and Arctic grayling included in the condition factor analysis by
mainstem geomorphic reach and tributary
Tributary/ Geomorphic Reach PRM Arctic Grayling Chinook Salmon
Oshetna River 235.1 128 1
Black River N/A 59 22
Goose Creek 232.8 316
Upper Extent Watana Reservoir PRM 232.5
Susitna River UR-3 224.9-234.5 27
Jay Creek 211 11
Kosina Creek 209.1 40 67
Tsisi Creek N/A 38
Susitna River UR-4 208.1-224.9 38
Susitna River UR-5 203.4-208.1 15
Watana Creek 196.9 264
Unnamed 194.8 194.8 8
Susitna River UR-6 187.1-203.4 96
Proposed Watana Dam Location PRM 187.1
Subtotal 1,040 90
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Table 4.8-1. Summary of otolith collection for Dolly Varden in 2013.
Dolly Varden
Index Date
Length
(mm) Location
1 10/4/2013 200 Watana Creek Site 14
2 10/4/2013 200 Watana Creek Site 14
3 10/4/2013 200 Watana Creek Site 14
4 10/4/2013 204 Watana Creek Site 14
5 10/4/2013 208 Watana Creek Site 14
6 10/4/2013 209 Watana Creek Site 14
7 10/4/2013 210 Watana Creek Site 14
8 10/4/2013 214 Watana Creek Site 14
9 10/4/2013 215 Watana Creek Site 14
10 10/4/2013 216 Watana Creek Site 14
11 10/4/2013 216 Watana Creek Site 14
12 10/4/2013 216 Watana Creek Site 14
13 10/4/2013 216 Watana Creek Site 14
14 10/4/2013 217 Watana Creek Site 14
15 10/4/2013 218 Watana Creek Site 14
16 10/4/2013 218 Watana Creek Site 14
17 10/4/2013 223 Watana Creek Site 14
18 10/4/2013 224 Watana Creek Site 14
19 10/4/2013 225 Watana Creek Site 14
20 10/4/2013 226 Watana Creek Site 14
21 10/4/2013 228 Watana Creek Site 14
22 10/4/2013 231 Watana Creek Site 14
23 10/4/2013 235 Watana Creek Site 14
24 10/4/2013 238 Watana Creek Site 14
25 10/4/2013 245 Watana Creek Site 14
26 10/4/2013 248 Watana Creek Site 14
27 10/4/2013 250 Watana Creek Site 14
28 10/4/2013 263 Watana Creek Site 14
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Table 4.9-1. Summary of tissue collection for baseline metal and mercury concentration evaluation, 2013.
Date Target Species
Size
(mm) Location
Baseline Metal
Tissue Samples
Mercury Tissue
Samples
8/11/12 Arctic Grayling 248 Watana Creek 1 1
8/11/12 Arctic Grayling 340 Watana Creek 1 1
6/25/13 Arctic Grayling 160 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 225 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 155 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 185 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 180 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 170 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 215 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 215 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 235 Kosina Creek TRM 2.2 1
6/25/13 Arctic Grayling 75 Kosina Creek TRM 2.2 1
6/26/13 Arctic Grayling 180 Kosina Creek TRM 2.3 1
8/4/13 Arctic Grayling 310 Kosina Creek TRM 2.2 1
8/4/13 Arctic Grayling 300 Kosina Creek TRM 2.2 1
8/4/13 Arctic Grayling 330 Kosina Creek TRM 2.2 1
8/5/12 Burbot 410 RM 186.8 1 1
8/5/12 Burbot 410 RM 192.6 1 1
8/9/13 Burbot 443 PRM 193.1 1 1
8/16/13 Burbot 467 PRM 224.3 1 1
8/17/13 Burbot 390 PRM 217.1 1 1
10/4/13 Burbot 451 PRM 214.7 1 1
10/4/13 Burbot 417 PRM 214.7 1 1
9/18/13 Dolly Varden 177 Watana Creek Site 04 1
9/18/13 Dolly Varden 187 Watana Creek Site 04 1
9/18/13 Dolly Varden 204 Watana Creek Site 04 1
10/3/13 Dolly Varden 195 Watana Creek Site 14 1
10/3/13 Dolly Varden 194 Watana Creek Site 14 1
10/3/13 Dolly Varden 186 Watana Creek Site 14 1
10/3/13 Dolly Varden 196 Watana Creek Site 14 1
8/3/12 Lake Trout 510 Sally Lake 1 1
8/3/12 Lake Trout 430 Sally Lake 1 1
9/20/13 Lake Trout 625 Deadman Lake 1
9/20/13 Lake Trout 450 Deadman Lake 1
9/20/13 Lake Trout 460 Deadman Lake 1
9/20/13 Lake Trout 590 Deadman Lake 1
9/20/13 Lake Trout 455 Deadman Lake 1
9/20/13 Lake Trout 355 Deadman Lake 1
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Date Target Species Size (mm) Location Baseline Metal Tissue Samples Mercury Tissue Samples
9/20/13 Lake Trout 380 Deadman Lake 1
8/9/13 Longnose Sucker 320 PRM 195.5 1
8/9/13 Longnose Sucker 320 PRM 193.1 1
8/13/13 Longnose Sucker 350 Oshetna River 1
8/13/13 Longnose Sucker 430 Oshetna River 1
8/13/13 Longnose Sucker 340 Oshetna River 1
8/13/13 Longnose Sucker 315 Oshetna River 1
8/13/13 Longnose Sucker 350 Oshetna River 1
9/12/13 Longnose Sucker 330 PRM 217.1 1
9/12/13 Slimy Sculpin 85 PRM 219.5 1
9/12/13 Slimy Sculpin 86 PRM 219.5 1
9/12/13 Slimy Sculpin 87 PRM 219.5 1
9/16/13 Slimy Sculpin 100 PRM 202.7 1
9/16/13 Slimy Sculpin 87 PRM 202.7 1
9/16/13 Slimy Sculpin 92 PRM 202.7 1
9/18/13 Slimy Sculpin 74 PRM 195.5 1
8/13/13 Whitefish, Humpback 340 Oshetna River 1
8/16/13 Whitefish, Round 130 Oshetna River 1
8/16/13 Whitefish, Round 450 PRM 219.5 1
8/18/13 Whitefish, Round 372 PRM 212.3 1
8/18/13 Whitefish, Round 317 PRM 209.9 1
8/29/13 Whitefish, Round 309 PRM 190.7 1
8/30/13 Whitefish, Round 278 Watana Creek Site 13 1
9/10/13 Whitefish, Round 140 PRM 233.9 1
9/10/13 Whitefish, Round 175 PRM 233.9 1
9/10/13 Whitefish, Round 342 PRM 233.9 1
8/13/13 Whitefish, Undifferentiated 190 Oshetna River 1
8/14/13 Whitefish, Undifferentiated 365 Kosina Creek 1
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Table 4.11-1. Summary of tissue collection for genetic baseline development, 2013.
Location Chinook salmon Arctic Grayling Burbot Dolly Varden Longnose sucker Salmonid, undifferentiated Sculpin Whitefish, humpback Whitefish, round Grand Total Black River 55 15 1 24 2 97
Oshetna River 3 4 8 2 1 15 1 8 42
Goose Creek 3 6 9
Upper Extent Watana Reservoir PRM 232.5
Susitna River-UR-3 7 3 10 20
Jay Creek 5 41 46
Kosina Creek 63 53 2 6 4 1 3 132
Susitna River UR-4 34 13 3 17 67
Susitna River UR-5 4 10 14
Watana Creek Tributary 44 2 46
Watana Creek 118 1 5 124
Unnamed Tributary 194.8 26 26
Susitna River UR-6 9 56 5 24 94
UR Study Area Total 121 57 84 229 85 1 51 2 87 717
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Table 5.1-1. Fish Distribution in the Upper Susitna River 2012 & 2013 and select historical records.
Location Poject River MileDrainage Basin Size (km2)Chinook salmon (juvenile)Arctic graylingBurbotDolly VardenLake troutLongnose suckerSculpinWhitefish, humpbackWhitefish, roundWhitefish, unspecifiedSusita River Devils Canyon to Watana Dam 2013 166.1-187.1 X X X X X X X X
Proposed Watana Dam Location 187.1 ---------------------------------
Susitna River UR-6 187.1-203.4 X X X X X X
Susitna River UR-5 203.4-208.1 X X X X X
Susitna River UR-4 208.1-224.9 X X X X X
Susitna River UR-3 224.9-234.5 X X X X X
Watana Reservoir at Full Pool 232.5 ---------------------------------
Susitna River above Oshetna >234.5 X
Aerial Mainstem - Dam site to Oshetna N/A X X
Deadman Creek 189.4 453.5 X, X
Unnamed Tributary 194.8 194.8 321.2 X X X
Watana Creek 196.9 452.7 X, O X, O X, X, O X, O
Watana Creek Tributary: Unnamed L1 N/A X X
Watana Creek Tributary: Unnamed L3 N/A X
Watana Creek Tributary: Unnamed R3 N/A X X
Watana Creek Tributary: Unnamed R5 N/A X X X X
Unnamed Tributary 197.7 197.7 <80.3 X X
Unnamed Tributary 198.4 198.4 X
Unnamed Tributary 203.4 203.4 X X
Unnamed Tributary 206.3 206.3 <80.3 X
Kosina Creek 209.1 1036.5 X, O X X, X, O X, X, O X, O X X
Kosina Creek Tributary: Tsisi Creek N/A X X X X
Kosina Creek Tributary: Gilbert Creek N/A X X, O
Kosina Creek Tributary: Unnamed N/A X
Jay Creek 211 106.1 X, O X, X, X
Goose Creek 232.8 269.1 X, O X X, O X
Oshetna River 235.1 1424.5 X, O X, O X X X X X X
Oshetna River Tributary: Black River N/A X X X, O X, O X, O X, O
Tyone River 247.3 X
Clearwater Creek 266.6 X
Deadman Basin Lake: Deadman Lake N/A X,
Deadman Basin Lake: Unnamed Lake N/A X
Watana Basin Lake: Sally Lake 196.9 X, X, X,
Kosina Basin Lake: Tsisi Lake N/A X
X: Fish Distribution and Abudance 2012-2013
: ADF&G 1981, 1983a, 1984
O: Buckwalter 2011
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Table 5.1-2. Upper Susitna fish observations, 2013. Includes all data sources: Early-Life History sampling (ELH), GRTS tributary sampling (GRTS), Direct
tributary sampling(Direct), mainstem transect sampling (Transect), rotary screw trap (RST), opportunistic sampling (Opportunistic), targeted
sampling for radio tagging (RT), and targeted sampling for genetics (Genetics), and targeted sampling for metals/mercury samples (Metals).
Observation data are provisional and subject to revision based on ongoing QA/QC
Geomorphic
Reach Habitat
Project
River Mile Sample Type Salmon, Chinook (adult)Salmon, Chinook (juvenile) Arctic graylingBurbotDolly VardenLongnose suckerSculpinTrout, lakeWhitefish, humpbackWhitefish, roundWhitefish, undifferentiatedTotalNA Clearwater Creek 266.6 RT 4 4
Tyone River 247.3 RT 6 6
Oshetna River 235.1 ELH, GRTS, RST, Genetics, Opportinstic, RT 4 952 22 191 2,031 11 86 45 3,342
Oshetna River: Off-Channel GRTS 7 84 91
Black River ELH, GRTS, Opportinstic 78 115 13 1 997 3 1,207
Black River: Off-Channel GRTS 2 19 1 121 143
Susitna River 224.9-234.5 Transect 57 12 4 44 2 17 136
Goose Creek 232.8 GRTS, RT 1,513 7 281 43 1,844
232.5
Susitna River 208.1-224.9 Transect, RT 70 48 13 127 19 277
Jay Creek 211 Direct, RT 44 3 137 37 221
Kosina Creek 209.1 ELH, GRTS, RST, Genetics, Opportinstic, RT 2 197 509 2 5 12 486 4 19 9 1,245
Tsisi Creek ELH, GRTS 310 487 4 1 802
Tsisi Creek: Off-Channel GRTS 23 32 55
UR-5 Susitna River 203.4-208.1 Transect, RT 22 8 4 25 22 81
Susitna River 187.1-203.4 Transect, RT 168 17 80 188 1 37 491
Susitna River: Off-Channel Transect 3 16 75 1 95
Watana Creek 196.9 GRTS, Opportunistic, RT 292 3 494 1 563 22 1,375
Watana Creek: Off-Channel GRTS 13 15 28
Watana Creek Unnamed Tributary GRTS 736 56 169 1 7 969
Watana Creek Unnamed Tributary: Off-Channel GRTS 2 24 26
Unnamed Tribuatry 194.8 GRTS 16 71 1 158 246
Deadman Creek & Lake 189.4 RT, Metals 9 7 16
187.1
2 281 4,869 129 778 336 5,944 8 18 280 55 12,700Upper River Total
Proposed Watana Dam Location
Watana Reservoir at Full Pool
UR-2
UR-3
UR-6
UR-4
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Table 5.1-3. Fish distribution and abundance (transect, GRTS, and direct sample) sampling total observations for
each gear type by species and life stage, 2013.
Note: Observation data are provisional and subject to revision based on ongoing QA/QC
Backpack Electrofish Snorkel Minnow Trap Angle Boat Electrofish Fyke Net Seine
Fry 1 6 2 9
Parr 8 6 14
Juvenile 84 12 18 3 117
Total 93 18 26 3 140
Adult 115 562 107 63 2 849
Juvenile 366 467 28 12 2 15 18 908
Juvenile or Adult 368 760 7 77 15 29 6 1,262
Unknown 3 2 3 8
Total 852 1,789 37 196 80 47 26 3,027
Adult 13 2 14 1 30
Juvenile 16 1 1 18
Juvenile or Adult 22 1 1 24
Total 51 4 16 1 72
Adult 69 23 5 5 102
Juvenile 84 150 22 256
Juvenile or Adult 111 189 32 1 5 338
Unknown 4 3 7
Total 268 362 62 6 5 703
Lake Trout Juvenile 1 1
Adult 14 4 5 18 41
Juvenile 5 8 12 25
Juvenile or Adult 17 1 7 1 14 40
Unknown 1 1
Total 36 5 15 6 45 107
Salmonid,
species unknown Juvenile 1 1
Adult 290 4 76 3 6 1 380
Juvenile 108 2 2 1 1 114
Juvenile or Adult 1,913 5 334 27 5 2,284
Unknown 31 2 23 56
Total 2,342 13 435 4 33 7 2,834
Species unknown Unknown 0 0 2 2 4 0 0 8
Adult 12 38 21 2 3 76
Juvenile 10 1 1 9 21
Juvenile or Adult 8 18 4 30
Unknown 1 1
Total 31 54 25 3 12 128
Whitefish, species
unknown Adult 1 1
Grand Total 3,675 2,245 581 204 135 91 91 7,022
Whitefish, round
Life stageSpecies Gear Type
Grand Total
Dolly Varden
Burbot
Arctic Grayling
Longnose Sucker
Chinook Salmon
Sculpin
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Table 5.2-1. Upper Susitna River rotary screw trap catch by species and life stage, 2013.
Note: Catch data are provisional and subject to revision based on ongoing QA/QC
Kosina Creek Oshetna River
UR-4 UR-2
Species Life stage
Parr 1 1
Smolt 9 1 10
Adult 1 1
Juvenile 91 233 324
Juvenile/Adult 22 335 357
Adult 4 38 42
Juvenile 3 3
Juvenile/Adult 1 1
Dolly Varden Juvenile/Adult 2 2
Juvenile 97 97
Juvenile/Adult 1 42 43
Adult 46 46
Juvenile 5 11 16
Juvenile/Adult 21 21
Adult 3 38 41
Juvenile 5 5
Juvenile/Adult 2 5 7
Juvenile 1 12 13
Juvenile/Adult 7 33 40
Juvenile 34 34
Juvenile/Adult 4 39 43
Adult 7 7
153 1,001 1,154
Whitefish, undifferentiated
Whitefish, round
Grand Total
Grand
Total
Geomorphic reach
Project River Mile 209.1 235.1
Arctic grayling
Burbot
Longnose sucker
Sculpin
Whitefish, humpback
Chinook salmon
Rotary screw trap location
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Table 5.2-2. Movement and survival of Arctic grayling during 2 week periods, by tagging group, Upper Susitna River,
2013.
Arctic Grayling
Zone Name Rls *1 Aug15 Aug30 AugRls *1 Aug15 Aug30 AugRls *1 Aug15 Aug30 AugRls *1 Aug15 Aug30 AugRls *1 Aug15 Aug30 AugRls *1 Aug15 Aug30 AugRls *30 AugIndian River
Indian River trib
MOB - Indian trib 1 1 1
MOB - Indian - Slough 21
MOB - Slough 21
Powerline
MOB - above Powerline
MOB - abv Powerline - Portage
MOB - Jack Long Creek
MOB - Portage trib
MOB - Portage - Impediment1
MOB - Impediment1 - Cheechako
MOB - Cheechako Creek
MOB - Cheechako - Impediment2
MOB - Impediment2 - Chinook 1
MOB - Chinook Creek
MOB - Chinook - Impediment3
MOB - Devils Creek
Devils Island 1 1
MOB - Impediment3 - Devil Stn
MOB - Devil Stn - Fog
MOB - Fog Creek
MOB - Fog - Dam Site 1 1 1
MOB - Tsusena Creek 2 2
MOB - Dam Site - Deadman 4 3 1
Deadman Creek
MOB - Deadman Creek 2
MOB - Deadman - Watana 7 1 2 1
MOB - 'Creek 192'
MOB - Watana Creek 3 1 1 1 1
MOB - Wantana - Kosina 1 1 1 1 1
Kosina Creek 5 4 3 1 1 1
MOB - Kosina Creek 8
MOB - Kosina - Oshetna 2 3 2 1
Oshetna River
MOB - Oshetna River 8 7 7 7
MOB - above Oshetna 2 2 2 2
Total Tags Live 7 6 6 4 3 3 3 2 8 7 7 6 3 3 3 1 8 8 8 8 2 2 2 2 1 1
Mort tags **0 1 1 3 0 0 0 1 0 1 1 2 0 0 0 2 0 0 0 0 0 0 0 0 0 0
* unique time and location
** mortality tags not shown in table
Rls
8/15 -
8/30
Rls 7/15 -
7/31
Rls 7/15 -
7/31
Rls 7/15 -
7/31
Rls 7/15 -
7/31
Rls 7/15 -
7/31
Rls 7/15 -
7/31
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Table 5.2-3. Movement and survival of longnose sucker during 2 week periods, by tagging group, Upper Susitna
River, 2013.
Longnose Sucker Released 7/15 - 7/31
Zone Name eased * 1 Aug 15 Aug 30 Aug MOB - Deshka - Kashwitna 1 1
MOB - Caswell area tribs
Montana
MOB - Kashwitna - Montana
MOB - Montana Creek
MOB - Montana - Sunshine
MOB - Sunshine Creek
MOB - Rabideux Creek
ADFG Sunshine
ADFG Talkeetna
MOB - Talkeetna River
ADFG Chulitna
MOB - Chulitna River
ADFG - Middle Chulitna
MOB - Sunshine - Talkeetna
Whiskers
MOB - Talkeetna - Lane
MOB - Whiskers Creek
MOB - Trib off zone 95
Lane Creek
MOB - Lane - Gateway
MOB - Lane Creek
MOB - 5th of July Creek
MOB - Slough 8A
Gateway
MOB - Gateway - 4th of July
MOB - Slough 9
MOB - Sherman Creek
Fourth of July
MOB - 4th of July Creek
MOB - 4th of July - Slough 11
MOB - Slough 11
MOB - Gold Creek
MOB - Slough11 - Indian
Indian River
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Longnose Sucker Released 7/15 - 7/31
Zone Name eased * 1 Aug 15 Aug 30 Aug Indian River trib
MOB - Indian trib
MOB - Indian - Slough 21
MOB - Slough 21
Powerline 1
MOB - above Powerline
MOB - abv Powerline - Portage 1 1
MOB - Jack Long Creek
MOB - Portage trib
MOB - Portage - Impediment1 1
MOB - Impediment1 - Cheechako
MOB - Cheechako Creek
MOB - Cheechako - Impediment2
MOB - Impediment2 - Chinook
MOB - Chinook Creek
MOB - Chinook - Impediment3
MOB - Devils Creek
Devils Island 1
MOB - Impediment3 - Devil Stn
MOB - Devil Stn - Fog
MOB - Fog Creek
MOB - Fog - Dam Site
MOB - Tsusena Creek
MOB - Dam Site - Deadman
Deadman Creek
MOB - Deadman Creek
MOB - Deadman - Watana
MOB - 'Creek 192'
MOB - Watana Creek
MOB - Wantana - Kosina
Kosina Creek
MOB - Kosina Creek
MOB - Kosina - Oshetna
Oshetna River
MOB - Oshetna River
MOB - above Oshetna 5 2 1 1
2
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Longnose Sucker Released 7/15 - 7/31
Zone Name eased * 1 Aug 15 Aug 30 Aug Total Tags Live 5 5 3 3
Mort tags * 0 0 2 2
* unique time and location
** mortality tags not shown in table
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Table 5.2-4. Number of fish in the Upper Susitna River implanted with PIT tags, detected by stationary antennas, and
recaptured during subsequent sampling events, by species, 2013.
Species
Tagged
Subsequently Observed
Detected at Antenna Recaptured Total
N N % N % N %
Chinook salmon 22 0 0% 0 0% 0 0%
Arctic grayling 913 29 3% 6 1% 35 4%
Burbot 31 1 3% 0 0% 1 3%
Dolly Varden 109 0 0% 2 2% 2 2%
Lake Trout 1 0 0% 0 0% 0 0%
Longnose sucker 20 0 0% 1 5% 1 5%
Whitefish, humpback a 9 0 0% 0 0% 0 0%
Whitefish, round 98 3 3% 0 0% 3 3%
Whitefish,
undifferentiated 21 0 0% 0 0% 0 0%
Total 1,224 33 3% 9 1% 42 3%
Notes: aOne humpback whitefish (PIT tag 000183327483) from the Upper River, tagged and released in the Oshetna River,
was subsequently recaptured in the Middle River at the Curry Station downstream migrant trap and then detected at
the Whiskers Slough PIT antenna.
Values exclude a small number of PIT tags with missing implant records, multiple implant records, or inconsistent
species identification upon recapture. Longnose sucker are not a target species
Data are provisional and subject to revision based on ongoing QA/QC
Table 5.2-5. Number of individual fish detected and total number of detectionsa by species at Upper River PIT
antenna stations at Kosina Creek and the Oshetna River in 2013.
Kosina Creek Antenna Oshetna River Antenna Total
Species Fish Detections Fish Detections Fish Detections
Arctic grayling 9 77 21 19,195 29b 19,272
Burbot 1 10 1 10
Round whitefish 1 94 2 9,671 3 9,765
Total 10 171 24 28,876 33 29,047
Note: a“Detections” reflects the number of unique records for a given fish encounter with an antenna; each “detection” is
typically comprised of many consecutive readings of the PIT tag by the antenna reader.
bIncludes one Arctic grayling (PIT tag 000183327467) that was detected at both antenna stations.
Values exclude a small number of PIT tags with missing implant records, multiple implant records, or inconsistent
species identification upon recapture.
Data are provisional and subject to revision based on ongoing QA/QC
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Table 5.2-6. Arctic grayling movement between macrohabitat types in the Upper River in 2013 based on a
comparison of initial tagging events versus subsequent recapture or detection at PIT antennas. Values indicate
the number of individual fisha
Detection/Recapture Macrohabitat
Single Tributary Channelb Split Tributary Channelc Complex Tributary
Channeld Tagging Macrohabitat Single Tributary Channelb 4 10 8
Split Tributary Channel 10 Complex Tributary
Channel 1
Split Main Channel 1
Not reported 2 Notes:
a Values include one fish that was detected in two different macrohabitat types.
b Includes Oshetna River and Kosina Creek rotary screw traps c Includes Oshetna River PIT antenna d Includes Kosina Creek PIT antenna
Data are provisional and subject to revision based on ongoing QA/QC
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Table 5.3-1. Early life history sampling catch by location and gear type, 2013.
Tributary Black River Kosina Creek Oshetna River Tsisi Lake Outlet Tsisi Creek
Grand Total Gear type
Backpack e-fish Fyke net Backpack e-fish Backpack e-fish Fyke net Backpack e-fish Species Life stage
Chinook salmon Fry 6 6
Total 6 6
Arctic grayling
Adult 4 80 3 10 4 1 102
JOA 1 22 22 14 3 62
JUV 5 8 9 9 31
Total 10 110 34 33 4 4 195
Burbot
Adult 1 1 2
JOA 2 2
JUV 1 1 1 3
Total 3 2 2 7
Dolly Varden
Adult 2 2
JOA 1 1
Total 3 3
Longnose sucker
Adult 2 2 4
JUV 1 5 6
Total 1 7 2 10
Sculpin JOA 81 54 89 1 225
Whitefish, humpback Adult 1 1 2
Whitefish, round
Adult 7 1 1 9
JUV 1 1
Total 7 1 2 10
Grand Total 100 121 99 129 4 5 458
Data are provisional and subject to revision based on ongoing QA/QC
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Table 5.4-1. Number PIT-tagged recaptured PIT-tagged juvenile Chinook salmon and Arctic grayling available for
growth analysis for the Upper Susitna River, 2013.
River Location Species Name Implanted (N) Detected (N) Recaptured (N) Recaptured or Detected (N)
UR Chinook salmon 22 0 0 0
UR Arctic grayling 913 29 6 35
Total 935 29 6 35
Data are provisional and subject to revision based on ongoing QA/QC
Table 5.4-3. Condition factor of juvenile Chinook salmon by tributary, Upper Susitna River, 2013.
Location PRM Sample Size Mean Condition Factor Mean Standard Error Median Condition factor (N)
Oshetna River 235 1 0.79 n/a 0.79
Black River N/A 22 0.86 0.045 0.84
Kosina Creek 209 67 1.04 0.023 1.08
Data are provisional and subject to revision based on ongoing QA/QC
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Table 5.4-4. Condition factor of Arctic grayling by macrohabitat type and tributary, Upper Susitna River, 2013.
Macrohabitat Tributary/
Geomorphic Reach
Sample
Size Mean Condition
Factor
Mean Standard Error Median
(N)
Main Channel
UR-3 27 0.9 0.018 0.9
UR-4 11 0.81 0.031 0.85
UR-5 15 0.88 0.015 0.9
UR-6 66 0.94 0.015 0.92
Split Main Channel UR 30 0.85 0.026 0.85
Side Channel UR 10 0.96 0.061 0.9
Clear Water Plume UR 15 0.88 0.036 0.85
Side Slough UR 8 0.92 0.09 0.87
Side Slough,
Beaver UR n/a n/a n/a n/a
Upland Slough UR 15 0.92 0.04 0.97
Tributary
Black River 59 0.90 0.024 0.91
Goose Creek 316 0.94 0.012 0.93
Jay Creek 11 0.85 0.025 0.87
Kosina Creek 40 0.77 0.021 0.78
Oshetna River 128 0.89 0.02 0.89
Tsisi Creek 34 0.89 0.027 0.91
Unnamed 194.8 8 0.88 0.037 0.89
Watana Creek 264 0.83 0.013 0.86
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9. FIGURES
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Figure 3-1. Upper Susitna River fish distribution and abundance study area.
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Figure 4.1-1. Salmon Early Life History sampling sites in the Upper Susitna River basin, 2013.
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Figure 4.1-2. Locations of 13 tributaries upstream of the proposed Watana Dam location selected for sampling up to the 3,000 ft contour, 2013.
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Figure 4.1-3. GRTS fish distribution and abundance sampling targets and field sampling locations (including oversamples) in Unnamed Tributary
194.8, Watana Creek, Watana Creek Tributary, and Unnamed Tributary 197.7, 2013.
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Figure 4.1-4. GRTS fish distribution and abundance sampling targets and field sampling locations (including oversamples) in Unnamed Tributary
204.3, Unnamed Tributary 206.3, Kosina Creek, and Tsisi Creek, 2013.
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Figure 4.1-5. GRTS fish distribution and abundance sampling targets and field sampling locations (including oversamples) in Goose Creek, the
Oshetna River, and the Black River, 2013.
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Figure 4.1-6. Fish distribution and abundance transect sampling locations in the Upper Susitna River, 2013.
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Figure 4.1-7. Outmigrant (rotary screw) trap, PIT tag array, and radio fixed receiver locations in the Upper Susitna River Study Area, 2013.
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Figure 4.2-1. Summary of PIT tag interrogation system operation in the Upper Susitna River, 2013. Black indicates continuous operation; gray
indicates partial or interrupted operation.
15-Jun 15-Jul 14-Aug 13-Sep 13-Oct
2013 Upper Susitna River PIT Antenna Operations
Oshetna River
Kosina Creek
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Figure 4.2-2. Screw trap operation in the Upper Susitna River, 2013.
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Figure 4.5-1. Summary of PIT tagging effort in the vicinity of the Oshetna River, 2013.
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Figure 4.5-2. Summary of PIT tagging effort in the vicinity of Kosina Creek, 2013.
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Figure 4.5-3. Illustration of swim over Oshetna River PIT tag interrogation antenna orientation
positioning at high (top) and low flow (bottom), 2013.
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Figure 4.5-4. Swim through PIT tag interrogation antenna on Kosina Creek side channel at RM 0.2, 2013.
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Figure 4.7-1. Condition factor by size (fork length mm) for juvenile Chinook salmon (top) and Arctic
Grayling (bottom) for Lower, Middle, and Upper Susitna River, 2013.
0
0.5
1
1.5
2
2.5
0 20 40 60 80 100 120 140 160 180 200Condition FactorLength (mm)
Chinook Salmon
0
0.5
1
1.5
2
2.5
3
0 50 100 150 200 250 300 350 400 450 500Condition FactorLength (mm)
Arctic Grayling
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Figure 5.2-1. Kosina Creek rotary screw trap catch by species and life stage, 2013. Adt=adult, Juv=juvenile, JoA= Juvenile/Adult,
Smt=smolt, Unk=unknown
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Figure 5.2-2. Oshetna River rotary screw trap catch by species and life stage, 2013. Adt=adult, Juv=juvenile, JoA= Juvenile/Adult,
Smt=smolt, Unk=unknown
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Figure 5.4-1. Box-and-whisker plot of juvenile Chinook salmon condition factor in Upper River
tributaries, 2013.
Figure 5.4-2. Box-and-whisker plot of Arctic Grayling condition factor in Upper River Tributaries (Trib)
various mainstem Susitna River macrohabitats. MC=main channel, SMC=split main channel, SC=side
channel, SS=side slough, US=upland slough, CWP= clear water plume (special mesohabitat type).
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APPENDIX A: DISTRIBUTION OF FISH RADIO-TAGGED IN THE UPPER
SUSITNA RIVER, 2013
[See separate file for Appendix.]
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APPENDIX B: FISH DISTRIBUTION MAPS FOR THE UPPER SUSITNA
RIVER 2012 AND 2013
[See separate file for Appendix.]
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APPENDIX C: SEASONAL FISH DISTRIBUTION, UPPER SUSITNA
RIVER 2012 AND 2013
[See separate file for Appendix.]
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APPENDIX D: UPPER RIVER FISH OBSERVATIONS AND RELATIVE
ABUNDANCE, 2013
[See separate file for Appendix.]