U.S. Department of Commerce | National Oceanic and Atmospheric Administration | National Marine Fisheries Service

WEST 

COAST

REGION

WEST COAST 

REGION

ESA Recovery Plan for Snake River 

Sockeye Salmon

(Oncorhynchus nerka)

June 8, 2015
ESA Recovery Plan: Snake River Sockeye Salmon | 2

June 2015 NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 3

June 2015| NOAA Fisheries 

DISCLAIMER

Endangered Species Act (ESA) recovery plans delineate reasonable actions that the best available 

information indicates are necessary for the conservation and survival of listed species. Plans are 

published by the National Marine Fisheries Service (NMFS), usually with the assistance of recovery 

teams, state agencies, local governments, salmon recovery boards, non-governmental organizations, 

interested citizens of the affected area, contractors, and others. ESA recovery plans do not necessarily 

represent the views, official positions, or approval of any individuals or agencies involved in the plan 

formulation, other than NMFS. They represent the official position of NMFS only after they have been 

signed by the West Coast Regional Administrator. ESA recovery plans are guidance and planning 

documents only; identification of an action to be implemented by any public or private party does not 

create a legal obligation beyond existing legal requirements. Nothing in this plan should be construed as 

a commitment or requirement that any Federal agency obligate or pay funds in any one fiscal year in 

excess of appropriations made by Congress for that fiscal year in contravention of the Anti-Deficiency 

Act, 31 U.S.C. 1341, or any other law or regulation. Approved recovery plans are subject to 

modification as dictated by new information, changes in species status, and the completion of recovery 

actions.

ESA recovery plans provide important context for NMFS determinations pursuant to section 7(a)(2) of 

the Endangered Species Act. However, recovery plans do not place any additional legal burden on 

NMFS or the action agency when determining whether an action would jeopardize the continued 

existence of a listed species or adversely modify critical habitat. The procedures for the section 7 

consultation process are described in 50 CFR 402 and are applicable regardless of whether or not the 

actions are described in a recovery plan.

Additional copies of this plan can be obtained from:

NOAA NMFS

West Coast Region

1201 NE Lloyd Blvd.

Suite 1100

Portland, OR 97232

503-230-5400

Cover Photo: 2008 Adult release into Redfish Lake. Photo: Mike Peterson, IDFG
ESA Recovery Plan: Snake River Sockeye Salmon | 4

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 5

June 2015| NOAA Fisheries 

Acknowledgements

The Snake River Sockeye Salmon ESA Recovery Plan represents the dedicated effort of numerous 

individuals over many years. The National Marine Fisheries Service would like to thank the individuals, 

agency and tribal representatives listed below (alphabetically) for their contributions to this plan. 

Special thanks go to the Snake River Sockeye Salmon Technical Committee members for their input, 

support and guidance throughout this recovery planning process.

Recovery Plan Contributors and Reviewers

David Arthaud - National Marine Fisheries Service, West Coast Region

Gordon Axel - Northwest Fisheries Science Center

Laurie Beale - NOAA Office of the General Counsel

John Chatel - U.S. Forest Service, Pacific Northwest Region

Thomas Cooney - NMFS Northwest Fisheries Science Center

Peter Dygert - National Marine Fisheries Service, West Coast Region

Tom Flagg - Northwest Fisheries Science Center

Kurt Fresh - Northwest Fisheries Science Center

Rosemary Furfey - National Marine Fisheries Service, West Coast Region

Ritchie Graves - National Marine Fisheries Service, West Coast Region

Robert Griswold - Contractor for Shoshone Bannock Tribes

Tracy Hillman - BioAnalysts, Inc.

Lyndal Johnson - Northwest Fisheries Science Center

Paul Kline – Idaho Department of Fish and Game

Chris Kozfkay - Idaho Department of Fish and Game

David Mabe - National Marine Fisheries Service, West Coast Region

Des Maynard – Northwest Fisheries Science Center

Jonathan McCloud – Bonneville Power Administration

Brenda Mitchell – U.S. Forest Service, Sawtooth National Forest

Enrique Patino – National Marine Fisheries Service, West Coast Region

Mike Peterson – Idaho Department of Fish and Game

Larissa Plants - National Marine Fisheries Service, Office of Protected Resources

Scott Rumsey - National Marine Fisheries Service, West Coast Region

Gina Schroeder - National Marine Fisheries Service, West Coast Region

Doug Taki – Shoshone Bannock Tribes

Barbara Taylor – BioAnalysts, Inc. and NMFS contractor

Michael Tehan - National Marine Fisheries Service, West Coast Region

Chris Toole - National Marine Fisheries Service, West Coast Region

Snake River Sockeye Salmon Technical Committee

Brenda Mitchell - U.S. Forest Service, Sawtooth National Forest

Thomas Cooney - NMFS Northwest Fisheries Science Center

Tom Flagg - Northwest Fisheries Science Center
ESA Recovery Plan: Snake River Sockeye Salmon | 6

June 2015| NOAA Fisheries 

Rosemary Furfey - National Marine Fisheries Service, West Coast Region

Ritchie Graves - National Marine Fisheries Service, West Coast Region

Robert Griswold - Contractor for Shoshone Bannock Tribes

Lyndal Johnson - Northwest Fisheries Science Center

Paul Kline – Idaho Department of Fish and Game

Chris Kozfkay - Idaho Department of Fish and Game

David Mabe - National Marine Fisheries Service, West Coast Region

Des Maynard – Northwest Fisheries Science Center

Jonathan McCloud – Bonneville Power Administration

Rick Mogren – Federal Caucus Coordinator

Scott Rumsey - National Marine Fisheries Service, West Coast Region

Doug Taki – Shoshone Bannock Tribes

Interior Columbia Technical Recovery Team

Rich Carmichael – Oregon Department of Fish and Wildlife

Thomas Cooney – National Marine Fisheries Service, Co-Chair

Peter Hassemer – Idaho Department of Fish and Game

Phillip Howell – U.S. Forest Service

Michelle McClure – NMFS, Northwest Fisheries Science Center, Co-Chair

Dale McCullough – Columbia River Inter-Tribal Fish Commission

Charles Petrosky – Idaho Department of Fish and Game

Howard Schaller – US Fish and Wildlife Service

Paul Spruell – Department of Biology, Southern Utah University

Fred Utter – School of Aquatic and Fisheries Science, University of Washington

Casey Baldwin – Washington Department of Fish and Wildlife

Authors of the Snake River Modules:

NMFS Columbia River Estuary ESA Recovery Plan Module for Salmon and Steelhead

NMFS Snake River Hydro Module

NMFS Snake River Harvest Module

NMFS Snake River Ocean Module
ESA Recovery Plan: Snake River Sockeye Salmon | 7

June 2015| NOAA Fisheries 

Contents

Acknowledgements ................................................................................................................................... 5

Contents..................................................................................................................................................... 7

List of Tables........................................................................................................................................... 13

List of Figures.......................................................................................................................................... 15

Abbreviations and Acronyms ................................................................................................................ 17

Terms and Definitions............................................................................................................................ 19

Snake River Sockeye Salmon Recovery............................................................................................................ 27

Plan Executive Summary............................................................................................................................... 27

Introduction............................................................................................................................................... 27

About This Recovery Plan........................................................................................................................ 30

Scientific Foundation................................................................................................................................ 32

Recovery Goals and Criteria..................................................................................................................... 33

Current Status of the ESU......................................................................................................................... 37

Historical Snake River Sockeye Salmon Life Cycle ................................................................................ 39

Limiting Factors and Threats Analysis..................................................................................................... 40

Recovery Strategies and Actions.............................................................................................................. 43

Redfish Lake Sockeye Salmon Population............................................................................................... 47

Pettit Lake Sockeye Salmon Population................................................................................................... 49

Alturas Lake Sockeye Salmon Population................................................................................................ 51

Stanley Lake and Yellowbelly Lake Sockeye Salmon Populations......................................................... 53

Adaptive Management, Research, Monitoring, and Evaluation............................................................... 54

Implementation ......................................................................................................................................... 56

Time and Cost Estimates .......................................................................................................................... 57

Section 1: Introduction........................................................................................................................... 59

1. Introduction......................................................................................................................................... 61

1.1 Purpose of the Plan ............................................................................................................................. 65

1.2 Endangered Species Act Requirements.............................................................................................. 65

1.3 Context of Plan Development............................................................................................................. 66

1.3.1 Recovery Domains and Technical Teams................................................................................ 67

1.3.2 Snake River Sockeye Salmon Stakeholder Groups................................................................. 68

1.4 Tribal Trust and Treaty Responsibilities............................................................................................. 69

1.5 Recovery Planning Modules............................................................................................................... 70

1.6 How NMFS Intends to Use the Plan................................................................................................... 71

Section 2: Biological Background.......................................................................................................... 73

2. Biological Background ....................................................................................................................... 75

2.1 Geographic Setting.............................................................................................................................. 75
ESA Recovery Plan: Snake River Sockeye Salmon | 8

June 2015| NOAA Fisheries 

2.2 Sockeye Salmon Overview................................................................................................................. 80

2.3 Snake River Sockeye Salmon ............................................................................................................. 81

2.3.1 Recent History ......................................................................................................................... 84

2.3.2 Life History.............................................................................................................................. 86

2.3.3 Genetic Analyses ..................................................................................................................... 90

2.3.4 Lake Hydrology, Limnology, and Carrying Capacity ............................................................. 91

2.3.5 Other Fish Species ................................................................................................................... 95

2.3.6 Captive Broodstock Program................................................................................................... 97

2.3.7 Watershed Land Use and Demographics................................................................................. 99

2.4 Critical Habitat.................................................................................................................................. 102

2.5 Salmonid Biological Structure.......................................................................................................... 104

2.5.1 Evolutionarily Significant Units (ESUs) and Distinct Population Segments (DPSs)............ 105

2.5.2 Major Population Groups....................................................................................................... 106

2.5.3 Independent Populations........................................................................................................ 106

2.5.4 Snake River Sockeye Salmon ESU Structure........................................................................ 107

2.6 Viable Salmonid Populations............................................................................................................ 107

2.6.1 Abundance and Productivity.................................................................................................. 108

2.6.2 Spatial Structure and Diversity .............................................................................................. 109

Section 3: Recovery Goals and Delisting Criteria.............................................................................. 111

3. Recovery Goals and Delisting Criteria ........................................................................................... 113

3.1 Background on Developing Biological Viability Criteria ................................................................ 114

3.1.1 Viability Criteria for ESUs with One MPG........................................................................... 115

3.1.2 Recovery Scenarios................................................................................................................ 116

3.2 Recovery Goals and Biological Viability Criteria for Snake River Sockeye Salmon...................... 117

3.2.1 Recovery Goals...................................................................................................................... 117

3.2.2 Biological Viability Criteria .................................................................................................. 118

3.3 Listing Factors/Threats Criteria ........................................................................................................ 122

3.4 Delisting Decision............................................................................................................................. 126

Section 4: Current Status Assessment of Snake River Sockeye Salmon ESU................................. 127

4. Current Status Assessment of Snake River Sockeye Salmon ESU............................................... 129

4.1 Abundance and Productivity............................................................................................................. 129

4.1.1 Current Abundance Data........................................................................................................ 130

4.1.2 Productivity............................................................................................................................ 131

4.2 Spatial Structure and Diversity ......................................................................................................... 139

4.3 ESU Status........................................................................................................................................ 139

Section 5: Threats and Limiting Factors............................................................................................ 141

5. Threats and Limiting Factors.......................................................................................................... 143

5.1 Habitat............................................................................................................................................... 145

5.1.1 Sawtooth Valley Lakes.......................................................................................................... 145

5.1.2 Salmon River ......................................................................................................................... 163
ESA Recovery Plan: Snake River Sockeye Salmon | 9

June 2015| NOAA Fisheries 

5.1.3 Lower Mainstem Snake River to Lower Granite Reservoir .................................................. 171

5.1.4 Mainstem Migration Corridor................................................................................................ 173

5.1.5 Estuary and Plume ................................................................................................................. 173

5.1.6 Ocean ..................................................................................................................................... 174

5.2 Hydropower ...................................................................................................................................... 175

5.2.1 Migrating Juveniles................................................................................................................ 175

5.2.2 Migrating Adults.................................................................................................................... 176

5.2.3 Summary of Hydropower Threats and Limiting Factors....................................................... 177

5.3 Hatcheries ......................................................................................................................................... 177

5.3.1 Snake River Sockeye Salmon ................................................................................................ 178

5.3.2 Summary of Hatchery Threats and Limiting Factors ............................................................ 180

5.4 Fisheries............................................................................................................................................ 181

5.4.1 Natal Lake Fisheries .............................................................................................................. 181

5.4.2 Salmon River and Snake River Fisheries............................................................................... 182

5.4.3 Mainstem Columbia River Fisheries ..................................................................................... 182

5.4.5 Ocean Fisheries...................................................................................................................... 184

5.4.6 Summary of Fishery-related Threats and Limiting Factors................................................... 185

5.5 Predation and Disease ....................................................................................................................... 185

5.5.1 Sawtooth Valley Lakes.......................................................................................................... 185

5.5.2 Salmon River ......................................................................................................................... 186

5.5.3 Lower Snake River ................................................................................................................ 186

5.5.4 Lower Columbia River and Estuary ...................................................................................... 186

5.5.5 Ocean ..................................................................................................................................... 189

5.5.6 Summary of Predation and Disease Threats and Limiting Factors........................................ 190

5.6 Competition....................................................................................................................................... 190

5.6.1 Natal Lakes ............................................................................................................................ 190

5.6.2 Salmon River ......................................................................................................................... 191

5.6.3 Mainstem Migration Corridor, Estuary, Plume and Ocean ................................................... 191

5.6.4 Summary of Competition Threats and Limiting Factors....................................................... 192

5.7 Toxics................................................................................................................................................ 192

5.7.1 Sawtooth Valley Lakes.......................................................................................................... 193

5.7.2 Salmon River Migration Corridor.......................................................................................... 196

5.7.3 Lower Snake River and Columbia River Migration Corridor ............................................... 197

5.7.4 Contaminant Exposure, Uptake, and Risk in Snake River Sockeye Salmon......................... 200

5.7.5 Summary of Threats and Limiting Factors Related to Toxics............................................... 202

5.8 Climate Change................................................................................................................................. 202

Section 6: Recovery Strategy ............................................................................................................... 209

6. Recovery Strategy ............................................................................................................................. 211

6.1 Analysis of Causes of Decline .......................................................................................................... 211

6.2 Basic Assumptions............................................................................................................................ 212

6.3 Recovery Strategy............................................................................................................................. 213
ESA Recovery Plan: Snake River Sockeye Salmon | 10

June 2015| NOAA Fisheries 

6.3.1 Strategies to Recover Snake River Sockeye Salmon at the Local Level (Sawtooth Valley and 

Upper Salmon River)...................................................................................................................... 217

6.3.2 Strategies to Recover Snake River Sockeye Salmon at the Regional Level (Migration 

Corridor in the Mainstem Salmon, Snake, and Columbia Rivers; Estuary; Plume; and Ocean).... 235

6.4 Key Information Needs..................................................................................................................... 248

Section 7: Site-Specific Actions............................................................................................................ 255

7. Site-Specific Actions.......................................................................................................................... 257

7.1 Building on Current Efforts.............................................................................................................. 260

7.2 Site-Specific Actions to Recover Snake River Sockeye Salmon at the Local Level (Sawtooth Valley 

and upper Salmon River) ............................................................................................................ 261

7.2.1 Conserve Population Genetic and Life History Diversity, and Spatial Structure.................. 261

7.2.2 Increase Naturally Spawning Snake River Sockeye Salmon Abundance ............................. 263

7.2.3 Improve Sockeye Salmon Passage to Natal Lakes................................................................ 263

7.2.4 Reestablish a Self-sustaining Anadromous Sockeye Salmon Population in Redfish Lake ... 264

7.2.5 Investigate and Develop Strategies and Implement Actions to Support and Enhance Sawtooth 

Valley Sockeye Salmon Reintroduction and Adaptation Phases for Pettit Lake............................ 264

7.2.6 Investigate and Evaluate the Potential for Restoring Natural Production of Anadromous 

Sockeye Salmon from returning Kokanee Outmigrants from Alturas Lake................................... 264

7.2.7 As Sufficient Numbers of Natural-Origin Adults Return, Develop an Integrated Approach to 

Manage Natural and Hatchery-Origin Adults in the Hatchery Program and in the Wild............... 265

7.2.8 As Sufficient Numbers of Hatchery-Origin Anadromous Adults Return to the Basin, Identify 

Options for Future Fisheries ........................................................................................................... 265

7.2.9 Continue Research and Actions to Reestablish Natural Populations in Other Natal Lakes.. 265

7.2.10 Continue Research on Natal Lakes’ Carrying Capacity, Nutrients, and Ecology ............... 266

7.2.11 Protect and Conserve Natural Ecological Processes at the Watershed Scale that Support 

Population Viability: Salmon River Habitat and Natal Lakes Watershed...................................... 266

7.2.12 Protect, Restore, and Manage Spawning and Rearing Habitat ............................................ 267

7.2.13 Maintain Unimpaired Water Quality and Improve Water Quality as Needed..................... 267

7.2.14 Investigate and Improve Conditions in Salmon River and Tributaries to Support Increased 

Survival of Migrating Snake River Sockeye Salmon ..................................................................... 267

7.2.15 Monitor and Control Predation, Disease, Aquatic Invasive Species, and Competition and 

Develop Actions as Needed............................................................................................................ 268

7.2.16 Create an Adaptive Management Feedback Loop to Track Progress and Refine Strategies 

and Actions ..................................................................................................................................... 269

7.3 Actions to Recover Snake River Sockeye Salmon at the Regional Level (Migration Corridor in the 

Mainstem Salmon, Snake, and Columbia Rivers and Estuary, Plume and Ocean).................... 294

7.3.1 Implement the FCRPS BiOp’s Reasonable and Prudent Alternative to Reduce Mortalities 

Associated with Migration Through the Mainstem Salmon, Snake and Columbia Rivers, Estuary 

and Plume........................................................................................................................................ 294

7.3.2 Continue Research and Monitoring on Snake River Sockeye Salmon Survival/Mortality in 

Mainstem Salmon, Snake, and Columbia Rivers Migration Corridor; Estuary; Plume; and Ocean

......................................................................................................................................................... 295
ESA Recovery Plan: Snake River Sockeye Salmon | 11

June 2015| NOAA Fisheries 

7.3.3 Update Snake River Sockeye Salmon Life Cycle Models Using Latest Information on 

Survival Through Mainstem Salmon, Snake and Lower Columbia River Migration Corridor; 

Estuary; Plume; and Ocean............................................................................................................. 296

7.3.4 Manage to Maintain Current Low Impact Fisheries and Reduce Fishery Impacts in Those 

Fisheries that Affect Snake River Sockeye Salmon: Fishery Management ................................... 296

7.3.5 Protect and Conserve Natural Ecological Processes that Support the Population Viability.. 297

7.3.6 Improve Degraded Water Quality and Maintain Unimpaired Water Quality........................ 297

7.3.7 Address Ecosystem Imbalances in Predation, Competition, Invasive Species, and Disease 

through the Strategies and Actions in this Plan, the Estuary Module, and Reasonable and Prudent 

Alternatives identified in Biological Opinions............................................................................... 298

7.3.8 Respond to Climate Change Threats by Implementing Research, Monitoring, and Evaluation 

to Track Indicators Related to Climate Change and by Preserving Biodiversity ........................... 300

7.3.9 Implement the Snake River Sockeye Salmon Recovery Plan through Effective 

Communication, Education, Coordination, and Governance ......................................................... 301

7.3.10 Continue Research, Monitoring, and Evaluation for Adaptive Management...................... 302

7.3.11 Prioritize and Address Key Information Needs, and Create an Adaptive Management 

Feedback Loop to Revise Recovery Actions as Needed ................................................................ 303

Section 8: Potential Effects of Proposed Actions ............................................................................. 3045

8. Potential Effects of Proposed Recovery Actions............................................................................ 307

Section 9: Time and Cost...................................................................................................................... 309

9. Cost and Time Estimates.................................................................................................................. 311

9.1 Cost Estimates................................................................................................................................... 311

9.2 Time Estimate ................................................................................................................................... 313

Section 10: Implementation ................................................................................................................. 315

10. Implementation ............................................................................................................................... 317

10.1 Implementation Framework............................................................................................................ 318

10.2 Implementation Progress and Status Assessments ......................................................................... 321

Section 11: Research, Monitoring, and Evaluation for Adaptive Management ............................. 323

11. Research, Monitoring, and Evaluation for Adaptive Management........................................... 325

11.1 Research, Monitoring, and Evaluation............................................................................................ 327

11.1.1 Types of Monitoring Efforts................................................................................................ 330

11.1.2 Monitoring Framework........................................................................................................ 331

11.1.3 Phase 1 Monitoring.............................................................................................................. 334

11.1.4 Phase 2 Monitoring.............................................................................................................. 348

11.1.5 Phase 3 Monitoring.............................................................................................................. 356

11.2 Adaptive Management.................................................................................................................... 370

11.2.1 Tributary Habitat.................................................................................................................. 371

11.2.2 Hatcheries ............................................................................................................................ 373

11.2.3 Harvest ................................................................................................................................. 375

11.2.4 Mainstem Hydropower System............................................................................................ 377
ESA Recovery Plan: Snake River Sockeye Salmon | 12

June 2015| NOAA Fisheries 

11.2.5 Integration of Adaptive Management Processes.................................................................. 378

12 Literature Cited ............................................................................................................................... 379

Appendix A: Summary of Recovery Measures and Estimated Costs.............................................. 407

Appendix B: Module for Ocean Environment................................................................................... 431

Appendix C: Estuary Module.............................................................................................................. 431

Appendix D: Snake River Harvest Module........................................................................................ 431

Appendix E: Supplemental Recovery Plan Module for Snake River Salmon and Steelhead 

Mainstem Columbia River Hydro System.......................................................................................... 431
ESA Recovery Plan: Snake River Sockeye Salmon | 13

June 2015| NOAA Fisheries 

List of Tables

Table ES-1. Viable salmonid population (VSP) parameters and proposed biological viability criteria for Snake 

River Sockeye Salmon. ......................................................................................................................36

Table ES-2. Hatchery and natural-origin Sockeye Salmon returns to Sawtooth Valley, 1999 – 2014 ..................37

Table 2-1. Physical and morphometric characteristics of the Sawtooth Valley lakes.............................................79

Table 2-2. Characteristics of Sawtooth Valley lakes with comparison to Lake Wenatchee and Lake Oosyoos.....91

Table 2-3. Seasonal mean (June-October) water temperatures (o

C) for 0-10 m depth. ...........................................92

Table 2-3. Fish species present in the Sawtooth Valley Lakes................................................................................96

Table 2-4. Recreation facilities and activities on Sawtooth Valley lakes..............................................................100

Table 2-5. Types of sites and essential physical and biological features designated as PCEs for anadromous 

salmonids, and the life stage each PCE supports .............................................................................103

Table 3-1. VSP parameters and proposed biological viability criteria for Snake River Sockeye Salmon. ...........118

Table 4-1. Hatchery and natural-origin Sockeye Salmon returns to Sawtooth Valley, 1999 - 2014.....................131

Table 4-2. Cormak Jolly Seber-based survival estimates for PIT-Tagged Snake River Sockeye Salmon with 95% 

confidence intervals..........................................................................................................................136

Table 4-3. Adult Sockeye Salmon passage at Lower Granite Dam, adjusted for fallback and reascension using 

PIT-tagged adult return data and survival rates to the Sawtooth Valley..........................................137

Table 5-1. Reaches of the mainstem Salmon River that do not support the beneficial use “Cold Water Aquatic 

Life” .................................................................................................................................................169

Table 5-2. Historical Sockeye Salmon harvest......................................................................................................183

Table 5-3. Sockeye Salmon harvest rate schedule.................................................................................................184

Table 6-1. Monitoring and evaluation programs for Snake River Sockeye Salmon. ............................................253

Table 7-1. Summary of proposed local-level (Sawtooth Valley and upper Salmon River) recovery actions.......270
ESA Recovery Plan: Snake River Sockeye Salmon | 14

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 15

June 2015| NOAA Fisheries 

List of Figures

Figure ES-1. Snake River Sockeye Salmon migration corridor from Columbia River estuary to Sawtooth Valley 

lakes....................................................................................................................................................27

Figure ES-2. Map of the Sawtooth Valley, Idaho. ..................................................................................................28

Figure ES-3. Historical Snake River Sockeye Salmon Life Cycle..........................................................................39

Figure ES-4. The adaptive management process. ...................................................................................................54

Figure ES-5. Snake River Sockeye Salmon Recovery Plan implementation framework. ......................................56

Figure 1-1. Snake River Sockeye Salmon migration corridor, from estuary to Sawtooth Valley Lakes in Idaho..62

Figure 1-2. Historical populations of Sockeye Salmon in the Snake River basin ...................................................64

Figure 1-3. Columbia Basin recovery domains for NMFS West Coast Region......................................................68

Figure 2-1. Hydropower facilities on Snake River Sockeye Salmon migration route.............................................75

Figure 2-2. Land use and cover in the Snake River basin. ......................................................................................77

Figure 2-3. Map of the Sawtooth Valley, Idaho. .....................................................................................................78

Figure 2-4. Land ownership in the spawning range of the Snake River Sockeye Salmon ESU..............................80

Figure 2-5. The Snake River Sockeye Salmon ESU with current status designations............................................84

Figure 2-6. Historical Snake River Sockeye Salmon Life Cycle. ...........................................................................87

Figure 2-7. Spawning locations for Sockeye Salmon in Redfish Lake. ..................................................................89

Figure 2-8. Box and whisker charts depicting mean upper and lower quartile and range of zooplankton biomass 

over time (2000-2011) in Redfish, Pettit, and Alturas Lakes in the Sawtooth Valley, Idaho. ...........94

Figure 2-9. Seasonal mean zooplankton biomass for the Sawtooth Valley lakes (June-October), 1996-2012. ......94

Figure 2-10. Comparison of zooplankton biomass and weight of individual Daphnia sampled during September 

2007 in Redfish, Pettit, Alturas and Yellowbelly Lakes, Idaho. ........................................................95

Figure 2-11. Hierarchical levels of salmonid species structure as defined by the TRTs for ESU/DPS recovery 

planning............................................................................................................................................106

Figures 3-1a & b. Viability curves for application to Snake River Sockeye Salmon lake populations. a) Redfish 

Lake and Alturas Lake (Intermediate). b) small lake populations (Stanley Lake)...........................121

Figure 5-1. Extent of recent Mountain pine beetle epidemic beginning in 1996. .................................................162

Figure 5-2. Streams in the Salmon subbasin, Idaho, that are included on the 303(d) list .....................................170

Figure 5-3. Shows locations of breeding colonies of piscivorous birds in estuary and Columbia River basin.....188

Figure 5-4. NPDES permit sites and 303(d) listed streams in Snake River Sockeye Salmon migratory corridor 193

Figure 5-5. Preliminary maps of predicted hydrologic regime for (A) the period 1970-1999 and (B) the period 

2070-2099.........................................................................................................................................203

Figure 10-1. Snake River Sockeye Salmon recovery plan implementation framework........................................320

Figure 11-1. The adaptive management cycle.......................................................................................................326
ESA Recovery Plan: Snake River Sockeye Salmon | 16

June 2015| NOAA Fisheries 

Figure 11-2. Flow diagram outlining the decision framework used by NMFS to assess the status of biological 

viability criteria and limiting factors criteria....................................................................................328
ESA Recovery Plan: Snake River Sockeye Salmon | 17

June 2015| NOAA Fisheries 

Abbreviations and Acronyms

2008 SCA 2008 Supplemental Comprehensive Analysis

BACI before after control influence

BiOp biological opinion

BPA Bonneville Power Administration

CERCLA Comprehensive Environmental Response Compensation and Liability 

Act

CA Comprehensive Analysis

CHaMP Columbia Habitat Monitoring Program

CWT coded wire tags

DDT Dichlorodiphenyltrichloroethane

DPS distinct population segment

ERTG Expert Regional Technical Group

ESA Endangered Species Act

ESU evolutionarily significant unit

FCRPS Federal Columbia River Power System

GIS geographic information system

GM geometric mean

HGMP Hatchery Guidance Management Plan

HSRG Hatchery Scientific Review Group

ICTRT Interior Columbia Basin Technical Recovery Team

IDFG Idaho Department of Fish and Game

IHOT Integrated Hatchery Operations Team

ISDA Idaho State Department of Agriculture

ISRP Independent Scientific Review Panel

MCR Middle Columbia River

MPG major population group

NAWQA National Water Quality Assessment

NMFS National Marine Fisheries Service

NOAA National Oceanic and Atmospheric Administration

NPCC Northwest Power and Conservation Council

NPDES National Pollutant Discharge Elimination System

NRCS Natural Resources Conservation Service

NWFSC Northwest Fisheries Science Center

ODFW Oregon Department of Fish and Wildlife

OSC Office of Species Conservation

PAHs polycyclic aromatic hydrocarbons

PBDEs polybrominated diphenyl ethers

PBT parental based tagging

PCBs polychlorinated biphenyls

PIBO Pacfish - Infish Biological Opinion
ESA Recovery Plan: Snake River Sockeye Salmon | 18

June 2015| NOAA Fisheries 

PIT passive integrated transponder

PNI proportionate natural influence

RIST Recovery Implementation Science Team

RM river mile

Rkm river mile in kilometers

RME research, monitoring, and evaluation

RPA reasonable and prudent alternative

SAR smolt-to-adult return

SBSTOC Stanley Basin Sockeye Technical Oversight Committee

SBT Shoshone Bannock Tribe

SCA Supplemental Comprehensive Analysis

Sawtooth NRA Sawtooth National Recreation Area

SR Snake River

TCDDs tetra-chlorinated dibenzo-p-dioxius

TDG total dissolved gas

TMDL total maximum daily load

TOC Technical Oversight Committee

TRT Technical Recovery Team

UCR Upper Columbia River

UI University of Idaho

USFS U.S. Forest Service

VIC variable infiltration capacity
ESA Recovery Plan: Snake River Sockeye Salmon | 19

June 2015| NOAA Fisheries 

Terms and Definitions

Abundance In the context of salmon recovery, abundance refers to the number 

of adult fish returning to spawn.

Acre-feet A common measure of the volume of water in the river system. It is

the amount of water it takes to cover one acre (43,560 square feet) 

to a depth of one foot.

Adaptive Management The process of adjusting management actions and/or directions 

based on new information.

All-H Approach The idea that actions could be taken to improve the status of a 

species by reducing adverse effects of the hydrosystem, predators, 

hatcheries, habitat, and/or harvest.

Anadromous Fish Species that are hatched in freshwater, migrate to and mature in salt 

water, and return to freshwater to spawn. 

Baseline Monitoring In the context of recovery planning, baseline monitoring is done 

before implementation, in order to establish historical and/or current 

conditions against which progress (or lack of progress) can be 

measured.

Biogeographical Region An area defined in terms of physical and habitat features, including 

topography and ecological variations, where groups of organisms (in 

this case, salmonids) have evolved in common.

Broad Sense Recovery 

Goals

Goals defined in the recovery planning process, generally by local 

recovery planning groups, that go beyond the requirements for ESA 

delisting, to address, for example, other legislative mandates or 

social, economic, and ecological values.

Brood Cycles Salmon and steelhead mature at different ages so their progeny 

return as spawning adults over several years. When all progeny at 

all ages have returned to spawn, the brood cycle is complete.

Comprehensive Analysis 

(CA) 

The analysis conducted by the FCRPS Action Agencies to assess 

impacts of proposed operation of major projects in the Federal 

Columbia River Power System (FCRPS). The CA provides the basis 

underlying the biological assessments on the FCRPS and Upper 

Snake River projects. 

Compliance Monitoring Monitoring to determine whether a specific performance standard, 

environmental standard, regulation, or law is met.

Conservation Gap The difference between a population’s baseline status and its target 

status.

Contributing Population A population for which some restoration will be needed to achieve 

the MPG-wide average viability recommended by the Interior 

Columbia Technical Recovery Team.
ESA Recovery Plan: Snake River Sockeye Salmon | 20

June 2015| NOAA Fisheries 

Delisting Criteria Criteria incorporated into ESA recovery plans that define both 

biological viability (biological criteria) and alleviation of the causes 

for decline (threats criteria based on the five listing factors in ESA 

section 4(a)(1), and that, when met, would result in a determination 

that a species is no longer threatened or endangered and can be 

proposed for removal from the Federal list of threatened and 

endangered species.

Distinct Population 

Segment (DPS)

A listable entity under the ESA that meets tests of discreteness and 

significance according to USFWS and NOAA Fisheries policy. A 

population is considered distinct (and hence a “species” for 

purposes of conservation under the ESA) if it is discrete from and 

significant to the remainder of its species based on factors such as 

physical, behavioral, or genetic characteristics, it occupies an 

unusual or unique ecological setting, or its loss would represent a 

significant gap in the species’ range.

Diversion Refers to taking water out of the river channel for municipal, 

industrial, or agricultural use. Water is diverted by pumping directly 

from the river or by filling canals.

Diversity All the genetic and phenotypic (life history, behavioral, and 

morphological) variation within a population. Variations could include 

anadromy versus lifelong residence in freshwater, fecundity, run 

timing, spawn timing, juvenile behavior, age at smolting, age at 

maturity, egg size, developmental rate, ocean distribution patterns, 

male and female spawning behavior, physiology, molecular genetic 

characteristics, etc. 

Effectiveness Monitoring Monitoring set up to test cause-and-effect hypotheses about RPA 

actions intended to benefit listed species and/or designated critical 

habitat. Did the management actions achieve their direct effect or 

goal? For example, did fencing a riparian area to exclude livestock 

result in recovery of riparian vegetation?

Endangered Species A species in danger of extinction throughout all or a significant 

portion of its range.

ESA Recovery Plan A plan to recover a species listed as threatened or endangered 

under the U.S. Endangered Species Act (ESA). The ESA requires 

that recovery plans, to the maximum extent practicable, incorporate 

(1) objective, measurable criteria that, when met, would result in a 

determination that the species is no longer threatened or 

endangered; (2) site-specific management actions that may be 

necessary to achieve the plan's goals; and (3) estimates of the time 

required and costs to implement recovery actions.

Evolutionarily Significant 

Unit (ESU)

A group of Pacific salmon or steelhead trout that is (1) substantially 

reproductively isolated from other conspecific units and (2) 

represents an important component of the evolutionary legacy of the 

species. Equivalent to a distinct population segment and treated as 

a species under the Endangered Species Act.

Extinct No longer in existence. No individuals of this species can be found.
ESA Recovery Plan: Snake River Sockeye Salmon | 21

June 2015| NOAA Fisheries 

Extirpated Locally extinct. Other populations of this species exist elsewhere. 

Functionally extirpated populations are those of which there are so 

few remaining numbers that there are not enough fish or habitat in 

suitable condition to support a fully functional population.

Factors for Decline Five general categories of causes for decline of a species, listed in 

the Endangered Species Act section 4(a)(1)(b): (A) the present or 

threatened destruction, modification, or curtailment of its habitat or 

range; (B) overutilization for commercial, recreational, scientific, or 

educational purposes; (C) disease or predation; (D) the inadequacy 

of existing regulatory mechanisms; or (E) other natural or humanmade factors affecting its continued existence.

FCRPS Action Agencies The three agencies that operate the Federal Columbia River Power 

System: Bonneville Power Administration, U.S. Army Corps of 

Engineers and Bureau of Reclamation. 

Fish Ladder A series of stair-step pools that enables adult salmon and steelhead 

to migrate upstream past a dam. Swimming from pool to pool, adult 

salmon and steelhead work their way up the ladder to the top where 

they continue upriver.

Flow Augmentation Water released from system storage at targeted times and places to 

increase streamflows to benefit migrating juvenile salmon and 

steelhead.

Freshet The heavy runoff that occurs in the river when streams are at their 

peak flows with spring snowmelt. Before the dams were built, these 

freshets moved spring juvenile salmon quickly downriver.

Functionally Extirpated Describes a species that has been extirpated from an area; although 

a few individuals may occasionally be found, there are not enough 

fish or habitat in suitable condition to support a fully functional 

population.

Heterozygosity The presence of different alleles at one or more loci on homologous 

chromosomes.

Hyporheic Zone The hyporheic zone is a region beneath and alongside a stream bed 

where shallow groundwater and surface water mix.

Implementation Monitoring Monitoring to determine whether an activity was performed and/or 

completed as planned.

Independent Population A group of fish of the same species that spawns in a particular lake or 

stream (or portion thereof) at a particular season and which, to a 

substantial degree, does not interbreed with fish from any other group 

spawning in a different place or in the same place at a different season. 

For NMFS’ purposes in recovery planning, not interbreeding to a 

‘substantial degree’ means that two groups are considered to be 

independent populations if they are isolated to such an extent that 

exchanges of individuals among the populations do not substantially 

affect the population dynamics or extinction risk of the independent 

populations over a 100-year time frame (McElhany et al. 2000). 
ESA Recovery Plan: Snake River Sockeye Salmon | 22

June 2015| NOAA Fisheries 

Independent Scientific 

Review Panel (ISRP)

The Independent Scientific Review Panel reviews individual fish and 

wildlife projects funded by Bonneville Power Administration and 

makes recommendations to the Northwest Power and Conservation 

Council on matters related to those projects.

Indicator A variable used to forecast the value or change in the value of 

another variable.

Intrinsic Potential The estimated relative suitability of a habitat for spawning and 

rearing of anadromous salmonid species under historical conditions 

inferred from stream characteristics including channel size, gradient, 

and valley width.

Intrinsic Productivity Productivity at very low population size; unconstrained by density.

Introgression The incorporation of genes from one species into the gene pool of 

another as a result of hybridization.

Interoparity The ability to reproduce more than once during a lifetime.

Jack and Jill salmon Jack and Jill salmon return to freshwater one or two years earlier 

than their counterparts. They are usually smaller but are sexually 

mature and return to spawn at an earlier age. 

Juvenile salmon Juvenile salmon is the term applied to a salmonid fish between the 

egg and adult stages. Juvenile salmonid stages include sac fry or 

alevin, fry, parr, and smolts. The juvenile stage last until the fish are 

grown and sexually mature. 

Kokanee A self-perpetuating, generally non-anadromous form of 

Oncorhynchus nerka that is distinct from sockeye. Kokanee occur in 

balanced sex-ratio populations where the parents, for several 

generations back, have spent their whole lives in fresh water. 

Kokanee are genetically distinct from sockeye and are not the focus 

of this recovery plan.

Large Woody Debris (LWD) A general term for wood naturally occurring or artificially placed in 

streams, including branches, stumps, logs, and logjams. Streams 

with adequate LWD tend to have greater habitat diversity, a natural 

meandering shape, and greater resistance to flooding.

Legacy Effects Impacts from past activities (usually a land use) that continue to 

affect a stream or watershed in the present day.

Limiting Factors Impaired physical, biological, or chemical features (e.g., inadequate 

spawning habitat, high water temperature, insufficient prey 

resources) that result in reductions in viable salmonid population 

(VSP) parameters (abundance, productivity, spatial structure, and 

diversity). Key limiting factors are those with the greatest impacts on 

a population’s (or major population group’s or species’) ability to 

reach its desired status. 

Major Population Group An aggregate of independent populations within an ESU that share 
ESA Recovery Plan: Snake River Sockeye Salmon | 23

June 2015| NOAA Fisheries 

(MPG) similar genetic and spatial characteristics.

Maintained Status Population status in which the population does not meet the criteria 

for a viable population but does support ecological functions and 

preserve options for ESU recovery.

Management Unit A geographic area defined for recovery planning purposes on the 

basis of state, tribal or local jurisdictional boundaries that 

encompass all or a portion of the range of a listed species, ESU, or 

DPS.

Metrics Something that quantifies a characteristic of a situation or process; 

for example, the number of natural-origin salmon returning to spawn 

to a specific location is a metric for population abundance.

Morphology The form and structure of an organism, with special emphasis on 

external features.

Natural-origin Fish Fish that were spawned and reared in the wild, regardless of 

parental origin.

Northern Pikeminnow A large member of the minnow family, the Northern Pikeminnow 

(formerly known as Squawfish) is native to the Columbia River and

its tributaries. Studies show a Northern Pikeminnow can eat up to 15 

young salmon a day.

Parr The stage in anadromous salmonid development between 

absorption of the yolk sac and transformation to smolt before 

migration seaward.

Peak Flow The maximum rate of flow occurring during a specified time period 

at a particular location on a stream or river.

Persistence Probability The complement of a population’s extinction risk (i.e., persistence 

probability = 1 – extinction risk).

Phenotype Any observable characteristic of an organism, such as its external 

appearance, development, biochemical or physiological properties, 

or behavior.

Photic Zone The depth of the water in a lake or ocean that is exposed to 

sufficient sunlight for photosynthesis to occur.

Piscivorous Describes any animal that preys on fish for food.

Primary Population A population that is targeted for restoration to high or very high 

persistence probability.

Productivity The average number of surviving offspring per parent. Productivity is 

used as an indicator of a population’s ability to sustain itself or its 

ability to rebound from low numbers. The terms “population growth 

rate” and “population productivity” are interchangeable when 

referring to measures of population production over an entire life 

cycle. Can be expressed as the number of recruits (adults) per 

spawner or the number of smolts per spawner.
ESA Recovery Plan: Snake River Sockeye Salmon | 24

June 2015| NOAA Fisheries 

Reach A length of stream between two points.

Reasonable and Prudent 

Alternative

Recommended alternative actions identified during formal 

consultation that can be implemented in a manner consistent with 

the purposes of the action, that can be implemented consistent with 

the scope of the Federal agency’s legal authority and jurisdiction, 

that are economically and technologically feasible, and that the 

Service finds would avoid the likelihood of jeopardizing the 

continued existence of the listed species or the destruction or 

adverse modification of designated critical habitat.

Recovery Domain An administrative unit for recovery planning defined by NMFS based 

on ESU boundaries, ecosystem boundaries, and existing local 

planning processes. Recovery domains may contain one or more 

listed ESUs.

Recovery Goals Goals incorporated into a locally developed recovery plan. These 

goals may go beyond the requirements of ESA de-listing by 

including other legislative mandates or social values. 

Recovery Scenarios Scenarios that describe a target status for each population within an 

ESU, generally consistent with TRT recommendations for ESU 

viability.

Recovery Strategy A statement that identifies the assumptions and logic—the 

rationale—for the species’ recovery program.

Redd A nest constructed by female salmonids in streambed gravels where 

eggs are deposited and fertilization occurs.

Resident Fish Fish that are permanent inhabitants of a water body. Resident fish 

include trout, bass, and perch.

Residual Sockeye Sockeye that are genetically aligned with the anadromous form of 

sockeye but have adopted a resident life history pattern, remaining 

in freshwater to mature and reproduce.

Riparian Area Area with distinctive soils and vegetation between a stream or other 

body of water and the adjacent upland. It includes wetlands and 

those portions of floodplains and valley bottoms that support riparian 

vegetation.

River Reach A general term used to refer to lengths along the river from one 

point to another, as in the reach from the John Day Dam to the 

McNary Dam.

Runoff Precipitation, snowmelt, or irrigation water that runs off the land into 

streams or other surface water.

Salmonid Of, belonging to, or characteristic of the family Salmonidae, which 

includes salmon, steelhead, trout, and whitefish. In this document, it 

refers to listed steelhead distinct population segments (DPS) and 

salmon evolutionarily significant units (ESU).
ESA Recovery Plan: Snake River Sockeye Salmon | 25

June 2015| NOAA Fisheries 

Shoal A shallow place in a lake or other body of water. Sockeye shoal 

spawners return to spawn along the shoreline of the lake.

Smolt A juvenile salmon or steelhead migrating to the ocean and 

undergoing physiological changes to adapt from freshwater to a 

saltwater environment.

Smoltification The transformation from parr to smolt. The transformation involves 

a series of physiological changes where juvenile salmonid fish adapt 

from living in freshwater to living in saltwater.

Spatial structure The geographic distribution of a population or the populations in an 

ESU.

Spill Water released from a dam over the spillway instead of being 

directed through the turbines.

Stabilizing Population A population that is targeted for maintenance at its baseline 

persistence probability, which is likely to be low or very low.

Streamflow Streamflow refers to the rate and volume of water flowing in various 

sections of the river. Streamflow records are compiled from 

measurements taken at particular points on the river, such as The 

Dalles, Oregon.

Supplemental 

Comprehensive Analysis 

(SCA)

An analysis by NOAA Fisheries of the environmental baseline and 

cumulative effects on ESA-listed Columbia River salmon and 

steelhead species from operations of the Federal Columbia River 

Power System (FCRPS) and the Upper Snake River water 

management systems and the U.S. v. Oregon Harvest Management 

Agreement. The SCA used the most recent available scientific data 

and information to update a previous Comprehensive Analysis 

prepared by the FCRPS Action Agencies. The SCA provides the 

analysis underlying the evaluations in the FCRPS Biological 

Opinions on the effects of the three actions on the species. 

Technical Recovery Team 

(TRT)

Teams convened by NOAA Fisheries to develop technical products

related to recovery planning. Technical Recovery Teams are 

complemented by planning forums unique to specific states, tribes, 

or regions, which use TRT and other technical products to identify 

recovery actions. See SCA Section 7.3 for a discussion of how TRT 

information is considered in these Biological Opinions.

Threatened Species A species likely to become endangered within the foreseeable future 

throughout all or a significant portion of its range.

Threat Reduction Scenario A specific combination of reductions in threats from various sectors 

that would lead to a population achieving its target status.

Threats Human activities or natural events (e.g., road building, floodplain 

development, fish harvest, hatchery influences, volcanoes) that 

cause or contribute to limiting factors. Threats may exist in the 

present or be likely to occur in the future.
ESA Recovery Plan: Snake River Sockeye Salmon | 26

June 2015| NOAA Fisheries 

Total Maximum Daily 

Loads (TMDLs)

A calculation of the maximum amount of a pollutant that a water body 

can receive and still safely meet water quality standards. 

Viability criteria Criteria defined by NOAA Fisheries-appointed Technical Recovery 

Teams based on the biological parameters of abundance, 

productivity, spatial structure, and diversity, which describe a viable 

salmonid population (VSP) (an independent population with a 

negligible risk of extinction over a 100-year time frame) and which 

describe a general framework for how many and which populations 

within an ESU should be at a particular status for the ESU to have 

an acceptably low risk of extinction. See SCA Section 7.3 for a 

discussion of how TRT information is considered in these Biological 

Opinions.

Viability Curve A curve describing combinations of abundance and productivity that 

yield a particular risk of extinction at a given level of variation over a 

specified time frame.

Viable Salmonid 

Population (VSP)

An independent population of any Pacific salmon or steelhead that 

has a negligible risk of extinction due to threats from demographic 

variation (random or directional), local environmental variation, and 

genetic diversity change (random or directional) over a 100-year 

time frame.

VSP Parameters Abundance, productivity, spatial structure, and diversity. These 

describe characteristics of salmonid populations that are useful in 

evaluating population viability. See NOAA Technical Memorandum 

NMFS-NWFSC-42, Viable salmonid populations and the recovery of 

evolutionarily significant units (McElhany et al. 2000).

Yearling A fish that is in its second year of life; sometimes used 

synonymously with smolt.
ESA Recovery Plan: Snake River Sockeye Salmon | 27

June 2015| NOAA Fisheries 

Snake River Sockeye Salmon Recovery 

Plan Executive Summary

Introduction

This recovery plan (Plan) serves as a blueprint for the protection and restoration of Snake River Sockeye 

Salmon (Oncorhynchus nerka). Snake River Sockeye Salmon were listed as an endangered species 

under the Endangered Species Act (ESA) in 1991. The listing was reaffirmed in 2005. The species 

remains at risk of extinction. 

Today, the last remaining Snake River Sockeye Salmon spawn in Sawtooth Valley lakes, high in the 

Salmon River drainage of central Idaho in the Snake River basin. While very few Sockeye Salmon 

currently follow an anadromous life cycle, the small remnant run of the historical population migrates 

900 miles downstream from the Sawtooth Valley through the Salmon, Snake and Columbia Rivers to the 

ocean (Figure ES-1). After one to three years in the ocean, they return to the Sawtooth Valley as adults, 

passing once again through these mainstem rivers and through eight major federal dams, four on the 

Columbia River and four on the lower Snake River. Anadromous Sockeye Salmon returning to Redfish 

Lake in Idaho’s Sawtooth Valley travel a greater distance from the sea, 1,448 kilometers (900 miles), to 

a higher elevation (1,996 meters [6,500 feet]) than any other Sockeye Salmon population. They are the 

southernmost population of Sockeye Salmon in the world.

Figure ES-1. Snake River Sockeye Salmon migration corridor from Columbia River estuary to Sawtooth Valley lakes.
ESA Recovery Plan: Snake River Sockeye Salmon | 28

June 2015| NOAA Fisheries 

Before the turn of the twentieth century, large runs of Sockeye Salmon returned annually to the Snake 

River basin (Evermann 1896; Selbie et al. 2007). In fact, one of the major historical spawning areas, 

Redfish Lake, was named for the large numbers of Sockeye Salmon that returned to spawn each year 

turning the lake a shimmering red during the spawning season. Sockeye Salmon ascended the Snake 

River to the Wallowa River basin in northeastern Oregon and the Payette and Salmon River basins in 

Idaho to spawn in natural lakes. Within the Salmon River basin, Sockeye Salmon spawned in Warm 

Lake in the South Fork Salmon River basin, as well as in the Sawtooth Valley lakes: Stanley, Redfish, 

Yellowbelly, Pettit and Alturas Lakes (Figure ES-2). A smaller Sawtooth Valley lake, Hell Roaring 

Lake, may have also supported some Sockeye Salmon production. The historical relationships between 

the different fish populations are not known. 

Figure ES-2. Map of the Sawtooth Valley, Idaho.
ESA Recovery Plan: Snake River Sockeye Salmon | 29

June 2015| NOAA Fisheries 

The Sockeye Salmon populations declined through the 

early- and mid-1900s, leading to the National Marine 

Fisheries Service (NMFS) proposed ESA-listing of the 

species as endangered in April 1991 (56 FR 14055) and 

final ESA-listing in November 1991 (56 FR 58619). 

NMFS reaffirmed the listing in 2005 (70 FR 2853). 

NMFS is a branch of the National Oceanic and 

Atmospheric Administration (NOAA) and is sometimes 

referred to as NOAA Fisheries. As the federal agency 

charged with stewardship of the nation’s marine resources, 

NMFS has the responsibility for listing and delisting 

salmon and steelhead species under the ESA. 

When Snake River Sockeye Salmon were ESA-listed as 

endangered in 1991, all of the Snake River Sockeye 

Salmon populations but one, the Redfish Lake population 

in the Sawtooth Valley, were gone, and that population 

had dwindled to fewer than 10 fish per year. In some years 

before 1998, no anadromous Sockeye Salmon returned to 

the Snake River basin. This major decline in the number of 

Sockeye Salmon returning to the Sawtooth Valley put the 

population at significant risk of extinction. Many human 

activities contributed to the near extinction of Snake River 

Sockeye Salmon. The NMFS status review that led to the 

original listing decision attributed the decline to 

“overfishing, irrigation diversions, obstacles to migrating 

fish, and eradication through poisoning.” NMFS’ 1991 

listing decision for Snake River Sockeye Salmon noted 

that such factors as hydropower development, water 

withdrawal and irrigation diversions, water storage, 

commercial harvest, and inadequate regulatory 

mechanisms represented a continued threat to the species’ 

existence. 

In 1991, a partnership of state, tribal and federal fish 

managers initiated a captive broodstock hatchery program 

to save the Redfish Lake Sockeye Salmon population. 

Between 1991 and 1998, all 16 of the natural-origin adult 

Sockeye Salmon that returned to the weir at Redfish Lake 

were incorporated into the captive broodstock program, as well as out-migrating smolts captured 

between 1991 and 1993, and residual Sockeye Salmon captured between 1992 and 1995. The program 

Why restore Snake River Sockeye Salmon?

Snake River Sockeye Salmon are listed as 

endangered under the Endangered Species Act 

because they are in danger of becoming extinct.

Their numbers have dramatically declined from 

historical levels. In some years before 1998, no 

anadromous Sockeye Salmon returned to the 

Snake River basin. 

What is the captive broodstock program?

A captive broodstock program for Snake River 

Sockeye Salmon began in May 1991. The 

program has prevented extinction in the near term 

and preserved the genetic lineage of Redfish Lake 

Sockeye Salmon. The program was developed 

using captured adult Sockeye Salmon that 

returned to Redfish Lake (1991-98), out-migrating 

smolts (1991-93), and residual adult Sockeye 

Salmon (1992-95). Reintroduction of captive 

broodstock progeny has followed a “spread-therisk” philosophy, incorporating multiple release 

strategies into Redfish, Pettit, and Alturas Lakes. 

What does “recovery” mean?

Biological recovery for a salmon species means 

that it is naturally self-sustaining  enough fish 

spawn in the wild and return year after year so 

they are likely to persist in the long run, defined as 

the next 100 years. The species also has to be 

resilient enough to survive catastrophic changes in 

the environment, including natural events such as 

floods, storms, earthquakes, and decreases in 

ocean productivity.

What about other fish species in the lakes?

Other fish species will also benefit from habitat and 

passage improvements for Snake River Sockeye 

Salmon. 
ESA Recovery Plan: Snake River Sockeye Salmon | 30

June 2015| NOAA Fisheries 

has used multiple rearing sites to minimize chances of catastrophic loss of broodstock and has produced 

several million eggs and juveniles, as well as several thousand adults, for release into the wild. 

The Sawtooth Valley is seeing results from the captive broodstock program. Sockeye Salmon returns to 

the valley have increased, especially in recent years, to 646 in 2008 (including 140 natural-origin fish), 

832 in 2009 (including 86 natural-origin fish), 1,355 in 2010 (including 178 natural-origin fish), 1,117 in 

2011 (including 145 natural-origin fish), 257 in 2012 (including 52 natural-origin fish), 272 in 2013 

(including 79 natural-origin fish), and 1,579 in 2014 (including 453 natural-origin fish). However, while 

the program has successfully prevented extinction and preserved the genetic lineage of Redfish Lake 

Sockeye Salmon, the species remains at risk of extinction. Snake River Sockeye Salmon cannot be said 

to be recovered until it is made up of natural-origin fish spawning in the wild and surviving their twoway journey in far greater numbers. 

About This Recovery Plan

The ESA requires NMFS to develop recovery plans for species listed under the ESA. This Plan was 

developed to comply with the law. 

This Plan provides information required by NMFS to satisfy the requirements of section 4(f) of the ESA. 

It describes: (1) recovery goals and objective, measurable criteria which, when met, will result in a 

determination that the species be removed from the threatened and endangered species list; (2) sitespecific management actions necessary to achieve the plan’s goals; and (3) estimates of the time 

required and cost to carry out the actions needed to achieve the plan’s goals. It also includes direction 

for monitoring and evaluation and adaptive management to fine-tune the course towards recovery when 

needed.

NMFS has directed preparation of this Plan. The Plan is the product of a collaborative process with 

contributions by a wide group of governments, sovereigns (tribes), and organizations with the potential 

to contribute to recovery. Participants included Idaho Department of Fish and Game, Shoshone-Bannock 

Tribes, NMFS’ Northwest Fisheries Science Center, members of NMFS’ Interior Columbia Technical 

Recovery Team, Bonneville Power Administration, Stanley Basin Sockeye Salmon Technical Oversight 

Committee, and the U. S. Forest Service. The goal is to produce a Plan that meets NMFS’ ESA 

requirements for recovery plans as well as State of Idaho’s needs. NMFS intends to use the Plan to 

organize and coordinate recovery of the species in partnership with state, tribal, and federal resource 

managers.

The Plan builds upon ongoing Snake River Sockeye Salmon recovery and research efforts. It describes 

the limiting factors and threats that impact survival and recovery. It then identifies a set of strategies and 

actions to address the limiting factors and threats, and restore natural Sockeye Salmon populations in 

Sawtooth Valley lakes to levels that will achieve Snake River Sockeye Salmon recovery. It also 

describes a comprehensive research, monitoring, and evaluation program so that species status is 

evaluated over time, and based on new information, recovery actions can be adjusted as part of an 
ESA Recovery Plan: Snake River Sockeye Salmon | 31

June 2015| NOAA Fisheries 

adaptive management strategy. The actions are voluntary and may be taken to restore the species to a 

healthy, naturally self-sustaining condition. 

Several modules developed by NMFS provide key support to the Plan. NMFS produced these modules, 

which address regional-scale issues affecting Snake River Sockeye Salmon, as well as other ESA-listed 

Columbia River salmon and steelhead species, to assist in recovery planning. These modules provide a 

consistent set of assumptions and recovery actions that recovery planners incorporated into speciesspecific recovery plans. The following modules are used in the Snake River Sockeye Recovery Plan: (1) 

Columbia River Estuary ESA Recovery Plan Module for Salmon and Steelhead (herafter Estuary 

Module) (NMFS 2011a), (2) Supplemental Module for Snake River Salmon and Steelhead , Mainstem 

Columbia River Hydropower Projects (hereafter Hydro Module) (NMFS 2014a), (3) Columbia River 

Harvest Module (Harvest Module), and (4) Module for the Ocean Environment (Ocean Module). The 

modules will be updated periodically to reflect new data. 

Contents of Recovery Plan

The document describes:

• Purpose and uses of the Plan, and context of Plan development (Section 1).

• Relationship of the Plan to other planning processes and other ESA mandates (Section 1).

• The geographic area that supports the historical population (Section 2).

• Characteristics that define the species, including critical habitat (Section 2).

• Salmonid biological structure used in recovery planning (Section 2).

• Recovery goals and ESA requirements for delisting (Section 3).

• Desired Status —biological and threats criteria for delisting; broad sense recovery goals (Section 3).

• Current status of Snake River Sockeye Salmon and populations (Section 4).

• Limiting factors and threats (habitat, hydropower, hatcheries, fisheries, predation, competition, toxics, climate 

change) and critical uncertainties (Section 5).

• Recovery strategies for Snake River Sockeye Salmon (Section 6).

• Site-specific actions for recovery of Snake River Sockeye Salmon (Section 7).

• Predicted effectiveness of proposed actions (Section 8).

• Time and Cost estimates for recovery (Section 9).

• Framework for implementation, defining progress, and status assessment (Section 10).

• Framework for research, monitoring, and evaluation for adaptive management (Section 11).
ESA Recovery Plan: Snake River Sockeye Salmon | 32

June 2015| NOAA Fisheries 

Scientific Foundation

NMFS’ belief that it is critically important to 

base recovery plans on a solid scientific 

foundation that sets the stage for developing 

recovery plans. NMFS appointed teams of 

scientists with geographic and species 

expertise to develop recovery plans for each 

ESA-listed species from a common scientific 

foundation. The team responsible for Snake

River Sockeye Salmon, the Interior Columbia 

Technical Recovery Team (ICTRT), includes 

biologists from NMFS and several states, 

tribal entities, and academic institutions.

This common approach recognizes that, 

historically, most salmon or steelhead species 

contained multiple populations connected by 

some small degree of genetic exchange with 

spawners straying in from other areas. Thus, 

the overall biological structure of a species is 

hierarchical. The species is essentially a 

metapopulation defined by the common 

characteristics of populations within a 

geographic range. 

The ICTRT treats Sawtooth Valley Sockeye 

Salmon as the single major population group 

(MPG) within the Snake River Sockeye 

Salmon evolutionarily significant unit (ESU). 

The MPG contains one extant population 

(Redfish Lake) and two (Alturas Lake and 

Pettit Lake) to four (Stanley and Yellowbelly 

Lakes) other historical populations.

What is an evolutionarily significant unit (ESU)?

An ESU is a group of Pacific salmon that is (1) substantially 

reproductively isolated from other groups of the same species and 

(2) represents an important component of the evolutionary legacy 

of the species. ESUs are defined based on geographic range as 

well as genetic, behavioral and other traits. 

All Pacific salmon belong to the family Salmonidae and the genus 

Oncorhynchus. Sockeye Salmon belong to the species 

Oncorhynchus nerka. 

The Snake River Sockeye Salmon ESU

The Sawtooth Valley supports three forms of O. nerka. The Snake 

River Sockeye Salmon ESU includes two of the forms: 

anadromous and residual Sockeye Salmon. 

• Anadromous Sockeye Salmon usually spend 1 to 3 years in 

the nursery lakes before migrating to sea as smolts. They 

remain at sea for 1 to 3 years before returning to natal areas 

to spawn.

• Residual Sockeye Salmon are genetically aligned with the 

anadromous form but have adopted a resident life history 

pattern, remaining in freshwater to mature and reproduce.

• Kokanee are a type of O.nerka (O. nerka kennerlyi) that is 

genetically distinct from Sockeye Salmon and is not included 

in the Snake River ESA listing. Kokanee are a selfperpetuating, generally non-anadromous form of O.nerka

whose parents, for several generations, have spent their 

whole lives in freshwater. While Kokanee are generally a 

resident fish, and mostly segregated from Sockeye Salmon 

during spawning, the Alturas Lake early stream spawning 

Kokanee produce considerable numbers of smolts and some 

anadromous returns. Consequently, Kokanee represent an 

important life history type and add to the spatial diversity of 

anadromous O. nerka in the Sawtooth Valley. 
ESA Recovery Plan: Snake River Sockeye Salmon | 33

June 2015| NOAA Fisheries 

Recovery Goals and Criteria

The Plan (Section 3) identifies the recovery goals and 

criteria that NMFS will use in future status reviews of the 

Snake River Sockeye Salmon ESU. The primary goal is to 

ensure that the species is viable and no longer needs ESA 

protection. Two types of criteria are used to describe 

viability and inform future ESA-delisting decisions: 

“Biological viability” criteria define population or 

demographic parameters. “Threats” criteria relate to the five 

listing factors detailed in the ESA. This Plan addresses these 

criteria for Snake River Sockeye Salmon populations. In 

addition, broad sense recovery goals identify a future 

species status beyond ESA delisting. 

Biological Viability Criteria: The primary goal is for biological 

recovery to support removal of Snake River Sockeye 

Salmon from the threatened and endangered species list. 

The delisting decision must be based on the best available 

science. Biological recovery for a salmon species (the basis 

for delisting) means that it is naturally self-sustaining 

enough fish spawn in the wild and return year after year so 

they are likely to persist in the long run, defined as the next 

100 years. The species also has to be resilient enough to 

survive catastrophic changes in the environment, including 

natural events, such as floods and changes in ocean 

productivity. A viable ESU is naturally self-sustaining, with 

a high probability of persistence over a 100-year time 

period. The viability of an ESU reflects the viability of its 

populations. A Viable Salmonid Population is an

independent population of Pacific salmon or steelhead that 

has a negligible risk of extinction due to threats from 

demographic variation (random or directional), local 

environmental variation, and genetic diversity changes 

(random or directional) over a 100-year time frame.

The ICTRT proposed biological criteria for the ESU define a viable salmonid population based on four 

viable salmonid population (VSP) parameters: population abundance, productivity, spatial structure, and 

diversity. The ICTRT criteria are hierarchical, with ESU- level objectives expressed in terms of the VSP 

status of the individual populations. The viability criteria are summarized here and discussed in more 

depth in Chapter 3.

What is the goal of this recovery plan?

The primary recovery goal for Snake River 

Sockeye Salmon is to ensure that the species is 

self-sustaining in the wild and no longer needs 

the protection of the ESA. The ESU-level 

objectives are the following:

• Population-level persistence in the face of 

year-to-year variations in environmental 

influences.

• Resilience to the potential impact of 

catastrophic events.

• Maintaining long-term evolutionary potential. 

Once the fish achieve recovery under the ESA, 

the recovery plan will help meet other “broad 

sense” goals that go beyond delisting and 

provide social, cultural, or economic values.

What is delisting? 

Who makes the decision?

Under the ESA, listing and delisting of marine 

species, including salmon, are the responsibility 

of NMFS. If a fish or other species is listed as 

threatened or endangered, legal requirements 

to protect it come into play. When NMFS 

decides through scientific review that the 

species is doing well enough to survive without 

ESA protection, NMFS will “delist” it. The 

decision must reflect the best available science 

concerning the current status of the species and 

its prospects for long-term survival.
ESA Recovery Plan: Snake River Sockeye Salmon | 34

June 2015| NOAA Fisheries 

Abundance/Productivity: Abundance is expressed in terms of natural-origin spawners (adults on the 

spawning ground) measured over a time series. The ICTRT used a recent 10-year geometric mean of 

natural-origin spawners as a measure of current abundance. Productivity is defined in terms of the 

average number of surviving offspring per parent, or a population’s ability to sustain itself. The ICTRT 

measured productivity as returns per spawner or recruits per spawner. 

Abundance and productivity are linked, as populations with low productivity can still persist if they are 

sufficiently large, and small populations can persist if they are sufficiently productive. A viable 

population needs sufficient abundance to maintain genetic health and to respond to normal 

environmental variation, and sufficient productivity to enable the population to quickly rebound from 

periods of poor ocean conditions or freshwater perturbations. Viable populations should demonstrate 

sufficient productivity to support a net replacement rate of 1:1 or higher at abundance levels established 

as long-term targets.

The ICTRT developed viability curves that used quantitative metrics to evaluate the abundance and 

productivity of the populations. A viability curve describes combinations of abundance and productivity 

that correspond to a range of extinction risks: 1% (very low), 5% (low), and 25% (moderate) over a 100-

year period. The ICTRT set the minimum spawning abundance threshold at 1,000 natural-origin 

spawners, measured as a ten-year geometric mean, for the Redfish and Alturas Lake populations, and 

500 natural-origin spawners for the smaller Pettit, Yellowbelly, and Stanley Lake populations. The 

productivity needed to achieve an average natural-origin spawning abundance at the minimum threshold 

varies as a function of population size and target risk level. For example, an average productivity 

exceeding 1.2 and a minimum average natural-origin spawner abundance of 1,000 would be required to 

achieve Highly Viable status, with very low (<1%) risk projected over 100 years for the Redfish Lake 

and Alturas Lake populations (Figure ES-3). 
ESA Recovery Plan: Snake River Sockeye Salmon | 35

June 2015| NOAA Fisheries 

Figure ES-3. Viability curve for intermediate-size Redfish Lake and Alturas Lake Sockeye Salmon populations. 

Spatial Structure/Diversity: A population’s spatial structure reflects both the geographic distribution of 

individuals in the population and the processes that generate that distribution. Diversity refers to the 

distribution of traits within and among populations. The ICTRT defined two primary goals to address 

the spatial structure and diversity criteria: 1) maintain natural rates and levels of spatially mediated 

processes, and 2) maintain natural patterns of variation. It also identified mechanisms, factors and 

metrics for assessing a population’s spatial structure and diversity. The ICTRT defined population 

structure/diversity risk levels by integrating across the measures of spatial structure and diversity. 

Populations with restricted distribution and few spawning areas are at a higher risk of extinction as a 

result of catastrophic environmental events than are populations with more widespread and complex 

spatial structures. A population with a complex spatial structure, including multiple spawning areas, 

experiences more natural exchange of gene flow and life history characteristics. For Snake River 

Sockeye Salmon, the ICTRT determined that risks to ESU life history diversity and spatial structure 

could be diminished by reestablishing or reintroducing independent Sockeye Salmon populations to 

Alturas and Pettit Lakes, and possibly eventually into Stanley or Yellowbelly Lake. Risks to ESU life

history patterns could also be reduced by reestablishing historical life history patterns that may have 

been present in the natal lakes. 

Table ES-1 shows the ICTRT’s biological viability criteria for Snake River Sockeye Salmon. The 

ICTRT-recommended quantitative criteria (including minimum abundance thresholds) reflect the best 

information currently available. Information gained from ongoing studies of production potential and 

exchange rates among the lakes as natural reintroduction efforts progress will be periodically reviewed 
ESA Recovery Plan: Snake River Sockeye Salmon | 36

June 2015| NOAA Fisheries 

to determine if the basic assumptions behind the current quantitative criteria are valid, or if updates are 

warranted. 

Table ES-1. Viable salmonid population (VSP) parameters and biological viability criteria for Snake River Sockeye Salmon.

VSP Parameter Biological Viability Criteria

Abundance

• Minimum spawning abundance threshold measured as a ten-year 

geometric mean of estimated natural-origin spawners: 1,000 for 

Redfish Lake and Alturas Lake populations (intermediate size 

category);

• Minimum spawning abundance threshold measured as a tenyear geometric mean of estimated natural-origin spawners: 500 

for populations in the smaller historical size category (Pettit, 

Stanley, or Yellowbelly Lakes)

Productivity • Population growth rate is stable or increasing

Spatial Structure and 

Diversity

• Very low to low risk rating for a highly viable population; and 

• Moderate risk rating for a viable population

Threats Criteria: At the time of a delisting decision for Snake River Sockeye Salmon, NMFS will examine 

whether five listing factors (or threats) detailed in section 4(a)(1) of the ESA have been addressed:

A. Present or threatened destruction, modification, or curtailment of [the species’] habitat or range; 

B. Over-utilization for commercial, recreational, scientific, or educational purposes; 

C. Disease or predation; 

D. Inadequacy of existing regulatory mechanisms; or 

E. Other natural or human-made factors affecting [the species’] continued existence.

The listing factors, or threats, need to have been addressed to the point that delisting is not likely to 

result in their re-emergence. NMFS also expects that the relative priority of threats will change over 

time and that new threats may emerge. NMFS will examine whether the listing factors have been 

addressed during its five-year reviews. 

The Plan identifies threats criteria for each of the relevant listing/delisting factors. Addressing these 

criteria will help to ensure that underlying causes of decline have been addressed and mitigated before a 

species is considered for delisting. NMFS expects that if the proposed actions described in the Plan are 

implemented, they will make substantial progress toward meeting the threats criteria.

Broad Sense Recovery: The immediate goal of this Plan is ESA delisting. Once the fish achieve recovery 

under the ESA, the recovery plan will help meet broader goals. These “broad sense” goals may go 
ESA Recovery Plan: Snake River Sockeye Salmon | 37

June 2015| NOAA Fisheries 

beyond the requirements for delisting to acknowledge social, cultural, or economic values regarding the 

listed species. 

Current Status of the ESU

The endangered Snake River Sockeye Salmon ESU has a long way to go before it will meet the 

biological viability criteria that signal it is self-sustaining and naturally producing at targeted levels. 

Still, annual returns of Snake River Sockeye Salmon through 2013 show that more fish are returning 

than before initiation of the captive broodstock program (Table ES-2). Between 1999 and 2007, more 

than 355 adults returned from the ocean from captive brood releases  almost 20 times the number of 

wild fish that returned in the 1990s. However, this total is primarily due to large returns in the year 2000. 

Returns dropped from 2003 through 2007, but began building in 2008. Adult returns the last six years 

have ranged from a high of 1,579 fish in 2014 (including 453 natural-origin fish) to a low of 257 adults 

in 2012 (including 52 natural-origin fish). Two-thirds of the fish were captured at the Redfish Lake 

Creek weir and the remaining fish were captured at the Sawtooth Hatchery weir on the mainstem 

Salmon River upstream of the Redfish Lake Creek confluence. Sockeye Salmon returns to Alturas Lake 

ranged from one fish in 2002 to 14 fish in 2010. No fish returned to Alturas Lake in 2012, 2013, or 

2014. 

Table ES-2. Hatchery and natural-origin Sockeye Salmon returns to Sawtooth Valley, 1999 – 2014 (IDFG, in prep).

Return Year Total Return Natural Return Hatchery Return Alturas Returns*

Observed Not 

Trapped

1999 7 0 7 0 0

2000 257 10 233 0 14

2001 26 4 19 0 3

2002 22 6 9 1 7

2003 3 0 2 0 1

2004 27 4 20 0 3

2005 6 2 4 0 0

2006 3 1 2 0 0

2007 4 3 1 0 0

2008 646 140 456 1 50

2009 832 86 730 2 16

2010 1,355 178 1,144 14 33

2011 1,117 145 954 2 18

2012 257 52 190 0 15

2013 272 79 191 0 2

2014 1,579 453 1,062 0 63

*These fish were assigned as Sockeye Salmon returns to Alturas Lake and are included in the natural return numbers.
ESA Recovery Plan: Snake River Sockeye Salmon | 38

June 2015| NOAA Fisheries 

Survival by life stage

Building to target levels of adult hatchery returns and gaining knowledge of key survival rates are 

important steps towards successfully reestablishing natural production in the Sawtooth Valley. Recent

increased returns of anadromous Snake River Sockeye Salmon from captive brood releases have made it 

possible to compare survival/mortality during different life stages, and to determine key areas, concerns 

and strategies for recovery. Recent survival estimates during different life stages are summarized below.

• Spawner to smolt survival - Currently, the hatchery program controls productivity and survival 

for this life stage. An increase in parent spawning levels in the lakes will provide insights into 

juvenile production and survival levels in the lakes.

• Juvenile migrant survival - Sawtooth Valley to Lower Granite Dam: Juveniles migrate quickly 

through the Salmon River to Lower Granite Dam. Estimated survival of hatchery juveniles in the 

reach has been highly variable, ranging from 11.4% in 2000 to 77.6% in 2008. 

• Juvenile migrant survival - Lower Granite Dam to Bonneville Dam: Juvenile survival from 

Lower Granite to Bonneville Dam since 2008 has ranged from 40% to 57%. Within this reach, 

mean survival is estimated at 60% from Lower Granite to McNary Dam (1996-2010) and at 54% 

from McNary to Bonneville Dam (1998-2003, 2006-2010).

• Juvenile and adult migrant survival - Estuary, Plume and Ocean: Survival rates for Snake River 

Sockeye Salmon during this life stage remain unknown due to small numbers of migrants.

• Adult migrant survival - Bonneville Dam to Lower Granite Dam: Estimated survival rates for 

2010-2013 show that survival averaged 56% to 83% from Bonneville to McNary, 92% to 99% 

from McNary to Ice Harbor, and 71% to 97% from Ice Harbor to Lower Granite.

• Adult migrant survival - Lower Granite Dam to Sawtooth Valley: Estimated survival rates for 

PIT-tagged Sockeye Salmon show that 73% of the adults that passed Lower Granite Dam (2008-

2012) were recovered at Redfish Lake, the Sawtooth Hatchery weir or other locations.

Adult Sockeye Salmon in Redfish Lake. Photo courtesy Mike Peterson, Idaho Fish & Game.
ESA Recovery Plan: Snake River Sockeye Salmon | 39

June 2015| NOAA Fisheries 

Historical Snake River Sockeye Salmon Life Cycle

Figure ES-3. Historical Snake River Sockeye Salmon Life Cycle.
ESA Recovery Plan: Snake River Sockeye Salmon | 40

June 2015| NOAA Fisheries 

Limiting Factors and Threats Analysis

NMFS biological review teams have concluded that the 

decline of the Snake River Sockeye Salmon ESU is the 

result of widespread habitat degradation, impaired 

mainstem and tributary passage, historical commercial 

fisheries, chemical treatment of Sawtooth Valley lakes in 

the 1950s and 1960s, and poor ocean conditions. These 

combined factors reduced the number of Sockeye Salmon to 

the single digits. The decline in abundance itself has 

become a major limiting factor, making the remaining 

population vulnerable to catastrophic loss and posing 

significant risks to genetic diversity. 

Today, some threats that contributed to the original listing 

of Snake River Sockeye Salmon now present little harm to 

the ESU, while others continue to threaten viability. 

Fisheries are now better regulated through ESA constraints 

and management agreements, significantly reducing harvest-related mortality. Potential habitat-related 

threats to the fish, especially in the Sawtooth Valley, pose limited concern since most passage barriers 

have been removed and much of the natal lakes area and headwaters remain protected. Efforts to 

eradicate the species from the natal lakes through chemical treatment ended decades ago. Hatcheryrelated concerns have also been reduced through improved management actions. 

The mainstem hydropower system, while less of a constraint than in the past, continues to threaten 

Sockeye Salmon viability. Both juvenile and adult losses occur during travel through the Salmon, Snake,

and Columbia River migration corridor. In addition, the combined and relative effects of different 

threats across the life cycle, including threats from climate change and other unknowns, remain poorly 

understood. Consequently, while the Plan presents the full range of threats and limiting factors 

throughout the life cycle, the different threats do not carry equal weight in their impact on Sockeye 

Salmon. Our recovery strategy focuses on gaining a better understanding of combined threats to Snake 

River Sockeye Salmon through the life cycle, and targeting actions effectively to achieve recovery. 

The Idaho Department of Fish and Game, Shoshone-Bannock Tribes, NMFS, and many independent 

researchers have conducted decades of scientific research and analysis concerning Snake River Sockeye 

Salmon. Key findings are summarized below. Section 5 of the Plan provides a detailed discussion of 

these limiting factors and threats. 

Sawtooth Valley Lakes

Sockeye Salmon historically spawned and reared in five nursery lakes in the Sawtooth Valley: Redfish, 

Pettit, Alturas, Yellowbelly, and Stanley Lakes. They usually spent one to three years in the nursery 

lakes before migrating to sea as smolts. Because of the captive broodstock program and reintroduction 

What are limiting factors and 

threats? 

Limiting factors are the biological and 

physical conditions that limit a species’ 

viability (e.g. high water temperature).

Threats are the human activities or natural 

processes that cause the limiting factors. 

The term “threats” carries a negative 

connotation; however, they are often 

legitimate and necessary activities that at 

times may have unintended negative 

consequences on fish populations. These 

activities can be managed to minimize or 

eliminate the negative impacts.
ESA Recovery Plan: Snake River Sockeye Salmon | 41

June 2015| NOAA Fisheries 

work, Sockeye Salmon currently spawn in Redfish, Alturas, and Pettit Lakes. The lakes lie within the 

Sawtooth National Recreation Area, managed by the U.S. Forest Service. The headwaters of each lake 

drain lands in the Sawtooth Wilderness Area. Overall, habitat conditions for Snake River Sockeye 

Salmon in these high mountain lakes remain in relatively pristine condition. The lakes are, and were 

historically, oligotrophiclacking in nutrients and with relatively low natural aquatic productivity 

compared to lower elevation lakes in other areas. In addition, zooplankton abundance and composition 

vary across the lakes, which may be an important factor in successfully reintroducing anadromous 

Sockeye Salmon production. Lake nutrient supplementation has been implemented in Redfish, Pettit,

and Alturas Lakes to increase Sockeye Salmon carrying capacity. Summer water temperatures in the 

lakes also temporarily spike to levels that make Sockeye Salmon more susceptible to disease and 

infection. Introduction and continued stocking of non-native fish species such as brook trout, lake trout,

and kokanee creates competition and predation risks. Potential interbreeding between hatchery-origin 

fish and natural-origin spawners could further reduce genetic diversity. Providing connectivity of 

migratory corridors and increasing spatial distribution is critical to successful Sockeye Salmon recovery.

Passage is now available to Redfish Lake, but a weir at Sawtooth Hatchery blocks passage in the Salmon 

River to upstream lakes. Providing passage at the weir is critical to reestablishing production in Alturas 

and Pettit Lakes important early steps in the recovery strategy. An artificial barrier on Stanley Lake 

Creek also prevents access to Stanley Lake. Potential removal of this barrier will receive further 

consideration.

Salmon River Mainstem

The Salmon River runs 684 kilometers (410 miles) through central Idaho to join the Snake River in 

lower Hells Canyon, almost half the length of the Sockeye Salmon migration route. Juvenile Sockeye 

Salmon leave the natal lakes in late spring and early summer, often arriving at Lower Granite Dam about 

seven days later. Juvenile Sockeye Salmon survival varies between years and reaches. Tracking studies 

indicate that a large portion of the loss of outmigrating juvenile hatchery Sockeye Salmon in the Salmon 

River occurs between release sites and the North Fork Salmon confluence, with higher losses occurring 

within Little Redfish Lake, in the reach just above Valley Creek near Stanley, between the Pahsimeroi 

and Lemhi Rivers, and in the slow-river reach at Deadwater Slough. Predation appears to cause much of 

the juvenile mortality in the upper Salmon River; however, loss of juvenile migrants may also reflect 

competition with non-native species, environmental conditions, or rearing and release strategies. 

Adult Sockeye Salmon return to the Salmon River in late summer and travel approximately 30 days up 

the free-flowing river to reach the Sawtooth Valley. A number of adult migrants are lost in the Salmon 

River corridor. The factors responsible for the losses of adult Sockeye Salmon migrants are not fully 

established, but are believed to be strongly related to stream flow and temperature. Adult Sockeye 

Salmon return to the Salmon River in late summer, when flows often reach low levels and water 

temperatures peak. Research continues to identify how and where these conditions in the Snake and 

Salmon Rivers affect Sockeye Salmon migrants. A weir at Sawtooth Hatchery on the Salmon River and 

a barrier below the Stanley Lake outlet restrict Sockeye Salmon passage to natal lakes.
ESA Recovery Plan: Snake River Sockeye Salmon | 42

June 2015| NOAA Fisheries 

Columbia and Snake River Mainstem

The Columbia and Snake River hydrosystem remains a threat to the viability of Snake River Sockeye 

Salmon. Four federal dams on the lower Snake River mainstem (Lower Granite, Little Goose, Lower 

Monumental and Ice Harbor) and four federal dams on the lower Columbia River mainstem (McNary, 

John Day, The Dalles and Bonneville) limit passage for juvenile Sockeye Salmon migrating to the 

ocean, and adult Sockeye Salmon returning to their natal lakes. All eight dams are part of the Federal 

Columbia River Power System (FCRPS). Specific limiting factors that impact viability include mortality 

and delayed upstream passage (adults), direct and indirect mortality on downstream migrants (juveniles), 

alteration of the hydrograph and riverine habitat, delayed migration and reduced survival due to high 

water temperatures, and predation by birds, pinnipeds, and non-native fish species. Some incidental take 

of Snake River Sockeye Salmon occurs in mainstem fisheries. The length and duration of the species’ 

migration (900 miles) also increases their risk of exposure to agricultural and industrial chemicals. 

Columbia River Estuary, Plume and Ocean

The cumulative impacts of past and current land use (including dredging, filling, diking, and 

channelization) and alterations to the Columbia River flow regimes have reduced the quality and 

quantity of estuarine and plume habitat. Snake River Sockeye Salmon, like other stream-type salmonids, 

move relatively quickly through the estuary, probably passing through the area within two to three days. 

Juveniles Sockeye Salmon may use the low-salinity gradients of the plume to achieve growth and 

gradually acclimate to saltwater. They would be affected by changes in flow and sediment in these areas. 

They are also vulnerable to bird predation in the estuary, as well as to pinniped predation when they 

return to the estuary as adults. High concentrations of urban and industrial contaminants in some areas 

of the lower Columbia River and estuary may affect fish health and behavior. 

Ocean conditions and food availability contribute to the health and survival of Sockeye Salmon 

returning to the Columbia Basin, and eventually the Sawtooth Valley. Early ocean life is a critical time

for the fish. Most early marine mortality likely occurs during two periods: first, predation-based 

mortality that occurs during the first few weeks to months; second, mortality due to food availability/ 

starvation during and following the first winter at sea. Poor ocean condition from 1977 through the late 

1990s was one of several factors that drove the stock to a very small remnant population.

Future Implications from Climate Change

Likely changes in temperature, precipitation, wind patterns, and sea-level height due to climate change 

have profound implications for survival of Snake River Sockeye Salmon populations in both freshwater 

and marine habitats. Stream flows and temperaturesthe environmental attributes that climate change 

will affectalready limit Sockeye Salmon productivity in areas of the Sawtooth Valley lakes, Salmon 

River, and mainstem Columbia and Snake Rivers. In the ocean, climate-related changes are expected to 

alter primary and secondary productivity, the structure of marine communities, and in turn, the growth, 

productivity, survival, and migrations of salmonids, although the degree of impact on listed salmonids is 

currently poorly understood. All other threats and conditions remaining equal, future deterioration of 

water quality, water quantity, and/or physical habitat due to climate change can be expected to reduce 

viability or survival of naturally produced adult Sockeye Salmon returning to the Sawtooth Valley lakes.
ESA Recovery Plan: Snake River Sockeye Salmon | 43

June 2015| NOAA Fisheries 

Recovery Strategies and Actions

Strategies and actions for the Snake River Sockeye Salmon 

ESU aim to recover self-sustaining, naturally spawning 

populations that are likely to persist for at least 100 years. 

Consistent with the long-term recovery scenario for Snake 

River Sockeye Salmon (discussed in Section 3), the strategies 

(Section 6) and actions (Section 7) intend to restore at least 

two of the three historical lake populations in the ESU to 

highly viable status, and one to viable status. The recovery 

strategies focus on Redfish, Alturas, and Pettit Lakes. As 

recovery efforts progress over time, expansion of 

reintroductions into Stanley Lake and Yellowbelly Lake will 

be considered.

Overall Recovery Strategy

Overall, the strategy aims to reintroduce and support 

adaptation of naturally self-sustaining Sockeye Salmon populations in the Sawtooth Valley lakes. An 

important first step toward that objective has been the successful establishment of anadromous returns

from natural-origin Redfish Lake resident stock gained through a captive broodstock program. That 

program is transitioning as higher levels of anadromous Sockeye Salmon return to spawn in Redfish 

Lake. The long-term strategy is for the naturally produced population to achieve escapement goals in a 

manner that is self-sustaining and without the reproductive contribution of hatchery spawners. 

Our recovery strategy recognizes that efforts to address habitat, fisheries, hatchery, and hydrosystem

issues affecting Snake River Sockeye Salmon need to be planned and implemented with a clear 

understanding of ecological processes  both biological and habitat processes  and how past and 

current activities affect these processes. Since the ESU is at risk for extinction, the first phase in 

recovery, the captive broodstock program, helped maintain the population and prevent species 

extinction. The second phase, recolonization, which we are now entering, will incorporate more naturalorigin Sockeye Salmon returns in the hatchery-spawning program to maintain the genetic fitness of the 

natural population and to provide anadromous adults to recolonize available habitat in Redfish, Pettit,

and Alturas Lakes. Ultimately, the program will move to a third phase emphasizing natural adaptation

and viability. At the same time, recovery efforts will address habitat, fisheries, and hydro-related issues 

affecting Snake River Sockeye Salmon. Together, these efforts aim to provide sufficient fish to restore 

populations adapted to the specific conditions of lakes in the Sawtooth Valley, while also protecting and 

improving habitat conditions, and addressing passage, competition and predation concerns, to support a 

self-sustaining population. 

The approach is adaptive in nature. The strategy for Redfish Lake is based on the working assumption 

that fostering relatively high numbers of returns from hatchery releases will lead to increasing numbers 

of naturally produced adult returns in the future, ultimately leading to natural production at selfPrinciples for sound salmon recovery

• Assess, protect and maintain biological 

and habitat processes.

• Reconnect isolated habitat to increase 

spatial structure.

• Restore ecological processes.

• Restore degraded habitat.

• Conserve or restore evolutionary 

processes.

• Develop goals and objectives based on a 

deep understanding of ecological 

properties of the system.

• Manage actions to be adaptive and 

minimally intrusive.
ESA Recovery Plan: Snake River Sockeye Salmon | 44

June 2015| NOAA Fisheries 

sustaining levels. This strategy is based on a careful assessment of the best available scientific 

information and has associated monitoring and evaluation studies targeting key assumptions and 

uncertainties to support future adaptations to achieve the recovery objectives. In addition, the strategies 

for Pettit and Alturas Lakes are tailored to specific circumstances associated with each lake and are 

designed to evaluate variations on the basic restoration strategy. Taken as a whole, the information from 

each of the approaches in combination will guide future adaptation of the overall program to meet 

natural production recovery objectives. 

The proposed recovery strategy contains elements to address limiting factors and threats at the local 

level (Sawtooth Valley and upper Salmon River) and regional level (Salmon, Snake and Columbia 

Rivers, Columbia River estuary and plume, and ocean). The recovery strategy for Snake River Sockeye 

Salmon is summarized in the box: Recovery Strategy for Snake River Sockeye Salmon ESU. 

Site-Specific Actions

Section 7 of the Plan describes specific actions proposed under each of the local and regional recovery 

strategies discussed in Section 6 to address problems for Sockeye Salmon. The actions build on recovery 

actions that have been implemented over the last 20 years. Table 7-1 defines over 90 specific actions 

that correspond to the different local-level recovery strategies and address problems for Sockeye Salmon

in the natal lakes and upper Salmon River. The table identifies the actions as well as the sites, VSP 

parameters, limiting factors, and threats that each action targets. The table also provide estimated costs 

and potential implementing entities for each action, and priority for implementation. The Plan also 

identifies actions needed at the regional level (mainstem Salmon, Snake and Columbia Rivers and the 

estuary, plume and ocean) to support recovery of Snake River Sockeye Salmon. Many of these proposed 

actions are designed to be integrated with current, ongoing programs and regulations. 
ESA Recovery Plan: Snake River Sockeye Salmon | 45

June 2015| NOAA Fisheries 

RECOVERY STRATEGY FOR SNAKE RIVER SOCKEYE SALMON ESU

At the local level (Sawtooth Valley and upper Salmon River):

• Conserve population genetic and life history diversity, and spatial structure. 

• Increase naturally spawning Snake River Sockeye Salmon abundance. 

• Improve Sockeye Salmon passage to natal lakes. 

• Reestablish a self-sustaining anadromous Sockeye Salmon population in Redfish Lake.

• Investigate/develop strategies for future actions to support Sawtooth Valley Sockeye Salmon reintroduction and 

adaptation phases for Pettit Lake.

• Investigate and evaluate the potential for restoring natural production of anadromous Sockeye Salmon from 

returning early stream-spawning outmigrants produced by Alturas Lake kokanee.

• As sufficient numbers of natural-origin adults return, develop an integrated approach to manage natural- and 

hatchery-origin adults in the hatchery program and in the wild.

• As sufficient numbers of hatchery-origin anadromous adults return to the basin, identify options for future harvest.

• Continue research and actions to reestablish natural populations in other natal lakes.

• Continue research on natal lakes’ carrying capacity, nutrients, and ecology.

• Protect and conserve natural ecological processes at the watershed scale that support population viability. 

• Protect, restore and manage spawning and rearing habitat.

• Maintain unimpaired water quality and improve water quality as needed.

• Investigate and improve conditions in Salmon River and tributaries to support increased survival of migrating 

Snake River Sockeye Salmon.

• Monitor for predation, disease, aquatic invasive species, and competition and develop actions as needed. 

• Create an adaptive management feedback loop to track progress toward recovery, monitor and evaluate key 

information needs, assess results, and refine strategies and actions accordingly.

At the regional level (mainstem Salmon, Snake and Columbia Rivers; estuary; plume; and ocean): 

• Implement 2008/2010 FCRPS BiOp’s reasonable and prudent alternative to reduce mortalities associated with 

migration through the mainstem Salmon, Snake and Columbia Rivers, estuary and plume.

• Continue research and monitoring on Snake River Sockeye Salmon survival/mortality in mainstem Salmon, Snake 

and Columbia River migration corridor; estuary; plume; and ocean.

• Update Snake River Sockeye Salmon life cycle models using latest information on survival through mainstem 

Salmon, Snake, and lower Columbia River migration corridor; estuary; and plume.

• Manage to maintain current low impact fisheries and reduce fishery impacts in those fisheries that affect Snake 

River Sockeye Salmon.

• Protect and conserve natural ecological processes that support population viability.

• Improve degraded water quality and maintain unimpaired water quality.

• Address ecosystem imbalances in predation, competition, and disease through the strategies and actions in this 

Plan, the Estuary Module and FCRPS BiOp.

• Respond to climate change threats by implementing research, monitoring and evaluation to track indicators related 

to climate change and by preserving biodiversity. 

• Implement this recovery plan through effective communication, coordination and governance.

• Continue research, monitoring and evaluation for adaptive management.

• Prioritize and address key information needs and create an adaptive management feedback loop to revise 

recovery actions as needed.
ESA Recovery Plan: Snake River Sockeye Salmon | 46

June 2015| NOAA Fisheries 

Considerations for Setting Priorities

Based on the current endangered status of the Snake River Sockeye Salmon ESU, our goal is to have 

viable independent populations in at least three or more natal lakes to expand spatial distribution and 

diversity, and protect the relatively healthy habitat conditions in the Sawtooth Valley. The following are 

recommendations for prioritizing the sequence of implementing recovery actions. These 

recommendations reflect the principles for sound salmon recovery:

1. Implement the current captive broodstock program. Actions support conservation of life histories 

and genetic attributes. 

2. Reestablish self-sustaining anadromous Sockeye Salmon populations in Redfish, Pettit, and 

Alturas Lakes. Actions enhance viability and protection of multiple Sockeye Salmon populations 

through continued implementation of the Redfish Lake program, implementation of introduction 

strategies for Pettit and Alturas Lakes, and reconnection of isolated habitat to improve spatial 

structure and diversity.

3. Protect and enhance existing habitat conditions and conserve natural ecological processes.

Actions support the viability of the populations and their primary life history strategies 

throughout their entire life cycle. Continued implementation of the Management Plan for the 

Sawtooth National Recreation Area, together with continued wilderness protections in the 

Sawtooth Valley will protect habitat processes for the natal lakes watersheds. Additional habitat 

protection and restoration actions for the migration corridor are identified in Sections 6 and 7. 

4. Improve survival for all life stages in the migration corridor. Strategies and actions to improve 

survival in the migration corridor are described in Section 6.3.2.

5. Carry out research, monitoring, and evaluation actions. Actions provide critical information 

needed to assess fish viability responses and adapt management decisions as needed based on 

this information. Section 11 identifies the adaptive management approach, together with 

research, monitoring, and evaluation actions to continually adapt recovery actions over time. 

 

We believe the recovery strategies and management actions identified in the Plan will be effective in 

improving survival of Snake River Sockeye Salmon; however, we have uncertainties about whether they 

will be sufficient to achieve viability. Thus, the Plan depends on an adaptive management framework 

that implements the actions based on best available science, monitors to improve the science, and 

updates actions based on new knowledge. 

Summaries describing strategies and actions for Sockeye Salmon recovery in Redfish Lake, Pettit Lake 

and Alturas Lake, and potentially in Stanley and Yellowbelly Lakes, follow.
ESA Recovery Plan: Snake River Sockeye Salmon | 47

June 2015| NOAA Fisheries 

Redfish Lake Sockeye Salmon Population

Recovery Strategy

As the only extant population of Snake River Sockeye Salmon, the Redfish Lake population plays a key role in ESU recovery. 

A captive broodstock program has successfully prevented the population’s extinction in the near term and preserved its 

genetic lineage. That program will now transition to increase hatchery releases to support sufficient natural-origin anadromous 

Sockeye Salmon returns. Next, it will shore up adaptation to reestablish a natural self-sustaining anadromous Sockeye 

Salmon population. 

Redfish Lake. Photo courtesy of Andy Kohler,Shoshone-Bannock Tribes.

Redfish Lake Sockeye Salmon Population

Current Status

▪ Extant population; at high risk of extinction in its current state. 

Proposed Recovery Scenario

▪ Achieve highly viable (<1% extinction risk) or viable (<5% extinction risk) status for population. 

▪ Achieve a minimum spawning abundance threshold measured as a ten-year geometric mean of 1,000 naturalorigin spawners, with a stable or increasing population growth rate. 

▪ Achieve a spatial structure/diversity rating of low risk for highly viable status or maintained for viable status. 
ESA Recovery Plan: Snake River Sockeye Salmon | 48

June 2015| NOAA Fisheries 

Key Strategies and Actions 

 

▪ Conserve population genetics and life history diversity by establishing a composite hatchery and natural Sockeye Salmon

population in Redfish Lake.

▪ As natural-origin adult returns increase, reestablish a self-sustaining anadromous Sockeye Salmon population in the lake.

▪ Maintain current wilderness protection and protect pristine habitat and natural ecological processes. 

▪ Continue research on lake carrying capacity, nutrients, and ecology. 

▪ Investigate whether water quality, including temperatures, affects Sockeye Salmon carrying capacity in the lake and 

improve water quality as needed.

▪ Protect and enhance spawning and rearing habitat in Redfish Lake and Fishhook Creek. 

▪ Investigate and improve conditions in Salmon River and tributaries to support increased survival of migrating juvenile and 

adult Sockeye Salmon. 

▪ Implement FCRPS BiOp actions to reduce mortalities associated with passage through the mainstem Columbia and 

Snake River hydroelectric projects. 

▪ Continue research on Sockeye Salmon survival/mortality in Snake and Columbia Rivers, estuary, plume, and ocean. 

▪ Manage risks from mainstem Columbia River and lower Snake River fisheries through U.S. v. Oregon. 

▪ Identify options for future fisheries as sufficient numbers of hatchery-origin Sockeye Salmon adults return to basin. 

▪ Monitor and control predation, disease, aquatic invasive species, and competition.

▪ Respond to climate change threats by implementing research, monitoring, and evaluation (RM&E) to track indicators and 

by preserving biodiversity.
ESA Recovery Plan: Snake River Sockeye Salmon | 49

June 2015| NOAA Fisheries 

Pettit Lake Sockeye Salmon Population

Recovery Strategies

Reintroduction strategies for the extirpated Pettit Lake Sockeye Salmon population will be further developed and refined 

during implementation of the Redfish Lake strategy. An interim strategy may include initial reintroductions to Pettit Lake from 

volitional spawning of Pettit Lake-origin anadromous adults and release of captive broodstock. The reintroduction plan will be 

refined over time through an adaptive management process to achieve a naturally adapted anadromous population. 

Pettit Lake. Photo courtesy Andy Kohler, Shoshone-Bannock Tribes.

Pettit Lake Sockeye Salmon Population

Current Status

▪ Potential historical population; now functionally extirpated. 

Proposed Recovery Scenario

• Achieve highly viable (<1% extinction risk) or viable (<5% extinction risk) status for population. 

• Achieve a minimum spawning abundance threshold measured as a ten-year geometric mean of 500 

natural-origin spawners, with a stable or increasing population growth rate. 

• Achieve a spatial structure/diversity rating of low risk for highly viable status or maintained for viable 

status. 
ESA Recovery Plan: Snake River Sockeye Salmon | 50

June 2015| NOAA Fisheries 

Key Strategies and Actions 

 

▪ Improve Sockeye Salmon passage at the Sawtooth Hatchery weir on the Salmon River.

▪ Improve/replace juvenile trapping structure on Pettit Lake Creek.

▪ Allow anadromous adult Sockeye Salmon to return to Pettit Lake for volitional spawning.

▪ Release captive broodstock adults into Pettit Lake representing the entire genetic diversity of the broodstock for several 

years.

▪ After several years of direct outplanting of adults sourced from the Redfish Lake population, stop stocking and evaluate

the natural production response; continue to allow anadromous Pettit Lake-origin adults to return for volitional spawning.

▪ Evaluate and refine the reintroduction program as needed to reestablish a locally adapted population in Pettit Lake.

▪ Maintain current wilderness protection and protect pristine habitat and natural ecological processes. 

▪ Continue research on lake carrying capacity, nutrients, and ecology. 

▪ Investigate whether water quality affects Sockeye Salmon carrying capacity in the lake and improve water quality as 

needed.

▪ Protect and enhance spawning and rearing habitat in Pettit Lake. 

▪ Investigate and improve conditions in Salmon River and tributaries to support increased survival of migrating Sockeye 

Salmon. 

▪ Implement FCRPS BiOp actions to reduce mortalities associated with passage through the mainstem Columbia and 

Snake River hydroelectric projects. 

▪ Continue research on Sockeye Salmon survival/mortality in Snake and Columbia Rivers, estuary, plume, and ocean. 

▪ Manage risks from mainstem Columbia River and lower Snake River fisheries through U.S. v. Oregon. 

▪ Identify options for future fisheries as sufficient numbers of hatchery-origin Sockeye Salmon adults return to basin. 

▪ Monitor and control predation, disease, aquatic invasive species, and competition.

▪ Respond to climate change threats by implementing RM&E to track indicators and by preserving biodiversity.
ESA Recovery Plan: Snake River Sockeye Salmon | 51

June 2015| NOAA Fisheries 

Alturas Lake Sockeye Salmon Population

Recovery Strategies

The recovery strategy for Alturas Lake Sockeye Salmon focuses on rebuilding the population using the lake’s existing native 

kokanee population. The Alturas Lake kokanee population exhibits an earlier return time than the Redfish Lake population and 

maintaining this diversity is important. Reintroduction strategies for Alturas Lake will be developed based on investigations and 

evaluations regarding the potential to restore natural production of anadromous Sockeye Salmon from early returning, early

stream spawning outmigrants produced by kokanee in the lake. Careful steps will be taken to maintain the population’s unique 

genetic diversity and spatial structure, and capture the benefits of local adaptation. Reintroduction options will be refined over 

time through adaptive management. 

Alturas Lake. Photo courtesy Andy Kohler, Shoshone-Bannock Tribes.

Alturas Lake Sockeye Salmon Population

Current Status

▪ Historical population; now functionally extirpated. 

Proposed Recovery Scenario

• Achieve highly viable (<1% extinction risk) or viable (<5% extinction risk) status for population. 

• Achieve a minimum spawning abundance threshold measured as a ten-year geometric mean of 1,000

natural-origin spawners, with a stable or increasing population growth rate. 

• Achieve a spatial structure/diversity rating of low risk for highly viable status or maintained for viable 

status. 
ESA Recovery Plan: Snake River Sockeye Salmon | 52

June 2015| NOAA Fisheries 

Key Strategies and Actions

▪ Improve Sockeye Salmon passage at the Sawtooth Hatchery weir on the Salmon River.

▪ Trap and transport or allow volitional migration of anadromous adults identified as Alturas Lake origin to Alturas Lake for 

volitional spawning. 

▪ Establish a new hatchery program for Alturas Lake anadromous Sockeye Salmon using returning anadromous Alturas 

Lake-origin adults.

▪ Identify appropriate donor stocks and investigate strategies to establish a new hatchery captive broodstock program for 

anadromous Alturas Lake Sockeye Salmon. Investigate alternative strategies for the early stream spawning Alturas Lake 

population that will support and enhance anadromy. 

▪ Construct and operate trapping structure in Alturas Lake Creek.

▪ Maintain current wilderness protection and protect pristine habitat and natural ecological processes. 

▪ Continue research on lake carrying capacity, nutrients, and ecology. 

▪ Investigate whether water quality affects Sockeye Salmon carrying capacity in the lake and improve quality as needed.

▪ Protect and enhance spawning and rearing habitat in Alturas Lake. 

▪ Investigate and improve conditions in Salmon River and tributaries to increase survival of migrating Sockeye Salmon. 

▪ Implement FCRPS BiOp actions to reduce mortalities associated with passage through the mainstem Columbia and 

Snake River hydroelectric projects. 

▪ Continue research on Sockeye Salmon survival/mortality in Snake and Columbia Rivers, estuary, plume, and ocean. 

▪ Manage risks from mainstem Columbia River and lower Snake River fisheries through U.S. v. Oregon. 

▪ Identify options for future fisheries as sufficient numbers of hatchery-origin Sockeye Salmon adults return to basin. 

▪ Monitor and control predation, disease, aquatic invasive species, and competition.

▪ Respond to climate change threats by implementing RM&E to track indicators and by preserving biodiversity.
ESA Recovery Plan: Snake River Sockeye Salmon | 53

June 2015| NOAA Fisheries 

Stanley Lake and Yellowbelly Lake Sockeye Salmon Populations

Recovery Strategies

The long-term recovery scenario for the Snake River Sockeye Salmon ESU focuses initial efforts on restoring self-sustaining, 

naturally producing populations in Redfish, Pettit, and Alturas Lakes. Currently, stocking Sockeye Salmon in Stanley and 

Yellowbelly Lakes is not a priority. This may change as adult returns increase and passage to the upper basin is restored. It is 

likely that Sockeye Salmon may return to Yellowbelly Lake through straying and natural recolonization. Reintroduction efforts 

for Stanley Lake would include developing a lake trout management strategy and reestablishing adult passage at the outlet of 

Stanley Lake that currently prevents adult Sockeye Salmon immigration.

Key Potential Strategies and Actions

▪ Continue research on lake carrying capacity, nutrients, and ecology. 

▪ Investigate whether water quality affects Sockeye Salmon carrying capacity in the lakes; improve conditions as needed.

▪ Take actions to prevent the spread of non-native lake trout to other Sawtooth Valley nursery lakes.

▪ Remove an upstream fish passage barrier in Stanley Lake Creek. Develop program to support Sockeye Salmon recovery. 

▪ Investigate and manage risks to native kokanee in Stanley Lake. 

▪ Develop and implement a study in Yellowbelly Lake to evaluate lake-carrying capacity of Sockeye Salmon in the absence 

of resident kokanee.

▪ Determine under what migratory conditions (timing, water flows, temperatures) and how often returning adult Sockeye 

Salmon can currently migrate through a boulderfield (lag deposit) in the outlet stream of Yellowbelly Lake.

▪ Investigate whether varying flow regimes affect Sockeye Salmon migration and passage below/ above Yellowbelly Lake. 

▪ Evaluate the potential effects of cutthroat trout on Sockeye Salmon in Yellowbelly Lake.

▪ Maintain current wilderness protection and protect pristine habitat and natural ecological processes. 

▪ Protect and enhance spawning and rearing habitat in Stanley and Yellowbelly Lakes. 

▪ Investigate and improve conditions in Salmon River and tributaries to increase survival of migrating Sockeye Salmon. 

▪ Implement FCRPS BiOp actions to reduce mortalities associated with passage through the mainstem Columbia and 

Snake River hydroelectric projects. 

▪ Continue research on Sockeye Salmon survival/mortality in Snake and Columbia Rivers, estuary, plume, and ocean. 

▪ Manage risks from mainstem Columbia River and lower Snake River fisheries through U.S. v. Oregon. 

▪ Identify options for future fisheries as sufficient numbers of hatchery-origin Sockeye Salmon adults return to basin. 

▪ Monitor and control predation, disease, aquatic invasive species, and competition.

▪ Respond to climate change threats by implementing RM&E to track indicators and by preserving biodiversity.

Stanley Lake and Yellowbelly Lake Sockeye Salmon Populations

Current Status

▪ Historical populations; now functionally extirpated. 

Proposed Recovery Scenario

• As recovery efforts progress over time, expansion of Snake River Sockeye Salmon reintroductions into 

Stanley Lake and Yellowbelly Lake will be considered. 
ESA Recovery Plan: Snake River Sockeye Salmon | 54

June 2015| NOAA Fisheries 

Adaptive Management, Research, Monitoring, and Evaluation

Adaptive management plays a critical role in recovery planning. The long-term success of recovery 

efforts will depend on the effectiveness of incremental steps taken to move the one remaining extant 

Snake River Sockeye Salmon population from its current status to a viable level, and to restore naturally 

self-sustaining Sockeye Salmon populations in other Sawtooth Valley lakes. Adjustments will be needed

if actions do not achieve desired goals, and to take advantage of new information and changing 

opportunities. Adaptive management provides the mechanism to facilitate these adjustments. 

Adaptive management works by binding decision making with data collection and evaluation. Most 

importantly, it offers an explicit process through which alternative approaches and actions can be 

proposed, prioritized, implemented, and evaluated. Successful adaptive management requires that 

monitoring and evaluation plans be incorporated into overall implementation plans for recovery actions. 

These plans should link monitoring and evaluation results explicitly to feedback on the design and 

implementation of actions.

Figure ES-4. The adaptive management process.

The research, monitoring, and evaluation plan described in Section 11 identifies the level of monitoring 

and evaluation needed to determine the effectiveness of recommended actions, and whether they are 

leading to improvements in population viability. The RM&E plan also identifies critical data gaps in 

species and habitat knowledge. The data obtained through RM&E plan implementation will be used to 

assess and, if necessary, correct current restoration strategies. The Snake River Recovery 

Implementation and Science Team will oversee implementation of the adaptive management process in 

coordination with participating agencies, tribes, and entities (Section 10). 
ESA Recovery Plan: Snake River Sockeye Salmon | 55

June 2015| NOAA Fisheries 

A major challenge facing the development and implementation of an effective adaptive management 

strategy for Snake River Sockeye Salmon is the large number of organizations that implement 

management actions, as well as the complexity in jurisdictional and management decision authority. 

These organizations include, but are not limited to: Idaho Department of Fish and Game, Idaho 

Governor’s Office of Species Conservation, Shoshone-Bannock Tribes, state agencies, counties, 

irrigation districts, agriculture and private forest land managers, NMFS, U.S. Forest Service, BLM, other 

federal agencies, utilities, citizen groups, and others. The intent of the adaptive management plan is to 

develop a collaboration and coordination process that uses the current implementation structures and 

allows for sharing of information and decisions that influence recovery of Snake River Sockeye Salmon.
ESA Recovery Plan: Snake River Sockeye Salmon | 56

June 2015| NOAA Fisheries 

Implementation 

Implementation of recovery actions has been occurring for all threats since ESA listing in 1991.

Successful implementation of recovery actions, research and monitoring projects will build upon the 

over 20 years of leadership and Sockeye Salmon recovery work carried out by the Stanley Basin 

Sockeye Salmon Technical Oversight Committee, with the Idaho Department of Fish and Game, 

Shoshone-Bannock Tribes, U.S. Forest Service, NMFS and other partners to prevent ESU extinction. 

Plan implementation will also involve counties, other state and federal agencies, private landowners and 

individuals. 

Section 10 proposes an overall framework for coordinated implementation of this Plan. The 

implementation framework includes several integrated components with different responsibilities, 

including the Snake River Sockeye Salmon Implementation and Science Team, Stanley Basin Sockeye 

Salmon Technical Oversight Committee, and the NMFS’ Snake River Coordination Group. The figure 

below illustrates how these different groups will work together. The different groups will work closely 

with existing groups and seek collaborative initiatives to recover Snake River Sockeye Salmon 

populations. 

Figure ES-5. Snake River Sockeye Salmon Recovery Plan implementation framework.
ESA Recovery Plan: Snake River Sockeye Salmon | 57

June 2015| NOAA Fisheries 

Time and Cost Estimates

It is important to consider the unique challenges of estimating time and cost for salmon and steelhead 

recovery, given the complex relationship of these fish to the environment and to human activities on 

land and water. NMFS estimates that recovery of Snake River Sockeye Salmon could take 50 to 100 

years. The recovery plan (Section 7) contains an extensive list of actions to recover the populations; 

however, it recognizes that there are many uncertainties involved in predicting the course of recovery 

and in estimating total costs over such a long recovery period. Such uncertainties include biological and 

ecosystem responses to recovery actions. 

NMFS believes it is feasible to focus on the first five years of implementation and in five-year intervals 

thereafter, with the understanding that before the end of each five-year implementation period, specific 

actions and costs will be estimated for subsequent years. The Plan (Section 9) discusses cost estimates 

for all projects judged to be feasible and projected to occur over the initial five-year period of Plan 

implementation, fiscal years (FY) 2014 through 2018. It also estimates the total cost of recovery over the 

next 25 years. The estimated total cost for implementation of all actions during the initial five-year 

period, FY 2014 to FY 2018, where costs are available, is approximately $20,293,955. The total 

estimated cost of recovery actions for the ESA-listed Snake River Sockeye Salmon ESU over the next 

25 years is projected to be about $101,469,775. The Recovery Cost Summary Table in Appendix A 

provides the estimated costs for specific recovery actions identified in the Plan for the first five-year 

period.

There are several cautions that must be highlighted regarding these costs. Many of these costs may be 

incomplete in scope, scale, or magnitude until actions are better defined. Specifically, costs for 

potentially expensive projects such as land and water acquisition, water leasing, and research, 

monitoring, and evaluation have not yet been estimated for this ESU. Costs estimates may be adjusted 

up or down, as unit cost estimates, scale of projects, total number of actions, and currently unforeseen 

costs for actions are determined.
ESA Recovery Plan: Snake River Sockeye Salmon | 58

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 59

June 2015| NOAA Fisheries 

Section 1: Introduction

1.1 Purpose of the Plan

1.2 Endangered Species Act Requirements

1.3 Context of Plan Development

1.4 Tribal Trust and Treaty Responsibilities

1.5 Recovery Planning Modules

1.6 How NMFS Intends to Use the Plan
ESA Recovery Plan: Snake River Sockeye Salmon | 60

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 61

June 2015| NOAA Fisheries 

1. Introduction

NOAA’s National Marine Fisheries Service (NMFS) is required, pursuant to section 4(f) of the 

Endangered Species Act (ESA), to develop and implement recovery plans for species listed under the 

ESA. This is a recovery plan (Plan) for the protection and restoration of Snake River Sockeye Salmon

(Oncorhynchus nerka), proposed for listing on April 5, 1991 (56 FR 14055) and listed under the ESA as 

endangered on November 11, 1991 (56 FR 58619) (NMFS 1991); the listing was reaffirmed on June 28, 

2005 (NMFS 2005a). The anadromous and residual forms of Snake River Sockeye Salmon are listed 

under the ESA and are the focus of this Plan.

Historically, a number of lakes throughout the Columbia River basin supported Sockeye Salmon

production (Gustafson et al. 1997; Waples et al. 1991). Sockeye Salmon are native to the Snake River 

basin and historically were abundant in several lake systems in Idaho and Oregon. Today, the last 

remaining Snake River Sockeye Salmon spawn in Sawtooth Valley lakes high in the Salmon River 

drainage of the Snake River basin in Idaho. While very few Sockeye Salmon currently follow an 

anadromous life cycle, the small remnant run of the historical population migrates downstream from the 

lakes through the Salmon River, Snake River, and Columbia River to the ocean (Figure 1-1). After one

to three years in the ocean, they return as adults, passing once again through these mainstem rivers and 

through eight major Federal dams, four on the Columbia River and four on the lower Snake River. 

Anadromous Sockeye Salmon returning to Redfish Lake in Idaho’s Sawtooth Valley1 travel a greater 

distance from the sea (1,448 km [900 miles]) to a higher elevation (1,996 m [6,500 feet]) than any other 

Sockeye Salmon population in the world (Waples et al. 1991). They are the southernmost population of 

Sockeye Salmon (Bjornn et al. 1968; Foerster 1968).

Adult release into Redfish Lake. Photo: C. Kozfkey, IDFG.

 

1 Previous studies frequently did not differentiate the Stanley Basin from the Sawtooth Valley, or they called the whole area 

the Stanley Basin. In this Plan, the term “Sawtooth Valley” will be used to encompass both the Sawtooth Valley and the 

associated lakes, except where the Stanley Basin specifically is referred to.
ESA Recovery Plan: Snake River Sockeye Salmon | 62

June 2015| NOAA Fisheries 

Figure 1-1. Snake River Sockeye Salmon migration corridor, from estuary to Sawtooth Valley Lakes in Idaho.

Reports by Barton W. Evermann, an ichthyologist commissioned by the U.S. Bureau of Fisheries to 

investigate the status of salmon in the Snake and Columbia Basins, provide an indication of Sockeye 

Salmon abundance before the turn of the twentieth century. During his investigations, early settlers 

reported that many Sockeye Salmon returned to the Snake River basin (Evermann 1896; Selbie et al. 

2007). In fact, one of the major historical spawning areas, Redfish Lake, was named for the large 

numbers of Sockeye Salmon that returned to spawn each year turning the lake a shimmering red during 

the spawning season. Sockeye Salmon ascended the Snake River to the Wallowa, Payette, and Salmon 

River basins to spawn in natural lakes (Figure 1-2). Within the Salmon River basin, Sockeye Salmon

spawned in Warm Lake in the South Fork Salmon River basin, as well as in the Sawtooth Valley lakes: 

Stanley, Redfish, Yellowbelly, Pettit, and Alturas Lakes. A smaller Sawtooth Valley lake, Hell Roaring 

Lake, probably also supported some Sockeye Salmon production historically, but it may not have been 

large enough to support an independent population. Therefore, the lake is not included in the recovery 

strategy (ICTRT 2005a). The historical relationships between the different Snake River Sockeye Salmon

populations are not known. Because of the large geographic separation between the Wallowa, Payette, 

and Salmon River lakes, it is possible that each drainage supported a separate evolutionarily significant 

unit (ESU) (ICTRT 2005a). 

The Sockeye Salmon populations declined through the early- and mid-1900s. When ESA listing of 

Snake River Sockeye Salmon was completed in 1991, all of the Snake River Sockeye Salmon

populations but one, the Redfish Lake population in the Sawtooth Valley, were gone and that population 
ESA Recovery Plan: Snake River Sockeye Salmon | 63

June 2015| NOAA Fisheries 

had dwindled to fewer than 10 fish per year and was at a high risk of extinction. In 2003, the Interior 

Columbia Basin Technical Recovery Team (ICTRT) recognized the Redfish Lake population as the

single extant Sockeye Salmon population in the Snake River Sockeye Salmon ESU. In 2005, The 

ICTRT designated three historical Sockeye Salmon populations within the Sawtooth Valley; Redfish 

Lake, Alturas Lake, and Stanley Lake. They also determined that Pettit Lake and Yellowbelly Lake may 

have supported independent Sockeye Salmon populations but, because of the uncertainty, characterized 

these as potential populations. Accordingly, only the five Sockeye Salmon populations in the Sawtooth 

Valley are included in the listed Snake River Sockeye Salmon ESU.

Building on Early Recovery Efforts

In 1991, a group of agencies began collaborating to recover the species. The group’s near-term goal was 

to avoid extinction and to maintain remaining genetic diversity and population heterozygosity. In the 

long term they hoped to rebuild the population to facilitate delisting and to increase abundance to levels 

sufficient to support sport and tribal harvest needs. Central to this effort has been a captive broodstock 

program for the Redfish Lake population that has prevented extinction in the near term and preserved

the genetic lineage of Redfish Lake Sockeye Salmon. The program began with 16 remaining adult 

Sockeye Salmon ─ 11 males and 5 females ─ taken into captivity from 1991 to 1998. 

Today, the program continues to gain ground in reaching its goals. Using advanced aquaculture 

techniques, the 20-year program has retained about 95 percent of the species' remaining genetic 

variability, while releasing more than 3.8 million Sockeye Salmon eggs and fish into Sawtooth Valley 

lakes and streams. Further, the program has produced more than 10,000 adult descendants from the 

program’s initial 16 wild anadromous adult Sockeye Salmon (Kline and Flagg 2014). The program is 

coordinated by the Stanley Basin Sockeye Technical Oversight Committee (SBSTOC). SBSTOC 

members include representatives of the Idaho Department of Fish and Game (IDFG), Bonneville Power 

Administration (BPA), NMFS, Oregon Department of Fish and Wildlife (ODFW), the University of 

Idaho (UI), U.S. Forest Service (USFS or U.S. Forest Service), and the Shoshone-Bannock Tribes

(SBT). The program includes hatchery facilities in Idaho, Washington, and Oregon. 
ESA Recovery Plan: Snake River Sockeye Salmon | 64

June 2015| NOAA Fisheries 

Figure 1-2. Historical populations of Sockeye Salmon in the Snake River basin (NWFSC 2011).

Between 1999 and 2007, more than 355 adult Snake River Sockeye Salmon from captive broodstock 

releases returned to Redfish Lake from the oceanalmost 20 times the number of wild fish that returned 

in the 1990s (Flagg et al. 2004; Peterson et al. 2011). These returns have increased within the last seven

years, to 646 in 2008 (including 140 natural-origin fish), 832 in 2009 (including 86 natural-origin fish), 

1,355 in 2010 (including 178 natural-origin fish), 1,117 in 2011 (including 145 natural-origin fish), 257

in 2012 (including 52 natural-origin fish), 272 in 2013 (including 79 natural-origin fish), and 1,579 in 

2014 (including 453 natural-origin fish) (IDFG, in prep.). 

Nevertheless, the ESU cannot be said to be recovered until it is made up of natural-origin fish spawning 

in the wild and surviving their two-way journey in far greater numbers. This Plan identifies the 

minimum required number of annual natural adult Sockeye Salmon returns and the spatial distribution to 

the natal Sawtooth Valley lakes to support recovery. It also describes a set of strategies and actions to 

restore natural Sockeye Salmon populations in Sawtooth Valley lakes to levels that will achieve ESU 

recovery. 
ESA Recovery Plan: Snake River Sockeye Salmon | 65

June 2015| NOAA Fisheries 

This Plan identifies the conditions that led to the listing of Snake River Sockeye Salmon as an 

endangered species and the designation of critical habitat under the ESA, and builds upon the work of 

the Stanley Basin Sockeye Technical Oversight Committee and other ongoing Sockeye Salmon research 

and recovery efforts. The Plan presents the biological viability and threats criteria for assessing 

biological recovery and describes recovery strategies and actions to improve the Snake River Sockeye 

Salmon’s environment and long-term chances for survival. The Plan also presents other delisting 

considerations that will be used in future ESU delisting evaluations. 

1.1 Purpose of the Plan

The purpose of a recovery plan is to identify actions needed to restore threatened and endangered 

species to the point that the ecosystems upon which the species depend are conserved such that the ESU 

is self-sustaining in the wild and no longer need the protections of the ESA. A recovery plan serves as a 

roadmap for species recovery—it sets out where we need to go and how best to get there. Without a plan 

to organize, coordinate, and prioritize the many possible recovery actions on the part of Federal, state, 

and tribal agencies, local watershed councils and districts, and private citizens, our efforts may be 

inefficient or even ineffective. Prompt development and implementation of a recovery plan will help 

target limited resources effectively.

1.2 Endangered Species Act Requirements

Although recovery plans are guidance, not regulatory documents, the ESA clearly envisions recovery 

plans as the central organizing tool for guiding species’ recovery. Section 4(f) of the ESA requires that a 

recovery plan be developed and implemented for species listed as endangered or threatened under the 

statute. 

ESA section 4(a)(1) lists factors for delisting that are to be addressed in recovery plans:

A. The present or threatened destruction, modification, or curtailment of [the species’] 

habitat or range 

B. Over-utilization for commercial, recreational, scientific or educational purposes

C. Disease or predation

D. The inadequacy of existing regulatory mechanisms 

E. Other natural or human-made factors affecting its continued existence

ESA section 4(f)(1)(B) directs that recovery plans, to the maximum extent practicable, incorporate:

• a description of such site-specific management actions as may be necessary to achieve 

the plan’s goal for the conservation and survival of the species; 
ESA Recovery Plan: Snake River Sockeye Salmon | 66

June 2015| NOAA Fisheries 

• objective, measurable criteria which, when met, would result in a determination, in 

accordance with the provisions of this section, that the species be removed from the list; 

and

• estimates of the time required and the cost to carry out those measures needed to achieve 

the plan’s goal and to achieve intermediate steps toward that goal.

In addition, it is important for recovery plans to provide the public and decision makers with a clear 

understanding of the goals and strategies needed to recover a listed species and the science underlying 

those conclusions (NMFS 2006). 

Once a species is deemed recovered and therefore removed from a listed status, section 4(g) of the ESA 

requires monitoring of the species for a period of not less than five years to ensure that it retains its 

recovered status. 

1.3 Context of Plan Development

This Plan is the product of a collaborative process initiated by NMFS with contributions by a wide 

group of governments, sovereigns (tribes), and organizations with the potential to contribute to recovery. 

The goal was to produce a plan that meets NMFS’ ESA requirements for recovery plans as well as the 

State of Idaho’s needs. Participants included Idaho Department of Fish and Game, Shoshone-Bannock 

Tribes, NMFS’ Northwest Fisheries Science Center, members of NMFS’ Interior Columbia Technical 

Recovery Team (ICTRT), Bonneville Power Administration, Stanley Basin Sockeye Technical 

Oversight Committee, and the U.S. Forest Service. This Plan builds upon the ongoing efforts of the 

Technical Oversight Committee, including hatchery programs, research, restoration, and habitat 

assessment activities. 

This collaborative effort reflects NMFS’ belief that it is critically important to base ESA recovery plans 

on state, regional, tribal, local, and private conservation efforts already underway throughout the region.

Local support for recovery plans by those whose activities directly affect the listed species, and whose 

actions will be most affected by recovery measures, is essential. NMFS, therefore, supports and 

participates in locally led collaborative efforts to develop recovery plans, involving local communities, 

state, tribal, and Federal entities, and other stakeholders.
ESA Recovery Plan: Snake River Sockeye Salmon | 67

June 2015| NOAA Fisheries 

1.3.1 Recovery Domains and Technical Teams

Currently, 19 evolutionarily significant units (ESUs) and distinct population segments (DPSs)2 of 

Pacific salmon and steelhead in the Pacific Northwest are listed under the ESA as endangered or 

threatened. For the purpose of recovery planning for these species, the NMFS West Coast Region 

designated five geographically based “recovery domains”: Interior Columbia; Willamette-Lower 

Columbia; Puget Sound and Washington Coast; the Oregon Coast; and the Southern Oregon/Northern 

California Coast (Figure 1-3). The range of the Snake River Sockeye Salmon is in the Snake River subdomain of the Interior Columbia domain. 

For each domain, NMFS appointed a Technical Recovery Team (TRT) of scientists, nominated for their 

geographic and species expertise, to provide a solid scientific foundation for recovery plans. The charge 

of each TRT was to define the populations and major population groups (MPGs) within each ESU/DPS, 

develop recommendations on biological viability criteria for each ESU/DPS and its component 

populations, provide scientific support to local and regional recovery efforts, and provide scientific

evaluations of proposed recovery plans. The TRT responsible for Snake River Sockeye Salmon, the 

Interior Columbia Technical Recovery Team, includes biologists from NMFS and several states, tribal 

entities, and academic institutions.

All the TRTs used the same biological principles in developing their recommendations for species and 

population viability criteria—criteria to be used, along with criteria based on mitigation of the factors for 

decline, to determine whether a species has recovered sufficiently to be down-listed or delisted. The 

principles are described in NMFS’ technical memorandum, Viable Salmonid Populations and the 

Recovery of Evolutionarily Significant Units (McElhany et al. 2000). Viable salmonid populations 

(VSPs) are defined in terms of four parameters: abundance, population productivity or growth rate, 

population spatial structure, and diversity. A viable ESU or DPS is naturally self-sustaining, with a high 

probability of persistence over a 100-year time period. Each TRT made recommendations using the VSP 

framework. Their recommendations were also based on data availability, the unique biological 

characteristics of the species and habitats in the domain, and the members’ collective experience and 

expertise. Although NMFS has encouraged the TRTs to develop regionally specific approaches to 

evaluating viability and identifying factors limiting recovery, all the TRTs worked from a common 

scientific foundation.

 

2 An ESU of Pacific salmon (Waples et al. 1991; NMFS 1991) and a DPS of steelhead (NMFS 2006) are considered to be 

“species” as the word is defined in section 3 of the ESA. In addition, it should be noted that the terms “artificially 

propagated” and “hatchery” are used interchangeably in this Plan, as are the terms “naturally propagated” and “natural.”
ESA Recovery Plan: Snake River Sockeye Salmon | 68

June 2015| NOAA Fisheries 

Figure 1-3. Columbia Basin recovery domains for NMFS West Coast Region.

1.3.2 Snake River Sockeye Salmon Stakeholder Groups

In each recovery domain, NMFS has worked with state, tribal, local, and other Federal stakeholders to 

develop planning forums that build, to the extent possible, on ongoing locally led recovery efforts. 

While these forums are working from a consistent set of assumptions regarding needed recovery plan 

elements, the process by which they develop those elements, and the form they take, may differ among 

domains.

NMFS formed two stakeholder groups to assist in development of the Snake River Sockeye Salmon

recovery plan. First, in 2010 it created the Snake River Coordination Group with representatives from 

state, tribal and Federal governments and agencies to review and provide guidance to NMFS on 

development of the three recovery plans for the four Snake River species listed under the ESA. The 

Coordination Group has met periodically to review draft information as the recovery plan was developed 

and NMFS will edit the draft Plan based on comments received.

Second, in May 2012, NMFS formed the Snake River Sockeye Salmon Technical Team (Technical 

Team) made up of technical staff from state, tribal, and Federal entities. The Technical Team reviews

and provides input on technical content during writing, revision, and completion of the draft Plan.
ESA Recovery Plan: Snake River Sockeye Salmon | 69

June 2015| NOAA Fisheries 

1.4 Tribal Trust and Treaty Responsibilities

The salmon and steelhead that were once abundant in the watersheds throughout the Snake River basin 

were crucial to Native Americans throughout the region. Pacific Northwest Indian tribes today retain 

strong spiritual and cultural ties to salmon and steelhead, based on thousands of years of use for tribal 

religious/cultural ceremonies, subsistence, and commerce. Many Northwest Indian tribes have treaties 

reserving their right to fish in usual and accustomed fishing places, including areas covered by this 

recovery plan. Additionally, four Washington coastal tribes have treaty rights to ocean salmon harvest 

that may include some fish that are destined for the Snake River basin. These Columbia Basin and 

Washington coast treaty tribes are co-managers of salmon stocks, and participate in management 

decisions including those related to hatchery production and harvest. Some other tribes in the Columbia 

River basin, whose reservations were created by Executive Order, do not have reserved treaty rights but 

do have a trust relationship with the Federal government and an interest in salmon and steelhead 

management, including harvest and hatchery production. 

The NMFS Regional Administrator, in testimony before the U.S. Senate Indian Affairs Committee (June 

2003), emphasized the importance of this co-manager relationship: “We have repeatedly stressed to the 

region’s leaders, tribal and non-tribal, the importance of our co-management and trust relationship to the 

tribes. NMFS enjoys a positive working relationship with our Pacific Northwest tribal partners. We view 

the relationship as crucial to the region’s future success in recovery of listed salmon.” 

Native American treaty-reserved fishing rights in the Columbia Basin are under the continuing 

jurisdiction of the U.S. District Court for the District of Oregon in the case United States v. Oregon, No. 

68-513 (filed in 1968). In U.S. v. Oregon, the Court affirmed that the treaties reserved for the tribes up to 

50% of the harvestable surplus of fish destined to pass through their usual and accustomed fishing areas. 

The U.S. v. Oregon process has the potential to affect Snake River populations as some co-managing 

tribes assert their reserved fishing rights.

Restoring and sustaining a sufficient abundance of salmon and steelhead for harvest is important in 

fulfilling tribal fishing aspirations. It is NMFS’s policy to promote restoration of salmon and steelhead 

runs sufficient for tribal harvest. This policy is described in a July 21, 1998, letter from Terry D. Garcia, 

Assistant Secretary for Oceans and Atmosphere, U.S. Department of Commerce, to Mr. Ted Strong, 

Executive Director of the Columbia River Inter-Tribal Fish Commission (CRITFC). This letter states 

that recovery “must achieve two goals: 1) the recovery and delisting of salmonids listed under the 

provisions of the ESA; and 2) the restoration of salmonid populations over time, to a level to provide a 

sustainable harvest sufficient to allow for the meaningful exercise of tribal fishing rights.” 

Thus, it is appropriate for recovery plans to acknowledge tribal harvest goals. Where tribal harvest goals 

can only be met through hatchery production, recovery plans will identify strategies and actions to 

ensure the hatchery production is consistent with recovery of naturally spawning populations.
ESA Recovery Plan: Snake River Sockeye Salmon | 70

June 2015| NOAA Fisheries 

1.5 Recovery Planning Modules

NMFS has produced modules to assist in recovery planning for ESA-listed Columbia Basin salmon and 

steelhead species. These modules provide consistent information that can be referenced in speciesspecific recovery plans. Modules will be updated periodically to reflect new data. The following 

modules are incorporated into the Plan by reference: (1) Module for the Ocean Environment (hereafter

Ocean Module) (Fresh et al. 2014), (2) Columbia River Estuary ESA Recovery Plan Module for Salmon 

and Steelhead (herafter Estuary Module) (NMFS 2011a), (2) Supplemental Module for Snake River 

Salmon and Steelhead , Mainstem Columbia River Hydropower Projects (hereafter Hydro Module) 

(NMFS 2014a), and (4) Columbia River Harvest Module (hereafter Harvest Module) (NMFS 2014b).

These modules contain information specific to the four ESA-listed Snake River Salmon ESUs and 

Steelhead DPS, including Snake River Sockeye Salmon.

The Ocean Module (Fresh et al. 2014) uses the latest science to a) synthesize what is known about how 

each of the four listed Snake River species uses ocean ecosystems, b) identify major uncertainties 

regarding their use of the ocean environment, and c) define the role of the ocean in recovery planning 

and implementation of each species. The module is available on the NMFS web site: 

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/drft-sr-ocean-mod.pdf.

The Estuary Module (NMFS 2011a) discusses limiting factors and threats that affect all the salmonid 

populations in the mainstem Columbia River estuary and plume, and presents actions to address these 

factors. The 2011 Estuary Module was prepared for NMFS by the Lower Columbia River Estuary 

Partnership (contractor) and PC Trask & Associates, Inc. (subcontractor). It provides the basis of 

estuary recovery actions for ESA-listed salmon and steelhead in the Columbia River basin. This module 

is available on the NMFS web site: 

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/estuary-mod.pdf. This Plan 

summarizes actions identified in the Estuary Module to address threats to Snake River Sockeye Salmon. 

The Estuary Module discusses these actions in more detail.

NMFS completed the Hydro Module in June 2014 (NMFS 2014a). The document supplements the 2008 

Hydro Module for Snake River anadromous fish species listed under the ESA: Snake River steelhead, 

Snake River spring/summer Chinook salmon, Snake River fall Chinook salmon, and Snake River 

Sockeye Salmon (NMFS 2008a). The 2008 Hydro Module overviews limiting factors, summarizes 

current recovery strategies, and provides survival rates associated with the Federal Columbia River 

Power System (FCRPS). The FCRPS consists of 14 Columbia and Snake River hydropower and water 

storage projects that are operated as a coordinated system for power production and flood control. The 

2014 Snake River Hydro Module provides new information relevant to the Snake River species, 

including the most recent survival estimates and discussion of latent and delayed mortality. The Snake 

River Hydro Module is available on the NMFS web site: 

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/drft-sr-hydro-mod.pdf.
ESA Recovery Plan: Snake River Sockeye Salmon | 71

June 2015| NOAA Fisheries 

The 2014 Harvest Module describes fishery policies, programs, and actions affecting the fish species 

covered by the Snake River Recovery Plan (NMFS 2014b). The Harvest Module is available on the 

NMFS web site: 

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/drft-sr-hrvst-mod.pdf.

A captive broodstock program for the Redfish Lake population has been successful in preventing 

extinction in the near term and preserving the genetic lineage of Redfish Lake Sockeye Salmon. The 

program is coordinated by the Stanley Basin Sockeye Technical Oversight Committee, which was 

formed in 1991 to guide new research, coordinate ongoing research, and actively participate in all 

elements of the Snake River Sockeye Salmon recovery effort (Baker et al. 2011; Lewis et al. 1998). 

Stanley Basin Sockeye Technical Oversight Committee members include representatives of the 

Bonneville Power Administration, NMFS, Idaho Department of Fish and Game, the University of Idaho, 

U.S. Forest Service, and the Shoshone-Bannock Tribes, with hatchery facilities in Idaho, Washington, 

and Oregon. 

Hatchery effects on Sockeye Salmon and potential actions contributing to recovery are also discussed in 

NMFS’ Appendices C and D of the Supplemental Comprehensive Analysis (SCA) of the FCRPS 

Biological Opinion (NMFS 2008b). Additional actions will likely be identified through the Hatchery 

Scientific Review Group’s work and in hatchery management plans (Paquet et al. 2011). These 

hatchery reform proposals will be addressed and implemented through the development of Hatchery and 

Genetic Management Plans (HGMPs), ESA section 7 consultations, and the U.S. v. Oregon process. 

1.6 How NMFS Intends to Use the Plan

Although recovery plans are not regulatory and their implementation is largely voluntary, they are 

important tools that help to do the following:

• Provide context for regulatory decisions.

• Guide decision making by Federal, state, tribal, and local jurisdictions.

• Provide criteria for status reporting and delisting decisions.

• Organize, prioritize, and sequence recovery actions.

• Organize research, monitoring, and evaluation efforts.

NMFS will encourage Federal agencies and non-Federal jurisdictions to take recovery plans under 

serious consideration as they make the following sorts of decisions and allocate their resources:

• Actions by federal agencies carried out to meet their ESA section 7(a)(1) obligations to 

use their programs in furtherance of the purposes of the ESA and to carry out programs 

for the conservation of threatened and endangered species.
ESA Recovery Plan: Snake River Sockeye Salmon | 72

June 2015| NOAA Fisheries 

• Actions that are subject to ESA sections 4(d), 7(a)(2), or 10.

• Hatchery and Genetic Management Plans and permit requests.

• Harvest plans and permits.

• Selection and prioritization of subbasin planning actions.

• Development of research, monitoring, and evaluation programs.

• Revision of land use and resource management plans.

• Other natural resource decisions at the state, tribal, and local levels.

NMFS will emphasize recovery plan information in ESA section 7(a)(2) consultations, section 10 permit 

development, and application of the ESA section 4(d) Rule by considering:

• The importance of affected populations to listed species viability.

• The importance of the action area to affected populations and species viability.

• The relation of the action to recovery strategies and management actions.

• The relation of the action to the research, monitoring, and evaluation plan for the affected 

species.

In implementing these programs, recovery plans will be used as a reference and a source of context, 

expectations, and goals. NMFS staff will encourage the Federal Action Agencies to describe in their 

biological assessments how their proposed actions will affect specific populations and limiting factors 

identified in the recovery plans, and to describe any conservation measures and voluntary recovery 

activities in the action area.
ESA Recovery Plan: Snake River Sockeye Salmon | 73

June 2015| NOAA Fisheries 

Section 2: Biological Background

2.1 Geographic Setting

2.2 Sockeye Salmon Overview

2.3 Snake River Sockeye Salmon

2.4 Critical Habitat

2.5 Salmonid Biological Structure

2.6 Viable Salmonid Populations
ESA Recovery Plan: Snake River Sockeye Salmon | 74

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 75

June 2015| NOAA Fisheries 

2. Biological Background

This section provides a summary of the Snake River Sockeye Salmon ESU: its geographic 

setting, overview of the ESU, life history, distribution, and designated critical habitat. The 

section also reviews key concepts in salmonid biology, i.e. the hierarchical structure of salmonid 

species, from independent population to major population group to evolutionarily significant 

unit; and the parameters that measure viability for salmonid populations: abundance, 

productivity, spatial structure, and diversity.

2.1 Geographic Setting 

The geographic setting for the Snake River Sockeye Salmon life cycle includes the Pacific 

Ocean, the Columbia River estuary, the mainstem Columbia River, the Snake River, the Salmon 

River, and the Sawtooth Valley lakes. Snake River Sockeye Salmon also migrate through eight 

major dams and their reservoirs (four on the Columbia River and four on the lower Snake River) 

more than any other Columbia Basin salmonids except Snake River fall Chinook salmon, Snake 

River Steelhead, Snake River Spring/Summer Chinook salmon and salmonids migrating above 

Wells Dam on the upper Columbia River (Figure 2-1).

Figure 2-1. Hydropower facilities on Snake River Sockeye Salmon migration route. 
ESA Recovery Plan: Snake River Sockeye Salmon | 76

June 2015| NOAA Fisheries 

The Snake River basin is characterized by dramatic changes in elevation, from 3,859 meters 

(12,662 feet) at Mount Borah in the headwaters of the Pahsimeroi basin to 104 meters (340 feet)

at the Snake River confluence with the Columbia River. Terrestrial habitats in the basin include 

high elevation deserts, alpine peaks, temperate rain forests, and the deepest river canyon in North 

America (Hells Canyon – 2,346 m. [7,993 ft.] from the rim at its deepest point). Temperatures 

and precipitation vary widely, usually depending on elevation, with cooler and wetter climates in 

the mountainous areas and warmer and drier climates in the lower elevations. 

Within the Snake River basin, land use varies from wilderness to agriculture and rangeland to 

developed cities. The Snake River basin contains the largest contiguous wilderness in the lower 

48 states. Of the 83 square kilometers (31,862 square miles) of land in the Snake River recovery 

domain, 69.4% is federally owned, 24.3% is privately held, and 6.5% is state or tribal. Although

population growth in the basin is not keeping pace with other areas in the Pacific Northwest, 

development is occurring and tends to be concentrated in the valley bottoms. The twin port cities 

of Lewiston, Idaho and Clarkston, Washington at the confluence of the Snake and Clearwater 

Rivers send inland commodities such as wheat and forest products downriver and receive 

industrial products such as gasoline and other fuel oils from downstream sources (Makaryan et 

al. 2005). Figure 2-2 shows land use and cover in the Snake River basin.

The Sawtooth Valley, where the only extant Snake River Sockeye Salmon spawn, is a scenic, 

glaciated intermontane basin bordered on the west by the Sawtooth Mountains and on the east by 

the White Cloud Mountains. The Sawtooth Mountains are part of the Idaho batholith, made up of 

granite-like rock, consisting of granodiorite, quartz diorite, and quartz monzonite (Emmett 

1975). The Stanley Basin lies in the northern portion of the Sawtooth Valley and is the location 

of the small town of Stanley, Idaho. The Sawtooth Valley lakes, carved by glaciers, receive 

runoff from the Sawtooth Mountains and drain to the upper Salmon River. The upper Salmon 

River runs south to north through the Sawtooth Valley, from its headwaters high in the Sawtooth 

range. Elevation in the valley and basin varies between 1,890 and 2,134 meters (6,200 and 7,000

feet), while many of the surrounding peaks rise above 3,048 meters (10,000 feet). The climate is 

characterized by severe winter weather and dry, hot summers. Vegetation varies with altitude, 

soils, and exposure; lodgepole pine and aspen groves predominate in the higher altitudes, while 

sagebrush and grass cover the hills formed by moraines and the alluvial flats.
ESA Recovery Plan: Snake River Sockeye Salmon | 77

June 2015| NOAA Fisheries 

Figure 2-2. Land use and cover in the Snake River basin.

The five Sawtooth Valley lakes that historically supported Sockeye Salmon ─ Stanley Lake, 

Redfish Lake, Yellowbelly Lake, Pettit Lake, and Alturas Lake ─ range in elevation from 1,985 

m to 2,157 m (6,512 ft to 7,077 ft), and are located in central Idaho (Figure 2-3). A neighboring 

smaller Sawtooth Valley lake, Hell Roaring Lake, also probably supported some Sockeye 

Salmon production at one time. NMFS did not include this lake in the recovery strategy because 

it may not have been large enough to support an independent population.

The lakes lie at the western edge of the Sawtooth Valley and south of the town of Stanley, except 

Stanley Lake, which is slightly to the north and west of the Sawtooth Valley. They all drain into 

the upper Salmon River mainstem. The lakes are oligotrophic (low in nutrients) but high in 

oxygen, especially in the depths. They are underlain by granitic bedrock. Redfish Lake is the 

largest, at 615 hectares (1,520 acres), and Alturas is next largest, with about half the area. Table 

2-1 shows the surface area, depth, and other characteristics of the lakes. Redfish Lake is 

approximately 1,450 km (900 miles) from the mouth of the Columbia River. There are 616 km 
ESA Recovery Plan: Snake River Sockeye Salmon | 78

June 2015| NOAA Fisheries 

(380 miles) of free-flowing river from Redfish Lake to the mouth of the Salmon River and an 

additional 835 km (520 miles) impacted by eight dams on the Snake and Columbia Rivers.

Figure 2-3. Map of the Sawtooth Valley, Idaho.
ESA Recovery Plan: Snake River Sockeye Salmon | 79

June 2015| NOAA Fisheries 

Table 2-1. Physical and morphometric characteristics of the Sawtooth Valley lakes (BPA 1995).

Lake Surface 

Area (ha)

Elevation 

(m)

Volume 

(m3 x 106)

Mean Depth 

(m)

Maximum 

Depth (m)

Drainage 

Area (km2)

Redfish Lake 615 1,996 269.9 44 91 108.1

Alturas Lake 338 2,138 108.2 32 53 75.7

Pettit Lake 160 2,132 45.0 28 52 27.4

Stanley Lake 81 1,985 10.4 13 26 39.4

Yellowbelly Lake 73 2,157 10.3 14 26 30.4

Land use in the Sawtooth Valley is primarily recreation, with some ranching. Land ownership is 

90% Federal and 6% private, with a very small amount owned by the state of Idaho (Figure 2-4). 

The Sawtooth National Recreation Area (Sawtooth NRA), administered by the U.S. Forest 

Service, encompasses the Salmon River corridor from its headwaters to Stanley; the Sawtooth 

Valley and surrounding lakes; and the eastern foothills of the Sawtooth Mountains and western 

portion of the White Cloud Mountains. The Sawtooth NRA lies in Custer, Blaine, and Boise 

Counties. It encompasses roughly 3,150 km2 (778,000 acres), of which the U.S. Forest Service

administers 89%. Another 10% is private land and 1% is state land (USFS 2003). Virtually all of 

the private and state inholdings lie along the Salmon River or Valley Creek corridors. The 

Sawtooth Valley lakes and Redfish Lake in particular, are recreational destinations and are 

highly valued for their scenic qualities and clear water. In the summer, the area is used for 

fishing, boating, hiking, picnicking, and camping, and in the winter, for cross-country skiing, 

snowmobiling, and other outdoor activities.

The vision for the Sawtooth NRA is embodied in its enabling legislation, the Sawtooth National 

Recreation Area Act (PL 92-400). PL 92-400 identifies the specific values and purposes that the 

Sawtooth NRA is to emphasize. On August 22, 1972 Congress passed PL 92-400 to establish the 

Sawtooth NRA “...in order to assure the preservation and protection of the natural, scenic, 

historic, pastoral, and fish and wildlife values and to provide for the enhancement of the 

recreation values associated therewith...” These features are often referred to as the Sawtooth 

NRA’s “core values.” The vision of PL 92-400 tips the balance toward protection and 

preservation. Some development and use is welcome, but it must not “substantially impair” the 

primary values. The restoration of the salmon and other fisheries was one of the key purposes for 

establishing the Sawtooth NRA.
ESA Recovery Plan: Snake River Sockeye Salmon | 80

June 2015| NOAA Fisheries 

Figure 2-4. Land ownership in the spawning range of the Snake River Sockeye Salmon ESU.

Until recently, hatchery rainbow trout were stocked in Redfish, Alturas, Pettit, and Stanley 

Lakes. Currently, only Alturas and Stanley Lakes are stocked. Sport fishing for salmonid fishes 

is open during specified fishing seasons on all lakes as well as on inlet and outlet streams.

As described in Selbie et al. 2007, “Redfish Lake has a large, relatively pristine watershed that 

drains from the granitic Sawtooth Mountains. Lower elevation portions of the drainage area are 

vegetated and support a mixed aspen and coniferous forest (Wurtsbaugh et al. 1997). Redfish 

Lake is a steep-sided system of Pleistocene glacial origin (deglaciation occurred by about 14,000 

years before the present), impounded behind a large glacial moraine (Killsgaard et al. 1970; Alt 

and Hyndman 1989; Thackray et al. 2004). Redfish Lake is classified as an ultraoligotrophic 

lake system. The paleolimnological data are in agreement with this and indicate that the lake was 

consistently oligotrophic throughout the past 500 years.” The other Sawtooth Valley lakes are 

physically, geologically, and visually quite similar to Redfish Lake. 

2.2 Sockeye Salmon Overview

All Pacific salmon belong to the family Salmonidae and the genus Oncorhynchus. Sockeye 

Salmon are the species Oncorhynchus nerka. Snake River Sockeye Salmon are an ESU of O. 

nerka. ESUs are defined based on geographic range as well as genetic, behavioral, and other 
ESA Recovery Plan: Snake River Sockeye Salmon | 81

June 2015| NOAA Fisheries 

traits. Sockeye Salmon are the second most abundant of the seven Pacific salmon species (Quinn 

2005). 

The vast majority of Sockeye Salmon populations spawn in or near lakes. Spawning can take 

place in lake tributaries, lake outlets, rivers between lakes, and on lake shorelines or beaches 

where suitable upwelling or intra-gravel flow is present. Spawn timing is often determined by 

water temperature. In spawning habitats with cooler water temperatures, Sockeye Salmon

typically spawn earlier (August) than in warmer habitats (November) (Burgner 1991). Sockeye 

Salmon fry spawned in lake tributaries typically exhibit a behavior of rapid downstream or 

upstream migration to the nursery lake after emergence, whereas lake/beach spawned Sockeye 

Salmon rapidly migrate to open limnetic waters after emergence. Lake-rearing juveniles typically 

spend 1 to 2 years in their nursery lake before emigrating to the marine environment (Gustafson 

et al. 1997). 

Upon smoltification, Sockeye Salmon emigrate to the ocean. Peak emigration to the ocean 

occurs in mid-April to early May in southern Sockeye Salmon populations (<52oN latitude) and 

as late as early July in northern populations (62oN latitude) (Burgner 1991). Upon entering 

marine waters, Sockeye Salmon may reside in the nearshore or coastal environment for several 

months but are typically distributed offshore by fall (Burgner 1991). Section 2.3.2 provides a 

detailed description of the life history characteristics specific to Snake River Sockeye Salmon. 

In North America, Sockeye Salmon spawn from the Columbia River north to the Noatak River in 

Alaska, but historically ranged as far south as the Sacramento River (California) and as far north 

as Kotzebue Sound (Alaska) (Atkinson et al. 1967; Burgner 1991). Sockeye Salmon in 

commercially important numbers occur only from the Columbia River to the Kuskokwim River 

in the Bering Sea (Foerster 1968; Burgner 1991; Quinn 2005). In the Western Pacific, Sockeye 

Salmon can be found from the Kuril Islands (Japan) to Cape Chaplina (Russia) (Burgner 1991; 

Gustafson et al. 1997). 

2.3 Snake River Sockeye Salmon

Five lakes in the Sawtooth Valley historically contained anadromous Sockeye Salmon: Alturas, 

Pettit, Redfish, Stanley, and Yellowbelly Lakes (Bjornn et al. 1968). Currently, only the Redfish 

Lake population, supported by a captive broodstock program, is considered extant (Figure 2-5).

However, reintroduction efforts have been ongoing in Redfish Lake since 1993, Pettit Lake since 

1995, and Alturas Lake since 1997 with Redfish Lake stock (Hebdon et al. 2004).

The Sawtooth Valley lakes support three forms of O. nerka:

• Anadromous Sockeye Salmon  Sockeye Salmon in the Sawtooth Valley 

generally display an anadromous life history strategy. They spend 1 to 2 years in 

nursery lakes before migrating to sea as smolts during the spring of the year. They
ESA Recovery Plan: Snake River Sockeye Salmon | 82

June 2015| NOAA Fisheries 

remain at sea for an additional one to three years before returning to natal areas to 

spawn (Bjornn et al. 1968; Foerster 1968; Groot and Margolis 1991). 

• Residual Sockeye Salmon  These Sockeye Salmon are genetically aligned with

the anadromous form but have adopted a resident life history pattern, remaining in 

freshwater to mature and reproduce. They mature earlier (males earlier than 

females) and at a smaller size than anadromous Sockeye Salmon and have a sex 

ratio biased toward males. They spawn in the vicinity of anadromous individuals. 

Due to the low carotenoid resources available in freshwater lakes, residuals are 

normally a dusky color at spawning rather than the more vibrant red/green of 

ocean return fish (Waples 1992, as referenced in Flagg et al. 1995). They can 

produce either resident or anadromous offspring (Rieman et al. 1994), but 

generally produce anadromous offspring (Ricker 1938; Foerster 1968; Groot and 

Margolis 1991). Residuals may act as a safety net against failure of year-classes 

at sea. They are ESA-listed along with the anadromous portion. 

• Kokanee  Kokanee are a type of O. nerka (O. nerka kennerlyi) that is 

genetically distinct from Sockeye Salmon and is not included in the Snake River 

ESA listing. Therefore, they are not the main focus of this recovery plan;

however, they represent important life history and spatial diversity and may 

contribute to recovery. Kokanee are a self-perpetuating, generally nonanadromous form of O. nerka that occurs in balanced sex-ratio populations and 

whose parents, for several generations back, have spent their whole lives in fresh 

water. Kokanee have adapted to the carotenoid-poor forage environment of lakes, 

appear more efficient than Sockeye Salmon at storing carotenoid, and have a 

vibrant red/green color at spawning (Waples 1992, as referenced in Flagg et al. 

1995). Kokanee are generally a resident fish and mostly segregated from Sockeye 

Salmon during spawning, both temporally and spatially. However, in Alturas 

Lake the early stream spawning kokanee produce considerable numbers of smolts

and some anadromous adult returns.

The five Sawtooth Valley lakes support different forms of O. nerka:

Redfish Lake

Redfish Lake remains the only lake with returning anadromous Sockeye Salmon adults. The lake 

supports both anadromous and residual Sockeye Salmon, as well as a genetically distinct and 

non-ESA-listed form of native kokanee. Kokanee in Redfish Lake are segregated from 

anadromous and residual Sockeye Salmon during spawning, both temporally and spatially. The 

anadromous and residual forms are shoal spawners that reproduce in the lake in late September 

and October, whereas kokanee spawn in a tributary to the lake in August and early September 

(Peterson et al. 2011). Kokanee are native to Redfish Lake; the previous stocking from a range 

of hatchery sources beginning in 1930 and continuing through 1972 (Bowler 1990) has appeared 

to have no lasting impacts (Waples et al. 2011).
ESA Recovery Plan: Snake River Sockeye Salmon | 83

June 2015| NOAA Fisheries 

Stanley Lake

While anadromous Sockeye Salmon were historically indigenous to Stanley Lake, an artificial 

fish passage barrier below the lake’s outlet has prevented recolonization of the lake by 

anadromous Sockeye Salmon since its installation in 1956. The lake continues to support two 

kokanee populations, one native and one non-native. Recent data analysis suggests that the 

current population constitutes a native population of kokanee with low levels of non-native 

introgression and a non-native stock descended from the introduction(s) of Wizard Falls stock 

kokanee (Kozfkay 2013a). 

Yellowbelly Lake

Yellowbelly Lake historically contained Sockeye Salmon but currently O. nerka, Sockeye 

Salmon or kokanee, are not present in the lake. The lake’s historical Sockeye Salmon population 

likely displayed anadromous and residual life history strategies. Prior passage issues existed at 

the outlet stream due to an outlet barrier constructed by IDFG in 1962. The U.S. Forest Service

removed the barrier in 2000 to reestablish connectivity with the mainstem Salmon River. 

Biologists reported in 1968 that fish found in the lake following chemical treatment appeared to 

be residual Sockeye Salmon (Bjornn et al. 1968). There is no record of Sockeye Salmon or 

kokanee salmon stocking in the lake.

Pettit Lake

Pettit Lake historically supported an anadromous Sockeye Salmon population but an outlet 

barrier prevented all upstream fish migration from 1960 until 1996 when the barrier was 

removed by the Shoshone-Bannock Tribes. The downstream Salmon River mainstem weir at 

Sawtooth Hatchery continues to prevent anadromous returns to Alturas, Pettit, and Yellowbelly 

Lakes. Since 2000, a residualized/anadromous Sockeye Salmon population appears to be 

developing in Pettit Lake from reintroductions of Redfish Lake stock (egg boxes, pre-smolts). In 

addition, the Shoshone-Bannock Tribes have captured unmarked outmigrants at a fish trap below 

the lake. These fish were most likely produced from the descendants of fish introduced in eggboxes or as pre-smolts that residualized in the lake. Kokanee are also native to Pettit Lake; 

however, genetic analyses indicate that the native population of kokanee may have been 

completely replaced by non-native introductions of kokanee from northern Idaho (Winans et al.

1996; Waples et al. 2011).

Alturas Lake

Alturas Lake supports a native predominately resident population of kokanee (not ESA listed)

that also produces anadromous O. nerka. The lake has also received reintroductions of Redfish 

Lake Sockeye Salmon, primarily through pre-smolt and egg-box releases. It is not uncommon 

for these anadromous O. nerka to outmigrate as one- or two-year old smolts during the typical 

spring smolt outmigration window. Adults produced from these experimental releases were not 

provided direct access back to Alturas Lake from 1991 to 2014; however, one fish was released 

into Alturas Lake in 2011 following genetic confirmation. In addition to these adults, 
ESA Recovery Plan: Snake River Sockeye Salmon | 84

June 2015| NOAA Fisheries 

approximately 20 Sockeye Salmon of Alturas Lake-origin (anadromous offspring of early stream 

spawning kokanee) have been identified at the Sawtooth Fish Hatchery weir as early-returning 

anadromous adults since the inception of the program in 1991 (IDFG, in prep.). The anadromous 

Alturas Lake O. nerka population exhibits an earlier spawn time than the Redfish Lake Sockeye 

Salmon population. Studies indicate that kokanee from Redfish and Alturas Lakes are 

genetically similar (Monan 1991). 

Figure 2-5. The Snake River Sockeye Salmon ESU with current status designations (Ford 2011).

2.3.1 Recent History

It is not known what proportion of all Snake River Sockeye Salmon, including those from the 

Payette and Grande Ronde River systems, originated in the Sawtooth Valley. Historically, 

Sawtooth Valley lakes and streams were described as “teeming with redfish” (Evermann 1895), 

but numerical estimates are not available (Spaulding 1993). Evermann reported that in 1881, 

nearly 1,360 kgs (3,000 lbs) of Sockeye Salmon were harvested from Alturas Lake for mining 

camps, and there were plans to build a cannery at Redfish Lake (Evermann 1895, cited by 

Bowles and Cochnauer 1984). Historical evidence from upstream anglers suggests that 

noticeable reductions in upriver spawner returns to Idaho coincided in the 1890s with the peak of 

the downriver commercial harvest of Sockeye Salmon from the entire Columbia and Snake River 
ESA Recovery Plan: Snake River Sockeye Salmon | 85

June 2015| NOAA Fisheries 

basins. More than 1.1 to 1.3 million Sockeye Salmon were harvested annually during that period

(Evermann 1895; Beiningen 1976).

Selbie et al. (2007) noted that “The intensification of the commercial fishery occurred 

concurrently with other documented negative human influences on salmon in the Columbia 

River basin, including mining, logging, and agriculture (Beiningen 1976). As such, it is difficult 

to attribute the trends . . . solely to the effects of the commercial harvest.” However, Selbie et al. 

(2007) conducted paleolimnological studies in the Sawtooth Valley lakes, finding corroborating

evidence “that the onset of a decline in Snake River Sockeye Salmon was concurrent with the 

inception and intensification of the commercial fishery, and it probably had a substantial early 

and persistent negative influence on these fish” (Selbie et al. 2007).

In 1910, Sunbeam Dam was constructed on the Salmon River approximately 32.1 kilometers (20 

miles) downstream of Redfish Lake. Although it is generally believed that Sunbeam Dam largely 

prevented adult Sockeye Salmon from returning to the Sawtooth Valley from 1910 to 1934 

(Chapman et al. 1990), it has also been hypothesized that some passage occurred while the dam 

was in place, allowing the Sawtooth Valley population or populations to persist (see Bjornn et al. 

1968; Waples et al. 1991). Sockeye Salmon runs to Redfish Lake may have been sustained by an 

inadequate fish ladder and a diversion tunnel through the dam (Waples et al. 1991), downstream 

lakes (e.g., Sullivan Lake) functioning as refugia (Foerster 1968), and/or residual outmigrants 

from Redfish Lake. In 1934, the 9.1 meter-high (30-foot) Sunbeam Dam was partially removed. 

Sunbeam Dam currently poses no migration problem.

An irrigation diversion on Alturas Creek is thought to have blocked the entire adult Sockeye 

Salmon migration to Alturas Lake and also entrained juvenile outmigrants from 1914 until the 

Sawtooth National Forest purchased the water right in 1992. The U.S. Forest Service removed 

and rehabilitated the headgate, screen and ditch in 1997 (Chapman et al. 1990). The early stream 

spawning kokanee population in Alturas Lake continues to produce smolts and some 

anadromous adult returns in spite of the fact that anadromous adults have had little to no access 

to the lake for approximately 100 years. Adult Sockeye Salmon returns to Alturas Lake that 

were produced by the early stream spawning kokanee include one fish in 2002, one fish in 2008,

two fish in 2009, fourteen fish in 2010 and two fish in 2011. No adult Sockeye Salmon returned 

to Alturas Lake in 2012, 2013, or 2014 (IDFG, in prep: see Table 4-1). 

From 1954 to 1990, the IDFG chemically treated Pettit, Stanley, Yellowbelly, and Hell Roaring 

Lakes to eradicate Sockeye Salmon and other unwanted species, preparatory to planting the lakes 

with trout. (Stanley Lake was treated with Rotenone. Yellowbelly and Pettit Lakes received 

Toxaphene treatments in the 1950s and 1960s. Yellowbelly Lake was treated a second time with 

Rotenone in 1990. Stanley Lake was treated with Fish-Tox (a compound that is a mix of 

Toxaphene and Rotenone)). Hell Roaring Lake was chemically treated in 1970. The IDFG then 

built permanent structures on each of these three lake outlets to prevent re-entry of anadromous 

Sockeye Salmon (Chapman and Witty 1993). A fish barrier may have been constructed in the 
ESA Recovery Plan: Snake River Sockeye Salmon | 86

June 2015| NOAA Fisheries 

outlet stream to Hell Roaring Lake using natural materials (M. Moulton, personal 

communication). Redfish and Alturas Lakes were not chemically treated. 

In the 1990s, non-game fish barriers were removed from the outlet of Yellowbelly Lake by the 

Sawtooth National Forest (USFS 2011) and from the outlet of Pettit Lake by the ShoshoneBannock Tribes. The fish barrier on Alturas Lake Creek (an irrigation intake) was also removed 

(Teuscher and Taki 1996, cited in Flagg et al. 2004). The only remaining non-game fish barrier 

is on Stanley Lake Creek. However, the Sawtooth Fish Hatchery weir prevents Sockeye Salmon 

from accessing Alturas, Pettit, Yellowbelly, and Hell Roaring Lakes.

From 1960 to 1973, commercial and tribal Sockeye Salmon fisheries in the Columbia River 

harvested an average of 35,956 fish per year. In that period, returns to Redfish Lake declined by 

about 85%, from an average of about 1,250 fish to about 170 (Bjornn et al. 1968). Commercial 

fisheries were closed from 1974 to 1983 (NMFS 1991). During the commercial closure, tribal 

harvest averaged approximately 1,000 fish annually. Snake River Sockeye Salmon may have 

been susceptible to proportionately higher harvest rates than other stocks because of their low 

abundance relative to other Sockeye Salmon populations and also because Redfish Lake Sockeye 

Salmon are relatively large compared to other Columbia River stocks and harvest practices 

selected for larger fish (Bjornn et al. 1968). Although little data are available on exploitation 

rates specific to Snake River Sockeye Salmon, the NMFS listing decision noted commercial 

fisheries on Sockeye Salmon in the lower Columbia River and historical harvest on the spawning 

grounds as primary factors for decline of the ESU (NMFS 1999a). Recreational fishing impacts 

were considered negligible.

The construction of Federal dams on the Columbia and Snake Rivers from 1938 to 1975

presented further challenges to the Sockeye Salmon returning to Redfish Lake (Figure 2-1). A 

description of limiting factors and threats related to hydropower and water storage projects is

described in Section 5.2 and in NMFS’ Hydro Module (NMFS 2014a).

2.3.2 Life History

Historically, adult Snake River Sockeye Salmon entered the Columbia River in June and July, 

migrated upstream through the Snake and Salmon Rivers, and arrived at the Sawtooth Valley

lakes in August and September (Bjornn et al. 1968). Spawning in lakeshore gravels peaked in 

October. Fry emerged in late April and May and moved immediately to the open waters of the 

lake where they feed on plankton for one to three years before migrating to the ocean. Juvenile 

Sockeye Salmon generally left the Sawtooth Valley lakes from late April through May and 

migrated nearly 900 miles to the Pacific Ocean. While pre-dam reports indicate that Sockeye 

Salmon smolts passed through the lower Snake River in May and June, passive integrated 

transponder (PIT)-tagged smolts from Redfish Lake recently passed Lower Granite Dam from 

mid-May to mid-July (SCA, NMFS, 2008b). Collaborative PIT tag and radiotelementry studies 

conducted by NMFS and IDFG during the 2012 and 2013 outmigration determined that median 
ESA Recovery Plan: Snake River Sockeye Salmon | 87

June 2015| NOAA Fisheries 

travel time for Sawtooth and Oxbow Hatchery releases was approximately 7 days to Lower 

Granite Dam (Axel et al. 2013, 2014).

Figure 2-6. Historical Snake River Sockeye Salmon Life Cycle.

For hatchery juvenile Sockeye Salmon, estimated survival between the Sawtooth Valley and 

Lower Granite Dam has been highly variable between release locations, rearing strategies, 

origin, and years. Measuring the magnitude of mortality, as well as determining where, when

and why mortality is occurring, is critical to successful restoration and recovery of endangered 

Snake River Sockeye Salmon. Based on detections of Sockeye Salmon hatchery juveniles 

tagged with a PIT-tag and released in spring, estimates of survival to Lower Granite Dam have 

ranged from 0.114 in 2000 (Zabel et al. 2001) to 0.776 in 2008 (Faulkner et al. 2008). The 

tagging studies indicate that timing of juvenile migration may influence survival. For example, 

for groups of PIT-tagged fish released to Redfish Lake Creek in 2013, estimated survival to 

Lower Granite Dam ranged 51.0% to 59.2%, with earliest released fish groups often 

experiencing the highest mortality (Axel et al. 2014). Study findings also indicate that a large 

portion of the observed mortality is occurring in reaches of the upper Salmon River, with 
ESA Recovery Plan: Snake River Sockeye Salmon | 88

June 2015| NOAA Fisheries 

physical observations of removal by bull trout Salvelinus confluentus, osprey Pandion haliaetus, 

common mergansers Mergus merganser, and western grebes Aechmophorus occidentalis.

Snake River Sockeye Salmon enter the estuary at a large size as a result of the long time they 

spend in the natal lakes before emigrating as juveniles to the ocean. Although they experience 

significant mortality in the Columbia River estuary, juvenile Snake River Sockeye Salmon are 

presumably affected to a lesser degree by limiting factors and threats in the estuary because of

their shorter residency times in the reach (NMFS 2011a). Snake River Sockeye Salmon spend 

the majority of their life in the Pacific Ocean, generally returning as four-year old or older fish 

to their natal Sawtooth Valley lake to spawn. Similar to many species of salmon, some 

anadromous O. nerka return as three-year-olds, which are referred to as jacks or jills, depending 

on their sex. 

Brannon et al. (1994) reported that the anadromous Sockeye Salmon spawned only along a 400-

meter section of shallow beach on the northeast shoreline of Redfish Lake during the months of 

October and November. Current spawning locations for anadromous and residual Sockeye 

Salmon include: (1) the transfer dock area near the inlet of Redfish Lake Creek at the southwest 

corner of the lake, (2) a small section of substrate at the southeast corner of Redfish Lake Creek, 

(3) the southern snorkel transect, also at the southern end of Redfish Lake; (4) Sockeye Beach at 

the northeastern end of the lake, and recently (5) Fishhook Creek (Figure 2-7) (IDFG 2013a). 
ESA Recovery Plan: Snake River Sockeye Salmon | 89

June 2015| NOAA Fisheries 

Figure 2-7. Spawning locations for Sockeye Salmon in Redfish Lake. 
ESA Recovery Plan: Snake River Sockeye Salmon | 90

June 2015| NOAA Fisheries 

2.3.3 Genetic Analyses

At the time of the first status review for Snake River Sockeye Salmon (Waples et al. 1991), the 

relationship between kokanee and Sockeye Salmon in Redfish Lake was uncertain. Monan 

(1991) concluded that kokanee from Redfish and Alturas Lakes were genetically similar but 

distinct from samples collected in other lakes in Idaho, Washington, and British Columbia. 

Waples et al. (1991) suggested that Redfish Lake Sockeye Salmon were genetically distinct from 

other Sockeye Salmon populations. 

After the first status review, genetic analyses were conducted that included adult anadromous 

Sockeye Salmon that returned to Redfish Lake and residual Sockeye Salmon. Adult Redfish 

Lake Sockeye Salmon samples collected from 1991, 1992, and 1993 were genetically distinct 

from Fishhook Creek kokanee, and similar to residual Sockeye Salmon samples (Waples et al. 

1997). Alturas Lake kokanee were most similar to Redfish Lake kokanee (Winans et al. 1996). 

Two important findings presented by Winans et al. (1996) were that 1) stock transfers of O. 

nerka in the Sawtooth Valley did not result in any substantial genetic effects and 2) Sawtooth 

Valley kokanee are genetically distinct from all other kokanee and Sockeye Salmon sampled in 

Idaho, Washington, and British Columbia. The dissimilarity between Fishhook Creek kokanee 

and anadromous and resident Sockeye Salmon was confirmed through analysis of mitochondrial 

DNA (Faler and Powell 2003). Waples et al. (2011) used variation at 64 allozyme loci to 

examine genetic relationships among 32 samples of Sockeye Salmon and kokanee from the 

Snake River basin and other North American locations. Results confirm findings from the 

previous studies, Griswold et al. (2012) provides an additional review.

Two gene pools of kokanee were identified in Stanley Lake (WCSBRT 2003; Waples et al. 

2011). One appears to have originated from introductions of Wizard Falls Hatchery (Oregon) 

kokanee and the other is a possible remnant of a native O. nerka population that survived 

Rotenone treatments in the 1950s and 1960s. Recent genetic analyses by the IDFG indicate that 

the native O. nerka population is still present within Stanley Lake, and that it has low levels of 

introgression from non-native introductions of kokanee (Kozfkay 2013a). In contrast, genetic 

analyses of Pettit Lake kokanee samples did not reveal any trace of the original O. nerka gene 

pool, and the current kokanee population spawning in the lake was traced to kokanee 

introductions from north Idaho lakes, whose origin was traced to Lake Whatcom (Washington) 

kokanee (WCSBRT 2003; Waples et al. 2011).

The ICTRT (2003) initially recognized a single extant Sockeye Salmon population in the Snake 

River ESU (Redfish Lake) but later (ICTRT 2005a) designated three historical Sockeye Salmon

populations within the Sawtooth Valley; Redfish Lake (including Little Redfish Lake), Alturas 

Lake, and Stanley Lake. They also determined that Pettit Lake and Yellowbelly Lake may have 

supported independent Sockeye Salmon populations, but because of the uncertainty, 

characterized these as potential populations. All five populations fall within the geographic area 

of the Snake River Sockeye Salmon ESU.
ESA Recovery Plan: Snake River Sockeye Salmon | 91

June 2015| NOAA Fisheries 

2.3.4 Lake Hydrology, Limnology, and Carrying Capacity

The Sawtooth Valley lakes are located on the east side of the relatively pristine, granitic 

Sawtooth Mountains with the majority of their watersheds designated as wilderness. The lakes 

were formed behind glacial moraines, are relatively deep and are classified as oligotrophic 

(Table 2-2). They are dimictic, mixing completely in the spring and fall, except for Pettit Lake, 

which is meromictic, meaning that it does not mix completely during spring and fall turnover. 

The lakes are thermally stratified during the summer and ice covered from December to early 

May. The lakes have no man-made hydraulic controls, thus water level elevation is relatively 

stable, with minor seasonal variation (Graves 2012.) There is no data available for water level 

elevations (Griswold 2013). Water and nutrient budgets were developed for Redfish Lake in 

1992 and 1993 (Gross 1995; Gross et al. 1998).

Table 2-2. Characteristics of Sawtooth Valley lakes with comparison to Lake Wenatchee and Lake Osoyoos 

(Columbia River basin lakes currently supporting natural Sockeye Salmon production) (BPA 1995).

Lake Elevation

M (ft.)

Secchi Reading

m (ft.)

Surface Area

hectares (acres)

Maximum Depth

m (ft.)

Stanley 1,985 (6,513) 7 (23) 81 (200) 26 (85)

Redfish 1,996 (6,548) 12 (39) 615 (1,519) 91 (299)

Alturas 2,138 (7,014) 10 (33) 338 (835) 53 (174)

Yellowbelly 2,157 (7,076) 9 (30) 73 (200) 26 (85)

Pettit 2,132 (6,996) 13 (43) 162 (400) 52 (171)

Lake Wenatchee 572 (1,877) 6.3 (21) 990 (2,446) 73 (240)

Lake Osoyoos 278 (912) 3.3 (11) 2,300 (5,683) 63 (207)

Researchers have conducted limnology studies in Redfish, Stanley, Yellowbelly, Pettit, and 

Alturas lakes since 1991. The studies help determine production potential and carrying capacity 

in the lakes for juvenile Sockeye Salmon. The Shoshone-Bannock Tribes monitor the 

limnological characteristics of the three largest lakes (Redfish, Pettit and Alturas) and have 

conducted similar research on Stanley Lake from 1993 to 2005 and Yellowbelly Lake during 

1992 and 1993. The monitoring program examines water temperature and dissolved oxygen 

profiles, water transparency, light penetration, nutrient concentrations, chlorophyll a

concentrations, phytoplankton and zooplankton abundance, biomass, and species composition. 

Monitoring shows that maximum surface water temperatures usually occur during July or August 

and range from approximately 17-20 o

C (62-68 °F). Mean seasonal (June-October) water 

temperatures between 0 and 10 m depth range from 10.7-15.8 oC (51-60 °F) for the four lakes

(Redfish, Pettit, Alturas, and Stanley) (Table 2-3). Mean surface water temperatures are 

inversely correlated with Salmon River discharge. Mean summer water transparencies (Secchi) 

range between 9.6 m and 15.2 m (31-50 ft) in Redfish, Pettit, and Alturas Lakes and 5.0-8.2 m 

(16-27 ft) in Stanley Lake. Mean summer total phosphorous concentrations in the epilimnion 
ESA Recovery Plan: Snake River Sockeye Salmon | 92

June 2015| NOAA Fisheries 

range from 4.9 to 11.8 ug/l. Seasonal mean epilimnetic chlorophyll a concentrations range from 

0.3 to 2.3 ug/l. For all lakes and years, epilimnetic chlorophyll a averages 0.8 ug/L without 

nutrient supplementation and 1.6 ug/L during years with nutrient supplementation. Algal 

productivity is generally considered low and limited by both nitrogen and phosphorus 

(Wurtsbaugh et al. 1997). Gross et al. (1992) conducted nutrient supplementation studies and 

conclude that it was unlikely that silicate or other micronutrients were controlling algal growth 

but could possibly become limiting with nutrient supplementation (N and P).

Table 2-3. Seasonal mean (June-October) water temperatures (oC) for 0-10 m depth (measured in 1 m intervals) for 

Redfish, Petti, Alturas, and Stanley Lakes, Idaho.

Surface temperature (oC ) 0-10m

Year Redfish Pettit Alturas Stanley

1992 14.9 15.1 14.7 14.7

1993 13.4 13.6 13.1 11.9

1994 14.7 15.6 14.3 14.6

1995 13.4 13.2 12.2 12.0

1996 12.0 12.2 11.5 10.7

1997 12.2 12.4 11.4 11.5

1998 13.3 13.6 12.6 11.8

1999 12.7 12.7 11.8 11.1

2000 14.2 14.4 13.8 12.4

2000 14.2 14.4 13.8 -

2001 14.3 14.8 14 -

2002 13.6 13.8 12.3 -

2003 13.9 13.7 12.9 -

2004 13.5 14 13.3 -

2005 14.1 13.7 13.1 -

2006 13.3 12.1 12.7 -

2007 13.9 13.6 13.6 -

2008 14.9 15.8 15.3 -

2009 13.9 13.2 13.1 -

2010 12.3 12.6 12.1 -

2011 12.1 12.3 11.9 -

Lake productivity is characterized by the existence of a seasonal, deep chlorophyll a maximum, 

probably due to a plunging inflow of colder, comparatively nutrient-enriched river water during 

the ice-free period. Planktonic algae are dominated by Chryso- and Cryptophycean nanoflagellates, autotrophic picoplankton, diatoms, and green algae (Budy et al. 1995; Griswold et al. 

2002). Primary productivity measurements were obtained in Redfish, Pettit, Alturas, and Stanley 
ESA Recovery Plan: Snake River Sockeye Salmon | 93

June 2015| NOAA Fisheries 

Lakes during 1993, 1995-1997, and 2002 to evaluate the effects of whole-lake nutrient 

supplementation (Griswold et al. 2002) and for use in the Photosynthetic Rate model (Shortreed 

et al. 2000). The Photosynthetic Rate model will be used to estimate the rearing capacity for 

juvenile Sockeye Salmon in Sawtooth Valley lakes. The model is based on a correlation 

between photosynthetic rate expressed as metric tons of carbon per year and Sockeye Salmon 

smolt biomass. From this, one can estimate the optimum spawning escapement and spring fry 

recruitment required to produce maximum smolt numbers and biomass.

Zooplankton biomass and species composition varies among lakes and over time (Figures 2-8

and 2-9). The presence of kokanee with highly variable annual escapement, particularly in 

Alturas Lake, creates “boom and bust” cycles that result in shifts in species abundance and 

composition. Zooplankton biomass, which is often the driver for Sockeye Salmon growth, is 

typically dominated by Daphnia rosea, calanoid copepods, and Bosmina longirostris with 

contributions from Holopedium gibberum, Polyphemus pediculus, and the calanoid copepod 

Epischura nevadensis (Budy et al. 1995; Griswold et al. 2002). 

Zooplankton data for Yellowbelly Lake is limited but Steinhart et al. (1993) reported that in 1992 

and 1993 the “highest zooplankton biomasses were observed in Yellowbelly and Pettit followed 

by Stanley Lake. The lowest total zooplankton biomass was observed in Redfish and Alturas 

Lakes in both years.” In 2007, zooplankton was sampled during September in Yellowbelly Lake 

and compared to several other Sawtooth Valley lakes. Results showed that zooplankton biomass 

was slightly lower in Yellowbelly than in Redfish and Pettit but the presence of large bodied 

Daphnia and calanoid copepods indicated low levels of planktivory (Figure 2-10). 

These data combined with O. nerka population data, such as rearing densities and size and 

growth of outmigrants, are beginning to provide insights into the relative carrying capacities for 

Sockeye Salmon production (e.g., Flagg et. al. 2004; Selbie et al. 2007). Detailed limnology 

methods and results can be found in the SBT annual reports to BPA (e.g. Kohler et al. 2000). 
ESA Recovery Plan: Snake River Sockeye Salmon | 94

June 2015| NOAA Fisheries 

Figure 2-8. Box and whisker charts depicting mean upper and lower quartile and range of zooplankton biomass over 

time (2000-2011) in Redfish, Pettit, and Alturas Lakes in the Sawtooth Valley, Idaho. (Shoshone-Bannock Tribes 

unpublished data).

Figure 2-9. Seasonal mean zooplankton biomass for the Sawtooth Valley lakes (June-October), 1996-2012. Zooplankton biomass (mg m2

)

0

500

1000

1500

2000

2500

3000

3500

Redfish Lake Pettit Lake Alturas Lake

0

500

1,000

1,500

2,000

2,500

3,000

3,500

Zooplankton biomass (mg/m2) .

Redfish Lake

Pettit Lake

Alturas Lake

Stanley Lake
ESA Recovery Plan: Snake River Sockeye Salmon | 95

June 2015| NOAA Fisheries 

Figure 2-10. Comparison of zooplankton biomass and weight of individual Daphnia sampled during September 

2007 in Redfish, Pettit, Alturas, and Yellowbelly Lakes, Idaho.

2.3.5 Other Fish Species

Native fish present in Sawtooth Valley waters include the following: Sockeye Salmon and 

kokanee O. nerka, Chinook salmon O. tshawytscha, rainbow trout/steelhead O. mykiss, 

westslope cutthroat trout O. clarkii lewisi, bull trout Salvelinus confluentus, sucker Catostomus

spp., northern pikeminnow Ptychocheilus oregonensis, mountain whitefish Prosopium 

williamsoni, redside shiner Richardsonius balteatus, dace Rhinichthys spp., and sculpin Cottus

spp. (Peterson et al. 2010). Kokanee live in Redfish, Alturas, Pettit, and Stanley Lakes. Bull 

Zooplankton biomass (ug/L) September 7-12, 2007

0

10

20

30

40

50

60

70

80

90

100

Redfish Pettit Alturas Yellowbelly

Zooplankton biomass (ug/L)

Cyclops

Calanoid

Polyphemus

Bosmina

Holopedium

Daphnia

Daphnia weight (ug) September 7-12, 2007

0

2

4

6

8

10

12

Redfish Pettit Alturas Yellowbelly 

Daphnia weight (ug/)
ESA Recovery Plan: Snake River Sockeye Salmon | 96

June 2015| NOAA Fisheries 

trout, pikeminnow and suckers are found in Redfish and Alturas Lakes. Alturas Lake includes 

whitefish at lower frequencies. 

Non-native species present in Sawtooth Valley waters include lake trout S. namaycush (Stanley 

Lake only), rainbow trout O. mykiss, and brook trout S. fontinalis. Yellowbelly Lake was 

chemically treated in 1990 to reduce brook trout populations and it was then stocked with 

westslope cutthroat trout. Non-native kokanee salmon were introduced into Pettit, Redfish, 

Alturas, and Stanley Lakes to establish non-native recreational sport fisheries. Kokanee are 

native to Pettit Lake, however, genetic analyses indicate that the native population of kokanee 

may have been completely replaced by non-native introductions of kokanee from northern Idaho 

(Winans et al. 1996). Stanley Lake continues to support two kokanee populations, one native 

and one non-native. Recent data analysis suggests that the current population constitutes a native 

population of kokanee with low levels of non-native introgression and a non-native stock 

descended from the introduction(s) of Wizard Falls stock kokanee (Kozfkay 2013a). 

According to Peterson et al. (2011), rainbow trout are released into Alturas and Stanley Lakes in 

the summer to increase sport fishing opportunities. Sport fishing on Alturas and Stanley Lakes is 

covered by Idaho’s statewide general fishing regulations, which allow harvest of 6 trout per day 

(excluding bull trout, which must be released if caught) and 25 kokanee per day with no seasonal 

closures. Beginning in 2011, trout stocking was discontinued in Pettit Lake (Peterson 2013a).

Sport fishing regulations on Redfish Lake restrict kokanee fishing/harvest to January 1 through 

August 7 to protect residual Sockeye Salmon. No trout have been stocked in Redfish Lake since 

1992 (Peterson et al. 2010).

Table 2-3. Fish species present in the Sawtooth Valley Lakes.

Fish Species Redfish Lake Alturas Lake Pettit Lake Stanley Lake Yellowbelly Lake

Sockeye salmon √ √ √

Kokanee √ √ √ √

Rainbow/steelhead √ √

W. cutthroat trout √

Bull trout √ √ √ √ √

Lake trout √

Brook trout √ √ √ √ √

Sucker √ √

N. Pikeminnow √ √

Mountain whitefish √

Reside shiner √

Dace √
ESA Recovery Plan: Snake River Sockeye Salmon | 97

June 2015| NOAA Fisheries 

Predation on Sockeye Salmon 

Several fish species that occupy the lakes potentially prey on Sockeye Salmon, including bull 

trout, northern pikeminnow, and brook trout. Research shows that Sockeye Salmon and kokanee 

are part of the diet of bull trout and northern pikeminnow. See Section 5.5, Predation for more 

information.

2.3.6 Captive Broodstock Program

At the time that NMFS listed Snake River Sockeye Salmon as endangered, a group of Federal, 

state, and tribal partners initiated a captive broodstock program in hopes of preventing the ESU’s 

extinction. Sixteen adult Sockeye Salmon that returned to Redfish Lake from 1991 to 1998, as 

well as 886 out-migrating smolts captured between 1991 and 1993 and 26 residual Sockeye 

Salmon captured between 1992 and 1995, were used to develop the program (Hebdon et al. 

2004; Flagg et al. 2004). The captive broodstock program has focused on maintaining remaining 

genetic diversity and population heterozygosity, while striving to rebuild the populations to 

support delisting and harvest needs. Recent restoration releases aim to restore anadromous O. 

nerka to Redfish, Pettit, and Alturas Lakes (Kline and Flagg 2014). 

The captive broodstock program is coordinated by the multi-agency Stanley Basin Sockeye 

Technical Oversight Committee, whose members include representatives of BPA, NMFS, Idaho 

Department of Fish and Game, U.S. Forest Service, Oregon Department of Fish and Wildlife,

and the Shoshone-Bannock Tribe. The BPA provides funding for the captive broodstock

program through the Northwest Power and Conservation Council’s Fish and Wildlife Program. 

NMFS manages the permitting of activities and the captive-rearing program hatchery operations 

in Manchester and Burley Creek, Washington. The IDFG monitors a variety of fisheries 

parameters in the field and is responsible for the hatchery operations in Eagle, Stanley, and 

Springfield, Idaho. The ODFW rears Sockeye Salmon smolts at Oxbow Hatchery near Cascade 

Locks, Oregon. The U.S. Forest Service participates in permitting activities and habitat 

improvements. The SBT monitors a variety of fisheries biology parameters and evaluates 

spawning and rearing habitat characteristics in the Sawtooth Valley nursery lakes (Taki et al. 

2006).
ESA Recovery Plan: Snake River Sockeye Salmon | 98

June 2015| NOAA Fisheries 

Adult Sockeye Salmon at direct release event at Redfish Lake. Photo: N. Nokkentved, IDFG

Reintroduction plans for the captive broodstock progeny have followed a “spread-the-risk” 

philosophy, incorporating multiple release strategies into Redfish, Pettit, and Alturas Lakes

(Hebdon et al. 2004). Monitoring and evaluation efforts have focused on maximizing the use of 

limited hatchery rearing space and on identifying and prioritizing the most successful 

reintroduction strategies. Further, the genetic focus of the program and adherence to principles 

of conservation aquaculture has retained approximately 95% of the original variability that 

remained in the population (Kalinowski et al.2012; Kline and Flagg 2014).

Today, the captive broodstock program continues to play a key role in the recovery of the Snake 

River Sockeye Salmon ESU, and is considered as a key component of this recovery plan for the 

species, as discussed in recovery strategy, Section 6.3.11. The program applies a tiered or 

phased approach that includes increasing the number of adult Redfish Lake Sockeye Salmon 

returns, incorporating more natural-origin returns in hatchery spawning designs and on spawning 

grounds, and moving toward the development of an integrated conservation program that takes 

advantage of local adaptation (IDFG 2010; Kline and Flagg 2014). 

The SBSTOC continues to provide technical recommendations and coordination for the Sockeye 

Salmon captive broodstock program implemented by IDFG and other agencies. The captive 

broodstock program continues to evolve as the total number of hatchery and natural-origin 

Sockeye Salmon returning to Redfish Lake increases. As this Snake River Sockeye Salmon 

recovery plan is implemented and Sockeye Salmon recovery efforts move beyond the captive 

broodstock phase, IDFG plans to meet future demand for increased juvenile Sockeye Salmon
ESA Recovery Plan: Snake River Sockeye Salmon | 99

June 2015| NOAA Fisheries 

production at the recently constructed Springfield Hatchery near the town of Springfield in 

Bingham County, Idaho, which was completed in 2013. IDFG’s 2010 Springfield Hatchery 

Master Plan estimates production of up to one million Sockeye Salmon smolts annually to 

support continued re-colonization of Sockeye Salmon into Redfish, as well as potential 

reintroduction programs developed for Pettit, Alturas, and other Sawtooth Valley lakes (IDFG 

2010). The program includes specific biological triggers to guide the transition to the final phase 

(local adaptation), including the ramp-down and ultimate discontinuation of captive broodstock 

efforts at the facilities.

2.3.7 Watershed Land Use and Demographics

Sawtooth Valley lakes and streams form the headwaters of the Salmon River, a major tributary to 

the Snake River. Located entirely within the Sawtooth National Recreation Area, most of the 

land in the valley is higher than 1,970 m (6,463 ft.) above sea level. The watersheds of these 

major lakes lie mostly within the Sawtooth Wilderness Area, and drain the east side of the 

granite Sawtooth Mountains. The U-shaped lake basins were once heavily glaciated, leaving 

large moraines behind which the lakes are impounded (Killsgaard et al. 1970; Alt and Hyndman 

1989). 

Land use in the Sawtooth Valley is predominantly cattle ranching and recreation. The private 

lands, with ranches and scattered residences, are primarily used as pasture. Alturas Lake Creek 

is the only outlet stream from the lakes that crosses these private agricultural lands before 

entering the Salmon River. The town of Stanley had a population of 63 in the 2010 census. More 

than 1 million people per year visit the Sawtooth National Recreation Area, mostly in the 

summer (Griswold et al. 2002). 

The Sawtooth National Recreation Area encompasses roughly 3,150 km2 (778,000 acres) and is 

heavily used in the summer for fishing, boating, hiking, picnicking, camping, and livestock 

grazing. In the winter, the area is used for cross-country skiing, snowmobiling, and other 

outdoor activities. The Sawtooth National Recreation Area contains five major road-accessible 

lakes (Alturas, Pettit, Yellowbelly, Redfish, and Stanley) and numerous other lakes and streams. 

The Sawtooth National Recreation Area is managed by the U.S. Forest Service. 

The lakes of the Sawtooth National Recreation Area have numerous recreational facilities such 

as campgrounds and picnic areas. Camping, fishing, scuba diving, hiking, sightseeing, 

swimming, boating, jet skiing, and other day-use activities are common on each of the five major 

Sawtooth Valley lakes. Table 2-4 lists the recreational facilities and activities at each lake.
ESA Recovery Plan: Snake River Sockeye Salmon | 100

June 2015| NOAA Fisheries 

Table 2-4. Recreation facilities and activities on Sawtooth Valley lakes (BPA 1995).

Lake Facilities Activities

Stanley campgrounds (39 sites)

1 boat ramp

1 picnic and overlook area

Fishing, motor boating, sail boating, 

canoeing, and snowmobiling 

Redfish Visitor Center

Lodge (holds 125 persons)

5 campgrounds (105 sites)

1 boat ramp

2 swimming beaches

3 picnic areas

Fishing, swimming, all types of 

boating, waterskiing on 615-acre lake, 

5 miles in length cross-country skiing, 

horseback riding and boat tours

Yellowbelly No improved facilities Fishing, dispersed camping, and 

boating with horsepower restrictions

Pettit Campgrounds (5 sites)

Boat ramp

Day use area

All types of boating, waterskiing, 

fishing, snowmobiling, and crosscountry skiing

Alturas campgrounds (55 sites)

Picnic area for up to 125 persons

All types of boating, waterskiing, 

fishing, snowmobiling, cross-country 

skiing and amphitheater events

The Shoshone-Bannock and Nez Perce Tribes have hunting and fishing rights in the Sawtooth

National Forest that have been reserved by treaty.

Stanley Lake 

Stanley Lake supports rainbow trout, kokanee, and lake trout. The self-sustaining population of 

lake trout is present in Stanley Lake as a result of a one-time introduction by IDFG in 1975 

(USFS 2011). It is regularly stocked with rainbow trout by IDFG. Brook trout, Chinook salmon, 

westslope cutthroat trout, steelhead, and various species of sculpin and sucker are found in 

Stanley Lake Creek, the outlet of the lake. In 1956, a barrier was installed at the outlet of 

Stanley Lake by IDFG to prevent fish from migrating into the lake; it remains today. 

Stanley Lake was stocked with non-native kokanee from 1988 to 1991, an early spawning stock. 

The 1990s data from Waples (1991) suggests that kokanee are a mix of native and non-native 

fish within this lake. IDFG has re-sampled the kokanee population to identify the current genetic 

composition of kokanee. Results of this recent analysis suggest that the current Stanley Lake 

population constitutes a native population of kokanee with low levels of non-native introgression 

(Kozfkay 2013a). 

Recreation facilities at Stanley Lake include three campgrounds, a day use area, a boat launch, 

and hiking trails. The lake is a common fishing destination for both shore and boat anglers. 
ESA Recovery Plan: Snake River Sockeye Salmon | 101

June 2015| NOAA Fisheries 

Redfish Lake

Redfish Lake remains the only lake with returning Sockeye Salmon adults. The recovery 

program continues to introduce Sockeye Salmon adults and juveniles into Redfish Lake and 

IDFG operates a weir within Redfish Lake Creek. Successful adult returns have occurred since 

2000, with a high of 1,117 Sockeye Salmon returning in 2011 (including 142 natural-origin fish); 

1,355 returning in 2010 (including 179 natural-origin fish); 833 fish returning in 2009 (including 

85 natural-origin fish); and 650 fish in 2008 (including 142 natural-origin fish). 

Kokanee are a target game fish species in Redfish Lake. Fishhook Creek, a tributary to Redfish 

Lake, was stocked with non-native kokanee from 1930 to 1987, with an early spawning stock 

from the Anderson Ranch Reservoir. Similar to the kokanee in Alturas Lake, genetic analyses 

suggest no remaining impacts from these earlier stocking events (Waples et al. 2011). 

Salmonid species present in the lake include Chinook salmon and steelhead. Sockeye Salmon

are released into the lake to spawn naturally as part of the Sockeye Salmon recovery program. 

Between Redfish Lake and the Salmon River, Little Redfish Lake and Redfish Lake Creek also 

contain bull trout and cutthroat trout.

Yellowbelly Lake 

Target game fish species in Yellowbelly Lake include brook trout and cutthroat trout; the latter 

are stocked in most years. An outlet barrier was constructed by IDFG in 1961 to prevent access 

by anadromous fish and it was removed by the U.S. Forest Service in 2000. A lag deposit

formation located 402 meters (a quarter-mile) below the outlet of the lake, where Yellowbelly 

Lake Creek flows through pore spaces of a boulder field, that did not historically restrict Sockeye 

Salmon passage. Yellowbelly Lake hosts no developed campgrounds and development around 

the lake is minimal. 

Pettit Lake

Pettit Lake contains kokanee, rainbow trout, and Sockeye Salmon. Sockeye Salmon are planted 

in the lake annually. The lake was stocked with non-native kokanee from 1932-1968. In the 

early 1960s, it was chemically treated. The kokanee that exist today are a non-native north Idaho 

late spawning stock. Development on Pettit Lake is limited to one campground and day use area, 

mountain cabins, and a boat launch. Pettit Lake Sockeye Salmon/kokanee are shoal spawners.

Alturas Lake

Alturas Lake is a highly oligotrophic lake located at an elevation of 2,138 m (7,014 ft). The lake 

has a surface area of 338.2 ha (835 ac) and 7.9 km (4.9 miles) of shoreline. Its source (inlet) and 

drainage (outlet) is Alturas Lake Creek. The lake supports a population of bull trout, along with 

kokanee, mountain whitefish, suckers, northern pikeminnow, and hatchery rainbow trout. 

“Historically, spring Chinook salmon spawned and reared in Alturas Lake Creek above and 

below the lakes and in Alpine Creek, a tributary of Alturas Lake Creek, for approximately (2.4 

km (1.5 miles). Some summer steelheads also use Alturas Lake Creek. Sockeye Salmon spawned 
ESA Recovery Plan: Snake River Sockeye Salmon | 102

June 2015| NOAA Fisheries 

in the upper drainage and reared in Alturas Lake” (Andrews et al. 1987). Spring Chinook 

salmon still spawn in Alturas Lake Creek, though at reduced levels from historical abundance.

Fisheries for kokanee and rainbow trout occur in Alturas Lake. Brook trout, bull trout, and the 

occasional Chinook salmon or steelhead can also be found. Rainbow trout and Sockeye Salmon

are stocked in Alturas Lake annually. Alturas Lake is one of the more developed lakes in the 

Sawtooth Valley, with three campgrounds, day use areas and a boat launch (IDFG 2010).

2.4 Critical Habitat

The ESA requires the Federal government to designate “critical habitat” for any species it lists 

under the ESA. The Act defines critical habitat as areas that contain physical or biological 

features that are essential for the conservation of the species, and that may require special 

management or protection. Critical habitat designations must be based on the best scientific 

information available, in an open public process, within specific timeframes. The designations 

are one factor to consider during the identification and prioritization of recovery actions in 

recovery plans.

A critical habitat designation applies only when Federal funding, permits, or projects are 

involved. Under section 7 of the ESA, all Federal agencies must ensure that any actions they 

authorize, fund, or carry out are not likely to jeopardize the continued existence of a listed 

species, or destroy or adversely modify its designated critical habitat. Before critical habitat is 

designated, careful consideration must be given to its economic impacts, impacts on national 

security, and other relevant impacts. The Secretary of Commerce may exclude an area from 

critical habitat if the benefits of exclusion outweigh the benefits of designation, unless excluding 

the area will result in the extinction of the species concerned. A critical habitat designation does 

not set up a preserve or refuge. Critical habitat requirements do not apply to citizens engaged in 

activities on private land that do not involve a Federal agency; however, activities that impair 

habitat used by listed species may constitute a violation of the ESA in some circumstances. 

The physical and biological elements, also called “primary constituent elements,” or PCEs, that 

support one or more life stages and are considered essential to the conservation of the species are 

described in detail in the final rule designating critical habitat for 12 West Coast salmon and 

steelhead ESUs/DPSs (NMFS 2005b). Essential salmon habitat consists of four components: (1) 

spawning and juvenile rearing areas: (2) juvenile migration corridors; (3) areas for growth and 

development to adulthood; and (4) adult migration corridors. Essential features of spawning and 

rearing areas include adequate (1) spawning gravel; (2) water quality; (3) water quantity; (4) 

water temperature; (5) food; (6) riparian vegetation; and (7) access (NMFS 1993). Essential 

features of juvenile migration corridors include adequate: (1) substrate; (2) water quality; (3) 

water quantity; (4) water temperature; (5) water velocity; (6) cover/shelter; (7) food; (8) riparian 

vegetation; (9) space; and (10) safe passage conditions (NMFS 1993). The adult migration 
ESA Recovery Plan: Snake River Sockeye Salmon | 103

June 2015| NOAA Fisheries 

corridors are the same areas, and the essential features are the same with the exception of 

adequate food (adults do not eat on their return migration to natal streams).

The Pacific Ocean areas used by listed salmon for growth and development to adulthood are not 

well understood and essential areas and features in the ocean have not been identified (NMFS 

1993). 

Table 2-5 is a summary of the physical and biological features considered essential for 

anadromous salmon and steelhead.

Table 2-5. Types of sites and essential physical and biological features designated as PCEs for anadromous 

salmonids, and the life stage each PCE supports (NMFS 2005b).

Site Essential Physical and Biological 

Features ESU/DPS Life Stage

Freshwater spawning Water quality, water quantity, and 

substrate

Spawning, incubation, and larval 

development

Freshwater rearing Water quantity and floodplain 

connectivity

Juvenile growth and mobility

Water quality and forage Juvenile development

Natural covera Juvenile mobility and survival

Freshwater migration Free of artificial obstructions, water 

quality and quantity, and natural 

coverb

Juvenile and adult mobility and survival

Estuarine areas Free of obstruction, water quality and 

quantity, and salinity

Juvenile and adult physiological 

transitions between salt and freshwater

Natural covera, forageb and water 

quantity

Growth and maturation

Nearshore marine areas Free of obstruction, water quality and 

quantity, natural covera and forageb

Growth and maturation, survival

Offshore marine areas Water quality and forageb Growth and maturation

a Natural cover includes shade, large wood, log jams, beaver dams, aquatic vegetation, large rocks and boulders, side 

channels, and undercut banks.

b Forage includes aquatic invertebrate and fish species that support growth and maturation.

Critical habitat for Snake River Sockeye Salmon was designated on December 28, 1993 (NMFS 

1993). It includes the juvenile and adult migration corridor to the Pacific Ocean: the Columbia 

River and its estuary, the Snake River, and the main fork of the Salmon River up to the Sawtooth 

Valley and the site of current spawning, Redfish Lake. Other historical nursery areas that are 

essential to the conservation of the species and identified as critical habitat include Alturas, 
ESA Recovery Plan: Snake River Sockeye Salmon | 104

June 2015| NOAA Fisheries 

Pettit, Stanley, and Yellowbelly Lakes and their inlet and outlet creeks, Alturas Lake Creek, and 

that portion of Valley Creek between Stanley Lake Creek and the Salmon River (NMFS 1993). 

NMFS is currently working to produce a map showing critical habitat for this ESU and will add 

the map to the recovery plan when it becomes available. 

The lower Columbia River corridor is among the areas of high conservation value to all 

Columbia and Snake River basin species because it connects every population with the ocean 

and is used by rearing/migrating juveniles and migrating adults. The Columbia River estuary is a 

unique and essential area for juveniles and adults making the physiological transition between 

life in freshwater and marine habitats. 

For Snake River Sockeye Salmon designated areas consist of the water, waterway bottom, and 

the adjacent riparian zone (defined as an area 300 feet from the normal high water line on each 

side of the river channel) (NMFS 1999). Specific watersheds constituting critical habitat for each 

species were identified in the respective final rules (NMFS 1993, NMFS 1999b, and NMFS

2005b).

NMFS recognizes that salmon habitat is dynamic and that present understanding of areas 

important for conservation will likely change as recovery planning sheds light on areas that can 

and should be protected and restored, such as areas upstream of barriers where fish could be 

reestablished in historical habitat. 

NMFS will update its critical habitat designations as needed as new information becomes 

available, including information developed during recovery plan implementation. Critical habitat 

designations are one element to consider in identifying and prioritizing recovery actions.

2.5 Salmonid Biological Structure

Most of the time salmon return to spawn in the streams or lakes where they were born. However, 

they occasionally “stray” and choose to spawn where conditions are right, perhaps in an adjacent 

stream or lake. The result is that salmon populations that are geographically widespread may 

have some amount of genetic similarity. They are linked because of straying, and differentiated 

because of long-term adaptation to different environments. Diverse genetic, life history, and 

morphological characteristics that have evolved over generations give the species as a whole the 

resilience to persist over time.

Historically, most salmon or steelhead species typically contained multiple populations 

connected by some small degree of genetic exchange with spawners straying in from other areas,

(exceptions to this general pattern, however, are the examples of single lake ESUs for Sockeye 

Salmon, e.g., Lake Ozette Sockeye Salmon.) Thus, the overall biological structure of the species 

is hierarchical; spawners in the same area of the same stream will share more characteristics than 
ESA Recovery Plan: Snake River Sockeye Salmon | 105

June 2015| NOAA Fisheries 

those in the next stream over. Fish whose natal streams are separated by hundreds of miles will 

have less genetic similarity. The species is essentially a metapopulation defined by the common 

characteristics of populations within a geographic range (Figure 2-10).

McElhany et al. (2000) formally identified two levels in this hierarchy for recovery planning 

purposes: the evolutionarily significant unit (ESU), which is a special type of distinct population 

segment (DPS) applicable to Pacific salmon, and the independent population. (An independent 

populaions is a group of fish of the same species that spawns in a particular lake or stream (or 

portion thereof) at a particular season and which, to a substantial degree, does not interbreed with 

fish from any other group spawning in a different place or in the same place at a different season. 

For NMFS’ purposes in recovery planning, not interbreeding to a ‘substantial degree’ means that 

two groups are considered to be independent populations if they are isolated to such an extent 

that exchanges of individuals among the populations do not substantially affect the population 

dynamics or extinction risk of the independent populations over a 100-year time frame 

(McElhany et al. 2000)). The ICTRT identified an additional level between the population and 

ESU/DPS levels, which they call a major population group (MPG) (McClure et al. 2003). 

Unlike most Chinook salmon ESUs and steelhead DPSs, the lake-spawning Sockeye Salmon

ESUs may comprise only a single population, such as, for example, the Lake Ozette Sockeye 

Salmon ESU, which is made up of Sockeye Salmon that spawn exclusively in Lake Ozette, on 

the Olympic Peninsula in Washington State. Different spawning aggregates may represent spatial 

diversity for these Sockeye Salmon: beach locations vs. lake tributaries, lake outlets, rivers 

between lakes. In the case of Snake River Sockeye Salmon, spawners returning to the various 

lakes within the Sawtooth Valley may historically have constituted separate ESUs.

2.5.1 Evolutionarily Significant Units (ESUs) and Distinct Population Segments 

(DPSs)

A salmon ESU or steelhead DPS is a distinctive group of Pacific salmon or steelhead that is 

uniquely adapted to a particular area or environment. Because of the hierarchical structure of 

salmonid populations, the concept of “distinctive group” has received considerable attention and 

refinement. An ESU is defined as “a group of Pacific salmon that is (1) substantially 

reproductively isolated from other conspecific units and (2) represents an important component 

of the evolutionary legacy of the species. Equivalent to a distinct population segment and treated 

as a species under the Endangered Species Act.” (Waples et al. 1991). A “population segment” is 

considered “distinct” (a DPS and hence, like ESUs, considered a “species” for purposes of 

conservation under the ESA) if it is discrete from and significant to the remainder of its species 

based on factors such as physical, behavioral, or genetic characteristics, or if it occupies an 

unusual or unique ecological setting, or if its loss would represent a significant gap in the 

species’ range. ESUs/DPSs may contain multiple populations that are connected by some degree 

of migration, and hence may have a broad geographic range across watersheds and river basins. 
ESA Recovery Plan: Snake River Sockeye Salmon | 106

June 2015| NOAA Fisheries 

2.5.2 Major Population Groups

Within an ESU/DPS, independent populations can be grouped into larger populations that share 

similar genetic, geographic, and/or habitat characteristics (McClure et al. 2003). These "major 

population groups" (MPGs) are isolated from one another over a longer time scale than that 

defining the individual populations, but retain some degree of connectivity greater than that 

between ESUs/DPSs. The relationship between ESU/DPS, MPG, and independent populations is 

depicted in Figure 2-11.

Hierarchy in Salmonid Population Structure

Figure 2-11. Hierarchical levels of salmonid species structure as defined by the TRTs for ESU/DPS recovery 

planning.

2.5.3 Independent Populations

McElhany et al. (2000) defined an independent population as follows: 

...a group of fish of the same species that spawns in a particular lake or stream (or 

portion thereof) at a particular season and which, to a substantial degree, does not 

interbreed with fish from any other group spawning in a different place or in the same 

place at a different season. For our purposes, not interbreeding to a ‘substantial degree’ 

means that two groups are considered to be independent populations if they are isolated 

to such an extent that exchanges of individuals among the populations do not 

substantially affect the population dynamics or extinction risk of the independent 

populations over a 100-year time frame.

Population 

Attributes 

Populations

Major Population Group/ 

Stratum/Geographic Unit 

Evolutionarily Significant Unit/

Distinct Population Segment

ESU/DPS

MPG 1 MPG 2 MPG 3
ESA Recovery Plan: Snake River Sockeye Salmon | 107

June 2015| NOAA Fisheries 

2.5.4 Snake River Sockeye Salmon ESU Structure

The ICTRT defined Snake River Sockeye Salmon as a single ESU with a single major 

population group, the Sawtooth Valley Lakes MPG. The group determined that the one MPG 

historically supported at least three independent sockeye salmon populations (Redfish, Alturas,

and Stanley Lakes) (ICTRT 2007). The MPG is currently made up of one extant population 

(Redfish Lake) and two (Alturas Lake and Stanley Lake) to four (possibly also Pettit and 

Yellowbelly Lakes) other historical populations (Figure 2-12). 

Hierarchy in Snake River Sockeye Salmon ESU Structure

Figure 2-12. Hierarchial levels in Snake River Sockeye Salmon ESU. Redfish Lake (shown in green) is the ESU’s 

only extant population. The Alturas, Pettit, Stanley and Yellowbelly Lake populations are currently extirpated. 

Historically, the Snake River basin likely supported additional Sockeye Salmon populations and 

MPGs, and possibly other separate ESUs. As discussed earlier in the Plan, Sockeye Salmon once 

ascended the Snake River to the Wallowa, Payette, and Salmon River basins to spawn in natural 

lakes. Within the Salmon River basin, Sockeye Salmon spawned in Warm Lake in the South 

Fork Salmon River basin, as well as in the Sawtooth Valley lakes. The historical relationships 

between the different Snake River Sockeye Salmon populations are not known. 

2.6 Viable Salmonid Populations

A Viable Salmonid Population is an independent population of any Pacific salmon or steelhead

that has a negligible risk of extinction due to threats from demographic variation (random or 

directional), local environmental variation, and genetic diversity changes (random or directional) 

over a 100-year time frame (McElhany et al. 2000). NMFS scientists measure salmon recovery 

in terms of four parameters, called the viable salmonid population (VSP) parameters: abundance, 

Snake River Sockeye Salmon ESU

Sawtooth Valley Lakes MPG 

Redfish Lake Alturas Lake Pettit Lake Stanley Lake Yellowbelly Lake
ESA Recovery Plan: Snake River Sockeye Salmon | 108

June 2015| NOAA Fisheries 

productivity, spatial structure, and diversity. Biological viability criteria, described in more detail 

in Section 3, establish threshold values for the VSP parameters appropriate to population size.

2.6.1 Abundance and Productivity

Abundance is expressed in terms of spawners (adults on the spawning ground), measured over a 

time series, i.e. some number of years. The ICTRT often uses a recent 10- or 12-year geometric 

mean of natural spawners as a measure of current abundance.

The productivity of a population (the average number of surviving offspring per parent) is a 

measure of the population’s ability to sustain itself. Productivity can be measured as spawner:

spawner ratios (returns per spawner or recruits per spawner) (or adult progeny to parent), annual 

population growth rate, or trends in abundance. Population-specific estimates of abundance and 

productivity are derived from time series of annual estimates, typically subject to a high degree 

of annual variability and sampling-induced uncertainties. The ICTRT recommends estimating 

current intrinsic productivity using spawner-to-spawner return pairs from low to moderate 

escapements over a recent 20-year period.

Abundance and productivity are linked, as populations with low productivity can still persist if 

they are sufficiently large, and small populations can persist if they are sufficiently productive. A 

viable population needs sufficient abundance to maintain genetic health and to respond to normal 

environmental variation, and sufficient productivity to enable the population to quickly rebound 

from periods of poor ocean conditions or freshwater perturbations.

The VSP guidelines for abundance recommend that a viable population should be large enough 

to have a high probability of surviving environmental variation observed in the past and expected 

in the future; be resilient to environmental and anthropogenic disturbances; maintain genetic 

diversity; and support/provide ecosystem functions (McElhany et al. 2000).

Viable populations should demonstrate sufficient productivity to support a net replacement rate 

of 1:1 or higher at abundance levels established as long-term targets. Productivity rates at 

relatively low numbers of spawners should, on the average, be sufficiently greater than 1.0 to 

allow the population to rapidly return to abundance target levels (ICTRT 2005b).

Abundance should be high enough that 1) declines to critically low levels would be unlikely, 

assuming recent historical patterns of environmental variability and intrinsic productivity; 2) 

compensatory processes provide resilience to the effects of short-term perturbations; and 3) 

subpopulation structure is maintained (e.g., multiple spawning tributaries, spawning patches, life 

history patterns) (ICTRT 2005b).
ESA Recovery Plan: Snake River Sockeye Salmon | 109

June 2015| NOAA Fisheries 

2.6.2 Spatial Structure and Diversity

A population’s spatial structure is made up of both the geographic distribution of individuals in 

the population and the processes that generate that distribution (McElhany et al. 2000, p. 18). 

Diversity refers to the distribution of traits within and among populations. Some traits are 

completely genetically based, while others, including nearly all morphological, behavioral, and 

life history traits, vary as a result of a combination of genetic and environmental factors 

(McElhaney et al. 2000). Spatial structure and diversity considerations are combined in the 

evaluation of a salmonid population’s status because they are so interrelated.

Populations with restricted distribution and few spawning areas are at a higher risk of extinction 

as a result of catastrophic environmental events, such as a landslide, than are populations with 

more widespread and complex spatial structures. A population with a complex spatial structure, 

including multiple spawning areas, experiences more natural exchange of gene flow and life 

history characteristics.

Population-level diversity is similarly important for long-term persistence. Populations 

exhibiting greater diversity are generally more resilient to short-term and long-term 

environmental changes. Phenotypic diversity, which includes variation in morphology and life 

history traits, allows more diverse populations to use a wider array of environments, and protects 

populations against short-term temporal and spatial environmental changes. Underlying genetic 

diversity provides the ability to survive long-term environmental changes.

Because neither the precise role that diversity plays in salmonid population viability nor the 

relationship of spatial processes to viability is completely understood, the ICTRT adopted the 

principle from McElhany et al. that historical spatial structure and diversity should be taken as a 

“default benchmark,” on the assumption that historical, natural populations did survive many 

environmental changes and therefore must have had adequate spatial structure and diversity.
ESA Recovery Plan: Snake River Sockeye Salmon | 110

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 111

June 2015| NOAA Fisheries 

Section 3: Recovery Goals and Delisting Criteria

3.1 Background on Developing Biological Viability Criteria

3.2 Recovery Goals and Biological Viability Criteria for Snake River Sockeye Salmon

3.3 Listing Factors / Threats Criteria

3.4 Delisting Decision
ESA Recovery Plan: Snake River Sockeye Salmon | 112

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 113

June 2015| NOAA Fisheries 

3. Recovery Goals and Delisting Criteria

This section describes the biological recovery goals and delisting criteria that NMFS will use in 

future ESA status reviews of the Snake River Sockeye Salmon ESU. These reviews will 

contribute to NMFS’ larger objective of delisting the Snake River Sockeye Salmon ESU. 

The recovery goals that are incorporated into a recovery plan may include delisting, 

reclassification (e.g., from endangered to threatened), and/or other “broad sense” goals that may 

go beyond the requirements for delisting to acknowledge social, cultural, or economic values 

regarding the listed species. Delisting criteria must meet ESA requirements, while recovery may 

be defined more broadly. The ESA requires that recovery plans, to the maximum extent 

practicable, incorporate objective, measurable criteria which, when met, would result in a 

determination in accordance with the provisions of the ESA that the species should be removed 

from the Federal List of Endangered and Threatened Wildlife and Plants (50 CFR 17.11 and 

17.12; 50 CFR 223.102 and 224.101). These criteria are of two kinds: the biological viability 

criteria, which deal with population or demographic parameters, and the “threats” criteria, which 

relate to the five listing factors detailed in the ESA (see Section 3.2 and 3.4 of this Plan). The

threats criteria define the conditions under which the listing factors, or threats, can be considered 

to be addressed or mitigated. Together these make up the “objective, measurable criteria” 

required under section 4(f)(1)(B) for the delisting decision.

The delisting criteria are based on the best available scientific information and incorporate the 

most current understanding of the ESU and the threats it faces. As this recovery plan is 

implemented, additional information will become available that can increase certainty about 

whether the threats have been abated, whether improvements in population and ESU status have 

occurred, and whether linkages between threats and changes in salmon status are understood. 

These delisting criteria will be assessed through an adaptive management program and NMFS 

may review whether the criteria may warrant revision during its five-year reviews of the ESU. 

As the biological status of natural-origin spawners improves over time, the ESA five-year status 

review process can be used to articulate the changes in viability parameters and ESA listing 

factors that might warrant a review of whether the ESU’s listing status should be changed from 

endangered to threatened, as well as to delist. Given the current abundance of natural-origin 

spawners, however, NMFS is not proposing downlisting criteria in this recovery plan. The fiveyear status review process will be used to evaluate this ESU's progress toward recovery and 

determine if any future change in ESA listing status is warranted.

As described in Section 4, NMFS convened the ICTRT and requested that they develop 

biological viability criteria specifically adapted for listed Interior Columbia salmon and 

steelhead. The ICTRT developed its viability criteria based on a set of general guidelines set out 

in McElhany et al. (2000), expressed in terms of population level abundance, productivity, 

spatial structure, and diversity (the VSP parameters). The ICTRT criteria represent a consistent 

framework with examples of metrics that are intended to be evaluated and adapted to fit the 
ESA Recovery Plan: Snake River Sockeye Salmon | 114

June 2015| NOAA Fisheries 

specific characteristics and conditions of a particular ESU or DPS. The criteria are hierarchical, 

with ESU/DPS level objectives being expressed in terms of the viability status of individual 

populations considered in aggregate major population groupings (MPGs). 

NMFS has adopted recovery plans covering listed species in two of the three major sub-regions 

of the Columbia River domain: Middle Columbia River steelhead and Upper Columbia River 

steelhead in the Middle Columbia subregion, and spring Chinook salmon in the Upper Columbia

subregion. Both of these plans incorporated biological recovery criteria that build on the 

viability criteria developed by the ICTRT (ICTRT 2007). 

The following sections describe background information for developing biological viability 

criteria, proposed recovery goals, and biological viability criteria for Snake River Sockeye 

Salmon, listing factors/threats criteria, and delisting decision evaluation considerations that 

describe conditions on the basis of which, if met, NMFS would decide to remove the species 

from the Federal list of endangered and threatened species. 

3.1 Background on Developing Biological Viability Criteria

In 2007, the ICTRT completed its Technical Review Draft of Viability Criteria for Application 

to Interior Columbia Basin Salmonid ESUs (ICTRT 2007). Biological viability criteria are 

quantitative metrics that describe ESU/DPS characteristics associated with a low risk of 

extinction for the foreseeable future. These criteria are based on the VSP parameters of 

abundance, productivity, spatial distribution, and diversity, according to guidelines developed by 

NOAA’s Northwest Fisheries Science Center and published as a NOAA Technical 

Memorandum, Viable Salmonid Populations and the Recovery of Evolutionarily Significant 

Units (McElhany et al. 2000, ICTRT 2007).

Sections 2.5 and 2.6 of this Plan describe salmonid biological structure and the viable salmonid 

population parameters of abundance, productivity, spatial structure, and diversity to characterize 

the viability status of salmon and steelhead (McElhany et al. 2000). The ICTRT used these 

parameters to describe biological viability criteria applicable to each of the ESA-listed Interior 

Columbia Basin salmonid ESUs (ICTRT 2007). Following the guidance in McElhany et al. 

(2000), the ICTRT developed ESU-level criteria expressed in terms of the status of component 

populations organized into major population groups (MPGs). These criteria can then be used to 

understand the status of Interior Columbia Basin ESA-listed salmon and steelhead ESUs and 

DPSs with the goal of having ESUs be at low risk and provide for the greatest probability for 

persistence of the ESU (ICTRT 2007). 
ESA Recovery Plan: Snake River Sockeye Salmon | 115

June 2015| NOAA Fisheries 

3.1.1 Viability Criteria for ESUs with One MPG

In 1991, NMFS determined that the Snake River Sockeye Salmon is a “species,” an ESU, under 

the ESA and concluded that it should be listed as endangered (NMFS 1991). The ESU includes 

“all naturally spawned anadromous and residual Sockeye Salmon originating from the Snake 

River basin. Also, sockeye salmon from one artificial propagation program: the Redfish Lake 

Captive Broodstock Program” (70 FR 37160, Jun 28, 2005, (NMFS 2005b); reaffirmed 79 FR 

20802, April 14, 2014).

Further investigations have clarified our understanding of the different Sockeye Salmon life 

history forms in the Sawtooth Valley natal lakes. For example, following the 1991 listing 

decision, a “residual” form of Snake River Sockeye Salmon was identified in Redfish Lake. In 

1993 NMFS determined that the residual population of Snake River Sockeye Salmon that exists 

in Redfish Lake is substantially reproductively isolated from kokanee and represents an 

important component in the evolutionary legacy of the species and should be included in the 

listed ESU (NMFS 1993).

Kokanee are defined as the self-perpetuating, generally non-anadromous form of O. nerka that 

occurs in balanced sex-ratio populations and whose parents, for several generations back, have 

spent their whole lives in fresh water. The NMFS Biological Review Team determined in its 

status review that Redfish Lake Sockeye Salmon are genetically distinct from kokanee and did 

not include the fish in the ESA listing (Waples et al. 1991). NMFS continues to reevaluate the 

situation. Genetic analysis in 1997 showed that Redfish Lake sockeye and kokanee are 

genetically distinct, and that Alturas Lake kokanee are most similar to Redfish Lake kokanee 

(Waples et al. 1997). NMFS recognizes, however, that in some situations where there is 

presumably some regular, or at least episodic, genetic exchange between resident and

anadromous forms, they should be considered part of the same ESU. The key issue is evaluating 

the strength and duration of reproductive isolation between the resident and anadromous forms. 

If in the future it is determined that kokanee are part of the ESU’s genetic and evolutionary 

legacy, or that extant kokanee populations are contributing to the anadromy, their relationship 

will be re-evaluated. As recovery progresses over time, and as anadromous or residual fish in the 

natal lakes re-emerge or are reestablished, any new information about kokanee will be 

considered regarding whether it should be part of the listed ESU. 

NMFS’ subsequent 1997 Technical Memo discusses O. nerka life history and non-anadromous 

life history forms. NMFS cites Ricker’s 1938 definition of the terms "residual Sockeye Salmon" 

and "residuals" to identify resident, non-migratory progeny of anadromous Sockeye Salmon

parents. For the purposes of NMFS’ 1997 review, “resident Sockeye Salmon” referred to those 

fish that are the progeny of anadromous parents, yet spend their adult life in freshwater and are 

observed together with their anadromous siblings on the spawning grounds. 
ESA Recovery Plan: Snake River Sockeye Salmon | 116

June 2015| NOAA Fisheries 

A number of lakes ranging widely in size within the Columbia River basin historically supported 

Sockeye Salmon production. In the Snake River drainage, Wallowa Lake, the Payette Lake 

basin, and Warm Lake formerly supported Sockeye Salmon. However, these lake groups are 

separated by distances that are consistent with those between other Sockeye Salmon ESUs. The 

ICTRT concluded that it is unclear, and currently unresolvable, whether these lake groups were 

MPGs of the same ESU or separate ESUs (ICTRT 2007). Given this uncertainty, the ICTRT 

treats the Snake River Sawtooth Valley Sockeye Salmon as a single ESU with a single MPG 

made up of one extant population (Redfish Lake) and two (Alturas Lake and Stanley Lake) to 

four (possibly also Pettit and Yellowbelly Lakes) other historical populations (ICTRT 2010). 

The ICTRT has used the best available scientific information to make these ESU/MPG 

determinations; however, these delineations will be re-evaluated as new information becomes 

available. 

ESUs that contain only one MPG are inherently at greater extinction risk than salmon species 

with several MPGs (ICTRT 2007). Such species will, by definition, have a more limited spatial 

structure, less diversity, and potentially less abundance and productivity than those with multiple 

MPGs. In addition, such ESUs typically have fewer component populations, which increases 

their risk level (Boyce 1992; Tear et al. 2005; ICTRT 2007). The ICTRT developed more 

stringent applications of their biological criteria for ESUs with a single MPG to mitigate this 

inherently higher risk. The persistence of multiple single population Sockeye Salmon ESUs 

across the range of the species supports the assumption that long-term sustainability in the face 

of year-to-year variations in environmental effects and localized catastrophic events is possible 

with sufficiently high levels of abundance, productivity, diversity and spatial structure. 

ESUs that contained only one MPG historically, or that include only one MPG critical for proper 

function, should meet the ICTRT’s MPG criteria, as well as the following additional criteria 

(ICTRT 2007):

1. Two-thirds or more of the historical populations within the MPG should meet viability 

standards; and

2. At least two populations should meet the criteria to be “Highly Viable.”

3.1.2 Recovery Scenarios

For most ESUs, the ICTRT viability criteria could be met with alternative combinations of 

populations meeting their individual objectives. The possible combinations of risk status for 

populations in each MPG that would allow the ESU/DPS to meet the viability criteria are called 

“recovery scenarios.”

The ICTRT included examples of possible recovery scenarios that would allow each Snake River 

ESU/DPS to meet the viability criteria (ICTRT 2007). The ICTRT selected these combinations 

of risk status based on the populations’ unique characteristics, such as run timing, population 
ESA Recovery Plan: Snake River Sockeye Salmon | 117

June 2015| NOAA Fisheries 

size, or genetics; major production areas in the MPG; and spatial distribution of the populations. 

The ICTRT cautioned against prematurely restricting the options for any population. In most 

cases, the ICTRT recovery scenarios reflected information on current and historical production 

from the target ESU. In other cases, including Snake River Sockeye Salmon, longer-term 

viability analyses and estimates of current natural production characteristics must depend largely 

on inferences from monitoring populations in other areas (e.g. Upper Columbia River, Fraser 

River system). The current ICTRT recovery scenarios and the ESU specific applications reflect 

the best available information. The following section includes a summary of the example 

developed by the ICTRT for the Snake River Sockeye Salmon ESU. 

3.2 Recovery Goals and Biological Viability Criteria for Snake River 

Sockeye Salmon

Snake River Sockeye Salmon are still close to extinction, supported primarily by a captive 

broodstock program. This program has substantially improved the numbers of hatchery-produced 

O. nerka for use in supplementation, and in recent years the levels of naturally produced Sockeye 

Salmon returns have increased. Nevertheless, substantial increases in survival rates across life 

history stages must occur in order to reestablish sustainable natural production (Ford 2011). 

3.2.1 Recovery Goals

This Plan aims to meet two types of recovery goals. The primary goal is for biological recovery 

to support removal of the Snake River Sockeye Salmon ESU from the threatened and endangered 

species list. Once the fish achieve recovery under the ESA, this Plan also aims to meet broader 

goals. These “broad sense” goals strive to rebuild the populations to provide for sustainable 

fisheries and other benefits. 

Biological Recovery Goals

The recovery goal for the Snake River Sockeye Salmon, as for all ESUs/DPSs, is to ensure that 

the ESU is self-sustaining and no longer needs the protection of the ESA. The ESU-level 

objectives are the following:

• Population-level persistence in the face of year-to-year variations in 

environmental influences.

• Combination of abundance and productivity sufficient to sustain a population (in 

the absence of hatchery supplementation) at levels that will maintain genetic and 

spatial diversity. 

• Resilience to the potential impact of catastrophic events.

• Populations distributed in a manner that insulates against loss from a local 

catastrophic event and provides for recolonization of a population that is affected 

by such an event.
ESA Recovery Plan: Snake River Sockeye Salmon | 118

June 2015| NOAA Fisheries 

• Maintaining long-term evolutionary potential.

• Sustaining natural production across a range of conditions, allowing for 

adaptation to changing environmental conditions.

Broad-Sense Recovery Goals

The immediate goal of this Plan is ESA delisting of Snake River Sockeye Salmon. This Plan also 

recognizes that while the goal of recovering Sockeye Salmon to the point that it no longer 

requires protective measures of the ESA is an immediate priority, building on this success with 

continued recovery efforts will be important to achieve broader goals. The broad sense goal is 

that naturally spawning Snake River Sockeye Salmon populations are sufficiently abundant, 

productive, and diverse (in terms of life histories and geographic distribution) to provide 

significant ecological, cultural, social, and economic benefits. Recovery of Snake River Sockeye 

Salmon populations throughout the full life cycle will require actions that preserve, enhance and 

restore healthy watershed conditions where ecosystem functions, processes and dynamics are 

intact ─ including instream conditions, riparian habitat diversity and complexity, and upland 

watershed health in concert with complementary management of harvest, hatcheries, and 

hydropower. Recovery is a process that leads to Sockeye Salmon populations that are not only 

viable, but that also provide a harvestable surplus for the treaty tribes, citizens of Idaho, and for 

others in the region. 

3.2.2 Biological Viability Criteria

The ICTRT adapted its approach to accommodate the biological characteristics and available 

data for the Snake River Sockeye Salmon, but generated a viability curve for this ESU following 

the same analytical steps as applied to the stream-type Chinook salmon and steelhead ESUs 

(ICTRT 2010). Table 3-1 shows the biological viability criteria for Snake River Sockeye 

Salmon.

Table 3-1. VSP parameters and biological viability criteria for Snake River Sockeye Salmon.

VSP Parameter Biological Viability Criteria

Abundance

• Minimum spawning abundance threshold 

measured as a ten-year geometric mean of 

estimated natural-origin spawners: 1,000 for 

Redfish Lake and Alturas Lake populations 

(intermediate size category);

• Minimum spawning abundance threshold 

measured as a ten-year geometric mean of 

estimated natural-origin spawners: 500 for 

populations in the smaller historical size 

category (Pettit, Stanley, or Yellowbelly 

Lakes)
ESA Recovery Plan: Snake River Sockeye Salmon | 119

June 2015| NOAA Fisheries 

Productivity • Population growth rate is stable or 

increasing

Spatial Structure and Diversity

• Very low to low risk rating for a highly viable 

population; and 

• Moderate risk rating for a viable population

3.2.2.1 Abundance and Productivity

Redfish Lake is approximately 62% of the size of Lake Wenatchee in the upper Columbia Basin, 

yet the other Sawtooth Valley lakes are relatively small compared to other lake systems in the 

Columbia Basin that historically supported Sockeye Salmon production. The ICTRT developed 

a general approach for assigning individual populations to one of four size categories based on 

historical habitat intrinsic potential (ICTRT 2007). For each ESU, populations in the smallest 

size category based on habitat intrinsic potential were assigned a minimum abundance level of 

500 spawners (measured as a ten-year geometric mean of estimated natural-origin spawners). 

The minimum abundance levels for larger historical size categories were assigned systematically 

to ensure that average spawning densities were sufficient to provide for within population 

diversity and spatial structure (ICTRT 2007). These viability criteria may be revised as new 

information becomes available, and as the production potential of other natal lakes becomes 

more certain. This is a critical uncertainty and key information need that is further discussed in 

Section 6.4. 

For Sockeye Salmon, intrinsic potential was estimated in terms of lake surface area (hectares) 

based on relationships reported for Sockeye Salmon lakes in Alaska and Canada (e.g., Burgner 

1991). Stanley, Pettit, and Yellowbelly Lakes are assigned to the smallest size category. Redfish 

and Alturas Lakes are classified as intermediate in size. For Snake River Sockeye Salmon, the 

ICTRT minimum abundance thresholds for Redfish Lake (intermediate) and Pettit Lake (small) 

were the same as recommended by the Snake River Recovery Team (Bevan et al. 1994). Alturas 

Lake was assigned to the intermediate-size category in the historical size analysis conducted by 

the ICTRT, which resulted in a higher recommended target minimum abundance threshold of 

1,000 (measured as a ten-year geometric mean of estimated natural-origin spawners). It is 

important to note that the Sawtooth Valley lakes are generally smaller than the lakes used to 

generate the general relationship between lake area and average Sockeye Salmon production, and 

that the Sawtooth Valley is at a significantly higher elevation. The ICTRT recommended criteria 

(including the minimum abundance thresholds) reflect the best information currently available. 

Still, information gained from ongoing studies of the production potential in each of the 

Sawtooth Valley lakes, and the rates of exchange among them, should be periodically reviewed 

to determine if the basic assumptions behind the current criteria remain valid, or if updates would 

be warranted. 

The ICTRT recommended considering average natural-origin abundance and productivity in 

combination when assessing viability and expressed criteria for these parameters in terms of 

viability curves corresponding to particular risk thresholds (ICTRT 2007). ESU-specific curves 
ESA Recovery Plan: Snake River Sockeye Salmon | 120

June 2015| NOAA Fisheries 

corresponding to thresholds of 1%, 5%, and 25% risk over 100 years were generated and used to 

define very low, low, and moderate extinction risk categories. These criteria were specifically 

designed to inform longer-term status and recovery evaluations of listed ESUs. Variations on 

these basic criteria for use in assessing short-term performance and risk are possible, and could 

be developed and incorporated into recovery implementation strategies as an aid to assessing 

progress. The ICTRT did not have a sufficient trend data set for Redfish Lake Sockeye Salmon

to use in directly generating a viability curve. They set the minimum spawning abundance 

threshold at 1,000 natural-origin spawners measured as a ten-year geometric mean for the 

Redfish and Alturas Lake populations, and 500 natural-origin spawners measured as a ten-year 

geometric mean for populations in the smallest historical size category (e.g., Pettit, Yellowbelly 

or Stanley Lake). They used a run reconstruction of Lake Wenatchee Sockeye Salmon as the 

basis for a representative set of variance and autocorrelation input values along with average age 

structure from historical Redfish Lake data (ICTRT 2007, Appendix A). The viability curves that 

correspond to the two size categories of Sawtooth Valley lakes (e.g., intermediate and small) are 

depicted in Figures 3-1 a & b. The productivity associated with achieving an average naturalorigin spawning abundance at the minimum threshold varies as a function of population size 

category and target risk level. For example, an average productivity exceeding 1.2 and a 

minimum average natural-origin spawner abundance of 1,000 would be required to achieve a 

very low risk rating (<1% risk projected over 100 years) for abundance and productivity for 

intermediate category populations (Redfish Lake and Alturas Lake). 
ESA Recovery Plan: Snake River Sockeye Salmon | 121

June 2015| NOAA Fisheries 

Figure 3-1. a.

Figure 3-1. b.

Figures 3-1a & b. Viability curves for application to Snake River Sockeye Salmon lake populations. a) Redfish 

Lake and Alturas Lake (Intermediate). b) small lake populations (Stanley Lake). Age structure used was 60% age-4 

and 40% age-5 adult returns. Adjusted variance (variance unexplained by autocorrelation) and autocorrelation 

parameters (derived from Lake Wenatchee data) were 0.42 and 0.41, respectively.
ESA Recovery Plan: Snake River Sockeye Salmon | 122

June 2015| NOAA Fisheries 

3.2.2.2 Spatial Structure and Diversity

Reintroduction or reestablishment of independent Sockeye Salmon populations in Alturas and 

Pettit Lakes will increase the spatial structure and diversity of the MPG/ESU. An important 

recent development is that Alturas Lake native kokanee have produced early-returning and 

earlier spawning anadromous O. nerka (than adults returning to Redfish Lake). Recent trucking 

of these early-returning fish above the Sawtooth Hatchery weir to Alturas Lake presents promise 

of improving ESU spatial structure and diversity. After successful reintroductions in Alturas and 

Pettit Lakes, the feasibility of reestablishing a population in Stanley Lake will be explored.

It is possible that distinct naturally spawning aggregations in Redfish Lake could develop.

Recently, some Redfish Lake Sockeye Salmon have been spawning in Fishhook Creek. More 

detailed information on the spatial structure within and among the Sawtooth Valley lakes

populations will be generated as recovery efforts progress. As with abundance and productivity, 

results from these specific investigations may provide for more specific expressions of viability 

criteria for application to Snake River Sockeye Salmon to ensure the underlying objectives are 

met. The risks to ESU life-history diversity will be diminished by reestablishing life-history 

patterns that may have been present in the natal lakes. It appears that we may have such an 

opportunity to restore both shoal beach and stream spawning life-history types in the ESU. 

3.2.2.3 Recovery Scenario

The ICTRT recommended that the long-term recovery scenario should include restoring at least 

two of the three historical lake populations in the ESU to highly viable, and one to viable status, 

using Redfish Lake, Alturas Lake, and Pettit Lake. As recovery efforts progress over time, the 

ICTRT recommended considering expansion of reintroductions into Yellowbelly Lake and 

Stanley Lake.

3.3 Listing Factors/Threats Criteria

Threats, in the context of salmon recovery, are understood as the activities or processes that 

cause the biological and physical conditions that limit salmon survival (the limiting factors). 

Threats also refer directly to the listing factors detailed in section 4(a)(1) of the ESA. Listing 

factors are those features that are evaluated under section 4(a)(1) when initial determinations are 

made whether to list species for protection under the ESA. 

ESA section 4(a)(1) listing factors are the following:

A. Present or threatened destruction, modification, or curtailment of [the species’] habitat or 

range; 

B. Over-utilization for commercial, recreational, scientific, or educational purposes; 

C. Disease or predation; 

D. Inadequacy of existing regulatory mechanisms; or 
ESA Recovery Plan: Snake River Sockeye Salmon | 123

June 2015| NOAA Fisheries 

E. Other natural or human-made factors affecting [the species’] continued existence.

At the time of a delisting decision for the Snake River Sockeye Salmon ESU, NMFS will 

examine whether the section 4(a)(1) listing factors have been addressed. To assist in this 

examination, NMFS will use the listing factors (or threats) criteria described below, in addition 

to evaluation of biological recovery criteria and other relevant data and policy considerations. 

The threats need to have been addressed to the point that delisting is not likely to result in their 

re-emergence. 

NMFS recognizes that perceived threats, and their significance, can change over time due to 

changes in the natural environment or changes in the way threats affect the entire life cycle of 

salmon. Indeed, this has already happened. As discussed earlier, some threats perceived as 

significant effects on Snake River Sockeye Salmon at the time of listing, such as harvest 

mortality, have since been addressed through management adjustments and now pose little 

danger to species viability. Other threats, such as the mainstem hydropower system, continue to 

limit recovery efforts. At the same time, new threats, such as those posed by climate change, may 

be emerging. Consequently, NMFS expects that the relative priority of threats will continue to 

change over time and that new threats may be identified. During its five-year reviews, NMFS 

will review the listing factor criteria as they apply at that time.

The specific criteria listed below for each of the relevant listing/delisting factors help to ensure 

that underlying causes of decline have been addressed and mitigated before a species is 

considered for delisting. NMFS expects that if the proposed actions described in the Plan are 

implemented, they will make substantial progress toward meeting the following listing factor 

(threats) criteria for Snake River Sockeye Salmon. Section 5 discusses the threats and limiting 

factors that currently affect Snake River Sockeye Salmon viability. 

Factor A: The present or threatened destruction, modification, or curtailment of [the 

species’] habitat or range.

To determine that the ESU is recovered, threats to habitat should be addressed as outlined below:

1. Passage obstructions (e.g., dams, artificial fish barriers, weirs, and culverts) are removed 

or modified to improve survival and restore access to historically accessible habitat where 

necessary to support recovery goals. Reestablish the conditions necessary for residual 

Sockeye Salmon to express anadromy.

2. Flow conditions that support adequate rearing, spawning, and migration are achieved 

through management of mainstem and tributary irrigation and hydropower operations, 

and through increased efficiency and conservation in other consumptive water uses such 

as municipal supply.

3. Forest management practices that protect watershed and stream functions are 

implemented on Federal, state, tribal, and private lands.
ESA Recovery Plan: Snake River Sockeye Salmon | 124

June 2015| NOAA Fisheries 

4. Agricultural practices, including grazing, are managed in a manner that protects and 

restores riparian areas, floodplains, and stream channels, and protects water quality from 

sediment, pesticide, herbicide, and fertilizer runoff.

5. Urban, rural, and recreational development does not reduce water quality or quantity, or 

impair natural stream or lake conditions so as to impede achieving recovery goals.

6. Limnetic processes are protected and restored so that ecological inputs (of sediment, 

instream and groundwater flows, insects, leaves and wood) and ecological habitat 

processes support properly functioning lake and shoreline habitat conditions, which in 

turn support adequate adult migration, rearing, and spawning habitat for Sockeye Salmon

and the species they prey upon.

7. The effects of toxic contaminants on salmonid fitness and survival are understood and are 

sufficiently limited so as not to affect recovery.

8. Channel function, including vegetated riparian areas, canopy cover, stream-bank stability, 

off-channel and side-channel habitats, natural substrate and sediment processes, and 

channel complexity are restored to provide adequate rearing and spawning habitat. 

9. Floodplain function and the availability of floodplain habitats for salmon are restored to a 

degree sufficient to support a viable ESU/DPS. This restoration should include 

connectedness between river and floodplain and the restoration of impaired sediment 

delivery processes.

Factor B: Over-utilization for commercial, recreational, scientific, or educational purposes.

To determine that the ESU is recovered, any utilization for commercial, recreational, scientific, 

or educational purposes should be managed as outlined below:

1. Fishery management plans are in place that (a) accurately account for total fishery 

mortality (i.e., both landed catch and non-landed mortalities) and constrain mortality rates 

to levels that are consistent with recovery; and (b) are implemented in such a way as to 

avoid deleterious genetic effects on populations or negative effects on the distribution of 

populations. 

2. Federal, tribal, and state rules and regulations are effectively enforced. 

3. Technical tools accurately assess the effects of the harvest regimes so that harvest 

objectives are met but not exceeded. 

4. Handling of fish is minimized to reduce indirect mortalities associated with educational 

or scientific programs, while recognizing that monitoring, research, and education are key 

actions for conservation of the species. 

5. Routine construction and maintenance practices are managed to reduce or eliminate 

mortality of listed species.
ESA Recovery Plan: Snake River Sockeye Salmon | 125

June 2015| NOAA Fisheries 

Factor C: Disease or predation.

To determine that the ESU is recovered, any disease or predation that threatens its continued 

existence should be addressed as outlined below: 

1. Hatchery operations do not subject targeted populations to deleterious diseases and 

parasites and do not result in increased predation rates of wild fish.

2. Predation by avian predators is managed in a way that allows for recovery of Sockeye 

Salmon populations.

3. Populations of introduced exotic predators such as smallmouth bass, walleye, and catfish 

are managed such that competition or predation does not impede recovery.

 4. Physiological stress and physical injury that may cause disease or increase susceptibility 

to pathogens during rearing or migration is reduced during critical low flow periods (e.g. 

low water years) or poor passage conditions (e.g. at diversion dams or bypasses).

Factor D: The inadequacy of existing regulatory mechanisms.

To determine that the ESU is recovered, any inadequacy of existing regulatory mechanisms that 

threatens its continued existence should be addressed as outlined below:

1. Adequate resources, priorities, regulatory frameworks, and coordination mechanisms are 

established and/or maintained for effective enforcement of land and water use regulations 

that protect and restore habitats, including water quality and water quantity, and for the 

effective management of fisheries. 

2. Habitat conditions and watershed functions are protected through land-use planning that 

guides human population growth and development.

3. Habitat conditions and watershed function are protected through regulations that govern 

resource extraction such as timber harvest and gravel mining.

4. Habitat conditions and watershed functions are protected through land protection 

agreements as appropriate, where existing policy or regulations do not provide adequate 

protection.

5. Regulatory, control, and education measures to prevent additional exotic plant and animal 

species invasions are in place.

6. Sufficient priority instream water rights for fish habitat are in place.

Factor E: Other natural or human-made factors affecting [the species’] continued 

existence.

To determine that the ESU is recovered, other natural and man-made threats to its continued 

existence should be addressed as outlined below:
ESA Recovery Plan: Snake River Sockeye Salmon | 126

June 2015| NOAA Fisheries 

1. Hatchery programs are being operated in a manner that is consistent with individual 

watershed and region-wide recovery approaches; appropriate criteria are being used for 

integration of hatchery Sockeye Salmon populations and extant natural populations 

inhabiting watersheds where the hatchery fish return. 

2. Hatcheries operate using appropriate ecological, genetic, and demographic risk 

containment measures for (1) hatchery-origin adults returning to natural spawning areas, 

(2) release of hatchery juveniles, (3) handling of natural-origin adults at hatchery 

facilities, (4) withdrawal of water for hatchery use, (5) discharge of hatchery effluent, and 

(6) maintenance of fish health during their propagation in the hatchery.

3. Monitoring and Evaluation plans are implemented to measure population status, hatchery 

effectiveness, and ecological, genetic, and demographic risk containment measures.

4. Nutrient enrichment programs are implemented where it is determined that nutrient 

limitations are a significant limiting factor for Sockeye Salmon production and that 

nutrient enrichment will not impair water quality.

5. Recovery actions, together with monitoring and evaluation programs, seek to understand 

the impacts of climate change on the marine environment and marine survival of Pacificorigin Sockeye Salmon, and adapt recovery actions to address information on the impacts 

of climate change. 

3.4 Delisting Decision

In accordance with its responsibilities under section 4(c)(2) of the ESA, NMFS will conduct 

reviews of Snake River Sockeye Salmon every five years to evaluate the status of the species and 

gauge progress toward delisting. Such evaluations will take into account the following:

• The biological recovery criteria (ICTRT 2007) and listing factor (threats) criteria 

described above.

• The management programs in place to address the threats.

• Principles presented in the Viable Salmonid Populations paper (McElhany et al. 

2000).

• Best available information on population and ESU status and new advances in 

risk evaluation methodologies.

• Other considerations, including: the number and status of extant spawning groups; 

the status of the major spawning groups; linkages and connectivity among groups; 

the diversity of life history and phenotypes expressed; and considerations 

regarding catastrophic risk.
ESA Recovery Plan: Snake River Sockeye Salmon | 127

June 2015| NOAA Fisheries 

Section 4: Current Status Assessment of Snake River 

Sockeye Salmon ESU

4.1 Abundance and Productivity

4.2 Spatial Structure and Diversity

4.3 ESU Status
ESA Recovery Plan: Snake River Sockeye Salmon | 128

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 129

June 2015| NOAA Fisheries 

4. Current Status Assessment of Snake River Sockeye 

Salmon ESU

In 2011, NMFS determined in its five-year review of the Snake River Sockeye Salmon that the 

ESU should retain its “endangered” classification (NMFS 2011b,

http://www.nmfs.noaa.gov/pr/pdfs/species/snakeriver_salmonids_5yearreview.pdf).

The five-year review depended in part on Ford (2011), which provided an updated scientific 

summary of the risk status of the subject species. 

Before the initiation of the captive brood-based hatchery program, Snake River Sockeye Salmon

had declined to remnant population components apparently maintained by residual spawning in 

one or two lakes  in some years no anadromous Sockeye Salmon returned to the basin. In 

terms of natural production, this ESU remains at a very high risk of extinction. As a result, the 

most recent five-year review discussed long-term natural production objectives and indicators 

measuring progress on key initial phase restoration steps. These included building a sufficient 

level of anadromous returns from captive brood releases for outplanting assessments and 

measures of key life stage survivals (e.g., egg or adult outplant to outmigrant smolt and lake 

migrant to Lower Granite Dam). Building to target levels of adult hatchery returns and gaining 

knowledge of key survival rates are important steps towards successfully reestablishing natural 

production in the Sawtooth Valley. 

NMFS’ biological viability criteria for salmonid populations and the methods for assessing risk 

of extinction are based on the VSP parameters of abundance, productivity, spatial structure, and 

diversity, described in detail in Section 3. In this section we review the most recent data on 

Snake River Sockeye Salmon status for these parameters, based on NMFS 2008 Supplemental 

Comprehensive Analysis (NMFS 2008b), as updated with IDFG’s more recent adult return data;

the ICTRT’s 2010 status assessment (ICTRT 2010); and the most recent five-year review of 

West Coast ESA-listed salmonids (Ford 2011).

4.1 Abundance and Productivity

Adult Sockeye Salmon returns to Redfish Lake during the period 1954 through 1966 were of 

natural-origin and ranged from 11 to 4,361 fish (Bjornn et al. 1968). In 1985, 1986, and 1987, 

11, 29, and 16 Sockeye Salmon, respectively, were counted at the Redfish Lake weir (WCSBRT 

2003; Good et al. 2005). In 1991, at the time of the listing, only one, one, and zero Sockeye 

Salmon had returned to Redfish Lake in the three preceding years, respectively. 

Biologists have also counted Sockeye Salmon at the Sawtooth Fish Hatchery weir since its 

installation on the Salmon River above Redfish Lake Creek in 1985. The weir captured three 

anadromous Sockeye Salmon in 1985 and two in 1987, but no Sockeye Salmon in 1986. Since 

then, captures of additional unmarked adult Sockeye Salmon of unknown origin at the Sawtooth 
ESA Recovery Plan: Snake River Sockeye Salmon | 130

June 2015| NOAA Fisheries 

Fish Hatchery weir included one in 1988, one in 1996, three in 2002, three in 2004, one in 2006 

and three in 2007. Known adult returns from Alturas Lake (confirmed by genetic analysis) have 

been trapped at the Sawtooth Fish Hatchery weir in recent years: one, one, fourteen, and two

Sockeye Salmon in 2008, 2009, 2010, and 2011, respectively (Kozfkey 2013b).

Between 1991 and 1998, all 16 of the natural-origin adult Sockeye Salmon that returned to the 

weir at Redfish Lake were incorporated into the captive broodstock program, as well as outmigrating smolts captured between 1991 and 1993, and residual Sockeye Salmon captured 

between 1992 and 1995 (Hebdon et al. 2004). The program has used multiple rearing sites to 

minimize chances of catastrophic loss of broodstock and has produced several million eggs and 

juveniles, as well as several thousand adults, for release into the wild. 

4.1.1 Current Abundance Data

Estimates of annual returns are now available through 2014 (Table 4-1) (IDFG, in prep.). 

Between 1999 and 2007, more than 355 adults returned from the ocean from captive broodstock 

releases – almost 20 times the number of wild fish that returned in the 1990s (Flagg et al. 2004). 

However, this total is primarily due to large returns in the year 2000 (number: 257). Returns for 

2003-2007 were relatively low, similar to the range observed between 1987 and 1999. Sockeye 

Salmon returns have increased since 2008. Adult returns the last seven years include 646 fish in 

2008 (including 140 natural-origin fish), 832 in 2009 (including 86 natural-origin fish), 1,355 in 

2010 (including 178 natural-origin fish), 1,117 in 2011 (including 145 natural-origin fish), 257 

adults in 2012 (including 52 natural-origin fish, 272 adults in 2013 (including 79 natural-origin 

fish), and 1,579 adults in 2014 (including 453 natural-origin fish) (IDFG, in prep.). 

Approximately two-thirds of the adults captured in each year were taken at the Redfish Lake 

Creek weir; the remaining adults were captured at the Sawtooth Hatchery weir on the mainstem 

Salmon River upstream of the Redfish Lake Creek confluence (Ford 2011). In addition, Sockeye 

Salmon (adults derived from early stream spawning kokanee) attempting to return to Alturas 

Lake, but stopped by the Sawtooth Fish Hatchery weir, have ranged from 1 adult in 2002 to 14

adults in 2010. No Sockeye Salmon attempted to return to Alturas Lake in 2012, 2013, or 2014

(IDFG, in prep.). 
ESA Recovery Plan: Snake River Sockeye Salmon | 131

June 2015| NOAA Fisheries 

Table 4-1. Hatchery and natural-origin Sockeye Salmon returns to Sawtooth Valley, 1999 - 2014 (IDFG, in prep.).

Return

Year

Total Return

Natural

Return Hatchery Return

Observed

(Not trapped)

Assigned 

Alturas 

Returns*

1999 7 0 7 0 0

2000 257 10 233 14 0

2001 26 4 19 3 0

2002 22 6 9 7 1

2003 3 0 2 1 0

2004 27 4 20 3 0

2005 6 2 4 0 0

2006 3 1 2 0 0

2007 4 3 1 0 0

2008 646 140 456 50 1

2009 832 86 730 16 2

2010 1,355 178 1,144 33 14

2011 1,117 145 954 18 2

2012 257 52 190 15 0

2013 272 79 191 2 0

2014 1,5793 453 1,062 63 0

*These fish are included in the natural return numbers.

4.1.2 Productivity

The ICTRT defines productivity as the expected return per spawner (or other measure of 

population growth rate) from low to moderate escapements averaged over the most recent 20-

year period. During the reintroduction phase, assessing productivity of naturally spawning 

Sockeye Salmon in each of the lakes as adults returning from the hatchery supplementation 

program will be an important indicator of progress towards recovery goals. Until spawning is 

reestablished in at least one lake (a major intermediate term objective of the recovery strategy for 

this ESU), direct estimates of population productivity will not be possible. However, measures of 

key components of overall life cycle productivity will be very informative for assessing progress 

towards recovery during the initial reintroduction phases. For example, with recent increased 

returns from the hatchery program and from outplants of anadromous spawners to Redfish Lake, 

it has been possible to estimate adult returns with greater accuracy, to compare juvenile

survival/mortality by inriver migration vs. transport, and to compare adult survival between 

various reaches during upstream passage. The reintroduction of spawners into each lake, 

initially comprised of returns or outplants from the hatchery program, will provide for an 

 

3 Note: Including one unknown origin Sockeye Salmon in 2014.
ESA Recovery Plan: Snake River Sockeye Salmon | 132

June 2015| NOAA Fisheries 

opportunity to directly evaluate juvenile production rates and, ultimately, gain insights into 

carrying capacity relationships. As the program progresses, direct information on another key 

question, a potential increase in parr production rates from naturally produced adult returns, 

should also become available. In the short term, periodic status reviews are summarizing

information on survival estimates for key sub-elements of overall productivity as it becomes 

available (i.e., from life stage survival studies focusing on hatchery releases and initial 

outplanting evaluations). Recent data on the survival of juvenile and adult migrants, which 

determine productivity in the smolt-to-adult portion of the life cycle, are described in the 

following sections.

Juvenile production from natural spawning

As adults from the reintroduction program begin to spawn in Redfish Lake, an important element 

of the adaptive management program will involve sampling designed to produce direct estimates 

of the levels of parr and outmigrant smolt abundance as a function of annual estimates of adult 

spawning. Evaluating juvenile production levels as parent spawning levels increase will provide 

important early indications of a key life stage component of overall productivity, spawner to 

juvenile survivals. As juvenile production levels increase, monitoring efforts should also provide 

direct information on density dependent limitations on production.

Juvenile migrant survival  Sawtooth Lakes to Lower Granite Dam

Hatchery releases from the captive broodstock program have allowed fish managers to track the 

migration of hatchery juvenile Sockeye Salmon after release in the Sawtooth Valley. These 

monitoring and evaluation studies show that the fish move quickly through the reach, often arriving 

at Lower Granite Dam in approximately seven days. Estimated survival for the hatchery juveniles in 

the reach has been highly variable among different release locations, rearing strategies, origin, and 

years (Axel et al. 2014). Based on detections of Sockeye Salmon hatchery juveniles that were tagged 

with a PIT-tag and released in spring, survival estimates have ranged from 11.4% in 2000 (Zabel et 

al. 2001) to 77.6% in 2008 (Faulkner et al. 2008). 

IDFG and NMFS continue to conduct studies to characterize migration and survival for juvenile 

Snake River Sockeye Salmon between the upper Snake River basin and Lower Granite Dam. 

This project applies a multifaceted tracking approach, utilizing PIT-tag and radio-telemetry 

methodologies to demonstrate where and when mortality is occurring. Data collected from the 

studies indicates that release timing of hatchery smolts may have a direct impact on survival 

estimates. High flows in the upper Salmon River also likely contribute to shorter travel times 

between release sites and Lower Granite Dam (Axel et al. 2014). 

In addition, data indicate that the majority of juvenile mortality occurs between the release 

location and the North Fork Salmon River, after which mortality appears to level off to Lower 

Granite Dam (Axel et al. 2014). Higher losses appear to occur within Little Redfish Lake, in the 

reach just above Valley Creek near Stanley, between the Pahsimeroi and Lemhi Rivers, and in 

the slow-river reach at Deadwater Slough (Axel et al. 2014). Research continues to examine the 
ESA Recovery Plan: Snake River Sockeye Salmon | 133

June 2015| NOAA Fisheries 

causes of mortality in each reach and determine how release strategies might be changed to 

improve juvenile migrant survival. Currently, losses in several of these sections seem to be 

related to predation; however, other possible culprits include competition with non-native 

species, environmental conditions, or the results of rearing and release strategies. Upon 

completion, the research should provide a better understanding of where mortality occurs during 

downstream migration to Lower Granite.

Juvenile migrant survival  Lower Granite Dam to Bonneville Dam

Survival rates for juvenile Sockeye Salmon migrants in the reach from Lower Granite Dam to 

Bonneville Dam reflect aggregate rates for two major downstream migration routes: inriver 

passage and downstream transport to below Bonneville Dam. Based on data for yearling Snake 

River Chinook salmon, NMFS estimates that the proportion of Snake River Sockeye Salmon

migrants transported each year has ranged from approximately 98% in 2001 to 23% in 2012 

(Table 23 in Faulkner et al. 2013). About 36% of yearling Chinook salmon (and potentially 

Sockeye Salmon) migrants were transported in 2013 (Zabel 2013). The mean estimated survival 

of juvenile inriver Snake River Sockeye Salmon migrants from Lower Granite to McNary Dam 

was 60% for the period 1996-2010; individual year estimates ranged from 28% (1996) to 76%

(2008) (Ferguson 2010). Mean survival from McNary Dam to Bonneville Dam (1998-2003, 

2006-2010) was 54%, which should be interpreted with caution due to small sample sizes and 

associated low detection probabilities for many of the individual year estimates (Ferguson 2010). 

Juvenile survival from Lower Granite to Bonneville Dam since 2008 has ranged from 40% to 

57% (NMFS 2014c).

Juvenile and adult migrant survival  Estuary, Plume, and Ocean

The following discussion of factors that affect the survival of Columbia Basin Sockeye Salmon

in the estuary, plume, and ocean is excerpted from Fresh et al. (2014). 

The effects of variability in ocean productivity can mask, enhance, or even override underlying 

trends in freshwater habitat productivity and lead to a misinterpretation of the causes of

variability in adult returns. However, the estuarine and ocean ecology of this ESU is largely 

unknown. After its near extirpation by the mid-1990s, the ESU remains at very low abundance 

levels and only a handful of the Sockeye Salmon caught in surveys off the west coast of 

Vancouver Island since 1998 were confirmed as originating from the Snake River (M. Trudel, 

Department of Fisheries and Oceans Canada, personal communication). We must use 

information on Sockeye Salmon originating from other spawning areas, including the unlisted 

Okanogan and Lake Wenatchee ESUs and the populations in British Columbia and Alaska, to 

draw inferences about the estuarine and marine life history of Snake River Sockeye Salmon.

Based on PIT-tag detections, peak passage of juvenile Snake River Sockeye Salmon at 

Bonneville Dam is generally in late May, about two weeks later than that of all Columbia Basin

Sockeye Salmon juveniles combined. Catches of all juvenile Sockeye Salmon in the estuary peak 

in early June, with most fish caught between May 15 and June 15 (Weitkamp et al. 2012). There 
ESA Recovery Plan: Snake River Sockeye Salmon | 134

June 2015| NOAA Fisheries 

is relatively little annual variation in migration timing through the estuary: peak catches occurred

on June 1, 2007, June 5, 2008, and June 10, 2010 (no peak observed in 2009) (Weitkamp et al. 

2012). Two PIT-tagged Sockeye Salmon migrated from Redfish Lake to RM 9 in 15 and 21 

days, respectively; one of the fish detected at RM 9 had been detected at Bonneville Dam three 

days earlier.

Sockeye Salmon immediately begin migrating north when they leave the Columbia; none have 

been caught south of the river’s mouth in 15 years of sampling. They are most abundant off 

Washington in May and June, but some have migrated as far as the northern coast of British 

Columbia (Tucker et al. 2009) by June. Sockeye Salmon are absent from the ocean off 

Washington by September. They move north, with some evidence of migration along the 

Alaskan coast, entering the offshore waters of the Gulf of Alaska by winter (Tucker et al. 2009), 

although these observations were overwhelmingly dominated by fish from British Columbia 

populations.

4

Evidence from a variety of salmon ESUs and steelhead DPSs, including some from the 

Columbia Basin, supports the hypothesis that early marine life is a critical period that largely 

determines the strength of adult returns years in the future (Ricker 1976; Beamish et al. 2004; 

Mueter et al. 2005; Farley et al. 2007; Wells et al. 2008; MacFarlane 2010; Moore et al. 2010; 

Duffy at al. 2011; Thomson et al. 2012; Tomaro et al. 2012; Miller et al. 2013; Burke et al. 

2013). Most early marine mortality is thought to occur during two critical periods within the first 

year of ocean life. The first period is thought to be predation-based mortality that occurs during 

the first few weeks to months (e.g., Brosnan et al. 2014; Freidland et al. 2014). The second 

occurs during and following the first winter at sea and is thought to be driven by food 

availability/starvation (Beamish and Mahnken 2001; Moss et al. 2005). That is, juvenile fish 

have to consume enough food during their first spring and summer at sea to achieve a critical 

size with enough accumulated energy reserves that they can survive the following winter. Studies 

with a variety of salmonid stocks (including Columbia River spring Chinook salmon) have found 

that body size and survival are often positively related (Bilton et al. 1982; Holtby et al. 1990; 

Henderson and Cass 1991; Mortensen et al. 2000; Duffy et al. 2011; Tomaro et al. 2012; 

Woodson et al. 2013). In general, larger bodied fish are less likely to die than smaller bodied fish 

although this relationship may not be true under all ocean environmental conditions (Irvine et al. 

2013; Woodson et al. 2013) or for all species (Welch et al. 2011). Fish size can affect

vulnerability to predation as well as starvation (Willette et al. 2001). The marine diet of Sockeye 

Salmon is dominated by invertebrates, especially euphausiids (krill) in the Gulf of Alaska and 

Bering Sea (Peterson et al. 1982; Brodeur 1990; Myers et al. 1999).

 

4 Of the 4,156 juvenile Sockeye Salmon analyzed by Turner et al. (2012), 4,062 were allocated to regional 

populations and Columbia Basin fish accounted for about 4% of these.
ESA Recovery Plan: Snake River Sockeye Salmon | 135

June 2015| NOAA Fisheries 

Adult migrant survival  Bonneville Dam to Lower Granite Dam

Adult PIT-tag detectors, in place since 2002 at Bonneville, McNary, and Lower Granite dams,

allow NMFS to monitor the survival of specific stocks (e.g., those from the Oxbow versus 

Sawtooth hatcheries) through the Bonneville to Lower Granite Dam migration corridor. 

Before the number of returning adult Snake River Sockeye Salmon increased due to releases 

through the captive broodstock program, PIT-tag detections from upper Columbia River Sockeye 

Salmon stocks were used to extrapolate the survival rates for Snake River Sockeye Salmon in the 

Bonneville to Lower Granite Dam migration corridor. This changed after enough known-origin 

adult Snake River Sockeye Salmon returned to the Columbia Basin in 2010–2012 to make PITtag-based direct (rather than extrapolated) conversion rate estimates for the reach. 

The Corps of Engineers recently installed PIT-tag detectors in both ladders at The Dalles Dam.

These detectors are allowing estimates of survival rates between Bonneville and The Dalles 

dams and between The Dalles and McNary dams, helping regional managers assess where losses

are occurring. NMFS and the Action Agencies are assessing the need for additional detectors at 

John Day Dam, as discussed in the 2010 and 2014 Supplemental FCRPS BiOp. The Corps is also 

planning to install temporary (2 to 4 years) adult PIT-tag detectors at Lower Monumental and 

Little Goose dams within the lower Snake reach, which should similarly help isolate the 

subreaches where losses are occurring.

Recent Cormak Jolly Seber-based survival estimates for PIT-tagged Snake River Sockeye 

Salmon indicate that for 2010-2013, survival rates averaged from 56% to 83% for the Bonneville 

to McNary reach; 92% to 99% for the McNary to Ice Harbor reach; and 71% to 97% for the Ice 

Harbor to Lower Granite reach (Table 4-2). ). Crozier et al. (2014) present similar adult survival 

estimates through the FCRPS dams, and from Bonneville to the Sawtooth Valley for 2008 to 

2013. Survival through the entire hydrosystem (Bonneville Dam to Lower Granite Dam) 

exceeded 70% from 2008 to 2010, but then declined to a low of 44% in 2013. The bulk of the 

loss occurred in the reach between Bonneville Dam and McNary Dam, with a survival estimate 

of only 58% in 2012. Crozier et al. describe survival from Lower Granite to the Sawtooth

Valley, which peaked in 2010 and 2011, declined in 2012, and then dropped by half in 2013. 

These results are similar to the estimates in Table 4-2. 
ESA Recovery Plan: Snake River Sockeye Salmon | 136

June 2015| NOAA Fisheries 

Table 4-2. Cormak Jolly Seber-based survival estimates for PIT-Tagged Snake River Sockeye Salmon with 95% confidence intervals (Bellerud 2014). These 

estimates include the effects of the existence and operation of the FCRPS, straying of adults in the migration corridor, delayed effects of attacks by marine 

mammals below Bonneville Dam, harvest, and any other sources “natural” morality (i.e., that would have occurred without the influence of human activity).

Year

Number of Fish 

Detected at 

BON

Bonneville to McNary McNary to Ice 

Harbor

Ice Harbor to 

Lower Granite

Bonneville To Lower 

Granite Lower Granite to Sawtooth Valleya Bonneville to Sawtooth Valleya

2010 41

83%

(72.2% -95.2%)

98%

(92.3% - 100%)

93%

(83.2%-100%)

76%

(63.6%-89.9%)

77%

(64.0%-93.6%)

58%

(42.1%-73.7%)

Median travel time 5.1 days 6.5 days − 35.5 days −

2011 516

68%

(63.5%-71.6%)

99%

(97.7%-100%)

97%

(94.9%-99.2%)

65%

(61.2%-69.5%)

74%

(69.5%-79.0%)

48%

(44.0%-52.9%)

Median travel time 5.9 days 6.5 days − 39.3 days −

2012 127

56%

(47.3%-64.4%)

97%

(91.6%-100%)

93%

(85.1%-99.1%)

51%

(42.5%-58.8%)

62%

(51.0%-75.1%)

32%

(23.5%-40.3%)

Median travel time 5.5 days 6.2 days − 36 days −

2013 207

67%b

92%

(85.2%-98.2%)

71%

(63.3%-80.3%)

44%

(37.1%-51.0%)

33% b

15%

10.0%-20.0%

Bonneville 

to The 

Dallesc

The Dalles to 

McNary

LGR to 

Salmon RM 

262c

Salmon RM 

262 to RM 

276c

Salmon RM 

276c to 

Sawtooth 

Valleya

83% 81% 50.2% 87.6% 75.0%

(77.8%-

88.2%)

(75.5%-

87.3%)

(39.7%-

63.4%)

(69.0%-

100%)

(58.3%-

96.5%)

Median travel time 5.2 days 7.1 days − 39.7 days −

Average 69% 98% 89% 59% 62% 38%

aThese are minimum survival estimates because the detection efficiency of the Sawtooth Valley PIT-tag detection arrays is unknown. That is, some adults that are detected at Salmon RM 276 may 

have returned to the Sawtooth Valley, but have been outside the area interrogated by the detectors.

bThe 67% survival estimate for the Bonneville to McNary reach for 2013 is the product of the estimates for the Bonneville-The Dalles and The Dalles-McNary subreaches in the rows underneath. In 

the same manner, the 33% estimate for the Lower Granite to Sawtooth Valley reach is the product of the LGR-Salmon RM 262 through Salmon RM 276-Sawtooth Valley reaches in the rows 

underneath. 

cPIT-tag detectors came on line in 2013 at The Dalles Dam and at Salmon RMs 262 and 276.
ESA Recovery Plan: Snake River Sockeye Salmon | 137

June 2015| NOAA Fisheries 

Productivity of the Snake River Sockeye Salmon ESU is tied to adult run timing because 

survival through the 743 km (462-mile) reach from Lower Granite Dam to the Sawtooth Valley 

decreases as the season progresses (Crozier et al. 2011). Adult migration timing for Snake River 

Sockeye Salmon has been progressing earlier in the year over the 20th century and this trait may 

have evolved due to mortality of late migrants exposed to higher Columbia River temperatures 

(Crozier et al. 2011). The fish also show a strong annual response to river flow, such that they 

migrate earlier in low-flow years. 

Adult migrant survival  Lower Granite Dam to Sawtooth Valley

Beginning in 2008, PIT-tagged adults from the captive broodstock program began to return to 

the Sawtooth Valley in sufficient numbers to begin investigating adult return rates from Lower 

Granite Dam upstream to return locations. PIT-tagged adults returning each year have enabled us

to calculate survival rates from Lower Granite Dam to the Sawtooth Valley (Table 4-3). Of the 

5,574 adults that passed Lower Granite from 2008 to 2012, a total of 4,207 (75%) were 

recovered at Redfish Lake, the Sawtooth Hatchery weir or other basin trapping locations (IDFG 

2012). It is important to point out, however, that the average survival rate of 73% is only for the 

years 2008-2012, and does not reflect the lower rate for 2013 (Table 4-2).

Table 4-3. Adult Sockeye Salmon passage at Lower Granite Dam, adjusted for fallback and reascension using PITtagged adult return data and survival rates to the Sawtooth Valley (Peterson et al. 2012).

Year Total Passage % Fallback 95% CI # of PIT-Tags Adjusted 

Passage

# of Trapped Adults Conversion to 

Sawtooth Valley

2008 909 9.10% +/- 17.0% 10 826 599 72.52%

2009 1,219 5.60% +/- 10.6% 17 1.151 817 70.98%

2010 2,201 11.80% +/- 10.8% 30 1,941 1,306 67.28%

2011 1,502 13.40% +/- 3.4% 323 1,301 1,098 84.40%

2012 470 24.40% +/- 9.3% 62 355 243 68.45%

Average 72.73%

Estimates of survival from Lower Granite to the Sawtooth Valley presented in Table 4-3 vary 

slightly from those shown in Table 4-2. The estimates in Table 4-2 are based on detections of 

PIT-tagged Snake River Sockeye Salmon at Lower Granite and various sites in the Sawtooth 

Valley, corrected for detection efficiency. In comparison, Table 4-3 uses a ratio between the 

number of fish counted at Lower Granite (corrected for fallback and reascension using PIT-tag

information) and the total number of fish trapped in the Sawtooth Valley. Nevertheless, the 

findings presented in the two tables are similar. For the years 2010 through 2012, the average 

survival estimates are 71% for the data presented in Table 4-2 and 73% for the data presented in 

Table 4-3. A lower survival estimate for 2013, shown in Table 4-2, reflects losses due to high 

water temperatures at Lower Granite Dam in late July 2013, which blocked adult Snake River 

Sockeye Salmon passage for more than a week and resulted in high mortality rates for migrating 

adult Sockeye Salmon (see Section 3.3.3.1 in NMFS 2014c). 
ESA Recovery Plan: Snake River Sockeye Salmon | 138

June 2015| NOAA Fisheries 

Information gained from the PIT-tag detectors installed in 2013 also provides a snapshot of adult 

Sockeye Salmon survival through different Salmon River reaches. Minimum survival estimates5

for adult PIT-tagged Sockeye Salmon were 50% from Lower Granite Dam to Salmon RM 262, 

88% from Salmon RM 262 to RM 276, and 75% from Salmon RM 276 to the Sawtooth Valley 

(Table 4-2). Section 5.1.2, Salmon River, describes the limiting factors and threats affecting 

Snake River Sockeye Salmon in the mainstem from the Sawtooth Valley to the confluence with 

the Snake River. Limiting factors include elevated water temperatures, altered hydrologic 

regimes, reduced floodplain connectivity, and blocked passage to historical habitat. Determining 

the magnitude of this loss, as well as where and why mortality is occurring, is critical to the 

successful restoration and recovery of Sockeye Salmon populations. 

Sawtooth Valley-to-Sawtooth Valley Smolt-to-Adult Returns

Increased annual adult Sockeye Salmon returns since 2008 have allowed IDFG to develop 

Sawtooth Valley-to-Sawtooth Valley Smolt-to-Adult returns (SAR), a measure of productivity,

for the different release strategies, which helps identify and prioritize the most successful 

reintroduction strategies. For the 2004 through 2006 brood years, the natural-origin and full-term 

hatchery-raised smolts produced the highest SARs. These ranged from a low of 0.06% for brood 

year 2004 hatchery-raised pre-smolts to a high of 3.1% for brood year 2006 smolts that hatched 

in and emigrated from Redfish Lake (NMFS 2013; NMFS 2014c). The latter were derived from 

fish that spawned naturally in the lakes or hatched from eyed-eggs that had been fertilized in the 

hatchery, but then outplanted in the lake.

Information gained through monitoring allows researchers to evaluate the effectiveness of 

different supplementation strategies  information that is critical to defining the most effective 

strategies for increasing the abundance of natural spawners. The data indicates that adults from 

natural production and hatchery full-term smolts produce higher SARs than other release 

strategies. The data is being used to evaluate survival processes impacting each life-history 

phase. For example, PIT-tag data is providing valuable information on juvenile downstream 

passage survival and adult upstream survival, and the factors that influence survival at different 

stages and locations. These include the warm water temperatures that blocked adult Sockeye 

Salmon passage at Lower Granite Dam during late July in 2013; a factor that NMFS is working 

with the Corps, tribes and other co-managers to address. Juvenile and adult losses in the 

migration corridor between Lower Granite Dam and the natal lakes are not fully understood, but 

appear to be influenced by stream flow and temperature.

 

5 The survival estimates in Table 4-2 are corrected for detection efficiencies, except for the detector arrays in the 

Sawtooth Valley. Assuming that detection efficiency is less than 100%, the true conversion rates to the Sawtooth 

Valley are likely to be higher than those shown in Table 4.2.
ESA Recovery Plan: Snake River Sockeye Salmon | 139

June 2015| NOAA Fisheries 

4.2 Spatial Structure and Diversity

The same basic elements of the ICTRT spatial structure and diversity criteria that apply to stream 

type Chinook salmon and steelhead can be easily adapted to evaluate Sockeye Salmon

populations (ICTRT 2007). Within-population spatial structure can be expressed in terms of the 

number and distribution of spawning beaches and/or tributary reaches. Beach vs. river spawning 

sub- populations, where they were likely historically present, along with anadromous and 

residual components represent major life history patterns. The same basic criteria apply with 

respect to assessing within- and among-population indicators of genetic diversity and the longterm risks from continued high levels of hatchery spawners. 

Sockeye Salmon in the Snake River ESU display several different life history patterns, indicating 

population diversity within the ESU. Historically there may have been some Redfish Lake 

anadromous Sockeye Salmon that were tributary spawners, returning to habitat in Fishhook 

Creek, while others were shoal spawners, returning to spawning areas along the lake. Some 

anadromous Sockeye Salmon continue to spawn in Fishhook Creek. Information suggests that 

the historical Alturas Lake Sockeye Salmon population was also an early stream spawning type, 

similar to the Fishhook Creek kokanee population and the extant Alturas Lake kokanee. Native 

early stream spawning kokanee in Alturas Lake continue to produce smolts and adult returns and 

although they are not currently listed, they may be an important source of life history and spatial 

diversity. The historical Stanley Lake native kokanee population may have also expressed this 

early run timing. This suggests that the Alturas Lake population, and possibly the Stanley Lake 

population, remains genetically unique from the anadromous Sockeye Salmon population in 

Redfish Lake (see Griswold et al. 2012 for review). In addition, observations by Evermann 

(1894) indicate that the inlet to Pettit Lake supported Sockeye Salmon. Evermann reported 

seeing one Sockeye Salmon carcass along the inlet stream of Pettit Lake during 1894. In 1895 

they caught two Sockeye Salmon in a net set in the Pettit Lake inlet on August 14 and 22. 

Evermann also reported seeing two Sockeye Salmon in excellent condition on a shoal in Alturas 

Lake in 1895 as he was preparing to leave the area, and at a time when adults likely would have 

just begun returning to the shoal to spawn (Evermann 1896). 

At the current time, based on the low levels of naturally produced anadromous returns, the 

Redfish Lake population must be rated at high risk for diversity, since it is currently being 

maintained by captive propagation. It is at high risk of not being able to maintain: 1) natural 

patterns of phenotypic and genotypic expression, 2) natural patterns of gene flow, and 3) the 

integrity of natural systems (ICTRT 2010).

4.3 ESU Status

The captive propagation program has likely forestalled extinction of the Redfish Lake population 

and the ESU. This program has increased the total number of anadromous adults and has 

preserved what genetic diversity remained after the decline. However, the longer this program 
ESA Recovery Plan: Snake River Sockeye Salmon | 140

June 2015| NOAA Fisheries 

relies on captive broodstock to maintain the population, the greater the risks of domestication 

become. Although the program has increased the number of anadromous adults in some years, it 

has only begun to yield large numbers of returning adults (in part due to larger smolt releases and 

in part because of out-of-basin effects such as ocean conditions), and the long-term effects of 

captive propagation are unknown. 

In recent years, sufficient numbers of returning hatchery adults and their eggs and smolts have 

been available to make it feasible to use supplementation strategies to increase the abundance of 

natural spawners. Limnological studies and direct experimental releases are being conducted to 

learn more about production potential in the three Sawtooth Valley lakes that are candidates for 

Sockeye Salmon restoration. Lake habitat rearing potential, juvenile downstream passage 

survivals, and adult upstream survivals are also being studied. However, substantial increases in 

survival rates across all life history stages must occur in order to reestablish sustainable natural 

production (e.g. Hebdon et al. 2004; Keefer et al. 2008). 

The increased abundance of hatchery-reared Snake River Sockeye Salmon reduces the risk of 

immediate loss, but levels of Sockeye Salmon returns remain low. As a result, overall, although 

the risk status of the Snake River Sockeye Salmon ESU appears to be on an improving trend, the 

risk of extinction is still high and the ESU continues to be listed as endangered (Ford 2011). 
ESA Recovery Plan: Snake River Sockeye Salmon | 141

June 2015| NOAA Fisheries 

Section 5: Threats and Limiting Factors

5.1 Habitat

5.2 Hydropower

5.3 Hatcheries

5.4 Fisheries

5.5 Predation and Disease

5.6 Competition

5.7 Toxics

5.8 Climate Change
ESA Recovery Plan: Snake River Sockeye Salmon | 142

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 143

June 2015| NOAA Fisheries 

5. Threats and Limiting Factors

The reasons for a species’ decline are generally described in terms of limiting factors and threats. NMFS 

defines limiting factors as the biological and physical conditions that limit a species’ viability – e.g., 

high water temperature – and defines threats as those human activities or natural processes that cause the 

limiting factors. For example, removing the vegetation along the banks of a stream (threat) can cause 

higher water temperatures (limiting factor), because the stream is no longer shaded. 

Designing effective recovery strategies and actions requires understanding limiting factors and threats 

across the species’ entire life cycle. The term threats is often used as synonymous with the listing factors 

detailed in the ESA section 4(a)(1): destruction of habitat, over-utilization, disease or predation, 

inadequacy of existing regulatory mechanisms, or other natural or human-made factors affecting [the 

species’] continued existence. NMFS typically organizes discussions of threats according to the four Hs 

(habitat, hydro, hatcheries, and harvest), which represent the types of threats most relevant to salmonids.

While the term “threats” carries a negative connotation, it does not mean that activities identified as 

threats are inherently undesirable. They are often legitimate human activities that may at times have 

unintended negative consequences on fish populations—and that can usually be managed in a manner 

that minimizes or eliminates the negative impacts.

For Sockeye Salmon and other salmonids, survival to reproduce depends on a complex, interacting 

system of environmental conditions, with different conditions needed for each life stage. Optimal water 

temperature, for example, varies (within limits) for adult migration vs. egg incubation vs. juvenile 

rearing. In addition, the particular factors limiting production may vary across different sections of the 

tributary drainage used by a particular population. Data on a full range of potential limiting factors is 

rarely available at the reach level. As a result, the identification of limiting factors for salmonids often 

includes elements based on inference and expert opinion. 

Identification of limiting factors for Snake River Sockeye Salmon is based on a substantial body of 

research on salmonids, local field data and field observations, and the considered opinions of regional 

experts. These are implicitly hypothetical statements. They are made with the expectation that action 

will be taken in the face of some degree of scientific uncertainty. Through careful monitoring of the 

results, continuing research to resolve the uncertainties, and adapting management actions in response, 

the state of our knowledge will improve and so will the survival of these fish. 

Many human activities have contributed to the near extinction of Snake River Sockeye Salmon in the 

Snake River basin. The NMFS status review (Waples et al. 1991) that led to the original listing decision 

attributed the decline of this ESU to “overfishing, irrigation diversions, obstacles to migrating fish, and 

eradication through poisoning.” The NMFS 1991 listing decision noted that such factors as hydropower 

development, water withdrawal and irrigation diversions, water storage, commercial harvest, and 

inadequate regulatory mechanisms represented a continued threat to the ESU’s existence (NMFS 1991). 

NMFS’ 1991 listing decision also stated that predation impacts from piscivorous fish and marine 
ESA Recovery Plan: Snake River Sockeye Salmon | 144

June 2015| NOAA Fisheries 

mammals was increasing in Northwest salmonid fisheries; however, the extent of these impacts on 

Snake River Sockeye Salmon was unknown at that time. NMFS’ recent review of historical threats 

identified intense commercial harvest of Sockeye Salmon along with other salmon species beginning in 

the mid-1880s; the existence of Sunbeam Dam as a migration barrier between 1910 and early 1930s; the 

eradication of Sockeye Salmon from Sawtooth Valley lakes in the 1950s and 1960s; development of 

mainstem hydropower projects on the lower Snake and Columbia Rivers in the 1970s and 1980s; and 

poor ocean conditions in 1977 through the late 1990s as factors that contributed to the species’ decline 

(NMFS 2008c).

Today, some threats that contributed to the original listing of Snake River Sockeye Salmon now present 

little harm to the ESU while others continue to threaten viability. Impacts from ocean and inriver 

fisheries are now better regulated through ESA-listed constraints and management agreements, 

significantly reducing harvest-related mortality. Potential habitat-related threats to the fish, especially in 

the Sawtooth Valley, now pose limited concern. Several barriers that once blocked Sockeye Salmon 

passage to the natal lake have been removed or no longer obstruct fish migration. In addition, much of 

the natal lakes area and headwaters remain in excellent condition due to wilderness and other land use 

designations; almost 90% of the habitat in the Sawtooth Valley is within the U.S. Forest Service’s

Sawtooth National Recreation Area. Efforts to eradicate the species from the natal lakes through 

chemical poisoning ended decades ago. Hatchery-related concerns have also been reduced through 

management actions, particularly through the captive broodstock program that uses an integrated 

broodstock program to maintain and rebuild the species’ genetic resources; however, continued caution 

needs to be applied to ensure that hatchery releases do not influence the species natural genetic diversity 

and fitness.

Recovery efforts focus on addressing other remaining threats. Juvenile and adult losses during travel 

through the Salmon, Snake, and Columbia River migration corridor continue to present a significant 

threat to species recovery. In addition, the combined and relative effects of different threats across the 

life cycle, including threats from climate change and other unknowns, remain poorly understood. 

Consequently, while this section presents the full range of threats and limiting factors throughout the life 

cycle, the different threats do not carry equal weight in their impact on Sockeye Salmon. Our recovery 

strategy recognizes the need to better understand the effects of combined threats to Snake River Sockeye 

Salmon, and to focus recovery actions on the limiting factors and threats that are most important for 

recovery. The Plan directs actions to gain critical information regarding how different factors affect the 

fish. It also identifies considerations for prioritizing actions, and charges implementation groups with 

developing criteria to prioritize actions and scheduling implementation according. 

This section discusses the threats and limiting factors for Snake River Sockeye Salmon throughout their 

life cycle. Section 5.1 describes the threats and limiting factors for Snake River Sockeye Salmon related 

to habitat conditions in the natal lakes, Salmon River, Snake and Columbia River mainstems, Columbia 

River estuary and plume, and the ocean. Section 5.2 describes the impacts of hydro operations on the 

migration corridor through the mainstem Snake and Columbia Rivers. This section is followed by 

discussions of potential limiting factors associated with hatcheries (5.3), fisheries (5.4), predation and 
ESA Recovery Plan: Snake River Sockeye Salmon | 145

June 2015| NOAA Fisheries 

disease (5.5), competition (5.6), toxics (5.7), and climate change (5.8). Much of the following sections 

rely on NMFS (1991, 2008b, 2008c, 2014c) and NMFS Northwest Fisheriers Science Center five-year 

status assessment in Ford 2011.

The discussion of out-of-subbasin limiting factors and threats that affect all the salmonid populations in 

the mainstem Columbia River corridor is excerpted from the Estuary Module and from the 2008 and 

2014 FCRPS Biological Opinions (NMFS 2008c, 2014c). The discussions also reflect information 

presented in the Hydro Module, which summarizes FCRPS actions contained in the Biological Opinion 

(Hydro Module, NMFS 2014a) and the Ocean Module, which discusses ocean conditions and effects 

(Ocean Module, Fresh et al. 2014). (The Estuary Module underwent public review; the Hydro Module is 

a summary of the publicly reviewed BiOp.) 

5.1 Habitat

As described in Section 2.3.2, Life History, the Snake River Sockeye Salmon life cycle begins with 

emergence from the gravel in their natal lakes in the Sawtooth Valley and continues through rearing in 

the lakes; migration as smolts through the Salmon River to mainstem Snake River, Columbia River, 

estuary, and plume; maturation in the ocean; and the return migration to spawn. Threats and potential 

limiting factors in Snake River Sockeye Salmon habitat throughout the life cycle are described in this 

section, starting with the natal lakes and continuing to the ocean. 

5.1.1 Sawtooth Valley Lakes

Sockeye Salmon are historically native to five nursery lakes in the Sawtooth Valley: Redfish, Pettit, 

Alturas, Yellowbelly, and Stanley lakes. The lakes lie within the Sawtooth National Recreation Area and 

much of the headwaters of each drainage is designated as wilderness. The glacial-carved lakes range in 

elevation from 1,985 m to 2,157 m (6,512 to 7,077 feet) and collect flow from the Sawtooth and Smoky 

Mountains. Overall, habitat conditions for Snake River Sockeye Salmon in these high mountain lakes 

remain in excellent shape. Factors limiting Sockeye Salmon production in the lakes are discussed 

below.

5.1.1.1 Lake water quality

Researchers have conducted limnology studies in Stanley, Redfish, Yellowbelly, Pettit, and Alturas 

Lakes since 1991. The studies examine water temperature, oxygen, light, chlorophyll, phytoplankton, 

and zooplankton in each lake several times from May through October. Generally, the results from 

limnological sampling indicate that water quality in all five lakes provides suitable rearing habitat for 

juvenile Sockeye Salmon, although the lakes vary considerably in the species composition and 

abundance of zooplankton. 

Limnology monitoring between 2000 and 2010 shows that seasonal (June through October) mean 

surface water temperatures in the lakes generally range from 12-14 °C (53-57 °F) (Griswold et al. 
ESA Recovery Plan: Snake River Sockeye Salmon | 146

June 2015| NOAA Fisheries 

2011a). These water temperatures support Sockeye Salmon life stages for spawning, incubation, and 

rearing. The physiological optimum water temperature defined for Sockeye Salmon is in the range of 12 

to 15 °C (53-59 °F) (Brett 1971). Studies reported by Brett (1971) indicate that Sockeye Salmon

performance and distribution may be limited at temperatures above 18 °C (64 °F), despite their being 

able to tolerate temperatures of 24 °C (75 °F). Bell (1991) reported similar findings, stating a preferred 

water temperature range for Sockeye Salmon of between 11.6 and 14.4 °C (52.8 and 58 °F). 

The studies show that thermoclines are typically present in the Sawtooth Valley lakes from July through 

October, with maximum surface temperatures reaching approximately 18 °C (64 °F) in all lakes 

(Griswold et al. 2011a). The effects of temporary surface water temperature spikes above 15 °C (59 °F) 

on Sockeye Salmon may be minimal, particularly if the Sockeye Salmon can escape to deeper waters or 

to areas where groundwater inflow or shade reduce temperatures. However, in some cases, high water 

temperatures may make Sockeye Salmon more susceptible to disease and infection or promote fungal, 

bacterial infection or secondary wound infections that leave the Sockeye Salmon more susceptible to 

pre-spawning mortality (BOR 2007). 

Stanley Lake

U.S. Forest Service assessments have concluded that watershed conditions in Stanley Lake Creek are 

“functioning at risk” primarily because of loss of connectivity resulting from the fish passage barrier 

below the lake. Cattle grazing has been removed, but impacts to stream channels may still linger in 

some areas. Headwater streams and riparian areas remain in relatively good condition. However, the 

2006 Trailhead fire burned high elevation cirque basins, ridges, and steep-side slopes adjacent to Stanley 

Lake Creek. The main headwater channel of Stanley Lake Creek had a high severity burn for 

approximately one mile. In 2007, summer thunderstorms caused small debris flows and increased 

sediment downstream of the fire. While much of the sediment deposited upstream, some finer sediment 

and nutrients may have entered the lake.

A bloom of Didymosphenia geminate recently extended from the head of Stanley Lake Creek to Valley 

Creek. The bloom was first noted in 2008, and may have diminished the quantity and quality of the 

aquatic habitats for salmonids (USFS 2011). The U.S. Forest Service water temperature testing results 

in Stanley Lake Creek downstream of the lake to Valley Creek during several summer seasons from 

1994 to 2009 display daily maximum surface water temperatures typically between 23 and 25 °C (73-77 

°F) during the warmest summer periods. Natural heating of the lake’s surface is believed to be the 

primary cause of this condition and it is considered a natural phenomenon (USFS 2011). 

IDEQ assessed water quality at four locations within the Stanley Lake drainage between 1995 and 2008 

and concluded that beneficial uses were fully supported. As such, no waters within the Stanley Lake 

Creek drainage or downstream in Valley Creek were included in IDEQ’s 2008 integrated report of 

impaired waterbodies (IDEQ 2009). Currently, IDEQ considers Stanley Lake a Category 3 water body 

for which insufficient data and information, including on water temperatures, are available to determine 

if beneficial uses are being attained (IDEQ 2011).
ESA Recovery Plan: Snake River Sockeye Salmon | 147

June 2015| NOAA Fisheries 

In 1997, the U.S. Forest Service realigned Stanley Lake Road and closed and rehabilitated the associated 

former campsites to address a potential source of fine sediment in the watershed (USFS 2011). The 

popular recreation use of the lake and shoreline areas by motorized equipment continues to pose a 

potential risk of spilling chemical pollutants.

Redfish Lake

U.S. Forest Service assessments have concluded that watershed condition is “functioning appropriately” 

in the Redfish Lake Creek drainage. The large majority of the watershed remains in near natural 

condition with the exception of fire suppression that has resulted in most forests being in late seral (or 

“old growth”) condition. However, development on the north end of Redfish Lake has been extensive. 

Developed recreation sites and/or commercial activities occupy approximately two miles of shoreline. 

Less intensive development has occurred in one-half mile of shoreline on Little Redfish Lake. 

Given the high alpine headwaters and the generally unaltered riparian vegetation, maximum summer 

surface water temperatures naturally range from 12 to 15 °C (53-59 °F) in Fishhook Creek and 14 to 

16°C (57-61 °F) in Redfish Lake Creek (above the lake). Limnology monitoring by the ShoshoneBannock Tribes between 2000 and 2010 shows a seasonal (June through October) mean surface water 

temperature of 13.8 °C (56.7 °F) in Redfish Lake, ranging from 12.3°C (54 °F) (2010) to 14.9 °C (58.8 

°F) (2008). The maximum recorded surface water temperature is 18 °C (64 °F) (Griswold et al. 2011a).

This mean seasonal surface temperature is considered within the biological range for Sockeye Salmon; 

however, the maximum recorded temperatures fall above the preferred range. 

IDEQ’s 2010 303(d) list classifies Redfish Lake Creek from the source to Redfish Lake as a Category 1 

stream: waters within wilderness or roadless areas where water quality standards are presumed to be 

attained (IDEQ 2011). The 303(d) list identifies stream and river reaches listed as impaired by the Idaho 

Department of Environmental Quality under the guidelines of the Clean Water Act. The Clean Water 

Action requires all states to submit a list for U.S. Environmental Protection Agency (EPA) approval 

every two years that identifies all waters where required pollution controls are not sufficient to attain or 

maintain applicable water quality standards. 

Heating at the surface of the lakes is evident based on the temperatures observed near the outlet of the 

lake. Summer season daily maximum surface water temperatures routinely approach or exceed 20°C in 

Redfish Lake Creek below the lake (USFS 2011). IDEQ’s 2010 303(d) list classifies Redfish Lake and 

Redfish Lake Creek as Category 3 water bodies, for which insufficient data and information are 

available to determine if beneficial uses are being attained (IDEQ 2011). 

The calm waters of the lake allow incoming sediments to sink. Much of the lake shore is undeveloped 

and unaffected by upstream watershed activities in the Sawtooth National Recreation Area. However, 

shoreline development or lake recreation may result in elevated sediments in the lake bottom or water 

column in lake shoal habitats, as well as in the upper end of the outlet. These areas may need further 

monitoring to determine potential effects on fish habitat. Recreational development on the north end of 

the lake and seasonal motorized boating use in Redfish Lake has likely released some chemical 
ESA Recovery Plan: Snake River Sockeye Salmon | 148

June 2015| NOAA Fisheries 

pollutants (USFS 2011). Some conditions have been addressed (e.g. gas storage at the marina); 

however, with existing development, the potential for pollutant threats remains (USFS 2011). 

In the past, nearshore camping and a hotel facility created the potential for nutrient stresses on the lake; 

however, inputs from such activities are believed to be limited, as sewage, the main potential nutrient 

source, is removed from the area by contained sanitation systems (Gross et al. 1998). 

Yellowbelly Lake

U.S. Forest Service assessments have concluded that watershed condition is “functioning appropriately” 

in the Yellowbelly Lake Creek drainage. Few management activities occur within the drainage and 

habitat conditions are near pristine. Sediment is naturally high from granitic parent materials.

Yellowbelly Lake historically provided habitat for resident kokanee and residual Sockeye Salmon

(Bjornn et al. 1968; Waples et al. 1991), suggesting the lake supported anadromous production. The 

U.S. Forest Service monitored water temperatures above and below the lake in 2002 and 2005. IDEQ’s 

2010 303(d) list classifies Yellowbelly Lake as a Category 3 water body, for which insufficient data and 

information are available to determine if beneficial uses are being attained (IDEQ 2011). Yellowbelly 

Lake was treated with Rotenone in 1990 by IDFG. 

Pettit Lake

U.S. Forest Service assessments have concluded that watershed condition is “functioning appropriately” 

in the Pettit Lake drainage. Little management disturbance has occurred in the drainage, other than lake 

shore development. Habitat conditions are near pristine, although, sediment is naturally high from 

granitic parent materials. The U.S. Forest Service also monitors stream temperatures in reaches above 

and below Pettit Lake. The agency has determined that stream temperatures below the lake are likely 

natural and a result of heating of the lake surface. 

Extensive water quality monitoring has occurred as part of the Sockeye Salmon recovery actions. In 

limnology monitoring studies conducted by the Shoshone-Bannock Tribes, seasonal mean surface water 

temperatures (June-October) in Pettit Lake measured approximately 13.8 °C (56.8 °F) between 2000 and 

2010, and ranged from 12.1 °C (54 °F)(2006) to 15.8 °C (60.4 °F)(2008) (Griswold et al. 2011a). 

Generally, these mean temperatures remain within the physiological optimum water temperature range 

of 12-15 °C (53-59 °F) defined by Brett (1971) for Sockeye Salmon. 

Data from 2000-2010 show that 2008 was the only year when seasonal mean surface water temperatures 

in Pettit Lake rose above 15 °C; however, maximum recorded surface water temperatures reached 18 °C 

(Griswold et al. 2011a). The effects of temperatures above 15 °C on Sockeye Salmon generally depend 

on exposure time. The effects of 2- to 4-day exposure to temperatures between 18-24 °C (64-75 °F) are 

not well documented in scientific literature. However, the high temperatures may make Sockeye 

Salmon more susceptible to disease and infection, or promote fungal and bacterial infections, as well as 

secondary wound infection, leaving the Sockeye Salmon more susceptible to pre-spawning mortality. 
ESA Recovery Plan: Snake River Sockeye Salmon | 149

June 2015| NOAA Fisheries 

IDEQ’s 2010 303(d) list classifies Pettit Lake as a Category 3 water body, for which insufficient data 

and information are available to determine if beneficial uses are being attained (IDEQ 2011). 

Alturas Lake

Stream habitat is in good condition in the drainage, although fine sediment is likely elevated from 

headwater grazing and patented mining and granitic parent material. Historic intensive sheep grazing 

substantially altered stream banks in some localized areas, particularly near the corrals. However, the 

corrals were closed and removed in the mid-1990s, and the area is no longer authorized for grazing. As a 

result, streambank recovery is ongoing. In 2003, Alturas Lake Creek and lower Jakes Gulch were 

reviewed for impacts from domestic sheep grazing based on tracking collar data. No effects from sheep 

use were observed above the lake.

The Alturas Creek subwatershed has been a focus for restoration since 1999. In 2000, Alturas Lake 

Creek was returned to 1⁄4 mile of natural channel above the confluence with Alpine Creek where it had 

been previously captured by Road 205 a decade earlier. This capture had liberated thousands of yards of 

sediment into Alturas Lake Creek. In 2005 and 2006, 4.5 miles of headwater road were closed and 

rehabilitated, including the deteriorating ford through Alpine Creek. As restoration now occurs, these 

changes have essentially removed all chronic sources of management related sediment within the upper 

watershed.

A PACFISH/INFISH Biological Opinion Effectiveness Monitoring Program (PIBO) integrator reach is 

located on Alpine Creek 1.59 miles above the confluence with Alturas Lake Creek. The habitat index 

score ranged from 62.0 in a 2005 survey to 65.7 in 2010, indicating moderate to good habitat conditions 

when compared to reference streams. PIBO found habitat indices averaged 63.4 in unmanaged reference 

habitat. 

Sockeye Salmon have been reintroduced into Alturas Lake since 1997: hatchery adults were released 

into the lake for volitional spawning in 1997 and 2000. U.S. Forest Service temperature thermograph 

monitoring from 2002 to 2005 recorded maximum 7-day average daily maximum summer surface water 

temperatures at or below 15 °C in the lake. Limnology monitoring by the Shoshone-Bannock Tribes 

between 2000 and 2010 shows a seasonal mean water temperature of 13.3 °C in Alturas Lake, ranging 

from 12.1 °C (2010) to 15.3 °C (2008) Maximum surface temperatures in the lake can reach 18 °C 

(Griswold et al. 2011a). These water temperatures are generally within the biological range for Sockeye 

Salmon spawning, incubation, and rearing. Monitoring by the Shoshone-Bannock Tribes shows that 

mean surface temperatures in the lake rose above 15 °C in 1 of 10 years from 2000 to 2010 (Griswold et 

al. 2011a). As discussed earlier, effects to Sockeye Salmon from temporary water temperature spikes 

depend on when and how long the temperatures remain outside the preferred range. 

Sediment loading from granitic parent material results in a high natural sediment load that accumulates 

in the lake (USFS 2011). Historical effects of grazing and mining in the headwaters has likely 

exacerbated this condition. Extensive U.S. Forest Service restoration activities in the upper watershed in 
ESA Recovery Plan: Snake River Sockeye Salmon | 150

June 2015| NOAA Fisheries 

2005 and 2006, including road closures and habitat rehabilitation, are intended to address the sources of 

land use-related impairments to sediment processes within the upper watershed (USFS 2011). 

IDEQ’s 2010 303(d) list identifies both Alturas Lake to its mouth and Alturas Lake Creek as not 

meeting the conditions needed to support aquatic plants and animals, although the cause of impairment 

has not been identified (IDEQ 2011). Lake nutrient supplementation permitted by IDEQ has been 

occurring in Alturas Lake since 1995 implemented by BPA, via the Shoshone-Bannock Tribes. 

5.1.1.2 Lake food resources 

Growth of Sockeye Salmon in the Sawtooth Valley lakes is often density dependent and related to 

zooplankton density (Hyatt and Stockner 1985; Rieman and Meyers 1992). Juvenile Sockeye Salmon

rear one to three years in the lakes before emigrating to the ocean, and during their stay in the lakes 

Sockeye Salmon juveniles feed almost entirely on zooplankton. 

Changes in zooplankton levels in the lakes contributed to the decline of Sockeye Salmon production in 

the lakes (Selbie et al. 2007). Low zooplankton densities can restrict growth rates and ultimately the 

ability of Sockeye Salmon to achieve a level of fitness needed to survive the long seaward migration 

from their nursery lakes. Reductions in the lakes’ zooplankton communities developed after the 

Sockeye Salmon population drastically declined and other fish (trout, non-native kokanee) were 

introduced in mid-century. Ongoing studies of lake water quality seek to determine the current 

characteristics and carrying capacity of the lakes.

Overwintering conditions can be especially important for Sockeye Salmon in these high mountain lakes. 

Since Sockeye Salmon remain active at temperatures below 4 °C (39 °F), winter is not a period of 

dormancy (Burgner 1992). In fact, at 4 °C, Sockeye Salmon must consume about 0.1% of their wet 

weight per day to meet basic metabolic requirements (Brett et al. 1969). Winter productivity in the 

Sawtooth Valley lakes is limited because ice covers the lakes for long periods. This reduces light 

penetration and photosynthesis, which then limit winter productivity and Sockeye Salmon foraging 

ability (Steinhart and Wurtshaugh 2003).

Because of this limited winter productivity, Sockeye Salmon in the lakes may experience more 

competition from kokanee, as well as other Sockeye Salmon, when densities increase due to stocking. 

Increased competition for limited zooplankton supplies can exacerbate energetic losses during winter 

months, causing Sockeye Salmon to grow more slowly and to have fewer lipids, reducing outmigrant 

survival (Steinhart and Wurtshaugh 2003). 

Powell et al. (2010) concluded that diet and fatty acid composition differed between Redfish Lake 

smolts of hatchery origin (planted as pre-smolts) and those produced naturally in the lake. Wild 

outmigrants had fatty acid profiles indicative of the zooplankton diet typical of resident Sockeye Salmon

in the lake. In contrast, hatchery-produced juveniles introduced as pre-smolts had fatty acid profiles 

resembling those associated with hatchery diets. At outmigration, total lipids of hatchery-origin smolts 

were approximately half of that of wild fish despite having been nearly three times higher at planting. 
ESA Recovery Plan: Snake River Sockeye Salmon | 151

June 2015| NOAA Fisheries 

Studies by Griswold et al. (2011) also suggest that growth rates may affect emigrating smolt survival. 

The researchers found that successful smolt migrants from the Sawtooth Valley lakes to Lower Granite 

Dam often maintained their weight during the winter preceding migration. They also found that smaller 

parr and smolts survived better. The researchers suggest that the stocking of smaller parr with lower 

metabolic demand may be preferable to stocking larger parr when forage is limited (Griswold et al. 

2011a). 

Stanley Lake 

Studies consistently show lower seasonal mean zooplankton biomass (June through October) in Stanley 

Lake than in Pettit, Redfish and Alturas Lakes (Taki et al. 2006).

Redfish Lake

Nutrient supplementation has been implemented since 1995 by BPA through the Shoshone-Bannock 

Tribes to promote Sockeye Salmon growth in Redfish Lake’s highly oligotrophic water and to increase 

lake carrying capacity. Results from 1995 to 1998 show the effectiveness of nutrient supplementation in 

Redfish Lake. Following nutrient supplementation, tribal personnel measured large increases in surface 

chlorophyll a, primary productivity, and zooplankton biomass in comparison to smaller changes in 

Stanley Lake where no nutrient supplementation occurred (Griswold et al. 2002). 

Kokanee control measures are also implemented in Redfish Lake to reduce intraspecific competition. 

Section 5.6 provides more discussion on this competition factor. In addition, a variety of fishery and 

limnological parameters are monitored annually in association with these strategies. 

Yellowbelly Lake

Zooplankton data for Yellowbelly Lake is limited, but Steinhart et al. (1993) reported that in 1992 and 

1993 the “highest zooplankton biomasses were observed in Yellowbelly and Pettit followed by Stanley 

Lake. The lowest total zooplankton biomass was observed in Redfish and Alturas Lakes in both years.” 

In 2007, zooplankton was sampled during September in Yellowbelly Lake and compared to several 

other Sawtooth Valley Lakes. Zooplankton biomass was slightly lower in Yellowbelly than in Redfish 

and Pettit Lakes.

Pettit Lake

Lake nutrient supplementation permitted by IDEQ has been occurring in Pettit Lake since 1995 and 

implemented by BPA, via the Shoshone-Bannock Tribes to increase Pettit Lake’s carrying capacity. 

Nutrient supplementation of Pettit Lake may be creating short-term growth benefiting lake dwelling fish. 

Sockeye Salmon in Pettit Lake typically exhibit the highest growth rates compared to fish in Redfish and 

Alturas Lakes. Sockeye Salmon presmolts released into Pettit Lake during the fall of 2004 experienced 

relatively high total zooplankton biomass, composed primarily of Cyclopoids and Daphnia, for the first 

month after release. During the winter, moderate zooplankton biomass was present in the form of 

Cyclopoids and Bosmina. The fish had a higher growth rate than fish in Redfish and Alturas Lakes in 

terms of weight (Taki et al. 2006). 
ESA Recovery Plan: Snake River Sockeye Salmon | 152

June 2015| NOAA Fisheries 

Alturas Lake

The Shoshone-Bannock Tribes continue to provide nutrient supplementation to increase Alturas Lake’s 

carrying capacity. Nutrient supplementation of Alturas Lake may be creating short-term growth benefits 

to lake-dwelling fish (USFS 2011). Research by Taki et al. (2006), however, found that fall-release 

Sockeye Salmon presmolts experienced low zooplankton biomass and also low growth rates; growth 

rates were considerably lower than in Redfish and Pettit Lakes. 

5.1.1.3 Blocked access

At the time of the initial listing (NMFS 1991), the greatest habitat problem faced by the Snake River 

Sockeye Salmon ESU was the lack of physical access to any of the lakes but Redfish Lake. As described 

in Sections 2.6.2 and 3.2.2.2, improving Sockeye Salmon spatial structure with broader landscape 

distribution and access to multiple spawning areas will reduce the risk of extinction due to catastrophic 

environmental events. Therefore, providing connectivity of migratory corridors and increasing spatial 

distribution is still important to successful Sockeye Salmon recovery. Maintaining habitat connectivity 

within the population will promote gene flow and aid in establishing a locally adapted, naturally 

spawning population, and improve overall species viability. 

Local recovery actions to remove barriers to Sockeye Salmon migration and, therefore, improve spatial 

distribution are being implemented. For example, Sunbeam Dam, which blocked salmon passage on the 

Salmon River approximately 20 miles downstream from the mouth of Redfish Lake Creek, was removed 

in 1934. The fish barriers on Alturas and Pettit Lake creeks (an irrigation intake and a concrete nongame fish barrier, respectively) were modified to facilitate passage of anadromous Sockeye Salmon into 

these historical habitats in the early to late 1990s (Teuscher and Taki 1996, cited in Flagg et al. 2004). 

The fish barrier at Yellowbelly Lake was removed by the U.S. Forest Service in 2000. The only 

remaining fish barriers are the fish migration barrier at the outlet of Stanley Lake and the weir at 

Sawtooth Fish Hatchery. In order to improve spatial distribution, presmolt outplants into Redfish, 

Alturas and Pettit Lakes were initiated in the mid-1990s, with releases averaging approximately 80,000 

fish per year since 1995 (Ford 2011). Currently, however, anadromous returns are entirely precluded 

from Alturas, Pettit and Yellowbelly Lakes by the Sawtooth weir and from Stanley Lake by the fish 

barrier at the lake outlet. Plans are underway to begin allowing anadromous Sockeye Salmon adults to 

return to their lake of origin. This would entail trapping adults at the Sawtooth weir and transporting 

them to Alturas or Pettit Lakes, or alternatively to pass the adults to allow for volitional migration. 

Presently the trap does not effectively capture adult Sockeye Salmon.

Stanley Lake

The artificial barrier on the outlet of Stanley Lake, constructed in 1956 by IDFG as an upstream barrier 

to non-game fish, does not prevent downstream passage. The stocking of Stanley Lake with lake trout in 

1975 further changed the system (IDFG 2013). These lake trout are reproducing and pose a risk to native 

kokanee in Stanley Lake, as well as the other Sockeye Salmon nursery lakes in the Sawtooth Valley. 

Movement of lake trout from Stanley Lake has not been documented; however, the risk of lake trout 

moving to other tributaries and lakes in the basin, and thus impeding Sockeye Salmon recovery, remains 

high. Alternative lake trout management strategies must be carefully considered, including removal of 
ESA Recovery Plan: Snake River Sockeye Salmon | 153

June 2015| NOAA Fisheries 

the artificial barrier. The barrier prevents recolonization of the lake by Sockeye Salmon and other 

species, such as ESA-listed bull trout, steelhead, and Chinook salmon. 

One water diversion exists on Stanley Lake Creek. The diversion does not pose a barrier to fish 

migration because it is screened and sits on a side channel to the creek. However, the diversion serves 

eight water rights totaling about 2 cfs (IDWR 2013) that reduce critically low summer flows by 20% to 

60%. This level of flow depletion in the wide and shallow channel of Stanley Lake Creek reduces water 

depth and increases stream temperature enough to substantially impair upstream migration of adult 

Sockeye Salmon. There are no culvert barriers that impact historical Sockeye Salmon habitat within this 

subwatershed. 

Redfish Lake

IDFG operates an adult and juvenile weir on Redfish Lake Creek below the lake, which detains all 

migrants during the period of operation. The number of captive-reared or returning anadromous adults 

allowed to pass over the Redfish Lake weir or outplanted into the lake has increased substantially in 

recent years (Ford 2011). There are no culvert barriers on Redfish Lake or Fishhook Creek.

Yellowbelly Lake

Prior passage issues existed at the outlet stream due to an outlet barrier that was constructed in 1962 by 

IDFG (Chapman et al. 1990). The USFS removed the barrier in 2000 to reestablish connectivity with the 

mainstem Salmon River. There is no record of Sockeye Salmon or kokanee salmon stocking in 

Yellowbelly Lake and currently O. nerka are not present. A natural seasonal impediment exists 

approximately one-half mile above the mouth where Yellowbelly Lake Creek passes through onequarter mile of coarse glacial boulder deposits. Typically, at baseflow this results in subsurface 

streamflow as the creek continues within the interior of this boulder matrix (USFS 2011). Habitat access 

is also believed limited above the lake due to barrier cascade 3.5 km (2.2 miles) above the lake’s inlet. 

Future monitoring is needed to better understand Sockeye Salmon passage issues associated with these 

natural conditions. There are no water diversions or culvert barriers within this subwatershed. 

Pettit Lake

An outlet barrier was constructed in 1960 to keep native fish from recolonizing the lake after IDFG 

chemically treated the lake. For three decades, prior to 1996, a barrier at the lake outlet prevented all 

upstream fish migration. The Pettit Lake barrier was removed in 1996 to allow for passage for 

anadromous Snake River Sockeye Salmon into the lake. Today, the Shoshone-Bannock Tribes operate 

an adult/juvenile fish trap below the lake targeting Sockeye Salmon.

Alturas Lake

No manmade barriers exist within the watershed. In some years, a reach of Alturas Lake Creek from 

just above the confluence with Alpine Creek and extending as much as 805 m (one-half mile) becomes 

dry during late summer. This condition was first documented in 1895 by Evermann and is believed to 

be natural (USFS 2011).
ESA Recovery Plan: Snake River Sockeye Salmon | 154

June 2015| NOAA Fisheries 

5.1.1.4 Land use and other human activities

The Sawtooth Valley’s beauty and natural resources attracted 19th century European-American ranchers, 

miners, and loggers. Roads, scattered settlements, and recreational development followed. Current and 

legacy effects of land use and other human activities such as mining, lake poisoning, and introduction of 

non-native species have altered Sockeye Salmon habitat and may still constitute limiting factors for 

Sockeye Salmon survival. Land use practices may also be affecting Sockeye Salmon by reducing stream 

flows to critical levels; however, more information is needed to better understand this potential concern.

Future land and water use, such as development of new ponds for aesthetics and irrigation purposes, 

could potentially affect Sockeye Salmon populations by reducing water quality. More information is 

needed to understand the potential impacts of this and other possible emerging threats.

Land use

Intensive sheep and cattle grazing occurred within the watershed for a century until the 1993 Record of 

Decision for Grazing in the Stanley Basin mandated changes in grazing management. These changes 

included reduction in numbers, exclusion of grazing in some areas to protect salmon habitat, fencing, 

limitation on duration of grazing, and monitoring of riparian conditions. Since that time, many of the 

stream channels have shown significant recovery.

 

Stanley Lake

Overall, the U.S. Forest Service characterizes the Stanley Lake watershed as having high quality habitat 

conditions and integrity, with some areas of low integrity along the lakeshore. Past intensive uses such 

as mining have occurred in places within the watershed, and some within sensitive streamside and 

lakeside areas. Some mining activities occurred within the headwaters in the mid-1900s, including the 

construction of a small access road. The main access road was upgraded in the 1930s with lengthy 

segments located adjacent to Stanley Lake Creek. Intensive sheep and cattle grazing occurred within the 

watershed for a century until these activities were removed in 1993. Timber harvest, including road 

building, occurred in the reasonably accessible portion of the watershed on Elk Mountain in the 1960s 

(USFS 2011). 

Stanley Lake’s small size predominantly attracts fishing boat, kayak, and canoe use, although waterski 

boats and other personal watercraft are also allowed. The Stanley Lake Recreation Complex includes 

developed campgrounds, multiple areas of unconfined or dispersed camping, a trailhead, scenic 

overlook, and boat launch. Although equally accessible to passenger cars, Stanley Lake offers a vastly 

different experience than the larger and busier lakes. 

Recreational developments are located adjacent to, or in close proximity to 43% of the Stanley Lake 

shoreline. Visitor numbers and impacts are increasing at a time when the local natural environment is 

particularly vulnerable. The recent mortality of the majority of mature lodgepole pine has left much of 

the area with a loss of shading, screening, and natural restrictions to foot traffic. Regeneration of 

groundcover, shrubs and trees will be delayed until foot traffic is directed and managed. Condition 

assessments by the U.S. Forest Service in 2001 showed most of these shorelines had been altered, with 
ESA Recovery Plan: Snake River Sockeye Salmon | 155

June 2015| NOAA Fisheries 

no improving trend apparent. For example, when lakeshore developments were present, 100% of the 

survey area had severe or moderate bank alterations. In contrast, when development was absent, only 

21% of the survey area had severe or moderate bank alterations. The U.S. Forest Service is taking 

action to address fuel hazards in the developed recreation sites and along roads. The popular recreation 

use of the lake and shoreline areas by motorized equipment presents potential risks of contaminant 

spills. 

While the overall watershed habitat conditions are good and improving, campground and boat launch 

developments impact some habitat areas (USFS 2011). There are also concerns about shoreline impacts 

from uncontrolled access points due to mooring. The Forest Service plans to work in cooperation with 

the county to identify impacts and develop a mitigation plan.

In addition, the U.S. Forest Service has removed lakeshore trails and installed fences to encourage 

recovery of shoreline vegetation. In 2011, the U.S. Forest Service closed the Stanley Lake Inlet 

Campground and began rehabilitating several roads and trails located in streamside and lakeside riparian 

areas. If sufficient funding can be secured, the U.S. Forest Service plans to construct 14 new campsites 

and associated facilities on the northeast corner of Stanley Lake near the Stanley Lake Campground but 

outside of lakeside riparian areas. A new boat launch will also be developed near the existing Stanley 

Lake Inlet Campground site. 

Redfish Lake 

The large majority of the Redfish Lake watershed remains in near natural condition, with the exception 

of the results of fire suppression, which has allowed most of the surrounding forest to reach late seral 

condition. Currently, however, the majority of the mature lodgepole pines are now standing dead 

because of a recent natural infestation of mountain pine beetle (USFS 2011). Fuel reduction treatments 

are being carried out by the U.S. Forest Service. These treatments typically reduce risks of high 

intensity forest fires by thinning trees, conducting prescribed burns, and removing surface fuels (fallen 

branches, low flammable brush and other flammable understory vegetation.) 

Some recreational facilities sit at the north end of Redfish Lake. Facilities include the Redfish Lake 

Lodge (restaurant, cabin, and boat rentals), U.S. Forest Service campgrounds, boat launch, day-use 

areas, and a visitor center. Tours on the lake are common, as are motorized and non-motorized pleasure 

and fishing boats (IDFG 2010). At times during the summer months, the population of the Redfish Lake 

Complex is likely the largest “community” in Custer County. Developed recreation sites and/or 

commercial activities occupy approximately two miles of shoreline (USFS 2011). Sockeye Salmon

campground and Sandy Beach boat ramp occur adjacent to Sockeye Salmon Beach spawning grounds. 

The only other facilities near Sockeye Salmon spawning areas (e.g., the transfer dock area and southeast 

of the inlet of Redfish Lake Creek) are Redfish Inlet Campground and transfer dock. Redfish Lake 

lakeshore was surveyed in early August of 2007. Nearly 75% of Redfish Lake shoreline has no 

development and remains in near pristine condition. However, 25% of the shoreline was developed 

causing increased bank alteration and removal of riparian vegetation. 
ESA Recovery Plan: Snake River Sockeye Salmon | 156

June 2015| NOAA Fisheries 

The U.S. Forest Service has implemented several projects to remove lakeshore trails and install fences to 

encourage recovery of shoreline vegetation. In 2011, the U.S. Forest Service decided to replace two 

bridges on Road No. 214, realign Road No. 214 to access the new bridge, and construct a new road to 

bypass the second bridge, thus eliminating the need for one bridge. The U.S. Forest Service also will 

relocate the Visitor Center parking lot out of its current wet location, relocating the North Shore parking 

lot to provide for more day-use parking, and constructing a new pedestrian/bicycle trail near the Visitor 

Center. Abandoned roadways in the North Shore area would be removed to reestablish natural 

topography.

Yellowbelly Lake

Yellowbelly Lake habitat conditions are considered near pristine (USFS 2001). Recreation use on public 

land and minor development on private land near the mouth of Yellowbelly Lake have had a small 

influence in the watershed. Few U.S. Forest Service management activities occur within the watershed. 

Roads are believed to have little influence within the watershed (USFS 2001). IDFG management of the 

lake through a former fish barrier and chemical treatments has had the greatest influence on fish. 

Pettit Lake

There is little land use disturbance in the Pettit Lake watershed, other than lakeshore developments. 

Developed recreation sites and/or cabin lots occupy approximately two miles of the south end of Pettit 

Lake – nearly 50% of the shoreline. Currently these developments receive considerably less intensive 

use than similar lakeside areas at Redfish Lake, but use is increasing. Possible historical Sockeye 

Salmon shoal spawning habitats are adjacent to these lakeside developments (USFS 2011). There are 

also several recreation developments (Pettit Lake Campground, Day Use area, and boat launch near the 

lake’s outlet. Condition assessments by the U.S. Forest Service in 2006 showed that shoreline near 

developments had more trampled banks and less vegetation and downed woody debris.

Alturas Lake

Past irrigation diversions on Alturas Lake significantly affected the Sockeye Salmon population. The 

historic Breckenridge/Busterback Ranch in the Sawtooth Valley had three main diversions, including 

one on Alturas Lake Creek. The diversion had significant effects on stream flow and fish passage. The 

ranch had water rights for approximately 44 cfs from the Alturas Lake Creek which was used to flood 

irrigate summer cattle pasture. However, during the core of the irrigation season, natural flows were 

less than the appropriated flows such that, prior to 1992, Alturas Lake Creek was routinely dewatered 

during the summer irrigation season. Munther (1974) concluded that “no other diversion in Sawtooth 

Valley affects as many species as the Alturas Lake Creek diversion.” Even when not fully dewatered 

the diversion structure itself severely reduced available fish habitat by precluding or impairing upstream 

migration. In 1992 the U.S. Forest Service purchased much of the former Busterback Ranch and the 

associated water rights from both Alturas Lake Creek and the Salmon River for 3.2 million dollars. The 

rights from Alturas Lake Creek (35.6 cfs) were immediately returned to the creek to improve habitat and 

passage conditions. In 1997, immediately after the last private irrigator discontinued use, the U.S. 

Forest Service removed the former diversion structure and restored natural channel conditions.
ESA Recovery Plan: Snake River Sockeye Salmon | 157

June 2015| NOAA Fisheries 

Historical legacy effects of grazing and mining in the headwaters have exacerbated sediment loading 

impacts in Alturas Lake (USFS 2011). More recently, recreational development has occurred on the 

north side of Alturas Lake and developed recreation sites now occupy approximately 1.6 km (1 mile) of 

shoreline. Perhaps 60% or more of the potential historical Sockeye Salmon shoal-spawning habitat are 

now adjacent to lakeside developments (USFS 2011). Since 1999, the U.S. Forest Service has closed 

and rehabilitated more than eight kilometers (5 miles) of roads, and the remaining roads are paved 

within the Alturas Lake recreation complex. The visitor facilities have been altered to reduce streamside 

pressure (USFS 2011). By 2006, the objectives were believed to be essentially complete. As natural 

recovery of these areas now proceeds, habitat conditions are expected to improve.

Mining 

In 1862, gold was discovered in the Boise basin and miners rapidly pushed into the Payette River 

drainage on the west slope of the Sawtooth Mountains. In July 1864, a group of miners led by Captain 

John Stanley arrived in the Valley Creek area near present-day Stanley, Idaho and discovered gold. 

They named the valley “Stanley Basin.” In 1878, silver ore was discovered in the lower Sawtooth 

Valley, which proved to be an extraordinarily rich find. Mining towns were quickly established, yet the 

ore was soon depleted and the mine closed in 1887. Gold was discovered north and east of Stanley 

Basin in Loon Creek in 1869 and in the Yankee Fork region in 1870, where miners rushed in by 1879. 

In some areas, the scars of past mining activities remain today. Mining activities, particularly dredging, 

have affected aquatic habitat conditions by changing channel structure, removing riparian vegetation, 

reducing floodplain connectivity, and/or increasing fine sediment levels. Although little mining activity 

currently occurs in the area, the possibility of future mining remains a potential threat, particularly if the 

minerals increase in value. However, under Public Law 92-400, subject to valid existing rights, all 

Federal lands in the Sawtooth National Recreation Area are withdrawn from all forms of mineral 

location, entry, and patent (Sawtooth National Forest 2006). 

Stanley Lake

Placer mining occurred in some tributaries, such as Stanley Creek, and along the Salmon River within 

the canyon, and had severe local effects on stream habitat conditions. Some fine sediment accumulation 

above Stanley Lake may be due to historical effects of grazing and some mining in the headwaters. 

However, no mining activity has occurred for many decades (USFS 2011).

Alturas Lake

Hard rock or quartz mining boomed in 1879 at Sawtooth City. The discovery of ores that started this 

town did not sustain it and the supply of ore had declined rapidly by the late 1880s, although occasional 

spurts of activity occurred during the 1900s. Historical legacy effects, particularly grazing and patented 

mining in the headwaters, have exacerbated sediment loading into the lake (USFS 2001). 
ESA Recovery Plan: Snake River Sockeye Salmon | 158

June 2015| NOAA Fisheries 

Lake poisoning

In the mid-1950s, based on very low levels of adult Sockeye Salmon returns to Stanley, Pettit, and 

Yellowbelly Lakes, the IDFG made the decision to develop these lakes for resident species sport 

fisheries (IDFG 1959). Yellowbelly (1961), Pettit (1961), and Stanley (1954) Lakes were chemically 

treated with Toxaphene, Rotenone, and Fish-Tox, but the larger Alturas and Redfish Lakes were not. 

Stanley Idaho resident John Rember reports that the 1961 fish kill extended down the upper Salmon 

River as far as the town of Stanley (Rember 2003), which suggests that a cohort of smolts from all the 

lakes may have been depleted by the poisoning.

Stanley Lake

Treated with Fish-Tox in 1954 and an upstream fish barrier was constructed.

Yellowbelly Lake

Native fish were chemically removed from Yellowbelly Lake with Toxaphene in the 1950s and in 1961 

by IDFG and an outlet barrier was constructed at that time (Chapman et al. 1990). Bjornn et al. 1968 

observed dead residual Sockeye Salmon after treatment. Bjornn stated, “Fish found in Pettit and 

Yellowbelly Lakes, after chemical treatment in 1961 and 1962, appeared to be residual Sockeye Salmon. 

The fish were darker in coloration than the bright red kokanee and would have spawned later than the 

kokanee populations in Redfish and Alturas Lakes. We found no record of kokanee being planted in

Yellowbelly Lake.” The lake was chemically treated again with Rotenone in 1990. 

Pettit Lake

In the 1950s and 1960s, IDFG treated the lake with Toxaphene to remove native fish (Chapman et al. 

1990). 

Hell Roaring Lake

In the 1970s, Hell Roaring Lake was chemically treated. Stacey Gebbards reported seeing numerous 4 to 

5 inch kokanee during treatment, an indication that the lake may have supported anadromous Sockeye 

Salmon at some point in time (Bowler 1990).

Introduction of Non-native Fish Species

Non-native species present in Sawtooth Valley waters include lake trout S. namaycush (Stanley Lake 

only), various hatchery strains of rainbow trout, brook trout S. fontinalis, and non-native kokanee.

Stanley Lake

Disturbance to the lake’s biological processes began early in the 1900s with the introduction of exotic 

brook trout and again in 1975 with the introduction of lake trout (Curet et al. 2009; IDFG 2013). In 

1993, Teuscher (1999) reported a wide range of lake trout lengths, from approximately 200 to 680 mm 

total length. The shorter lengths of lake trout identified by Teuscher served as the first indicator of 

natural reproduction within the lake trout population. Stanley Lake was stocked with non-native 
ESA Recovery Plan: Snake River Sockeye Salmon | 159

June 2015| NOAA Fisheries 

kokanee from 1988 to 1991, an early spawning stock. The 1990s data from Waples (1991) suggests that 

kokanee in this lake are a mix of native and non-native fish. IDFG has recently re-sampled the kokanee 

population to identify the current genetic composition of kokanee. The recent study found that the native 

population of kokanee still exists within Stanley Lake but that it has been slightly introgressed with nonnative kokanee. U.S. Forest Service electrofishing surveys in 2008 found brook trout in Stanley Lake 

Creek above the lake. Brook trout are also present in Stanley Lake Creek below the lake. 

Redfish Lake

Kokanee are native to Redfish Lake. Previous kokanee stocking from a range of hatchery sources 

beginning in 1930 and continuing through 1972 (Waples et al. 2011; Bowler 1990) has appeared to have 

no lasting impacts. IDFG recently re-sampled the kokanee population to identify the current genetic 

composition of these fish and found the same results (Kozfkay 2013c). 

Electrofishing surveys conducted by the Sawtooth National Forest in 2008 observed numerous brook 

trout in Redfish Creek above the lake. Brook trout have also been observed in Fishhook Creek in 2006 

and 2012 Sawtooth National Forest surveys. Brook trout may indirectly impact Sockeye Salmon and 

kokanee that use lower Fishhook Creek by aggressively defending feeding territories and outcompeting 

anadromous salmon (Hutchison and Iwata 1997). Brook trout are also voracious predators, and they 

frequently consume juvenile salmonids (Sigler and Sigler 1987; Karas 1997). Additionally, brook trout 

appear to consume salmon eggs (Karas 1997). Johnson (Johnson and Ringler 1979; Johnson 1981), for 

example, reported that salmon eggs comprised between 38 and 95% of the diet of brook trout in a 

tributary of Lake Ontario.

Yellowbelly Lake

Yellowbelly Lake was chemically treated in 1990 to reduce brook trout populations and was then 

stocked with westslope cutthroat trout. Brook trout are numerous and widely distributed in Yellowbelly 

Lake Creek above and below the lake due to historic stocking. 

Pettit Lake

Non-native kokanee salmon from north Idaho stock were stocked repeatedly from 1930 to 1968. 

Genetic analyses have confirmed that the native population of kokanee has been completely replaced by 

non-native introductions of kokanee from northern Idaho. The kokanee compete with listed Sockeye 

Salmon for the zooplankton forage base. Electrofishing surveys conducted by the Sawtooth National 

Forest above Pettit Lake in 2007 observed numerous brook trout. Brook trout are likely the result of 

emigration from Alice and Pettit Lake stocking in the 1950s and 1960s.

Alturas Lake

Alturas Lake was stocked with non-native kokanee from 1921 to 1968 with an early spawning stock of 

kokanee from the Anderson Ranch Reservoir. The current data from Waples et al. (2011) indicates that 

the fish within Alturas Lake are native and that there is no lasting impact from these past stocking 

activities based on the results of the genetic analyses that were conducted. Brook trout were found in 

eight electrofishing sites in 2012 within Alturas Lake Creek and lower Alpine Creek. Brook trout 
ESA Recovery Plan: Snake River Sockeye Salmon | 160

June 2015| NOAA Fisheries 

densities ranged from 1.18-2.36 fish/100m2 with the highest densities occurring in the headwaters of 

Alturas Lake Creek. 

Introduction of Aquatic Invasive Species

Currently very few waters on the Sawtooth National Recreation Area have been infested with aquatic 

invasive species. New Zealand mud snails (Potamopyrgus antipodarum) have only been found in a 

small pond on private property near Squaw Creek. Mudsnails can grow in such great densities that they 

endanger the food chain by outcompeting native snails and water insects for food, leading to sharp 

declines in the native populations. Fish populations then suffer because the native snails and insects are 

their main food source. Mud snails can also damage infrastructure used to manage hatcheries, weirs and 

other structures used to manage water resources. Mud snails were first detected in the United States in 

the Snake River in 1987 and have since spread to most western states. Fortunately, Eurasian water 

milfoil, Quagga and Zebra Mussels, and Chytrid fungus have not yet been detected in any waters on the 

Sawtooth National Recreational Area. 

The parasite (Myxobolus cerebralis), which affects salmonids and causes whirling disease, is also an 

invasive species of concern. Myxobolus cerebralis spores can cause whirling disease and have been 

detected in rainbow trout left in live traps in the Salmon River, Pole Creek and Alturas Lake. The 

disease affects juvenile fish and causes skeletal deformation and neurological damage. The parasite has 

caused rates of high mortality of fish species important in several recreational sport fishing rivers in the 

West, including Idaho where it can further impact species that are already threatened or endangered. 

Didymosphenia geminate (Didymo) has been confirmed in localized areas within the Salmon River 

below Slate Creek and in Stanley Lake Creek below the lake. The extreme risk posed by the potential 

for aquatic invasive species could be mitigated by setting up check points at the three portals entering 

the Sawtooth Valley (Hwy 75 from Ketchum, Hwy 75 from Challis and Hwy 21 from Boise).

Redfish Lake

The greatest risk of aquatic species infestations to the upper Salmon River region comes from boats 

launching in large glacial lakes (e.g., Redfish, Alturas, Stanley and Pettit), commercial floatboat 

outfitters and private floatboaters on the Salmon River, and public fishing. The Sawtooth National 

Forest has worked with the Idaho State Department of Agriculture (ISDA) since 2009 to maintain a boat 

inspection station at the Redfish Lake Sandy Beach boat ramp (Chatel 2013). Boat inspections 

conducted at Redfish Lake from 2009-2011 have found a number of boaters coming from infected 

waters both within Idaho and outside the state. Some boats have come from as far a Maine and Florida. 

In 2011, eight boats were washed at the Redfish check station. Two boats had been in Utah waters (an 

impacted state), one boat was found with Eurasian water milfoil (from the Snake River), two boats were 

generally dirty, and three watercrafts were found with snails. All watercraft with snails found on them 

had previously launched in Magic Reservoir and the snails were determined to be a native pond snail 

species. In 2012, the inspectors examined 1,518 watercrafts (ISDA 2013). Four boats were washed in 

2012. Two boats were washed by the ISDA crew, including a jet ski with dead quagga mussels on it and 
ESA Recovery Plan: Snake River Sockeye Salmon | 161

June 2015| NOAA Fisheries 

Nevada registration. Two boats were washed by the Student Conservation Association crew. Three of 

the boats were just dirty, with no plants or animals visible. 

Wildfire Risks

Mountain pine beetle populations are a natural part of the ecosystem. Several mountain pine beetle 

infestations have occurred and been recorded in the Sawtooth Valley area throughout the past century. 

The most recent mountain pine beetle epidemic started in 1996 (Figure 5-1). Even though mountain 

pine beetle epidemics are a natural part of the ecosystem, concerns have been raised about how the 

epidemics may influence wildfire risk. In general, the potential for high-intensity crown fires is great 

during two periods in the life of a lodgepole stand. The first period is in young stands, when the crowns 

of the growing lodgepole are in proximity to dead woody fuels. The second period is when over mature

stands break up and are being replaced by shade-tolerant associates. During this period, dead fuels 

accumulate as lodgepole snags fall, and young shade-tolerant conifers provide a fuel ladder to the 

crowns of overstory trees.

In 2005, the 16,524 hectare (40,831 acre) Valley Road Fire, located 22.5 km (14 miles) southeast of 

Stanley, Idaho, started on private property from human causes. Weather and fuel conditions created 

extreme fire behavior. In 2012, the 72,461 hectare (179,055 acre) Halstead Fire started by a lightning 

strike on the Salmon Challis National Forest north of Stanley. In 2013, the 210 Fire was aggressively 

fought and contained at 93 hectares (230 acres) along Highway 75 near the Redfish Lake Road, 

approximately 5 miles south of Stanley, Idaho. 

Although no large fires have occurred on the westside of the Sawtooth Valley, several smaller fires have 

occurred, including the Road 210, Gold, and Hell Roaring Fires in 2013 and 2014. The accumulation of 

fuel within lodgepole pine and adjacent stands place several subwatersheds that support Sockeye 

Salmon at risk from changed watershed conditions. How change may occur is dependent on the burn 

severity, fire intensity, burn area, topography, soil properties, climate, and channel proximity (Baker

1988; Beschta 1990; DeBano et al., 1998; Robichaud 2000). If kept small, wildfire and post-fire effects 

may have only localized impacts to watersheds and aquatic systems. However, larger fires have the 

potential to accelerated soil erosion and sediment delivery to streams until enough vegetative recovery 

occurs. Some streams with adequate wood and other obstructions may be able to temporarily store the 

finer sediments; however, most streams will transport material to lower gradient reaches because they 

are very steep and have confined channels. Spawning gravel quality may decrease in localized areas 

depending on how large a sediment pulse enters the channel and how much of it is stored in lower 

gradient areas. Pool volume may also decrease until higher flows transport the fine sediment 

downstream. Wildfires may also change lake water chemistry by adding nutrient-laden sediment, or 

through atmospheric deposition of smoke and ash. 
ESA Recovery Plan: Snake River Sockeye Salmon | 162

June 2015| NOAA Fisheries 

Figure 5-1. Extent of recent Mountain pine beetle epidemic beginning in 1996.

5.1.1.5 Summary of natal lakes threats and limiting factors

Threat: Introduction and continued stocking of non-native fish species such as brook trout, rainbow 

trout, lake trout, and kokanee.

Potential limiting factors: Unfavorable changes in lake ecology; genetic introgression and intraspecific 

competition between Sockeye Salmon and kokanee for food resources; predation and competition by 

hatchery steelhead (Cannamela 1993), rainbow trout, brook trout, and potentially lake trout if Sockeye 
ESA Recovery Plan: Snake River Sockeye Salmon | 163

June 2015| NOAA Fisheries 

Salmon are allowed to enter currently inaccessible Stanley Lake or if lake trout spread to other lakes and 

streams. 

Threat: Recreational use and development.

Potential limiting factors: Potential unfavorable changes to water quality; localized impacts to lakeshore 

and wetland habitats, access roads impact sediment processes and habitat if located adjacent to lakeshore 

or outlet streams, potential interference in historical Sockeye Salmon spawning areas; potential for 

chemical spill from recreational boat use in lakes; projected future increase in recreational use and 

development pressures on natal lakes may increase the impact of this threat in future years.

Threat: Legacy impacts from historical land use, irrigation diversions, and mining practices.

Potential limiting factors: Increased sediment inputs and lingering historical habitat impacts due to 

sheep and cattle grazing, timber harvest, road building, and mining; reduced flow and blocked migration 

due to water withdrawals and irrigation diversion structures; lake poisoning and stocking of non-native 

fish. 

Threat: Blocked access to lakes.

Potential limiting factor: Inability to spawn in historical habitat, restricted Sockeye Salmon spatial 

diversity, and impacts to natal lake biological processes due to loss of connectivity of fish into lakes.

Potential Future Threat: Aquatic invasive species.

Potential limiting factors: Impacts to natal lake biological processes due to impacts in food chain 

species important to lake ecosystem and salmonid food sources; increased mortality at different life 

stages due to parasites.

Potential Future Threat: Wildfire risks.

Potential limiting factors: Impacts to watersheds may include accelerated soil erosion and sediment 

delivery to streams, decreased spawning gravel quality, decreased pool volume and changes to lake 

water chemistry due to nutrient laden sediment or through atmospheric deposition of smoke and ash.

Potential Future Threat: New pond development.

Potential limiting factors: Impacts to natal lake biological processes due to impacts from sediment 

delivery to streams; potential unfavorable changes to water quality, including temperature; potential 

introduction of aquatic invasive species. 

5.1.2 Salmon River

This section discusses the threats and potential limiting factors for Snake River Sockeye Salmon in the 

Salmon River migration corridor. It discusses land use practices and the resulting habitat conditions that 

Sockeye Salmon migrants face as they make their way to and from the Sawtooth Valley lakes. The 

possible effects from contaminants are discussed in Section 5.7, Toxics.
ESA Recovery Plan: Snake River Sockeye Salmon | 164

June 2015| NOAA Fisheries 

The Salmon River, flowing 660 km (410 miles) through central Idaho to join the Snake River in lower 

Hells Canyon, represents almost half the length of the Sockeye Salmon migration route. Juvenile 

Sockeye Salmon migrants move quickly through the Salmon River after leaving the natal lakes in late 

spring and early summer, often arriving at Lower Granite Dam in about seven days. Adult Sockeye 

Salmon migrate upstream through the river in late summer, returning to the Sawtooth Valley lakes in 

August and September. Adult Sockeye Salmon migrants generally spend more than 30 days traveling up 

the Salmon River before reaching the Sawtooth Valley. 

Much of the upper Salmon basin is managed for public use, with some of the Salmon subbasin protected 

in wilderness or roadless areas. High watershed and aquatic integrity is found in the Upper Middle Fork, 

Lower Middle Fork, and Middle Salmon–Chamberlain watersheds (NPCC 2004a). Habitats tend to be 

more modified or degraded in the major watersheds that have broad valleys and easier access for 

humans and development, such as the Little Salmon, lower Salmon, Pahsimeroi, and Lemhi watersheds. 

Much of the subbasin is managed by the USFS or BLM for multiple uses. 

Private lands tend to be concentrated along the valley bottoms, i.e. near the river. The small towns in the 

subbasin are located along the river (Stanley, Challis, Salmon, Riggins, New Meadows, and White 

Bird), with rural populations scattered in the surrounding areas. Most of these towns have populations 

under 500. Salmon is the largest, with slightly more than 3,000 people (NPCC 2004a). Cattle ranching 

and agriculture are the main economic activities, and irrigation diversions are common; logging and 

mining were important historically but have declined since the 1990s (NPCC 2004a). Water quality in 

many areas of the subbasin is affected to varying degrees by land uses that include livestock grazing, 

road construction, irrigation withdrawals, logging, and mining (NPCC 2004a). A potential emerging 

threat is the development of new ponds for aesthetics and irrigation purposes, even when there are other 

means to meet existing water rights. The development of new ponds could increase losses through 

evaporation, reduce water quality, raise water temperature and sediment delivery, and create additional 

stressors to the aquatic environment. More information is needed about this potential land use issue to 

better understand its impacts. 

5.1.2.1 Sockeye Salmon migration and survival in the Salmon River

Despite the relatively sparse human population and expanse of public lands, both juvenile and adult 

Sockeye Salmon experience unexplained mortality in the 743 km (462-mile) migration corridor between 

Redfish Lake and Lower Granite Dam. Determining the magnitude of this loss, as well as where and 

why mortality is occurring, is critical to the successful restoration and recovery of the Sockeye Salmon

populations. 

Annual tracking of hatchery Sockeye Salmon juveniles between release sites in the Sawtooth Valley and 

Lower Granite Dam shows that juvenile survival through this Salmon River reach varies between years. 

Based on detections of juvenile hatchery Sockeye Salmon that were PIT-tagged and released in the 

spring of each year, survival estimates have ranged from 11.4% in 2000 (Zabel et al. 2001) to 77.6% in 

2008 (Faulkner et al. 2008). 
ESA Recovery Plan: Snake River Sockeye Salmon | 165

June 2015| NOAA Fisheries 

The studies show that survival of juvenile hatchery Sockeye Salmon in the Salmon River varies between 

release strategies and different reaches (Axel et al. 2014 ). Researchers track and compare survival and 

travel times for PIT-tagged and radio-tagged hatchery Sockeye Salmon juveniles from Sawtooth and 

Oxbow hatcheries. The fish have been released in separate groups to compare day and night survival 

rates. The tracking studies also indicate that a large portion of the loss of outmigrating juvenile hatchery 

Sockeye Salmon in the Salmon River occurs between release sites and the North Fork Salmon 

confluence, with higher losses occurring within Little Redfish Lake, in the reach just above Valley 

Creek near Stanley, between the Pahsimeroi and Lemhi Rivers, and in the slow-river reach at Deadwater 

Slough (Axel et al. 2014 ). 

Predation appears to be responsible for much of the juvenile mortality in the upper Salmon River. 

During fish releases, researchers have observed multiple predation events on recently released juvenile 

Sockeye Salmon. In 2013, common merganser Mergus merganser, osprey Pandion haliaetus, doublecrested cormorant Phalacrocorax auritus, and western grebe Aechmophorus occidentalis were actively 

feeding in Little Redfish Lake, located below the release site, as fish were moving through the area. Bull 

trout Salvelinus confluentus were also chasing juvenile Sockeye Salmon schools as they migrated 

through Little Redfish Lake (Axel et al. 2014). Loss of migrating juvenile Sockeye Salmon may also be 

related to competition with non-native species, environmental conditions, natural mortality, or rearing 

and release strategies. 

Adult migrants are also lost in the Salmon River corridor (Keefer et al. 2008). Of the 5,574 adult 

Sockeye Salmon that passed Lower Granite between 2008 and 2012, a total of 4,207 (75%) were 

recovered at Redfish Lake, the Sawtooth Hatchery weir, or other basin trapping locations (IDFG 2012). 

The factors responsible for the losses of adult Sockeye Salmon migrants are not fully established, but are 

believed to be strongly related to stream flow and temperature (Arthaud 2012). Adult Sockeye Salmon

return to the Salmon River in late summer, when flows often reach low levels and water temperatures 

peak. Research continues to identify how and where these conditions in the Snake and Salmon Rivers

affect Sockeye Salmon migrants. It is not clear where adult Sockeye Salmon mortality is occurring 

upstream of Lower Granite Dam.

5.1.2.2 Salmon River mainstem habitat in Sawtooth Valley

Sockeye Salmon utilize the upper mainstem Salmon River in the Sawtooth Valley as a migratory 

corridor to and from the natal lakes. Legacy effects from historical mining, private land grazing, and 

irrigated pasture use may still influence local habitat and sediment processes and conditions. However, 

ongoing restoration work to eliminate impacts from irrigation diversions and fence stream corridors to 

exclude livestock are improving habitat conditions over time.
ESA Recovery Plan: Snake River Sockeye Salmon | 166

June 2015| NOAA Fisheries 

Water Temperature and Sediment

The Salmon River from Redfish Creek to Valley Creek is currently listed on IDEQ’s 2010 303(d) list 

(under the Clean Water Act) as “not supporting” the beneficial use “cold water aquatic life”6 due to 

“water temperature and sediment/siltation” (Table TT in IDEQ 2011). Grazing and localized 

development pressures, numerous diversions on tributaries, irrigation return flows, and some large 

diversions on the mainstem Salmon River (e.g., Decker Flats), are major factors. In tributaries 

throughout the Sawtooth basin, Rothwell and Moulton (2001) found reductions in streamflow caused by 

diversions correlated with increases in stream temperature. Reductions in water quality, especially from 

water temperature and sediment, are widespread where tributaries cross the flat, grazed, and exposed 

valley floor. Water temperatures in the Salmon River rise as the river collects the warmer streamflow 

from these tributaries. The higher water temperatures impact Sockeye Salmon migration survival 

through the Salmon River. The quality of source water from the Salmon River for the Sawtooth 

Hatchery is also limited when temperatures warm during late summer.

Physical Barriers

Multiple diversions occur on the mainstem Salmon River upstream of Stanley, Idaho. Most of these 

have fish screens and head gates, but some still may entrain fish into irrigation ditches or cause 

significant bypass mortality. Diversions also reduce stream flows, but most mainstem diversions below 

the Redfish Lake Creek confluence do not currently reduce flow enough to create passage barriers. 

Diversions upstream of Redfish Lake Creek confluence have historically limited fish passage, especially 

during drought years. 

A weir at Sawtooth Hatchery on the Salmon River also restricts Sockeye Salmon passage. Plans are 

underway to begin allowing anadromous Sockeye Salmon adults to return to their lake of origin. This 

would entail trapping adults at the Sawtooth weir and transporting them to Alturas or Pettit Lakes, or 

alternatively to pass the adults to allow for volitional migration. Presently the trap does not effectively 

capture adult Sockeye Salmon. The Sawtooth Hatchery on the Salmon River upstream of the mouth of 

Redfish Lake Creek has been in operation since 1985 as a mitigation hatchery for Chinook salmon and 

summer steelhead. The hatchery includes a weir on the Salmon River, a fish ladder and adult holding 

ponds. Adult Sockeye Salmon trapped at the Sawtooth weir are transported to the Eagle Fish Hatchery 

where they are identified (genetically) and either held for incorporation in subsequent spawning designs 

or returned to Sawtooth Valley lakes for natural spawning. 

Floodplain Modification and Connectivity

Some localized floodplain modification has occurred, including road fill (particularly from Highway 

75), bridges, channel modifications on private lands, residential and commercial development in Stanley 

and lower Stanley, and construction of the Sawtooth Hatchery (USFS 2011). River bank modifications 

 

6 Supporting the beneficial use “Cold Water Aquatic Life” means that water quality is appropriate for the protection and 

maintenance of a viable aquatic life community for coldwater species (e.g., salmon, steelhead, and bull trout).
ESA Recovery Plan: Snake River Sockeye Salmon | 167

June 2015| NOAA Fisheries 

and bank stabilization treatments have been applied to control or prevent natural movement of the river 

channel. 

Mining

Mining activities have occurred throughout the Salmon River headwaters of the population since the 

latter part of the nineteenth century. However, the legislation that established the Sawtooth National 

Recreation Area withdrew the area from additional mineral entry under the 1872 Mining Law, and 

directed validation of existing mining claims. The vast majority of claims present in 1972 have since 

been invalidated. Valid claims remain, but active mining is not currently occurring (Sawtooth National 

Forest 2006).

5.1.2.3 Salmon River mainstem habitat from Sawtooth Valley to Snake River

Snake River Sockeye Salmon are affected by conditions in the Salmon River as they migrate between 

the Sawtooth Valley and lower Snake River. Several factors potentially influence Sockeye Salmon

survival in this reach including floodplain modification, mining, irrigation withdrawals, water quality, 

and introduction of non-native species. 

Floodplain Modification and Connectivity

The Salmon River floodplain downstream from the Sawtooth Valley has been modified considerably by 

conversion to cropland, such as irrigated cut hay, alfalfa, and wheat, and by residential development. 

Riverbanks have been altered by the construction of numerous dikes and diversions associated with 

agriculture, residential development, and State Highways 75 and 93. Much of the natural sinuosity of 

the river has been reduced and side channels filled in an effort to protect residential and agricultural 

lands on either side of the river channel (IDEQ 2003). 

Historical and Current Mining

Many upper Salmon River watersheds have experienced mining activities in the past, with some activity 

remaining today. Mining and associated activities severely reduced habitat and water quality of the 

Salmon River. Hydraulic mining and placer mining were widely used historically, followed by shaft 

mines and adit mines (where the entrance to an underground mine is horizontal or nearly horizontal). 

Mine-related ground disturbance removed hill-slope and riparian vegetation, exposed and compacted 

soils, and altered drainage patterns. 

Mining activities in the basin began more than 100 years ago. In 1910, Sunbeam Dam was constructed 

on the upper Salmon River to generate power for a mine on the Yankee Fork. The dam was used only 

one year, yet blocked fish passage to the entire upper Salmon River for 23 years until breached in 1934 

by IDFG. In the early 1940s and 1950s, the substrate of the lower Jordan Creek and Yankee Fork was 

mined for gold using a floating dredge, severely affecting the Yankee Fork and mainstem Salmon River. 

Much of the natural meander pattern of the Yankee Fork was lost, along with associated instream habitat 

and riparian vegetation. Extensive unconsolidated and unvegetated dredge tailings continue to increase 

sedimentation and reduce water quality of the Salmon River.
ESA Recovery Plan: Snake River Sockeye Salmon | 168

June 2015| NOAA Fisheries 

Mining activities in recent decades include Grouse Creek Mine, a large surface silver mine operated in 

the 1990s in the Yankee Fork, which is now closed as a Comprehensive Environmental Response 

Compensation and Liability Act (CERCLA) site, commonly known as a superfund site. The largest 

active mine in the region is the Thompson Creek Molybdenum Mine located within the Thompson 

Creek and Squaw Creek watersheds. Potential exists for future mining opportunities in many tributary 

watersheds to the Salmon River (IDEQ 2003).

Irrigation withdrawals

One of the largest impacts to salmonid habitat in the upper Salmon River comes from the effects of 

irrigation diversions and evapotranspiration of crops (USBWP 2005). Consumptive water use in the

upper Salmon River basin reduces streamflow in individual tributaries and cumulatively in the Salmon 

River. Reductions during juvenile spring migration and during summer and fall adult migrations reduce 

the amount and function of available habitat, leading to reduced survival (Arthaud and Morrow 2007, 

2013). 

Diversions on the mainstem Salmon River near Challis and downstream from Salmon withdraw large 

proportions of water available in the mainstem. Entrainment and bypass of Sockeye Salmon is common 

and reduced survival may occur. Through their Anadromous Fish Screen Program, IDFG has installed 

fish screens on most of the diversions on the mainstem Salmon River, but tributary diversions are 

largely unscreened and number in the hundreds throughout the Salmon River basin (IDFG 2003). These 

flow reductions in tributaries contribute to flow depletions and higher water temperatures in some 

reaches of the Salmon River mainstem and reduce salmon rearing and migration survival. One of the 

most critical reaches of the Salmon River for juvenile migration is likely from Challis to Shoup, which 

includes the most and larger diversions, least tributary contributions, and most associated habitat and 

water quality degradation. The development of new ponds for aesthetics and irrigation is a potential

emerging threat to water quality and stressor to the aquatic environment. More information is needed 

about this potential land use issue to better understand its impacts. 

Water quality 

The land and water uses described above have led to some stream and river reaches in upper Salmon 

River being listed as impaired on the Clean Water Act 303(d) list. In 2008, Idaho Department of 

Environmental Quality (IDEQ) listed various stream reaches as impaired by sediment, high 

temperatures, and nutrients (IDEQ 2008). Multiple tributaries, along with the main Salmon River 

downstream from the Pahsimeroi River, are also listed on the 303(d) list as not supporting cold-water 

aquatic life for unknown reasons. This section of the Salmon River mainstem, for example, received 

low scores on IDEQ’s combined biota and habitat bioassessments, but the specific pollutants causing the 

low scores are not known. IDEQ has written a Total Maximum Daily Load (TMDL) for sediment for 

Challis Creek, recommending a substantial reduction in streambank erosion. Temperatures in portions of 

the mainstem Salmon River migration corridor do not support the beneficial use “Cold Water Aquatic 
ESA Recovery Plan: Snake River Sockeye Salmon | 169

June 2015| NOAA Fisheries 

Life”7 (Table 5-1) which is likely to reduce the survival of adult Sockeye Salmon returning to the 

Sawtooth Valley in late July and August.

Table 5-1. Reaches of the mainstem Salmon River that do not support the beneficial use “Cold Water Aquatic Life” (Source: 

Table TT, IDEQ 2011).

Mainstem Reach Reach Pollutant

Upper Salmon Fisher Cr to Decker Cr Sedimentation/siltation

Redfish Lake Cr to Valley Cr Sedimentation/siltation/

Water temperature

Valley Creek to Yankee Fork 

Creek

Sedimentation/siltation/

Water temperature

Thompson Cr to Squaw Cr Sedimentation/siltation/

Water temperature

Middle Salmon-Panther

Pahsimeroi to NF Salmon R 

(includes multiple assessed 

reaches)

“Cause unknown”

Eighty water bodies in the Salmon subbasin are classified as impaired under the guidelines of section 

303(d) of the Clean Water Act (IDEQ 2011) (Figure 5-2). The primary parameters of concern are 

sediments, nutrients, flow alteration, water temperatures, and habitat alteration. 

 

7 IDEQ defines support of the beneficial use “Cold Water Aquatic Life” as water quality is appropriate for the protection and 

maintenance of a viable aquatic life community for coldwater species (e.g., salmon, steelhead, and bull trout).
ESA Recovery Plan: Snake River Sockeye Salmon | 170

June 2015| NOAA Fisheries 

Figure 5-2. Streams in the Salmon subbasin, Idaho, that are included on the 303(d) list ( Source: IDEQ 2011).

Introduction of non-native species

Smallmouth bass thrive in the lower Salmon River mainstem extending upstream to Salmon, Idaho. 

Introduced smallmouth bass, brook trout, hatchery steelhead, and hatchery rainbow trout compete with 

and prey upon emigrating juveniles (Peterson 2013b). 

5.1.2.4 Summary of Salmon River threats and limiting factors

Threat: Irrigation withdrawals.

Potential limiting factors: Reduced baseflows, altered hydrologic regime, elevated water temperatures, 

and reduced refugia at tributary mouths reduce juvenile and adult Sockeye Salmon survival and impede 

migrations. 
ESA Recovery Plan: Snake River Sockeye Salmon | 171

June 2015| NOAA Fisheries 

Threat: Toxic pollutants (See Section 5.7).

Potential limiting factors: Impaired fitness and research needed to assess potential impacts.

Threat: Historical and current land use, roads and erosion control, floodplain development, and mining 

activities.

Potential limiting factors: Degraded riparian habitat, elevated water temperatures, reduced floodplain 

connectivity, narrowed and simplified channels, barriers to migration, and elevated sediment levels.

Threat: Blocked access to migration corridor and natal lakes.

Potential limiting factor: Inability to spawn in historical habitat, restricted Sockeye Salmon spatial 

structure, and impacts to biological processes due to loss of connectivity into migration corridors and 

lakes.

Threat: Introduction and continued stocking of non-native fish species.

Potential limiting factors: Unfavorable changes in species composition; competition for food resources; 

predation on emigrating Sockeye Salmon juveniles by smallmouth bass, hatchery steelhead, rainbow 

trout, and brook trout.

Potential Future Threat: New pond development.

Potential limiting factors: Impacts to natal lake biological processes due to impacts from sediment 

delivery to streams; potential unfavorable changes to water quality, including temperature; potential 

introduction of aquatic invasive species. 

5.1.3 Lower Mainstem Snake River to Lower Granite Reservoir

The Salmon River joins the lower Snake River at river kilometer (RKm) 302 (river mile (RM) 188). The 

Grande Ronde River also contributes flow to this reach, along with some smaller tributaries, including 

the Imnaha River and Asotin Creek. The channel widens near RKm 290 (RM 180), with gently sloping 

shorelines. Downstream of the Salmon and Grande Ronde Rivers there are long, deep pools and runs 

and low-gradient rapids (Groves and Chandler 1999). The free-flowing reach ends at RKm 236 (RM 

147), where it enters the Lower Granite Reservoir near Lewiston, Idaho. 

5.1.3.1 Altered flows

Although unimpounded, flows in this reach of the lower Snake River have been altered by power 

peaking operations at the Hells Canyon Complex (Snake River RKm 398, RM 247) since the 1960s. 

Flow fluctuations can strand or entrap juveniles in shallow water areas. There is no indication that this is 

a significant issue for Snake River Sockeye Salmon which migrate quickly through the mainstem and 

spend limited time in nearshore areas. PIT-tag and radiotelementry studies during the 2012 and 2013 

outmigration season showed that median travel time for Sawtooth and Oxbow Hatchery Sockeye 

Salmon was approximately 7 days from the Sawtooth Valley to Lower Granite Dam (Axel et al. 2013, 

2014).
ESA Recovery Plan: Snake River Sockeye Salmon | 172

June 2015| NOAA Fisheries 

The fluctuations in flow caused by the upstream Hells Canyon Dam complex have altered riparian 

vegetation in this free-flowing reach of the lower Snake. Over the decades, this has created a large 

degraded riparian zone along each side of the river where the vegetation community and associated prey 

communities are highly altered. The food is now dominated by phytoplankton and zooplankton instead 

of the prey produced in the floodplain, but the effect of this change on juvenile Sockeye Salmon growth, 

condition, and survival has not been studied.

5.1.3.2 Water quality

The potential effects of toxics in this reach are discussed in Section 5.7 Toxics.

High water temperatures may be a limiting factor in this reach. IDEQ has begun a TMDL for 

temperature for the lower mainstem reach (Zaroban 2011). A preliminary comparison of USGS 

temperature gage data from 1999 to 2005 found peak summer water temperatures in the Salmon River 

and the mainstem Snake quite similar, reaching 24°C (75°F) in both (Zaroban 2011).

Sockeye Salmon adults migrate upstream during summer in depleted flows and warm temperatures. 

Arthaud et al. (2010) estimated spring flows of the Snake and Columbia Rivers were depleted about 30-

50%, although peak runoff exceeded historical averages some years. Summer depletions of the upper 

Salmon River may also reach 10-30% (Rothwell 2009). From 1999 to 2012, survival of PIT-tagged

adult Sockeye Salmon from Lower Granite Dam to Sawtooth return sites was closely and negatively 

related (r2 = 0.53) to water temperature of the Snake River (Arthaud 2012). When Snake River (at 

Anatone, Washington gage) average July water temperatures exceed 22oC (71.6°F), the percent

conversion was less than 20%, yet reached 90% as temperature declined to 18oC (64°F). Current efforts 

to control summer water temperatures in the lower Snake River include regulating outflow temperatures 

at Dworshak Dam.

5.1.3.3 Adjacent land uses

Dryland and irrigated farming and livestock grazing are widespread in the lower Snake River subbasin. 

Lands adjacent to the river are mostly privately owned (NPCC 2004b). Riparian vegetation tends to be 

absent or degraded (NPCC 2004b.). The Lewiston-Clarkston area near the mouth of the Snake River is 

the only significant industrial, commercial, and residential development in the subbasin.

5.1.3.4 Summary of lower mainstem Snake River to Lower Granite Reservoir threats and limiting factors 

Threat: Upstream dam operations.

Related limiting factors: Altered flows, riparian function, and food webs

Threat: Land uses adjacent to Snake River and tributaries.

Related limiting factors: Degraded water quality, altered thermal regime.
ESA Recovery Plan: Snake River Sockeye Salmon | 173

June 2015| NOAA Fisheries 

5.1.4 Mainstem Migration Corridor

Moving downstream, the mainstem Columbia and Snake River migration corridor runs from the 

contiguous reservoirs formed by Lower Granite, Little Goose, Lower Monumental, and Ice Harbor 

Dams on the lower Snake River; through McNary, John Day, The Dalles, and Bonneville Dams on the 

lower Columbia River; and on through the estuary and plume to the ocean. Hydrosystem modifications 

to the mainstem habitat are significant, affecting both juvenile and adult migration. Hydropower and 

flood control have altered stream habitat conditions through the creation of passage barriers, conversion 

of riverine habitat to reservoirs, and water withdrawals. The effects of the hydrosystem are discussed in 

Section 5.2.

5.1.5 Estuary and Plume

As stream-type salmonids, Snake River Sockeye Salmon are assumed to move relatively quickly 

through the estuary; however data are sparse because of their small numbers. They, like PIT-tagged

Chinook salmon and steelhead tracked from below Bonneville Dam to the mouth of the Columbia River, 

may pass through this area within two to three days (McMichael et al. 2011), but this hypothesis has not 

been tested. Snake River Sockeye Salmon may stay in the plume before moving to the ocean but only 

limited information exists regarding this potential habitat use.

5.1.5.1 Diking and reduced spring flows

In the lower Columbia River and estuary, diking and reduced peak spring flows have eliminated much 

of the shallow water and low velocity habitat needed by juvenile salmonids for feeding, growth, refuge 

from predators, and to complete the physiological transition to salt water. Dikes are constructed to 

protect agriculture and other development in riparian areas; spring flows are managed in the FCRPS and 

upper Snake hydrosystems for power production, flood control, navigation, fish and wildlife, and other 

purposes (Hydro Module, NMFS 2014a and Estuary Module, NMFS 2011a).

Changes in the volume and timing of Columbia River flow caused by upstream water management have 

altered both the size and structure of the plume during the spring and summer months. Reductions in 

spring freshets and associated sediment transport processes have permanently changed the food web in 

the estuary and plume (Casillas 1999 cited in the Estuary Module, NMFS 2011a). 

5.1.5.2 Water temperature

Higher water temperatures have reduced habitat quality for salmonids that use the estuary during 

summer months. Since 1938, average summer water temperatures entering the estuary at Bonneville 

Dam have increased 2.2°C (4° F) (Lower Columbia Fish Recovery Board 2004). Among-year variability 

in temperature has been reduced by 63% since 1970 (Lower Columbia Fish Recovery Board 2004). 

5.1.5.3 Latent mortality

Mortality of juveniles after passing Bonneville Dam that would not occur in a free-flowing river is 

called differential latent mortality (Williams et al. 2005). Latent mortality could result from injuries, 
ESA Recovery Plan: Snake River Sockeye Salmon | 174

June 2015| NOAA Fisheries 

stress, disease, or depletion of energy reserves caused by passage through the hydropower system. 

However, it can also result because of other factors, including conditions in the subbasins that produced 

the fish and contributed to their age, fitness and arrival time at Bonneville Dam, and/or environmental 

factors that the fish could also experience in a free-flowing system. Because there are no mortality 

estimates for the reference condition (no mainstem dams), latent mortality cannot be measured directly. 

Currently, the range of estimates of latent mortality is extremely wide (0.01 to 64%) and depends on 

strong, but unverifiable assumptions (ISAB 2007; NMFS 2014a). The degree to which mortality in the 

estuary and ocean is caused by prior experience of juveniles passing through the FCRPS (delayed or 

latent mortality) remains unknown. 

5.1.5.4 Summary of estuary and plume threats and limiting factors

Threat: Dikes and levees that have disconnected the river from its historical floodplain.

Related limiting factors: Lack of access to floodplain habitat; altered food web.

Threat: FCRPS flow management: reduced spring flows and other flow alterations.

Related limiting factors: Flow-related changes in access to off-channel habitat and the size of the 

plume; reduced macrodetrital inputs and increased microdetrital inputs.

5.1.6 Ocean

Ocean conditions and food availability contribute to the health and survival of Sockeye Salmon

returning to the Columbia Basin, and eventually the Sawtooth Valley. Poor ocean conditions in 1977 

through the late 1990s probably contributed, together with other factors, to drive the stock to a very 

small remnant population (NMFS 2008b).

Once Sockeye Salmon enter the ocean they immediately began migrating north; no sockeye salmon 

from the Columbia River (Snake River Sockeye Salmon and unlisted Upper Columbia River Sockeye 

Salmon) have been caught south of the river’s mouth in 16 years of sampling in the Northern California 

Current. In May and June, Columbia River sockeye salmon are most abundant off the coast of 

Washington but some fish have migrated as far north as North and Central British Columbia (Tucker et 

al. 2009). As the Sockeye Salmon leave the Northern California Current, they likely move north into the 

Gulf of Alaska (GOA), Bering Sea, and up the coast into Alaska. By winter, the fish have disappeared 

from coastal areas and have entered the GOA (Tucker et al. 2009). In general, maturing Sockeye 

Salmon are distributed in the GOA and into the Bering Sea but are migratory within this region (Burgner 

1991; Myers et al. 1996). Water temperatures affect the distribution of fish in the GOA with warmer 

temperatures pushing fish further north, thereby increasing the distance fish migrating south to the 

Columbia River will need to travel on their return journey. A study by Myers et al. (1996) found six 

maturing sockeye salmon from the Columbia River in the GOA. 

As the fish mature in the GOA and Bering Sea region, they eventually begin their return migration to the 

Snake River. Water temperatures during the last months of ocean residence affect their body size at 

return, with warmer temperatures leading to a smaller body size (Pyper and Peterman 1999). The date 
ESA Recovery Plan: Snake River Sockeye Salmon | 175

June 2015| NOAA Fisheries 

when Snake River Sockeye Salmon begin their return migration is likely a population specific trait that 

is independent of where the fish are at sea (Hodgson et al. 2006). Water temperature also plays an 

important role in determining when the fish arrive back to coastal areas near the mouth of the Columbia 

River. The Ocean Module provides additional information on ocean-related threats and limiting factors 

for Snake River Sockeye Salmon, including potential effects related to future climate change.

5.2 Hydropower

Dam development and operations have affected the viability of Snake River Sockeye Salmon and other 

Columbia River basin anadromous salmon and steelhead. This section summarizes the general effects of 

the mainstem hydropower system on Snake River Sockeye Salmon. The Hydro Module also describes 

the impacts in more detail. The goal in this section is to consider specific effects these factors may have 

on Snake River Sockeye Salmon. 

Compared to Snake River spring/summer Chinook salmon, there is relatively little route-specific 

information on the survival of Snake River Sockeye Salmon through the FCRPS. Most available reach 

survival estimates  especially in the lower Columbia River  are relatively imprecise because sample 

sizes of migrants from the Snake River are small (NMFS 2008c).

5.2.1 Migrating Juveniles

Federal Columbia River Power System

Juvenile Snake River Sockeye Salmon enter the mainstem hydropower corridor in Lower Granite 

Reservoir. Three U.S. government agencies ─ the Bonneville Power Administration, U.S. Army Corps 

of Engineers, and Bureau of Reclamation, also called, collectively, the “Action Agencies” ─ collaborate 

to run the Federal Columbia River Power System (FCRPS), under various congressional authorities, as a 

coordinated system for power production, flood control, and other purposes. The 31 Federally owned 

multipurpose dams on the Columbia, Snake River and tributaries that make up the FCRPS provide about 

60% of the hydroelectric generating capacity in the northwestern United States. The dams supply 

irrigation water to more than a million acres of land in Washington, Oregon, Idaho, and Montana. The 

river is used for barge navigation from the Pacific Ocean to Lewiston, Idaho, 748 km (465 miles) inland.

A substantial proportion of juvenile Sockeye Salmon can be killed while migrating through the dams, 

both directly through collisions with structures and abrupt pressure changes during passage through 

turbines and spillways, and indirectly, through non-fatal injury and disorientation which leave fish more 

susceptible to predation and disease, resulting in delayed mortality. Concerns include:

• Juvenile mortality while passing through the mainstem lower Snake and lower Columbia 

River hydropower system.

• Scarcity of cover in mainstem reservoirs as refuge from fish predators such as 

smallmouth bass and northern pikeminnows.

• Increased mortality from cormorants and other avian predators.
ESA Recovery Plan: Snake River Sockeye Salmon | 176

June 2015| NOAA Fisheries 

• Altered seasonal flow and temperature regimes.

The Action Agencies have implemented a number of actions in recent years to improve conditions in the 

migration corridor for all listed Columbia Basin salmon and steelhead species. By 2009, each of the 

eight mainstem lower Snake and lower Columbia River dams was equipped with a surface passage 

structure (spillbay weirs, powerhouse corner collectors, or modified ice and trash sluiceways). Smolts 

primarily migrate in the upper 20 feet of the water column in the lower Snake and Columbia Rivers. 

Water is drawn through these surface passage routes from the same depths as juveniles migrate, whereas 

conventional spillbays or turbine unit intakes draw water from depths greater than 15 meters (50 feet). 

The surface passage routes provide a safe and effective passage route for migrating smolts by reducing 

migration delay (time spent in the forebay of the dams) and increasing the proportion of smolts passing 

the dams via the spillway rather than via the turbines or juvenile bypass systems (spill passage 

efficiency). Changes have included the relocation of juvenile bypass system outfalls to avoid areas 

where predators collect; as well as other operational and structural changes. Other changes include 

changes to spill operations, the installation of avian wires to reduce juvenile losses to avian predators, as 

well as changes to reduce dissolved gas concentrations that might otherwise limit spill operations. 

Together, these factors have improved the inriver survival of Snake River Sockeye Salmon (NMFS 

2014c).

5.2.2 Migrating Adults

While the upstream migration of adults can be slowed as fish search for fishway entrances and navigate 

through the fishways themselves, adults migrate more quickly through the relatively slow velocity 

reservoir environments. Large upstream water storage and flood control projects and mainstem run-ofriver hydropower projects have affected the thermal regime of the mainstem Snake and Columbia 

Rivers. Together, they have generally increased minimum winter temperatures, delayed spring warming, 

reduced maximum summer temperatures, and delayed fall cooling. These alterations may benefit

Sockeye Salmon adults that migrate during the spring and summer, but may negatively affect those 

migrating in the late summer and fall by increasing their exposure to relatively high temperatures. To 

mitigate for (or, in some instances, enhance) these thermal effects, Dworshak Dam, on the North Fork 

Clearwater River, releases cool water during July, August, and September to reduce mainstem Snake 

River temperatures.

Adult fish passage, in the form of fish ladders, is provided at each of the eight mainstem projects in the 

lower Snake and lower Columbia Rivers. In general, these adult passage facilities are highly effective, 

but average survival from Bonneville to McNary dams (including the reservoirs) is lower than that in the 

Snake River reach (Table 4-2). Section 4 discusses recent Sawtooth Valley-to-Sawtooth Valley smoltto-adult return rates for Snake River Sockeye Salmon.

The FCRPS 2014 Supplemental Biological Opinion included actions to add adult detectors at The Dalles 

and/or John Day Dam to better understand where these losses are occurring in the lower Columbia 
ESA Recovery Plan: Snake River Sockeye Salmon | 177

June 2015| NOAA Fisheries 

River. This information should help managers identify the factors likely contributing to these losses and 

develop corrective actions (NMFS 2014c).

Conditions at the dams can affect Sockeye Salmon adult migration in some years. In late July 2013, low 

summer flows, high temperatures, and a period of little or no wind created conditions that allowed 

Lower Granite reservoir to thermally stratify to a greater extent than had been the case for many years. 

The result was warmer water entering the ladder exit, and a refusal by adult Snake River Sockeye 

Salmon (and summer Chinook salmon and steelhead) to pass the project for more than a week. NMFS 

worked with the Corps, IDFG, the tribes, and other co-managers to resolve this issue. However, 

unadjusted PIT-tag based conversion rate estimates from Ice Harbor to Lower Granite Dam indicated 

that a substantial proportion of the migrating adult Sockeye Salmon (~30%) failed to successfully pass 

Lower Granite Dam and most likely died without spawning (NMFS 2014c). NMFS and other comanagers continue to develop short- and long-term measures to resolve this passage problem.

5.2.3 Summary of Hydropower Threats and Limiting Factors 

Threat: Impaired mainstem passage conditions for migrating juveniles.

Related limiting factors: Reduced spring flows and the existence and operation of mainstem hydropower 

projects directly (dam passage) or indirectly (exposure to predators, delayed migration, etc.) can increase 

mortality and injury rates of juveniles compared to migrants in a free-flowing reach.

Threat: Impaired mainstem passage conditions for migrating adults.

Related limiting factors: Fish ladders operating outside criteria, high flows, high spill levels, and thermal 

blockages can impair adult passage through the mainstem migration corridor resulting in increased prespawning mortalities.

Threat: Large storage reservoirs in the upper Columbia and on the Clearwater River in the Snake basin 

reduce annual peak spring flows and increase late summer mainstem temperatures.

Related limiting factors: Water withdrawals reduce spring and summer flows, contributing to increased 

travel times and exposure to elevated summer water temperatures. This exposes adult Sockeye Salmon 

(especially those migrating during late July and August) to factors that can delay migration past the 

dams and cause pre-spawning mortality and outbreaks of virulent disease.

5.3 Hatcheries

Several things are unique about artificial propagation programs (hereafter referred to as hatcheries)

relative to the other factors addressed in this section. First, hatcheries can reduce extinction risk in the 

short-term; second, no two hatcheries are alike; and third, there remains substantial uncertainty over the 

efficacy and the effects of hatcheries on salmon and steelhead recovery.

Although it is generally accepted that hatcheries may contribute to the conservation of salmon and 

steelhead, it is unclear whether or how much hatchery propagation during the recovery process will 
ESA Recovery Plan: Snake River Sockeye Salmon | 178

June 2015| NOAA Fisheries 

compromise the distinctiveness of natural populations. Artificial propagation has been an important 

element in recovery plans for several species, including plants such as Knowlton’s cactus (Pediocactus 

knowltonii), birds such as the peregrine falcon (Falco peregrinus), mammals such as the black-footed 

ferret (Mustela nigripes), and fishes, including pupfishes (Cyprinodon spp.) and several trouts

(Oncorhynchus spp.). 

For salmon and steelhead, the presence of hatchery fish can positively affect the overall status of an ESU 

or DPS by increasing the number of natural spawners, by serving as a source population for repopulating 

unoccupied habitat and increasing spatial distribution, and by conserving genetic resources. Conversely, 

a hatchery program can adversely affect an ESU or DPS by reducing adaptive genetic diversity and by 

reducing reproductive fitness and productivity (Griswold et al. 2012; NMFS 2005c). Although the 

Snake River Sockeye Salmon captive broodstocks are apparently functioning well at this time, NMFS 

recognizes that most hatchery efforts are likely to eventually result in some degree of genetic change and 

fitness reduction in hatchery fish and in the progeny of naturally spawning hatchery fish relative to 

desired levels of diversity and productivity for natural populations (Rand et al. 2012). Hatchery fish 

thus pose a threat to natural population rebuilding and recovery when they interbreed with fish from 

natural populations. That risk is outweighed under circumstances where demographic or short-term 

extinction risk to a natural population is greater than risks to population diversity and productivity. 

However, the extent and duration of genetic change and fitness loss and the short and long-term 

implications and consequences for different species, for species with multiple life-history types, and for 

species subjected to different hatchery practices and protocols remains unclear and should be the subject 

of further scientific investigation. Recently, the Columbia River Hatchery Scientific Review Group 

(HSRG) expanded on theories developed by Ford (2002) to develop scenarios for managing hatcheryand natural-origin salmon and steelhead. The HSRG developed possible population-specific solutions 

for integrating hatchery- and natural-origin fish that minimize potential impacts to wild populations 

associated with hatchery selection. 

Consequently, NMFS believes hatchery intervention is a legitimate and useful tool to help avert, at least 

in the short term, salmon and steelhead extinction, but otherwise managers should seek to limit 

interactions between hatchery and natural-origin fish as they implement a plan for transitioning from 

current practices to those consistent with recovery of listed populations, implementation of treaty Indian 

fishing rights, and harmony with other applicable laws and policies. 

5.3.1 Snake River Sockeye Salmon

The goal of this Snake River Sockeye Salmon Recovery Plan is the restoration of natural Sockeye 

Salmon populations in Sawtooth Valley lakes. The captive broodstock hatchery program has provided a 

useful tool towards achieving this goal; indeed, Snake River Sockeye Salmon might be extinct if not for 

the captive broodstock hatchery program. The natural stock reintroduction and adaptation strategy for 

Sockeye Salmon is evolving and has three phases: prevent extinction and build genetic resources using a 

captive broodstock program in Phase 1; secure the Redfish Lake population and develop strategies to 

support Sawtooth Valley Sockeye Salmon reintroduction in Pettit Lake and evaluate the potential for 
ESA Recovery Plan: Snake River Sockeye Salmon | 179

June 2015| NOAA Fisheries 

restoring natural production of anadromous Sockeye Salmon from returning residual outmigrants from 

Alturas Lake in Phase 2; and reduce hatchery releases and transition the program to follow integrated 

broodstock guidelines and build local natural adaptation in Phase 3. The program was initiated in 1992 

and is now ready to transition from Phase 1 to Phase 2. 

Before Sockeye Salmon were protected under the ESA, one, one, and zero fish returned to the Sawtooth 

Valley in the three preceding years. For the four most recent years (2011-2014), natural-origin Sockeye 

Salmon returns have been 145, 52, 79, and 453 fish respectively, and total returns for the ESU (natural 

and hatchery-origin returns combined) have been 1,117, 257, 272, and 1,579 adults. Between 1991 and 

1998, all 16 of the natural-origin adult Sockeye Salmon that returned to the Sawtooth Valley were 

incorporated into the captive broodstock program. The program has used multiple rearing sites to 

minimize chances of catastrophic loss of broodstock and progeny, and has produced several hundred 

thousand eggs and juveniles, as well as several hundred adults for release into the wild to spawn 

naturally.

In addition to “standard” hatchery production releases of both pre-smolt and full-term smolts to 

Sawtooth Valley waters, the program also has used “natural production” release strategies by outplanting both pre-spawn adults and fertilized eyed-eggs. Progeny produced from adults that spawn 

naturally as well as juveniles that successfully hatch from eyed egg releases are better adapted to lake 

environments and avoid potential hatchery selection concerns that are typically associated with hatchery 

environments. Parentage analyses are used to determine first generation pedigrees for all fish in the 

population, genetic importance, and relative relatedness (Kozfkay et al. 2007). Spawning plans for the 

hatchery also consider heterozygosity and genetic diversity among and within individuals. The 

development and implementation of a spawning matrix has allowed the program to spawn the least 

genetically related individuals within the population (Baker et al. 2011; Kozfkay et al. 2007). 

Monitoring results to date show that patterns of genetic variation have not changed significantly as a 

result of the hatchery program. 

The Redfish Lake Sockeye Salmon Captive Broodstock Program has been vital to helping the 

population avoid extinction. For groups of Redfish Lake Sockeye Salmon in captive broodstock culture, 

eyed-egg survival has averaged about 80% over the last decade and fry-to-adult survival also averages 

about 80%. The fish culture successes for the Redfish Lake program have resulted in the production of 

over 10,000 adult descendants from the 16 wild adult Sockeye Salmon that returned to the Sawtooth 

Valley during the 1990s. Almost 4,300 adults have returned from the ocean to collection sites in the 

Sawtooth Valley; over 250 times the number that returned from wild spawners during the entire decade 

of the 1990s. The genetic focus of the program, and adherence to various central tenets of conservation 

aquaculture, has enabled program managers to retain approximately 95% of the original founding 

genetic variability of the population. 

The hatchery program has been successful in its purpose of conserving genetic resources (Kalinowski et 

al. 2012) and reducing extinction risk, in the short term, and it is now ready to transition to a larger scale 
ESA Recovery Plan: Snake River Sockeye Salmon | 180

June 2015| NOAA Fisheries 

supplementation program. The next step is to secure the primary population in Redfish Lake and 

amplify the number of fish available for reintroduction into the ESU’s former range.

The program is now transitioning to Phase 2, with an emphasis on supporting relatively high levels of 

anadromous return spawners in Redfish Lake. IDFG completed construction of the Springfield Hatchery

in 2013. This new Sockeye Salmon smolt-rearing hatchery will be capable of producing up to one 

million full-term Sockeye Salmon smolts annually (IDFG 2013). Eggs for the expanded smolt program 

will be produced at the IDFG Eagle Fish Hatchery broodstock station and from increased production 

from NMFS’ facilities in Washington State. Using a conservative smolt-to-adult return rate of 0.50%

for hatchery-reared and released smolts (based on empirical program information), managers anticipate 

that a release of up to one million smolts from the Springfield Hatchery could consistently return an 

annual average of 5,000 anadromous adults to Redfish Lake, and to other lakes as determined through 

the adaptive management nature of the reintroduction strategy. 

The program will move to Phase 3, local adaptation, when program triggers are reached, signaling that 

five-year running average returns are more than 2,150 Sockeye Salmon adults, including over 750 

natural-origin adults. During this phase the program transitions to an integrated broodstock management 

program that follows a sliding scale to meet escapement and broodstock objectives. These expansion 

efforts are consistent with expectations established through the Biological Opinion developed by NMFS 

to address risks associated with the operation of the Federal Columbia River Power System. 

5.3.2 Summary of Hatchery Threats and Limiting Factors 

Threat: Hatchery fish interbreed with natural-origin spawners.

Related limiting factors: Potential loss of genetic diversity.
ESA Recovery Plan: Snake River Sockeye Salmon | 181

June 2015| NOAA Fisheries 

Pre-smolts being released into Redfish Lake. Photo: T. Brown, IDFG.

5.4 Fisheries

The potential exists for Snake River Sockeye Salmon to be incidentally caught in fisheries throughout 

the migration corridor, from the ocean to natal lakes (NMFS 2008c). For the near term, fisheries that 

currently impact Snake River Sockeye Salmon through incidental harvest should be managed, with 

accompanying adequate monitoring programs, to minimize their impacts on the ESU. Fishery-related 

limiting factors and threats are summarized here and discussed in more detail in the Harvest Module 

(NMFS 2014b).

5.4.1 Natal Lake Fisheries 

Sport fisheries targeting kokanee occur in Redfish Lake from Memorial Day through the first week in 

August. One goal, or reason, for the fishery is to crop the kokanee population in the lake because 

kokanee compete with Sockeye Salmon for food. Once kokanee leave the lake to spawn in tributary 

streams, the fishery is closed to protect Sockeye Salmon. Creel surveys are conducted to estimate the 

number of juvenile Sockeye Salmon encountered incidental to the kokanee fishery. Sport-caught 

kokanee are sampled (by removing a small piece of fin) for DNA analysis to estimate the proportion of 

Sockeye Salmon taken in the fishery. Analysis to date shows that the fishery removes significant 

numbers of kokanee without depleting the Sockeye Salmon ESU. In addition, residual Sockeye Salmon 
ESA Recovery Plan: Snake River Sockeye Salmon | 182

June 2015| NOAA Fisheries 

that live in Pettit Lake are subject to sport harvest, as are the native kokanee in Alturas and Stanley 

Lakes.

5.4.2 Salmon River and Snake River Fisheries 

There are no fisheries targeting Sockeye Salmon. There are fisheries targeting hatchery spring/summer 

Chinook salmon and steelhead and these fisheries are managed to protect Sockeye Salmon. ESA 

biological opinions require appropriate monitoring and evaluation of the fisheries; when Sockeye 

Salmon are encountered or show up in the catch the IDFG fisheries are closed (NMFS 2011c) and the 

Shoshone-Bannock Tribes operate with a one percent ESA limit, although Sockeye Salmon have yet to 

be encountered in that fishery (NMFS 2013).

State fishery management agencies and tribes submit to NMFS a Fishery Implementation Plan (FIP) 

each year as part of ESA compliance. FIPs are used pre-season by NMFS to determine if year-specific 

fishery plans are consistent with Fishery Management and Evaluation Plans (FMEPs) and Tribal 

Resource Management Plans (TRMPs) that have ESA authorization, and to confirm ESA compliance in 

the long term for the duration of the respective biological opinion. FIPs describe year-specific preseason details for fisheries in the Snake River that affect ESA-listed species, such as harvest numbers 

and ESA take that is expected on a given year, and that may have occurred in prior years under a given 

biological opinion. 

Annual Snake River spring/summer Chinook fisheries are a good example of how fisheries are 

managed under the ESA. States and tribes submit FIPs to NMFS each year describing year-specific 

projected fishing season goals based on pre-season run size estimates. Post season, States and tribes 

report to NMFS fishery-related ESA take based on creel surveys, and this includes any projected 

incidental take of Sockeye Salmon. Snake River spring/summer Chinook fisheries are carefully 

managed to avoid any potential take of Sockeye Salmon and no incidental take has been reported thus 

far.

5.4.3 Mainstem Columbia River Fisheries

Within the mainstem Columbia River, treaty tribal net fisheries and non-tribal fisheries directed at 

Chinook salmon do incidentally take a small percentage of Sockeye Salmon. Mainstem Columbia River 

fisheries are managed under an abundance-based harvest rate schedule that limits the resulting ESA take 

(Table 5-3). Because of stock composition in the mainstem Columbia River, most of the Sockeye 

Salmon harvested are from the upper Columbia River (Canada and Lake Wenatchee), but an equal 

proportion of Snake River Sockeye Salmon are taken incidentally to mainstem fisheries directed at 

Chinook salmon. Fishery impact rates in the 1980s increased briefly due to directed Sockeye Salmon

fisheries on large runs of upper Columbia River stocks (Table 5-2). 
ESA Recovery Plan: Snake River Sockeye Salmon | 183

June 2015| NOAA Fisheries 

Table 5-2. Historical Sockeye Salmon harvest (WDFW 20127).

Snake River Sockeye Salmon

Columbia Non- Bonn. At Non- Lower

River Treaty Dam Treaty Col R. Treaty Treaty Granite Escapement

Year Mouth1 Catch2 Count Catch3 Mouth Catch2 Catch3 Esc.4 Wenatchee5 Okanogan6

1980 58,886 4 58,882 636 108 0 1 96 22,752 26,573

1981 56,037 0 56,037 1,507 236 0 6 218 16,490 28,234

1982 50,319 100 50,219 775 261 1 4 211 23,732 19,005

1983 100,628 83 100,545 3,349 241 0 8 216 60,345 27,925

1984 161,886 9,345 152,541 24,616 148 9 23 105 35,795 81,054

1985 200,724 32,213 166,340 49,969 59 10 15 35 49,137 52,989

1986 59,963 1,840 58,123 6,672 28 1 3 20 16,077 34,788

1987 145,546 28,553 116,993 39,560 55 11 15 29 29,558 40,120

1988 99,757 17,632 79,714 30,990 45 8 14 23 15,069 33,978

1989 47,475 36 41,884 2,138 4 0 0 4 21,184 15,976

1990 49,754 173 49,581 2,716 1 0 0 1 34,847 7,609

1991 76,484 3 76,481 3,271 10 0 0 9 35,094 27,490

1992 85,000 8 84,992 2,185 2 0 0 2 26,555 41,951

1993 91,710 64 80,178 5,020 18 0 1 17 37,311 27,849

1994 12,858 1 12,678 472 3 0 0 3 9,314 1,666

1995 9,662 1 8,773 445 5 0 0 5 4,474 4,892

1996 30,896 25 30,255 1,414 3 0 0 3 7,559 17,701

1997 47,470 12 46,927 2,046 18 0 1 17 11,064 25,754

1998 13,220 2 13,218 425 4 0 0 3 3,379 4,669

1999 17,878 1 17,877 704 20 0 1 18 4,260 12,388

2000 93,755 364 93,391 2,910 352 1 11 337 19,084 59,944

2001 120,314 1,688 114,933 7,300 49 1 3 45 38,618 74,490

2002 50,461 14 49,610 2,564 77 0 4 73 31,946 10,659

2003 39,375 0 39,375 1,090 28 0 1 26 4,424 28,820

2004 129,932 672 123,320 4,317 117 1 4 113 25,328 77,492

2005 77,329 0 72,448 2,766 20 0 1 19 15,656 53,218

2006 37,067 1 37,066 1,596 79 0 3 16 9,756 22,064

2007 26,059 0 24,376 1,414 58 0 3 55 4,439 22,282

2008 214,402 821 213,607 9,017 983 4 41 907 32,396 165,334

2009 178,959 1,160 177,823 9,731 1,625 11 88 1,406 29,724 134,937

2010 387,858 242 386,355 26,125 2,596 2 175 2,406 42,672 291,764

2011 187,307 1,708 185,796 12,849 1,919 18 132 1,502 14,015 111,508

1. Upriver run is larger of (Bonn. Count + Zones 1-5 harvest) or (Priest Rapids count + Snake River count + Zones 1-6 

harvest). 

2. Non-Treaty harvest may include kept fish and incidental release mortalities in Zones 1-6.

3. Treaty harvest includes Sockeye Salmon kept in Zones 1-6, which includes harvest downstream of Bonneville Dam.
ESA Recovery Plan: Snake River Sockeye Salmon | 184

June 2015| NOAA Fisheries 

4. Prior to 1992, Lower Granite Dam Sockeye Salmon counts may include kokanee. Since 1992 video counts or length 

measurements are used to identify true Sockeye Salmon. 

5. Beginning in 1979, the Wenatchee estimate is based on Rock Island or Priest Rapids Dam counts minus Rocky Reach Dam 

totals, except Priest Rapids count minus Wells count in 1995.

6. The Okanogan estimate is based on the Rocky Reach Dam counts until 1966. Wells Dam counts are used beginning with 

1967.

7. Source: http://wdfw.wa.gov/publications/01354/wdfw01354.pdf.

Fisheries in the mainstem Columbia River that affect Snake River Sockeye Salmon are currently 

managed subject to the terms of the U.S. v. Oregon Management Agreement for 2008-2017. These 

fisheries are managed to ensure that the incidental take of ESA-listed Snake River Sockeye Salmon does 

not jeopardize the Sockeye Salmon ESU. Management provisions for Sockeye Salmon in the 2008 U.S. 

v. Oregon Management Agreement are the same as those in the 2005-2007 agreement. Non-Indian 

fisheries in the lower Columbia River are limited to an incidental take rate of 1% of the Snake River 

Sockeye Salmon adults reaching the Columbia River mouth, and Treaty Indian fisheries are limited to an 

incidental take rate of 5 to 7%, depending on the run size of upriver Sockeye Salmon stocks (Table 5-3). 

Actual incidental take rates ranged from zero to 1.41% (non-Indian), and 2.8 to 6.9% (Treaty Indian 

fisheries) in the 10-year period 1998-2007.

Table 5-3. Sockeye Salmon harvest rate schedule (Harvest Module, NMFS 2014b).

River Mouth Sockeye Salmon Run 

Size

Treaty Harvest 

Rate

Non-Treaty Harvest 

Rate

Total Harvest Rate

< 50,000 5% 1% 6%

50,000 -75,000 7% 1% 8%

> 75,000 7% * 1% 8% *

*If the upriver Sockeye Salmon run size is projected to exceed 75,000 adults over Bonneville Dam, any party may propose harvest 

rates exceeding those specified in Part II.C.2. or Part II.C.3. of the 2008-2017 Management Agreement. The parties shall then 

prepare a revised biological assessment of proposed Columbia River fishery impacts on ESA-listed Sockeye Salmon and shall submit 

it to NMFS for consultation under Section 7 of the ESA.

5.4.5 Ocean Fisheries

Ocean fisheries do not significantly affect Snake River Sockeye Salmon. Research indicates that the 

migration path and ocean distribution of Snake River Sockeye Salmon is such that the fish are not 

present in near shore areas where ocean salmon fisheries traditionally occur (NMFS 2014b). Also, 

Sockeye Salmon are not attracted to baits or lures; they are plankton feeders, and thus they are rarely 

caught in commercial or recreational fisheries. There are no net fisheries in the ocean that target 

salmonids.
ESA Recovery Plan: Snake River Sockeye Salmon | 185

June 2015| NOAA Fisheries 

5.4.6 Summary of Fishery-related Threats and Limiting Factors 

Threat: Ongoing Columbia River harvest.

Related limiting factors: Reduced abundance/productivity due to incidental take.

5.5 Predation and Disease

This section summarizes predation on Snake River Sockeye Salmon from the natal lakes in the Sawtooth 

Valley, through the Salmon River, lower Snake River, Columbia River mainstem and estuary, and 

ocean. 

5.5.1 Sawtooth Valley Lakes

Several fish species that occupy the Sawtooth Valey lakes potentially prey on Sockeye Salmon, 

including bull trout, northern pikeminnow, and brook trout. Research shows that Sockeye Salmon and 

kokanee are part of the diet of bull trout and northern pikeminnow.

Bull trout are believed to be the top native piscivorous predator of the Sawtooth Valley lakes fish 

community. Based on limited information, a 1984 study estimated that native bull trout (Salvelinus 

confluentus) and introduced rainbow trout (Oncorhynchus mykiss) consumed up to 60% of Sockeye 

Salmon eggs, fry, and pre-smolts in Alturas Lake (Bowles and Cochnauer 1984). The estimated 

predation rate was based on the multi-species impact and apparent high predation abundance and used to 

model Sockeye Salmon production potential in Alturas Lake. Monitoring associated with Sockeye 

Salmon habitat and limnological research has found that the bull trout diet is composed primarily of fish 

prey (Taki et al. 1999), with juvenile Sockeye Salmon and kokanee found in the stomach contents of 

bull trout from Pettit Lake in February 2004 (Taki et al. 2006). Bull trout, however, were ESA-listed as 

a threatened species in 1998. Any predation by the species on Sockeye Salmon is considered a natural 

process and no control measures will be implemented. 

Concern has been expressed about the potential predation of northern pikeminnow on juvenile Sockeye 

Salmon. Northern pikeminnow are known to prey on juvenile salmon and are the subject of control 

efforts in the mainstem Columbia and Snake Rivers. Northern pikeminnow are also one of the most 

abundant species found in the Sawtooth Valley lakes. Despite their abundance, diet analysis has only 

positively identified Sockeye Salmon/kokanee in the stomach of one northern pikeminnow (Taki et al. 

2006). A 1998 study found no salmonids, including kokanee/Sockeye Salmon, in the stomachs of any 

of the northern pikeminnow or brook trout sampled in four of the lakes (Lewis et al. 1998). Since the 

juvenile Sockeye Salmon tend to stay in the deeper areas and northern pikeminnow are found in the 

littoral areas, the northern pikeminnow may have limited opportunities for predation on Sockeye Salmon

in these lakes (Taki et al. 2006). 
ESA Recovery Plan: Snake River Sockeye Salmon | 186

June 2015| NOAA Fisheries 

Other species that prey on Sockeye Salmon include mink, otter, and several bird species including 

grebes, mergansers, and osprey (Peterson 2013c). Research is needed to document the extent and 

impact of predation. 

Introduced invasive species can also negatively impact juvenile Sockeye Salmon survival. The parasite 

(Myxobolus cerebralis) which causes whirling disease has been detected in the headwaters of Alturas 

Lake Creek and is being monitored by the U.S. Forest Service. This parasite affects juvenile salmonids 

and causes skeletal deformation and neurological damage. Fish “whirl” forward in an awkward pattern 

instead of swimming normally, find feeding difficult, and are more vulnerable to predators. 

5.5.2 Salmon River

Snake River Sockeye Salmon juveniles migrate relatively quickly from the upper Salmon basin to the 

Snake River. Little is currently known regarding predation in this reach, but potential predators include 

smallmouth bass (Micropterus dolomieui), bull trout, northern pikeminnow (Ptychocheilus oregonensis), 

juvenile steelhead, and rainbow trout.

Recent tagging studies and associated observational data conducted through a collaborative effort 

between NMFS and IDFG indicate that predation may be responsible for some of the juvenile mortality 

that occurs during outmigration. Researchers have observed multiple predation events on recently 

released PIT-tagged juvenile Sockeye Salmon during the studies. In 2013, common merganser, osprey, 

double-crested cormorant, and western grebe were actively feeding in Little Redfish Lake, located 

below the release site, as fish were moving through the area. Bull trout were also preying on juvenile 

Sockeye Salmon as they migrated through Little Redfish Lake (Axel et al. 2014). Predation also likely 

contributes to losses of juvenile Sockeye Salmon migrants in the upper Salmon River reach known as 

Deadwater Slough. This reach is one of east-central Idaho’s best birding locations due to quality riparian 

habitat, good water quality, and adjacent diverse upland habitats for raptors and other species. Flow in 

the reach is visibly slower and juvenile Sockeye Salmon travel at a considerably reduced rate in the 

reach, increasing their risk to predation (Axel et al. 2014). 

 

5.5.3 Lower Snake River 

Smallmouth bass are the most abundant predator on salmonids in the lower Snake River reservoirs. The 

reservoir habitat formed by the dams creates slow backwater areas and warmer water temperatures 

benefiting non-native species such as smallmouth bass and channel catfish (Ictaluras punctatus).

Additional research, monitoring, and evaluation is needed to quantify the impacts of this predation on 

Snake River Sockeye Salmon recovery efforts.

5.5.4 Lower Columbia River and Estuary

Anthropogenic changes in the Columbia River have altered the relationships between salmonids and 

other fish, bird, and pinniped species. Some of the predator species’ abundance levels have increased 
ESA Recovery Plan: Snake River Sockeye Salmon | 187

June 2015| NOAA Fisheries 

dramatically, particularly in localized areas, with associated changes in predation of juvenile and adult 

Sockeye Salmon as well as other species of salmon and steelhead (LCREP 2006). 

5.5.4.1 Avian predation

Ecosystem alterations attributable to hydropower dams and modification of estuarine habitat have 

increased predation on Snake River salmon and steelhead populations. In the estuary, the number and/or 

effectiveness of Caspian terns, double-crested cormorants, and a variety of gull species has increased 

because of habitat modification (LCREP 2006; Fresh et al. 2005). Caspian tern predation has decreased 

in recent years because of management efforts reducing available island habitat, but double-crested 

cormorant predation has increased (Collis and Roby 2011). The draft 2010 season summary of Research, 

Monitoring, and Evaluation of Avian Predation on Salmonid Smolts in the Lower and Mid-Columbia 

River (Collis and Roby 2011) estimates that double-crested cormorants nesting on East Sand Island near 

the mouth of the Columbia River consumed 19.2 million juvenile salmonids in 2010. 

Yearling type juvenile salmonids like Sockeye Salmon are vulnerable to avian predation in the estuary 

because they use deep-water habitat channels that have relatively low turbidity and are close to island 

habitats. Recent information on cormorant consumption of Sockeye Salmon smolts in the estuary 

indicates that Snake River Sockeye Salmon smolts were taken by cormorants at an annual rate of 1.3% 

during 1998 to 2012 (NMFS 2014c).

Tern, cormorant, and gull colonies on islands in the Columbia River and the lower Snake River also 

prey on juvenile salmonids, but predation in the estuary is an order of magnitude greater (NMFS 2014c). 

In the Columbia Plateau region, 2012 PIT-tag-derived predation rates by double-crested cormorants 

nesting on Foundation Island indicated that predation rates were highest on Snake River Sockeye 

Salmon (2.5%) (Roby et al. 2012). Data on PIT-tag deposition rates for American white pelicans nesting 

at the colony on Badger Island are not currently available. Minimum predation rate estimates (not 

corrected for PIT-tag deposition rates) indicate that American white pelicans consumed less than 0.3% 

of the available smolts in 2012, regardless of species (Roby et al. 2012). 
ESA Recovery Plan: Snake River Sockeye Salmon | 188

June 2015| NOAA Fisheries 

Figure 5-3. Shows locations of breeding colonies of piscivorous birds in estuary and Columbia River basin (Collis and Roby

2011).

5.5.4.2 Piscivorous fish predation

There is no specific information on predation rates on Sockeye Salmon in the Columbia Basin but 

habitat modifications by the hydropower system have generally provided conditions that support both

native and introduced piscivorous fish along the migratory route. Northern pikeminnows and non-native 

predatory species (e.g., smallmouth bass, walleye, channel catfish, etc.) congregate near dams or at 

hatchery release sites to feed on migrating smolts. Many of these species are also abundant in freeflowing river reaches and feed on rearing juveniles in these areas. Warmer water temperatures can 

enhance conditions for fish that prey on or compete with juvenile salmonids. Northern pikeminnow, 

walleye, smallmouth bass, and channel catfish were estimated to consume between 9 and 19% of the 

juvenile salmonids entering John Day Reservoir, with northern pikeminnow accounting for 78% of the 

loss (NMFS 2004). Bonneville Power Administration has implemented the Northern Pikeminnow 

Management Program since 1990. The program’s goal of removing 10-20% of predatory-sized 

pikeminnow has been achieved in 18 of 22 years with an estimated 4.05 million fish removed from the 

lower Snake and Columbia Rivers by sport fishermen who receive monetary awards. BPA estimates that 

the program has reduced predation on juvenile salmonids by 37% (BPA 2013).

Within the Columbia River basin, juvenile Pacific salmon could encounter no fewer than eight 

documented non-native predator and competitor fish species en route to the estuary (Sanderson et al. 

2009). Salmonids can compose up to 100% of the diets of various non-native predators, such as channel 

catfish, smallmouth bass, and walleye. 
ESA Recovery Plan: Snake River Sockeye Salmon | 189

June 2015| NOAA Fisheries 

Predation by nonnative fishes on outmigrating smolts is roughly equivalent to the productivity declines 

attributed to habitat loss and degradation (Beechie et al. 1994). Although it is difficult to make direct 

comparisons between adult and juvenile mortality with respect to population impacts, predation rates on 

juvenile outmigrants are also similar in magnitude to harvest-related mortality rates on adults, 3% to 

84% (McClure et al. 2003).

Beamesderfer and Nigro (1989) estimated that walleye annually consumed an average of 400,000 

salmonids (250,000 to 2,000,000), or up to 2% of the salmonid run from 1983-1986. Abundance of 

walleye in the lower Columbia River appears highly variable, but losses of juveniles and smolts to 

walleye was estimated at up to 2 million fish per year, which compares to 4 million for pikeminnow 

(Tinus and Beamesderfer 1994).

Sculpins, suckers, and cyprinids (including northern pikeminnow) made up the majority of smallmouth 

bass diets in the John Day Reservoir; however, bass still ate a large number of salmonids, primarily 

young-of-the-year Chinook salmon that co-inhabit littoral areas in July and August (Poe et al. 1991). 

Downstream of Bonneville Dam, bass diets consisted of sculpins (46%), cyprinids (19%), suckers 

(16%), and salmonids (12%).

In the Snake River, Shively et al. (1991) and Nelle (1999) found lower consumptive rates of juvenile 

salmonids in the areas they studied compared to the Columbia River studies mentioned above. 

However, even though consumption rates are relatively low, the large number of individual predators 

can result in substantial losses of migrating juveniles.

5.5.4.3 Marine mammals

Predation by marine mammals is also a concern. Marine mammals (pinnipeds) prey on winter and spring 

migrating adult salmon and steelhead in the lower Columbia River including the tailrace of Bonneville 

Dam. There is no additional information available regarding pinniped predation rates on Sockeye 

Salmon.

5.5.5 Ocean

Although there is still much to be learned about the marine ecology of Sockeye Salmon, several major 

marine predators have been identified. Juvenile Sockeye Salmon are preyed on by sablefish 

(Anoplopoma fimbra) and murres (Uria spp.) (Sturtevant et al 2009; Ogi and Tsujita 1973). Juvenile 

Oncorhynchus spp. are fed upon by both murres (Uria aalge) and rhinocerrous auklets (Cerorhinca 

monocerata) (Lance and Thompson 2005). Older Sockeye Salmon are preyed on by mesopelagic 

daggertooth (Anotopterus pharao) that move into the epipelagic zone to forage on larger Sockeye 

Salmon (Welch et al 1991; Savinykh and Glebov 2003; Svirindov et al. 2004). Salmon sharks (Lamna 

ditropis) prey on larger Sockeye Salmon during their marine residence (Nagasawa 1998). Sockeye 

Salmon are also fed upon by lamprey during their oceanic migration (Lampetra tridentate) (Pelenev et 

al. 2008). Although these marine predators may limit Snake River Sockeye Salmon survival they are 
ESA Recovery Plan: Snake River Sockeye Salmon | 190

June 2015| NOAA Fisheries 

primarily natural forms of predation whose population size have not been increased by anthropogenic 

activities.

As maturing Sockeye Salmon near their natal rivers they become subject to harbor seal (Phoca vitulina) 

predation (Hauser et al. 2008; Forrest et al. 2009). In general, salmonids of the genus Onchoryhnchus

are important prey items in the diet of Stellar sea lions (McKenzie and Wynne 2008). Resident killer 

whales (Orca orcinus) specialize in feeding on chinook and chum salmon; and thus far Sockeye Salmon

have not been a significant component of their diet (Ford et al. 2006). 

5.5.6 Summary of Predation and Disease Threats and Limiting Factors 

Threat: Non-native and native fishes in Sawtooth Valley lakes and the mainstem Salmon, Snake, and 

Columbia Rivers.

Related limiting factors: Predation by non-native and native fishes could reduce Sockeye Salmon

productivity.

Threat: Predation by birds in the Sawtooth Valley lakes; mainstem Salmon, Snake, and Columbia 

Rivers; and estuary.

Related limiting factors: Predation could reduce Sockeye Salmon abundance.

Threat: Predation by marine mammals in the Columbia River and estuary and ocean

Related limiting factors: Predation could reduce Sockeye Salmon productivity 

Threat: Introduction of invasive parasite that causes whirling disease in salmonids in natal lakes and 

other water bodies

Related limiting factors: Infestation by parasite can reduce Sockeye Salmon productivity

5.6 Competition

Competition can refer to competition among salmonids or other species for food resources, or 

competition between hatchery fish and wild fish for food or spawning areas. 

5.6.1 Natal Lakes

In sockeye salmon systems, intraspecific competition is much stronger than interspecific competition 

(Burgner 1987). In Takala Lake in British Columbia, Canada, a comparison of the diet and distribution 

of kokanee (resident form) and anadromous sockeye salmon detected no significant niche differences 

between the two forms (Wood et al. 1999) suggesting high intraspecific competition. Both density and 

fertilization experiments have demonstrated that sockeye salmon compete intraspecifically for available 

food resources (Hartman and Burgner 1972; Reiman and Myers 1992; Rich et al. 2009; Hyatt and 

Stockner 1985). 
ESA Recovery Plan: Snake River Sockeye Salmon | 191

June 2015| NOAA Fisheries 

This intraspecific competition also appears to be the case in the Sawtooth Valley lakes, where like 

Sockeye Salmon, kokanee tend to stay in the deeper areas and feed almost entirely on zooplankton prey 

species. There is no indication the two life history forms in Redfish Lake compete for spawning habitat,

as the listed anadromous fish are lake spawners and the sympatric kokanee are stream spawners that 

spawn earlier than the anadromous fish. It is the aforementioned competition among juveniles for food 

and space that leads to the conclusion that kokanee in the Sawtooth Valley lakes may limit the growth 

and survival of Snake River Sockeye Salmon during the lake rearing phase of their life cycle. 

Historical actions for the management of game fish in the Sawtooth Valley lakes reduced the available 

habitat for Sockeye Salmon for a period of some 60 years and introduced competition for food 

resources. Kokanee salmon were stocked by the IDFG in Redfish Lake as early as the 1920s (Bowler 

1990). Since then, measures to control kokanee have been implemented in Redfish Lake to reduce 

intraspecific competition. Various fishery and limnological parameters have been monitored in 

association with these strategies (Taki et al. 2006). IDFG maintains sport fishing seasons on kokanee 

for the purpose of having anglers harvest them to decrease competition with Sockeye Salmon.

Potential competition for food occurs between anadromous Sockeye Salmon and planted rainbow trout 

and kokanee although recent studies by Taki et al. (2006) found no overlap in diet between rainbow 

trout and Sockeye Salmon in Pettit Lake. Age-zero Sockeye Salmon, the life stage of primary interest, 

fed almost exclusively on zooplankton while rainbow trout diets consisted of aquatic insects (Taki et al. 

2006).

5.6.2 Salmon River

Non-native species, including smallmouth bass, hatchery steelhead, and rainbow trout both prey upon 

Sockeye Salmon and reduce Sockeye Salmon productivity by competing with outmigrating juveniles for 

limited food and space in the mainstem Salmon River. Competition for limited food sources also likely 

occurs between outmigrating juvenile Sockeye Salmon and steelhead and Chinook salmon from 

hatchery releases. Limited information currently exists on competition in the Salmon River. Additional 

research, monitoring, and evaluation are needed to better determine the extent of this threat to Snake 

River Sockeye Salmon viability.

5.6.3 Mainstem Migration Corridor, Estuary, Plume and Ocean

The migratory corridor and marine environment present additional opportunities for intraspecific and 

interspecific competition to limit the ESU. In the lower Snake and Columbia River migratory corridor, 

Snake River Sockeye Salmon potentially encounter both reservoir-rearing kokanee and anadromous 

sockeye salmon smolts from the upper Columbia migrating to the sea. 

Upon entering the ocean and migrating north, they will be placed in competition with hatchery and 

natural sockeye salmon stocks originating along the entire North Pacific rim. Although salmon use only 

a small percentage of the North Pacific's food resource, they are major factors in the epipelagic zone 
ESA Recovery Plan: Snake River Sockeye Salmon | 192

June 2015| NOAA Fisheries 

resources they do use. In a survey of the epipelagic nekton in the western North Pacific Ocean, the 

most abundant species (68% by number) were the six species of Pacific salmon (Ishida et al. 1999). 

Pacific salmon have also been observed to be a dominant daytime biomass in offshore surface waters 

(Beamish et al. 2005). Given this abundance and limited forage base, it is not surprising that both 

intraspecific and interspecific competition have been observed in the marine environment. Using 

growth and abundance data, Pyper and Peterman (1999) demonstrated intraspecific competition for food 

resources in sockeye salmon in the North Pacific Ocean. The observation of Bugaev et al. (2001) that 

the size of sockeye salmon returning to the Ozernaya River is reduced in years when sockeye salmon

abundance in the marine environment is high also supports the concept of intraspecific marine 

competition. These observations indicate that in years when food resources in the North Pacific 

ecosystem are scarce the release of hatchery fish from lower Columbia River species into the ecosystem 

may have the potential to limit Snake River Sockeye Salmon marine growth and survival. 

Sockeye Salmon are believed to face their greatest interspecific marine competition from pink and chum 

salmon. Research indicates diet overlap between these three species can be high for small and medium 

size fish and moderate for large salmon (Zavolokin et al. 2007). Depending on season and location, the 

dietary overlap between Sockeye Salmon and chum salmon rearing in the Bering Sea ranges from low to 

high (Davis et al. 2003). As expected, studies indicate the Sockeye Salmon, pink, and chum dietary and 

habitat use is diverging in a manner that reduces interspecific competition (LeBrasseur 1966; Kanno and 

Hamai 1971; Azuma 1995). Research indicates that Sockeye Salmon marine growth and survival is 

reduced in years of high pink salmon abundance (Bugaev et al. 2001; Ruggerone and Nielsen 2004;

Ruggerone et al. 2005). This suggests that hatchery releases of pink and chum salmon into the North 

Pacific may have the potential to limit Snake River Sockeye Salmon growth and survival.

5.6.4 Summary of Competition Threats and Limiting Factors 

Threat: Competition with planted rainbow trout and kokanee in the Sawtooth Valley lakes.

Related limiting factors: Competition for limited food could reduce Sockeye Salmon productivity.

Threat: Potential competition with non-native fishes and hatchery salmonids in the Salmon, Snake, and 

Columbia Rivers and ocean.

Related limiting factors: Competition for limited food supplies could reduce Sockeye Salmon

productivity.

5.7 Toxics

Although Snake River Sockeye Salmon spawn and rear in an undeveloped area with very little industry 

or cropland, they have the longest migration of any Sockeye Salmon, traveling 1,448 km (900 miles)

inland. Much of the migratory path includes waters listed as impaired on the 303(d) lists for Oregon and 

Washington; Figure 5-4 shows 303(d) listed streams and NPDES permit sites in the region. These waters 

are contaminated by drift and runoff from both agricultural and urban areas. Exposure to toxic 
ESA Recovery Plan: Snake River Sockeye Salmon | 193

June 2015| NOAA Fisheries 

chemicals during adult and juvenile migration may contribute to low survival and impede recovery of 

this stock.

Figure 5-4. NPDES permit sites and 303(d) listed streams in Snake River Sockeye Salmon migratory corridor. (Source: 

NMFS 2009).

5.7.1 Sawtooth Valley Lakes

Most of the historical spawning and rearing area for Sockeye Salmon in Redfish, Pettit, Alturas Stanley, 

and Yellowbelly Lakes, lies within an undeveloped wilderness area. For example, only about 1% of the 

land surrounding Redfish Lake has been developed, and another 1% is used for agriculture, primarily 

hay and pasture (NMFS 2010a). No areas within the spawning habitat of the ESU are designated for 

water quality violations due to the presence of toxic contaminants. However, Stanley Lake, Pettit Lake, 

and Yellowbelly Lake, as well portions of Alturas Creek, Redfish Lake Creek, Pettit Lake Stream, and 

Stanley Creek are listed on IDEQ’s 303 (d) list as Category 3 water bodies for which there are 

insufficient data on water quality, including toxics, to determine if beneficial uses are being met (IDEQ 

2014). 

Some monitoring for toxic metals has been conducted in resident fish from the Sawtooth Valley lakes. 

The Idaho Department of Environmental Quality sampled kokanee, rainbow trout, and bull trout in 

Alturas and Yellowbelly Lakes for mercury, selenium, and arsenic (Essig and Kosterman 2008). Results 
ESA Recovery Plan: Snake River Sockeye Salmon | 194

June 2015| NOAA Fisheries 

showed that selenium concentrations ranged from 0.23 to 0.34 mg/kg wet weight at Yellowbelly Lake 

and from 0.30 to 0.37 mg/kg wet wt in fish from Alturas Lake. All these samples were well below 

Idaho’s proposed draft fish tissue criterion of 7.91 mg/kg dry wt or 1.58 mg/kg wet wt for protection of 

aquatic life for selenium, as well as the 1.0 ug/g wet wt threshold proposed by Lemly (1996, 2002) for 

protection of larval fish. Arsenic concentrations were below detection limits in all samples from 

Yellowbelly Lake, but in fish from Alturas Lake, total arsenic ranged from 0.12 to 0.35 mg/kg wet, the 

highest arsenic concentration observed in any samples from the study. Biochemical effects such as 

changes in enzyme activity have been reported in carp with tissue arsenic concentrations in this range 

(Ventura-Lima et al. 2009), and increased mortality and reduced growth have been observed in rainbow 

trout at tissue concentrations in the 0.38-0.4 range (Dixon and Sprague 1981; Erickson et al. 2011), 

suggesting this might be a cause for concern if Snake River Sockeye Salmon were reintroduced to this 

lake. Mercury levels ranged from 103 to 162 ug/kg in fish sampled at Yellowbelly Lake and from 76 to 

163 ug/kg in fish sampled from Alturas Lake. These levels are all below Idaho’s human health criterion 

for mercury of 300 ug/kg wet wt, as well as the estimated effects threshold for fish of 200 ug/kg wet wt 

proposed by Beckvar et al. (2005). Overall, these results suggest that Snake River Sockeye Salmon

would not be at risk for toxic injury due to these metals, although there is some uncertainty about 

whether these criteria would be protective for both lethal and sublethal effects to all life stages of salmon 

that may be present.

The recent NMFS Biological Opinion on the Idaho water quality criteria for toxic pollutants (NMFS 

2014d) found that approval of the proposed chronic water quality criterion for mercury would likely 

cause adverse modification to critical habitat or lethal and sublethal effects to Snake River Sockeye 

Salmon, and supports Idaho’s human health fish tissue criterion as a reasonable means of protecting 

Snake River Sockeye Salmon until a more protective water quality criterion can be established. This 

Biological Opinion also found that approval of the chronic water quality criteria for arsenic, copper, 

cyanide, and selenium, as well as calculation of metals toxicity levels using the 25 mg/l proposed

hardness floor, would result in jeopardy for the Snake River Sockeye Salmon ESU. According to the 

Opinion, the chronic mercury, arsenic, and selenium criteria would not protect salmon against adverse 

effects on growth, reproduction, and survival mediated through food chain contamination and uptake of 

these metals in the diet. The acute and chronic copper criteria could have adverse behavioral effects 

from loss of sense of smell. The cyanide acute criterion could lead to lethality under cold winter 

temperatures, while the cyanide chronic criterion is close to threshold for adverse effects on swimming 

ability and reproduction. 

The NMFS Biological Opinion on the Oregon water quality criteria for toxic pollutants (NMFS 2012a) 

similarly found that the proposed criteria for arsenic, copper, and selenium would not be protective of 

Snake River Sockeye Salmon. This Biological Opinion additionally found that adoption of the proposed 

criteria for aluminum, ammonia, lindane, cadmium, dieldrin, endosulfan-alpha, endosulfan-beta, endrin, 

nickel, pentachlorophenol, silver, tributyltin, and zinc could jeopardize the recovery of Snake River 

Sockeye Salmon, based on the potential of these contaminants to contribute to mortality at the 

population level. It should be noted that the NMFS decisions on these criteria do not necessarily 

indicate that waters in the Sawtooth Valley lakes or other critical habitat are currently impaired by these 
ESA Recovery Plan: Snake River Sockeye Salmon | 195

June 2015| NOAA Fisheries 

compounds, but that the proposed criteria would not prevent such impairment from occurring. Adoption 

of the reasonable and prudent alternatives proposed in these two Biological Opinions on Oregon and 

Idaho water quality should provide additional protection for Snake River Sockeye Salmon against the 

potential adverse effects of these toxic compounds.

Several other potential threats associated with toxic contaminants are present within the area. First, the 

Redfish Lake area has become a popular recreational destination (Selbie et al. 2007). It is unlikely that 

nearshore camping and a hotel facility contribute to pollution via wastewater contaminants because 

sewage, the main source, is removed from the area by contained sanitation systems (Gross et al. 1998). 

Fuel spills from recreational boats present in the lake are another potential hazard, which could have 

especially serious effects on early life stages of Snake River Sockeye Salmon. Larval exposure to 

certain polycyclic aromatic hydrocarbons (PAHs) can cause cardiac developmental toxicity that may 

result in death or, at lower exposure concentrations, lead to heart defects that can reduce swimming 

speed and fitness and contribute to increased mortality later in life (Incardona et al. 2009; Hicken et al. 

2011). Fuel spills associated with motorized boating could also be a concern for Snake River Sockeye 

Salmon re-introduced to Stanley and Pettit Lakes; motorized boating is prohibited at Yellowbelly Lake. 

In Yellowbelly, Pettit, and Stanley Lakes, there is the possibility of toxaphene contamination. In the 

mid-1950s, based on very low levels of adult Sockeye Salmon returns to Stanley, Pettit, and Yellowbelly 

Lakes, the IDFG made the decision to develop these lakes for resident species sport fisheries (IDFG 

1959). Yellowbelly (1961), Pettit (1961), and Stanley (1954) Lakes were chemically treated with 

Toxaphene, but Alturas and Redfish Lakes were not. Stanley Idaho resident John Rember reports that 

the 1961 fish kill extended down the upper Salmon River as far as the town of Stanley (Rember 2003), 

which suggests that a cohort of smolts from all the lakes may have been depleted by the poisoning. 

Yellowbelly Lake was poisoned a second time in 1990 using rotenone, and again the fish kill extended 

down the outlet creek and then down the Salmon River approximately 4 miles (Curet et al. 2010). 

Yellowbelly Lake was poisoned again in the late 1990s (Kline 2013). It is possible that Toxaphene is 

still present in lake sediments and biota, but no monitoring data are available.

As more than 50% of the ESU’s critical habitat is composed of evergreen forests, forestry pesticide uses 

may affect spawning and rearing activities. Researchers have conducted some studies on herbicides that 

may be used in forested and riparian areas for weed control. Stehr et al. (2009) screen six herbicides 

(picloram, clopyralid, imazapic, glyphosate, imazapyr, and triclopyr) and several technical formulations 

(Tordon K, Transline, Habitat, Plateau, Garlon 3A, and Renovate) for developmental toxicity using 

zebrafish as a model system. No developmental toxicity was observed in response to the six individual 

herbicides or the different technical formulations. On this basis, the authors concluded that noxious 

weed control activities were not likely to pose a direct threat to the health of salmonids at early life 

stages.

The Sawtooth National Forest recently (SNF 2012) completed consultation on herbicide treatment using 

11 active ingredients (Aminopyralid, 2,4-D, Chlorsulfuron, Clopyralid, Triclopyr, Dicamba, Glyphosate, 

Imazapic, Metsulfuron methyl, Picloram, and Diflufenzopyr). NMFS concluded that the applications 
ESA Recovery Plan: Snake River Sockeye Salmon | 196

June 2015| NOAA Fisheries 

proposed by the U.S. Forest Service were likely to have only short-term, non-lethal effects on salmonids 

including Sockeye Salmon.

Use of fire retardants to fight forest fires might also pose a threat to this habitat. These products are 

normally applied by aircraft and are specifically intended for terrestrial application, but fire retardants 

have incidentally entered aquatic habitats and resulted in fish kills. The toxicity of these chemicals to 

salmon is currently under investigation in joint studies conducted by the U.S. Forest Service, USGS, and 

NMFS. Dietrich et al. (2010, 2013) examined the lethal and sub-lethal effects of two currently approved 

fire retardants, PHOS-CHEK 259F and LC-95A. These retardants contain diamonium phosphates and 

ammonium polyphosphates, and their toxic mode of action is similar in many aspects to ammonia. 

Concentrations of the products that caused 50% mortality (LC50 or ‘median lethal dose’) were 140.5 

and 339.8 mg/L for 259F and LC-95A, respectively, levels that could occur during accidental drops into 

aquatic habitats. Sub-lethal exposure to PHOS-CHEK significantly reduced salmon survival during a 

study which tested juvenile salmon’s ability to adapt to saltwater, suggesting that exposure to this fire 

retardant could interfere with smoltification. Exposed fish also displayed some unusual behavior, such 

as swirling and apparent disorientation, that could increase their susceptibility to predation. Because 

Redfish Lake is located in a watershed that is 92% Federal land, any forestry uses of the chemicals are 

being considered in consultations with the U.S. Forest Service.

5.7.2 Salmon River Migration Corridor

Water quality problems in the Salmon River basin are generally associated with factors such as 

temperature or siltation rather than toxic contaminants (IDEQ 2002, 2003, 2011), although there is also 

some risk of toxic exposure in the region, including metals contamination from mine wastes in the 

Middle Salmon-Panther subbasin (IDEQ 2001). Arsenic, cobalt, and copper are three metals of concern 

in this subbasin (IDEQ 2001). Historically, the Blackbird Mine in the Middle Salmon-Panther 

watershed released high concentrations of these and other metals into the environment, and several 

creeks near the mine have been listed under section 303(d) of the Clean Water Act for impairment due to 

copper and other metals. This reach of the Salmon River itself is not listed as impaired due to metals 

contamination, although some portions have been listed as impaired due to unknown contaminants 

(IDEQ 2011). The Blackbird Mine was listed as a superfund site in 1993 and cleanup and remedial 

actions are ongoing (see: http://yosemite.epa.gov/r10/cleanup.nsf/sites/blackbird), but because of 

historical releases there may still be some potential for Snake River Sockeye Salmon exposure to toxic 

metals in the Salmon River migration corridor. Copper is especially problematic, as even short-term 

exposure to at relatively low concentrations of copper in the water column can affect salmon olfaction 

and related behaviors (Sandahl et al. 2007; Hecht et al. 2007). By interfering with critical activities such

as prey capture, predator avoidance, and homing, copper exposure could reduce adult spawning success 

and juvenile growth and survival (Hecht et al. 2007; Baldwin et al. 2011). 

Mercury is a concern in the Salmon River, as mercury at concentrations sufficient to impair fish health 

and be a risk to humans and wildlife have been reported in bass and northern pike minnow from some 

sites in the area (Hinck et al. 2006; Essig 2010). However, concentrations of mercury in the toxic range 
ESA Recovery Plan: Snake River Sockeye Salmon | 197

June 2015| NOAA Fisheries 

appear to be restricted to longer-lived, piscivorous fish. Reported concentrations in salmonid species 

including trout and mountain white fish are relatively low (Essig 2010), suggesting that the risk to Snake 

River Sockeye Salmon is limited.

Exposure to current-use pesticides, including organophoshates, carbamates, herbicides, and fungicides is 

another also a possible risk in the Salmon River (NMFS 2008d, 2009, 2010a, 2011d). NMFS (2008d, 

2009) stated that areas where exposure to these pesticides was most likely included dryland agricultural 

areas within the lower Salmon River basin. While most of the pesticides reviewed in NMFS’ Biological 

Opinions were considered to be of low risk to Snake River Sockeye Salmon populations, NMFS found 

that exposure to the compounds chlorpyriphos, diazanon, malathion, naled, and 2,4-D was likely to

jeopardize the continued existence of the ESU and recommended a reasonable and prudent alternative

(NMFS 2008d, 2010a, 2011d). As a high proportion of the Salmon River migration corridor is 

comprised of forested lands, concerns about forestry pesticides and fire retardants would apply to this 

area as well as the Sawtooth lakes region. 

Legacy pesticides may be less of a concern in the Salmon River than current use pesticides, although 

data are limited. For example, Clark and Maret (1998) found DDTs in resident large-scale sucker from 

the Salmon River only at relatively low concentrations (600 ng/g lipid), well below concentrations 

associated with health effects for DDTs in fish (Beckvar et al. 2005). For Snake River Sockeye Salmon, 

which are present in the area for a limited time during migration, uptake of DDTs and related legacy 

pesticides would likely be even lower. However, there is no information on concentrations of these 

chemicals in juvenile Snake River Sockeye Salmon to confirm this.

5.7.3 Lower Snake River and Columbia River Migration Corridor

Snake River Sockeye Salmon are unique compared to other sockeye salmon populations. Sockeye 

Salmon returning to Redfish Lake in Idaho’s Sawtooth Valley travel a greater distance from the sea 

(approximately 1,500 km or 900 miles) to a higher elevation (1,982 meters or 6,500 ft.) than any other 

sockeye salmon population (Bjornn et al. 1968). The length of and duration of their migration puts them 

at increased risk for exposure to agricultural and industrial chemicals.

Throughout the Snake and Columbia River migration corridor, agricultural land uses may affect Snake 

River Sockeye Salmon. Irrigation began on lands adjacent to the Snake River around 1880. Irrigated 

agriculture is developed in a band several miles wide on either side of the river, and agriculture is a 

predominant land use to this day. Agricultural runoff returns to the river and also recharges the aquifer. 

It may carry various contaminants from pesticides, fertilizers, and/or animal wastes, but water quality 

monitoring data on current use of pesticides in the lower Snake River is limited (Watson et al. 2008). 

Bio-accumulative legacy pesticides are also a concern in this region. A recent study by the Washington 

State Department of Ecology sampled resident fish (bluegill, channel catfish, common carp, largemouth 

bass mountain whitefish, northern pikeminnow, peamouth, pumpkinseed, smallmouth bass, and yellow 

perch) at several sites on the Snake River between Clarkston and the Ice Harbor Dam (Seiders et al. 

2011). All five sites showed water quality violations for the legacy pesticides DDTs, dieldrin, and 
ESA Recovery Plan: Snake River Sockeye Salmon | 198

June 2015| NOAA Fisheries 

toxaphene, based on concentrations of these contaminants in fish. However, concentrations in sediments 

appear to be declining (Watson et al. 2008).

The mainstem Columbia River from its confluence with the Snake River near Pasco, Washington to its 

mouth also serves as a migration corridor for Snake River Sockeye Salmon. Like the Snake River, the 

Columbia River passes through agricultural lands, and receives pesticides, fertilizers and animals in both 

the mainstem and tributaries. In the 198-km (123-mile) reach of the Columbia River between the 

McNary and Dalles Dams, dominant land uses are irrigated and non-irrigated agriculture, livestock 

grazing, and timber harvest, and agricultural and forest pesticides, biological wastes, fertilizers, and 

pharmaceuticals are all considered potential contaminants of concern (CBFWA 2008). The region 

exhibits a number of water quality issues including elevated concentrations of water-soluble pesticides 

and herbicides and elevated concentrations of organochlorine pesticides including DDTs in both bed 

sediment and fish (Clark et al. 1998; Williamson et al. 1998; Hinck et al. 2006; Wagner et al. 2006;

McCarthy and Gale 2001; Johnson and Norton 2005; Watson et al. 2008). The USGS found particularly 

high concentrations and detection frequencies for current-use pesticides in the Pasco, Washington area 

(Williamson et al. 1998). 

In the Columbia Gorge, in the reach of the river bounded by Bonneville Dam at river kilometer 233

(river mile 145) and The Dalles Dam at river kilometer 307 (river mile 191), pesticide usage is also high, 

especially in the Hood River basin (Jenkins 2003; Jenkins and Catignoli 2004). Various current use 

pesticides and herbicides have been detected at various sites in the Hood River subbasin, including at the 

mouth of the Hood River at its confluence with the Columbia River (Temple and Johnson 2011). 

Agricultural pesticides enter the lower Columbia River, below Bonneville Dam, at various locations, 

including the confluence with the Willamette River. The Willamette River basin is a region of heavy 

pesticide use (Anderson et al. 1996; Wentz et al. 1998), and may be also source of pesticide 

contamination in the Columbia River. Throughout the Columbia Gorge and lower Columbia River, 

there are reaches that are listed as impaired under section 303(d) of the Clean Water Act because of high 

concentrations of DDTs in resident fish (Davis et al. 1998; Coots 2007; Seiders et al. 2007). In both the 

Columbia Gorge and lower Columbia River and estuary, much of the region is forested, and most 

contaminants in this region isare low (Anderson et al. 1996; Johnson and Norton 2005); however, they 

could contribute some forestry herbicides and insecticides, similar to those described in earlier sections 

of this Plan. 

In addition to agricultural chemicals, Snake River Sockeye Salmon may be exposed to contaminants 

from urban and industrial sources at many points in their migration corridor. The Snake River passes 

through Lewiston, Idaho, Clarkston, Washington, and the tri-cities of Kennewick, Pasco, and Richland 

Washington, before its confluence with the Columbia River. These population centers are sources of 

contaminants associated with urban and industrial activity. A recent study by Washington State 

Department of Ecology sampled resident fish (bluegill, channel catfish, common carp, largemouth bass 

mountain whitefish, northern pikeminnow, peamouth, pumpkinseed, smallmouth bass, and yellow 

perch) at several sites on the Snake River between Clarkston and the Ice Harbor Dam (Seiders et al. 

2011). All five sites showed water quality violations for polychlorinated biphenyls (PCBs) and dioxins, 
ESA Recovery Plan: Snake River Sockeye Salmon | 199

June 2015| NOAA Fisheries 

based on concentrations of these contaminants in fish. Polybrominated diphenyl ethers (PBDEs) may

also be a problem at some locations; Arkoosh et al. (2011) reported some accumulation of PBDEs in 

spring Chinook salmon during passage through reaches of the Snake River close to population centers 

such as Lewiston before reaching Lower Granite Dam. The Columbia River between the McNary and 

The Dalles dams is influenced by inputs of contaminants from urbanized and industrial areas of the TriCities and Hanford. At a site near Pasco, Hinck et al. (2006) reported high concentrations of mercury 

and selenium in resident fish. A recent Washington State Department of Ecology report (Sandvick 

2010) reported concentration of PCBs near McNary Dam that exceeded Washington State and EPA 

national water quality criteria. Higher than average levels of PBDEs in sediments and resident fish have 

also been reported near the Tri-Cities by EPA (Watson et al. 2008). 

Industrial chemicals are generally found at lower concentrations in the Columbia Gorge, but some 

portions of the Columbia River in this reach are listed as impaired water bodies under section 303(d) of 

the Clean Water Act due to elevated concentrations of PCBs in resident fish or in the water column 

(Coots 2007; Seiders and Deligeannis 2009). Bradford Island, on the Oregon side of the Columbia 

River, and part of the Bonneville Dam facility in Cascade Locks, is a source of PCB contamination in 

the Columbia Gorge region (URS 2010). In the past, an old landfill at Bradford Island served as a 

disposal site for electrical components and other materials containing PCBs. The Oregon Department of 

Environmental Quality is currently working with the Army Corps of Engineers to clean up PCB wastes 

at this site. In resident fish sampled from Cascade Locks, Hinck et al. (2006) found mercury, PCBs, and 

tetra-chlorinated dibenzo-p-dioxins (TCDDs).

Urban and industrial contaminants are present at especially high concentrations in the lower Columbia 

River and estuary near the confluence of the Columbia and Willamette Rivers, as this region contains 

multiple population centers, including Portland, the largest city in Oregon, and Vancouver, the fourth 

largest in Washington. Because of its high population density and industrialization, this area has major 

impacts on water quality. The majority of wastewater discharges, as well as non-point source runoff 

from paved roads and urban areas, originate in the region (USEPA 2009). Major classes of 

contaminants that have been detected in water, sediments, and fish in this area include PAHs, PCBs, 

dioxins, various semi-volatile industrial organic compounds, and metals (e.g., see Tetra Tech 1996; 

Buck et al. 2005; McCarthy and Gale 2001; Johnson and Norton 2005; Fuhrer et al. 1996; Weston 1998; 

Sethajintanin et al. 2004; Hinck et al. 2006; Sandvick 2010; LCREP 2007; Johnson et al. 2007, 2013); 

and there is evidence that other contaminants of emerging concern, including polybrominated diphenyl 

ethers (PBDEs) and pharmaceuticals, personal care products, and surfactants present in wastewater may 

be entering the river as well (Morace 2006, 2012; LCREP 2007; Sloan et al. 2010). There is also some 

evidence of contamination in some stretches of the Columbia River below Portland and Vancouver. 

Reaches near the Cowlitz and Lewis Rivers are listed as impaired water bodies because of elevated 

concentrations of PCBs in resident fish from these water (Davis et al. 1998; Coots 2007). High 

concentrations of PAHs, PCBs, and PBDEs were also detected in juvenile fall Chinook salmon from 

sites near Columbia City and Beaver Army Terminal (LCREP 2007; Sloan et al. 2010; Johnson et al. 

2013).
ESA Recovery Plan: Snake River Sockeye Salmon | 200

June 2015| NOAA Fisheries 

5.7.4 Contaminant Exposure, Uptake, and Risk in Snake River Sockeye Salmon

Land use activities and available data on contaminant concentrations in areas designated as critical 

habitat for Snake River Sockeye Salmon suggest that although a substantial proportion of their spawning 

habitat is relatively undeveloped, both juveniles and adults are likely at risk for exposure to several 

classes of contaminants, including mercury, legacy and current use pesticides, industrial contaminants 

such as PCBs and PBDEs, and wastewater contaminants during juvenile outmigration and adult 

spawning migration. However, very little is known about actual exposure to and uptake of contaminants 

in outmigrant juvenile Snake River Sockeye Salmon, or returning adults, and no data are available on 

contaminant body burdens in this species. Moreover, water quality data for much of this ESU’s habitat 

is incomplete. For example, there are only three USGS National Water-Quality Assessment (NAQWA) 

monitoring sites within the migration corridor of Snake River Sockeye Salmon, and no sites within the 

spawning and rearing habitat (NMFS 2011d). Water quality assessments are lacking for several lakes 

that comprise historical spawning habitat. In general, toxics monitoring in the Columbia Basin has been

concentrated primarily in the lower Columbia River and estuary, and data for the middle and upper 

Columbia, Snake River and Salmon River basins are lacking (USEPA 2009). 

Snake River Sockeye Salmon juveniles generally move rapidly downstream and spend little time rearing 

in the migration corridor. Consequently, they may be especially at risk from contaminants such as 

current use pesticides, which can affect behavior and other endpoints after only short-term exposure 

(NMFS 2008d, 2009, 2010a, 2011d). In a series of biological opinions, NMFS evaluated the likely 

impacts of a wide range of current use pesticides, including fifteen organophosphate insecticides, three 

carbamate insecticides, four herbicides, and two fungicides, on Snake River Sockeye Salmon (NMFS 

2008d, 2009, 2010a, 2011d). NMFS concluded that individual Snake River Sockeye Salmon would 

likely show some reductions in viability due to use of most of the reviewed pesticides. For a more 

limited number of pesticides (diazinon, chlorpyriphos, malathion, 2,4-D, and nalad), NMFS determined 

that there was a risk of jeopardy to Snake River Sockeye Salmon if these chemicals were applied 

imprudently (NMFS 2008d, 2009, 2010a, 2011d). 

Like current-use pesticides, dissolved copper may be a particular risk for Snake River Sockeye Salmon

because of its ability to affect olfactory function and behavior after relatively short-term exposure 

(Hecht et al. 2007). A variety of studies have shown that copper in the water column may have 

sublethal effects on juvenile salmonids at concentration in the 1-4 ug/L range (Hecht et al. 2007; 

Mebane and Arthaud 2010), concentrations that are not uncommon in the Snake and Columbia Rivers 

(Morace 2006, 2012; Anderson 2009). This suggests that some short-term effects on olfaction and 

behavior are likely for Snake River Sockeye Salmon juveniles and adults, but it is difficult to know if 

their exposure to variable concentrations would be of sufficient severity or duration to affect growth, 

mortality, or population viability. 

Snake River Sockeye Salmon may also be exposed to PAHs during both juvenile and adult migration. 

While no data are available on this stock, PAH metabolites in bile have been measured in juvenile fall 

Chinook salmon from the lower Columbia River and Estuary (Yanagida et al. 2011) and in juvenile 

spring Chinook salmon samples from the Snake and Middle Columbia Rivers between the Lower 
ESA Recovery Plan: Snake River Sockeye Salmon | 201

June 2015| NOAA Fisheries 

Granite and Bonneville Dams (Arkoosh et al. 2011). Of the bile samples collected from spring Chinook 

salmon collected from the Snake and Middle Columbia by Arkoosh et al. (2011), 36% exceeded the 

PAH-metabolite effect threshold estimated by Meador et al. (2008), while 47% of fall Chinook salmon

samples collected from sites in the lower Columbia River exceeded the threshold (Yanagida et al. 2011). 

Moreover, in both studies, levels of PAH metabolites above threshold concentrations were observed at 

multiple sites throughout the sampling areas, suggesting that exposure may be occurring throughout the 

region. This suggests that PAH exposure is highly likely in Snake River Sockeye Salmon moving 

through the Snake and Columbia River migration corridor, although there is much uncertainty about 

whether the duration of exposure would be sufficient to have health impacts on these fish. 

Because of the Snake River Sockeye Salmon’s stream-type life history strategy, their likelihood of 

accumulating high concentrations of bioaccumulative contaminants such as PCBs, PBDEs, and DDTs 

may be limited in comparison to ocean-type stocks such as Snake River fall Chinook salmon, which use 

the migration corridor and estuary as a rearing environment. Studies with Snake River spring Chinook 

salmon, another stream-type stock, indicated that juvenile Snake River spring Chinook salmon

accumulated DDTs and related agricultural pesticides during outmigration through the Snake and 

Columbia Rivers, but showed less uptake of PCBs and PBDEs, industrial chemicals present in especially 

high concentrations in the lower Columbia River and estuary (Sloan et al. 2010; Arkoosh et al. 2011; 

Johnson et al. 2012). However, because of lipid loss during outmigration, lipid-adjusted concentrations 

of all three classes of contaminants, which are better predictors of toxicity than wet weight 

concentrations, increased, putting some fish at risk for toxic effects. Concentrations of DDTs as high as 

8700 ng/g lipid and PCBs as high as 3100 ng/g lipid were reported, levels above those associated with 

toxic effects in juvenile salmon (Meador et al. 2002; Arkoosh et al. 2011; Johnson et al. 2013). 

Comparable results might be expected for juvenile Snake River Sockeye Salmon, but this is uncertain. 

No specific information is available on concentrations of the PCBs, DDTs, and related bioaccumulative 

contaminants in adult Snake River Sockeye Salmon, but the EPA has collected some information on 

concentrations these contaminants in adult spring Chinook salmon, which have a somewhat comparable 

life history. The average concentrations of DDTs and PCBs in whole body samples were 225 ng/g lipid 

and 333 ng/g lipid, respectively, given an average lipid content of 12% of these fish (USEPA 2002). 

Thus, risks of injury appear higher in outmigrant juveniles than in adult fish. 

Mercury is also considered a contaminant of concern in the several reaches of the Salmon, Snake, and 

Columbia Rivers that are critical habitat for Snake River Sockeye Salmon. Concentrations are not 

especially high in resident fish species captured from the Sawtooth Valley lakes, but high concentrations 

have been detected in resident fish from other areas in the Salmon, Snake, and Columbia Rivers (Hinck 

et al. 2006; Essig 2010). However, reported mercury concentrations are typically much lower in 

salmonids, including returning adults, than in resident piscivorous fish species (USEPA 2002; Essig 

2010). Mercury has also been measured in egg samples of returning fall and spring Chinook salmon, 

and steelhead trout from various sites in the Columbia Basin, and levels were below detection limits in 

all samples (USEPA 2002). These data suggest that risks associated with mercury contamination are 
ESA Recovery Plan: Snake River Sockeye Salmon | 202

June 2015| NOAA Fisheries 

low for Snake River Sockeye Salmon. However, the lack of information on mercury levels in this 

species makes it difficult to be certain of the impacts. 

In addition to these contaminants discussed above, there are many other contaminants of concern in the 

Snake and Columbia Rivers with potential effects on salmon (USEPA 2009). These include metals such 

as arsenic and lead; radionuclides; combustion byproducts such as dioxin; and “contaminants of 

emerging concern” such as pharmaceuticals and personal care products. Additional information, 

including toxicity evaluations and geographically targeted studies on these contaminants is needed to 

evaluate their potential risk to Snake River Sockeye Salmon. 

5.7.5 Summary of Threats and Limiting Factors Related to Toxics

Threats: Agricultural runoff, legacy mining contaminants, urban and industrial runoff, effluent, and 

wastes in the migration corridor and legacy toxaphene in Sawtooth Valley lakes.

Related limiting factors: Contaminants such as DDTs, PCBs, PBDEs, toxaphene, mercury, copper, and 

other metals, current use agricultural and forest pesticides, wildfire retardants, radionuclides, dioxin, 

etc., causing mortality, disease, reduced fitness.

Threat: Recreational development.

Potential limiting factors: Unfavorable changes to water quality; interference in spawning areas could 

reduce Sockeye Salmon productivity.

Threat: Forestry pesticide and fire retardant use.

Potential limiting factors: Toxic runoff resulting in lake water pollution could reduce Sockeye Salmon

productivity.

Threat: Legacy pesticide presence due to lake poisoning.

Potential limiting factors: Persistent and bioaccumuative toxicants (i.e., toxaphene) in lake sediments 

and biota could reduce Sockeye Salmon productivity by causing mortality, disease, or reduced fitness.

5.8 Climate Change

Likely changes in temperature, precipitation, wind patterns, and sea level height have profound 

implications for survival of Snake River salmon and steelhead, including Sockeye Salmon, in both their 

freshwater and marine habitats. Recent descriptions of expected changes in Pacific Northwest climate 

that are relevant to listed salmon and steelhead include Elsner et al. (2009), Mantua et al. (2009), Mote 

and Salathe (2009), Salathe et al. (2009), Mote et al. (2010), Chang and Jones (2010), and Crozier 

(2012, 2013). Reviews of the effects of climate change on salmon and steelhead in the Columbia River 

basin include ISAB (2007), NMFS (2010), Hixon et al. (2010), Dalton et al. (2013), and NMFS (2014c). 

The NMFS Northwest Fisheries Science Center will also be producing annual updates describing new 

information regarding effects of climate change relevant to salmon and steelhead as part of the FCRPS 
ESA Recovery Plan: Snake River Sockeye Salmon | 203

June 2015| NOAA Fisheries 

Adaptive Management Implementation Plan. The following is a short summary of expected climate 

change effects on listed Snake River salmon and steelhead derived from the above sources. 

Freshwater Environments

Climate records show that the Pacific Northwest has warmed about .07°C since 1900, or about 50%

more than the global average warming over the same period (Dalton et al. 2013). The warming rate for 

the Pacific Northwest over the next century is projected to be in the range of 0.1°C to 0.6°C per decade. 

While total precipitation changes are predicted to be minor (+1% to 2%), increasing air temperature will 

alter the snow pack, stream flow timing and volume, and water temperature in the Columbia Basin

(Figure 5-5). Climate experts predict the following physical changes to rivers and streams in the 

Columbia Basin:

• Warmer temperatures will result in more precipitation falling as rain rather than snow.

• Snow pack will diminish, and stream flow volume and timing will be altered. More 

winter flooding is expected in transitional and rainfall-dominated basins. Historically 

transient watersheds will experience lower late summer flows. 

A trend towards loss of snowmelt-dominant and transitional basins is predicted. Summer and fall water 

temperatures will continue to rise. 

 Figure 5-5. Preliminary maps of predicted hydrologic regime for (A) the period 1970-1999 and (B) the period 2070-2099 

using emission scenario A1B and global climate model CGCM3.1(T47), based on classification of annual hydrographs as in 

(Beechie et al. 2006). Data from University of Washington Climate Impacts Group 

(http://www.hydro.washington.edu/2860/).

Recent intensive modeling of stream flow and temperature in the Pacific Northwest (Wu et al. 2012) 

indicates that the Salmon River basin and similar watersheds may be particularly impacted by climate 

change. The model simulations projected that climate change will have greater impacts on snow-
ESA Recovery Plan: Snake River Sockeye Salmon | 204

June 2015| NOAA Fisheries 

dominant streams, such as those found in the upper Columbia Basin and Salmon and Clearwater basins. 

Increased water temperatures could affect migrating adult Sockeye Salmon by increasing the metabolic 

cost of swimming and holding prior to spawning, which can increase prespawn mortality (Crozier 2012). 

An assessment by the Sawtooth National Forest also suggests that climate change may impact flows and 

water temperatures in the Salmon basin. The Sawtooth National Forest conducted a climate change 

vulnerability assessment (US U.S. Forest Service 2011) on winter peak and summer base flows, and 

water temperatures in the upper Salmon drainage on the Sawtooth National Recreation Area. Results 

include: 

Summer Baseflows (Mean Summer)

Assessment results project a general trend of declining summer baseflows for the entire Sawtooth 

National Recreation Area as air temperatures and evapotranspiration increase. As discussed in the 

assessment (2011), increasing winter air temperatures will reduce the amount of snow (e.g., more 

precipitation falling as rain than snow), as already observed in several parts of the western United States. 

In addition, higher spring temperatures will also initiate earlier runoff and peak streamflows in 

snowmelt-dominated basins.

The prediction of lower baseflow is consistent with studies and empirical trends at flow gages on the 

Salmon National Forest. Since 1950, stream discharge in both the Colorado and Columbia River basins 

has decreased (Walter et al., 2004). Regonda et al. (2005) and Stewart et al. (2005) found that stream 

runoff steadily advanced during the latter half of the twentieth century and now occur 1 to 3 weeks 

earlier due largely to concurrent decreases in snowpack and earlier spring melt (Mote et al. 2005). These 

changes diminished recharge of subsurface aquifers that support summer baseflows (Hamlet et al. 2005). 

Luce and Holden (2009) found that three-fourths of the 43 gage records they examined from the Pacific 

Northwest exhibited statistically significant declines in summer low flows. Luce and Holden (2009) also 

found that the driest 25% of years are getting drier across the majority of the Pacific Northwest sites, 

with most streams showing decreases exceeding 29% and some showing decreases approaching 50% 

between 1948 and 2006. Sites on or near the Sawtooth National Forest showed similar declines in mean 

annual flow.

Summer Water Temperatures (Maximum weekly maximum temperature) 

Assessment results predict that summer maximum weekly maximum water temperatures will increase 

over the next 70 years relative to 2008, with possible increases by +0.9 oC (2033), +1.1 oC (2040), +1.7 o

C (2058), and +2.5 oC (2080) on the Sawtooth National Recreation Area.

These changes in air temperatures, river temperatures, and river flows are expected to cause changes in 

adult Sockeye Salmon migration rates and survival. Higher temperatures during adult migration in late 

summer may lead to increased mortality or reduced spawning success due to lethal temperatures, delay, 

increased fallback at dams, or increased susceptibility to disease and pathogens. Low late-summer flows 

in tributaries below natal lakes may preclude adult passage to spawning areas.
ESA Recovery Plan: Snake River Sockeye Salmon | 205

June 2015| NOAA Fisheries 

Effects of climate change on the limnology of natal lakes in the Salmon River is uncertain, so effects of 

climate change on Snake River Sockeye Salmon spawning, emergence, and juvenile rearing are 

currently unknown. If lakes are warmer during incubation, fry may emerge earlier, which could be either 

beneficial or detrimental, depending upon location and prey availability. If lake temperatures are warmer

during juvenile rearing, metabolism will increase, which may either increase or decrease juvenile growth 

rates and survival, depending upon availability of food. Higher temperatures may also increase predation 

rates on juvenile Sockeye Salmon or favor food competitors of Sockeye Salmon.

In the Salmon, Snake, and Columbia Rivers, modified timing of the spring freshet may alter timing of 

smolt migration, such that there is a mismatch with ocean conditions and predators. Reduced flow in late 

spring may lead to delayed migration and higher mortality passing dams. 

The degree to which phenotypic or genetic adaptations may partially offset these effects is being studied 

but is currently poorly understood. For example, potential impacts on Snake River Sockeye Salmon

could be reduced if the fish continue to adjust their migration timing. Adult migration timing in Snake 

River and upper Columbia Sockeye Salmon has been progressing earlier in the year in the Columbia 

River over the 20th century. Crozier et al. (2011) explored how changes in river temperature and flow, 

as well as ocean conditions might be driving this advance. They found evidence that this trait evolved 

genetically due to mortality of late migrants exposed to higher Columbia River temperatures during the 

historical migration period. The fish also show a strong annual response to river flow, such that they 

migrate earlier in low-flow years. These two processes combined suggest both plastic and evolutionary 

responses are involved in an adaptive shift likely to continue in response to climate change (Crozier 

2012).

Estuarine and Plume Environments

Climate change will also affect Sockeye Salmon in the estuarine and plume environments. In the 

estuary, Sockeye Salmon would be primarily affected by increased predation. Juvenile Sockeye Salmon

and other stream-type salmonids move quickly through the estuary on their way to the plume and ocean 

and are less affected by the health of the estuarine ecosystem than are ocean-type salmonids. Juvenile 

Sockeye Salmon may be affected by habitat changes in the plume environment due to flow- or sedimentrelated changes; however, use of plume habitat by Sockeye Salmon remains poorly understood. Effects 

of climate change on Sockeye Salmon in the estuary and plume may include the following:

• Higher winter freshwater flows and higher sea levels may increase sediment deposition in 

the plume, possibly reducing the quality of rearing habitat.

• Lower freshwater flows in late spring and summer may lead to upstream extension of the 

salt wedge, possibly influencing the distribution of salmonid prey and predators.

• Increased temperature of freshwater inflows and seasonal expansion of freshwater 

habitats may extend the range of non-native, warm-water species that are normally found 

only in freshwater. 

In all of these cases, the specific effects on Sockeye Salmon abundance, productivity, spatial distribution 

and diversity are poorly understood. 
ESA Recovery Plan: Snake River Sockeye Salmon | 206

June 2015| NOAA Fisheries 

Marine Environments

Effects of climate change in marine environments include: increased ocean temperature, increased 

stratification of the water column, changes in intensity and timing of coastal upwelling, and ocean 

acidification. Hypotheses differ regarding whether coastal upwelling will decrease or intensify, but even 

if it intensifies, the increased stratification of the water column may reduce the ability of upwelling to 

bring nutrient-rich water to the surface. There are also indications in climate models that future 

conditions in the North Pacific region will trend toward conditions that are typical of the warm phases of 

the Pacific Decadal Oscillation, but the models in general do not reliably reproduce the oscillation 

patterns. Hypoxic conditions observed along the continental shelf in recent years appear to be related to 

shifts in upwelling and wind patterns that may be related to climate change.

Climate-related changes in the marine environment are expected to alter primary and secondary 

productivity, the structure of marine communities, and in turn, the growth, productivity, survival, and 

migrations of salmonids, although the degree of impact on listed salmonids is currently poorly 

understood. A mismatch between earlier smolt migrations (because of earlier peak spring freshwater 

flows and decreased incubation period) and altered upwelling may reduce marine survival rates. 

Ocean warming also may change migration patterns, increasing distances to feeding areas. Rising 

atmospheric carbon dioxide concentrations drive changes in seawater chemistry, increasing the 

acidification of seawater and thus reducing the availability of carbonate for shell-forming invertebrates, 

including some that are prey items for juvenile salmonids. This process of acidification is under way, 

has been well documented along the Pacific coast of the United States, and is predicted to accelerate 

with increasing greenhouse gas emissions.

Ocean acidification has the potential to reduce survival of many marine organisms, including Sockeye 

Salmon. However, because there is currently a paucity of research directly related to the effects of ocean 

acidification on salmon and their prey, potential effects are uncertain. Laboratory studies on salmonid 

prey taxa have generally indicated negative effects of increased acidification, but how this translates to 

the population dynamics of salmonid prey and the survival of salmon is uncertain. Modeling studies that 

explore the ecological impacts of ocean acidification and other impacts of climate change concluded that 

salmon landings in the Pacific Northwest and Alaska are likely to be reduced.

Conclusion

All other threats and conditions remaining equal, future deterioration of water quality, water quantity, 

and/or physical habitat as a result of climate change is expected to cause reductions in the numbers of 

naturally produced adult Sockeye Salmon. This possibility further reinforces the importance of 

achieving survival improvements throughout the entire life cycle.

Additional exposure to high water temperatures in the mainstem Salmon, Snake, and Columbia Rivers 

could pose a paramount concern for adult Snake River Sockeye Salmon, which generally migrate 

through the corridor in late summer when water temperatures are highest. For example, observations of 

high July through September 2013 Snake and Columbia River temperatures indicate dangerous 
ESA Recovery Plan: Snake River Sockeye Salmon | 207

June 2015| NOAA Fisheries 

conditions for adult Snake River Sockeye Salmon migrating through the FCRPS during that period. PITtag information indicates unusually low survival of adult Snake River Sockeye Salmon through the 

FCRPS in 2013 (Crozier 2013), particularly for Sockeye Salmon in July and August, which were 

exposed to the highest temperatures. The potential impacts on migrating Snake River Sockeye Salmon

may be reduced if the fish continue to adjust their migration timing.

Recent research reinforces the importance of maintaining habitat diversity, conducting studies to 

document climatic effects on freshwater, estuary, and ocean productivity and adjust actions accordingly 

through adaptive management. 
ESA Recovery Plan: Snake River Sockeye Salmon | 208

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 209

June 2015| NOAA Fisheries 

Section 6: Recovery Strategy

6.1 Analysis of Causes of Decline

6.2 Basic Assumptions

6.3 Recovery Strategy

6.4 Key Information Needs
ESA Recovery Plan: Snake River Sockeye Salmon | 210

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 211

June 2015| NOAA Fisheries 

6. Recovery Strategy 

The recovery strategy is designed to meet the recovery goal of ESA delisting, and the delisting goals are 

provided in Section 3. In this section, NMFS presents the reasoning behind the recovery program 

recommended for the Snake River Sockeye Salmon ESU. The recovery strategy links this program to 

the ESU’s current status and limiting factors, described in preceding sections, and the recovery goals, 

biological viability criteria, and recovery scenario set by NMFS in cooperation with regional and local 

stakeholders. 

The Snake River Sockeye Salmon ESU currently is still close to extinction. This ESU is now on the 

equivalent of life support, with a captive broodstock program sending hundreds of thousands of smolts 

on their migration to the sea. In recent years of favorable ocean conditions, hundreds of adult fish have 

returned, but natural production levels for anadromous returns remain extremely low for the species. As 

previously stated, the ESU cannot be said to have recovered until there is a self-sustaining, naturally 

spawning population likely to persist over the next century. We must first address the ESU’s current 

high-risk status, while also anticipating future actions that can be implemented as natural production 

increases. 

6.1 Analysis of Causes of Decline

The Idaho Department of Fish and Game, Shoshone-Bannock Tribes, NMFS, and many independent 

researchers have conducted decades of scientific research and analysis concerning Snake River Sockeye 

Salmon. Successive NMFS biological review teams have concluded that the decline of the ESU is the 

result of widespread habitat degradation, impaired mainstem and tributary passage, historical 

commercial fisheries, chemical treatment of Sawtooth Valley lakes in the 1950s and 1960s, and poor 

ocean conditions. These combined factors reduced the number of Sockeye Salmon to the single digits. 

The decline in abundance itself has become a major limiting factor, making the remaining population 

vulnerable to catastrophic loss and posing significant risks to genetic diversity. 

Based on this analysis, actions taken to improve, change, mitigate, and reduce those factors will result in 

reduced risks and increased survival. Because of the species’ complex life cycle and the many changes 

that have taken place in its environment, the factors limiting its survival must be addressed in concert 

and in an integrated way. The work needs to occur both at a regional level, in terms of commitment to 

actions and funding, and at the local level, as reintroduction actions are implemented. 
ESA Recovery Plan: Snake River Sockeye Salmon | 212

June 2015| NOAA Fisheries 

6.2 Basic Assumptions

In designing an effective recovery strategy, we make a number of assumptions, including the following: 

1. We have accurately identified the limiting factors and threats affecting the fish.

• This recovery strategy reflects the best technical information available and our current 

understanding of the limiting factors and threats that affect the fish throughout their life 

cycle. 

2. Addressing the limiting factors and threats will improve the viability of the existing population 

and the ESU. 

• Multiple causes are responsible for the decline of this ESU due to limiting factors and 

threats throughout the entire life cycle. To improve population and ESU viability, our 

strategy focuses on a wide range of hatchery, habitat, fishery, and hydropower systemrelated actions to address the many threats that currently impact Snake River Sockeye 

Salmon recovery. The strategy also recognizes the many remaining unknowns regarding 

our understanding of the factors that affect the fish now, or might influence their recovery

in the future. It recognizes the risks in taking various steps toward recovery. As a result, 

it directs actions to gain critical information regarding how different factors affect the 

fish and address potential risks linked to the recovery actions. 

3. This Plan is based on technically sound ecological principles and an effective adaptive 

management approach. 

• Our recovery strategy recognizes that efforts to address habitat, fisheries, hatchery and 

hydropower system-related issues affecting Snake River Sockeye Salmon need to be 

planned and implemented with a clear understanding of ecological processes  including 

both biological and habitat processes  and how past and current activities affect these 

processes. 

• An understanding of these biological and habitat processes frames our approach to 

rebuild Snake River Sockeye Salmon viability. The ESU is at risk for extinction. The 

captive broodstock program has helped maintain the Sockeye Salmon population and 

prevent species extinction. We are now entering a new phase that will incorporate more 

natural-origin Sockeye Salmon returns in the hatchery-spawning program to maintain the 

genetic fitness of the natural population and to provide anadromous adults to recolonize 

available habitat in the natal lakes. Our goal is for the naturally produced population to 

achieve escapement goals in a manner that is self-sustaining in the wild and without the 

reproductive contribution of hatchery spawners. This will require a combination of 

efforts that support biological and habitat processes. Together, these efforts aim to 

provide sufficient fish to restore populations adapted to the specific conditions of lakes in 

the Sawtooth Valley, while also protecting and improving habitat conditions, and 

addressing passage, competition, and predation concerns, to support a self-sustaining 

population. Further, the Plan supports the conservation of native residual and resident 
ESA Recovery Plan: Snake River Sockeye Salmon | 213

June 2015| NOAA Fisheries 

forms of O. nerka. We recognize that while the focus of this Plan is on the recovery of 

ESA-listed anadromous Sockeye Salmon, residual Sockeye Salmon and kokanee 

represent important life history and spatial diversity characteristics that may contribute to 

the recovery of the anadromous Sockeye Salmon.

4. Through an understanding of each limiting factor, actions can modify the ESU’s environment 

and result in a biological response (through improvements in productivity, abundance, spatial 

structure and diversity).

• The recovery strategies and subsequent actions reflect our current understanding of 

limiting factors and threats for the population and ESU. However, we acknowledge that 

actions may not yield the desired result, gaps in data may emerge, and recovery efforts 

may need to be adapted to new information. Acknowledging these limitations and 

integrating adaptive management into the recovery plan is an essential part of the 

recovery strategy. The recovery strategies will be reevaluated and updated as new 

information becomes available. 

6.3 Recovery Strategy

Our strategic vision for recovery of Snake River Sockeye Salmon is to establish viable self-sustaining, 

naturally spawning populations in the wild that are sufficiently abundant, productive, and diverse and no 

longer need Endangered Species Act protection. As the species continues to recover over time, broader 

goals that go beyond achieving species recovery may also be met to provide multiple ecological, 

cultural, social, and economic benefits. 

Overall, our strategy aims to reintroduce and support adaptation of natural Sockeye Salmon populations 

in the Sawtooth Valley lakes. An important first step toward that objective has been the successful 

establishment of anadromous returns from natural-origin Redfish Lake stock gained through a captive 

broodstock program. That program is transitioning as higher levels of anadromous Sockeye Salmon

return to spawn in Redfish Lake. Ultimately, the program will transition to a third phase emphasizing 

natural adaptation and viability. The NMFS’ five-year reviews will track our progress toward recovery 

and allow us to adjust actions in response. 

Our strategic vision for recovery recognizes that reestablishing natural Sockeye Salmon populations in 

the lakes, as well as life history strategies and habitats, requires use of well-formulated, scientifically 

sound approaches. Since multiple causes are responsible for impairing population viability and 

disrupting ecosystem functions, limiting factors and threats across the entire life cycle will need to be 

addressed in concert. Development and implementation of management actions that lead to recovery 

will require a sound understanding of conservation biology principles and ecosystem management as 

well as integration of planning, funding, and monitoring such that each contributes to reaching our end 

goal.
ESA Recovery Plan: Snake River Sockeye Salmon | 214

June 2015| NOAA Fisheries 

We also recognize the importance of learning as we go and adjusting our efforts accordingly to achieve 

ESU recovery as quickly and effectively as possible. Thus, a key element of the approach to restoring 

natural production of Sockeye Salmon in the Sawtooth Valley is the adaptive nature of the recovery

strategy. The strategy depends on implementation of an adaptive management framework that 

implements site-specific actions based on best available science, monitors to improve the science, and 

updates actions based on new knowledge. The ESA section 4(f) requires site-specific actions “as may 

be necessary to achieve the plan’s goals for conservation and survival of the species.” There are two 

types of site-specific actions in this plan: management actions (Section 7) and research, monitoring, and 

evaluation actions (Section 11). Our hypothesis is that the management actions will be effective in 

improving survival; however, we have uncertainties about whether they will be sufficient to achieve 

viability. Thus, this plan depends on an adaptive management framework as follows:

1. Establish recovery goals and viability and threats criteria for delisting (Section 3).

2. Determine the species’ present status and the gaps between the present status and viability 

criteria (Section 4).

3. Assess the threats and limiting factors in each of the major sectors that are contributing to the 

gaps between present status and viability criteria (Section 5). Also, assess the threats in the 

context of variable ocean conditions and emerging climate change.

4. Implement management actions (Section 7) that target the limiting factors and threats associated 

with each of the major sections.

5. Implement research, monitoring, and evaluation actions (Section 11) to evaluate the status and 

trend of the species and the status and trend of limiting factors and threats, including action 

implementation and action effectiveness.

6. Address key information needs. There are key information needs about the species status, effects 

of ongoing and proposed actions, the role of the ocean and climate change, and the best 

opportunities for further improving survival sufficiently to meet the viability criteria. These key 

information needs are described in Section 6.

7. Develop and apply criteria for prioritizing recovery actions and develop an implementation plan. 

We need to prioritize and stage the implementation of recovery actions so we can achieve 

recovery in a timely and effective manner. Section 7, Actions, describes prioritization 

considerations that will be used to develop prioritization criteria for management actions. Section 

10, Implementation, discusses the process for developing the prioritization criteria and the 

implementation schedule and plan.

8. Establish a contingency process: We need to be prepared if the species’ status does not continue 

to improve in a timely manner, and also if there are significant declines in status. A contingency 

process should be established that sets intermediate goals and timeframes and also sets early 

warning indicators and significant decline triggers. As part of this process, additional actions 

should be developed that are “on the shelf,” if needed, to address long-term trends toward 
ESA Recovery Plan: Snake River Sockeye Salmon | 215

June 2015| NOAA Fisheries 

recovery and to prevent precipitous declines. The contingency process is addressed in Section 

10, Implementation.

9. Review progress and identify best opportunities for survival improvements. Regular major 

reviews of implementation progress, species response, and new information are needed. These 

progress reviews are addressed in Section 10, Implementation. 

10. Adjust actions according to progress reviews. The success of this recovery plan depends on an 

implementation structure that takes action in response to the results of progress reviews.

11. Repeat the adaptive management cycle. Adaptive management should be a continuous loop of 

action implementation, monitoring and evaluation, new information, assessment of information 

and updated actions. Section 11 discusses the adaptive management process.

Achieving species recovery will require coordinated and collaborative management and implementation 

of actions at local, watershed, and regional levels as described in Section 10. Multiple causes are 

responsible for the decline of this ESU due to limiting factors and threats throughout the entire life 

cycle. Addressing these impaired conditions and factors will require management of hatcheries, habitat, 

fisheries, and hydro-related actions based on the following elements in this recovery strategy. In turn, 

this strategy recognizes the need to adaptively manage programs, agreements and actions over time as 

they are implemented and new information becomes available.

The strategies and actions identified in this Plan will also provide key information aimed to answer 

critical recovery strategy questions through an adaptive management process. Addressing these 

questions will increase the certainty that the underlying assumptions in the Plan are correct and that 

implementation of the proposed actions will lead to recovery of the species. Key questions include: 

1. Will the proposed actions translate into the benefits expected? 

2. Will the benefits achieved by the actions allow the populations and MPG to recover to desired 

levels where the species can be delisted? 

3. Are survivals that result from current conditions and management actions enough to provide for 

life history survival through variations in ocean and climate conditions? 

Section 11 describes the research, monitoring, and evaluation that will address these questions. The 

research, monitoring, and evaluation program is designed to assess the status of the listed species and 

their habitat, track progress toward achieving recovery goals, and provide information needed to refine 

recovery strategies and actions through the process of adaptive management.

 

The proposed recovery strategy for Snake River Sockeye Salmon contains elements to address limiting 

factors and threats at the local level (Sawtooth Valley and upper Salmon River) and the regional level 

(the mainstem lower Salmon, Snake and Columbia Rivers and estuary, and plume and ocean). The 

different elements are listed in Box 6-1 and discussed in Sections 6.3.1 and 6.3.2. 
ESA Recovery Plan: Snake River Sockeye Salmon | 216

June 2015| NOAA Fisheries 

Box 6-1. Recovery strategy for Snake River Sockeye Salmon

At the local level (Sawtooth Valley and upper Salmon River):

• Conserve population genetic and life history diversity, and spatial structure. 

• Increase naturally spawning Snake River Sockeye Salmon abundance. 

• Improve Sockeye Salmon passage to natal lakes. 

• Reestablish a self-sustaining anadromous Sockeye Salmon population in Redfish Lake.

• Investigate and develop strategies for future actions to support Sawtooth Valley Sockeye Salmon reintroduction and adaptation 

phases for Pettit Lake.

• Investigate and evaluate the potential for restoring natural production of anadromous Sockeye Salmon from returning kokanee

outmigrants from Alturas Lake.

• As sufficient numbers of natural-origin adults return, develop an integrated approach to manage natural- and hatchery-origin 

adults in the hatchery program and in the wild.

• As sufficient numbers of hatchery-origin anadromous adult’s return to the basin, identify options for future harvest.

• Continue research and actions to reestablish natural populations in other natal lakes.

• Continue research on natal lakes’ carrying capacity, nutrients, and ecology.

• Protect and conserve natural ecological processes at the watershed scale that support population viability. 

• Protect, restore and manage spawning and rearing habitat.

• Maintain unimpaired water quality and improve water quality as needed.

• Investigate and improve conditions in Salmon River and tributaries to support increased survival of migrating Snake River 

Sockeye Salmon.

• Monitor for predation, disease, aquatic invasive species, and competition and develop actions as needed.

• Create an adaptive management feedback loop to track progress toward recovery, monitor and evaluate key information needs, 

assess results, and refine strategies and actions accordingly.

At the regional level (the migration corridor, in the mainstem Salmon, Snake and Columbia Rivers; estuary; plume; and ocean): 

• Implement 2008/2010 FCRPS BiOp’s reasonable and prudent alternative, as modified in the 2014 Supplemental FCRPS BiOp to 

reduce mortalities associated with migration through the mainstem Salmon, Snake and Columbia Rivers, estuary and plume.

• Continue research and monitoring on Snake River Sockeye Salmon survival/mortality in mainstem Salmon, Snake and Columbia 

River migration corridor; estuary; plume; and ocean.

• Update Snake River Sockeye Salmon life cycle models using latest information on survival through mainstem Salmon, Snake, 

and lower Columbia River migration corridor; estuary; and plume.

• Manage to maintain current low impact fisheries and reduce fishery impacts in those fisheries that affect Snake River Sockeye 

Salmon.

• Protect and conserve natural ecological processes that support population viability.

• Improve degraded water quality and maintain unimpaired water quality.

• Address ecosystem imbalances in predation, competition, and disease through the strategies and actions in this Plan, the Estuary 

Module and reasonable and prudent alternatives identified in Biological Opinions.

• Respond to climate change threats by implementing research, monitoring and evaluation to track indicators related to climate 

change and by preserving biodiversity. 

• Implement this recovery plan through effective communication, education, coordination, and governance.

• Continue research, monitoring and evaluation for adaptive management.

• Prioritize and address key information needs and create an adaptive management feedback loop to revise recovery actions as 

needed.
ESA Recovery Plan: Snake River Sockeye Salmon | 217

June 2015| NOAA Fisheries 

6.3.1 Strategies to Recover Snake River Sockeye Salmon at the Local Level (Sawtooth 

Valley and Upper Salmon River)

Sections 6.3.1.1 through 6.3.1.16 describe strategies at the local level to improve Snake River Sockeye 

Salmon viability.

6.3.1.1 Conserve population genetic and life history diversity and spatial structure

Conserving population genetic diversity of Snake River Sockeye Salmon will require a series of actions 

corresponding to the expanding scope of the reintroduction efforts. In the short term, the Snake River 

Sockeye Salmon captive broodstock hatchery program and associated research and monitoring actions 

should continue to be implemented under the current IDFG and SBSTOC work plan (IDFG 2010) to 

reduce ESU extinction risk and promote recovery until criteria and benchmarks are reached and the 

program can be phased out. The current program places emphasis on maximizing the effective 

population size and the annual development of genetically diverse broodstock. Fish culture variables 

(broodstock mating designs, in-hatchery survival, maturations success, fecundity, egg survival to eyedegg stage, and fish health) are continuously monitored and evaluated to ensure maximum program 

success. 

The existing captive broodstock program will transition to a recolonization phase with the development 

of expanded smolt production through the Springfield Sockeye Salmon Hatchery program. The 

recolonization phase will aim to establish a self-sustaining anadromous broodstock and reduce reliance 

on captive broodstock for population maintenance. The production program will use anadromous 

Sockeye Salmon adults collected at Sawtooth Valley weirs as broodstock. This new program will allow 

gene banking (while the captive broodstock is on station) and provide anadromous adults to recolonize 

available habitat. As the number of available hatchery returns increases, more adults will be released 

into Redfish Lake to boost natural production. Outplanting and broodstocking strategies will be adapted 

to encourage the development of localized adaptations to habitat conditions and to protect genetic 

fitness.

Initial efforts under the Snake River Sockeye Salmon recovery strategy aim to reestablish the Sockeye 

Salmon population in Redfish, Pettit, and Alturas Lakes. The hatchery program and related hatchery 

and genetic management plan (NMFS 2012b) focus actions primarily on Redfish Lake because of its 

high production potential. Continued actions are needed to develop a reintroduction plan for Pettit Lake 

(e.g., when the program would use Redfish Lake fish in Pettit Lake, what life stage(s) would be released, 

etc.). Captive broodstock (or, if available, hatchery anadromous) adults will be released into Pettit Lake 

initially. These releases will cease after a defined period and strategies will be refined based on the 

response of initial reintroductions and the performance of the Redfish Lake program. Information is also 

needed regarding Pettit Lake’s production potential and whether targeted objectives for the lake can be 

achieved. Actions for Alturas Lake Sockeye Salmon recovery begin with identifying appropriate 

strategies for Alturas Lake anadromous Sockeye Salmon recovery, including (1) trap and transport of 

any anadromous adults of Alturas Lake origin for release in Alturas Lake and (2) possibly implementing 

a hatchery program for the population. As natural-origin adults begin returning from the reintroduction 
ESA Recovery Plan: Snake River Sockeye Salmon | 218

June 2015| NOAA Fisheries 

efforts in each lake, upstream passage and weir management strategies will be implemented to support 

continued adaptation to local conditions within each lake. 

Actions will also be taken to protect Sockeye Salmon population genetic makeup and fitness. Activities 

include evaluating the best possible broodstock sources, capturing broodstock throughout the return and 

spawning period, and using genetic testing to maintain the genetic diversity of the broodstock used in 

the hatchery program. Release strategies will be designed to support reestablishing natural populations 

adapted to local conditions. The Alturas Lake population, for example, exhibits an earlier return time 

than the Redfish Lake population and maintaining this diversity is important. The Snake River Sockeye 

Salmon HGMP includes performance standards, indicators of performance, and monitoring and 

evaluation requirements.

In the last phase, hatchery supplementation programs will transition to a longer-term role consistent with 

maintaining genetic variability. NMFS will develop guidance for how to recover O. nerka life history 

forms for Snake River Sockeye Salmon. Long-term guidelines will be developed that support and 

maintain localized adaptations within and among populations in the Sawtooth Valley. Section 6.4 Key 

Information Needs, expands on this discussion. Section 11 Research, Monitoring, and Evaluation for 

Adaptive Management, outlines actions to address the uncertainties. 

Recovery strategy questions:

• What was the historic genetic diversity and heterozygosity of Snake River Sockeye 

Salmon?

• What are the benefits/risks to genetic diversity of maintaining stocks adapted to each lake 

in the ESU? 

• How can remnant anadromous Sockeye Salmon gene resources that exist in other 

Sawtooth Valley lakes other than Redfish Lake be used for recovery efforts on a lake 

specific basis?

• Is the current Redfish Lake Sockeye Salmon captive broodstock genetic structure 

appropriate for use in rebuilding efforts in other Sawtooth Valley lakes? What will be the 

role of beach vs. stream spawning types?

6.3.1.2 Increase naturally spawning Sockeye Salmon abundance

As discussed in Section 3, the long-term recovery scenario for Snake River Sockeye Salmon is to restore 

at least two of the three historical lake populations in the ESU to highly viable, and one to viable status. 

The recovery scenario focuses on Redfish Lake, Alturas Lake, and Pettit Lake. As recovery efforts 

progress over time, expansion of reintroductions into Yellowbelly Lake and Stanley Lake will be 

considered.

Our recovery strategy aims to achieve viable, naturally spawning self-sustaining Sockeye Salmon

populations by increasing the number of anadromous adults that spawn naturally in the Sawtooth Valley 
ESA Recovery Plan: Snake River Sockeye Salmon | 219

June 2015| NOAA Fisheries 

lakes. The strategy builds on the current captive broodstock program and incorporates population 

recolonization programs for Redfish, Pettit, and Alturas Lakes. It implements a coordinated hatchery 

program to increase smolt production to increase the number of anadromous returns and subsequently 

the number of spawners in Redfish and Pettit Lake habitat. The program will emphasize supporting high 

levels of anadromous return spawners to Redfish Lake. The working hypothesis behind the approach 

assumes that the natural production that will result from the high levels of anadromous hatchery returns 

will lead to increases in relative productivity and downstream survivals sufficient to allow for transition 

to a third phase emphasizing natural adaptation. As natural-origin returns increase, smolt production 

and hatchery-origin returns would be reduced.

Natural production in Pettit Lake will be achieved through volitional spawning and short-term releases 

of captive broodstock. Initial hatchery releases to Pettit Lake will cease after a defined period and be 

revised based on natural production response. Volitional spawning of anadromous adults originating 

from Pettit Lake will continue. This program is discussed in Section 6.3.1.5. 

Natural production of anadromous Sockeye Salmon in Alturas Lake will be restored through steps that 

safeguard the early-spawning residual population’s spatial structure and genetic diversity. This program 

is discussed in Section 6.3.1.6.

The programs for the different Sawtooth Valley populations include steps to safeguard against potential 

risks. In the Sawtooth Valley lakes, potential risks associated with increased hatchery production include 

genetic and ecological risks to the residual populations (Griswold et al. 2012). Additional risks include 

disease and competition with residual Sockeye Salmon and kokanee, and competition within lakes for 

zooplankton resources, particularly with naturally produced fish. Increased hatchery production may 

also serve to increase the density of prey and attract predators. In addition, the effects that occur early in 

life history, especially those that impact growth, may impact survival at later life stages (Griswold et al. 

2011b). Redfish Lake residual Sockeye Salmon are a unique ecotype and it is not clear how they have 

developed or are maintained (Griswold et al. 2012). Consequently, it will be important to monitor the 

effects of increased hatchery production on the residual Sockeye Salmon populations. 

One of the primary overriding questions concerning Snake River Sockeye Salmon recovery is whether 

the survivals that result from current conditions and management actions will be enough to provide for 

life history survival through variations in ocean and climate conditions. As discussed in Section 5, 

climate experts project a warming trend for the Pacific Northwest over the next century. They predict 

that increasing air temperatures will alter the snow pack, stream flow timing and volume, and water 

temperature in the Columbia Basin. They also predict changes in ocean conditions due to climate 

change. Such likely changes in temperature, precipitation, wind patterns, and sea-level height could 

have profound implications for survival of Snake River Sockeye Salmon in both their freshwater and 

marine habitats, and need to be taken into consideration.

Recovery strategy questions:

• Is the hatchery program going to work?
ESA Recovery Plan: Snake River Sockeye Salmon | 220

June 2015| NOAA Fisheries 

• Is the current Redfish Lake Sockeye Salmon captive broodstock genetic structure 

appropriate for use in rebuilding efforts in other Sawtooth Valley lakes?

• Are the effects of the primary factors limiting the status of the populations increasing, 

decreasing or remaining stable?

• Can we get enough returning fish from outplants in the lakes to see natural production 

increase to levels needed for a self-sustaining population? 

• How is the hatchery program influencing abundance, productivity, and diversity of the 

natural populations? 

• Given regional temperature and precipitation patterns projected from climate models, 

how would potential changes in stream temperature and flows affect life-stage survivals 

and life-history characteristics for Snake River Sockeye Salmon?

6.3.1.3 Improve Sockeye Salmon passage to natal lakes

Improving fish passage throughout the Sockeye Salmon migration route and reestablishing access to 

historical spawning areas in natal lakes is a key recovery strategy. Improving habitat connectivity and 

allowing fish to occupy habitat over a wider landscape will improve ESU spatial distribution and reduce 

the risk of extinction due to catastrophic environmental events. This strategy is supported in 

conservation biology literature, which identifies reconnecting isolated habitat as the second most 

important element (after protecting and maintaining habitat) in a recovery strategy hierarchy of potential 

actions to improve salmon viability (Roni et al. 2002). Section 5 describes several limiting factors 

related to blocked access at different Sockeye Salmon life stages.

This strategy aims to improve Sockeye Salmon passage to the natal lakes by addressing passage barriers 

caused by artificial barriers, low stream flow, and other factors. It identifies actions to improve fish 

passage at the Sawtooth Hatchery weir on the Salmon River. It calls for actions to revise adult holding 

and handling practices at the Sawtooth Hatchery and Redfish Lake Creek trapping facilities to increase 

returns to Redfish, Pettit, and Alturas Lakes. The strategy also calls for actions to examine and address 

the lake trout management issue for Stanley Lake. Currently, an existing barrier on Stanley Lake Creek 

at the outlet of Stanley Lake prevents Sockeye Salmon migration into the lake; however, the barrier does 

not prevent lake trout in Stanley Lake from possibly moving to other tributaries and lakes in the basin. 

Any efforts to reintroduce Sockeye Salmon to Stanley Lake must include addressing the lake trout issue 

before the barrier can be removed. The strategy also aims to improve Sockeye Salmon passage survival 

in the Salmon and lower Snake Rivers, as well as Sockeye Salmon passage to Yellowbelly Lake.

Recovery strategy questions:

• How do we restore Sockeye Salmon migration to Stanley Lake without allowing lake 

trout movement to other tributaries and lakes in the basin?

• How do we prevent lake trout from spreading to other Sockeye Salmon natal lakes in the 

Sawtooth Valley?
ESA Recovery Plan: Snake River Sockeye Salmon | 221

June 2015| NOAA Fisheries 

• Under what migratory conditions (e.g., timing, water flows, temperatures) and how often 

can Sockeye Salmon currently migrate through the lag deposit boulder field at the outlet 

of Yellowbelly Lake?

• Are stream flows in the Salmon River above the Sawtooth Hatchery adequate to sustain 

migration of Sockeye Salmon to Alturas, Pettit and Yellowbelly Lakes during summer 

low flow conditions?

• How do SARs vary among lakes, years, natural vs. hatchery, and residual vs. anadromous 

Sockeye Salmon?

• Do high water temperatures in the lower Salmon and Snake Rivers affect upstream and 

downstream Sockeye Salmon survival and life-history characteristics?

• Is the mortality of adult returning anadromous Sockeye Salmon in the area between the 

upper Snake River basin and Lower Granite Dam related to natural causes (e.g., 

competition, predation, environmental conditions) or are extraneous causes involved?

• Are there local areas (hot spots) where mortality is concentrated during adult migration 

for anadromous Sockeye Salmon in the area between Lower Granite Dam and the upper 

Snake River basin, or are mortality rates uniform over the migration distance?

6.3.1.4 Reestablish a self-sustaining anadromous Sockeye Salmon population in Redfish Lake

Currently, Redfish Lake supports the only remaining substantial run of Snake River Sockeye Salmon. 

Our strategy aims to achieve viable, naturally spawning self-sustaining population(s) by increasing the 

number of anadromous adults that spawn naturally in Redfish Lake. 

The basis for the adaptive management strategy for Redfish Lake is laid out in detail in the Springfield 

Hatchery Master Plan and associated documents (IDFG 2010; ISRP 2011; IDFG 2013b). A key element 

of the approach to restoring natural production of Sockeye Salmon in the Sawtooth Valley is the 

adaptive management nature of the reintroduction strategy. Current plans are based on assumptions 

regarding a number of key factors including anticipated juvenile production relationships (productivity 

and density dependence) and survivals during migration and ocean rearing.

Phase 2 of the Snake River Sockeye Salmon natural stock reintroduction and adaptation program 

focuses efforts on securing the Redfish Lake population. During this recolonization phase, adequate and 

consistent returns of anadromous adults will allow managers to phase out the use of Redfish Lake 

captive broodstock and recolonize the naturally spawning Sockeye Salmon population in Redfish Lake. 

The existing captive broodstock program will transition to a new phase with an emphasis on supporting 

relatively high levels of anadromous return spawners to Redfish Lake using anadromous adults as 

broodstock. The path leading to long-term population viability will consist of a series of population 

status benchmarks, which if met will trigger the next level of recovery actions. For example, once the 

number of naturally produced fish in the population has stabilized to a certain level, measures will be 

taken to reduce the frequency of hatchery fish in the naturally spawning population. This staged 

approach to recovery is conceptually similar to the application of the sliding-scale hatchery management 

protocol already being implemented for other Snake River ESA-listed species. 
ESA Recovery Plan: Snake River Sockeye Salmon | 222

June 2015| NOAA Fisheries 

Recovery strategy questions:

• Can we get enough returning fish from outplants in Redfish Lake to see natural 

production increase to a level needed for a self-sustaining population of 1,000 naturalorigin spawners (Section 3.2.2. Biological Criteria)?

• What is the adult spawning carrying capacity for anadromous Sockeye Salmon in Redfish 

Lake? 

• Will the production of lake rearing parr and outmigrant smolts increase as the result of 

anadromous spawning in Redfish Lake? As natural-origin returns begins to contribute to 

spawning, are there indications of an increased pre-smolt per spawner rate relative to 

hatchery-origin fish?

• How does the lake’s juvenile carrying capacity affect pre-smolt per spawner production 

rates and abundance targets? How does it fit with recovery needs to address spatial 

structure and diversity needs?

• Has the Redfish Lake strategy been successful in preventing deleterious effects to the 

population from domestication, and has population productivity increased to a level 

where the dominant gene flow is moving from the natural population to the hatchery 

population?

Redfish Lake. Photo: Andy Kohler, Shoshone-Bannock Tribes.
ESA Recovery Plan: Snake River Sockeye Salmon | 223

June 2015| NOAA Fisheries 

6.3.1.5 Investigate and develop strategies for future actions to support Sawtooth Valley Sockeye Salmon

reintroduction and adaptation phases for Pettit Lake

The ultimate objective of the Snake River Sockeye Salmon Recovery Plan is the restoration of natural 

Sockeye Salmon populations in Sawtooth Valley lakes. An important first step toward that objective has 

been the successful establishment of anadromous returns originating from natural-origin Redfish Lake 

stock amplified through a captive broodstock program. That program is poised to transition to a second 

phase with an emphasis on supporting relatively high levels of anadromous return spawners in Redfish 

Lake. The working hypothesis behind this approach assumes that the introduction of increasing 

numbers of hatchery-origin spawners in Redfish Lake will result in increasing natural production of 

outmigrant smolts. Inherent in that hypothesis is an assumption that the smolt production capacity of 

Redfish Lake is sufficient to achieve natural-origin return targets. Those smolts will produce adult 

natural-origin returns that, if downstream and upstream survivals are sufficient, should allow for 

transition to a third phase emphasizing natural adaptation (local adaptation phase). As natural-origin 

returns increase in this phase, hatchery-origin returns would be reduced by reducing the number of 

released smolts.

The fact that there are multiple lakes in the Sawtooth Valley that historically supported anadromous 

Sockeye Salmon affords an opportunity to diversify the reintroduction strategy to promote the chances 

of sustainable natural production. The Snake River Sockeye Salmon Technical Committee that guided 

development of this Recovery Plan has worked together with NMFS’ scientists to develop the following 

strategy for the initial reintroduction phase for Pettit Lake, which is intended to complement the Redfish 

Lake strategy (described in Section 6.3.1.4).

The following proposed interim strategy for reintroductions to Pettit Lake will be further developed and 

refined as the Redfish Lake strategy is implemented. The Recovery Plan’s Implementation and Science 

Team, which will guide future Sockeye Salmon recovery reintroductions to Pettit Lake, will update this 

proposed interim strategy over time. 

1. Allow anadromous adults to return to Pettit Lake for volitional migration and spawning. Adults 

trapped at Sawtooth Fish Hatchery weir can be transported to their lake of origin and released, or 

passed over the weir and allowed to migrate. Anadromous adults trapped at the Sawtooth 

Hatchery weir may represent an important component of the proposed release strategy (e.g., of 

Pettit Lake origin). 

2. Release captive broodstock adults into Pettit Lake that represent the entire genetic diversity of 

the broodstock for several years. 

3. After several years of direct outplanting of adults sourced from the Redfish Lake population, 

adult stocking would cease to allow for evaluation of the natural production response; continue 

to allow anadromous adults originating from Pettit Lake to return to Pettit Lake for volitional 

spawning. 

4. Evaluation of the results of this reintroduction program will guide the future course of the Pettit 

Lake Sockeye Salmon program. Monitoring data will include relative trends in anadromous and 
ESA Recovery Plan: Snake River Sockeye Salmon | 224

June 2015| NOAA Fisheries 

resident production in Pettit Lake, as well as data that show whether hatchery inputs from the 

Redfish Lake stock are successful at increasing natural-origin production. Based on the results 

of this evaluation, the future action plan for Pettit Lake would be determined. Contingencies 

could include increasing Pettit Lake natural-origin returns without additional supplementation, 

using some Pettit Lake natural-origin returns to establish a broodstock to increase the rate of 

production, or using available hatchery returns from the Redfish Lake stock program to augment 

production. Sockeye Salmon could be added t in future years or not added based on the results

of future reintroduction strategies. 

5. A key step in the progression towards naturally adapted anadromous production from Pettit Lake 

will be the restoration of access to the lake for returning adults. Options for improving Sockeye 

Salmon passage to natal lakes above the Sawtooth Hatchery weir are being investigated and 

strategies are described in Section 6.3.1.3. 

Recovery Strategy Questions:

• Will the resident component (residual Sockeye Salmon and non-native kokanee) in Pettit 

Lake persist over time after stocking of adult Redfish Lake anadromous broodstock ends? 

• Will anadromous Sockeye Salmon intermingle and spawn with resident Sockeye Salmon

on the spawning grounds, and does this affect the presence and magnitude of anadromy 

in the Pettit Lake population over time? 

• What are the smolt-to-adult returns (SARs) of Pettit Lake outmigrants and are there 

systematic differences in production from anadromous vs. resident parents? 

• Will the production of outmigrant smolts increase as a result of returning adult Sockeye 

Salmon spawning in Pettit Lake?

• As pre-smolt production increases, is there evidence of density dependent limitations?

• How do zooplankton populations respond to potential shifts in grazing pressures as the 

proportion of fish with anadromous and resident life histories changes? How sensitive 

are zooplankton production dynamics in Pettit Lake to the size composition of O. nerka 

(e.g., is zooplankton biomass and species composition primarily influenced by the density 

of larger O. nerka)?

• How does lake productivity respond to external out-of-basin inputs of salmon derived 

nutrients?

• What is the adult spawning carrying capacity for anadromous Sockeye Salmon in Pettit 

Lake?
ESA Recovery Plan: Snake River Sockeye Salmon | 225

June 2015| NOAA Fisheries 

Pettit Lake. Photo: Andy Kohler, Shoshone-Bannock Tribes.

6.3.1.6 Investigate and evaluate the potential for restoring natural production of anadromous Sockeye 

Salmon from returning kokanee outmigrants from Alturas Lake. 

Alturas Lake currently supports a kokanee population. This early stream spawning type is similar to the 

Fishhook Creek kokanee population and different from the Redfish Lake late shoal spawning 

population. Accounts indicate that the lake once also supported Sockeye Salmon. Evermann observed 

stream spawning Sockeye Salmon in 1895 and 1896. He left the lake in both years before shoal 

spawning would have been underway, but did observe one pair of Sockeye Salmon on an Alturas Lake 

shoal as he was preparing to leave in 1895 (Evermann 1896). Since maintaining spatial structure, 

diversity, and capturing the benefits of local adaptation are critically important, careful steps will be 

taken to identify appropriate strategies for Alturas Lake anadromous Sockeye Salmon recovery efforts. 

Alternative strategies for the early-spawning Alturas Lake kokanee population might include the 

following options, beginning with No. 1 below, with the option to subsequently implement No. 2 and/or 

No. 3 at the same time or later. These options need to be refined in the future and the Sockeye Salmon

Implementation and Science Team and Stanley Basin Sockeye Technical Oversight Committee 

(SBSTOC) will make future reintroduction recommendations. 

1. Trap and transport any anadromous adults identified as Alturas Lake kokanee to Alturas Lake. 

Release the trapped ocean returning adults for volitional spawning. Radio telemetry should be 
ESA Recovery Plan: Snake River Sockeye Salmon | 226

June 2015| NOAA Fisheries 

considered as one means to identify spawning locations. Following the completion of the 

Sockeye Salmon juvenile rearing responsibilities at the Sawtooth Hatchery (tentatively June, 

2015), managers can consider allowing Alturas Lake-destined anadromous adults to volitionally 

migrate. If the lake of origin cannot be determined in a timely fashion, unmarked adults should 

be passed above the Sawtooth weir and allowed to volitionally migrate. 

2. Trap and transport any ocean returning adults identified as Alturas Lake kokanee to the IDFG 

Eagle Fish Hatchery for holding and spawning to establish a new hatchery program for Alturas 

Lake anadromous Sockeye Salmon, or transport ocean returning adults to Alturas Lake for 

volitional spawning. For the hatchery program, following spawning at the IDFG Eagle Fish 

Hatchery, the eggs and juveniles would be reared at the new Springfield Hatchery to the smolt 

stage. At the appropriate time, these smolts can be transported to and released into the outlet of 

Alturas Lake. Sufficient number of juveniles would be marked (genetic marks and PIT-tags) to 

facilitate the collection of life history information and to ensure that adults produced in the 

Alturas Lake hatchery program can be identified. If insufficient adults of both sexes are not 

available for effective artificial spawning, then adults would be transferred and released into 

Alturas Lake. One variation on this option would be to incorporate maturing, resident Alturas 

Lake kokanee in the spawning design along with ocean returning residual Alturas adults trapped 

at the Sawtooth weir. Juvenile outmigration and adult return success could be independently 

evaluated for progeny and F1 returning adults produced from anadromous or resident parents.

3. Establish a full-term captive broodstock to help amplify Alturas Lake O. nerka components 

(similar to Redfish Lake program). Follow guidelines for “2” above except, at smoltification, 

continue to rear fish to maturity in a captive broodstock facility. At this point, options include 

transferring all or a portion of maturing adults to Alturas Lake for release. Or, holding all or a 

portion of maturing adults for spawning at the hatchery. A portion of adults released to 

volitionally spawn could be fitted with radio transmitters to facilitate tracking and the 

identification of spawning locations. If adults are retained in the hatchery for spawning, eyedeggs should, preferably, be transferred to the IDFG Springfield Hatchery for final incubation and 

rearing through the smolt stage of development. Second generation smolts would be released in 

the outlet of Alturas Lake at an appropriate time.

In the interim while decisions are being made regarding anadromous Alturas Lake Sockeye Salmon

recovery efforts, any ocean returning Sockeye Salmon identified as of Alturas Lake origin will be 

transported to Alturas Lake and released.

Recovery strategy questions:

• What are the benefits and/or risks of alternative strategies for recovering the extant and/or 

historical life-history pattern in Alturas Lake? 

• What stock, or combination of stocks, is most appropriate for reintroduction into Alturas 

Lake?
ESA Recovery Plan: Snake River Sockeye Salmon | 227

June 2015| NOAA Fisheries 

• What strategy or combination of strategies should be used for reintroduction into Alturas 

Lake to achieve abundance goals of 1,000 natural-origin spawners (Section 3.2.2 

Biological Criteria)?

• What are the uncertainties or key assumptions that need to be addressed?

• Will the proposed actions listed above influence (e.g., establish) a residual life history 

strategy in Alturas Lake (not previously observed)?

• Will the production of lake rearing parr and outmigrant smolts increase as the result of 

anadromous spawning in Alturas Lake?

• As pre-smolt production increases, is there evidence of density dependent limitations?

• What are smolt-to-adult returns of Alturas Lake outmigrants and are there systematic 

differences for production from anadromous vs. resident parents?

• How do zooplankton populations respond to potential shifts in grazing pressures as the 

proportion of fish with anadromous life histories changes? How sensitive are 

zooplankton production dynamics in Alturas Lake?

• How does lake productivity respond to external out-of-basin inputs of salmon derived 

nutrients?

• What is the adult spawning carrying capacity for anadromous Sockeye Salmon in Alturas 

Lake?

Alturas Lake. Photo: Andy Kohler, Shoshone-Bannock Tribes.
ESA Recovery Plan: Snake River Sockeye Salmon | 228

June 2015| NOAA Fisheries 

6.3.1.7 As sufficient numbers of natural-origin adults return, develop an integrated approach to manage 

natural- and hatchery-origin adults in the hatchery program and in the wild

In its last phase, Phase 3, the Sockeye Salmon recovery strategy will be adapted to transition to an 

appropriate longer-term role consistent with maintaining genetic variability and limiting domestication. 

In this phase, the program will move toward the development of an integrated program. The Columbia 

River Hatchery Scientific Review Group considers a hatchery program to be an integrated program 

when the intent is for the natural environment to drive the adaptation and fitness of a composite 

population of fish that spawns both in a hatchery and in the wild (HSRG 2004). The approach centers on 

meeting the proportionate natural influence (PNI) criteria established by the Hatchery Scientific Review 

Group. 

During Phase 3, the hatchery program for Redfish Lake Sockeye Salmon will be converted into an 

integrated conservation program using broodstock returning to Redfish Lake. The program has three 

objectives in this phase: protecting the genetic resources of Snake River Sockeye Salmon, developing a 

composite hatchery and natural population in Redfish Lake that is locally adapted to the environmental 

conditions, and providing surplus adult hatchery fish to Pettit Lake to support initial Sockeye Salmon

recovery. The Plan includes using research, monitoring, and evaluation to assess the effectiveness and 

outcomes of the program, and trigger movement to the next phase of program implementation. 

We recognize that the overall program assumes that the fitness of the natural populations can be 

improved by restoring Sockeye Salmon to their native habitat and by following the Hatchery Scientific 

Review Group guidelines for integrated hatchery programs. Continued research is needed to track these 

and other assumptions and fill critical data gaps. These needs are further discussed in Section 6.4, Key 

Information Needs and in Section 11, Research, monitoring, and evaluation for Adaptive Management. 

Recovery strategy questions:

• Are we getting enough returning fish from outplants in the lake(s) to see natural 

production increase to the level needed for a self-sustaining Sockeye Salmon population?

• Will managing the proportion of hatchery-origin spawners on the spawning grounds 

improve population fitness?

• Is the status of each population trending toward the recovery criteria?

6.3.1.8 As sufficient numbers of hatchery-origin anadromous adults return to the basin, identify options 

for future fisheries

As the Sockeye Salmon recovery program transitions from the re-colonization phase into the local 

adaptation phase, the return of first generation adults is expected to generate large returns of anadromous 

hatchery-origin Sockeye Salmon to the Sawtooth Valley. These returns will be beyond levels needed to 

effectively manage broodstock composition, as well as spawner composition in the habitat. The natural 

production that will result from these high levels of anadromous hatchery returns is expected to lead to 

increases in relative productivity and overall life cycle survival. Resource managers will adaptively 

adjust the number of smolts released to help manage returning numbers of fish, yet having the added 
ESA Recovery Plan: Snake River Sockeye Salmon | 229

June 2015| NOAA Fisheries 

flexibility to use harvest as a tool will likely be needed. Future actions will include identifying options 

for potential state and tribal fisheries on Snake River Sockeye Salmon. 

Fisheries affecting Snake River Sockeye Salmon have been closed or severely constrained for decades. 

With the Springfield Hatchery coming online smolt production will increase fivefold over the next two 

or three years. Careful management of the resulting returns will provide the opportunity to accelerate the 

rebuilding process toward recovery. At some point in the rebuilding continuum it may be appropriate to 

relax current harvest constraints to provide access to otherwise harvestable fish. A new abundancebased harvest management strategy should be developed that relies on pertinent benchmarks related to 

species status in the Recovery Plan and calibrates varying harvest levels in such a way that it does not 

impede recovery.

Recovery strategy questions:

• Should harvest in the Snake basin be used as an action to reduce the number of Sockeye 

Salmon hatchery fish in the naturally spawning population?

• What is the annual incidental harvest rate on natural-origin Snake River Sockeye Salmon

that occurs outside the ESU?

• What is the annual incidental harvest rate that occurs on natural-origin Snake River 

Sockeye Salmon within the ESU?

• What is the cumulative incidental harvest rate on natural-origin Snake River Sockeye 

Salmon due to all fisheries (from within and outside of ESU)?

• What effect does total incidental harvest have on the abundance, productivity, and 

diversity of natural-origin Snake River Sockeye Salmon?

6.3.1.9 Continue research and actions to reestablish natural populations in other natal lakes

Snake River Sockeye Salmon rear in their natal lakes for one to three years. Protecting existing good 

quality habitat in Redfish, Pettit, and Alturas Lakes will benefit the spawning and rearing life stages. 

NMFS supports the ICTRT’s recommendation that the long-term recovery scenario should include 

restoring at least two of the three historical lake populations in the ESU to highly viable, and one to 

viable status, using Redfish Lake, Alturas Lake, and Pettit Lake. As recovery efforts progress over time, 

managers will consider reintroducing anadromous Sockeye Salmon into other natal lakes.

The Snake River Sockeye Salmon recovery scenario includes potential Sockeye Salmon reintroductions 

to Stanley and Yellowbelly Lakes. Currently, more information and consideration is needed to 

determine the potential benefits and risks associated with reintroduction to Stanley Lake. As discussed 

previously, efforts to reintroduce Sockeye Salmon to Stanley Lake must include developing a lake trout 

management strategy and removing the existing barrier on Stanley Lake Creek, at the outlet of Stanley 

Lake, which currently prevents Sockeye Salmon immigration. This is the only remaining artificial 

barrier to a natal lake in the Sawtooth Valley. 
ESA Recovery Plan: Snake River Sockeye Salmon | 230

June 2015| NOAA Fisheries 

Currently, stocking Sockeye Salmon in Yellowbelly Lake is not a priority. This may change as adult 

returns increase and passage to the upper Salmon River basin is restored. It is likely that Sockeye 

Salmon may return to Yellowbelly Lake through straying and natural recolonization by either early 

stream spawners (Alturas stock) and/or late shoal spawners (Redfish and Pettit stock). 

Recovery strategy questions:

• What is the carrying capacity of Stanley Lake for juveniles and spawning adults?

• How much zooplankton is available to support juvenile rearing and survival?

• Will the production of lake rearing parr and outmigrant smolts increase as the result of 

anadromous spawning in Stanley Lake?

• How much spawning habitat is available in lakes and streams not currently used by 

anadromous Sockeye Salmon?

• What spawning areas will be important as fish abundance recovers? 

• What will be the role of beach vs. stream spawning types?

• Will competition for food resources or spawning areas restrict efforts to reestablish 

natural Sockeye Salmon populations in the lakes?

• How should lake trout be managed in Stanley Lake?

• How do we reestablish a Sockeye Salmon population in Stanley Lake without 

encouraging lake trout movement to other tributaries and lakes in the basin?

6.3.1.10 Continue research on natal lakes’ carrying capacity, nutrients, and ecology

This strategy addresses the continuing need to understand the limnological characteristics of the 

Sawtooth Valley lakes and a lake’s relative carrying capacity for Sockeye Salmon production. The 

strategy builds upon the important research carried out for many years by the Shoshone-Bannock Tribes 

regarding assessing the period and frequency of lake stratification and subsequent turnover, together 

with research on lake algal productivity.

The carrying capacity of the natal lakes is often density dependent and linked to zooplankton levels. 

Changes in zooplankton levels in the lakes have contributed to the decline of Sockeye Salmon

production in the lakes (Selbie et al. 2007). Low zooplankton densities can restrict growth rates and, 

ultimately, the ability of Sockeye Salmon to achieve a level of fitness needed to survive the long 

migration to the ocean from their nursery lakes. Reductions in the lakes’ zooplankton communities 

developed after the Sockeye Salmon population declined and other fish (trout, non-native kokanee) were 

introduced. 

The Shoshone-Bannock Tribes have carried out nutrient supplementation to increase carrying capacity 

in Redfish, Pettit, and Alturas Lakes. Nutrient supplementation of the lakes may be creating short-term 

growth benefiting the lake-dwelling fish. Ongoing studies of lake water quality seek to determine the 

current characteristics and carrying capacity of the lakes.
ESA Recovery Plan: Snake River Sockeye Salmon | 231

June 2015| NOAA Fisheries 

Recovery strategy questions:

• What can be derived from limnological monitoring data regarding potential for juvenile 

anadromous Sockeye Salmon growth and survival in the different natal lakes?

• What is the carrying capacity of the different natal lakes? 

• Is nutrient supplementation increasing carrying capacity in the lakes?

• Will competition with kokanee for food resources or spawning areas restrict efforts to 

reestablish natural Sockeye Salmon populations in the natal lakes?

• Develop a time-table strategy for a whole-lake nutrification efforts compatible with 

reintroduction plans.

6.3.1.11 Protect and conserve natural ecological processes at the watershed scale that support 

population viability 

This recovery strategy is founded on the concepts presented in several salmonid habitat recovery 

planning documents and scientific studies (e.g., Beechie and Boulton 1999; Roni et al. 2002; Beechie et 

al. 2003; Roni et al. 2005; Stanley et al. 2005; Isaak et al. 2007; Roni et al. 2008; Beechie et al. 2010). 

These studies demonstrate that habitat conditions and aquatic ecosystems function are a result of the 

interaction between watershed controls (such as geology and climate), watershed processes (such as 

hydrology and sediment transport), and land use. Scientists and resource managers recognize that 

restoration planning that carefully integrates watershed or ecosystem processes is more likely to be 

successful at restoring depleted salmonid populations (Beechie et al. 2003). 

Actions to protect and improve watershed processes to support Snake River Sockeye Salmon viability 

play a key role in Sockeye Salmon recovery. Since much of the area surrounding the lakes is already 

designated as wilderness and in near pristine condition, the strategy focuses on maintaining current 

protection and consistently applying best management practices and existing laws to protect and 

conserve natural ecological processes. The strategy also supports protection and conservation through 

land acquisition and purchase of conservation easements, and actions that improve public understanding 

and support through education. 

The recovery strategy also addresses potential disturbance to biological processes that could be 

associated with movement of lake trout from Stanley Lake to areas in the Salmon River and other natal 

lakes. 

Recovery strategy questions:

• What is the risk that wildfire will have negative effects on sockeye habitat in historic 

natal lakes and their inlet/outlet streams? 

6.3.1.12 Protect, restore and manage spawning and rearing habitat

Protecting existing high quality habitat and restoring damaged habitat will specifically benefit Snake 

River Sockeye Salmon in the spawning and rearing life stages. Improved spawning and rearing means 
ESA Recovery Plan: Snake River Sockeye Salmon | 232

June 2015| NOAA Fisheries 

that more fish will reproduce, more juveniles will survive to migrate, and consequently more adults will 

return to the Sawtooth Valley. 

The strategy includes maintaining current wilderness protection in the natal lakes watersheds in the 

Sawtooth National Recreation Area, conserving rare and unique habitats, addressing water quality 

concerns, and consistently applying best management practices and existing laws to protect and improve 

habitat conditions. It supports land acquisition and purchase of conservation easements to protect 

habitats. The strategy also directs actions to determine if spawning and rearing habitat at the different 

lakes is adequate to meet Sockeye Salmon abundance goals, and to learn more about the potential roles 

of beach vs. stream spawners in reaching viability. 

Recovery strategy questions:

• What is the spawning capacity of the natal lakes? 

• What habitat areas will be important as fish abundance recovers? 

• What will be the role of beach vs. stream spawning types?

6.3.1.13 Maintain unimpaired water quality and improve water quality as needed

Limnology studies have been conducted in Stanley, Redfish, Yellowbelly, Pettit, and Alturas Lakes since 

1991. The studies have examined water temperature, oxygen, light, chlorophyll, phytoplankton, and 

zooplankton in each lake from May through October. Generally, the results from limnological sampling 

indicate that water quality in all five lakes provides suitable rearing habitat for juvenile Sockeye Salmon, 

although the lakes vary considerably in the species composition and abundance of zooplankton. 

The limnology studies show that surface water temperatures can reach 18°C (64°F) in all lakes during 

summer months (Griswold et al. 2011a). The effects of temporary surface water temperature spikes 

above 15°C (59°F) on Sockeye Salmon generally depend on exposure time. The effects may be minimal, 

particularly if the Sockeye Salmon can escape to deeper waters or to areas where groundwater inflow or 

shade reduce temperatures. However, in some cases, high water temperatures may make Sockeye 

Salmon more susceptible to disease and infection or promote fungal, bacterial or secondary wound 

infections that leave the Sockeye Salmon more susceptible to pre-spawning mortality (USBR 2007).

Where unimpaired, protecting and maintaining current water quality of the lakes, tributary streams and 

Salmon River are essential to providing suitable spawning and rearing habitat for Sockeye Salmon. Where 

elevated water temperatures have been identified, or other water quality standards are not being attained, this 

strategy promotes the use of best management practices, improved land use strategies, designation of 

minimum instream flows, and habitat restoration to address elevated water temperatures, and impaired 

sediment processes.

Recreational use at the lakes and along the Salmon River poses potential concerns to water quality. Access 

roads and recreational use on shores and waterways can increase sediment input, or result in a potential 
ESA Recovery Plan: Snake River Sockeye Salmon | 233

June 2015| NOAA Fisheries 

chemical spill. The strategy calls for continued management of recreational use and motorized boat activity to 

minimize these risks.

Recovery strategy questions:

• Do temporary surface water temperature spikes affect Sockeye Salmon carrying capacity 

in the different lakes? 

• Do reduced streamflows and high water temperatures in the lower Salmon and Snake 

Rivers affect upstream Sockeye Salmon survival?

6.3.1.14 Investigate and improve conditions in Salmon River and tributaries to support increased survival 

of migrating Snake River Sockeye Salmon

Protecting and restoring the migration corridor for Snake River Sockeye Salmon will require efforts on 

public and private lands in the lower Snake River mainstem above Lower Granite Dam and in the 

mainstem Salmon River. Currently, the stretch of the Salmon River from Redfish Creek to Valley Creek 

is listed on IDEQ’s 2010 303(d) list as not supporting the beneficial use “cold water aquatic life.” The 

pollutants are identified as water temperature and sediment/siltation. 

High water temperatures in the Salmon River impact migrating Snake River Sockeye Salmon. Adult 

Sockeye Salmon usually arrive in the Salmon River during baseflow conditions when water 

temperatures are highest. Adult Sockeye Salmon migration survival is inversely related to water 

temperature. High water temperatures may also limit survival of migrating Sockeye Salmon in the 

lower Snake River above Lower Granite Dam. Low flows in some years also affect juvenile Sockeye 

Salmon that migrate down the Salmon River in early summer. High temperatures can also affect fish in 

localized reaches, especially where temperatures are at or near their thermal tolerance levels, and 

increase susceptibility to predators and pathogens. 

Actions under this strategy are designed to improve water quantity and quality to support juvenile and 

adult migrations, with an emphasis on addressing flow, high summer temperature and sediment load 

concerns in the upper reaches of the mainstem Salmon River and mainstem lower Snake River. They 

are also designed to gain needed information on the magnitude of Sockeye Salmon mortality in the 

Salmon River, as well as determining where and why mortality is occurring. 

Recovery strategy questions:

• Do fluctuations in flows and water temperatures reduce Sockeye Salmon survival in the 

Salmon River? 

• What role do water diversions on the mainstem Salmon River and tributaries above the 

Sawtooth Hatchery contribute to elevated water temperatures and reduced fish passage 

and rearing habitat in the Salmon River?
ESA Recovery Plan: Snake River Sockeye Salmon | 234

June 2015| NOAA Fisheries 

6.3.1.15 Monitor for predation, disease, aquatic invasive species and competition and develop actions as 

needed

This strategy supports current state, Federal and tribal programs to monitor and control non-native fish, 

wildlife and aquatic species in the Sawtooth Valley and upper Salmon River mainstem that prey, 

compete, transmit diseases or otherwise reduce the productivity of Snake River Sockeye Salmon. 

Predation and disease

Several fish species occupy the natal lakes that potentially prey on Sockeye Salmon, including bull trout, 

northern pikeminnow, and brook trout. Sockeye Salmon may also experience predation from 

smallmouth bass, northern pikeminnow and other fish species while migrating through the Salmon 

River. The non-native fish may reduce Sockeye Salmon survival by preying on juvenile Sockeye 

Salmon and/or Sockeye Salmon eggs, or introducing disease. 

Aquatic invasive species

Invasive species are often harmful non-native plants, animals, and pathogens that could negatively 

impact Sockeye Salmon recovery. To date, no zebra and quagga mussels, Eurasian water Milfoil, and 

Chytrid fungus have been detected in the Sawtooth National Recreation Area. New Zealand mud snails 

have only been found in a small pond on private property near Squaw Creek. Whirling disease was 

detected in the headwaters of Alturas Lake Creek. The Idaho Department of Agriculture coordinates 

activities across the state to prevent aquatic species infestations by working with state and Federal

agencies, local governments and non-governmental organizations. The greatest risk of aquatic species 

infestations to the upper Salmon region comes from boats launching in Redfish, Alturas, Stanley, and 

Pettit Lakes; floatboaters on the Salmon River, and public fishing. Since 2009, the Sawtooth National 

Forest has worked with the Idaho Department of Agriculture to maintain a seasonal boat inspection 

station at the Redfish Lake Sandy Beach boat ramp. It is critically important that these efforts be 

maintained to prevent introduction of highly invasive aquatic species, such as quagga and zebra mussels. 

Competition

Competition with planted trout and kokanee for limited food supplies in the Sawtooth Valley lakes could 

potentially reduce Sockeye Salmon productivity. Brook trout, for example, can aggressively defend 

feeding territories and may outcompete juvenile Sockeye Salmon. Much remains unknown regarding 

the competitive effects of kokanee and Sockeye Salmon within the lakes. Redfish and Alturas Lakes 

contain native kokanee. Kokanee are also native to Pettit Lake; however, genetic analyses indicate that 

the native kokanee population in this lake may have been replaced by non-native kokanee introduced 

from northern Idaho. Efforts to control the kokanee populations and reduce competition with Sockeye 

Salmon are restricted because native kokanee are currently allowed to exist within the lakes without 

active control measures. A fishery exists to passively control the kokanee populations. Information 

about carrying capacity within the lakes and future evaluations regarding biomass (trawl, hydroacoustics coupled with genetic analyses to determine composition of the two forms) will help determine 

overall competition between the forms and appropriate management actions. 
ESA Recovery Plan: Snake River Sockeye Salmon | 235

June 2015| NOAA Fisheries 

Recovery strategy questions:

• Do juvenile Sockeye Salmon compete with kokanee in oligotrophic lakes? 

• Do we need to manage the kokanee population to make room for Sockeye Salmon

recovery?

• Will competition for food resources or spawning areas restrict efforts to reestablish 

natural Sockeye Salmon populations in the natal lakes?

• What habitat areas will be important as fish abundance recovers? 

• To what degree do juvenile Sockeye Salmon compete with other fish besides Sockeye 

Salmon in Sawtooth Valley lakes and how does this affect O. nerka carrying capacity 

estimates in each lake? Are additional watercraft inspection stations needed to protect 

lakes and streams from aquatic invasive species? If yes, where should they be located?

6.3.1.16 Create an adaptive management feedback loop to track progress toward achieving recovery 

goals, monitor and evaluate key information needs, assess information, and refine strategies and actions

Adaptive management will play a key role in the reintroduction strategy to restore natural production of 

Sockeye Salmon in the Sawtooth Valley. Current plans are based on assumptions regarding a number of 

key factors including anticipated juvenile production relationships and survivals during migration and 

ocean rearing. 

Successful implementation of the strategy requires a process to track progress, define weaknesses and 

adjust course appropriately. Section 11 describes research, monitoring evaluation to support adaptive 

management for the recovery of the Snake River Sockeye Salmon ESU. Section 10 describes a proposed 

framework for coordinated implementation of this Plan. It describes the key implementation teams that 

are part of this framework, including the Snake River Sockeye Salmon Implementation and Science 

Team, which will be responsible for coordinating implementation of the Adaptive Management and 

Research, monitoring, and evaluation Plan. 

NMFS will work with the Snake River Sockeye Salmon Implementation and Science Team and others 

to prioritize the key information needs identified in Section 6.4. It will also seek resources and form 

partnerships to address the key information needs during recovery plan implementation.

6.3.2 Strategies to Recover Snake River Sockeye Salmon at the Regional Level 

(Migration Corridor in the Mainstem Salmon, Snake, and Columbia Rivers; Estuary; 

Plume; and Ocean)

Sections 6.3.2.1 through 6.3.2.11 describe regional-level elements of the recovery strategy to improve 

Snake River Sockeye Salmon viability.
ESA Recovery Plan: Snake River Sockeye Salmon | 236

June 2015| NOAA Fisheries 

6.3.2.1 Implement the FCRPS BiOp’s Reasonable and Prudent Alternative to reduce mortality associated 

with migration through the mainstem Salmon, Snake, and Columbia Rivers, estuary and plume

Mainstem Salmon River 

Both juvenile and adult Sockeye Salmon are lost in the 462-mile Salmon River migration corridor 

between the natal lakes and Lower Granite Dam. While the factors responsible for the losses are not 

fully understood, they are believed to be influenced by stream flow, temperature, and predation. Adult 

Sockeye Salmon are often exposed to low flows and elevated water temperatures in the Salmon River, 

usually arriving in the river during baseflow conditions when water temperatures are highest. Juvenile 

Sockeye Salmon can also be affected by low flows; especially during dry years when irrigation 

withdraws can reduce streamflow in the Salmon River by early May, slowing migration rates for 

downstream migrating juvenile Sockeye Salmon and increasing exposure to predators and pathogens. 

Although the 2008/2010 FCRPS BiOp RPA as modified by the 2014 FCRPS Supplemental BiOp 

(hereafter ‘FCRPS RPA’) does not require the Action Agencies to increase habitat quality or survival 

for Snake River Sockeye Salmon through tributary habitat improvements, it does identify water 

transactions in the mainstem Salmon River to improve conditions for Snake River spring/summer 

Chinook salmon and steelhead. These actions will likely also improve the survival of adult migrant 

Sockeye Salmon returning to the Sawtooth Valley in July and August. Examples are projects in Pole 

Creek, Fourth of July Creek, Alturas Lake Creek, Beaver Creek, and the Salmon River. Improving flows 

in this area during late summer is likely to improve water temperature by increasing in-stream flow 

volume and velocity in this part of the adult Sockeye Salmon migration corridor.

Under the ESA, the Action Agencies are required to ensure that their actions are not likely to jeopardize 

the continued existence of listed salmon or adversely modify critical habitat, and that they seek NMFS’ 

opinion in the course of doing so. NMFS summarizes its findings in a Biological Opinion, or BiOp. 

The Biological Opinion issued on May 5, 2008 (NMFS 2008c), and supplemented on May 20, 2010

(NMFS 2010b) and on January 17, 2014 (NMFS 2014c), governs how the Columbia and Snake River 

mainstem dams (and upstream water storage facilities) are operated and configured through 2018. 

These documents are available at: http://www.nwr.noaa.gov/Salmon-Hydropower/Columbia-SnakeBasin/Final-BOs.cfm.

The FCRPS RPA includes hydro, habitat, hatchery, harvest and predation measures to address the 

biological needs of salmon and steelhead in every life stage within human control. The FCRPS RPA is 

the product of collaboration between NMFS, the Action Agencies, and the regional state and tribal 

sovereigns as ordered by the District Court. It is based on a comprehensive analysis of the salmon life 

cycle. The “Reasonable and Prudent Alternative Table” in the 2008 FCRPS Biological Opinion, as 

amended by the 2010 Supplemental FCRPS Biological Opinion and modified by the 2014 Supplemental 

FCRPS Biological Opinion, describes actions that NMFS expects will positively affect the viability of 

the Snake River Sockeye Salmon ESU.

The recovery strategy also proposes a number of actions to improve Snake River Sockeye Salmon

viability by addressing the effects of Columbia and Snake River hydro operations. The proposed actions 
ESA Recovery Plan: Snake River Sockeye Salmon | 237

June 2015| NOAA Fisheries 

include those summarized in the FCRPS Biological Opinion (NMFS 2008c) and the Hydro Module 

(NMFS 2014c). The actions are designed to improve juvenile and adult fish passage and to reduce 

predation. The release of cool water from Dworshak Dam to reduce lower Snake River temperatures per 

FCRPS RPA Action 4 is an example of such actions. Additional survival improvements may also result 

through the ongoing FCRPS adaptive management process. Amendments added to the FCRPS Adaptive 

Management Implementation Plan through the 2010 Supplemental BiOp and a new study implemented 

through the 2008 BiOp’s adaptive management approach are addressing the high fish ladder 

temperatures at Lower Granite Dam in 2013 that temporarily blocked Sockeye Salmon passage. Shortterm and longer-term measures adopted through these processes should substantially reduce, if not 

eliminate, the likelihood of future blocked passage at the project.

Lower Columbia River Estuary, Plume, and Ocean

As described in NMFS’ Estuary Module (2011a), habitat conditions in the Columbia River estuary are 

considerably degraded and those in the plume are altered compared to 200 years ago. In terms of

absolute size, the estuary tidal prism is about 20% smaller than it was when Lewis and Clark camped 

along the lower Columbia. This reduction in estuary size is due mostly to dike-and-fill practices used to 

convert the floodplain to agricultural, industrial, commercial, and residential uses. Spring flows entering 

the estuary have decreased 44% and the annual timing, magnitude, and duration of flows have also 

changed. The changes are attributed to hydrosystem regulation; water withdrawal for agricultural, 

municipal, and industrial purposes; and climate fluctuations. Further alterations in flow are likely to 

occur during the next century as a result of climate change, the effects of which are expected to include 

more precipitation falling as rain rather than snow. In the estuary this is likely to result in higher peak 

flows and reduced late-summer/early-fall stream flows (ISAB 2007).

Historically, vegetated wetlands within the floodplain supplied the estuary with its base-level food 

source: macrodetritus. The changes in flow volume and timing and the separation of the river from its 

floodplain by dikes and levees have altered the food web by reducing macrodetrital inputs (Bottom et al. 

2005). In addition, access to and use of floodplain habitats by juveniles that rear in the estuary have been 

compromised through alterations in the presence of and access to these critical habitats. 

At the same time, upstream dams have prevented sediments from entering the estuary, while dredging 

activities have exported sand and gravel out of the estuary. Studies have shown that sand is exported 

from the estuary at a rate three times higher than that at which it enters the estuary. The full impact of 

these changes is unknown; however, sediment transport is a primary habitat-shaping force that 

determines the type, location, and availability of habitats distributed in the estuary. In addition, 

decreases in suspended sediments have improved water clarity which increases the effectiveness of 

predators that consume juvenile and adult salmon and steelhead. 

The Estuary Module (NMFS 2011a) identifies 23 management actions to improve the survival of salmon 

and steelhead migrating through and rearing in the estuary and plume environments. These address 

changes in flow, habitat quality and availability, water quality, and prey resources. The BPA and Corps’ 
ESA Recovery Plan: Snake River Sockeye Salmon | 238

June 2015| NOAA Fisheries 

estuary restoration strategy is described in the Columbia Estuary Ecosystem Restoration Program 2012 

Strategy Report (BPA and USACE 2012).

The FCRPS Action Agencies are reconnecting tidal influence through breaching dikes and levees and 

replacing culverts, bridges, and tidegates, enhancing the quantity and quality of tidal channels, removing 

invasive species, and restoring riparian habitat conditions (BPA and USACE 2013). These projects are 

providing juvenile Sockeye Salmon access to quality habitat (Bottom et al. 2011, Roegner et al. 2012) 

and allowing the export of salmon prey (dipteran insects and the amphipod Americorophium) to the 

deeper water channel (Diefenderfer et al. 2012). 

Recovery strategy questions:

• How effective are hydropower management activities across the observed range of 

hydrologic conditions? Across a projected range of hydrologic conditions associated with 

climate change?

• How effective are estuary habitat improvement activities?

6.3.2.2 Continue research on Snake River Sockeye Salmon survival/mortality in mainstem Salmon, Snake 

and Columbia River migration corridors; estuary; plume; and ocean

Mainstem Salmon River 

As discussed previously, both juvenile and adult Sockeye Salmon are lost in the 743 km (462-mile)

Salmon River migration corridor between Redfish Lake and Lower Granite Dam. The factors 

responsible for the losses are not fully understood. More research is needed to determine where and 

why mortality occurs in the migration corridor between the natal lakes and Lower Granite Dam.

FCRPS BiOp RPA-directed studies to evaluate the feasibility of transporting adult Sockeye Salmon

from Lower Granite Dam to the Sawtooth Valley to avoid high mortality in that reach are resulting in a 

more detailed assessment of where adult losses are occurring along the entire Bonneville-to-Sawtooth 

migration route and a correlative analysis of factors, including water temperature, that may be 

responsible for adult Sockeye Salmon mortality. This study is ongoing (NMFS 2014c).

Federal Columbia River Power System

As discussed in Section 6.3.2.1, actions described in the FCRPS RPA and the Hydro Module, as well as 

any further improvements for fish survival that may result from the ongoing FCRPS adaptive 

management process, represent the near-term hydropower recovery strategy for Snake River Sockeye 

Salmon and other listed Columbia Basin salmonids. In 2009, after expansion of the Snake River 

Sockeye Salmon production facilities (FCRPS RPA Action 42), the Corps of Engineers was able to start 

PIT-tagging sufficient numbers of juvenile fish from this ESU to directly assess the survival of inriver 

migrants from the point of release in the Sawtooth Valley through the hydropower system to Bonneville 

Dam (FCRPS RPA Action 52). The Corps has also begun to compare the adult Snake River Sockeye 

Salmon return rates of fish that migrated inriver to those that were transported from the Snake River 

collector projects. Prior to this, estimates for unlisted Sockeye Salmon from the upper Columbia (Lake 
ESA Recovery Plan: Snake River Sockeye Salmon | 239

June 2015| NOAA Fisheries 

Wenatchee and Okanogan River ESUs), or even from other species (e.g., Snake River spring/summer 

Chinook salmon), were used as surrogates for Snake River Sockeye Salmon in this reach. Transportation 

effects could not be assessed using data for Upper Columbia River Sockeye Salmon, because fish from 

the upper Columbia are not transported. 

The increasing availability of smolts from the Snake River Sockeye Salmon production and 

supplementation program is further increasing the sample sizes of these studies, improving estimates of 

survival through the FCRPS and allowing the assessment of transport effects under current operations.

Researchers have now analyzed PIT-tag data from 920 adults that were detected at Bonneville Dam 

from 2008 through 2013. During this period, Snake River sockeye survival from Bonneville Dam to the 

Sawtooth Weir ranged from 60% down to 13% (Crozier et al. 2014). The researchers used the PIT-tag

data to examine several factors that might contribute to migration survival. These factors include 

juvenile history (hatchery origin, juvenile transportation, and age of adult return), migration 

characteristics (arrival timing, travel time, and fallback), and river environment (temperature, flow, spill, 

and percentage of dissolved gas) in the river reaches between Bonneville Dam and the Sawtooth Valley. 

They also used the data to explore the implications of potential triggers for Snake River Sockeye Salmon 

transportation. Research results to date indicate that the most important predictors of survival across 

reaches and years may be thermal exposure and fish travel time, with higher temperature exposure 

contributing to higher fallback rates and lower survival. As mentioned previously, adult Snake River 

Sockeye Salmon migrate through this long, strenuous river reach in July and August – the hottest time of 

year. The PIT-tag data show that migration survival dropped below 50% when the river surpassed 18°C. 

While additional years of PIT-tag data collection and analysis will improve research findings, the 

current data suggest that migration survival varies strongly as a function of temperature and that 

temperature should be considered in any decision to initiate fish transportation (Crozier et al. 2014). 

This strategy includes actions to investigate the observed SAR differential between Snake River 

Sockeye Salmon and Lake Wenatchee and Okanogan River Sockeye Salmon. Information gained from 

these investigations will inform further actions that could improve SARs for the Snake River ESU.

Lower Columbia River Estuary, Plume, and Ocean

As discussed in 6.3.2.1, actions described in the FCRPS RPA and the Estuary Module, as well as any 

further improvements for fish survival that may result from the ongoing FCRPS adaptive management 

process, represent the near-term estuary and plume recovery strategy for Snake River Sockeye Salmon

and other listed Columbia Basin salmonids. Under FCRPS RPA Actions 58-61, BPA and the Corps have 

been investigating fish and habitat status and trends in the estuary and developing estuary classification 

mapping layers to inform selection of habitat improvement projects. They are increasing the level of 

“action effectiveness” research to evaluate how fish and habitat actually respond to the improvement 

actions compared to pre-project predictions. The Expert Regional Technical Group (ERTG) considers 

and incorporates these new scientific findings into its habitat improvement scoring process. The group 

also assigns survival benefit units for ocean- and stream-type juvenile salmon for estuary habitat actions 

implemented by the Action Agencies.
ESA Recovery Plan: Snake River Sockeye Salmon | 240

June 2015| NOAA Fisheries 

The purpose of the plume and nearshore ocean research program has been to help understand the 

mechanisms by which the ocean and climate affect survival to increase the likelihood that Columbia 

Basin salmonid populations will persist over the full range of environmental conditions they are likely to 

encounter.

Recovery strategy questions:

• What are survival rates of juvenile and adult Snake River Sockeye Salmon through the 

mainstem Salmon River, lower Snake and Columbia Rivers, estuary, plume, and 

nearshore ocean?

• How and where do water quality and quantity conditions in the Salmon River affect 

Sockeye Salmon migrants between Lower Granite Dam and the natal lakes? What other 

factors (predation, competition, toxics) are causing juvenile Sockeye Salmon mortality 

during migration through the Salmon River?

• How do fluctuations in annual river flows (Columbia, Snake, and Salmon Rivers) affect 

survival through each of these stages?

• How are juvenile Snake River Sockeye Salmon using the estuary and plume (residence 

times, growth rates, survival to next life stage)?

• How do conditions in the estuary affect Sockeye Salmon rearing (residence times, growth 

rates and survival)?

• Does exposure to contaminants and bioaccumulation of contaminants in the estuary affect 

Snake River Sockeye Salmon survival?

• Is the mortality of juvenile outmigrating and adult returning anadromous Sockeye 

Salmon in the area between the Sawtooth Valley and Lower Granite Dam related to 

natural causes (e.g., competition, predation, environmental conditions) or effects of 

human activities?

• Are there local areas (hot spots) where mortality is concentrated during juvenile smolt 

and adult return migration for anadromous Sockeye Salmon in the area between the upper 

Snake River basin and Lower Granite Dam, or are mortality rates uniform over the 

migration distance?

• What are the effects of transportation on juvenile Sockeye Salmon survival?

• What estuary and ocean indicators (biological and physical) correlate with Sockeye 

Salmon growth rates and life stage survival and with SARs?

6.3.2.3 Update Snake River Sockeye Salmon life cycle models using latest information on survival 

through mainstem Salmon, Snake, and lower Columbia River migration corridor; estuary; and plume

Update appropriate life-stage inputs in the life cycle model and test hypotheses regarding whether 

strategies described in this plan, including those in Section 6.3.2.1, will be adequate to achieve recovery 

objectives for the ESU. 
ESA Recovery Plan: Snake River Sockeye Salmon | 241

June 2015| NOAA Fisheries 

6.3.2.4 Manage to maintain low impact fisheries and reduce fishery impacts in those fisheries that affect 

Snake River Sockeye Salmon

The strategy to reduce fishery impacts on Snake River Sockeye Salmon centers on the use of existing 

management agreements and monitoring activities. No fisheries directly target Snake River Sockeye 

Salmon; however, the fish are caught in fisheries targeting other species. 

In the Sawtooth Valley, sport fisheries in Redfish Lake targeting kokanee and rainbow trout may catch 

small numbers of Sockeye Salmon. DNA analysis of sport-caught fish, however, shows that the fishery 

removes significant numbers of kokanee but not Sockeye Salmon; therefore without negatively 

impacting the Sockeye Salmon ESU. 

Fisheries in the mainstem Salmon and Snake Rivers target hatchery spring/summer Chinook salmon and 

steelhead but the fisheries are managed to protect Sockeye Salmon. ESA biological opinions require 

substantial monitoring and evaluation of the fisheries; when Sockeye Salmon are encountered or show 

up in the catch the fisheries are closed.

Treaty tribal net fisheries and non-tribal fisheries in the lower Columbia River, i.e., below the 

confluence of the Snake River, that target Chinook salmon and steelhead also incidentally take small 

numbers of Snake River Sockeye Salmon. Most of the Sockeye Salmon harvested in these fisheries are 

from the upper Columbia River, but very small numbers of Snake River Sockeye Salmon are taken 

incidental to summer fisheries directed at Chinook salmon. Fisheries in the mainstem Columbia River 

that affect Snake River Sockeye Salmon are managed subject to the terms of the U.S. v. Oregon

Management Agreement for 2008-2017. These fisheries are managed to ensure that the incidental take 

of ESA-listed Snake River Sockeye Salmon does not jeopardize the ESU. 

Ocean fisheries may also take small numbers of Sockeye Salmon, but are not believed to significantly 

affect the Snake River Sockeye Salmon ESU. Ocean harvest is under the jurisdiction of the Pacific 

Fisheries Management Council and the Pacific Salmon Commission and is managed according to 

agreements through these jurisdictions. 

The recovery strategy calls to continue managing mainstem Columbia River and lower Snake River 

fisheries through the 2008-2017 U.S. v. Oregon Management Agreement, which retained the 2005-2007 

Interim Management Agreement to ensure that the incidental take of ESA-listed Snake River Sockeye 

Salmon does not exceed specified harvest rates. The strategy also implements monitoring and evaluation 

programs to ensure that fisheries minimize their impacts on this ESU. 

Tributary fisheries are managed to ensure that the incidental take of ESU-listed Snake River Sockeye 

Salmon does not exceed specific harvest rates. In addition, the strategy calls for actions to investigate the 

use of new technologies (PIT-tags and PIT-tag detectors, Parentage Based Tagging) to better manage 

inseason mainstem fisheries and assess seasonal harvest objectives and limitations.
ESA Recovery Plan: Snake River Sockeye Salmon | 242

June 2015| NOAA Fisheries 

Recovery strategy questions:

• Can we achieve recovery under the current U.S. v. Oregon sliding-scale fishery harvest 

regime, together with actions in the other Hs? 

• What are the effects of harvest on size selectivity and size of fish returning to spawn? 

• What research is needed to understand the role of Columbia River fishery harvest on 

adult Sockeye Salmon survival? Based on this research, what management actions can 

be taken to minimize take of Snake River Sockeye Salmon?

6.3.2.5 Protect and conserve natural ecological processes that support population viability

Actions to protect and improve habitat and fish passage in the Columbia/Snake River mainstem and 

estuary play a key a role in the overall recovery strategy for Snake River Sockeye Salmon. Protecting 

existing high quality habitat and restoring damaged habitat will specifically benefit Snake River 

Sockeye Salmon in the juvenile and adult migration life history stages. The Estuary Module describes 

strategies and actions to protect and conserve natural ecological processes to support salmonid viability 

in the lower Columbia River, estuary, and plume. The 2008 FCRPS Biological Opinion and 2010 

Supplemental FCRPS BiOp also provide direction for improving natural ecological processes in the 

mainstem Columbia and Snake Rivers. 

Relatively little information is available concerning Snake River Sockeye Salmon use of mainstem 

Snake and Columbia River habitat above Bonneville Dam, aside from passage through the dams. 

NMFS believes it is important to assess nearshore mainstem habitat and cold-water refugia in the 

mainstem Columbia and lower Snake Rivers and to explore opportunities for, and potential benefits 

from, restoration and protection of these areas. 

Recovery strategy questions:

• Are there shoreline, main channel, and/or cold-water refugia areas in the estuary that 

provide habitat for juvenile Snake River Sockeye Salmon during their migration? 

• What habitat conditions in the plume contribute to Sockeye Salmon viability?

• Where is predation on Sockeye Salmon occurring in the estuary and what changes in 

ecological conditions contribute to increased predation?

• What estuary and ocean indicators (biological and physical) correlate with Sockeye 

Salmon growth rates, life-stage survival, and with SARs? Protect existing high quality 

habitat and restore mainstem shoreline habitat (riparian and wetlands) in lower Snake and 

lower Columbia River reaches?

6.3.2.6 Improve degraded water quality and maintain unimpaired water quality

Summer water temperatures in portions of the mainstem Salmon River and the lower Snake River reach 

levels during late July and August that may affect the survival of migrating Snake River Sockeye 

Salmon. Besides delaying migration and/or causing direct or delayed Sockeye Salmon mortality, the 

high temperatures may also make Sockeye Salmon more susceptible to disease and infection if they are 
ESA Recovery Plan: Snake River Sockeye Salmon | 243

June 2015| NOAA Fisheries 

not able to escape to deep pools or other habitats with cooler temperatures. Higher water temperatures 

may also reduce the quality of shallow water estuarine habitats used by juvenile and adult Sockeye 

Salmon and other salmonids during summer months. Adult Sockeye Salmon have been known to suffer 

stress and disease as they are exposed to warm water in estuaries, waiting for cool runoff conditions in 

their natal stream (ISAB 2007). Warmer temperatures may also cause changes in the estuarine food web 

(NMFS 2011a).

Sections of the mainstem Salmon, Snake, and Columbia Rivers are also contaminated by drift and runoff 

from both agricultural and urban areas. Exposure to these chemicals during adult and juvenile migration 

may contribute to low survivorship and impede recovery of this stock. As discussed in Section 5, 

juvenile and adult Snake River Sockeye Salmon are likely at risk for exposure to several classes of 

contaminants, including mercury, legacy and current use pesticides, industrial contaminants such as 

PCBs and PBDEs, and wastewater contaminants their respective migrations. Currently, however, very 

little is known about the actual exposure to and uptake of contaminants in outmigrant juvenile Snake 

River Sockeye Salmon, or returning adults, and no data are available on contaminant body burdens in 

this stock. Moreover, water quality data for much of this ESU’s habitat is incomplete. Toxics 

monitoring in the Columbia Basin has been concentrated primarily in the lower Columbia River and 

estuary, and data for the middle and upper Columbia River, Snake River, and Salmon River basins are 

lacking (USEPA 2009). 

The Estuary Module lists several management actions that could improve water quality in the estuary for 

all Snake River Sockeye Salmon and other salmonids.

• Implement pesticide and fertilizer best management practices to reduce estuarine and 

upstream sources of nutrients and toxic contaminants entering the estuary. 

• Identify and reduce terrestrially and marine-based industrial, commercial, and public 

sources of pollutants.

• Restore or mitigate contaminated sites.

• Implement stormwater best management practices in cities and towns.

In addition, the strategy supports actions by IDEQ, Idaho Department of Water Resources, Oregon DEQ 

and Washington Department of Ecology to address water temperature concerns for the Salmon and 

lower Snake Rivers. The strategy calls for monitoring studies to determine how high temperatures and 

other water quality issues in the Salmon and lower Snake Rivers may be affecting Sockeye Salmon

survival and viability. 

Recovery strategy questions:

• How do high water temperatures in the lower Salmon and Snake Rivers affect upstream 

and downstream Sockeye Salmon survival and viability? 
ESA Recovery Plan: Snake River Sockeye Salmon | 244

June 2015| NOAA Fisheries 

• In what reaches of the lower Salmon and Snake Rivers are Sockeye Salmon particularly 

vulnerable to high water temperatures, and potential increases in predation by warmwater fish?

• How does exposure to contaminant and bioaccumulation affect Snake River Sockeye 

Salmon survival?

6.3.2.7 Address ecosystem imbalances in predation, competition, and disease through the strategies and 

actions in this Plan, the Estuary Module and reasonable and prudent alternatives identified in Biological 

Opinions

Predation

Avian Predation

While extensive research on predation and efforts at predator control in the Columbia Basin has been 

undertaken for decades, little is known regarding the extent of avian predation on Snake River Sockeye 

Salmon. Actions continue to reduce predation by cormorants and other birds. For example, altering 

habitat on Rice Island to prevent tern and cormorant nesting reduced avian predation in the estuary. The 

2008 FCRPS Biological Opinion (NMFS 2008c) recommended further reduction in bird habitat on East 

Sand Island. The Estuary Module and FCRPS RPA recommend further development of plans to control 

Caspian terns and double-crested cormorants that nest in the estuary and on islands upstream of 

Bonneville Dam. The Corps of Engineers plans to continue implementing “avian deterrent actions” at 

the lower Snake and Columbia River dams.

Piscivorous Fish Predation

Although predation of juvenile Sockeye Salmon undoubtedly occurs, there is little direct evidence that 

piscivorous fish in the Columbia River consume juvenile Sockeye Salmon (NMFS 2008c). Control of 

piscivorous predation has focused largely on targeted sports fisheries to remove more of the predators 

and /or direct removal by physical or chemical means (NMFS 2008c). 

A report by the Independent Scientific Advisory Board for the NPCC (ISAB) indicates that the methods 

of controlling non-native piscivores have not been sufficient, and that maintaining and restoring habitat 

is actually the better strategy. The ISAB report states “when native species are provided with habitat for 

which they are best adapted, they have an improved chance of out-competing or persisting with nonnative species” (ISAB 2008). NMFS supports this conclusion. Based on its report, the ISAB 

recommended that the NPCC urge state agencies to relax (or eliminate) fishing regulations that may be 

perpetuating populations of non-native species (both predators, such as walleye, smallmouth bass and 

channel catfish, and competitors, such as shad and brook trout); especially those that directly or 

indirectly interact with juvenile and adult salmonids. 

Competition

Evaluating the factors that influence how competition with hatchery fish and other species affects 

natural-origin populations under varying freshwater conditions and ocean conditions is an important area 
ESA Recovery Plan: Snake River Sockeye Salmon | 245

June 2015| NOAA Fisheries 

of future research. This is addressed in more detail in Appendix C of the 2008 FCRPS Biological 

Opinion (NMFS 2008c).

Disease 

Disease in salmonids is caused by multiple factors and probably cannot be directly addressed by 

recovery actions, except in specific instances of known causal factors. It is more likely that nearly all of 

the recommended recovery actions that improve spawning, rearing, and passage conditions for Sockeye 

Salmon and increase the survival, abundance, and productivity of naturally produced fish will result in 

decreasing incidence of disease. 

The Estuary Module, FCRPS BiOp, and other Biological Opinions, and this Plan identify strategies and 

actions to monitor and control predation, competition, and invasive species in the mainstem Columbia 

and Snake Rivers and estuary. The documents also direct additional research, monitoring, and 

evaluation activities to quantify the impacts of predation and competition on Snake River Sockeye 

Salmon recovery efforts. 

Recovery strategy questions:

• What is the predation rate and predatory effect of native and non-native fishes in the 

nursery lakes and migration corridor on Snake River Sockeye Salmon?

• What is the effect of predation from avian and fish predators in the Columbia River 

migration corridor on juvenile Snake River Sockeye Salmon?

• What is the effect of predation from marine mammals in the Columbia River migration 

corridor on adult Snake River Sockeye Salmon?

6.3.2.8 Respond to climate change threats by implementing research, monitoring, and evaluation to track 

indicators related to climate change and by preserving biodiversity 

Likely changes in temperatures, precipitation, wind patterns and sea-level height due to climate change 

have profound implications for survival of Snake River Sockeye Salmon. All other threats and 

conditions remaining equal, future deterioration of water quality, water quantity, and/or physical habitat 

due to climate change can be expected to cause a reduction in the number of naturally produced Sockeye 

Salmon returning to the ESU. This possibility reinforces the importance of implementing research, 

monitoring, and evaluation to track indicators and adapt actions to respond to climate change. It also 

reinforces the importance of maintaining habitat diversity and achieving survival improvements

throughout the entire life cycle.

The ISAB (2007) developed strategies and recommendations to incorporate climate change 

considerations into restoration and recovery planning. This Plan adopts the ISAB’s general strategy and 

recommendations as they apply to Snake River Sockeye Salmon. The strategy is three-pronged, 

addressing climate change concerns in freshwater habitats, the mainstem Snake/Columbia River 

corridor, and the ocean. 
ESA Recovery Plan: Snake River Sockeye Salmon | 246

June 2015| NOAA Fisheries 

• For freshwater lake habitats, the strategy is to: (1) conduct research and monitoring to 

predict and determine if climate change is affecting food supplies, predation and 

competition rates, spawning/rearing conditions and survival in the lakes; and (2) if so, 

determine if there are actions that can be implemented to reduce the effects of climate 

change. 

• For freshwater tributary migratory corridors, the strategy is to: (1) minimize increases in 

summer temperatures in affected streams by implementing measures to retain shade 

along stream channels and augment summer flow; (2) help alleviate both elevated 

temperatures and low stream flow in affected streams during summer and autumn by 

managing water withdrawals to maintain as high a summer flow as possible; and (3) 

provide mitigation for declining summer flows by protecting and restoring wetlands, 

floodplains, and other landscape features that store water. 

• For the mainstem Snake and Columbia migration corridor, the strategy includes releasing 

cool water from reservoirs during critical periods, improving juvenile passage through 

warm dam forebays, improving temperatures in adult fish passage structures, and 

reducing warm-water predators. For the estuary, removing dikes to open backwater, 

slough, and other off-channel habitats can increase flow through these areas and 

encourage hyporheic flow. 

• For the ocean, the climate change strategy is primarily to review mechanisms for timing 

arrival of smolts to avoid a mismatch with marine predators and prey and to review 

harvest practices to ensure that harvest quotas are adjusted to reflect changing conditions. 

Strategies and actions identified in this plan - including the research, monitoring, and evaluation plan -

define steps to track and guard against the effects of climate change. Strategies and actions identified in 

the Estuary and Hydro Modules, FCRPS BiOp, and other Biological Opinions also protect and improve 

habitats that could be affected by climate change. The climate change strategy necessitates a strong 

monitoring and evaluation program, along the lines of that included in the FCRPS Adaptive 

Management Strategy. The program will help detect physical and biological changes associated with 

climate change and determine the efficacy of responsive measures. 

Recovery strategy questions:

• Given regional temperature and precipitation patterns projected from climate models, 

how would potential changes in stream temperature and flows affect the limnology of 

lakes used for spawning and rearing of Snake River Sockeye Salmon?

• Given regional temperature and precipitation patterns projected from climate models, 

how might potential changes in limnology of the lakes affect Sockeye Salmon food 

supplies, predation and competition threats, migration timing and survival?

• Given regional temperature and precipitation patterns projected from climate models, 

how would potential changes in tributary and mainstem stream temperature and flows 

affect migration timing and survival of juvenile and adult Snake River Sockeye Salmon? 
ESA Recovery Plan: Snake River Sockeye Salmon | 247

June 2015| NOAA Fisheries 

What reaches are most vulnerable to potential increases in water temperature due to 

climate change? In particular:

• Will stream flows in the Salmon River above the Sawtooth Hatchery be adequate to 

sustain migration of Sockeye Salmon to Alturas, Pettit, and Yellowbelly Lakes under 

projected changes from climate change?

• Are there management strategies and actions that can affect life history survival across 

different climate and environmental conditions?

6.3.2.9 Implement the Snake River Sockeye Salmon Recovery Plan through effective communication,

education, coordination and governance

Recovery of Snake River Sockeye Salmon depends on the collective action of citizens and stakeholders 

in the region. Recovery actions will need to be implemented by diverse organizations, tribes, state and 

Federal agencies, landowners, private entities and the public. 

Implementation of recovery actions, research, and monitoring projects will build upon ongoing Sockeye 

Salmon recovery efforts carried out by the Stanley Basin Sockeye Technical Oversight Committee, 

IDFG, Shoshone-Bannock Tribes, U.S. Forest Service, NMFS and other partners that have prevented the 

extinction of this ESU. Implementation will need the continued coordinated actions and funding from 

diverse parties including IDFG, Shoshone-Bannock Tribes, Bonneville Power Administration, NMFS, 

U.S. Forest Service, counties, state and Federal agencies, private landowners, and individuals. NMFS 

will work with these various partners to define agreement on how best to implement the Snake River 

Sockeye Salmon recovery plan, especially regarding recovery action coordination, public education and 

interpretation, action tracking and reporting, scientific oversight, and adaptive management. 

6.3.2.10 Continue research, monitoring, and evaluation for adaptive management

Research, monitoring, and evaluation play a critical role in the recovery of the Snake River Sockeye 

Salmon ESU and are discussed in more detail in Section 11. As will be discussed in Section 6.4, Key 

Information Needs, many questions exist regarding the effects of the hydrosystem, fisheries, and land 

and water uses on survival of Snake River Sockeye Salmon in the mainstem migration corridor, estuary,

and ocean. We remain unsure whether Sockeye Salmon survivals resulting from current conditions and 

current and proposed management actions will be enough to provide for life history survival through 

variations in ocean and climate conditions. 

Strategies and actions in the FCRPS Biological Opinion, Hydro Module and Estuary Module identify 

research, monitoring, and evaluation activities that will aid recovery of Sockeye Salmon. In addition, the 

research, monitoring, and evaluation program discussed in Section 11 of this Plan provides direction to 

assess the status of the species and its habitat, track progress toward achieving recovery goals, and gain 

information needed to refine recovery strategies and adjust course as appropriate through the process of 

adaptive management. 
ESA Recovery Plan: Snake River Sockeye Salmon | 248

June 2015| NOAA Fisheries 

6.3.2.11 Prioritize and address key information needs and create an adaptive management feedback loop 

to revise recovery actions as needed

Successful implementation of the recovery plan requires a process to refine direction and adjust course 

appropriately. Section 10 describes a proposed framework for coordinated implementation of this Plan. 

It describes the key implementation teams that are part of this framework, including the Snake River 

Sockeye Salmon Implementation and Science Team, which will be responsible for coordinating 

implementation of the Adaptive Management and Research, Monitoring, and Evaluation Plan. 

NMFS will work with the Snake River Sockeye Salmon Implementation and Science Team and others 

to prioritize the key information needs identified in Section 6.4. It will also seek resources and form 

partnerships to address the key information needs during recovery plan implementation.

6.4 Key Information Needs

This section summarizes the key information needs to evaluate the status of Snake River Sockeye 

Salmon and identifies the high priority data gaps to guide recovery actions to support a future naturally 

spawning population. Key information needs include scientific investigations of critical assumptions 

and unknowns that constrain effective recovery plan implementation. They include pieces of 

information required for informed decision making, proper allocation of fish resources, or to decrease 

risks to Sockeye Salmon and their habitat that are not available at this time. They also include 

information needed to improve the outcome of fish supplementation and habitat enhancement projects.

Key information needs are first identified in the Section 5, which identifies hypotheses for how we think 

limiting factors and threats affect Sockeye Salmon, data gaps in our knowledge and understanding of 

Sockeye Salmon, and research needs to understand the factors affecting viability at each life stage. 

Section 6 describes the local and regional-level recovery strategies to address these limiting factors, 

together with relevant recovery strategy questions and information needs. 

This section does not list all the recovery strategy questions in Section 6; however, the intent of this 

section is to focus on those key information needs that are essential, timely and of high priority to guide 

recovery actions for this ESU. This section highlights the key priority information needs for the 

recovery actions in Section 7 and research, monitoring, and evaluation actions in Section 11. 

Strategy: Conserve population genetic and life history diversity, and spatial structure.

Several Sawtooth Valley lakes are believed to have supported Sockeye Salmon production historically. 

The last documented returns of Sockeye Salmon from the region were associated with Redfish Lake. 

The lakes vary in size and there may be important differences in environmental conditions and 

zooplankton communities. Limnological evaluations, juvenile growth studies and hatchery outplant 

survival evaluations can be used along with study results from Sockeye Salmon lakes outside of the 

Snake River basin to gain a better understanding of the opportunities to restore Sockeye Salmon

production.
ESA Recovery Plan: Snake River Sockeye Salmon | 249

June 2015| NOAA Fisheries 

1. Broodstocks - The current captive broodstock for Snake River Sockeye Salmon is exclusively 

composed of Redfish Lake fish/gene resources from an anadromous lineage adapted to beach 

spawning in the fall (late September through October).

• Is the current Redfish Lake Sockeye Salmon captive broodstock genetic structure 

appropriate for use in rebuilding efforts in other Sawtooth Valley lakes?

• Do remnant anadromous Sockeye Salmon gene resources exist in other Sawtooth Valley 

lakes and could they be utilized for recovery efforts on a lake-specific basis? 

• Is the current Redfish Lake Sockeye Salmon captive broodstock late September through 

October spawn timing structure appropriate for water temperature regimes in other 

Sawtooth Valley lakes?

• Is the current Redfish Lake Sockeye Salmon captive broodstock beach spawning 

propensity appropriate for rebuilding efforts in other Sawtooth Valley lakes, or would 

populations keyed to potential stream spawning habitats be more appropriate? 

2. Structure and size of restored natural spawning populations - Opportunities to restore Sockeye 

Salmon production in the lakes will depend greatly on their carrying capacity. The lakes differ in 

size, limnological condition, water quality, zooplankton communities, and other features that will 

determine the size and structure of a restored Sockeye Salmon population. We need a better 

understanding of the potential of different sites within each lake to support spawning. For example, 

there is strong evidence that Sockeye Salmon in Alturas Lake may spawn in the tributaries as well 

as along the lake shoreline, typical of Sockeye Salmon in other lakes. Consequently, the priorities 

for Sockeye Salmon production in the different lakes should be continually revisited as information 

from carrying capacity and survival rate studies becomes available. 

• Spatial Structure and Diversity: What are the options for population structure and 

diversity for restoration of a naturally spawning population(s)?

• What are the benefits/risks of alternative strategies for recovering extant and/or historical 

life-history patterns in the natal lakes (e.g., Alturas and Pettit)?

Strategy: Increase naturally spawning Snake River Sockeye Salmon abundance.

A key element of the plan for restoring natural production of Sockeye Salmon in the Sawtooth Valley 

lakes is its adaptive nature that allows opportunities to diversify reintroduction strategies for the lakes to 

promote the chances of successful reintroduction of sustainable natural production. 

• What is the potential of the individual lakes to support natural Sockeye Salmon

production? 

• What are the key constraints in each candidate lake? 

• How can additional limnological or experimental outplants be used to reduce 

uncertainties regarding restoration?
ESA Recovery Plan: Snake River Sockeye Salmon | 250

June 2015| NOAA Fisheries 

Strategy: Improve Sockeye Salmon passage to natal lakes.

Juvenile outmigration survival for Snake River Sockeye Salmon between the upper Snake River basin 

and Lower Granite Dam has ranged from about 20-80% and has been highly variable between years, 

release sites, origins, and rearing strategies. Likewise, adult upstream survival from Lower Granite Dam 

to the upper Snake River basin has ranged between a low of about 20% and a high of about 90%, and 

has been variable over years. Researchers have suggested that higher flows during the spring runoff 

period likely contribute to shorter travel times and higher survival to Lower Granite Dam. Lower stream 

flows and higher water temperatures may contribute to delayed upstream migration.

• Is the mortality of juvenile outmigrating and adult returning anadromous Sockeye 

Salmon in the area between the upper Snake River basin and Lower Granite Dam related 

to natural causes (e.g., competition, predation, environmental conditions) or are 

extraneous causes involved?

• Are there local areas (hot spots) where mortality is concentrated during juvenile smolt 

and adult return migration for anadromous Sockeye Salmon in the area between the upper 

Snake River basin and Lower Granite Dam, or are mortality rates uniform over migration 

distance?

Strategy: Investigate and develop strategies for future actions to support Sawtooth Valley in 

reintroduction and adaptation phases for Pettit Lake.

Evaluation of the initial reintroduction program will guide the future course of the Pettit Lake Sockeye 

Salmon program. This will depend greatly on the relative trends in anadromous and resident O. nerka

production in Pettit Lake. 

• Will the resident component (residual Sockeye Salmon and non-native kokanee) in Pettit 

Lake persist over time after stocking with Redfish Lake anadromous broodstock ends?

• Will anadromous Sockeye Salmon intermingle and spawn with resident Sockeye Salmon

on the spawning grounds? Does this impact the presence and magnitude of anadromy in 

the Pettit Lake population over time?

Strategy: Investigate and evaluate the potential for restoring natural production of anadromous 

Sockeye Salmon for returning residual outmigrants from Alturas Lake.

Information suggests that some of the Kokanee in Alturas Lake produce anadromous smolts that are 

genetically unique from the anadromous population found in Redfish Lake.

• What stock, or combination of stocks, is most appropriate for reintroduction into Alturas 

Lake to support the development of an anadromous O. nerka population?

Strategy: Continue research on natal lakes’ carrying capacity, nutrients, and ecology.

The Sawtooth Valley has a total of 1,267 surface hectares of lake habitat potentially available for 

anadromous Sockeye Salmon spawning and rearing (615 for Redfish Lake, 338 for Alturas, 160 for 

Pettit, 81 for Stanley, and 73 for Yellowbelly). Some primary questions of concern focus on how and if 
ESA Recovery Plan: Snake River Sockeye Salmon | 251

June 2015| NOAA Fisheries 

these potentially available habitats can be best used for recovery of Snake River Sockeye Salmon, 

including:

1. Lake rearing capacity

• What is the carrying capacity for adult spawning and juvenile rearing for anadromous 

Sockeye Salmon in each of the Sawtooth Valley lakes?

• How do these carrying capacities fit with recovery planning needs to address the 

abundance, productivity, spatial structure, and diversity of the ESU (e.g., is spawning and 

rearing capacity a limiting factor)?

• What can be derived from limnological monitoring data regarding the potential for 

juvenile anadromous Sockeye Salmon growth and survival in the various Sawtooth 

Valley lakes?

• How much zooplankton is available to support juvenile rearing and survival?

• We need to improve our understanding of the relationship between variability in 

zooplankton abundance and species composition vs. Sockeye Salmon juvenile density, 

survival, and anadromy vs. residency. 

• How would differing lake carrying capacity estimates affect the abundance targets?

2. Competition

• Do juvenile sockeye compete with kokanee for food resources in the oligotrophic lakes

of the Sawtooth Valley? Do we need to address the non-native kokanee population to 

make room for Sockeye Salmon recovery?

• Are other fish populations in Sawtooth Valley lakes limiting the production of juvenile 

anadromous Sockeye Salmon (e.g., does competition for food limit growth and survival)?

Strategy: Protect, restore and manage spawning, rearing, and migration habitat.

1. Habitat: spawning and rearing

• Uncertainty about the availability of spawning habitats. Is spawning capacity limiting in 

the natal lakes? 

• What habitat areas will be important as Sockeye Salmon numbers increase? What will be 

the role of beach vs. stream spawning types? 

2. Habitat: migration

• What are the causes of juvenile mortality for fish leaving natal lakes/ Sawtooth Valley?

• What are the causes of mortality of adults in certain reaches?
ESA Recovery Plan: Snake River Sockeye Salmon | 252

June 2015| NOAA Fisheries 

3. Habitat: estuary/ plume near shore

• How are juvenile Snake River Sockeye Salmon using the estuary and plume (arrival 

timing, residence times, habitat use, and prey consumption)?

• Effects of conditions in estuary and plume on growth, condition, and survival?

• What amount of benefit will this ESU gain from recovery actions in estuary?

4. Toxics

• Determine the sources of contaminant exposure and levels in body tissues in Snake River 

Sockeye Salmon.

• Gather toxics monitoring data from critical habitats for many contaminants.

• Gather information about the interactions of contaminants with other stressors.

Strategy: Implement FCRPS BiOp to reduce mortalities associated with passage through the 

mainstem Columbia and Snake River hydroelectric projects.

• Improve FCRPS passage survival rates.

• Continue survival studies for transported juveniles and in river migrants.

• Determine different survival rates through FCRPS system.

• Query existing tag information on survival to determine what happens during different 

climate/ocean conditions.

• Determine the physical and biological indicators of environmental conditions (in the 

mainstem and ocean) and how they are correlated with survival. Generate hypotheses of 

underlying mechanisms and where under human control, test alternatives.

Strategy: Maintain current low impact fisheries and reduce fishery impacts in those fisheries that 

affect the viability of the Snake River Sockeye Salmon ESU.

Harvest rate estimates of natural-origin fish are based on analyses of hatchery fish with Coded Wire 

Tags (CWTs).

1. Accuracy of harvest rate estimates

• Are estimates of harvest rates of natural-origin fish accurate? Are we meeting the sliding 

scale numbers in US v Oregon?

2. Potential effects of size selectivity

• What are the effects of harvest management on size selectivity and size of fish returning 

to spawn? 
ESA Recovery Plan: Snake River Sockeye Salmon | 253

June 2015| NOAA Fisheries 

Strategy: Respond to climate change threats by implementing research, monitoring, and 

evaluation to track indicators related to climate change and by taking actions designed to preserve

biodiversity.

1. Climate effects

• Given regional temperature and precipitation patterns projected from climate models, 

how would potential changes in stream temperature and flows impact the survival of

Snake River Sockeye Salmon at different points in the life cycle (e.g., natal lakes to lower 

Snake River, lower Snake River to lower Columbia, estuary and plume)?

Table 6-1. Monitoring and evaluation programs for Snake River Sockeye Salmon.

Types of Programs Activity Description Responsible Entities Status

Status and Trends 

Monitoring

Natural and hatchery 

origin adult returns to 

Redfish Lake

Adult returns to Lower 

Granite Dam

Adult returns to 

Bonneville Dam

Juvenile abundance at 

Redfish Lake, Lower 

Granite Dam

Smolt to adult survival 

studies

Trap counts at Redfish Lake

Ladder counts & PIT 

detections

PIT detections

Outmigrant trapping

Lower Granite smolt to adult 

returns.

IDFG, SBT

WDFW, IDFG

Corps of Engineers 

(COE)

IDFG and NOAA

NOAA and IDFG

Ongoing

Ongoing 

Ongoing

Ongoing

Ongoing

Hydro Evaluations

Downstream passage 

survival

Upstream passage 

survival

Representative PIT-tagging 

and monitoring

Adult counts, PIT-tag

monitoring

IDFG, NOAA, COE

Ongoing

Ongoing

Hatchery

Supplementation Parr per spawner production 

from Redfish Lake outplants, 

other lakes as they are 

initiated

Parr to outmigrant survivals 

IDFG, SBT

IDFG
ESA Recovery Plan: Snake River Sockeye Salmon | 254

June 2015| NOAA Fisheries 

Types of Programs Activity Description Responsible Entities Status

Harvest

Habitat

Salmon River 

migration survival

Lake production 

capacity evaluations

Status and trend of 

habitat conditions 

within historic Sockeye 

Salmon tributaries

Annual survivals of emigrant 

smolts from lakes to Lower 

Granite Dam, impact of 

environmental influences and 

annual survival rates of 

returning adults from Lower 

Granite Dam to the natal 

lakes

Limnological studies, prey 

dynamics, spatial temporal 

distribution of kokanee vs. 

anadromous presmolts

Five year rotating panel 

design monitoring of key 

habitat, riparian water 

quality, and water 

temperature variables

COE, IDFG,NMFS

SBT, IDFG

USFS (PIBO)

Ongoing

Ongoing

Ongoing

Other
ESA Recovery Plan: Snake River Sockeye Salmon | 255

June 2015| NOAA Fisheries 

Section 7: Site-Specific Actions

7.1 Building on Current Efforts

7.2 Site-Specific Actions for the Snake River Sockeye Salmon at the Local Level (Sawtooth Valley 

and Upper Salmon River)

7.3 Actions to Recovery Snake River Sockeye Salmon at the Regional Level (Migration Corridor in 

the Mainstem Salmon, Snake and Columbia Rivers and Estuary, Plume and Ocean)
ESA Recovery Plan: Snake River Sockeye Salmon | 256

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 257

June 2015| NOAA Fisheries 

7. Site-Specific Actions 

This section describes a suite of recommended actions that may be necessary to achieve recovery of the 

Snake River Sockeye Salmon ESU. These actions address the limiting factors and threats described in 

Section 5. They are also linked to the local and regional recovery strategies described in Section 6. This 

section begins by acknowledging the importance of recovery actions that have been implemented over 

the last 20 years. The proposed recovery actions are then summarized briefly, with specific recovery 

actions identified in Table 7-1. These proposed actions are designed to be integrated with current, 

ongoing programs and regulations that may benefit Sockeye Salmon and that are described in this Plan, 

such as current fishery management regulations, state water quality regulations, and U.S. Forest Service

forest management practices. Recovery actions addressing research and monitoring for adaptive 

management are included in Section 11. 

Setting Priorities to Implement Recovery Strategies and Actions

Priorities for recovery actions should be guided by viability criteria, best available scientific information 

concerning ESU status, the role of populations in meeting ESU viability, limiting factors and threats, 

and likelihood of action effectiveness. In addition, financial resources to implement recovery actions are 

limited which emphasizes the need to set priorities. Given the numerous recovery actions identified in 

this Plan, it is critically important to identify priorities for recovery action implementation to guide 

selection of near-term recovery actions.

Several key principles derived from conservation biology and ecosystem management help frame these 

priorities. Several scientific studies have illustrated the principle that habitat conditions and aquatic 

ecosystem function are the result of the interaction between watershed controls (such as geology and 

climate), watershed processes (such as hydrology and sediment transport), and land use. Scientists and 

resource managers have recognized that restoration planning that carefully integrates watershed or 

ecosystem processes is more likely to be successful at restoring depleted salmonid populations (Beechie 

et al. 2003). The strategy used in this recovery plan focuses on the concepts presented in several 

salmonid habitat recovery planning documents and scientific studies (e.g., Beechie and Boulton 1999; 

Roni et al. 2002; Beechie et al. 2003; Roni et al. 2005; Stanley et al. 2005). These principles for sound 

salmon recovery include:

• Assess, protect and maintain biological and habitat processes.

• Reconnect isolated habitat to increase spatial structure.

• Restore ecological processes.

• Restore degraded habitat used throughout the life cycle.

• Evolutionary processes must be conserved or restored.

• Develop goals and objectives based on a deep understanding of ecological properties of 

the system.

• Management must be adaptive and minimally intrusive.
ESA Recovery Plan: Snake River Sockeye Salmon | 258

June 2015| NOAA Fisheries 

The current endangered status of the ESU also frames our recovery efforts. The Plan’s goal is to have 

viable independent populations in at least three or more natal lakes to expand spatial distribution and 

diversity, and protect the relatively healthy habitat conditions in the Sawtooth Valley. The following 

features of our recovery strategy continue to influence the sequencing of recovery action

implementation:

• Implement the current captive broodstock program actions to support conservation of 

life histories and genetic attributes as described in Section 6.3.1.1. 

• Reestablish self-sustaining anadromous Sockeye Salmon populations in Redfish, 

Pettit, and Alturas Lakes. Actions that enhance viability and protection of multiple 

Sockeye Salmon populations through continued implementation of the Redfish Lake 

program, implementation of introduction strategies for Pettit Lake and Alturas Lake, and 

reconnection of isolated habitat to improve spatial structure and diversity as described in 

Sections 6.3.1.4, 6.3.1.5, and 6.3.1.6. Develop action prioritization criteria and then 

apply these criteria to develop a multi-year action implementation plan or schedule. 

• Protect and enhance existing habitat conditions and conserve natural ecological 

processes that support the viability of the extant populations and their primary life 

history strategies throughout their entire life cycle. Continued implementation of the 

Management Plan for the Sawtooth National Recreation Area, together with continued 

wilderness protections in the Sawtooth Valley will protect habitat processes for the natal 

lakes watersheds. Additional habitat protection and restoration actions for the migration 

corridor are identified in Sections 6.3.14 and 6.3.2.5.

• Improve survival for all life stages in the migration corridor as described in Section 

6.3.2.1.

• Carry out research, monitoring, and evaluation actions that provide critical 

information needed to assess fish viability responses and make adaptive management 

decisions as needed based on this information. Section 11 identifies the adaptive 

management approach, together with research, monitoring, and evaluation actions to 

continually adapt recovery actions over time. 

Strategy and Action Prioritization Considerations

Priorities for implementation of recovery strategies and management actions must consider the scientific 

complexities of addressing the different factors and threats, as well as diverse policy issues and 

economic implications. Priorities must be science based, but are ultimately policy choices. The 

following considerations will be used as guidance for the development of criteria, and prioritization and 

implementation of management strategies and actions for recovery of the Snake River Sockeye Salmon 

ESU and populations.
ESA Recovery Plan: Snake River Sockeye Salmon | 259

June 2015| NOAA Fisheries 

Highest priority actions:

• Actions that provide long-term protection of habitat conditions and conservation of 

natural ecological processes that support the viability of priority populations and their 

primary life history strategies throughout their entire life cycle. A population is 

considered a priority if it is critical for ESU viability.

• Actions that protect or enhance viability of multiple Sockeye Salmon populations.

• Actions that support conservation of unique and rare functioning habitats, habitat 

diversity, life histories, and genetic attributes.

• Actions that target the limiting factors and that contribute the most to closing the gap 

between current status and desired status of priority populations. 

• Actions that provide immediate benefits to enhancing the viability of priority populations. 

• Actions that provide critical information needed for assessing success and making 

adaptive management decisions.

High priority actions, but less than highest:

• Actions that enhance the habitat conditions and restore natural ecological processes of 

priority populations and their primary life history strategies throughout the entire life 

cycle.

• Actions that enhance the viability across the entire life cycle of priority populations. 

• Actions that are required to protect and enhance habitats for potential populations that are 

not critical for ESU viability but where reintroduction efforts may be implemented. 

Other things being equal, actions that demonstrate the following have enhanced priority:

• Actions where opportunity for success is high (rather than those of limited feasibility).

• Actions that likely produce a large (rather than small) improvement in viability attributes.

• Actions that support restoration of normative ecological processes rather than short-term

substitutions for normative processes.

• Actions that are complementary to other land management, water quality, environmental 

management, and recreational objectives as specified in fish management, conservation, 

recovery or other plans developed with and supported by regional and subbasin 

stakeholders (rather than those that are isolated, stand-alone efforts). 

• Actions that have regional and local support and generate increased participation.

• Actions that demonstrate cost effectiveness relative to alternative means of achieving the 

same objectives.

• Actions that have high degree of certainty in effectiveness and outcome.
ESA Recovery Plan: Snake River Sockeye Salmon | 260

June 2015| NOAA Fisheries 

7.1 Building on Current Efforts

Important recovery actions for Sockeye Salmon are already being implemented. The Stanley Basin 

Sockeye Technical Oversight Committee (SBSTOC), a team of biologists representing the BPA, IDFG, 

the Shoshone-Bannock Tribes, and NMFS, coordinates the ongoing captive broodstock program. This 

Sockeye Salmon captive broodstock program has been vital to helping the species avoid extinction, and 

remains an important part of this recovery plan.

In addition, numerous habitat conservation efforts have taken place over the past 20 to 30 years to 

protect, conserve, and restore Snake River Sockeye Salmon in Idaho. These conservation actions have 

balanced the biological and ecological needs of the species with the growing economic and resource 

management demands of the region. Water and land managers, private landowners, public interest 

groups and others have completed many tributary habitat restoration projects in the Sawtooth Valley and 

Snake River and Salmon River watersheds using a variety of funding sources. Implementing entities 

include BPA, Bureau of Reclamation, Natural Resource Conservation Service (NRCS), soil and water 

conservation districts, the Shoshone-Bannock Tribes, IDFG, U.S. Forest Service, irrigation districts, 

private landowners, and several public interest groups. Because of the collective habitat and hydropower 

improvements and education efforts by these various partners, instream, riparian, and upland habitat 

conditions in many parts of these watersheds continue to improve. 

Much of the Salmon River watershed displays near pristine habitat conditions, largely due to the many 

conservation efforts that have already taken place to protect, conserve, and restore habitats on public and 

private lands. As a result, the natural ecological processes needed to support a viable Sockeye Salmon

population already exist in many areas. In the Sawtooth Valley, Sockeye Salmon natal lakes lie within 

the Sawtooth National Recreation Area and much of the headwaters of each drainage is designated as 

wilderness. Overall, habitat conditions for Snake River Sockeye Salmon in these high mountain lakes 

remain in excellent shape and therefore this important habitat is relatively pristine. 

Steps to manage fisheries that could potentially affect Snake River Sockeye Salmon are also in place. 

Currently there are no fisheries targeting Snake River Sockeye Salmon. Incidental take of Sockeye 

Salmon in fisheries targeting other species is limited through careful monitoring and evaluation. 

Actions identified here build on fishery management efforts in the Salmon River basin.

Important hydropower-related efforts that will benefit recovery of Snake River Sockeye Salmon are also 

underway. As discussed in Section 6, the current mainstem hydro operations, the effects of which are 

summarized in the Hydro Module (NMFS 2014a), and any further improvements for fish survival that 

may result through the ongoing FCRPS collaborative process, represent the hydropower recovery 

strategy for Snake River Sockeye Salmon and all listed salmonids that migrate through the mainstem 

Columbia River.

NMFS acknowledges the important contributions made through these different efforts and recognizes 

their crucial role in Snake River Sockeye Salmon recovery. NMFS plans to work with all entities and 

interested landowners to effectively implement this recovery plan. Achieving recovery will require a 
ESA Recovery Plan: Snake River Sockeye Salmon | 261

June 2015| NOAA Fisheries 

cooperative local, regional, and ESU-specific approach that addresses threats to species viability 

throughout the life cycle — including those that affect tributary and estuary habitats, as well as harvest, 

hatcheries, and hydropower development and operations. Section10 describes a proposed organizational 

framework to implement and track implementation of proposed actions described in this recovery plan. 

Prioritizing recovery actions for Snake River Sockeye Salmon in Idaho would be a primary task of the 

proposed implementation teams (see Section 10); developed with local input from groups currently 

doing recovery work.

7.2 Site-Specific Actions to Recover Snake River Sockeye Salmon at the 

Local Level (Sawtooth Valley and upper Salmon River)

Actions identified in this section address local limiting factors and threats to recovery of the Snake River 

Sockeye Salmon ESU. The proposed actions are directly linked to the recovery strategies identified in 

Section 6.3.1. This section is organized by strategy with corresponding actions in the same order 

presented in Section 6.3.1. 

Sections 7.2.1 through 7.2.16 briefly describe the recovery strategies and actions to recover Snake River 

Sockeye Salmon at the local level (Sawtooth Valley and upper Salmon River). Table 7-1 defines the 

specific actions proposed under each strategy to address problems for Sockeye Salmon in the natal lakes 

and upper Salmon River. The table identifies the actions as well as the sites, VSP parameters, limiting 

factors, and threats that each action targets. The tables also provide estimated costs and potential 

implementing entities for each action, and priority for implementation. The actions address the limiting 

factors and threats identified in Section 5. 

7.2.1 Conserve Population Genetic and Life History Diversity, and Spatial Structure

The goal of this Snake River Sockeye Salmon Recovery Plan is the restoration of natural Sockeye 

Salmon populations in Sawtooth Valley lakes. Hatchery production has played a central role in the 

initial phase of the recovery strategy for the Snake River Sockeye Salmon ESU. Without the 

reproductive contribution that hatchery fish have made to natural production through the captive 

broodstock program, this ESU would likely be extinct. 

The Redfish Lake Sockeye Salmon Captive Broodstock Program has been vital to helping the 

population avoid extinction. The captive broodstock program is modeled, to the extent possible, on the 

population structure, mating protocol, growth, morphology, nutrient cycling, and other biological 

characteristics of the naturally spawning population. The number of program fish currently released at 

each life stage is conservative when considered in the context of the system’s historical carrying 

capacity. Paleolimnological information also indicates that the planned release of up to one million 

smolts from the Springfield Hatchery is also consistent with historical carrying capacity. The genetic 

focus of the program, and adherence to various central tenets of conservation aquaculture, has enabled 

program managers to retain approximately 95% of the original founding genetic variability of the 

population (Kalinowski et al. 2012). 
ESA Recovery Plan: Snake River Sockeye Salmon | 262

June 2015| NOAA Fisheries 

The existing captive broodstock program is now transitioning to a production program that will use 

anadromous Sockeye Salmon adults collected at Sawtooth Valley weirs as broodstock. This new 

program will allow gene banking (while captive adults are available) and provide high levels of 

anadromous adult returns to recolonize available habitat in Redfish Lake, Pettit Lake, and possibly other 

Sawtooth Valley lakes. Springfield Hatchery will play a central role in this new program. This new 

Sockeye Salmon smolt-rearing hatchery is capable of producing up to one million full-term smolts 

annually. Eggs for the expanded smolt program will be produced at the IDFG Eagle Fish Hatchery 

broodstock station and from increased production from NMFS’ facilities in Washington State. Using a 

conservative smolt-to-adult return rate of 0.50% for hatchery-reared and released smolts (based on 

empirical program information), managers anticipate that a release of up to one million smolts from the 

Springfield Hatchery could consistently return an average of 5,000 anadromous adults to the Sawtooth 

Valley annually. This level of adult returns will help jumpstart demographic processes for the Sockeye 

Salmon population in Redfish Lake. These expansion efforts are consistent with expectations 

established through the Biological Opinion developed by NMFS to address risks associated with the 

operation of the Federal Columbia River Power System. The recovery strategy includes the 

implementation of this conservation hatchery program, with the intent to balance the adverse short-term 

impacts on diversity and adaptation to captivity versus the long-term risk of population extirpation. 

Captive broodstock (or, if available, hatchery anadromous adults) will also be released into Pettit Lake 

for a defined period. Steps will be taken to ensure that these adults represent the entire genetic diversity 

of the broodstock for several years. These initial hatchery releases into Pettit Lake will cease after a few 

years to evaluate natural production response and refine the reintroduction program (see Section 

6.3.1.5). 

The recovery strategy for the Alturas Lake population aims to maintain the population’s genetically 

unique early stream spawning characteristics. Actions to restore this early spawning population will be 

developed based on recommendations from the Sockeye Salmon Implementation and Science Team and 

SBSTOC and as outlined in Section 6.3.1.6. 

Table 7-1 describes proposed hatchery recovery actions to address limiting factors and threats identified 

in Section 5.3 and Recovery Strategy 6.3.1.1. Conserve population genetic and life history diversity, and 

spatial structure. Proposed hatchery actions include:

1. Continue expansion of Snake River Sockeye Salmon captive brood program.

a. Fund and support infrastructure needs to increase smolt program to one million smolt 

release (i.e., at the Springfield Hatchery).

b. Describe conditions under which trapping would occur at various locations, including 

Lower Granite Dam.

c. Fund improvements to temporary adult holding capability at Sawtooth hatchery and 

Redfish Lake Creek (i.e., associated with operations of the weir).
ESA Recovery Plan: Snake River Sockeye Salmon | 263

June 2015| NOAA Fisheries 

2. Investigate alternatives and develop actions to support and enhance anadromy of the residual 

Alturas Lake population.

7.2.2 Increase Naturally Spawning Snake River Sockeye Salmon Abundance

The recovery strategy aims to achieve viable, naturally spawning self-sustaining Sockeye Salmon

populations by increasing the number of anadromous adults that spawn naturally in the Sawtooth Valley 

lakes. The strategy builds on the current captive broodstock program. It implements a coordinated 

conservation hatchery program focused primarily on achieving population recolonization goals for 

Redfish Lake. The program includes implementation of the 2011 Springfield Sockeye Salmon Hatchery 

Master Plan through construction of a new Sockeye Salmon smolt production hatchery (completed in 

2013) and implementation of associated program management goals. The Master Plan targets efforts to 

secure the Redfish Lake population. 

The recovery strategy also aims to increase spatial structure of the ESU by restoring natural production 

of Sockeye Salmon in Pettit, Alturas, and other Sawtooth Valley lakes. Programs for these lakes will be 

developed to promote the chances of successful reintroduction of sustainable natural production.

The proposed actions involve converting operations to Springfield Hatchery facilities that are capable of 

rearing up to one million Snake River Sockeye Salmon juveniles to the full-term smolt stage of 

development. Fish produced at the hatchery will be transported and released in the outlet of Redfish 

Lake. Adults produced through the captive broodstock program will also be released into Pettit Lake for 

a defined period. As adult run size increases, the goal is to eliminate redundant facilities (e.g., those 

needed for captive broodstock) and transition the program to the next phase of implementation.

The program includes monitoring the effects of increased hatchery production on the residual Sockeye 

Salmon populations. Monitoring will also be used to safeguard against potential risks, including 

potential genetic and ecological risks, and address uncertainties. 

7.2.3 Improve Sockeye Salmon Passage to Natal Lakes

Proposed actions will improve Sockeye Salmon passage to the natal lakes by addressing passage barriers 

caused by artificial barriers, low stream flow, hatchery practices, and other factors. The actions improve 

fish passage at the Sawtooth Hatchery weir on the Salmon River. They aim to revise adult holding and 

handling practices at Redfish Lake Creek to increase returns to Redfish Lake. The proposed actions also 

seek to examine and address the lake trout management issue for Stanley Lake. They also address 

concerns regarding Sockeye Salmon passage survival in the Salmon and lower Snake Rivers.
ESA Recovery Plan: Snake River Sockeye Salmon | 264

June 2015| NOAA Fisheries 

7.2.4 Reestablish a Self-sustaining Anadromous Sockeye Salmon Population in Redfish 

Lake

Actions to secure the Redfish Lake Sockeye Salmon population form the centerpiece of Phase 2 of the 

Snake River Sockeye Salmon natural stock reintroduction and adaptation program. Phase 1 focused on 

establishing anadromous returns from natal origin Redfish Lake Sockeye Salmon stock through a 

captive broodstock program. That program is poised to transition to Phase 2, with an emphasis on 

supporting relatively high levels of anadromous return Sockeye Salmon to Redfish Lake. Proposed 

actions will convert hatchery operations to Springfield Hatchery facilities that are capable of rearing up 

to one million Snake River Sockeye Salmon juveniles. The actions aim to reestablish a naturally 

spawning self-sustaining population in Redfish Lake by increasing the number of anadromous adults in 

the lake. The working hypotheses behind this approach assumes that the natural production that will 

result from relatively high levels of anadromous hatchery returns will lead to increases in productivity 

and downstream survivals sufficient to allow for transition to Phase 3, emphasizing natural adaptation. 

As adult run size to Redfish Lake increases, the goal is to transition to a phase that would focus on 

maintaining genetic variability and limiting domestication.

7.2.5 Investigate and Develop Strategies and Implement Actions to Support and 

Enhance Sawtooth Valley Sockeye Salmon Reintroduction and Adaptation Phases for 

Pettit Lake

Initially, Sockeye Salmon reintroduction efforts will focus primarily on the Redfish Lake population 

because of its high production potential and the availability of a hatchery stock derived from natal 

resident production. Adults produced through the captive broodstock program will also be released into 

Pettit Lake for a defined period based on the recovery strategy described in Section 6.3.1.5. Based on 

the response to the initial reintroductions and the performance of the Redfish Lake program in 

promoting natural production, the program for Pettit Lake will also be refined to reestablish a locally 

adapted population in Pettit Lake. This would include determining whether additional inputs of Redfish 

Lake fish in Pettit Lake would be warranted, and monitoring programs to track outmigrants and 

returning spawners.

7.2.6 Investigate and Evaluate the Potential for Restoring Natural Production of 

Anadromous Sockeye Salmon from returning Kokanee Outmigrants from Alturas Lake

Based on the recovery strategy for reintroduction to Alturas Lake that will be refined in the future, 

proposed actions may include (1) trap and transport any anadromous adults identified as Alturas Lake 

origin to Alturas Lake, and the option to subsequently implement a hatchery program at the same time or 

later by (2) identifying appropriate donor stocks and strategies to establish a new hatchery/captive 

broodstock program for anadromous Alturas Lake Sockeye Salmon recovery efforts (Section 6.3.1.6). 

Managers will investigate several alternative strategies for the Alturas Lake kokanee population that will 

support and enhance anadromy. In the interim, while decisions are being made regarding anadromous 

Alturas Lake Sockeye Salmon recovery efforts, any ocean-returning Sockeye Salmon identified as of 

Alturas Lake origin will be transported to Alturas Lake and released.
ESA Recovery Plan: Snake River Sockeye Salmon | 265

June 2015| NOAA Fisheries 

7.2.7 As Sufficient Numbers of Natural-Origin Adults Return, Develop an Integrated 

Approach to Manage Natural and Hatchery-Origin Adults in the Hatchery Program and 

in the Wild

In Phase 3 of the Sockeye Salmon recovery strategy, hatchery activities to assist Sockeye Salmon

reintroduction efforts will be transitioned to an appropriate longer-term role emphasizing natural 

adaptation consistent with maintaining genetic variability and limiting domestication. As natural-origin 

returns increase, hatchery-origin returns will be reduced by reducing the number of hatchery-origin 

smolts released. Triggers will be used to determine when hatchery-origin releases should be reduced or 

eliminated, thereby decreasing risk of the program to the natural population. Research, monitoring, and 

evaluation activities will also be implemented to assess the effectiveness and outcomes of the program. 

Collectively, information from these activities will be used to manage the hatchery program adaptively 

on a yearly basis.

7.2.8 As Sufficient Numbers of Hatchery-Origin Anadromous Adults Return to the Basin, 

Identify Options for Future Fisheries

As the Sockeye Salmon recovery program is implemented, the return of first generation adults is 

expected to generate large returns of anadromous hatchery-origin Sockeye Salmon to the Sawtooth 

Valley. These returns will be beyond levels needed to effectively manage broodstock composition as 

well as spawner composition in the habitat. The natural production that will result from these high 

levels of anadromous hatchery returns is expected to lead to increases in relative productivity and 

overall life cycle survival. Managers can adjust the number of smolts released to manage numbers of 

returning adults. However, another useful tool to manage returning fish is the potential for state and 

tribal fisheries on hatchery Snake River Sockeye Salmon. 

As returns increase, NMFS will work with the appropriate co-managers to develop a new abundancebased harvest management framework for Snake River Sockeye Salmon. Harvest levels will be 

calibrated to indicators of species’ status that are identified in the Recovery Plan and the operation and 

planning objectives of the Springfield Hatchery. A new harvest management framework will require 

decisions about where the harvest may occur along various points in the migration corridor and in the 

terminal areas. Those allocation choices will be developed by the state and tribal co-managers. Resulting 

recommendations will be consistent with provisions of the ESA, NEPA, and the U.S. v. Oregon

Agreement.

7.2.9 Continue Research and Actions to Reestablish Natural Populations in Other Natal 

Lakes

The Recovery Plan prioritizes the implementation of actions in Redfish Lake, the lake with the greatest 

production potential. The Recovery Plan also identifies high priority actions in Pettit Lake and Alturas 

Lake. Considering these priorities and when appropriate, managers will consider potential Sockeye 

Salmon reintroductions to Stanley and Yellowbelly Lakes. Currently, more information and 

consideration is needed to identify the role each of these lakes might play in future phases of the 
ESA Recovery Plan: Snake River Sockeye Salmon | 266

June 2015| NOAA Fisheries 

reintroduction efforts. For example, in the interim, as anadromous returns increase and connectivity to 

the upper Sawtooth Valley lakes is restored, it is anticipated that natural recolonization of Yellowbelly 

Lake may occur. In addition, more planning and evaluation is required to address uncertainties related 

to the presence of lake trout in Stanley Lake. Reintroduction efforts for Stanley Lake Sockeye Salmon

include developing a lake trout management strategy and removal of the barrier at the outlet of Stanley 

Lake that currently prevents Sockeye Salmon immigration, as well as immigration of other species (e.g., 

bull trout, suckers, pikeminnow). In addition, more information is needed to understand how varying 

flow regimes affect Sockeye Salmon migration and passage below and above Yellowbelly Lake. 

Further actions are also needed to investigate habitat capacity in the lakes, and potential predation and 

competition issues with non-native trout and kokanee in the lakes.

7.2.10 Continue Research on Natal Lakes’ Carrying Capacity, Nutrients, and Ecology 

Actions under this strategy continue research and monitoring to understand the limnological 

characteristics of the Sawtooth Valley lakes and the lakes’ carrying capacities for Sockeye Salmon

production. The actions build upon research carried out for many years by the Shoshone-Bannock 

Tribes to assess the period and frequency of lake stratification and subsequent turnover, together with 

research on lake algal productivity.

The carrying capacity of the natal lakes is believed to be linked to zooplankton levels. Since 1995, the 

Shoshone-Bannock Tribes have been supplementing Pettit and Alturas Lakes with nitrogen and 

phosphorus, and controlling non-native kokanee salmon in some years, which compete with Sockeye 

Salmon for food resources. Based on water quality and biological sampling described in their annual 

reports (e.g., Kohler et al. 2008), these management strategies are increasing the carrying capacities of 

the lakes for rearing juvenile Snake River Sockeye Salmon (based on newer genetic information, 

controlling kokanee salmon populations has been discontinued in Alturas Lake): 

• Continue limnological and ecological research and evaluations of the lakes. 

• Address nutrients as limiting factors in all lakes used for Sockeye Salmon recovery and 

study relationship to prey base in natal lakes.

• Research possible competition for food resources or spawning areas in natal lakes.

• Develop a time table and strategy for whole-lake nitrification efforts compatible with 

reintroduction plans.

7.2.11 Protect and Conserve Natural Ecological Processes at the Watershed Scale that 

Support Population Viability: Salmon River Habitat and Natal Lakes Watershed

Much of the area surrounding the lakes is designated as wilderness and displays near pristine habitat 

conditions, largely due to the many conservation efforts that have already taken place to protect, 

conserve, and restore habitats on public and private lands. As a result, the natural ecological processes 

needed to support a viable Sockeye Salmon population already exist in many areas. Actions aim to 

maintain current protection and consistently apply best management practices and existing laws to 
ESA Recovery Plan: Snake River Sockeye Salmon | 267

June 2015| NOAA Fisheries 

protect and conserve natural ecological processes. Actions to apply best management practices will also 

work to improve natural ecological processes and functions in degraded areas. 

These recommended recovery actions have been compiled from available publications (e.g., hatchery 

operating plan, listing decisions, agency work plans, sub-basin plans, FCRPS BiOp actions and USFS 

forest management plans, and from meetings and discussions with local biologists and natural resource 

specialists from IDFG, Shoshone-Bannock Tribes, USFS, NRCS, SWCD, BPA, and others).

7.2.12 Protect, Restore, and Manage Spawning and Rearing Habitat

Actions that protect and conserve natural ecological processes will also act to protect spawning and 

rearing habitats in the natal lakes. These actions include maintaining current wilderness protection in 

the natal lakes watersheds in the Sawtooth National Recreation Area. Additional actions aim to 

conserve rare and unique habitats for Sockeye Salmon. The actions will also improve water quality and 

address other concerns by consistently applying best management practices and existing laws. In 

addition, research and monitoring actions will help determine if spawning and rearing habitat at the 

different lakes is adequate to meet Sockeye Salmon abundance goals.

 

7.2.13 Maintain Unimpaired Water Quality and Improve Water Quality as Needed

Limnology studies conducted in Stanley, Redfish, Yellowbelly, Pettit, and Alturas Lakes since 1991 

indicate that water quality in all five lakes generally provides suitable rearing habitat for juvenile 

Sockeye Salmon, although zooplankton levels in the lakes can vary considerably. There is always a 

potential risk, however, that recreational use on the lakes and lakeshores could result in a chemical spill, 

or otherwise damage Sockeye Salmon spawning and rearing habitat. In addition, some reaches of the 

Salmon River and tributaries exhibit temporary elevated water temperatures and sediment levels that 

could restrict Sockeye Salmon production and survival. 

Recovery actions call to maintain current protection and consistently apply best management practices 

and existing laws to protect unimpaired water quality, improve degraded water quality, and minimize 

potential risks. 

7.2.14 Investigate and Improve Conditions in Salmon River and Tributaries to Support 

Increased Survival of Migrating Snake River Sockeye Salmon

Adult Sockeye Salmon usually arrive in the Salmon River when flows are low and water temperatures 

reach their highest levels. Monitoring efforts suggest that high water temperatures in some reaches of 

the Salmon River may be impacting adult Sockeye Salmon migration survival; however, it is not clear 

where this occurs. Currently, the stretch of the Salmon River from Redfish Creek to Valley Creek is 

included on IDEQ’s 2010 303(d) list due to elevated water temperatures and sediment levels above 

levels needed to support cold-water aquatic life. High water temperatures may also limit survival of 

migrating Sockeye Salmon in the lower Snake River above Lower Granite Dam. 
ESA Recovery Plan: Snake River Sockeye Salmon | 268

June 2015| NOAA Fisheries 

Juvenile Sockeye Salmon losses also occur in the Salmon River, particularly in reaches between release 

sites and the North Fork Salmon confluence. Predation appears to be a primary cause for these losses but 

other factors contribute to the losses. 

Recovery actions call for continued investigation to determine the impact of high water temperatures on 

the survival of migrating adult Sockeye Salmon in the Salmon and lower Snake Rivers. They also call 

for continued investigations of juvenile Sockeye Salmon migration to determine where and why losses 

are occurring. Actions will also improve stream tributary habitat leading from natal lakes to the Salmon 

River in the Sawtooth Valley through habitat restoration on public and private lands. Actions will also

be taken to restore habitat along the lower Snake River mainstem above Lower Granite Dam. 

Further, new information on the best methods for improving salmon habitat in the face of climate 

change will be used to help define and prioritize habitat restoration actions. New climate change 

research, such as Beechie et al. (2012), describes the best methods to apply for restoring salmon habitat 

in particular types of environments. Researchers found that restoring floodplain connectivity, restoring 

stream flow regimes, and regrading incised channels are the actions most likely to ameliorate stream 

flow and temperature changes, and increase habitat diversity and population resilience. 

7.2.15 Monitor and Control Predation, Disease, Aquatic Invasive Species, and 

Competition and Develop Actions as Needed

Actions that reduce predation, disease, and competition by introduced stocks on Snake River Sockeye 

Salmon should enhance the probability that the ESU can be recovered to a self-sustaining population. 

Ecological theory and confirming studies on Sockeye Salmon indicate that competition for food 

resources is greater within, than between species (Hartman and Burgner 1972, Reiman and Myers 1992, 

Rich et al. 2009, Hyatt and Stockner 1985). This suggests that population growth of anadromous Snake 

River Sockeye Salmon in Sawtooth Valley lakes may be limited by intraspecific competition for food 

resources with native and introduced kokanee (resident life history strategy). Actions proposed to 

reduce introduced kokanee numbers in lakes targeted for recovery of Snake River Sockeye Salmon

should enhance the survival of the listed ESU by reducing food resource competition. Similarly, actions 

to reduce the number of other introduced species that compete with or prey on anadromous Snake River 

Sockeye Salmon should also enhance the ESU’s chances for recovery. Actions to continue evaluations 

of the carrying capacity within the different lakes and biomass will help determine overall levels of 

competition between kokanee and Sockeye Salmon and identify appropriate management actions. 

Actions also address concerns regarding invasive species, such as zebra and quagga mussels, Eurasian 

water Milfoil, and Chytrid fungus. The Idaho Department of Agriculture coordinates activities across the 

state to prevent aquatic species infestations by working with state and Federal agencies, local 

governments and non-governmental organizations. The Sawtooth National Forest works with the Idaho 

Department of Agriculture to maintain a seasonal boat inspection station at the Redfish Lake Sandy 
ESA Recovery Plan: Snake River Sockeye Salmon | 269

June 2015| NOAA Fisheries 

Beach boat ramp. It is critically important that such efforts continue to prevent introductions of highly 

invasive aquatic species, such as quagga and zebra mussels. 

7.2.16 Create an Adaptive Management Feedback Loop to Track Progress and Refine 

Strategies and Actions

This Plan identifies actions to track progress, define weaknesses, and adjust course appropriately. 

Section 11 describes research, monitoring, and evaluation actions to support adaptive management for 

the recovery of the Snake River Sockeye Salmon ESU. Section 10 describes a proposed framework for 

coordinating implementation of the Plan and identifies the teams that will oversee implementation. The 

Snake River Sockeye Salmon Implementation and Science Team will be responsible for coordinating 

implementation of the Adaptive Management and Research, Monitoring, and Evaluation Plan. 
ESA Recovery Plan: Snake River Sockeye Salmon | 270

June 2015| NOAA Fisheries 

Table 7-1. Summary of proposed local-level (Sawtooth Valley and upper Salmon River) recovery actions (see Box 6-1 for recovery strategies listed below).

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

VSP*

Parameter 

Addressed

Limiting 

Factors 

Addressed

Threats

Addressed

Life Stages 

Affected

Estimated 

Costs

($K/year)

Timing

(near, mid and 

long-term)

Potential 

Implementing

Entity**

Comments

Recovery Strategy 7.2.1: Conserve population genetic and life history and spatial structure

7.2.1-1

1. Continue to fund 

annual operation of the 

Sockeye Salmon captive 

broodstock propagation 

program.

Sawtooth 

Valley

A, D

Reduced 

abundance

Reduced 

abundance

All life 

stages

3,014 Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-2

2. Fund modifications to 

Sawtooth Hatchery weir 

to improve Sockeye 

Salmon trapping 

efficiency and provide 

adult access to upper 

salmon nursery lakes. 

Sawtooth 

Valley A, SS, D

Reduced 

abundance, 

straying

Hatchery weir 

operation

Adult

To be 

determined

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

Capital project; 

Could be reduced 

abundance if fish don’t 

enter the trap and stray or 

spawn in other locations.

7.2.1-3

3. Determine additional 

detection needs (e.g., 

PIT-tag detectors) in the 

Salmon River.

Salmon 

River

A

Reduced 

migration 

survival

Downstream 

mortality

Juvenile 

outmigrants; 

adult returns

To be 

Determined 

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-4

4. Describe conditions 

under which trapping 

would occur at various 

locations, including 

Lower Granite Dam.

Snake River A, D

Reduced 

migration 

survival

Upstream 

mortality

Adult returns

IDFG, NMFS, 

ShoshoneBannock Tribes

This is currently being 

developed.

7.2.1-5

5. Determine changes in 

marking/tagging levels 

for increased precision to 

Salmon R. A

Reduced 

migration 

survival

Downstream 

mortality

Juvenile

To be 

Determined

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes
ESA Recovery Plan: Snake River Sockeye Salmon | 271

June 2015| NOAA Fisheries 

evaluate downstream 

sources of mortality.

7.2.1-6

6. In the near term at 

Sawtooth Hatchery, 

identify ways to improve 

handling of adults to 

collect genetic data of 

fish returning to Alturas 

Lake, Pettit Lake or 

Redfish Lake.

Sawtooth 

Valley A, SS, D

Reduced 

population 

structure and 

distribution

Hatchery weir 

operation

Adult

To be 

determined

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-7

7. Identify actions to 

improve fish passage at 

Sawtooth Hatchery weir 

to allow fish to return to 

natal lake of origin. 

Sawtooth 

Valley

A, SS, D

Reduced 

population 

structure and 

distribution

Hatchery weir 

operation

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term

IDFG, NMFS, 

ShoshoneBannock TribesAlso a predation issue.

7.2.1-8

8. Maintain current 

marking/tagging levels.

Sawtooth 

Valley

A

Reduced 

migration 

survival

Reduced 

population 

structure

Juvenile Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-9

9. Identify lake of origin 

for adults returning to 

basin collection facilities.

Sawtooth 

Valley SS, D

Reduced 

population 

structure

Reduced 

population 

structure

Adult

To be

determined

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-10

10. Mark sufficient 

numbers of outmigrants 

from each lake to enable 

collection of returning 

spawners specific to lake 

of origin.

Sawtooth 

Valley

SS, D

Reduced 

population 

structure

Reduced 

population 

structure

Juvenile 

outmigrants

To be 

determined

Near-term 

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-11

11. Continue to sort 

returning adults at basin 

Sawtooth 

Valley

SS, D

Reduced 

population 

Reduced 

population 

Adult

To be 

determined

Near-term

IDFG, NMFS, 

Shoshone-
ESA Recovery Plan: Snake River Sockeye Salmon | 272

June 2015| NOAA Fisheries 

weirs based on marks 

identifying lake of origin.

structure structure Bannock Tribes

7.2.1-12

12. Transport returning 

adults to lake of origin or 

to hatchery program 

based on lake of origin or 

allow passage of adults.

Sawtooth 

Valley SS, D

Reduced 

population 

structure

Reduced 

population 

structure

Adult

To be 

determined

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.1-13

13. Develop guidance 

and recommendations for 

a preferred recovery 

strategy (ies) for O. nerka

life history forms of 

Snake River Sockeye 

Salmon. 

Sawtooth 

Valley

D,SS

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

Not 

Applicable

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

Technical staff and policy 

action.

7.2.1-14

14. Develop long-term 

guidelines to support and 

maintain localized 

adaptations within and 

among populations. 

Sawtooth 

Valley

D,SS

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

Not 

applicable

Near-term NMFS Technical staff and policy 

action.

7.2.1-15

15. Investigate and 

address known or 

potential spawning 

security threats from lake 

and lakeshore recreation 

uses and/ or 

developments.

Sawtooth 

Valley Lakes

A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, 

rearing habitat

Potential 

habitat 

degrading 

recreation 

uses

Adult 

spawning, 

incubation, 

early juvenile

To be 

determined

Mid-term

USFS, NMFS, 

IDFG

Recovery Strategy 7.2.2: Increase naturally spawning Snake River Sockeye Salmon abundance

7.2.2-1

1. Manage Springfield 

Hatchery to meet 

Sockeye Salmon

Sawtooth 

Valley

A

Reduced 

abundance

Reduced 

abundance

All life 

stages

Near-term IDFG Springfield Hatchery 

opened in 2013.
ESA Recovery Plan: Snake River Sockeye Salmon | 273

June 2015| NOAA Fisheries 

recovery goals.

7.2.2-2

2. Increase annual 

hatchery smolt releases 

to 1 million through 

funding of additional 

hatchery facility(ies).

Sawtooth 

Valley

A

Reduced 

abundance

Reduced 

abundance

All life 

stages

Near-term

IDFG,

BPA

7.2.2-3

3. Replace Redfish Lake 

weir and trap to allow 

handling and holding of 

larger adult returns

3.5. Modify the Sawtooth 

Hatchery weir to improve 

Sockeye Salmon

trapping efficiency and 

provide adult access to 

upper salmon nursery 

lakes.

Redfish Lake A,P

Hatcheryrelated 

adverse 

effects

Hatchery 

operations’ 

limited space

Adult returns

To be 

Determined

Near-term IDFG, BPA

7.2.2-4

4. Increase adult holding 

capacity at Sawtooth 

Hatchery to provide 

separate holding for 

Sockeye Salmon and 

improve fish passage so 

fish more readily enter 

the trap.

Sawtooth 

Valley A, SS, D

Reduced 

abundance, 

straying, 

Hatcheryrelated 

adverse 

effects

Hatchery weir 

operation, 

Hatchery 

operations’ 

limited space

Adult 

To be 

determined

Near-term IDFG

7.2.2-5

5. Develop plan 

describing objectives for 

Pettit Lake, e.g., will the 

program use Redfish 

Lake fish in Pettit Lake, 

Pettit Lake

SS, D

Reduced 

population 

structure

Reduced 

abundance; 

Reduced 

population 

structure

All life 

stages

Not 

Applicable

Near-term

IDFG, 

ShoshoneBannock Tribes

Technical staff and policy 

issue.
ESA Recovery Plan: Snake River Sockeye Salmon | 274

June 2015| NOAA Fisheries 

and what life stage(s) to 

release into Pettit Lake.

7.2.2-6

6. Mark sufficient 

numbers of outmigrants 

from Pettit and Alturas 

Lakes to enable 

collection of returning 

spawners specific to this 

lake.

Pettit Lake SS, D

Reduced 

population 

structure

Reduced 

abundance

Juvenile 

outmigrants

To be 

determined

Near-term

IDFG,

ShoshoneBannock Tribes

7.2.2-7

7. Transport returning 

adults identified as 

originating from Pettit 

and Alturas Lakes to that 

lake, or pass above weir 

for volitional migration, or 

retain as broodstock 

specific for Pettit and 

Alturas Lake releases.

Pettit Lake SS, D

Reduced 

population 

structure

Reduced 

abundance; 

Reduced 

population 

structure

Adult

To be 

determined

Mid-term IDFG

Recovery Strategy 7.2.3: Improve Sockeye Salmon passage to natal lakes

7.2.3-1

1. In the near term at 

Sawtooth Hatchery, 

identify ways to improve 

adult holding and 

handling of fish returning 

to Alturas Lake, Pettit 

Lake, or Redfish Lake.

Sawtooth 

Valley

A, SS, D

Reduced 

population 

structure and 

distribution

Hatchery weir 

operation

adult returns

Not 

Applicable

Near-term

IDFG, USFWS, 

ShoshoneBannock Tribes

Also a viability and 

predation issue; technical 

staff and policy issue.

7.2.3-2

2. Identify actions to 

improve fish passage at 

Sawtooth Hatchery weir 

to allow fish to enter 

Sawtooth 

Valley

A, SS, D

Reduced 

population 

structure and 

distribution

Hatchery weir 

operation

adult returns

To be 

determined

Near-term

IDFG, USFWS, 

ShoshoneBannock Tribes

Also a viability and 

predation issue.
ESA Recovery Plan: Snake River Sockeye Salmon | 275

June 2015| NOAA Fisheries 

natal lakes.

7.2.3-3

3. Reestablish adult 

passage at Stanley Lake. Stanley Lake SS, D Impaired fish 

passage

Barrier

Adult 

returns; 

juvenile 

outmigrants

To be 

determined

Mid-term

IDFG, BPA, 

USFS

7.2.3-4

4. Manage lake trout in 

Stanley Lake to minimize 

threats to Sockeye 

Salmon and remove 

barrier to volitional 

Sockeye Salmon

passage.

Stanley Lake SS, D Impaired fish 

passage

Barrier

Adult 

returns; 

juvenile 

outmigrants

Not applicable Mid-term

IDFG, USFS,

ShoshoneBannock 

Tribes, NMFS

Technical staff and policy 

issue.

7.2.3-5

5. Investigating passage 

survival and mortality 

factors during migration 

between natal lakes and 

Lower Granite Dam.

Salmon 

River

Lower Snake 

River

SS,D

Impaired fish 

passage,

Impaired

water quality, 

predation

Irrigation 

diversions and 

land use 

practices

Adult 

returns; 

juvenile 

outmigrants

To be 

determined

Near-term

IDFG, NMFS, 

IDEQ

7.2.3-6

6. Improve instream 

flows in the Salmon River 

above the Sawtooth 

Hatchery to Alturas Lake 

Creek by improving 

irrigation efficiencies, 

using IDWR water bank 

and other conservation 

tools.

Sawtooth 

Valley

SS, D

Impaired fish 

passage and 

water quality

Irrigation 

diversions and 

land use 

practices

Adult 

returns; 

juvenile 

outmigrants

To be 

Determined

Mid-Term

IDFG, IDWR, 

NMFS, USFS, 

Custer/Blaine 

Counties

7.2.3-7

7. Collect information 

about new pond 

development and stream 

flow in the Sawtooth 

Sawtooth 

Valley

SS, D

Impaired fish 

passage; 

water quality

Irrigation 

diversions, 

land use 

practices, 

Adult 

returns; 

juvenile 

outmigrants

To be 

determined

Mid-Term

IDFG, IDWR, 

NMFS, USFS
ESA Recovery Plan: Snake River Sockeye Salmon | 276

June 2015| NOAA Fisheries 

Valley and identify next 

steps to address these 

issues.

pond 

development

Recovery Strategy 7.2.4: Reestablish a self-sustaining anadromous Sockeye Salmon population in Redfish Lake

7.2.4-1

1. Manage Springfield 

Hatchery to meet 

Sockeye Salmon

recovery goals.

Redfish Lake A

Reduced 

abundance

Reduced 

abundance

All life 

stages

Near-term IDFG Springfield Hatchery 

opened in 2013.

7.2.4-2

2. Replace Redfish Lake 

weir and trap to allow 

handling and holding of 

larger adult returns.

Redfish Lake A,P Hatchery-related 

adverse effects

Hatchery 

operations’ 

limited space

Adult returns

To be 

determined

Near-term IDFG

7.2.4-3

3. Once adequate and 

consistent returns of 

anadromous adults are 

achieved, phase out the 

use of Redfish lake 

captive broodstock.

Redfish Lake A, D Adult returns

To be 

determined IDFG, NMFS

7.2.4-4

4. Implement Redfish 

Lake Complex Road and 

Bridge Reconstruction:

Redfish Road relocation, 

phase II; Redfish

Northshore 

reconfiguration/

reconstruction; Visitors 

Center parking 

relocation; replace inchannel vehicle bridge 

with pedestrian bridge.

Redfish Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, rearing 

habitat

Potential 

habitat 

degrading 

land use 

practices

Adult 

spawning, 

incubation, 

early juvenile

To be 

determined

Near-term USFS

NEPA planning complete. 

Outcomes include core 

objectives to reconfigure 

the entire North Shore / 

VA facilities to restore and 

maintain appropriate 

shoreline conditions. 

Listed in prerequisite 

order.
ESA Recovery Plan: Snake River Sockeye Salmon | 277

June 2015| NOAA Fisheries 

7.2.4-5

5. Complete Sockeye 

Campground renovation. Redfish Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, rearing 

habitat

Potential 

habitat 

degrading 

land use 

practices

Adult 

spawning, 

incubation, 

early juvenile

To be 

determined

Near-term USFS

NEPA planning complete. 

Would improve shore 

conditions within facility 

adjacent to Sockeye 

Beach. Includes sockeye 

interpretive facilities.

7.2.4-6

6. Implement active 

restoration objectives at 

Sandy Beach boat 

launch/day use.

Redfish Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, rearing 

habitat

Potential 

habitat 

degrading 

land use 

practices

Adult 

spawning, 

incubation, 

early juvenile

To be 

determined

Mid-term USFS

Would reverse 

deteriorating shoreline 

conditions within facility 

adjacent to Sockeye 

Beach.

7.2.4-7

7. Implement physical 

and administrative 

changes at Redfish Inlet 

Campground, dispersed 

camping, and trailhead 

area.

Redfish Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, rearing 

habitat

Potential 

habitat 

degrading 

land use 

practices

Adult 

spawning, 

incubation, 

early juvenile

To be 

determined

Mid-term USFS

Would reverse 

deteriorating shoreline 

conditions within facility 

adjacent to Sockeye 

Beach.

7.2.4-8

8. Implement Redfish 

Lake complex trail 

system.

Redfish Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, rearing 

habitat

Potential 

habitat 

degrading 

land use 

practices

Adult 

spawning, 

incubation, 

early juvenile

To be 

determined

Mid-term USFS

Would reverse 

deteriorating shoreline 

conditions adjacent to inlet 

spawning areas.

7.2.4-9

9. Identify impacts due to 

mooring and coordinate 

with County to develop 

mitigation plan.

Redfish Lake A, P

Degraded water 

quality, ecological 

processes

Potential 

habitat 

degrading 

land use 

practices, 

pollutant risks

Spawning, 

incubation, 

early 

juveniles

Near-term

USFS and 

county
ESA Recovery Plan: Snake River Sockeye Salmon | 278

June 2015| NOAA Fisheries 

Recovery Strategy 7.2.5: Investigate and develop strategies for future actions to support Sawtooth Valley Sockeye Salmon reintroduction and adaptation for Pettit Lake

7.2.5-1

1. Release adults 

produced through the 

captive broodstock 

program into Pettit Lake 

for a defined period.

Pettit Lake A,P,SS

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

To be 

determined

Near-term IDFG, NMFS

7.2.5-2

2. Refine program as 

needed to reestablish a 

locally adapted 

population in Pettit Lake.

Pettit Lake SS,D

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

To be 

determined

Mid-term IDFG, NMFS

7.2.5-3

3. Investigate and 

address potential water 

quality threats from 

lakeshore recreation 

residences.

Pettit Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, 

rearing habitat

Potential 

introduction of 

toxics

Adult

spawning, 

incubation, 

early juvenile

To be 

determined Long-term USFS, IDEQ

Could require new 

infrastructure or relocation 

of some facilities.

7.2.5-4 4. Complete removal of 

former barrier. Pettit Lake A, P

Potential loss/ 

degradation of 

high quality 

habitat

Habitat 

degrading 

facilities

Juvenile

outmigrants; 

adult returns

To be 

determined Long-term

ShoshoneBannock 

Tribes, USFS

Remove remaining barrier 

abutments, etc., that 

occupy streamside 

habitats.

Recovery Strategy 7.2.6: Investigate and evaluate the potential for restoring natural production of anadromous Sockeye Salmon from returning kokanee outmigrants from Alturas Lake

7.2.6-1

1. Determine appropriate 

strategies and actions for 

restoring natural 

production in Alturas 

Lake. Options may 

include trap and 

transport or establishing 

a new hatchery program. 

Alturas Lake SS,D

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

Near-term

NMFS, IDFG,

SBSTOC

This is a key information 

need that will also be 

included in Section 11 

RM&E. Same as # 14 

above.

7.2.6-2 2.Determine whether Alturas Lake Reduced To be 
ESA Recovery Plan: Snake River Sockeye Salmon | 279

June 2015| NOAA Fisheries 

Alturas Lake still contains 

anadromous or residual 

genetic resources.

SS,D Reduced 

population 

structure

population 

structure

All life 

stages

Determined Near-term NMFS, IDFG, 

SBSTOC

7.2.6-3

3. Implement Smokey 

Bear Campground and 

boat launch shoreline 

protections.

Alturas Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, 

rearing habitat

Habitat 

degrading 

facilities; 

potential 

habitat 

degradation 

land use 

practices 

Spawning, 

incubation, 

early 

juvenile, 

juvenile 

outmigrants, 

adult returns

To be 

determined

Near-term USFS

Would reverse 

deteriorating shoreline 

habitat conditions adjacent 

to historic shoal spawning 

areas.

Recovery Strategy 7.2.7: As sufficient numbers of natural-origin adults return, develop integrated approach to manage natural- and hatchery-origin adults in the hatchery program and the wild

7.2.7-1

1. Examine the benefits 

and/or risks of alternative 

strategies for recovering 

extant and/or historical 

life-history patterns in the 

natal lakes.

Sawtooth 

Valley SS,D

Reduced 

population 

structure

Reduced 

abundance

All life 

stages

Not 

applicable

ShoshoneBannock 

Tribes, IDFG, 

NMFS

Technical staff and policy 

issue.

7.2.7-2

2. Develop long-term 

guidelines to support and 

maintain localized 

adaptations within and 

among populations. 

Sawtooth 

Valley

D,SS

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

Not 

Applicable 

Near-term NMFS, IDFG

Technical staff and policy 

issue.

7.2.7-3

3. Manage Springfield 

Hatchery to meet 

Sockeye Salmon

recovery goals.

Redfish Lake A

Reduced 

abundance

Reduced 

abundance

All life 

stages

Near-term IDFG Springfield Hatchery 

opened in 2013.

7.2.7-4

4. Once adequate and 

consistent returns of 

anadromous adults are 

Redfish Lake A

Reduced 

abundance

Reduced 

abundance

Adults

To be 

determined

Mid-term

IDFG, NMFS, 

ShoshoneBannock Tribes
ESA Recovery Plan: Snake River Sockeye Salmon | 280

June 2015| NOAA Fisheries 

achieved, phase out the 

use of Redfish lake 

captive broodstock.

Recovery Strategy 7.2.8: As sufficient numbers of hatchery-origin anadromous adult’s return to the basin, identify options for future harvest.

7.2.8-1

1. Develop a new 

abundance-based 

harvest management 

framework for Snake 

River Sockeye Salmon.

Sawtooth 

Valley 

Salmon 

River

A

Reduced 

population 

structure

Competition 

Predation

Adults

To be 

determined

Mid-term

NMFS, IDFG, 

ShoshoneBannock Tribes

and other 

appropriate comanagers

Recovery Strategy 7.2.9: Continue research and actions to reestablish natural populations in other natal lakes

7.2.9-1

1. Develop plan 

describing objectives for 

Pettit Lake, e.g., whether 

or not the program 

would use Redfish Lake 

fish in Pettit Lake, and 

what life stage(s) to 

release into Pettit Lake.

Pettit Lake

SS, D

Reduced 

population 

structure

Reduced 

abundance; 

Reduced 

population 

structure 

All life 

stages

Not

applicable

Near-term

IDFG, NMFS,

ShoshoneBannock Tribes

Technical staff and policy 

issue.

7.2.9-2

2. Mark sufficient 

numbers of outmigrants 

from Pettit Lake to 

enable collection of 

returning spawners 

specific to this lake.

Pettit Lake SS, D

Reduced 

population 

structure

Reduced 

abundance

Juvenile 

outmigrants

To be 

determined

Mid-term

ShoshoneBannock 

Tribes; IDFG

Same as No. 1 above.

7.2.9-3

3. Construct 

juvenile/adult trapping 

structure in Alturas Lake 

Creek.

Alturas Lake 

Creek

A, P

Reduced 

population 

structure

Reduced 

abundance

Juvenile 

outmigrants

To be 

Determined

Mid-term

BPA, IDFG,

ShoshoneBannock Tribes

7.2.9-4 4.Improve/replace Pettit Lake A, P Reduced Reduced Juvenile Mid-term BPA 
ESA Recovery Plan: Snake River Sockeye Salmon | 281

June 2015| NOAA Fisheries 

juvenile trapping 

structure in Pettit Lake

Creek.

Creek population 

structure

abundance outmigrants To be 

determined

ShoshoneBannock Tribes

7.2.9-5

5. Identify lake of origin 

from adults returning to 

basin collection facilities.

Sawtooth 

Valley A, P

Reduced 

population 

structure

Reduced 

abundance

Adults

To be 

determined

Near-term IDFG

7.2.9-6

6.Continue to sort 

returning adults at 

Sawtooth weir, based on 

marks identifying source 

of outmigrant.

Sawtooth 

Valley

A, P

Reduced 

population 

structure

Reduced 

abundance

Adults

To be 

determined

Near-term IDFG

7.2.9-7

7.For returning spawners 

that are to spawn in 

upper basin lakes, pass 

for volitional migration or 

transport to appropriate 

lake.

Sawtooth 

Valley A, P

Reduced 

population 

structure

Reduced 

abundance

Adults

To be 

Determined

Near-term

IDFG, 

ShoshoneBannock Tribes

7.2.9-8

8. Investigate strategies 

to enhance and support 

anadromy in extant 

Alturas Lake early stream 

spawning Sockeye 

Salmon.

Alturas Lake A, P

Reduced 

population 

structure

Reduced 

abundance

Adult

Not

applicable

Near-term

IDFG; 

SBSTOC, 

NMFS

Technical staff and policy 

issue.

7.2.9-9

9. Continue limnological 

and ecological research 

and evaluations of the 

lakes.

Sawtooth 

Valley lakes

A, P

Reduced 

population 

structure

Reduced 

abundance

Juvenile 

outmigrants

Near-term

ShoshoneBannock Tribes

7.2.9-10

10. Address nutrients as 

limiting factors in all lakes 

used for Sockeye 

Sawtooth 

Valley lakes

A, P

Reduced 

population 

structure

Reduced 

abundance

Juvenile 

outmigrants

Near-term

ShoshoneBannock Tribes
ESA Recovery Plan: Snake River Sockeye Salmon | 282

June 2015| NOAA Fisheries 

Salmon recovery and 

study relationship to prey 

base in natal lakes.

7.2.9-11

11. Investigate and 

manage risks to native 

kokanee in Stanley Lake: 

i.e., outlet barrier, lake 

trout and non-native 

kokanee.

Stanley Lake A, P

Reduced 

population 

structure

Reduced 

abundance

Juvenile 

outmigrants

To be 

determined

Near-term IDFG, NMFS

7.2.9-12

12. Research possible 

competition for food 

resources or spawning 

areas in natal lakes.

Sawtooth 

Valley lakes

Reduced 

population 

structure

Reduced 

abundance

All life 

stages

To be 

determined

ShoshoneBannock Tribes

7.2.9-13

13. Determine 

appropriate broodstock 

and strategies for 

recovery of Sockeye 

Salmon in Stanley Lake .

Stanley Lake SS,D

Reduced 

population 

structure

Reduced 

population 

structure

All life 

stages

To be 

determined

Near-term

NMFS, IDFG,

SBSTOC

This is a key information 

need that will also be 

included in Section 11 

RM&E.

7.2.9-14

14. Identify actions to 

improve fish passage at 

Sawtooth Hatchery weir 

to allow fish to enter 

natal lakes.

Sawtooth 

Valley

A, SS, D

Reduced 

population 

structure and 

distribution

Hatchery weir 

operation

adult returns

Not 

applicable

Near-term

IDFG, USFWS, 

ShoshoneBannock Tribes

Also a viability and 

predation issue.

7.2.9-15

15. Manage lake trout in 

Stanley Lake to minimize 

threats to Sockeye 

Salmon and remove

barrier to volitional 

Sockeye Salmon

passage.

Stanley Lake A, SS, D Predation Barrier Adult returns Not applicable

IDFG, USFS, 

NMFS
ESA Recovery Plan: Snake River Sockeye Salmon | 283

June 2015| NOAA Fisheries 

7.2.9-16

16.Based on resolution 

of lake trout 

management , develop a 

program for Stanley Lake 

to support Sockeye 

Salmon recovery.

Stanley Lake SS.D

Reduced 

population 

structure and 

distribution

Barrier

Adult 

returns; 

juvenile 

outmigrants

To be 

determined

Mid-term

SBSTOC,

IDFG, NMFS

7.2.9-17

17. Reestablish adult 

passage at Stanley Lake. Stanley Lake SS, D Impaired fish passage

Barrier

Adult 

returns; 

juvenile 

outmigrants

To be 

determined

Mid-term

IDFG, BPA, 

USFS

Recovery Strategy 7.2.10: Continue research on natal lakes’ carrying capacity, nutrients and ecology

7.2.10-1

1. Conduct limnological 

studies to evaluate 

nursery lake habitat 

conditions encountered 

by adult and juvenile 

Sockeye Salmon during 

freshwater phase.

Sawtooth 

Valley A, P

PredatorPrey, 

Intraspecific

Competition,

Nutrient 

conditions

Current 

habitat 

conditions, 

Fish and 

wildlife 

management

Adult,

juvenile

Near-term

ShoshoneBannock Tribes

7.2.10-2

2. Determine if lake 

fertilization is necessary 

for each lake used for 

Sockeye Salmon

recovery, and, if 

warranted, develop and 

implement a plan to 

fertilize lakes to increase 

rearing habitat 

productivity.

Sawtooth 

Valley

A,P

Food 

availability; 

food quality

Food resource 

competition

Juvenile 

rearing

Near-term

NMFS, IDFG,

ShoshoneBannock Tribes

The selection of lakes to 

fertilize should align with 

the IDFG Master Plan and 

its implementation. 

7.2.10-3 3. Develop and 

implement a study in 

Yellowbelly 

Lake

A,P

Food 

availability; 

Food resource 

competition

Juvenile 

rearing

To be 

Determined 

Mid-term

ShoshoneBannock Tribes
ESA Recovery Plan: Snake River Sockeye Salmon | 284

June 2015| NOAA Fisheries 

Yellowbelly Lake to 

evaluate lake carrying 

capacity of Sockeye 

Salmon in the absence of 

resident kokanee.

food quality

7.2.10-4

4. Continue limnological 

and ecological research 

and evaluations of the 

lakes reduced population 

structure, distribution, 

abundance, diversity.

Stanley and 

Yellowbelly 

Lakes

A, P

Food 

availability; 

food quality

Food resource 

competition

Juvenile 

rearing

Near-term

ShoshoneBannock Tribes

Recovery Strategy 7.2.11: Protect and conserve natural ecological processes at the watershed scale that support population viability

7.2.11-1

1. Construct and 

maintain NMFSapproved fish screens.

upper 

Salmon 

River

A, P

Altered 

hydrology Irrigation 

withdrawals

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term

NMFS, IDFG,

SWCDs,

Irrigation 

Districts

Identify costs based on 

each fish screen design 

and specifications.

7.2.11-2

2. Maintain current 

wilderness protection for 

the ESU in the Sawtooth 

Wilderness area and 

protect the currently 

pristine watershed 

habitat.

Sawtooth 

Wilderness 

area

A, P

Potential loss/ 

degradation of 

high quality 

habitats 

Potential 

Recreation 

Disturbance

Juvenile 

outmigrants; 

adult returns

Mid-term USFS

7.2.11-3

3. Continue to implement 

the Sawtooth National 

Recreation Area’s 

Management Plan and 

restoration actions.

Sawtooth 

National 

Recreation 

Area

A, P

Potential loss/ 

degradation of 

high quality 

habitats 

Potential 

Recreation 

Disturbance

Juvenile 

outmigrants; 

adult returns

Mid-term USFS

7.2.11-4 4. Implement BMPs to 

protect and conserve 

Sawtooth 

Valley

A, P

Potential loss/ 

degradation of 

Potential 

Recreation 

Juvenile 

outmigrants; 

To be 

determined

Mid-term

USFS, SWCDs, 

Counties, 
ESA Recovery Plan: Snake River Sockeye Salmon | 285

June 2015| NOAA Fisheries 

ecological processes. high quality 

habitats 

Disturbance adult returns landowners

7.2.11-5

5. Implement public 

education and 

interpretation actions 

Sawtooth 

Valley

A,P,SS, D

Potential loss/ 

degradation of 

high quality 

habitats

Potential 

disturbance

Juveniles 

and adults

To be 

determined

USFS, SWCDs, 

NMFS

Recovery Strategy 7.2.12: Protect, restore and manage spawning and rearing habitat

7.2.12-1

1. Maintain appropriate 

protections to manage 

lakeshore recreation to 

minimize any potential 

disturbance in areas 

where Sockeye Salmon

spawn.

Sawtooth 

Valley A, P

Potential loss/ 

degradation of 

high quality 

habitats 

Recreation 

Disturbance

Adult 

spawning; 

incubation; 

early juvenile

Mid-term

USFS, 

IDFG

7.2.12-2

2. Maintain appropriate 

protections to continue to 

protect, restore and 

maintain spawning and 

rearing habitat.

Sawtooth 

Valley A,P

Potential loss/ 

degradation of 

high quality 

habitats 

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

Mid-term USFS, county

7.2.12-3

3. Maintain current 

wilderness protection in 

Sawtooth Wilderness 

Area.

Sawtooth 

Valley 

A, P

Potential loss/ 

degradation of 

high quality 

habitats 

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

Mid-term USFS

7.2.12-4

4. Continue appropriate 

protections to manage 

other human 

development to restore 

or maintain native 

vegetation that provides 

Sawtooth 

Valley

A, P

Potential loss/ 

degradation of 

high quality 

incubation 

and rearing 

habitat

Potential 

Recreation 

Disturbance

Adult 

spawning; 

incubation; 

early juvenile

Mid-term

USFS, 

IDFG
ESA Recovery Plan: Snake River Sockeye Salmon | 286

June 2015| NOAA Fisheries 

naturally resilient and 

productive shoreline 

habitat.

7.2.12-5

5. Identify ways to 

maintain current 

protections for Sockeye 

Salmon critical habitat in 

the future, if ESU is 

delisted.

Sawtooth 

Valley

A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning, 

rearing habitat

Potential 

habitatdegrading 

land use 

practices 

Adult 

spawning; 

incubation; 

early juvenile

To be 

determined

Mid-term

USFS, 

IDFG, County

This is important because 

critical habitat protection 

will no longer be 

designated when ESU is 

not listed.

Recovery Strategy 7.2.13: Maintain unimpaired water quality and improve water quality as needed

7.2.13-1

1. Continue to manage 

recreational use and 

motorized boat activity to 

minimize the risk of fuel 

spill and introduction of 

wastewater contaminants 

into lakes.

Sawtooth 

Valley A,P

Potential 

loss/Degradati

on of high 

quality 

spawning/incu

bation habitat

Potential 

introduction of 

Toxics

Adult 

spawning; 

incubation; 

early juvenile

Mid-term USFS, IDFG

7.2.13-2

2. Implement TMDLs for 

impaired water bodies in 

Salmon River watershed.

Salmon 

River 

watershed

A, P

Degraded 

water qual.; 

altered 

sediment 

routing

Agriculture 

development; 

irrigation, 

livestock 

grazing

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term IDEQ

7.2.13-3

3. Monitor contaminants 

to determine whether 

there is residual 

contamination with 

Toxaphene in three lakes 

or arsenic contamination 

in Alturas Lake.

Sawtooth 

Valley

A,P

Potential 

loss/Degradati

on of high 

quality 

spawning/incu

bation habitat

Potential 

introduction of 

Toxics

Adult 

spawning; 

incubation; 

early juvenile

To be 

determined Long-term IDEQ

7.2.13-4 4. Improve water quality Salmon A, P Degraded Agriculture Juvenile To be Mid-term SWCDs, USFS
ESA Recovery Plan: Snake River Sockeye Salmon | 287

June 2015| NOAA Fisheries 

(sediment) to maintain, 

enhance and restore fish 

habitat and passage.

River basin water qual.; 

altered 

sediment 

routing

development; 

irrigation, 

livestock 

grazing

outmigrants; 

adult returns

determined

7.2.13-5

5. Improve water quality

(sed., temp.) between 

Redfish Lake Creek and 

East Fork Salmon River.

Salmon 

River

A

Degraded 

water qual.; 

altered 

sediment 

routing

Agriculture 

development; 

irrigation, 

livestock 

grazing, 

roadways

Juvenile 

outmigrants; 

adult returns

To be 

determined Mid-term

SWCDs, IDFG,

ShoshoneBannock Tribes

7.2.13-6

6. Increase stream flow 

to improve hydrology by 

implementing water 

conservation measures, 

improved water delivery, 

and improving water 

storage function of 

riparian areas and 

wetlands.

Salmon 

River

(between 

East Fork 

confluence 

and the 

headwaters)

A

Altered 

hydrology,

Elevated 

water 

temperature,

Reduced 

stream flow

Irrigation 

withdrawals

Juvenile 

outmigrants; 

adult returns

To be 

determined

Mid-term

IDFG,

SWCDs,

Irrigation 

Districts,

landowners

7.2.13-7

7. Collect information 

about effects of new 

pond development on

stream flow and water 

quality. Identify next 

steps to address these 

issues. 

Sawtooth 

Valley and 

Salmon 

River

A,P

Degraded 

water quality, 

elevated 

temperature; 

altered 

sediment 

routing

Pond 

development

Spawning; 

incubation; 

juveniles; 

outmigrants, 

adult returns

To be 

determined

SWCDs, 

IDEQ, 

USFS
ESA Recovery Plan: Snake River Sockeye Salmon | 288

June 2015| NOAA Fisheries 

7.2.13-8

8. Implement Stanley 

Lake Recreation 

Complex Reconstruction:

Construct new upland 

campground loop; 

remove Stanley Inlet 

campground/ boat 

launch; construct 

sustainable shoreline trail 

system; configure 

dispersed recreation.

Stanley Lake A, P

Potential loss/ 

degradation of 

high quality 

incubation, 

spawning and 

rearing habitat

Habitat 

degrading 

facilities; 

potential 

habitat 

degrading 

land uses

Spawning, 

incubation, 

early 

juvenile, 

outmigrants, 

adult returns

To be 

determined

Near-term USFS

NEPA planning complete. 

Sustainable habitat 

restoration a core 

objective of project. Nearterm to leverage current 

NEPA decision and 

funding opportunities. 

Listed in prerequisite 

order.

7.2.13-9

9. Investigate options for 

how to curtail threats 

from temperature 

pollutants via a 

moratorium on new pond 

development.

Sawtooth 

Valley

A, P

Degraded 

water quality, 

altered 

sediment 

routing

Residential/ 

agricultural 

pollutants

Juvenile 

outmigrants, 

adult returns

To be 

determined

Near-term

IDWR board, 

IDWR, USFS, 

IDEQ

Aesthetics, irrigation and 

stock ponds.

Recovery Strategy 7.2.14: Investigate and improve conditions in Salmon River and tributaries to support increased survival of migrating Snake River Sockeye Salmon

7.2.14-1

1. Protect and enhance 

stream tributary habitat 

leading from natal lakes 

to the Salmon River in 

the Sawtooth Valley. 

upper 

Salmon 

River and 

tributaries

A

Potential loss/ 

degradation of 

high quality 

habitats 

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term USFS

7.2.14-2

2. Protect and enhance 

watershed habitat to 

promote natural 

processes and 

watershed function.

Salmon and 

Lower Snake 

Rivers

A, SS

Potential loss/ 

degradation of 

high quality 

habitats 

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term USFS

7.2.14-3 3. Implement existing 

agreements on Federal

upper 

Salmon 

A, SS

Potential loss/ 

degradation of 

Potential 

habitatJuvenile outmigrants; 

Baseline Near-term USFS
ESA Recovery Plan: Snake River Sockeye Salmon | 289

June 2015| NOAA Fisheries 

lands in the Sawtooth 

Valley and Salmon River 

watersheds.

River and 

tributaries; 

Sawtooth 

Valley

high quality 

habitats 

degrading 

land use 

practices 

adult returns

7.2.14-4

4. Identify specific 

actions and responsible 

parties/entities to 

improve water quantity 

and the quality of juvenile 

and adult migration 

corridor habitats and 

monitor the actions. 

Especially in 

upper 

reaches of 

the 

mainstem 

Salmon 

River and 

mainstem 

lower Snake 

River

A, SS

Altered 

hydrology,

Elevated 

water 

temperature,

Reduced 

stream flow

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term USFS

7.2.14-5

5. Investigate the 

relatively high losses of 

juvenile and adult 

Sockeye Salmon in the 

Salmon River and 

identify actions that could 

reduce these losses.

Salmon 

River

A, SS

Altered 

hydrology,

Elevated 

water 

temperature,

Reduced 

stream flow

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

To be 

determined

Near-term NMFS, IDEQ

7.2.14-6

6. Continue to implement 

monitoring efforts to 

understand juvenile and 

adult survival in the 

Salmon River.

Salmon 

River

A, SS

Altered 

hydrology,

Elevated 

water 

temperature,

Reduced 

stream flow

Potential 

habitatdegrading 

land use 

practices 

Juvenile 

outmigrants; 

adult returns

Near-term IDEQ, NMFS

7.2.14-7 7. Implement TMDLs for 

impaired water bodies in 

Salmon 

River 

A, SS

Altered 

hydrology,

Potential 

habitatJuvenile outmigrants; 

To be 

determined

Near-term IDEQ
ESA Recovery Plan: Snake River Sockeye Salmon | 290

June 2015| NOAA Fisheries 

Salmon River watershed. watershed Elevated 

water 

temperature,

Reduced 

stream flow

degrading 

land use 

practices 

adult returns

7.2.14-8

8. Improve instream

flows in Stanley Lake 

Creek below SLC1 

diversion through 

increased efficiencies, 

alternative sources, and/ 

or conservation tools.

Stanley Lake SS, D

Impaired fish 

passage and 

water quality

Irrigation 

diversions and 

land use 

practices

Adult 

returns; 

juvenile 

outmigrants

To be 

determined

Mid-term

IDFG, IDWR, 

NMFS, USFS, 

ShoshoneBannock 

Tribes, Custer 

County

7.2.14-9

9. Investigate options to 

establish minimum 

stream flow on Salmon 

River above confluence 

with Alturas Lake Creek 

(aka Busterback reach).

Sawtooth 

Valley

A, SS, D

Reduced 

population 

structure and 

distribution

Irrigation 

diversions and 

land use 

practices

Adult 

returns, 

juvenile 

outmigrants

To be 

determined

Near-term

IDWR board, 

IDWR, USFS, 

IDEQ

Protect the substantial 

flow returned to the 

Salmon River currently 

from future appropriation.

7.2.14-

10

10. Acquire land or 

easement protections on 

parcels with river/stream 

frontage (development 

risks).

Salmon 

River (EF to 

headwaters)

A

Degraded 

water quality, 

altered 

sediment 

routing

Residential/ 

agricultural 

development, 

irrigation, 

livestock 

grazing, 

roadways

Juvenile 

outmigrants, 

adult returns

To be 

determined

All terms

BPA, SWCDs, 

IDFG, ESFS, 

ShoshoneBannock 

Tribes, NGOs

Acquisitions are often time 

sensitive.

7.2.14-

11

11. Weed Management –

protect healthy 

watersheds through 

controlling the spread 

and infestation of 

Salmon 

River (EF to 

headwaters)

Degraded

water quality, 

altered 

sediment 

routing

Habitat 

degrading 

facilities, 

potential 

habitat 

Spawning, 

incubation, 

early 

juveniles 

$20K/year Near-term USFS

Funds would facilitate 

monitoring and treatment. 

Treatments would comply 

with 2012 Sawtooth NF 

programmatic BA 
ESA Recovery Plan: Snake River Sockeye Salmon | 291

June 2015| NOAA Fisheries 

invasive plant species. degrading 

land uses

requirement.

Recovery Strategy 7.2.15: Monitor and control predation, disease, invasive species and competition and develop actions as needed

7.2.15-1

1. Implement plan for 

collection of returning 

spawners at Lower 

Granite Dam to reduce 

exposure to elevated 

temperatures in the 

mainstem Salmon River 

during late July and 

August.

Snake River A

Reduced 

abundance

Reduced 

Abundance

Adult returns Mid-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.15-2

2. Implement Idaho 

Department of 

Agriculture, U.S. Forest 

Service and IDFG 

whirling disease 

monitoring and control 

program.

Sawtooth 

Valley, upper 

Salmon 

River

A, P Disease

Reduced 

Abundance

Juvenile 

rearing

$ 29,000/

year

Mid-term

IDA, USFWS, 

IDFG

Whirling Disease has been 

detected.

7.2.15-3

3. Implement Idaho 

Department of 

Agriculture, U.S. Forest 

Service and IDFG 

invasive species 

monitoring and control 

programs.

Sawtooth 

Valley, upper 

Salmon 

River

A,P

Potential 

loss/Degradati

on of high 

quality 

spawning/incu

bation habitat, 

water quality 

and reduced 

food source

Human 

activity that 

may introduce 

invasive 

species 

Adult 

spawning; 

incubation; 

early juvenile

Same as No. 

2 above

Near-term

IDA, IDFG, 

USFS

New Zealand mud snails 

have been detected in 

Salmon River mainstem.

7.2.15-4

4. Reduce non-native 

kokanee in lakes used 

Pettit Lake, 

Stanley Lake

A, P, SS, D

Predation/ 

competition/ 

Food resource 

competition

Juvenile

To Be 

Determined

Mid-term

ShoshoneBannock 
ESA Recovery Plan: Snake River Sockeye Salmon | 292

June 2015| NOAA Fisheries 

for Sockeye Salmon

recovery.

disease Tribes; IDFG

7.2.15-5

5. Evaluate the effects of 

lake trout on Sockeye 

Salmon, develop an 

eradication strategy, if 

appropriate, and 

implement strategy as 

necessary.

Stanley Lake A, P

Predation/ 

competition/ 

disease

Non-native 

fish

Juvenile 

rearing

To be 

determined

Near-term IDFG

7.2.15-6

6. Develop strategy (ies) 

to prevent lake trout 

movement and 

colonization of additional 

Sockeye Salmon lakes. 

Sawtooth 

Valley

A,P 

Predation/com

petition

Non-native 

fish

Juvenile 

rearing

To be 

determined

Near-term IDFG

7.2.15-7

7. Evaluate the effects of 

cutthroat trout on 

Sockeye Salmon.

Yellowbelly 

Lake

A, P

Predation/ 

competition/ 

disease

Resource 

competition 

(vs. sympatry)

Juvenile 

rearing

To be 

determined

Mid-term IDFG

7.2.15-8

8. Develop and 

implement a study in 

Yellowbelly Lake to 

evaluate lake carrying 

capacity of Sockeye 

Salmon limiting factor in 

the absence of resident 

kokanee.

Yellowbelly 

Lake

A,P

Food 

availability; 

food quality

Food resource 

competition

Juvenile 

rearing

To be 

determined 

Mid-term

ShoshoneBannock Tribes

7.2.15-9

9. Identify criteria for 

transitioning to passing 

selected adults above 

weirs to migrate 

naturally, and for opening 

Sawtooth 

Valley

A, SS, D

Impaired fish 

passage; 

hatcheryrelated 

adverse 

Disease; 

impaired 

habitat 

connectivity

Adult

Not 

applicable

Near-term SBSTOC Technical staff or policy 

issue.
ESA Recovery Plan: Snake River Sockeye Salmon | 293

June 2015| NOAA Fisheries 

* Viable Salmonid Population (VSP) parameter abbreviations: A (abundance); P (productivity); SS (spatial structure); D (diversity).

** Potential implementing agencies abbreviations: BPA (Bonneville Power Administration); IDA (Idaho Department of Agriculture); IDFG (Idaho Department of Fish and Game); IDWR (Idaho 

Department of Water Resources); SBSTOC (Stanley Basin Sockeye Technical Oversight Committee); SWCDs (soil and water conservation districts); USFS (U.S. Forest Service); USFWS 

(U.S. Fish and Wildlife Service).

weirs to allow returns to 

distribute themselves 

naturally.

effects

7.2.15-

10

10. Identify ways to 

address predation at 

Sawtooth Hatchery weir.

Sawtooth 

Valley

A, SS, D

Predation due 

to impaired 

fish passage

Hatchery 

management 

Adult

To be 

determined

Near-term

IDFG, NMFS, 

ShoshoneBannock Tribes

7.2.15-

11

11. Aquatic invasive 

species (AIS) and 

prevention.

Alturas, 

Pettit, 

Stanley and 

Redfish 

Lakes

Degraded 

water quality, 

ecological 

processes

Potential 

introduction of 

AIS species to 

lakes

Spawning, 

incubation, 

early 

juveniles

$30/year Near-term USFS and IDA

Recovery Strategy 7.2.16: Create an adaptive management feedback loop to track progress toward achieving recovery goals, monitor and evaluate key information needs, assess information, 

and refine strategies and actions.

7.2.16-1

1. Implement Research, 

Monitoring and Adaptive 

Management Program.

Sawtooth 

Valley

A, SS, D, P All All

Juvenile 

rearing, 

Adult returns

To be 

determined

Near-term

IDFG, NMFS, 

BPA, 

ShoshoneBannock Tribes

This is a key 

implementation action.
ESA Recovery Plan: Snake River Sockeye Salmon | 294

June 2015| NOAA Fisheries 

7.3 Actions to Recover Snake River Sockeye Salmon at the Regional Level 

(Migration Corridor in the Mainstem Salmon, Snake, and Columbia Rivers 

and Estuary, Plume and Ocean)

Actions identified in Section 7.3 address regional limiting factors and threats to recovery of the Snake 

River Sockeye Salmon ESU. The proposed actions are directly linked to the recovery strategies 

identified in Section 6.3.2. This section is organized by strategy with corresponding actions in the same 

order presented in Section 6.3.2. 

Sections 7.3.1 through 7.3.11 briefly describe the recovery strategies and actions to recover Snake River 

Sockeye Salmon at the regional level (migration corridor in the mainstem Salmon, Snake, and Columbia 

Rivers and the estuary, plume, and ocean.) Table 7-1 defines the specific actions proposed under each 

strategy to address problems for Sockeye Salmon in the upper Salmon River. The table identifies the 

actions as well as the sites, VSP parameters, limiting factors, and threats that each action targets. The 

tables also provide estimated costs and potential implementing entities for each action, and priority for 

implementation. The actions address the limiting factors and threats identified in Section 5. 

7.3.1 Implement the FCRPS BiOp’s Reasonable and Prudent Alternative to Reduce 

Mortalities Associated with Migration Through the Mainstem Salmon, Snake and 

Columbia Rivers, Estuary and Plume

Mainstem Salmon River:

• Continue the current annual marking and tagging program as part of FCRPS BiOp to 

acquire consistent annual passage data.

• Evaluate pit tag program to determine SAR estimates.

Federal Columbia River Power System and Estuary: 

Actions identified in the 2008/2010 RPA (NMFS 2008c, 2010), as modified by the 2014 Supplemental 

Biological Opinion (NMFS 2014c); the Hydro Module (NMFS 2012a); and the Estuary Module (NMFS

2011a) are currently being implemented to reduce Snake River Sockeye Salmon mortalities associated 

with passage through the mainstem Columbia and Snake River hydroelectric projects and estuary. The 

suite of actions is designed to improve fish passage, reduce predation, and enhance habitat conditions 

and fish survival. The modules are available on the NMFS Web site: 

http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/recovery_planning_and_i

mplementation/snake_river/current_snake_river_recovery_plan_documents.html

The FCRPS RPA includes the following site specific actions to increase juvenile and adult survival: 

• Flow and water quality operations at the FCRPS storage projects (Libby, Hungry Horse, 

Albeni Falls, Grand Coulee, and Dworshak)—these include regulating outflow.
ESA Recovery Plan: Snake River Sockeye Salmon | 295

June 2015| NOAA Fisheries 

temperatures at Dworshak Dam to control summer water temperatures in the lower Snake 

River.

• Configuration and operational changes at the run-of-river mainstem projects—these 

include short- and long-term measures to prevent a temperature block in the adult ladder 

at Lower Granite Dam.

• Spill and juvenile transport improvements at the run-of-river mainstem projects to 

improve inriver and system survival.

• Predation control measures at the run-of-river mainstem projects and in the Columbia 

River estuary.

• Water transactions in the mainstem Salmon River8 and habitat improvements in the 

Columbia River estuary.

7.3.2 Continue Research and Monitoring on Snake River Sockeye Salmon

Survival/Mortality in Mainstem Salmon, Snake, and Columbia Rivers Migration Corridor; 

Estuary; Plume; and Ocean

As discussed in 7.3.1, the FCRPS RPA, as well as any further improvements for fish survival that may 

result from the ongoing FCRPS RM&E and adaptive management process, represent the near-term 

recovery strategy for Snake River Sockeye Salmon and other listed salmonids that migrate through the 

mainstem Columbia and Snake Rivers. The “Reasonable and Prudent Alternative Table” in the 2008 

FCRPS BiOp, as amended in the 2010 and modified in the 2014 Supplemental BiOps, respectively, 

describes research and monitoring actions that should demonstrate the success of these actions or the 

need to make adjustments or develop new measures to increase Snake River Sockeye Salmon survival 

during the migratory life stages.

Additional actions call for investigations concerning the apparent SAR differential between Snake River 

Sockeye Salmon and Lake Wenatchee and Okanogan River Sockeye Salmon. Information gained from 

these investigations will inform further actions that could improve SARs for the Snake River ESU.

• Determine changes in marking/tagging levels for more precise evaluations of downstream 

sources of mortality.

 

8 The FCRPS Action Agencies are implementing these water transactions specifically to improve the survival of Snake River

spring/summer Chinook and steelhead, but they are also likely to improve the survival of adult migrant Sockeye Salmon

returning to the Sawtooth Valley in July and August (NMFS 2014c).
ESA Recovery Plan: Snake River Sockeye Salmon | 296

June 2015| NOAA Fisheries 

7.3.3 Update Snake River Sockeye Salmon Life Cycle Models Using Latest Information 

on Survival Through Mainstem Salmon, Snake and Lower Columbia River Migration 

Corridor; Estuary; Plume; and Ocean

Use updated life cycle model to test hypotheses regarding whether actions described in this plan, 

including those in Section 7.3.2, will be adequate to achieve recovery objectives for the ESU. 

• Update appropriate life-stage inputs in life cycle model and test hypotheses regarding 

whether strategies described in this plan, including those corresponding recovery 

strategies in Section 6.3.2.1, will be adequate to achieve recovery objectives for the ESU. 

7.3.4 Manage to Maintain Current Low Impact Fisheries and Reduce Fishery Impacts in 

Those Fisheries that Affect Snake River Sockeye Salmon: Fishery Management

A number of different entities currently manage fisheries that could potentially affect Snake River 

Sockeye Salmon. Tributary fisheries for Snake River species are implemented by state and tribal 

entities, and reviewed under the ESA by NMFS. Fisheries in the mainstem Columbia River that affect 

Snake River Sockeye Salmon are subject to the terms of the U.S. v. Oregon Management Agreement, 

and are managed to ensure that the incidental take of ESA-listed Snake River Sockeye Salmon does not 

jeopardize the ESU. Snake River Sockeye Salmon are also exposed to incidental take as bycatch in the 

ocean troll, purse seine, and gill net salmon fisheries off the coasts of Alaska, British Columbia, and 

Washington. However, these ocean fisheries are believed to pose minimal threat to the species since 

Sockeye Salmon are not attracted to baits or lures and, thus, are rarely caught in commercial or 

recreational fisheries. 

This Plan supports current efforts under existing management agreements, including the 2008-2017 U.S. 

v. Oregon Management Agreement, to regulate fisheries. Actions to address fishery threats are identified 

by NMFS in the Harvest Module (NMFS 2014b). The Harvest Module is available on the NMFS Web 

site:

http://www.westcoast.fisheries.noaa.gov/protected_species/salmon_steelhead/recovery_planning_and_i

mplementation/snake_river/current_snake_river_recovery_plan_documents.html. 

Additional actions call for investigating the use of new technologies (PIT-tags and PIT-tag detectors, 

genetic data) to better manage in-season mainstem fisheries and assess seasonal harvest objectives and 

limitations.

• Continue to implement the 2008-2017 U.S. v. Oregon Agreement in mainstem Columbia 

River fisheries.

• Define appropriate levels of incidental take of Sockeye Salmon in fisheries in the Snake 

and Salmon Rivers and upper Salmon River lakes, based on Sockeye Salmon status.

• Monitor ocean fisheries databases for incidental take of Snake River Sockeye Salmon.

• As a future action, evaluate use of the harvest management sliding scale to manage 

hatchery-origin fish and protect natural-origin spawners returning to natal lakes.
ESA Recovery Plan: Snake River Sockeye Salmon | 297

June 2015| NOAA Fisheries 

• Identify and evaluate potential future changes to Sockeye Salmon harvest management 

when U.S. v Oregon is renegotiated after 2018.

• Investigate loss of PIT-tagged adult Sockeye Salmon between Bonneville and McNary 

dams.

7.3.5 Protect and Conserve Natural Ecological Processes that Support the Population 

Viability

Actions to protect and conserve the natural ecological processes that support Snake River Sockeye 

Salmon viability will play a key a role in the overall recovery strategy. Protecting and improving natural 

processes and functions will help maintain high quality habitat and restore damaged habitat, with 

specific benefits in the juvenile and adult migration life history stages.

The Estuary Module describes strategies and actions that will protect and conserve natural ecological 

processes to support salmonid viability in the lower Columbia River estuary. The 2008 FCRPS 

Biological Opinion, 2010 Supplemental FCRPS BiOp, 2014 Supplemental FCRPS BiOp and the Hydro 

Module also provide direction for improving natural ecological processes in the mainstem Columbia and 

Snake Rivers. 

• Assess nearshore mainstem habitat and cold-water refugia in the mainstem Columbia and 

lower Snake Rivers and explore opportunities for, and potential benefits from, restoration 

and protection of these areas.

• Protect intact riparian areas in the estuary and its tributaries and restore riparian areas that 

are degraded.

• Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries.

• Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health.

• Protect remaining high-quality off-channel habitat from degradation and restore degraded 

areas with high intrinsic potential for high-quality habitat.

• Breach, lower, or relocate dikes and levees to establish or improve access to off-channel 

habitats.

7.3.6 Improve Degraded Water Quality and Maintain Unimpaired Water Quality

Water quality issues affect Snake River Sockeye Salmon survival and viability in several areas of the 

migration corridor. In the lower Salmon and Snake Rivers, summer water temperatures in some reaches 

rise to levels that can restrict Sockeye Salmon production and survival. The high water temperatures can 

leave Sockeye Salmon more susceptible to disease and infection if they are not able to escape to deep 
ESA Recovery Plan: Snake River Sockeye Salmon | 298

June 2015| NOAA Fisheries 

pools or other habitats with cooler temperatures. Higher water temperatures also reduce habitat quality 

for Sockeye Salmon and other salmonids that use the estuary during summer months.

In addition, sections of the mainstem Salmon, Snake, and Columbia Rivers are also contaminated by 

drift and runoff from both agricultural and urban areas. Exposure to these chemicals during adult and 

juvenile migration may contribute to low survivorship and impede recovery of this stock.

The Estuary Module and FCRPS BiOp identify actions to improve reaches with degraded water quality 

and maintain reaches with good water quality in the mainstem corridor. Actions described in the 

Estuary Module include implementing best management practices to reduce the flow of nutrients and 

toxics to the estuary, and to restore or mitigate contaminated sites. The IDEQ is working with cities, 

counties, and landowners to implement actions that address water temperature concerns in the Salmon 

and lower Snake Rivers. This plan also call for monitoring studies to determine how high temperatures 

and other water quality issues in the Salmon and lower Snake Rivers may be affecting Sockeye Salmon

survival and viability.

• Implement pesticide and fertilizer best management practices to reduce estuarine and 

upstream sources of nutrients and toxic contaminants entering the estuary.

• Identify and reduce terrestrially and marine-based industrial, commercial, and public 

sources of pollutants.

• Restore or mitigate contaminated sites.

• Implement stormwater best management practices in cities and towns.

• Address water temperature concerns for the Salmon and lower Snake Rivers.

• Conduct monitoring studies to determine how high temperatures and other water quality 

issues in the Salmon and lower Snake Rivers may be affecting Sockeye Salmon survival.

• Implement Water Quality Plan for Total Dissolved Gas (TDG) and water temperature in 

the Mainstem Columbia and Snake Rivers to meet ESA and Clean Water Act 

responsibilities.

7.3.7 Address Ecosystem Imbalances in Predation, Competition, Invasive Species, and 

Disease through the Strategies and Actions in this Plan, the Estuary Module, and 

Reasonable and Prudent Alternatives identified in Biological Opinions

Snake River Sockeye Salmon experience predation and competition from other fish and birds in the 

mainstem Columbia, Snake, and Salmon Rivers and the estuary and ocean. In the Salmon River, 

Sockeye Salmon encounter predation from bull trout. In the Columbia River migratory corridor, Snake 

River Sockeye Salmon encounter both reservoir-rearing kokanee and anadromous Sockeye Salmon

smolts from the upper Columbia migrating to the sea. In the ocean, they must compete with hatchery 

and natural Sockeye Salmon stocks originating along the entire length of the North Pacific rim, as well 

as other salmon species. They are also exposed to a number of potential predators. Migrating Sockeye 

Salmon encounter predation from northern pikeminnow and other fish in the Columbia and lower Snake 
ESA Recovery Plan: Snake River Sockeye Salmon | 299

June 2015| NOAA Fisheries 

migration corridor. Predators in the estuary include Caspian terns, double-crested cormorants, and a 

variety of gull species. Currently, it is not clear if this potential predation poses a risk to Snake River 

Sockeye Salmon. 

The potential threat to Sockeye Salmon viability and habitat from invasive aquatic species is also a 

concern. Invasion of these harmful, non-native plants, animals, and pathogens could damage the 

environment and negatively influence Sockeye Salmon recovery. The Plan supports current programs to 

monitor and control invasive species that are being carried out in Idaho, Oregon and Washington in the 

Salmon River mainstem, Snake and Columbia Rivers and Columbia River estuary. In particular, it is 

critically important that these efforts be maintained to prevent introduction of highly invasive quagga 

and zebra mussels and other invasive species that can influence biological processes throughout the 

Sockeye Salmon migration route and reduce Sockeye Salmon productivity. 

Diseases in Sockeye Salmon also restrict efforts to recover the species. Diseases, however, can be 

caused by multiple factors and probably cannot be directly addressed by recovery actions, except in 

specific instances of known causal factors. It is more likely that nearly all of the recommended recovery 

actions that improve spawning, rearing, and passage conditions for Sockeye Salmon and increase the 

survival, abundance, and productivity of naturally produced fish will result in decreasing incidence of 

disease. 

Actions identified in this Plan, the Estuary Module, Ocean Module, FCRPS BiOp, and other Biological 

Opinions aim to monitor and control predation, competition, and invasive species in the mainstem 

Columbia, and Snake Rivers and in the estuary and ocean. The documents, including this Plan, also 

direct additional research, monitoring, and evaluation activities to quantify the impacts of predation and 

competition on Snake River Sockeye Salmon recovery efforts. 

• Investigate predation, disease, invasive species and competition; based on findings, 

implement actions in the migration corridor, estuary, plume and ocean.

• Evaluate the effectiveness and relative efficiency of a hook-and-line fishery at select 

dams on the mainstem Columbia and Snake Rivers to remove Northern Pikeminnow in 

areas inaccessible to sport-reward anglers.

• Continue to evaluate if inter-and intra-species compensation is occurring on surviving 

northern pikeminnow and other piscivorous species.

• Continue to conduct research on predation impacts of Columbia River avian predators on 

migrating juvenile salmonids, bioenergetics modeling, and habitat/population 

management strategies.

• Develop an avian management plan for other avian species as determined by RM&E for 

USACE owned lands and associated shallow-water habitat.

• Implement and improve deterrent devices and activities (e.g. bird wire, water cannons, 

hazing) at dams to keep avian predators away from bypass outfalls and other areas of 

juvenile salmonid concentration.
ESA Recovery Plan: Snake River Sockeye Salmon | 300

June 2015| NOAA Fisheries 

• Implement education and monitoring projects and enforce existing laws to reduce the 

introduction and spread of invasive plants.

• Implement projects to redistribute part of the Caspian tern colony currently nesting on 

East Sand Island.

7.3.8 Respond to Climate Change Threats by Implementing Research, Monitoring, and 

Evaluation to Track Indicators Related to Climate Change and by Preserving 

Biodiversity 

Projected changes in habitat conditions due to climate change could have profound implications for 

Snake River Sockeye Salmon survival and viability. All other threats and conditions remaining equal, 

future deterioration of water quality, water quantity, and physical habitat due to climate change could 

hinder efforts to recover Snake River Sockeye Salmon to viability levels needed to delist the species 

under the ESA. For example, lower flows and higher water temperatures in the Salmon and lower 

Snake Rivers in late summer and early fall when adult Sockeye Salmon are returning to the natal lakes 

to spawn could further reduce Sockeye Salmon survival and the number of naturally produced Sockeye 

Salmon returning to spawn. This possibility reinforces the importance of gaining information needed to 

detect and respond to changes in population viability or habitats related to climate change. It also 

reinforces the need to maintain habitat diversity and achieve survival improvements throughout the 

entire life cycle.

Actions identified in this Plan, the Estuary Module, Hydro Module, FCRPS BiOp, and other Biological 

Opinions to protect and improve habitat conditions will help to preserve and improve biodiversity, and 

guard against the effects of climate change. The climate change strategy also directs monitoring and 

evaluation actions, including those identified in Section 11, Research, Monitoring, and Evaluation for 

Adaptive Management, to help detect physical and biological changes associated with climate change 

and determine the efficacy of responsive measures.

• Implement research, monitoring, and evaluation actions identified in Section 11.

• Implement measures to retain shade along stream channels and augment summer flow.

• Manage water withdrawals to maintain as high a summer flow as possible.

• Implement measures to protect and restore wetlands, floodplains, and other landscape 

features that store water.

• Release cool water from mainstem reservoirs during critical periods.

• Improve juvenile passage through warm dam forebays.

• Improve temperatures in adult fish passage structures.

• Take steps to reduce predation and competition with non-native species.

• Remove dikes to open backwater, slough, and other off-channel habitats and to increase 

flow through these areas and encourage hyporheic flow.
ESA Recovery Plan: Snake River Sockeye Salmon | 301

June 2015| NOAA Fisheries 

• Protect remaining high-quality off-channel habitat from degradation and restore degraded 

areas with high intrinsic potential for high-quality habitat.

Implement habitat actions that are most likely to ameliorate stream flow and temperature changes due to 

climate change and increase habitat diversity and population resilience. Such actions include restoring 

floodplain connectivity, restoring stream flow regimes, reaggrading9 incised channels, removing 

barriers, and restoring riparian functions.

7.3.9 Implement the Snake River Sockeye Salmon Recovery Plan through Effective 

Communication, Education, Coordination, and Governance

Recovery of Snake River Sockeye Salmon depends on the collective action of citizens in the region. 

Recovery actions will need to be implemented by diverse organizations, tribes, state and Federal

agencies, landowners, private entities, and the public  all striving for the common goal of Sockeye 

Salmon recovery. 

Section 10 identifies an implementation framework to coordinate implementation of the Plan. 

Successful implementation of recovery actions, research, and monitoring projects will build upon the 

over twenty years of leadership and Sockeye Salmon recovery work carried out by the Stanley Basin 

Sockeye Technical Oversight Committee, together with IDFG, Shoshone-Bannock Tribes, U.S. Forest 

Service, NMFS, BPA, and other partners that have prevented the extinction of this ESU. 

Implementation will continue coordinated actions and funding from parties including IDFG, ShoshoneBannock Tribes, Bonneville Power Administration, NMFS, U.S. Forest Service, counties, state and 

Federal agencies, private landowners, and individuals. 

In addition, a key goal for the Sockeye Salmon recovery program is to engage the public as an active 

partner in implementing and sustaining recovery efforts. Actions to achieve this goal provide 

opportunities for public education and interpretation, and participation in recovery implementation 

activities. They also involve sharing information between scientists and the public as recovery projects 

and monitoring actions are carried out. 

• Develop multi-media public education, interpretation, and outreach information designed 

to reach different audiences describing what needs to be done for Sockeye Salmon

recovery and what the public and landowners can do to support recovery efforts. Post 

information on the web sites of cooperating agencies, entities, and tribes involved in 

Sockeye Salmon recovery actions.

 

9 Aggradation is a term used in geology for the increase in land elevation due to deposition of sediment.
ESA Recovery Plan: Snake River Sockeye Salmon | 302

June 2015| NOAA Fisheries 

• Produce educational materials that can be used in schools and at fairs, festivals, or other 

venues to communicate current status of the ESU and potential recovery actions needed 

to protect and restore Sockeye Salmon.

• Develop and implement education and outreach programs directed at anglers and the 

public regarding the negative impacts of invasive species on native species, habitat, and 

ecosystems.

• Work with the U.S. Forest Service, IDFG, Shoshone-Bannock Tribes, and other relevant 

parties to develop materials, posters, and signage to educate visitors to the Sawtooth 

National Recreation Area about the need to recover Sockeye Salmon and the recovery 

actions being carried out in the recreation area.

• Develop a clearinghouse of information on funding sources. Support local entities, 

landowners, tribes, and agencies seeking funding for recovery actions.

• Present briefings and presentations on Sockeye Salmon recovery to relevant civic, 

business, trade, environmental, and conservation organizations. 

• Lead seasonal tours of relevant sites so public and other interested groups can observe 

Sockeye Salmon and visit recovery projects. 

• Educate and work with landowners to implement recovery actions on private property 

with willing landowners.

7.3.10 Continue Research, Monitoring, and Evaluation for Adaptive Management

Research, monitoring, and evaluation efforts that allow groups and managers to make informed 

decisions through an adaptive management process will play a critical role in the recovery of the Snake 

River Sockeye Salmon ESU. As discussed in Section 6, many questions exist regarding the effects of 

the hydrosystem, fisheries, and land and water uses on survival of Snake River Sockeye Salmon in the 

mainstem migration corridor, estuary and ocean. We remain unsure whether Sockeye Salmon survivals 

resulting from current conditions and proposed management actions will be enough to support the ESU 

through downturns in ocean and climate conditions. 

The FCRPS BiOp, Hydro Module, and Estuary Module identify research, monitoring, and evaluation

activities that will help aid recovery of Sockeye Salmon. In addition, Section 11 of this Plan lays out a 

research, monitoring, and evaluation program designed to assess the status of the species and its habitat, 

track progress toward achieving recovery goals, and gain information needed to refine recovery 

strategies and adjust course as appropriate through the process of adaptive management.

• Continue to implement the monitoring and evaluation programs to track progress on 

meeting these recovery goals and objectives.

• Research critical uncertainties, monitor and evaluate implementation and effectiveness, 

and adjust course as appropriate through adaptive management.
ESA Recovery Plan: Snake River Sockeye Salmon | 303

June 2015| NOAA Fisheries 

7.3.11 Prioritize and Address Key Information Needs, and Create an Adaptive 

Management Feedback Loop to Revise Recovery Actions as Needed

Successful implementation of the Recovery Plan requires a process to refine direction and adjust course 

appropriately. Section 10 describes a proposed framework for coordinated implementation of this Plan 

and identifies the implementation teams that are part of this framework. The Snake River Sockeye 

Salmon Implementation and Science Team will coordinate implementation of the Adaptive Management 

and Research, Monitoring, and Evaluation Plan. Section 11 describes the aspects of the adaptive 

management process and the research, monitoring, and evaluation activities that will be implemented to 

inform future decisions and adjust our course toward Sockeye Salmon recovery. 

NMFS will work with the Snake River Sockeye Salmon Implementation and Science Team and others 

to prioritize the key information needs identified in Section 6.4. It will also seek resources and form 

partnerships to address the key information needs during recovery plan implementation.

• Work with the Snake River Sockeye Salmon Implementation and Science Team and 

others to prioritize the key information needs.

• Seek resources and form partnerships to address the key information needs during 

Recovery Plan implementation.
ESA Recovery Plan: Snake River Sockeye Salmon | 304

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 305

June 2015| NOAA Fisheries 

Section 8: Potential Effects of Proposed Actions
ESA Recovery Plan: Snake River Sockeye Salmon | 306

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 307

June 2015| NOAA Fisheries 

8. Potential Effects of Proposed Recovery Actions

This section describes a proposed approach to evaluate the effects of recovery actions on abundance and 

productivity of Snake River Sockeye Salmon in relation to the biological viability criteria described in 

Section 3.2. The ESU’s current risk of extinction remains high with the ESU being maintained in a 

captive broodstock program. The goal of this Plan is to have enough self-sustaining natural-origin 

Sockeye Salmon spawning in the wild and surviving the full life cycle in such numbers to maintain 

targeted viability over time and under varying environmental conditions. Based on an understanding of 

limiting factors and threats, we hypothesize that the recovery actions described in this Plan will increase 

the number of anadromous adults returning to spawn in natal lakes over time. Proposed monitoring 

actions will document Sockeye Salmon survival rates at each life stage through variations in ocean and 

climate conditions. 

Unlike effects analyses in other NMFS Columbia Basin recovery plans, we do not have an accurate 

understanding of past Sockeye Salmon productivity. In addition, the abundance of natural-origin fish is 

so low that modeling viability responses to recovery actions is not possible at this time. However, as 

numbers of natural-origin Sockeye Salmon increase, monitoring data will be available to calculate 

abundance and productivity over time

The following section proposes a framework for analyzing the effects of proposed recovery actions on 

Sockeye Salmon viability over time.

Hatchery Recovery Actions

These are the actions associated with the operation of the captive broodstock and conventional hatchery 

facilities to produce fish for reintroduction. These actions assume the demographic benefit hatchery 

production provides can be used to address abundance as a limiting factor. It is expected (hypothesized) 

that these actions will have the effect of increasing the number of naturally spawning anadromous 

Sockeye Salmon in the Sawtooth Valley basin. The actual effect of these actions can be tested by 

comparing long-term trends in reintroduction efforts and natural abundance. Redd counts, numbers of 

naturally produced spawners, and natural out-migrants are metrics that can be used to verify these 

actions generate the assumed effect and will lead to the end goal of producing a minimum of 1,000 

natural spawners per year in Redfish and Alturas Lakes and 500 spawners per year in one of the smaller 

Sawtooth Valley lakes. 

Reintroduction Recovery Actions

These actions are associated with populations chosen for amplification and the manner they are 

distributed to the available habitat. They assume that following the local adaptation concept during 

reintroduction actions will lead to increased spatial structure and diversity within the ESU. It is 

expected (hypothesized) that these actions will have the effect of increasing the number of natural 

spawning types (shoal and stream) and lake populations within the ESU. The actual effect of these 

actions can be tested by following long-term trends in number of Sawtooth Valley lakes and habitats 
ESA Recovery Plan: Snake River Sockeye Salmon | 308

June 2015| NOAA Fisheries 

supporting self-sustaining natural spawning populations of anadromous Sockeye Salmon. Location and 

number of redds and spawners can be monitored to verify that these actions lead to the increased 

numbers, productivity, spatial structure, and diversity associated with a low risk of extinction.

Migratory Corridor Recovery Actions

These actions are associated with reducing the physical, competitive, and predatory hazards in the 

migration corridor. They assume that reducing losses in the migratory corridor can be used to address 

abundance as a limiting factor. It is expected (hypothesized) that these actions will have the effect of 

increasing the number of anadromous Sockeye Salmon surviving to return to the Sawtooth Valley. The 

actual effect of these actions can be tested by comparing long-term trends in migration survival to the 

action implemented. Percentage of smolts surviving to Lower Granite Dam, percentage of adults 

surviving from Lower Granite Dam to the Sawtooth Valley, etc. can be monitored to verify that these 

actions lead to the end goal of producing a minimum of 1,000 natural spawners per year in Redfish and 

Alturas Lakes and 500 spawners per year in one of the smaller Sawtooth Valley lakes (Pettit, Stanley, or 

Yellowbelly Lakes).

Natal Lake Habitat Recovery Actions

These actions are associated with improving the physical and ecological condition of the natal lakes. 

They assume increasing the forage base and reducing predators, competitors, and pollutants will 

improve the overall abundance and productivity of anadromous Sockeye Salmon in the lakes. Enhancing 

the forage base, limiting kokanee competitors, controlling nonnative predators, and reducing pollutants 

is expected to increase anadromous spawner success, egg survival, fry carrying capacity, and smolt 

production. The actual effect of these actions can be tested by comparing long-term trends in these 

actions with natural abundance and productivity of anadromous Sockeye Salmon in the Sawtooth Valley 

lakes. Anadromous red counts, fry production, and smolt out-migrants numbers for each lake can be 

monitored to verify that these recovery actions will lead to the end goal of producing a minimum of 

1,000 natural spawners per year in Redfish and Alturas Lakes and 500 spawners per year in one of the 

smaller Sawtooth Valley lakes with a population that is stable or increasing.

Fishery Recovery Actions

These are the actions associated with managing ocean, river, and lake fisheries to limit take of the listed 

species. They assume limiting incidental harvest of Snake River Sockeye Salmon will improve overall 

abundance. It is expected (hypothesized) that these actions will have the effect of increasing the number 

of fish surviving to reach the spawning grounds in the Sawtooth Valley. The actual effect of these 

actions can be tested by comparing fishery recovery actions and natural abundance on the spawning 

ground. Incidental harvest, dam counts, weir counts, and the numbers of adults on the spawning ground 

can be monitored to verify that these actions will lead to the end goal of producing a minimum of 1,000 

natural spawners per year in Redfish and Alturas Lakes and 500 spawners per year in one of the smaller 

Sawtooth Valley lakes. 
ESA Recovery Plan: Snake River Sockeye Salmon | 309

June 2015| NOAA Fisheries 

Section 9: Time and Cost

9.1 Cost Estimates

9.2 Time Estimate
ESA Recovery Plan: Snake River Sockeye Salmon | 310

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 311

June 2015| NOAA Fisheries 

9. Cost and Time Estimates

ESA section 4(f)(1) requires that recovery plans, to the maximum extent practicable, include 

“estimates of the time required and the cost to carry out those measures needed to achieve the 

plan’s goal and to achieve intermediate steps toward that goal” (16 U.S.C. 1531-1544, as 

amended). This section is intended to meet this ESA requirement. 

9.1 Cost Estimates

This section provides five-year and total cost estimates as called for under ESA and NOAA 

Interim Recovery Planning Guidance, version 1.3, dated June 2010. Based on the limiting 

factors and threats identified in this Plan, the Sockeye Technical Advisory Committee made up 

of staff from NMFS, Northwest Fisheries Science Center, Idaho Department of Fish and Game, 

Shoshone-Bannock Tribes, Bonneville Power Administration, U.S. Forest Service, and other 

entities identified proposed actions to recover ESA-listed Snake River Sockeye Salmon. This list 

of recovery actions (Table 7-1) was developed using the most up-to-date assessment of current 

Snake River Sockeye Salmon status and recovery needs, without consideration of cost or 

potential funding. 

In order to prepare cost estimates for recovery actions, NMFS worked with the Sockeye 

Technical Committee staff familiar with the current and proposed recovery actions to estimate

costs where information was sufficient to allow reasonable estimates to be made. The approach 

taken to estimate the total cost of each project was to use the scale described for each action, 

where available, together with unit costs for each project type. For some actions, no scale 

estimate is available at this time, in which case no cost estimate is provided in Appendix A: 

Summary of Recovery Measures and Estimated Costs. 

The Recovery Cost Summary Table in Appendix A of this document provides the estimated 

costs for actions set forth in this recovery plan for fiscal years 2014 through 2018, where 

information was sufficient to provide them. It is a guide for meeting the recovery goals outlined 

in this Plan. The table includes the action numbers, action descriptions, the parties responsible 

for the actions (either funding or carrying out), and estimated costs. In many cases, research, 

monitoring, and evaluation costs have yet to be determined. Those that can be estimated at this 

point are included in Appendix A.

Responsible parties are entities, agencies, or organizations with authority, responsibility, or 

expressed interest to implement a specific recovery action. The listing of a party in the table 

does not require the identified party to implement the action(s) or to secure funding for 

implementing the action(s). 
ESA Recovery Plan: Snake River Sockeye Salmon | 312

June 2015| NOAA Fisheries 

All yearly costs identified in Appendix A are presented in present-year dollars (that is, without 

adjusting for inflation). Costs are estimates for the Fiscal Year (FY) in thousands of dollars 

($K). The total costs are the sum of the yearly costs without applying a discount rate.

As stated in Section 1, a coordinated partnership of multiple entities has implemented the captive 

broodstock program since the ESU was listed as endangered 1991. The estimated total costs for 

past Snake River Sockeye Salmon recovery actions from 1991 to 2013, including the captive 

broodstock program, total approximately $68 million. These actions were implemented as part of 

existing mandates and regulatory obligations to recover Sockeye Salmon. 

The estimated costs shown in the Summary of Recovery Measures and Estimated Costs Table in 

Appendix A correspond to proposed recovery actions in Section 7, Table 7-1. The actions range 

widely from relatively less expensive to more expensive projects. Actions also vary considerably 

in length of time over which they will take place. In some cases a length of time has yet to be 

determined. 

Recovery Actions and Corresponding Cost Estimates

The Summary of Recovery Measures and Estimated Costs Table in Appendix A lists available 

cost estimates for actions identified in the Plan. The action categories are the following:

• Baseline actions: These are actions categorized as part of ongoing, existing 

programs that will be carried out regardless of this Plan. No cost estimate is 

provided for these actions because they do not represent new costs that are a 

direct result of this Plan. 

• Cost Estimate Exists: These are actions for which an estimate and scale are 

available. 

• To Be Determined: These are actions that need costs to be developed, need unit 

costs, and/or need project scale estimates to be sufficiently detailed to support a 

cost estimate.

• Not Applicable: These actions are generally policy actions requiring staff time 

and do not have separate costs associated with them.

In the implementation phase, NMFS will work with regional experts and local implementers to 

identify costs, scale or unit costs for actions that require more information. The Recovery 

Measures and Estimated Costs Table in Appendix A will be updated as new cost information 

becomes available.

The Appendix A cost table summarizes the available cost estimates for the actions proposed in 

the Snake River Sockeye Salmon Recovery Plan, covering all projects judged to be feasible and 

projected to occur over the initial five year period of implementing the recovery plan, FY 2014 

to FY 2018. The overall total cost estimated for all actions during this five-year time period, 
ESA Recovery Plan: Snake River Sockeye Salmon | 313

June 2015| NOAA Fisheries 

where costs are available, is approximately $20,293,955. The total estimated cost of recovery 

actions for Snake River Sockeye Salmon over the next 25 years is about $101,469,775.

These costs do not include costs associated with implementing actions within the lower 

Columbia River, estuary, or Federal Columbia River Power System (FCRPS) because these are 

considered baseline actions. Preliminary research, monitoring, and evaluation costs have, in 

some cases, been estimated; however, these costs are not included at this time pending 

completion of research and monitoring plans and further development of each project.

There are several cautions that must be highlighted regarding these costs, because many of these 

costs may be incomplete in scope, scale, or magnitude until actions are better defined. 

Specifically, costs for potentially expensive projects such as land and water acquisition, water 

leasing, and research, monitoring, and evaluation have not yet been estimated for this ESU. For 

other projects, unit cost estimates or determination of project scale may also still need to be 

calculated. The Summary of Recovery Measures and Estimated Costs table in Appendix A

presents summary costs for recovery actions identified that will help promote recovery 

(delisting) of this ESU. Costs estimates may be adjusted up or down, as unit cost estimates, scale 

of projects, total number of actions, and currently unforeseen costs for actions are determined. 

9.2 Time Estimate

There are unique characteristics and challenges in estimating the time required for salmon and 

steelhead recovery given the complex relationship of these fish to their environment and to 

human activities in the water and on land. Examples of the uncertainties that preclude a more 

precise estimate of time include biological and ecosystem responses to recovery actions are the 

unknown impacts of future economic, demographic, and social developments.

NMFS estimates that recovery of the Snake River Sockeye Salmon ESU, like recovery for most 

of the ESA-listed Pacific Northwest salmon and steelhead, could take 50 to 100 years. While 

this recovery plan contains an extensive list of actions to recover Snake River Sockeye Salmon, 

there are many uncertainties involved in predicting the course of recovery and in estimating total 

costs. Such uncertainties include biological and ecosystem responses to recovery actions, as well 

as long-term and future funding. While continued programmatic actions in the management of 

habitat, hatcheries, hydro, and harvest will warrant additional expenditures beyond the first five 

years, NMFS believes it is impracticable to estimate all projected actions and costs over 50 to 

100 years, given the large number of economic, biological, and social variables involved. 

Consequently, NMFS believes it is appropriate to focus on the first 25 years of action 

implementation, with the provision that actions and costs will be estimated for subsequent years, 

to achieve long-term goals and to proceed until a determination is made that listing is no longer 

necessary. 
ESA Recovery Plan: Snake River Sockeye Salmon | 314

June 2015| NOAA Fisheries 

NMFS believes that is may take longer than 25 years for the biological effects of management 

actions to be fully realized and for recovery of Snake River Sockeye Salmon to occur. Rather 

than speculate on conditions that may or may not exist that far into the future, this Plan relies on 

ongoing monitoring and periodic plan review regimes to add, eliminate, or modify actions 

through adaptive management as information becomes available and until such time as the 

protection under the ESA is no longer required.

NMFS believes it most appropriate to focus on the first five years of implementation and in fiveyear intervals thereafter, with the understanding that before the end of each five-year 

implementation period, specific actions and costs will be estimated for subsequent years.
ESA Recovery Plan: Snake River Sockeye Salmon | 315

June 2015| NOAA Fisheries 

Section 10: Implementation

10.1 Implementation Framework

10.2 Implementation Progress and Status Assessments
ESA Recovery Plan: Snake River Sockeye Salmon | 316

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 317

June 2015| NOAA Fisheries 

10. Implementation

This section describes a proposed framework for coordinated implementation of this Plan. 

Successful implementation of recovery actions, research, and monitoring projects will build upon 

the over twenty years of leadership and Sockeye Salmon recovery work carried out by the 

Stanley Basin Sockeye Technical Oversight Committee, together with IDFG, Shoshone-Bannock 

Tribes, U.S. Forest Service, NMFS, and their partners that have prevented the extinction of this 

ESU. Implementation will need the continued coordinated actions and funding from diverse 

parties including IDFG, Shoshone-Bannock Tribes, Bonneville Power Administration, NMFS, 

U.S. Forest Service, counties, state and Federal agencies, private landowners, and individuals. 

Unlike other ESA-listed ESUs in the Pacific Northwest, the Snake River Sockeye Salmon ESU 

has not had a state-designated ESA recovery board (such as the SE Washington Snake River 

Recovery Board based in Dayton, Washington) that could take responsibility for developing a 

recovery plan. For that reason, NMFS is leading the development of this Plan in coordination 

with the state, tribes, and Federal agencies; however the process for implementing this Plan is yet 

to be determined.

NMFS will work with its Snake River Sockeye Salmon Technical Committee made up of 

representatives from the IDFG, the Shoshone-Bannock Tribes, U.S. Forest Service, BPA, and

together with the Idaho Governor’s Office of Species Conservation and other state and Federal

entities to review this proposed implementation framework and agree on how this Plan will be 

implemented.

Although the ESA requires NMFS to develop recovery plans, NMFS will rely, to a great extent, 

on local citizens, agencies, tribes, and jurisdictions to voluntarily implement actions the plan 

recommends or proposes. NMFS’ interim recovery planning guidance (NMFS 1996) 

acknowledges that recovery plans are not regulatory documents, and that it is not a requirement 

of ESA section 4(f) for any entity to implement the recovery strategy or specific actions in a 

recovery plan unless otherwise legally mandated. In many cases, the Plan acknowledges and 

recommends coordinating the pre-existing, ongoing recovery efforts and pre-existing laws or 

regulations that are expected to benefit the species and its environment, such as the ongoing 

hatchery, resource management, and habitat restoration activities of the IDFG, U.S. Forest 

Service, Shoshone-Bannock Tribes, soil and water conservation districts, and local land owners. 

Some of the ongoing actions that are in the Plan are required under other separate resource 

management regulatory processes, such as the implementation of forest practices, operation of 

fish hatcheries, and regulation of fisheries that may affect Snake River Sockeye Salmon. 

While organizations and individuals are not required to implement the Plan, it is anticipated that 

entities will choose to participate to further their own goals and seek funding partnerships to 

implement actions. This Plan acknowledges the leadership, hard work and dedication of 

organizations, entities, tribes, and individuals that have worked for many years on salmon 
ESA Recovery Plan: Snake River Sockeye Salmon | 318

June 2015| NOAA Fisheries 

recovery programs. It is also recognized that there may be alternative actions to those proposed 

in this plan that may also attain recovery goals. Actions to achieve a specific recovery strategy 

may vary due to logistics, project opportunities, willingness of landowners to participate, funding 

constraints, or an organization’s authorities and administrative processes. This Plan does not 

constrain or inhibit entities or individuals from implementing actions as opportunities or funding 

become available. 

10.1 Implementation Framework

This recovery plan implementation framework is presented below to begin the discussion about 

the best way to implement this Plan and engage interested parties on how best to coordinate 

future work. This anticipates close working relationships with existing groups, builds on the 

important recovery work of the last twenty years, and seeks continued collaborative initiatives to 

recover Snake River Sockeye Salmon. The roles of each of these implementation teams and the 

recovery coordinator are described below for discussion with interested parties. Similar 

frameworks are being used to coordinate other recovery plan implementation efforts in 

Washington and Oregon. 

The components of this implementation framework include the following (Figure 10-1):

• Snake River Sockeye Salmon Implementation and Science Team.

• Stanley Basin Sockeye Technical Oversight Committee (SBSTOC).

• NMFS’s Snake River Coordination Group.

Snake River Sockeye Salmon Implementation and Science Team

The Implementation and Science Team is responsible for overall leadership, coordination, 

direction, agenda setting, and communication with the action implementers and all parties 

involved in recovery plan implementation. It coordinates at relevant Federal, state, and regional 

levels, identifies and represents Sockeye Salmon recovery plan implementation in the Snake 

River Coordination Group meetings. This Team is made up of representatives from IDFG, 

Shoshone-Bannock Tribes, U.S. Forest Service, BPA, NMFS, and other entities and stakeholders 

as identified. The team will develop criteria to prioritize recovery actions and apply these 

criteria as it develops a three-year implementation schedule and plan. It will report annual 

progress on implementation and monitoring actions to the public.

The team coordinates implementation of the Adaptive Management and Research, Monitoring, 

and Evaluation Plan described in Section 11. It will coordinate with the Stanley Basin Sockeye 

Technical Oversight Committee, NMFS’ Northwest Fisheries Science Center’s Recovery 

Implementation Science Team (RIST), IDFG, Shoshone-Bannock Tribes, and NMFS to design 

research, monitoring, and evaluation protocols and actions for research, data collection, and 

reporting. It monitors and reports on status of populations in relation to recovery goals. It 
ESA Recovery Plan: Snake River Sockeye Salmon | 319

June 2015| NOAA Fisheries 

coordinates with technical teams from other Snake River management units to ensure 

consistency of across-ESU/DPS project design, data collection and reporting through 

communication with the Snake River Coordination Group.

This Team will also provide science input and advice on full life cycle Sockeye Salmon actions, 

strategies, research designs, and research and monitoring priorities, including scoping science 

needs at the ESU-level. This Team will ensure that rigorous and “best available science” 

informs implementation and is applied in research and monitoring activities and assist in 

translating information into status of species viability. This Team will be critical to five-year 

reviews of the ESU. This Team will interact with the Stanley Basin Sockeye Technical 

Oversight Committee and may have members on both groups.

Implementation Plan and Contingency Process

The Implementation and Science Team will develop action implementation prioritization criteria

and a three-year implementation schedule and plan. The prioritization criteria will build on the 

prioritization considerations described in Section 7, Actions. The ESA implementation schedule 

and plan will identify recovery actions, timeline and duration for completing the actions, lead 

agency/entity responsible for implementing the actions, and estimated cost over a specified 

period of time. 

The team will also develop a contingency process as part of its recovery tasks. As discussed in 

Section 6.3, this contingency process will identify steps so we are prepared if the species’ status 

does not continue to improve in a timely manner, and also if there are significant declines in 

status. A contingency process should set intermediate goals and timeframes, and also set early 

warning indicators and significant decline triggers. As part of this process, additional actions 

should be developed that are “on the shelf,” if needed, to address long-term trends toward 

recovery and to prevent precipitous declines. 

Stanley Basin Sockeye Technical Oversight Committee

In 1991, when Snake River Sockeye Salmon were listed as endangered under the Endangered 

Species Act, a cooperative effort began to conserve and rebuild the population. The ShoshoneBannock Tribes and the IDFG initiated the Snake River Sockeye Salmon Broodstock Program 

with funding from the BPA. The goal of this program is to conserve genetic resources and to 

rebuild Snake River Sockeye Salmon populations in Idaho. Coordination of this effort is carried 

out under the guidance of the Stanley Basin Sockeye Technical Oversight Committee, a team of 

biologists and technical experts representing the agencies involved in the recovery and 

management of Snake River Sockeye Salmon. Coordinated by BPA, the Stanley Basin Sockeye 

Technical Oversight Committee meets quarterly and is comprised of representatives from IDFG, 

Shoshone-Bannock Tribes, NMFS, and BPA.
ESA Recovery Plan: Snake River Sockeye Salmon | 320

June 2015| NOAA Fisheries 

NMFS’ Snake River Coordination Group

The Snake River Coordination Group, convened by NMFS, brings together representatives from 

the southeast Washington, northeast Oregon, and Idaho Snake River Recovery Plan management 

units and other relevant parties to coordinate policy and technical issues across the salmon and 

steelhead ESUs and DPS for the Snake River Recovery Plans. This Coordination Group 

provides organizational structure for communication and coordination on a tri-state and multitribal level across the Snake River recovery domain. This group will provide cross-species

communication and provide input to NMFS on recovery plan issues as the different Snake River 

Recovery Plans are being written and then promote recovery plan implementation. 

Figure 10-1. Snake River Sockeye Salmon recovery plan implementation framework.
ESA Recovery Plan: Snake River Sockeye Salmon | 321

June 2015| NOAA Fisheries 

10.2 Implementation Progress and Status Assessments

Evaluating a species for potential delisting requires an explicit analysis of population or 

demographic parameters (biological criteria) and also of threats under the five ESA listing 

factors in ESA section 4(a)(1) (listing factors (threats) criteria). Together these make up the 

“objective, measurable criteria” required under section 4(f)(1)(B). This Plan summarizes the 

biological criteria and threats criteria that will be used to evaluate the Snake River Sockeye 

Salmon ESU for potential change in listing status or delisting.

Five-Year Reviews and ESU/DPS Status Assessments 

The ESA requires that, at least every five years, the Secretary of Commerce shall conduct a 

review of all ESA-listed species and determine whether any species should: (1) be removed from 

such list; (2) be changed in status from an endangered species to a threatened species; or (3) be 

changed in status from a threatened species to an endangered species. Accordingly, at five-year 

intervals, NMFS will conduct reviews of the listed Snake River salmon ESUs and steelhead 

DPSs. These reviews will consider information that has become available since the most recent 

listing determinations, information specifically related to the limiting factors and threats 

identified in recovery plans, and make recommendations whether a change in listing status may 

be appropriate. Any status reviews will be based on the NMFS Listing Status Decision 

Framework and will be informed by the information obtained through implementation of 

monitoring, research, and evaluation programs in each management unit plan and the recovery 

modules.

Similarly, new information considered during five-year reviews may also compel more in-depth 

assessments of implementation and effectiveness monitoring and associated research to inform 

adaptive management decision at the management unit level.

Modifying or Updating the Recovery Plan

The ESA requires a review of all listed species at least once every five years. Guidance for these 

reviews developed jointly by NMFS and the U.S. Fish and Wildlife Service is on the NMFS 

website: http://www.nmfs.noaa.gov/pr/pdfs/laws/guidance_5_year_review.pdf. According to 

NMFS Interim Guidance (NMFS 2006), immediately following the five-year species review, an 

approved recovery plan should be reviewed in conjunction with implementation monitoring, to 

determine whether or not the plan needs to be brought up to date.

NMFS’ Recovery Guidance provides three types of plan modifications: (1) an update; (2) a

revision; or (3) an addendum. An update involves relatively minor changes. An update may 

identify specific actions that have been initiated since the plan was completed, as well as changes 

in species status or background information that do not alter the overall direction of the recovery 

effort. An update does not suffice if substantive changes are being made in the recovery criteria 

or if any changes in the recovery strategy, criteria, or actions indicate a shift in the overall 

direction of recovery; in this case, a revision would be required. Updates can be made by 
ESA Recovery Plan: Snake River Sockeye Salmon | 322

June 2015| NOAA Fisheries 

NMFS’ Interior Columbia Basin Office of the West Coast Region, which will seek input from 

the local stakeholder group prior to making any update. An update would not require a public 

review and comment period.

NMFS expects that updates will result from implementation of the adaptive management 

program for this Plan. Adaptive management depends on the flow of information from field staff 

to recovery managers and planners; hence, it requires frequent updates from monitoring and 

research on the effectiveness of recovery actions and the status and trends of the listed species. It 

may be most efficient to keep the Recovery Plan current by updating it frequently enough to 

forego the need for major revisions.

A revision is a substantial rewrite and is usually required if major changes are required in the 

recovery strategy, objectives, criteria, or actions. A revision may also be required if new threats 

to the species are identified, when research identifies new life history traits or threats that have 

significant recovery ramifications, or when the current plan is not achieving its objectives. 

Revisions represent a major change to the recovery plan and must include a public review and 

comment period.

An addendum can be added to a recovery plan after the plan has been approved and can 

accommodate minor information updates or relatively simple additions such as implementation 

strategies, or participation plans, by approval of the Area Office or NMFS' West Coast Region’s 

Regional Administrator. More significant addenda (for example, adding a species to a recovery 

plan) should undergo public review and comment before being attached to a Plan. Addenda are 

approved on a case-by-case basis because of the wide range of significance of different types of 

addenda. NMFS will seek input from stakeholders on minor addenda to this Plan.
ESA Recovery Plan: Snake River Sockeye Salmon | 323

June 2015| NOAA Fisheries 

Section 11: Research, Monitoring, and Evaluation for 

Adaptive Management

11.1 Research, Monitoring, and Evaluation

11.2 Adaptive Management
ESA Recovery Plan: Snake River Sockeye Salmon | 324

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 325

June 2015| NOAA Fisheries 

11. Research, Monitoring, and Evaluation for Adaptive 

Management

This section describes the proposed framework for research, monitoring, and evaluation

supporting adaptive management for the recovery of Snake River Sockeye Salmon ESU. The 

section begins with an introduction of the importance of adaptive management as a key 

component of Sockeye Salmon recovery. It then presents a proposed framework for research, 

monitoring, and evaluation and concludes with a proposed framework for carrying out adaptive 

management. 

Many different organizations, including state, tribal, Federal, local, and private entities, currently 

conduct programs and actions designed to improve survival across all “H’s” for Snake River 

Sockeye Salmon as they travel from natal lakes to the ocean and back. These entities also 

conduct various kinds of monitoring. Coordination of these diverse local and regional 

monitoring actions will be essential for future NMFS status reviews of the Snake River Sockeye 

Salmon ESU and understanding the effects of recovery actions to improve ESU viability and 

promote recovery. 

Adaptive Management

Adaptive management plays a critical role in recovery planning. The long-term success of 

recovery efforts will depend on the effectiveness of incremental steps taken to move this one 

remaining extant Snake River Sockeye Salmon population from its current status to a viable 

level. Adjustments will be needed if actions do not achieve desired goals, and to take advantage 

of new information and changing opportunities. Adaptive management provides the mechanism 

to facilitate these adjustments. 

Adaptive management is a structured process designed to improve understanding and 

management by helping managers and scientists learn from the implementation and 

consequences of natural resource policy decisions (Holling 1978; Walters 1986; Lee 1993). 

Research, monitoring, and evaluation associated with recovery plans need to gather the 

information that will be most useful in tracking and evaluating implementation and action 

effectiveness, and assessing the status of listed species. Planners and managers then need to use 

the information collected to guide and refine recovery strategies and actions. This process is 

crucial for salmon recovery because of the complexity of the species’ life cycle, the range of 

factors affecting survival, and the limits to our understanding of how specific actions affect 

species’ characteristics and survival. 

Adaptive management works by coupling decision making with data collection and evaluation. 

Most importantly, it offers an explicit process through which alternative approaches and actions 

can be proposed, prioritized, implemented, and evaluated. Successful adaptive management 
ESA Recovery Plan: Snake River Sockeye Salmon | 326

June 2015| NOAA Fisheries 

requires that monitoring and evaluation plans be incorporated into overall implementation plans 

for recovery actions. These plans should link monitoring and evaluation results explicitly to 

feedback on the design and implementation of actions. Figure 11-1 illustrates the adaptive 

management process. Section 11.2 describes the proposed adaptive management framework and 

approach. 

Figure 11-1. The adaptive management cycle. 

The research, monitoring, and evaluation (RM&E) plan described below identifies the level of 

monitoring and evaluation needed to determine the effectiveness of recommended actions, and 

whether they are leading to improvements in population viability. The plan also identifies critical 

data gaps in species and habitat knowledge. The data obtained through RM&E plan 

implementation will be used to assess and, if necessary, correct current restoration strategies. 

The Snake River Sockeye Salmon Implementation and Science Team will oversee 

implementation of an adaptive management plan in coordination with participating agencies, 

tribes, and entities (see Section 10). The group will:

• Confirm goals and objectives for Sockeye Salmon recovery; 

• Compare monitoring results with performance measures within the RM&E plan; 

• Review progress toward goals and objectives; and 

• Identify and recommend needed changes in strategies and/or actions to better 

meet goals/objectives, and revise strategies and/or actions accordingly.
ESA Recovery Plan: Snake River Sockeye Salmon | 327

June 2015| NOAA Fisheries 

A major challenge facing the development and implementation of an effective adaptive 

management strategy for Snake River Sockeye Salmon is the large number of organizations that 

implement management actions, as well as the complexity in jurisdictional and management 

decision authority. These organizations include, but are not limited to, Idaho Department of Fish 

and Game, Idaho Governor’s Office of Species Conservation, Shoshone-Bannock Tribes, state 

agencies, counties, irrigation districts, agriculture and private forest land managers, NMFS, U.S. 

Forest Service, BLM, other Federal agencies, utilities, citizen groups, and others. Adding to this 

complexity is the fact that there is no one single decision body that holds decision authority for 

management actions across all sectors (habitat, hatcheries, harvest, and hydro). It is unreasonable 

to expect centralization of all authorities and decision processes into a single decision 

framework. Therefore, the intent of this adaptive management plan is to develop a collaboration 

and coordination process that uses the current implementation structures and allows for sharing 

of information and decisions that influence recovery of Snake River Sockeye Salmon.

Pre-smolt Sockeye Salmon being released at Redfish Lake. Photo: T. Brown, IDFG.

11.1 Research, Monitoring, and Evaluation

This research, monitoring, and evaluation plan covers the Snake River Sockeye Salmon ESU. It 

describes the RM&E recommended for assessing the status and trends in population viability, 

statutory listing factors, and for evaluating the success of actions implemented to recover Snake 

River Sockeye Salmon. In addition, this plan identifies current efforts and additional RM&E 
ESA Recovery Plan: Snake River Sockeye Salmon | 328

June 2015| NOAA Fisheries 

needs. Although logistical and monetary limitations exist, this plan will focus on the common 

goal of assessing success in population and ESU recovery.

This RM&E plan is based in part on principles and concepts laid out in the NMFS document 

Guidance for Monitoring Recovery of Pacific Northwest Salmon and Steelhead Listed Under the 

Federal Endangered Species Act (January 2011) and Adaptive Management for ESA-Listed 

Salmon and Steelhead Recovery: Decision Framework and Monitoring Guidance (May 1, 2007). 

These guidance documents provide a listing status decision framework, which is a series of 

decision-questions that address the status and change in status of a salmonid ESU, and the risks 

posed by threats to the ESU (Figure 11-2).

Figure 11-2. Flow diagram outlining the decision framework used by NMFS to assess the status of biological 

viability criteria and limiting factors criteria.
ESA Recovery Plan: Snake River Sockeye Salmon | 329

June 2015| NOAA Fisheries 

A Three-Phased Approach

Given the status of the Snake River Sockeye Salmon ESU (a single extant population) and the 

recommendation to establish at least three viable populations, a multiphase RM&E Plan is 

needed to determine if the ESU meets recovery criteria. Thus, this plan adopts a three-phase 

approach:

• Phase 1 – Captive broodstock development and gene rescue;

• Phase 2 – Re-colonization of Redfish and other lakes; and

• Phase 3 – Local adaptation.

The ultimate objective of the three-phase approach is the restoration of natural Sockeye Salmon

populations in Sawtooth Valley lakes. A description of the three phases is summarized below.

A key element of the approach is the adaptive nature of the reintroduction strategy. Thus, 

evaluation of results will guide the course of future actions. Although the plan follows closely 

the phased approach associated with the hatchery program, it is important to note that in addition 

to monitoring the hatchery program, other environmental and biological conditions are 

monitored under each phase. That is, monitoring under each phase is not limited to monitoring 

the hatchery programs.

Phase 1

Phase 1 has not yet achieved Snake River Sockeye Salmon recovery objectives. Implementation 

of Phase 1 monitoring began in 1991 and focused on assessing best management practices for the 

captive brood program, genetic and phenotypic characteristics, reintroduction strategies, 

spawning success, limnological characteristics, and identification of factors limiting freshwater 

survival. 

Phase 2 

Phase 2 is being implemented to produce up to one million smolts at the Springfield Hatchery. 

The resulting anadromous returns from fish produced at the Springfield Hatchery will be used to 

meet re-colonization goals in Redfish Lake. 

Phase 2 will also implement a temporary adult supplementation program in Pettit Lake using 

Redfish Lake captive broodstock adults, or eggs produced by those adults, and residual 

production within Pettit Lake. Anadromous adults will be released upstream of the Sawtooth 

Hatchery after juvenile Sockeye Salmon rearing at that facility has been terminated. The 

reintroduction strategy will be further developed and refined as the Redfish Lake strategy is 

implemented. The future course will depend on the relative trends in anadromous production and 

resident production in Pettit Lake (Section 6.3.1.5), and performance of the Redfish Lake 

reintroduction strategy. 
ESA Recovery Plan: Snake River Sockeye Salmon | 330

June 2015| NOAA Fisheries 

In Phase 2 managers will evaluate and identify appropriate strategies for Alturas Lake Sockeye 

Salmon recovery (Section 6.3.1.6). This investigation will require careful steps to maintain the 

spatial structure and diversity of the Alturas Lake early stream spawning type, and capture the 

benefits of local adaptation. Alternative strategies for the early-spawning Alturas Lake residual 

population might include trap and transport of ocean-returning adults identified as Alturas Lake 

origin to Alturas Lake, or possibly to the IDFG Eagle Fish Hatchery to establish a new hatchery 

program for Alturas Lake anadromous Sockeye Salmon. 

Phase 2 monitoring would continue Phase 1 monitoring and would be refocused as needed to 

assess the abundance and trends in adult Sockeye Salmon spawners, phenotypic and genetic 

characteristics, and biological and environmental factors that limit survival.

Phase 3

Hatchery‐ and natural‐origin run sizes back to the Sawtooth Valley subbasin will be used to 

“trigger” management decisions such as reducing/eliminating the captive broodstock programs, 

reducing hatchery production, or shifting resources to new areas. As noted above, Pettit, Alturas, 

and Redfish Lake Sockeye Salmon restoration will require allocation of additional resources. 

Monitoring associated with Phase 3 will focus on determining if abundance, productivity, spatial 

structure, and diversity of Snake River Sockeye Salmon meet recovery criteria; tracking the 

status and trend in habitat conditions; assessing the effects of habitat actions on Sockeye Salmon

survival; and assessing the effects of hydro operations, harvest, predation, disease, and the Phase 

3 hatchery program on ESU viability. In addition, the Pettit and Alturas Lake strategies will be 

evaluated and refined to support naturally adapted anadromous production in the lakes.

11.1.1 Types of Monitoring Efforts

Several types of monitoring are needed to support adaptive management and to allow managers 

to make sound decisions.

Status and Trend Monitoring

Status monitoring describes the current state or condition of the population and their limiting 

factors at any given time. Trend monitoring tracks these conditions to provide a measure of the 

increasing, decreasing, or steady state of a status measure through time. Status and trend 

monitoring includes the collection of information used to describe broad-scale trends over time. 

This information is the basis for evaluating the cumulative effects of actions on fish and their 

habitats.

Action Effectiveness Monitoring

This type of monitoring addresses cause-and-effect. That is, action effectiveness monitoring is 

designed to determine whether a given action or suite of actions achieved the desired effect or 

goal. This type of monitoring is research oriented and therefore requires elements of 

experimental design (e.g., controls or reference conditions) that are not critical to other types of 
ESA Recovery Plan: Snake River Sockeye Salmon | 331

June 2015| NOAA Fisheries 

monitoring. Consequently, action effectiveness monitoring is usually designed on a case-by-case 

basis. Action effectiveness monitoring provides funding entities with information on benefit/cost 

ratios and resource managers with information on what actions or types of actions improved 

environmental and biological conditions.

Implementation and Compliance Monitoring

Implementation and compliance monitoring determines if actions were carried out as planned 

and meet established benchmarks. This is generally carried out as an administrative review and 

does not require any parameter measurements. Information recorded under this type of 

monitoring includes the types of actions implemented, how many were implemented, where they 

were implemented, and how much area or stream length was affected by the action. Success is 

determined by comparing field notes with what was specified in the plans or proposals (detailed 

descriptions of engineering and design criteria). Implementation monitoring sets the stage for 

action effectiveness monitoring by demonstrating that the restoration actions were implemented 

correctly and followed the proposed design.

Key Information Needs Research

Research of key information needs includes scientific investigations of critical assumptions and 

unknowns that constrain effective recovery plan implementation. Uncertainties include 

unavailable pieces of information required for informed decision making, as well as studies to 

establish or verify cause-and-effect and identification and analysis of limiting factors.

11.1.2 Monitoring Framework 

As discussed above, this framework consists of three phases that correspond to the phases of the 

hatchery program. Although monitoring of the hatchery program is a large part of the RM&E 

plan, other biological and environmental conditions are monitored in concert with the hatchery 

program. Below are the primary objectives associated with each of the monitoring phases.

Phase 1 Monitoring

The goal of the Phase 1 recovery effort is to develop captive broodstock for the purpose of 

preserving the genetic resources of the population. As an artifact of pursing this goal, eggs and 

fish not essential to this effort have been produced and re-introduced to the habitat using a 

“spread-the-risk” approach. Phase 1 recovery efforts were initiated in 1991 and much progress 

has been achieved in addressing the Phase 1 monitoring objectives. The objectives of Phase 1 

monitoring are to:

• Develop best management practices for rearing Snake River Sockeye Salmon to 

maturation in the hatchery environment (in both fresh and sea-water 

environments).

• Maintain the genetic resources of the Redfish Lake Sockeye Salmon.
ESA Recovery Plan: Snake River Sockeye Salmon | 332

June 2015| NOAA Fisheries 

• Release eggs and fish not essential for the maintenance of the captive broodstock 

to the habitat using multiple reintroduction strategies.

• Determine adult spawning capacity in recovery lakes.

• Identify the relative success of the different reintroduction strategies.

• Determine if full-term and hatchery-origin anadromous adults released to the 

habitat spawn successfully.

• Describe the life history and phenotypic characteristics of Snake River Sockeye 

Salmon.

• Determine the limnological characteristics of the nursery lakes of the upper 

Salmon River basin and assess their ability to aid in recovery efforts.

• Determine what factors may be limiting freshwater survival of Snake River 

Sockeye Salmon.

Phase 2 Monitoring

In Phase 2, returning adults will be used in a conventional hatchery program to support relatively 

high levels of anadromous return spawners in Redfish Lake. Initial efforts will prioritize the recolonization of Redfish and Pettit Lakes. Alturas Lake re-colonization objectives will be refined 

based on information gained during investigations. Yellowbelly and Stanley Lakes may 

experience some level of natural colonization during the implementation of Phase 2. An 

important component of this phase is to assess the capacity and production potential within the 

nursery lakes. The objectives of Phase 2 monitoring are to:

• Continue to implement elements of Phase 1 monitoring such as genetic and 

limnological monitoring, and determine the status and trend in habitat conditions 

for each population. 

• Continue to assess the number of adults returning to adult traps and nursery lakes 

in the Sawtooth Valley.

• Continue to assess the number of returning anadromous adult Sockeye Salmon

that spawn naturally in Sawtooth Valley lakes.

• Describe the life history and phenotypic characteristics of Sockeye Salmon in 

Sawtooth Valley lakes and evaluate strategies to recover Sockeye Salmon using 

existing populations in Pettit and Alturas Lakes.

• Determine if the five-year geometric mean (GM) of returning Snake River 

Sockeye Salmon adults (hatchery- and natural-origin) to the Sawtooth Valley 

meets adult abundance target objectives required to begin sun-setting captive 

broodstock programs (1,000 to sunset the NOAA programs and 2,150 to sunset 

the IDFG program).
ESA Recovery Plan: Snake River Sockeye Salmon | 333

June 2015| NOAA Fisheries 

• Determine if the five-year geometric mean (GM) of returning Snake River 

Sockeye Salmon natural-origin adults to Redfish Lake are sufficient to allow for 

transition to Phase 3 and integrated broodstock.

Phase 3 Monitoring

In Phase 3, the focus will be on natural adaptation. It is anticipated that once the populations 

build to self-sustaining numbers, the hatchery program will be phased out or greatly reduced. It 

may be necessary, however, to maintain a “safety-net” captive-broodstock program that will 

guard against environmental events that could cause large declines in the anadromous returns. 

The ultimate goal of Phase 3 monitoring is to assess the long-term persistence of viable 

populations of naturally produced Snake River Sockeye Salmon within the Snake River Sockeye 

Salmon ESU. In order to determine if the desired outcome has been achieved, answers to two 

overarching questions need to be addressed:

• Is the status of each population trending toward the recovery criteria?

• Are the effects of the primary factors limiting the status of the populations 

increasing, decreasing, or remaining stable? 

Although these two overarching questions provide the basis for developing Phase 3 of the 

RM&E plan, it is important to note that several specific objectives attend each of the two 

overarching questions. Below are the objectives associated with the two questions. 

• Determine the status and trend in abundance and productivity of O. nerka

spawners for each population. 

• Determine the status of the spatial structure of each population based on current 

and historically used habitat.

• Determine the status and trend in life history, genotypic, and phenotypic diversity 

for each population.

• Determine the status and trend in conditions of habitat for each population.

• Determine the effects of habitat degradation and habitat restoration actions on the 

abundance, productivity, and spatial structure of the natural populations.

• Determine the influence of the Phase 3 hatchery program on the abundance, 

productivity, spatial structure, and diversity of the natural populations.

• Determine the effect of mainstem hydropower operations and operational 

improvements on viability of Snake River Sockeye Salmon populations.

• Determine the effect of harvest on the abundance, productivity, and diversity of 

the natural populations.

• Determine the effect of predation on the abundance and productivity of the natural 

populations.
ESA Recovery Plan: Snake River Sockeye Salmon | 334

June 2015| NOAA Fisheries 

• Determine the transmission and effects of disease on the abundance, productivity, 

and diversity of the natural populations.

This plan is designed to assess current monitoring efforts and test new strategies for the

restoration and recovery of Snake River Sockeye Salmon. It is important to point out that there 

are several monitoring programs already in place that measure the status of Snake River Sockeye 

Salmon and several of its limiting factors. For example, there is an extensive plan to assess the 

hatchery program (IDFG 2010). In addition, current monitoring efforts include spawning ground 

surveys, assessments at weirs, limnological assessments, Columbia Habitat Monitoring Program 

(CHaMP) and the USDA PACFISH/INFISH Biological Opinion Monitoring Program (PIBO) 

habitat status and trend surveys in tributary streams, predator abundance estimates, genetic 

sampling, tagging studies, juvenile abundance estimates, juvenile smolt indices and smolt 

condition, adult ladder counts, adult conversion rates, juvenile survival rates, assessments of 

avian predators, measurements of mainstem environmental parameters (e.g., project flow; 

spillway flow; forebay and tailrace total dissolved gas levels; forebay, tailrace, and scrollcase 

temperatures; and turbidity), juvenile dam passage performance evaluations, and fishery 

assessments. Most of this work is conducted by IDFG, SBT, and NMFS. These monitoring 

programs, as they relate to each objective, are described below. Where there are gaps in 

monitoring, this plan intends to fill those gaps by building upon the existing monitoring efforts. 

Those additional efforts are also described below.

The following sections address the needed RM&E for each of the three monitoring phases. For 

each monitoring phase and objective, the plan identifies the type of monitoring needed (e.g., 

status and trend or implementation), key informational needs that were identified in Section 6, 

monitoring questions, performance metrics, possible approaches (monitoring methods), 

suggested analyses, and the status of monitoring associated with the objective. The approaches 

and analyses described for each objective are not exhaustive, but are intended to represent those 

actions considered to have potential to be implemented while recognizing logistical and 

monetary constraints. In addition, for many of the monitoring needs, regional review (e.g., ISRP) 

will suggest potentially different approaches and/or analyses. The intent of this Plan is to help 

standardize approaches and analyses for monitoring and evaluation purposes.

11.1.3 Phase 1 Monitoring

The purpose of Phase 1 monitoring is to determine if the captive brood program is preserving the 

genetic resources of the population and increasing adult abundance in both captive and natural 

environments. As noted above, Phase 1 monitoring includes more than just monitoring the 

success of the captive brood program. It also includes monitoring biological and environmental 

conditions. Much of the monitoring needed to address Phase 1 is described in IDFG (2010). 
ESA Recovery Plan: Snake River Sockeye Salmon | 335

June 2015| NOAA Fisheries 

Objective 1. Develop best management practices for rearing Snake River Sockeye Salmon

to maturation in the hatchery environment (in both fresh and sea-water environments).

Because of the precipitous decline of Snake River Sockeye Salmon, it was necessary to initiate a 

captive broodstock program with the primary goal of slowing the loss of critical population 

genetic diversity and heterozygosity, and to prevent extinction. The approach of the hatchery 

program under Phase 1 is to minimize inbreeding among closely related individuals and to slow 

the loss of critical genetic information. 

Type of monitoring effort: Implementation and effectiveness monitoring

Key Information Needs:

• None

Monitoring questions:

• Are hatchery best management practices to rear all life stages of Sockeye Salmon

adequately developed to address program objectives?

• What are the average life-stage survivals (e.g., green egg to the eyed-egg stage of 

development, first-feeding fry to maturation, etc.)?

Performance metrics:

• Number of fish collected for broodstock

• Life-stage survival in hatchery

• Number of fish spawned and released

Possible Approach: 

Record broodstock (numbers, origin, sex); sample numbers of fish monthly through 

rearing; and record number of fish released.

Suggested Analysis: 

Compare abundances and life-stage survival rates to standards from HGMP and other 

agreements.

Status: 

Most of this work is being conducted by IDFG with funding from BPA. Results can be 

found in (Ford 2011; Baker et al. 2012).
ESA Recovery Plan: Snake River Sockeye Salmon | 336

June 2015| NOAA Fisheries 

Objective 2. Maintain the genetic resources of the Redfish Lake Sockeye Salmon. 

To determine if the program is maintaining or slowing the loss of genetic diversity and 

heterozygosity, it is necessary to measure allelic diversity and heterozygosity, and track them 

over time. 

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• How can remnant anadromous Sockeye Salmon gene resources that exist in other 

Sawtooth Valley lakes be used for recovery efforts on a lake specific basis?

• Is the current Redfish Lake Sockeye Salmon captive broodstock genetic structure 

appropriate for use in rebuilding efforts in other Sawtooth Valley lakes? 

Monitoring questions:

• What was the historic genetic diversity and heterozygosity of Snake River 

Sockeye Salmon?

• To what degree have the genetic diversity and heterozygosity of Snake River 

Sockeye Salmon changed since the captive brood program began in 1991?

Performance metrics: 

• Indices of genetic diversity (allelic diversity, heterozygosity-microsatellites, 

single nucleotide polymorphisms)

Possible Approach: 

Collect and analyze genetic samples from a representative sample of adult and juvenile 

O. nerka. Samples are obtained from broodstock, smolt traps, mid-water trawls, and adult 

returns. Identify and analyze historic genetic samples (e.g., taxidermy, samples from 

biological surveys, etc.) of O. nerka from the Sawtooth Valley lakes.

Suggested Analysis: 

DNA tissue samples are analyzed using known genetic markers (including microsatellite 

loci and non-coding single nucleotide polymorphisms (SNPs), or base substitutions 

assayed via restriction enzyme analysis). 

Status: 

IDFG has been performing this work with funding from BPA. The most recent results 

can be found in Peterson et al. (2013).
ESA Recovery Plan: Snake River Sockeye Salmon | 337

June 2015| NOAA Fisheries 

Objective 3. Release eggs and fish not essential for the maintenance and annual rebuilding 

of the captive broodstock to the habitat using multiple reintroduction strategies.

When adult returns are in excess of hatchery program needs, adults are released back into the 

natural environment. Additionally, eggs from spawning events to maintain the captive 

broodstock are produced in excess of what is needed to maintain the broodstock and these 

hatchery eggs have been reared to various stages for release into the natal habitat. 

Type of monitoring effort: Effectiveness Monitoring.

Key information needs:

• None

Monitoring questions:

• Has the current “spread-the-risk” strategy of releasing eggs and fish to the habitat 

been sufficient to test the success of the different strategies used?

• Which release strategies result in the highest survival rate and successful 

spawning?

• Which release strategies improve spatial structure, life-history and genetic 

diversity, and productivity?

Performance metrics:

• Egg retention

• Distribution of spawners by release strategy

• Survival by release strategy

• Number of eggs or juveniles released

Possible Approach:

Record spawning data (sex, fecundity, release information per parent), numbers of fish 

monthly through rearing, and record number of fish released. Differentially mark fish at 

the time of release with physical marks or parentage-based tagging (PBT). 

Suggested Analysis:

Compare life-stage survival for each release strategy. Quantify the number of eggs 

produced and the number of fish released per strategy. 

Status: 
ESA Recovery Plan: Snake River Sockeye Salmon | 338

June 2015| NOAA Fisheries 

The SBT, Biolines Environmental Consulting, and IDFG have been performing this work 

with funding from BPA. The most recent results can be found in Griswold et al. (2011), 

Peterson et al. (2013), and Baker et al. (2013). Griswold et al. (2012) provides an 

evaluation of parr releases in Redfish, Pettit, and Alturas Lakes.

Objective 4. Identify the relative success of the different Phase 1 reintroduction strategies.

Since there are different strategies being used in Phase I to increase the number of fish returning 

to the Sawtooth Valley, it is important to evaluate which one(s) may be the most successful.

Type of monitoring effort: Status and trend monitoring and effectiveness monitoring.

Key information needs:

• None

Monitoring questions:

• How many juvenile Snake River Sockeye Salmon from each of the different 

rearing/release strategies pass Lower Granite Dam?

• How many adult Sockeye Salmon from each of the different rearing/release 

strategies return to the two adult traps in the Sawtooth Valley?

• How many returning adult Snake River Sockeye Salmon from each of the 

rearing/release strategies spawn naturally?

• What is the productivity of Sockeye Salmon that were produced under each 

rearing/release strategy?

Performance metrics:

• Survival by rearing/release strategy

• Growth by rearing/release strategy

• Adult age structure/release strategy

• Adult return numbers/release strategy

Possible Approach:

Marks and tags can be used to identify fish from a specific rearing/release strategy, 

census of adult returns; origin of adults returning to natal lakes; conduct multiple 

spawning surveys within all populations (see Approach under Objective 1).

Suggested Analysis:
ESA Recovery Plan: Snake River Sockeye Salmon | 339

June 2015| NOAA Fisheries 

Associating a hatchery spawner with a specific rearing/release strategy is needed in order 

to estimate the proportion of adults returning from a particular strategy. Analysis of 

marks and tags can be used to identify the return and survival of fish from different 

rearing/release strategies. Marks, tags, and parentage based tagging (PBT) analyses are 

used to identify fish from specific release strategies. A simple approach is to compare the 

number of PBT marked fish that returned by release strategy to the number of fish 

released within each strategy. Additional productivity measures (SARs, recruits per 

spawner) can also be reported. The number of naturally produced spawners can be 

estimated by PBT tagging of the released parents and returning unmarked adults.

Status: 

IDFG has been performing this work with funding from BPA. The most recent results 

can be found in Peterson et al. (2013).

Objective 5. Determine if full-term (captive brood) and hatchery-origin anadromous adults 

released to the habitat spawn successfully.

Both full-term and hatchery-origin adults will be released into the system to spawn naturally. 

This objective will determine if these releases are successful and if one is more successful than 

the other. 

Type of monitoring effort: Status and trend monitoring and effectiveness monitoring.

Key information needs:

• What are the various numerical adult spawning carrying capacities for 

anadromous Sockeye Salmon in the Sawtooth Valley lakes?

• How do these carrying capacity maximums fit with recovery planning needs to 

address abundance, spatial structure, and diversity needs (e.g., is spawning and 

rearing capacity a limiting factor)?

Monitoring questions:

• How many full-term and hatchery adult Sockeye Salmon spawn naturally on 

spawning grounds in the Sawtooth Valley lakes?

• How many redds are produced by full-term and hatchery adults?

• What is the spawn timing of full-term and hatchery adults in Sawtooth Valley 

lakes?

• How many adults return from full-term and hatchery adult Sockeye Salmon?

• How many residuals are observed on the spawning grounds?
ESA Recovery Plan: Snake River Sockeye Salmon | 340

June 2015| NOAA Fisheries 

Performance metrics:

• Number of full-term, hatchery, and residual spawners

• Number of redds

• Spawn timing

• Abundance of residual Sockeye Salmon

Possible Approach:

The number of full-term and hatchery-origin spawners will be estimated using redd 

surveys. The number of residual Sockeye Salmon spawners will be estimated using 

nighttime snorkel counts. Multiple redd surveys will cover the entire spawning areas. 

Suggested Analysis:

Genetic data from emigrating juveniles or returning adults can be used to assign fish to 

full-term spawners, hatchery-origin spawners, and potentially residual spawners. Spawn 

timing can be estimated using the temporal distribution of observed redds. The number of 

naturally produced spawners can also be estimated using proportions of hatchery and 

naturally produced fish, total number of redds, and fish/redd ratio. If weirs are used, 

abundance is based on weir counts, proportions of hatchery and naturally produced fish, 

and pre-spawn survival rates. 

Status: 

The SBT, Biolines Environmental Consulting, and IDFG have been performing this work 

with funding from BPA. The most recent results can be found in Griswold et al. (2011)

and Peterson et al. (2013).

Objective 6. Describe the life history and phenotypic characteristics of Snake River 

Sockeye Salmon.

For successful recovery of Snake River Sockeye Salmon to occur, fish will have to adapt to the 

local habitat conditions. Life history and phenotypic characteristics such as resident versus 

anadromous, size and age at migration, age at maturation, migration timing, and spawn timing 

can be affected by local habitat conditions. 

Type of monitoring effort: Long-term status and trend monitoring.

Key information needs:

• Is the current Redfish Lake Sockeye Salmon captive broodstock genetic structure 

appropriate for use in rebuilding efforts in other Sawtooth Valley lakes (especially 

Alturas)?
ESA Recovery Plan: Snake River Sockeye Salmon | 341

June 2015| NOAA Fisheries 

• How can remnant anadromous Sockeye Salmon gene resources in other Sawtooth 

Valley lakes be used for recovery efforts on a lake-specific basis? 

• What stock or stocks should be used for reintroduction into Alturas Lake?

• Is the current Redfish Lake Sockeye Salmon captive broodstock late September 

through October spawn timing structure appropriate for water temperature 

regimes in other Sawtooth Valley lakes?

• Is the current Redfish Lake Sockeye Salmon captive broodstock beach spawning 

propensity appropriate for rebuilding efforts in other Sawtooth Valley lakes, or 

would early stream spawning populations be more appropriate?

• What are the benefits/risks of alternative strategies for recovering extant and/or 

historical life-history patterns in the natal lakes?

• Do high water temperatures in the lower Salmon and Snake Rivers affect 

upstream and downstream Sockeye Salmon survival and life-history 

characteristics?

• What will be the role of beach vs. stream spawning types?

• Given regional temperature and precipitation patterns projected from climate 

models, how would potential changes in stream temperature and flows affect lifestage survivals and life-history characteristics for Snake River Sockeye Salmon?

Monitoring questions:

• What is the migration timing of adult Snake River Sockeye Salmon returning to 

the Snake River and adult trap sites in the Sawtooth Valley?

• What is the relationship between anadromous and residual Sockeye Salmon?

• Are residual populations viable?

• How long do adult Sockeye Salmon stage in Redfish Lake before spawning? 

• What is the migration timing of juvenile Sockeye Salmon leaving Redfish, Pettit, 

and Alturas Lakes?

• At what size and age do juvenile Sockeye Salmon exit the Sawtooth Valley lakes?

• What is the condition factor and lipid content of emigrating juvenile Sockeye 

Salmon and how does this affect survival?

• What is the fecundity of captive, hatchery- and natural-origin adult Snake River 

Sockeye Salmon?

• What is that size and age at maturity of captive, hatchery- and natural-origin 

anadromous adult Sockeye Salmon?

• Do hatchery fish exhibit reductions in life-history and phenotypic diversity and 

will these affect extant natural/wild O. nerka populations?
ESA Recovery Plan: Snake River Sockeye Salmon | 342

June 2015| NOAA Fisheries 

Performance metrics:

• Adult migration and spawning timing

• Age and length at maturity

• Fecundity

• Smolt age and size

Possible Approach:

Evaluation of life history and phenotypic characteristics will be accomplished by 

sampling live fish at weirs and observing fish on spawning grounds. Migration timing can 

be assessed at Lower Granite Dam and at weirs. Multiple spawning surveys will be 

conducted within all populations to determine spawn timing. Live and dead fish will be 

sampled for size (fork length), origin, marks and tags, and age (from ageing structures

and PBT). Adult females collected for the hatchery program can be used to assess 

fecundity. Age, size, and number of smolts will be measured at smolt traps located near 

the mouth of the lakes. 

Suggested Analysis:

The migration timing of Sockeye Salmon can be described by analyzing the temporal 

distribution of adults observed at Lower Granite Dam and at weirs within the basin. 

Spawn timing can be evaluated by analyzing the temporal distribution of spawners. 

Comparisons can be made between returning natural- and hatchery-origin fish using 

cumulative frequency plots. Age and length by origin and sex can be evaluated using 

ANOVA. Data collected from smolt traps can be analyzed to estimate the number of 

smolts that migrate out of the lakes at different ages, their size, and timing of migration 

(i.e., beginning, peak, and end of migration). 

Status: 

IDFG and SBT have been performing this work with funding from BPA. The most recent 

results can be found in Peterson et al. (2013) and Griswold et al. (2011). Powell et al. 

(2010) and Griswold et al. (2012) provided additional information on smolt condition and 

survival.
ESA Recovery Plan: Snake River Sockeye Salmon | 343

June 2015| NOAA Fisheries 

Objective 7. Determine the limnological characteristics of the nursery lakes of the upper 

Salmon River basin and assess their ability to aid in recovery efforts.

It is important to understand the current habitat conditions within the natal lakes that support 

Sockeye Salmon. Factors such as amount of spawning habitat, plankton composition, and O. 

nerka abundance are all important factors in understanding the probability of success of Sockeye 

Salmon reaching recovery levels.

Type of monitoring effort: Status and trend monitoring and effectiveness monitoring.

Key information needs:

• How do estimates of carrying capacity fit with VSP recovery criteria (e.g., is 

spawning and rearing capacity limiting such that VSP recovery criteria cannot be 

met)?

• What can be derived from limnological monitoring data regarding potential for 

juvenile anadromous Sockeye Salmon growth and survival in the various 

Sawtooth Valley lakes?

• How much zooplankton is available to support juvenile rearing and survival in the 

natal lakes?

• What is the relationship between variability in zooplankton abundance and 

species composition vs. juvenile O. nerka density, survival, anadromy v. 

residency? 

• Will competition for food resources or spawning areas restrict efforts to 

reestablish natural Sockeye Salmon populations in the natal lakes?

• What habitat areas will be important as fish abundance recovers? 

• To what degree do juvenile Sockeye Salmon compete with kokanee (or other fish) 

in Sawtooth Valley lakes and how does this affect O. nerka carrying capacity 

estimates in each lake? 

• Do the numbers of kokanee need to be reduced in order to recover Sockeye 

Salmon?

• What are the key rearing and spawning constraints within each natal lake?

Monitoring questions:

• What are the limnological characteristics (e.g., water clarity, water chemistry, 

phytoplankton and zooplankton abundance and composition) of the nursery lakes?

• What is the diet, growth rate, and estimated survival of juvenile Sockeye Salmon

in the nursery lakes?
ESA Recovery Plan: Snake River Sockeye Salmon | 344

June 2015| NOAA Fisheries 

• What is the carrying capacity for adult spawning and juvenile rearing within each 

nursery lake?

• What affects will anticipated increased adult returns of anadromous Sockeye 

Salmon have on resident O. nerka abundance and how will this affect lake 

productivity, zooplankton grazing pressure, and lake rearing capacities?

Performance metrics:

• Water quality

• Spawning and rearing habitat quality and quantity

• Limnological characteristics of lakes over time

• Primary productivity of lakes over time

• Zooplankton abundance over time

• Diet of juvenile Sockeye Salmon

• Growth and survival of juvenile Sockeye Salmon

Possible Approach:

Water quality and zooplankton abundance can be estimated from samples of water 

temperature (°C), dissolved oxygen (mg/L), conductivity (μS/cm), Secchi depth (m), 

compensation depth (m), nutrient concentrations (μg/L), chlorophyll a concentrations 

(μg/L), phytoplankton density (cells/mL) and biovolume (mm3

/L), and zooplankton 

density (number/L) and biomass (mg/m2) near the middle of each lake. Additional 

zooplankton samples can be collected from one or two other stations in each lake. 

Nutrients should be sampled in all lakes once per month in June, July, August, and 

October. Primary productivity estimates can be obtained and used with the 

Photosynthetic Rate Model to improve carrying capacity estimates. The Photosynthetic 

Rate Model carrying capacity estimates should be adjusted for kokanee grazing, which 

can be obtained using a bioenergetics model.

Juvenile fish abundance and density can be estimated by collecting hydroacoustic and 

trawl data. Mid-water trawl surveys provide biological data (e.g., length and weight at 

age and proportion of Snake River Sockeye Salmon vs. kokanee (based on genetic 

analysis)) necessary to estimate biomass, density, and age-specific abundance of O. nerka

within Redfish, Alturas, and Pettit Lakes from hydroacoustic methodology. In addition, 

horizontal and vertical gillnet sampling and trawl surveys can be conducted to quantify 

fish population characteristics including: species composition, habitat use (pelagic versus 

littoral), and diet analysis. Growth of presmolt releases can be estimated by recapturing 

marked fish and measuring them to the nearest 0.1 grams and fork length (mm). Diet 

analysis is estimated by sampling fish stomachs collected from gillnet and trawl samples. 
ESA Recovery Plan: Snake River Sockeye Salmon | 345

June 2015| NOAA Fisheries 

Zooplankton electivity indices can be developed from the relative proportion of 

zooplankton taxa in the lake environment and in stomach contents.

Suggested Analysis:

Target strengths and fish densities from hydroacoustic surveys can be processed using a 

Model 340 Digital Echo Processor and plotted with a Model 402 Digital Chart Recorder. 

Gillnet sampling can be used to estimate fish densities by using adjacent transects as 

replicates within a stratum (lake). Population estimates and variance for individual size 

classes can be obtained by using the equations found in Griswold et al. (2011) and 

Peterson et al. (2012) for hydroacoustic and mid-water trawl methods, respectively. 

Specific growth rates can be used to express growth relative to an interval of time and are 

commonly expressed as a percentage. Diet analysis can be estimated by enumerating 

zooplankton prey in a water bath under a compound microscope. Zooplankton could also 

be enumerated from vertical tows collected from the appropriate lakes during the same 

time period that stomachs are collected to develop electivity indices.

Status: 

The SBT and Biolines Environmental Consulting have been performing this work with 

funding from BPA. The most recent results can be found in Griswold et al. (2011) and

Peterson et al. (2013). 

Objective 8. Determine what factors may be limiting freshwater survival of Snake River 

Sockeye Salmon.

To reach recovery goals, it will be necessary to identify and understand the factors that may be 

reducing survival of juvenile and adult Snake River Sockeye Salmon.

Type of monitoring effort: Status and trend monitoring and effectiveness monitoring.

Key information needs:

• Is the mortality of juvenile outmigrating and adult returning anadromous Sockeye 

Salmon in the area between the upper Snake River basin and Lower Granite Dam 

related to natural causes (e.g., competition, predation, environmental conditions) 

or are extraneous causes involved?

• Are there local areas (hot-spots) where mortality is concentrated during juvenile 

smolt and adult return migration for anadromous Sockeye Salmon in the area 

between the upper Snake River basin and Lower Granite Dam, or are mortality 

rates uniform over migration distance?
ESA Recovery Plan: Snake River Sockeye Salmon | 346

June 2015| NOAA Fisheries 

• What are the effects of transportation on juvenile Sockeye Salmon survival?10

• Have lake trout (presently in Stanley Lake) colonized other Sawtooth Valley 

Sockeye Salmon nursery lakes?

• Does exposure to contaminants and bioaccumulation of contaminants in the 

estuary affect Snake River Sockeye Salmon survival?

Monitoring questions:

• What effect do sympatric kokanee have on anadromous Sockeye Salmon in the 

Sawtooth Valley lakes?

• How does O. nerka density affect zooplankton abundance, and growth and 

survival of juvenile Sockeye Salmon/resident O. nerka?

• How does size/condition of outmigrants affect smolt survival and SAR?

• What non-native predators in nursery lakes and in the migration corridor 

potentially limit juvenile Sockeye Salmon survival?

• What is the risk that non-native predators (e.g., lake trout) will colonize additional 

Sockeye Salmon nursery lakes in the Sawtooth Valley?

• What native predators in nursery lakes and in the migration corridor potentially 

limit juvenile Sockeye Salmon survival?

• What is the predation rate and predatory impact of exogenous fishes on the Snake 

River Sockeye Salmon ESU?

• What is the effect of predation from piscine predators in the Columbia River 

migration corridor on Snake River Sockeye Salmon?

• What is the effect of predation from avian predators in the Columbia River 

migration corridor on juvenile Snake River Sockeye Salmon?

• What is the effect of predation from marine mammals in the Columbia River 

migration corridor on adult Snake River Sockeye Salmon?

• What is the effect of Columbia River hydropower operations on juvenile Snake 

River Sockeye Salmon?

• What is the effect of Columbia River hydropower operations on returning adult 

Snake River Sockeye Salmon?

• How do conditions in the estuary affect Sockeye Salmon rearing, residence times, 

growth rates, and survival?

 

10 It would be useful if CSS included Sockeye Salmon in their analysis.
ESA Recovery Plan: Snake River Sockeye Salmon | 347

June 2015| NOAA Fisheries 

Performance metrics:

• Native and non-native predator abundance

• Juvenile and adult survival rates

• Kokanee abundance

• Lake productivity

• Water temperature 

• Stream flows

• Total dissolved gas (TDG)

Possible Approach:

Kokanee abundance is estimated through hydroacoustic surveys, trawl and net sampling, 

spawner counts, and redd counts. Juvenile fish survival to Lower Granite Dam (and to 

detection sites downstream) can be determined through mark and recapture of juvenile 

Sockeye Salmon using radio and potentially PIT-tags. Temperature and TDG are 

recorded at various locations.

Suggested Analysis:

Juvenile survivals at each FCRPS facility can be estimated using the SURPH model. 

Juvenile survival from release points (e.g., at lake outmigration traps) to Lower Granite 

Dam can be estimated using mark-recapture methods. Adult survival between facilities

can be estimated by comparing tag detections at adult ladders along the migration 

corridor. Rates can be expanded to population-level effects using the relative number of 

fish PIT-tagged and abundance estimates generated from mark-recapture studies. TDG 

levels and temperature at each facility will be compared to standards to determine timing 

and duration of exceedances. Active tags (radio and/or acoustic) can also be used to 

determine where mortality “hot spots” may be occurring.

Status: 

This work is ongoing and being conducted by NMFS, IDFG, and SBT with funding from 

BPA. The most current results can be found in Axel et al. (2013), Peterson et al. (2013), 

and Griswold et al. (2011). Additional information regarding smolt condition and 

subsequent smolt survival can be found in Powell et al. (2010) and Griswold et al. (2012).
ESA Recovery Plan: Snake River Sockeye Salmon | 348

June 2015| NOAA Fisheries 

11.1.4 Phase 2 Monitoring

One main purpose of Phase 2 monitoring is to determine if returning adults from a conventional 

hatchery program are leading to increased natural production of outmigrating smolts consistent 

with achieving natural-origin return targets for Redfish Lake. Initial efforts will prioritize the recolonization of Redfish Lake. Pettit and Alturas lake re-colonization strategies will be refined 

over time based on natural production responses. Yellowbelly and Stanley Lakes may experience 

some level of natural colonization during the implementation of Phase 2. Additional monitoring 

efforts will track life-stage survivals and assess environmental and biological conditions for 

spawning, rearing, and migration. 

Objective 1: Continue to implement elements of Phase 1 monitoring such as genetic and 

limnological monitoring, and determine the status and trend in habitat conditions for each 

population.

As described above, the purpose of Phase 1 monitoring is to determine if the captive brood 

program is preserving the genetic resources of the population and increasing adult abundance in 

both captive and natural environments. In addition, it tracks life-stage survivals and 

environmental and biological conditions. All the monitoring associated with Phase 1 monitoring 

is described in Section 11.1.3. What follows is the monitoring needed to determine the status and 

trend in habitat conditions for each population. 

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• How does lake productivity change as adult escapement increases and salmon 

derived nutrients increase?

• How do zooplankton populations respond to altered grazing patterns associated 

with increased anadromy?

• How do changes in nutrients and food abundance affect lake carrying capacity 

estimates for juvenile O. nerka?

• What are the various numerical adult spawning carrying capacities for 

anadromous Sockeye Salmon in the Sawtooth Valley lakes?

• What is the quantity and quality of spawning habitats used by anadromous adults?

• Can lake trout (presently in Stanley Lake) be prevented from colonizing other 

Sawtooth Valley Sockeye Salmon nursery lakes?

Monitoring questions:

• What is the status and trend in spawning and rearing habitat conditions for each 

population?
ESA Recovery Plan: Snake River Sockeye Salmon | 349

June 2015| NOAA Fisheries 

• How does increased anadromous production affect lake productivity and O. nerka

carrying capacity?

Performance metrics: 

• Water quality 

• Primary productivity

• Zooplankton abundance and species composition over time

• Limnological characteristics of the lakes over time

• Relative abundance of resident vs. anadromous O. nerka

• Habitat access 

• Habitat quality and quantity 

• Riparian condition 

• Watershed condition

Possible Approach:

Lake rearing and spawning conditions can be assessed by monitoring habitat 

characteristics within the lakes. Water quality and zooplankton abundance can be 

estimated from samples of water temperature (°C), dissolved oxygen (mg/L), 

conductivity (μS/cm), Secchi depth (m), compensation depth (m), nutrient concentrations 

(μg/L), chlorophyll a concentrations (μg/L), phytoplankton density (cells/mL) and 

biovolume (mm3/L), and zooplankton density (number/L) and biomass (mg/m2) near the 

middle of each Sawtooth Valley lake. Additional zooplankton samples can be collected 

from one or two other stations in each lake. Nutrients should be sampled in all lakes once 

per month in June, July, August, and October. 

Habitat conditions for stream spawning and migration can be obtained by applying the 

protocols outlined in the Columbia Habitat Monitoring Program (CHaMP; Ward et al. 

2012) or the USDA PACFISH/INFISH Biological Opinion Monitoring Program (PIBO; 

Archer et al. 2012). Although both programs collect habitat status and trend data, the two 

programs are designed somewhat differently, because of different objectives and goals. 

Nevertheless, the programs are currently working on merging their protocols so that 

habitat information can be shared between the two programs. Thus, information on 

instream habitat conditions, riparian conditions, and watershed conditions can be assessed 

under both programs.

Instream habitat variables to be measured include riparian cover, sinuosity, valley form, 

gradient, solar input, bankfull distance and height, geomorphic channel unit type, thalweg 

profile, channel depth, wetted width, substrate composition, undercut banks, woody 

debris, fish cover, pool tail fines, subsurface fines, conductivity, alkalinity, and 
ESA Recovery Plan: Snake River Sockeye Salmon | 350

June 2015| NOAA Fisheries 

macroinvertebrates. PIBO and CHaMP have developed databases, data dictionaries, 

meta-data support, and tools to help biologists collect, process, and store the habitat data.

Suggested Analysis: 

Water quality and zooplankton abundance can be analyzed as a time series. The 

Photosynthetic Rate Model can be used to estimate carrying capacity. The Photosynthetic 

Rate Model can also be modified to account for competition with resident O. nerka. 

Relative zooplankton consumption by juvenile Sockeye Salmon versus mixed age classes 

of kokanee can be assessed using limnological data and a bioenergetics model. These 

results can be used to refine carrying capacity estimates. Instream and watershed habitat 

status can be analyzed with the Horvitz-Thompson or π-estimator and trend can be 

analyzed with multi-phase regression analyses. The database and GIS formatting of data 

will also allow associations with land use, land vegetation coverage, and many other 

attributes at watershed and population scales.

Status: 

The SBT, Biolines Environmental Consulting, and IDFG have been performing most of 

the lake monitoring with funding from BPA. The most recent results can be found in 

Griswold et al. (2011) and Peterson et al. (2013). Additional funding will be needed to 

derive the information needed to specifically address this objective and to collect the 

necessary information from additional Sawtooth Valley lakes. Additional funding will 

also be needed to conduct instream and watershed monitoring if there are gaps in PIBO 

and CHaMP coverage in the Sawtooth Valley basin. 

Objective 2: Continue to assess the number of adults returning to adult traps and nursery 

lakes in the Sawtooth Valley.

Abundance of returning adults to the Sawtooth Valley is an important indicator of success and an 

important component of VSP. 

Type of monitoring effort: Long-term status and trend monitoring.

Key information needs:

• Is the mortality of adult returning anadromous Sockeye Salmon in the area 

between the upper Snake River basin and Lower Granite Dam related to natural 

causes (e.g., competition, predation, environmental conditions) or are extraneous 

causes involved?

• Are there local areas (hot-spots) where mortality is concentrated during adult 

migration for anadromous Sockeye Salmon in the area between Lower Granite 
ESA Recovery Plan: Snake River Sockeye Salmon | 351

June 2015| NOAA Fisheries 

Dam and the upper Snake River basin, or are mortality rates uniform over the 

migration distance?

• What estuary and ocean indicators (biological and physical) correlate with 

Sockeye Salmon growth rates, life-stage survival, and with SARs?

• Do high water temperatures in the lower Salmon and Snake Rivers affect 

upstream Sockeye Salmon survival?

• How do SARs vary among lakes, years, natural vs. hatchery, and residual vs. 

Sockeye Salmon?

Monitoring questions:

• How many natural- and hatchery-origin adults return to the Sawtooth Valley adult 

traps and lakes annually?

Performance metrics:

• Number of returning adults (hatchery and natural-origin) 

Possible Approach:

Adult abundance is determined by enumerating hatchery- and natural-origin adults 

trapped at Sawtooth Valley locations. The number of adults released to spawn naturally 

in Sawtooth Valley lakes is currently controlled and known.

Suggested Analysis:

Total abundance of returning hatchery and naturally produced fish is determined by 

summing the number of each stock (origin) collected at the adult traps. Regression 

analysis could be used to develop relationships between key environmental factors such 

as flow or water temperature and survival of upstream migrating adults.

Status: 

IDFG has been performing this work with funding from BPA. The most recent results 

can be found in Peterson et al. (2013) and Baker et al. (2013).

Objective 3: Continue to assess the number of returning anadromous adult Sockeye 

Salmon that spawn naturally in Sawtooth Valley lakes.

Not all adults that are enumerated at the adult traps will survive to spawn (i.e., pre-spawn loss). 

The productivity of each population is determined in part by knowing the number of successful 

spawners. Thus, the spawning escapement of hatchery and natural-origin Sockeye Salmon is one 

of the most important indicators of success.
ESA Recovery Plan: Snake River Sockeye Salmon | 352

June 2015| NOAA Fisheries 

Type of monitoring effort: Status and trend monitoring.

Key information needs:

• How much spawning habitat is available in lakes and streams not currently used 

by anadromous Sockeye Salmon?

• What spawning areas will be important as fish abundance recovers? 

• What will be the role of beach vs. stream spawning types?

• Will competition for spawning areas restrict efforts to reestablish natural Sockeye 

Salmon populations in the natal lakes?

Monitoring questions:

• How many adult Sockeye Salmon spawn naturally in Sawtooth Valley lakes?

• What percentage of the spawning escapement consists of hatchery- and naturalorigin anadromous Sockeye Salmon?

• How many residual Sockeye Salmon are observed on spawning grounds?

• How many kokanee are observed on spawning grounds?

Performance metrics:

• Number of hatchery and natural-origin spawners

• Number of residual Sockeye Salmon spawners 

• Number of kokanee spawners

Possible Approach:

The number of spawners will be estimated using redd surveys. Multiple redd surveys will 

cover the entire spawning areas. Genetic samples collected from smolts and returning 

adults can be used to assess representation of spawners to offspring. 

Suggested Analysis:

The number of naturally produced spawners is estimated using proportions of hatchery 

and naturally produced fish, total number of redds, and a fish/redd ratio. If weirs are used, 

abundance is based on weir counts, proportions of hatchery and naturally produced fish, 

and pre-spawn survival rates. Genetic analysis (see Objective 2 under Phase 1 

Monitoring) will assign outmigrants and returning adults to spawners. As returning adults 

are assigned to spawners, percentage of hatchery and natural-origin fish that contribute to 

the return can be calculated.
ESA Recovery Plan: Snake River Sockeye Salmon | 353

June 2015| NOAA Fisheries 

Status: 

IDFG and SBT have been performing this work with funding from BPA. The most recent 

results can be found in Griswold et al. (2011) and Peterson et al. (2013).

Objective 4: Describe the life history and phenotypic characteristics of Sockeye Salmon in 

Sawtooth Valley lakes.

See Objective 6 under Phase 1 monitoring.

Objective 5: Determine if the five-year geometric mean (GM) of returning Snake River 

Sockeye Salmon adults (hatchery- and natural-origin) to the Sawtooth Valley meets adult 

abundance target objectives.

To understand when the captive broodstock programs can be terminated, specific performance 

standards need to be met. This objective will enable managers to determine if performance 

metrics have been met and when it is appropriate to terminate these programs. 

Type of monitoring effort: Long-term status and trend monitoring.

Key information needs:

• None 

Monitoring questions:

• What is the number and origin of anadromous Sockeye Salmon that return to 

adult traps and lakes in the Sawtooth Valley annually?

Performance metrics:

• Number and origin of adult anadromous Sockeye Salmon

Possible Approach:

Adult abundance is determined by enumerating hatchery- and natural-origin adults 

trapped at Sawtooth Valley locations.

Suggested Analysis:

Total abundance of returning hatchery and naturally produced fish is determined by 

summing the number of each stock (origin) collected at the adult traps and sampling 

locations. Five-year running geometric means are then calculated and these estimates are 

compared to the target values. 
ESA Recovery Plan: Snake River Sockeye Salmon | 354

June 2015| NOAA Fisheries 

Status: 

IDFG has been performing this work with funding from BPA. The most recent results 

can be found in Peterson et al. (2013). In addition, NMFS evaluates the status of the 

species every five years and the latest stock status can be found in Ford (2011).

Objective 6: Determine if the five-year geometric mean (GM) of returning Snake River 

Sockeye Salmon adults to the Sawtooth Valley exceeds the targets to transition to Phase 3.

To understand when it is appropriate to transition to Phase 3, specific performance standards 

need to be met. This objective will enable managers to understand when it is appropriate to make 

the transition. 

Type of monitoring effort: Long-term status and trend monitoring.

Key information needs:

• None.

Monitoring questions:

• What is the number of naturally produced anadromous Sockeye Salmon that 

return to adult traps and lakes in the Sawtooth Valley annually?

Performance metrics:

• Number of naturally produced adult anadromous Sockeye Salmon

Possible Approach:

Adult abundance is determined by enumerating natural-origin adults trapped at Sawtooth 

Valley locations. Origin is confirmed genetically from tissue samples collected from all 

trapped adults. 

Suggested Analysis:

Total abundance of returning hatchery and naturally produced fish is determined by 

summing the number of each stock (origin) collected at the adult traps and sampling 

locations. Five-year running geometric means are then calculated and these estimates are 

compared to the target values. 

Status: 

IDFG has been performing this work with funding from BPA. The most recent results 

can be found in Peterson et al. (2013). Additional funding may be needed to derive the 

information needed to specifically address this objective.
ESA Recovery Plan: Snake River Sockeye Salmon | 355

June 2015| NOAA Fisheries 

Objective 7: Determine the transmission and effects of disease on the abundance, 

productivity, and diversity of the natural populations. 

A goal of the Phase 2 hatchery program will be to release large numbers of hatchery fish to 

support high levels of anadromous return spawners in Redfish Lake. It will be important to 

release fish into the system that are known to have a healthy disease history during rearing to 

minimize impacts on naturally and hatchery-produced fish. 

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

Monitoring questions:

• What are the prevalence and level of pathogens in natural and hatchery-origin 

Snake River Sockeye Salmon?

• What are the magnitude and pathways of disease transmission between hatchery 

and natural-origin Snake River Sockeye Salmon?

• What are the magnitude and pathways of disease transmission between hatchery 

and residual Sockeye Salmon and kokanee?

Performance metrics:

• Number of infected hatchery and naturally produced fish 

• Spatial distribution of disease 

Possible approach: 

The health of hatchery fish will be monitored starting with broodstock and continuing 

through rearing and release of juveniles. The health of naturally produced fish will be 

assessed on dead parr, smolts, and spawners encountered during monitoring activities. All 

sampling, diagnostic, and statistical analyses will comport with the Integrated Hatchery 

Operations Team (IHOT) and the Pacific Northwest Fish Health Protection committee 

guidelines. All disease monitoring will be consistent with the IDFG fish health policy and 

the native fish conservation policy. In addition, dead, naturally produced fish collected as 

parr or smolts during smolt trapping and juvenile sampling will be examined for diseases. 

Hatchery fish are sampled before release, during spring outmigration from the lakes, and 

throughout their life cycle within the hatchery.

Suggested analysis: 
ESA Recovery Plan: Snake River Sockeye Salmon | 356

June 2015| NOAA Fisheries 

Analysis of samples will follow standard protocols defined in the latest edition of the 

American Fisheries Society “Suggested Procedures for the Detection and Identification of 

Certain Finfish and Shellfish Pathogens (Blue Book).”

Status: 

The IDFG Eagle Fish Health Lab has been doing comprehensive fish health work on 

Snake River Sockeye Salmon since 1991.

11.1.5 Phase 3 Monitoring

Once the program transitions to Phase 3, a robust monitoring phase will begin that focuses on the 

VSP parameters and recovery criteria. For this phase of RM&E, abundance, productivity, spatial 

structure, and diversity will be compared to the criteria that are described in Section 3 of this 

Plan to determine if Snake River Sockeye Salmon are trending towards or meeting the recovery 

objectives. Importantly, monitoring conducted under Phase 1 and 2 also applies to Phase 3. That 

is, in many cases, Phase 3 monitoring is a continuation of Phase 1 and 2 monitoring.

Objective 1: Determine the status and trend in abundance and productivity of O. nerka

spawners for each population. 

The status of a population is determined by estimating the VSP parameters. The status of adult 

abundance, population productivity, and growth rate is compared to the population-specific 

recovery criteria resulting in an overall determination of the status of the ESU. Tracking these 

parameters over time within each population also allows estimation of long-term trends. 

Monitoring long-term trends will be critical to assessing the performance of restoration projects.

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

Monitoring questions:

• Is the 10-year GM for natural-origin Snake River Sockeye Salmon spawners in 

each population greater than or equal to the recovery criteria for natural 

spawners?

• What are the current natural-origin spawner abundance and five-year trend in 

abundance for each population?

• What are the current and trend in the natural-origin spawner 20-year population 

growth rate for each population?
ESA Recovery Plan: Snake River Sockeye Salmon | 357

June 2015| NOAA Fisheries 

• What is the current productivity for each natural population compared to the 

delisting criteria?

Performance metrics: 

• Number of spawners (hatchery plus natural) 

• Number of natural recruits 

• Recruits per spawner (smolts per spawner and spawner-to-spawner ratios)

• Age of returning adults 

Possible Approach: 

Adult abundance is determined by enumerating hatchery- and natural-origin adults 

trapped at Sawtooth Valley locations. Origin is confirmed genetically from tissue samples 

collected from all trapped adults. The number of adults released to spawn naturally in 

Sawtooth Valley lakes is currently controlled and known. Estimates of juvenile 

emigration are generated annually for Redfish, Pettit, and Alturas Lakes. 

Suggested Analysis: 

The number of naturally produced spawners is estimated using proportions of hatchery 

and naturally produced fish (confirmed using genetic analyses), total number of redds, 

and fish/redd ratio. If weirs are used, abundance is based on weir counts, proportions of 

hatchery and naturally produced fish (confirmed using genetic analyses), and pre-spawn 

survival rates. The latter can be determined by estimating the conversion rate from Lower 

Granite Dam window counts to the number of fish surviving post-release into the lake.

The 10-year GM for abundance of naturally produced fish is calculated. Productivity is 

based on an evaluation of the most recent 20-year period of spawner abundance (hatchery 

plus natural fish) and an estimate of natural recruits based on a run re-construction that 

includes age structure and downstream fishery information. These abundance and 

productivity estimates are analyzed in a time series and compared to recovery criteria. 

Status: 

IDFG and SBT have been performing this work with funding from BPA. The most recent 

results can be found in Griswold et al. (2011) and Peterson et al. (2013). Additional 

funding may be needed to derive the information needed to specifically address this 

objective. In addition, NMFS evaluates the status of the species every five years and the 

most recent five-year review can be found in Ford (2011).
ESA Recovery Plan: Snake River Sockeye Salmon | 358

June 2015| NOAA Fisheries 

Objective 2: Determine the status of the spatial structure of each population based on 

current and historically used habitat. 

Snake River Sockeye Salmon spawners can escape differentially to each watershed because of 

habitat conditions, migration barriers, pre-spawn mortality, hatchery programs, and stochasticity. 

The production of juveniles can vary among lake systems because of density-dependent and 

density-independent factors. Understanding the spatial and temporal variance in both spawner 

and juvenile distribution is therefore necessary to address uncertainties.

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

• What is the productivity of each population?

• What are the anadromous tendencies of each population and are they changing?

Monitoring questions:

• What is the spatial and temporal distribution of natural-origin spawners within 

each population?

• What is the density of natural-origin spawners within each population?

• What is the current spatial extent and distribution of spawning and rearing habitat 

used by natural-origin Sockeye Salmon within each population?

Performance metrics: 

• Spawner distribution 

• Redd distribution 

• Spawn timing 

• Juvenile distribution and density

• Smolt production

Possible Approach: 

The above parameters are currently being investigated in Phase 1 and 2. Spawner success 

and redd distribution within Redfish Lake is currently estimated using ocular methods. 

This method is also being used to estimate redd distribution of residual spawners in Pettit 

Lake and kokanee in Alturas Lake. Spawn timing in the wild is currently compared to 

spawn timing within the captive broodstock. Juvenile abundance and density are 

estimated using mid-water trawl and hydroacoustic methods. 
ESA Recovery Plan: Snake River Sockeye Salmon | 359

June 2015| NOAA Fisheries 

Suggested Analysis: 

The spatial spawning distribution is based on ocular observations of redd distribution. 

Data can be analyzed as distribution data in a GIS format and compared to recovery 

criteria. Juvenile abundance and density methods and analyses are presented in Objective 

7 under Phase I monitoring.

Status: 

The SBT, Biolines Environmental Consulting, and IDFG have been performing this work 

with funding from BPA. The most recent results can be found in Griswold et al. (2011)

and Peterson et al. (2013). Additional funding may be needed to derive the information 

needed to specifically address this objective or to collect the necessary information from 

all Sawtooth Valley lakes.

Objective 3: Determine the status and trend in life history, genotypic, and phenotypic 

diversity for each population. 

The artificial propagation of Sockeye Salmon includes risks that may reduce the likelihood of 

recovery. It is important, therefore, to monitor the genetic characteristics of hatchery and naturalorigin fish to ensure that the artificially produced fish resemble the naturally produced fish 

genetically, that adequate effective population sizes are maintained to prevent genetic drift, and 

that outbreeding depression does not reduce the reproductive success of the populations.

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

Monitoring questions:

• What is the population-level genetic composition of each population?

• What is the status and trend of life-history patterns and variation within each 

population?

Performance metrics: 

• Adult run timing 

• Size at maturity

• Age at maturity 

• Adult sex ratio

• Spawn timing
ESA Recovery Plan: Snake River Sockeye Salmon | 360

June 2015| NOAA Fisheries 

• Effective population size 

• Genetic variation 

• Fecundity 

• Spawning location (beach or stream)

• Juvenile age at migration

• Juvenile run timing

• Juvenile size at migration

Possible Approach: 

Evaluation of life history, genotypic, and phenotypic characteristics will be accomplished 

by sampling live fish at weirs and at screw traps for juveniles. Multiple spawning surveys 

will be conducted within all populations (see Approach under Objective 1). Fish will be 

sampled for size (fork length), origin, marks and tags, age (from scales), and genetics 

(operculum punch or fin tissue for DNA analysis). 

Suggested Analysis: 

DNA tissue samples are analyzed using known microsatellite markers (including 

microsatellite loci and non-coding single nucleotide polymorphisms (SNPs), or base 

substitutions assayed via restriction enzyme analysis). Microsatellite loci are analyzed to 

estimate levels of gene flow and to identifying geographic areas that contain genetically 

differentiated populations. Data collected from rotary screw traps can be analyzed to 

estimate the number of smolts that migrate out of the populations, the size of migrants, 

and the timing of migration (i.e., beginning, peak, and end of migration). Parentage-based 

tagging is used to estimate the number of returning hatchery-origin adults that stray to 

trapping locations where they were not released as smolts.

Status: 

IDFG and SBT have been performing this work with funding from BPA. The most recent 

results can be found in Griswold et al. (2011) and Peterson et al. (2013). Additional 

funding may be needed to derive the information needed to specifically address this 

objective and to collect information from other Sawtooth Valley lakes.

Objective 4: Determine the status and trend in conditions of habitat for each population.

The abundance, survival, and productivity of Snake River Sockeye Salmon are affected by the 

quantity and quality of spawning and rearing habitat. It is important to monitor changes in 

spawning and rearing habitat condition over time. 

See Objective 1 under Phase 2 monitoring.
ESA Recovery Plan: Snake River Sockeye Salmon | 361

June 2015| NOAA Fisheries 

Objective 5: Determine the effects of habitat degradation and habitat restoration actions on 

the abundance, productivity, and spatial structure of the natural populations.

The Recovery Plan identifies restoration actions such as habitat restoration and protection, flow 

augmentation, and passage restoration that should increase natural productivity, abundance, and 

spatial structure of natural-origin Snake River Sockeye Salmon. There are several RM&E 

information needs that must be addressed if the benefits of these management actions are to be 

effectively detected. 

Type of monitoring effort: Status and trend monitoring; implementation and compliance 

monitoring; and action effectiveness monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

• How will managers prevent the colonization of other tributaries and lakes by lake 

trout?

• Can the Sawtooth Fish Hatchery weir be modified so that Sockeye Salmon will 

enter the trap and allow them access to the upper Sawtooth Valley lakes?

Monitoring questions:

• Status and Trend Monitoring—What is the current status and trend of Snake River 

Sockeye Salmon habitat within each population (see Objective 4)?

• Implementation and Compliance Monitoring—Was the habitat restoration action 

implemented in the prescribed manner and did it achieve its objectives?

• Action Effectiveness Monitoring—Have the habitat restoration actions improved 

the viability of the Snake River Sockeye Salmon populations?

Performance metrics: 

• Abundance 

• Distribution 

• Survival 

• Growth 

• Condition 

• Habitat characteristics

• Spawning time and location

• Zooplankton abundance over time

• Limnological characteristics of lake over time
ESA Recovery Plan: Snake River Sockeye Salmon | 362

June 2015| NOAA Fisheries 

Possible Approach: 

Habitat status and trend monitoring was described under Objective 4. Compliance 

monitoring of restoration projects includes record keeping and reporting of activities. 

This type of monitoring is conducted by the implementing party and should include any 

parameters identified in work statements. All habitat restoration projects need to be 

monitored for compliance. Finally, action effectiveness monitoring should be conducted 

at both the project and population (lake system) scales. Action effectiveness monitoring 

designs should incorporate a before-after (BA) design, before-after-control-influence 

(BACI) design, or modified BACI designs (e.g., MBACI or MBACI(P)). Control or 

reference areas should be as similar as possible to the treatment site and must be 

independent of the influence of the treatment. Before-after designs can be used to monitor 

effects at larger spatial scales (e.g., population scale), but a long time series of before 

(pre-treatment) data are generally needed to tease out treatment effects. Entities 

implementing habitat restoration actions must coordinate with monitoring groups before 

scheduled activities, preferably years in advance to allow measurement of pre-treatment 

variables. Temporal scales must account for time lags related to life history and life-cycle 

timeframes.

Suggested Analysis:

Biotic and habitat data can be analyzed using time series analysis for before-after or 

intervention time series designs and ANOVA, t-tests, regression, or time series methods 

can be used with BACI designs. Randomization procedures, such as randomized 

intervention analysis, can also be used to analyze BACI designs. Data collected at the 

population scale should be compared directly with recovery criteria. Habitat data can also 

be included in fish-habitat models to assess the potential effects of habitat quantity and 

quality changes on potential fish survival and productivity.

Status: 

This work, which is ongoing in Redfish, Pettit, and Alturas Lakes for zooplankton 

abundance and limnological characteristics, is being carried out by SBT and Biolines 

Environmental Consulting with funding from BPA. The most recent results can be found 

in Griswold et al. (2011). Additional funding will be needed to collect and analyze 

information for other Sawtooth Valley lakes. Information pertaining to abundance and 

distribution is currently being collected by IDFG with funding from BPA and the most 

recent results can be seen in Peterson et al. (2013). Additional funding will be needed to 

extend these efforts to other Sawtooth Valley lakes. 
ESA Recovery Plan: Snake River Sockeye Salmon | 363

June 2015| NOAA Fisheries 

Objective 6: Determine the influence of the Phase 3 hatchery program on the abundance, 

productivity, spatial structure, and diversity of the natural populations.

The Phase 3 hatchery program is designed to play a critical role in providing reproductive 

support to depressed populations and thereby promote the conservation of the Snake River 

Sockeye Salmon populations. The program may also pose threats to natural-origin fish. 

Hatchery-induced genetic change may reduce the fitness of both hatchery and natural-origin fish 

in the wild, and hatchery-induced ecological effects (competition for food and space) can 

potentially reduce population productivity and abundance. Understanding the balance between 

the adverse long-term fitness impacts of the hatchery program and the benefits it may provide 

against demographic extinction is the crux of a successful monitoring and evaluation program.

Type of monitoring effort: Status and trend monitoring; implementation and compliance 

monitoring; and action effectiveness monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

• What effects will increased returns of anadromous adults have on resident O. 

nerka abundance and how will this affect zooplankton grazing pressure and lake 

rearing capacity?

Monitoring questions:

• Do hatchery fish alter the life history or genetic characteristics of naturally 

produced fish?

• Do hatchery fish alter the abundance and productivity of naturally produced fish?

• What is the spatial and temporal distribution of hatchery-origin spawners?

• What effect do changes in phenotypic traits (e.g., size, age, and fecundity) 

observed in hatchery fish have on population viability?

• Do these potential effects on life history, genetic characteristics, or phenotypic 

traits change in utility or severity over time?

Performance metrics: 

• Abundance

• Productivity

• Spatial structure

• Adult run timing 

• Size at maturity 
ESA Recovery Plan: Snake River Sockeye Salmon | 364

June 2015| NOAA Fisheries 

• Age at maturity 

• Effective population size 

• Genetic variation 

• Fecundity 

• Migration and spawning timing

• Spawning location (beach or stream)

Possible Approach: 

Approaches needed to address this objective are described under Phases 1 and 2, and 

under Objectives 1, 2, and 3 under Phase 3. 

Suggested Analysis: 

Analysis of the effects of hatchery programs is basically the same as those presented 

earlier for monitoring Objectives 1, 2, and 3. 

Status: 

IDFG and SBT have been performing this work with funding from BPA. The most recent 

results can be found in Griswold et al. (2011) and Peterson et al. (2013). Additional 

funding may be needed to extend data collection to other Sawtooth Valley populations.

Objective 7: Determine the effect of mainstem hydropower operations and operational 

improvements on viability of Snake River Sockeye Salmon populations. 

Snake River Sockeye Salmon are affected either directly (passage at a specific project) or 

indirectly (primarily through flow releases and water quality effects from upstream projects) by 

the hydrosystem. It is therefore important that all hydro-related effects be monitored. 

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Recovery Strategy Phase 1 and 2 monitoring. 

• Effects of transportation on juvenile survival.

Monitoring questions:

• What is the effect of Columbia River hydropower operations on juvenile Snake 

River Sockeye Salmon?

• What are the effects of the Columbia River hydropower system on habitat quality, 

predation, and competition?
ESA Recovery Plan: Snake River Sockeye Salmon | 365

June 2015| NOAA Fisheries 

• What is the effect of Columbia River hydropower operations on returning adult 

Snake River Sockeye Salmon?

• What are the effects of Columbia River hydropower operations on temperature 

and dissolved gas concentrations in the river?

• What are the timing and duration of fish passage through the hydrosystem?

Performance metrics:

• Juvenile and adult survival 

• Temperature

• Total dissolved gas (TDG)

• Water flow

Possible Approach:

Survival of migrating Sockeye Salmon is usually estimated with tags (PIT-tags, radio 

tags, or acoustic tags). Smolts can be PIT-tagged as they leave natal areas within the 

ESU. These PIT-tagged fish are then monitored for detections at FCRPS facilities along 

the migration corridor at both juvenile and adult life stages using DART and PTAGIS 

databases. Detection probabilities of juvenile salmonids migrating downstream at FCRPS 

facilities are modeled using the SURPH analytical tool (Survival with Proportional 

Hazards; Axel et al. 2013). Adult detection is currently available at ladders on several 

dams. TDG and temperature are measured hourly with calibrated electronic instruments 

at each FCRPS facility during fish passage. 

Suggested Analysis:

Juvenile survivals at each FCRPS facility can be estimated using the SURPH model

(Axel et al. 2013). Conversion rates between facilities can be estimated by comparing tag 

detections at adult ladders along the migration corridor. Rates can be expanded to 

population-level impacts using the relative number of fish PIT-tagged and abundance 

estimates generated from mark-recapture studies. TDG levels and temperature at each 

facility will be compared to standards to determine timing and duration of exceedances. 

Active tags may be needed to understand adult Sockeye Salmon entrance tendencies at 

hydroelectric projects under varying project operations. This will give managers 

information needed to pass adults quickly through the tailraces of the projects. 

Status: 

Currently, information pertaining to hydro operations and river characteristics are 

recorded through various programs like the Fish Passage Center’s Smolt Monitoring 

Program and results are listed on their website and others (e.g., Data Access in Real 

Time; DART), both of which are funded through BPA. In addition, there is currently a 
ESA Recovery Plan: Snake River Sockeye Salmon | 366

June 2015| NOAA Fisheries 

research program (Axel et al. 2013) that is collecting information on juvenile survival 

from the Sawtooth Valley to Lower Granite Dam that will partly inform this objective. 

Additional funding is needed to continue PIT-tag studies and to include them in the CSS 

suite of work. 

Objective 8: Determine the effect of harvest on the abundance, productivity, and diversity 

of the natural populations.

Restoring and optimizing fishery opportunities are a primary goal of local and regional fisheries 

managers and are important to meet Tribal and treaty trust obligations. This can be challenging, 

however, because of changes in fishing effort, run sizes, catch and harvest that are likely to occur 

as environmental and anthropogenic conditions vary and the fisheries restoration program 

matures. In addition, fisheries are also managed to keep unintended impacts to natural and 

hatchery production and non-target species within acceptable limits. As Plan implementation

progresses and we learn more about the recovery of the populations, under certain conditions, it 

may be desirable to use harvest to control the proportion of hatchery-origin spawners returning to 

the spawning grounds.

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

• Accuracy of harvest rates.

• Effects of harvest management on size selectivity and size of fish returning to 

spawn.

Monitoring questions:

• What is the annual incidental harvest rate on natural-origin Snake River Sockeye 

Salmon that occurs outside the ESU?

• What is the annual incidental harvest rate that occurs on natural-origin Snake 

River Sockeye Salmon within the ESU?

• What is the cumulative incidental harvest rate on natural-origin Snake River 

Sockeye Salmon due to all fisheries (from within and outside of ESU)?

• What effect does total incidental harvest have on the abundance, productivity, and 

diversity of natural-origin Snake River Sockeye Salmon?

Performance metrics:

• Fisher hours (effort) 

• Catch 
ESA Recovery Plan: Snake River Sockeye Salmon | 367

June 2015| NOAA Fisheries 

• Harvest 

• Stock identification 

• Spawning escapement 

• Recruits/spawner 

• Genetic composition

Possible Approach:

Outside the ESU, Snake River Sockeye Salmon can be incidentally harvested in two main 

fishery areas: ocean and Columbia River. Fishery-related mortality is reported for tribal 

and non-tribal ocean and Columbia River fisheries by the TAC of the Columbia River 

Compact. Within the ESU, incidental harvest rates on Sockeye Salmon are assessed 

during Chinook salmon roving creel surveys. Creel surveys should include angler counts; 

interviews to obtain information on catch rate, harvest rate, gear types, and angler 

demographics; and collection of biological and mark/tag information from the catch. This 

information can then be used to identify spatial and temporal relationships among fishing 

effort, catch, and harvest, and the incidental capture of Snake River Sockeye Salmon. 

Within the ESU, incidental take can occur within the existing kokanee fishery.

Suggested Analysis: 

The number of O. nerka caught by interviewed anglers will be totaled and used for an 

expanded estimate of the number of fish caught throughout the season. Expanded 

estimates will be based on sample strata and proportional coverage rates. Catch per unit 

effort (CPUE) will be estimated directly from interview responses. Total fishing effort 

will be estimated based on time period, week period, and site encounter probabilities. For 

each population, natural-origin abundance and productivity will be calculated with and 

without incidental harvest to determine if incidental harvest reduces the likelihood of 

meeting recovery criteria. The proportion of Sockeye Salmon within the creel will be 

estimated based on genetic data.

Status: 

Within the ESU, IDFG (Peterson et al. 2013), with funding through BPA, is currently 

collecting information that can address this objective. Outside of the ESU, information is 

collected in lower Columbia and Snake River fisheries from the co-managers (state 

agencies and Tribes) and is reported through the U.S. v Oregon ongoing litigation 

process.
ESA Recovery Plan: Snake River Sockeye Salmon | 368

June 2015| NOAA Fisheries 

Objective 9: Determine the effect of predation on the abundance and productivity of the 

natural populations.

Several fish species occupy the natal lakes that potentially prey on Sockeye Salmon, including 

non-native lake trout and brook trout, and native bull trout and northern pikeminnow. Sockeye 

Salmon may also experience predation from smallmouth bass, walleye, northern pikeminnow, 

and other fish species while migrating through the Salmon, Snake, and Columbia Rivers. These 

fishes may reduce Sockeye Salmon survival by preying on juvenile Sockeye Salmon and/or 

Sockeye Salmon eggs, or by introducing disease. 

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

• Abundance and distribution of predators.

Monitoring questions:

• What is the predation rate and predatory effect of native and non-native fishes in 

the nursery lakes and migration corridor on Snake River Sockeye Salmon?

• What is the effect of predation from avian predators in the Columbia River 

migration corridor on juvenile Snake River Sockeye Salmon?

• What is the effect of predation from marine mammals in the Columbia River 

migration corridor on adult Snake River Sockeye Salmon?

Performance metrics: 

• Number of juvenile Snake River Sockeye Salmon

• Number of predators 

• Number of juvenile Snake River Sockeye Salmon consumed by piscine and avian 

predators 

• Mortality rates 

• Proportion of SAR associated with predation

Possible Approach: 

Using appropriate sampling techniques, conduct annual sampling of exogenous piscine 

predators in the lakes and Salmon River to determine the abundance of predators (based 

on mark-recapture) and stomach contents. These data are then incorporated into a 

bioenergetics model to derive a population-level (or ESU-level) consumption estimate 

imposed by exogenous fishes. Sampling of predatory fish diets will occur during times 
ESA Recovery Plan: Snake River Sockeye Salmon | 369

June 2015| NOAA Fisheries 

and locations when and where their distribution overlaps with juvenile Sockeye Salmon. 

Interpretation of the predatory impact in the migration corridor should be conducted with 

methods established in the published literature (e.g., Fritts and Pearsons 2006). 

To evaluate avian predation on juvenile Snake River Sockeye Salmon, bird colonies are 

monitored for the presence of PIT-tags originating from specific populations within the 

Snake River Sockeye Salmon ESU. Bioenergetics models are then used to expand tag 

recoveries at colonies to population-level impacts.

Collect trend data from spawning tributaries for native and non-native predator 

abundance in the Sawtooth Valley basin. Peak counts and total redds produced would 

provide data to determine if the populations are changing over time.

Suggested Analysis:

The proportion of SAR attributable to predatory mortality can be estimated from the 

bioenergetics modeling results. 

Status: 

Within the ESU, IDFG (Peterson et al. 2013), with funding through BPA, is currently 

collecting information that can address this objective. Outside of the ESU, information is 

collected in lower Columbia and Snake River by various researchers. For example, for 

avian predation estimates see Roby et al. (2012) and for piscine predators see Porter 

(2011). 

Objective 10: Determine the transmission and effects of disease on the abundance, 

productivity, and diversity of the natural populations. 

An important goal of the Phase 3 hatchery program will be to release fish into the system that are 

known to have a healthy disease history during rearing to minimize impacts on naturally and 

hatchery-produced fish. 

Type of monitoring effort: Long-term status and trend monitoring.

Key Information Needs:

• Results from Phase 1 and 2 monitoring. 

Monitoring questions:

• What are the prevalence and level of pathogens in natural and hatchery-origin 

Snake River Sockeye Salmon?
ESA Recovery Plan: Snake River Sockeye Salmon | 370

June 2015| NOAA Fisheries 

• What are the magnitude and pathways of disease transmission between hatchery 

and natural-origin Snake River Sockeye Salmon?

• What are the magnitude and pathways of disease transmission between hatchery 

and residual Sockeye Salmon and kokanee?

Performance metrics:

• Number of infected hatchery and naturally produced fish 

• Spatial distribution of disease 

Possible approach: 

The health of hatchery fish will be monitored starting with broodstock and continuing 

through rearing and release of juveniles. The health of naturally produced fish will be 

assessed on dead parr, smolts, and spawners encountered during monitoring activities. All 

sampling, diagnostic, and statistical analyses will comport with the Integrated Hatchery 

Operations Team (IHOT) and the Pacific Northwest Fish Health Protection committee 

guidelines. All disease monitoring will be consistent with the IDFG fish health policy and 

the native fish conservation policy. In addition, dead, naturally produced fish collected as 

parr or smolts during smolt trapping and juvenile sampling will be examined for diseases. 

Hatchery fish are sampled before release, during spring outmigration from the lakes, and 

throughout their life cycle within the hatchery.

Suggested analysis: 

Analysis of samples will follow standard protocols defined in the latest edition of the 

American Fisheries Society “Suggested Procedures for the Detection and Identification of 

Certain Finfish and Shellfish Pathogens (Blue Book).”

Status: 

The IDFG Eagle Fish Health Lab has been doing comprehensive fish health work on 

Snake River Sockeye Salmon since 1991.

11.2 Adaptive Management 

Adaptive management provides a mechanism to incorporate the data obtained through RM&E 

into the design and implementation of an effective recovery strategy. It allows recovery planners 

to use monitoring and evaluation results to make adjustments on the path to recovery. Because of 

the large number of organizations in Idaho, and elsewhere in the basin, implementing 

management actions that affect Snake River Sockeye Salmon viability, the adaptive management 

strategy for the species outlines a collaboration and coordination process that uses the current 

implementation structures. The process allows for sharing of information and decisions that will 
ESA Recovery Plan: Snake River Sockeye Salmon | 371

June 2015| NOAA Fisheries 

influence recovery. What follows is a brief summary of the various management decision 

processes and associated adaptive management plans that affect management actions for 

tributary habitat, hatcheries, harvest, and the hydrosystem as they relate to Snake River Sockeye 

Salmon recovery.

11.2.1 Tributary Habitat

Several funding sources and various entities are involved with implementing tributary habitat 

restoration actions. In all cases, these entities have well established decision-making processes 

for prioritizing actions. It is beyond the scope of this document to identify and describe all the 

processes used. What follows are a few examples that illustrate ongoing decision processes.

Idaho Department of Fish and Game

Beginning in 1991 when Snake River Sockeye Salmon were listed as endangered, the Idaho 

Department of Fish and Game (IDFG) initiated a captive broodstock program to maintain Snake 

River Sockeye Salmon and prevent species extinction. Cooperating with NMFS, the ShoshoneBannock Tribes, Oregon Department of Fish and Wildlife, and BPA on the overall recovery 

program, IDFG develops and maintains captive broodstock, conducts field monitoring and 

evaluations, such as investigating the success of outplanted groups. IDFG genetic staff provide 

genetics monitoring and support for the program, such as background genetic identify analysis 

and development of spawning designs. IDFG manages the Eagle Fish Hatchery captive 

broodstock program, the Sawtooth Hatchery and the Springfield Sockeye Salmon

Hatchery. IDFG is a member of the Sockeye Technical Oversight Committee and the Technical 

Advisory Committee that developed this ESA Recovery Plan.

U.S. Forest Service

The U.S. Forest Service manages the Sawtooth National Recreation Area (Sawtooth NRA) 

which is located within the 2.1 million acre Sawtooth National Forest. The Sawtooth NRA 

consists of over 750,000 acres of protected land encompassing the Sawtooth Valley. The U.S. 

Congress established the Sawtooth NRA in 1972 with the passage of Public Law 92-400, which

sought to preserve and protect the area's "natural, scenic, historic, pastoral and fish and wildlife 

values and to provide for the enhancement of the recreation values associated therewith." The 

U.S. Forest Service actively manages the Sawtooth NRA for multiple purposes to meet its 

mission, including habitat restoration and protection actions supporting Snake River Sockeye 

Salmon recovery. The U.S. Forest Service has actively participated in development of the Snake 

River Sockeye Salmon recovery plan through participation on the Technical Advisory 

Committee.

Idaho Office of Species Conservation 

The state of Idaho Office of Species Conservation (OSC) coordinates policies and programs for 

the state of Idaho related to the conservation of threatened, endangered, and candidate species. 

The OSC, which is part of the Idaho governor’s office, heads the state ́s actions on all ESA 
ESA Recovery Plan: Snake River Sockeye Salmon | 372

June 2015| NOAA Fisheries 

recovery plans, management plans, public comment periods, biological opinions, guidance 

programs and species-specific recovery projects. Serving primarily as project coordinator, it 

works with various state natural resource agencies, including IDFG, IDEQ, IDWR, and Idaho 

Department of Lands, to implement recovery actions consistent with state laws and ongoing 

efforts. The OSC also coordinates and administers grant-funding programs that fund cooperative 

salmon habitat restoration for a wide variety of implementers. It leads project prioritization for 

funding consideration by the NPCC and BPA, and works to increase the reliable use of “best 

available data” in ESA recovery efforts. Adaptive management is implemented through strategic 

guidance, project review, and selection and prioritization processes. 

Shoshone-Bannock Tribes

The Shoshone-Bannock Tribes (SBT) implement tributary habitat actions and associated 

monitoring under an ESA Memorandum of Agreement with the Action Agencies for listed 

salmon and steelhead species. The SBT implements projects within the Salmon and upper Snake 

River subbasins to protect, restore and enhance ecosystem processes. These projects include the 

Snake River Sockeye Salmon Habitat and Limnological Research Project, which was 

implemented in 1991. The SBT receives funding from BPA and collaborates on the projects 

with NMFS, IDFG, and the University of Idaho. Project tasks include: 1) monitoring 

limnological parameters of the Sawtooth Valley lakes to assess lake productivity; 2) conducting 

lake fertilization in Pettit and Alturas Lakes; 3) reducing the number of mature kokanee salmon 

spawning in Alturas Lake Creek; 4) monitoring, enumerating, and evaluating Sockeye Salmon

smolt migration from Pettit and Alturas Lakes; 5) monitoring spawning kokanee salmon 

escapement and estimating fry recruitment in Fishhook and Alturas Lake creeks; 6) conducting 

Sockeye Salmon and kokanee salmon population surveys; 7) evaluating potential competition 

and predation between stocked juvenile Sockeye Salmon and a variety of fish species in Redfish, 

Pettit, and Alturas Lakes; and 8) assisting IDFG with captive broodstock production activities. 

Bonneville Power Administration and Northwest Power and Conservation Council 

Columbia Basin Fish and Wildlife Program

The Bonneville Power Administration (BPA) is a major funding source for salmon recovery 

projects in the Columbia Basin as part of its obligation to mitigate the effects of the operation of 

the FCRPS on fish and wildlife. Under the Columbia Basin Fish and Wildlife Program, the 

Northwest Power and Conservation Council recommends projects for funding by BPA. BPA 

currently provides funding for implementation of the Snake River Sockeye Salmon captive 

broodstock program and the associated monitoring and evaluation. Together, the two 

organizations function as coordinators of RM&E, both in terms of the habitat protection, 

restoration and RM&E actions they fund within the Salmon River and Sawtooth Valley, and the 

information-sharing processes they initiate and approve. Proposed projects undergo a rigorous 

scientific review (by an Independent Science Review Panel) and revision process to ensure the 

implementation of scientifically sound projects that are based on best available science and use 

state-of-the-art restoration approaches. For more information, see 

http://efw.bpa.gov/IntegratedFWP/anadfishresearch.aspx and http://www.nwcouncil.org/fw/.
ESA Recovery Plan: Snake River Sockeye Salmon | 373

June 2015| NOAA Fisheries 

Community-Level Partnerships 

Several community-level organizations collaborate with state and Federal agencies to implement 

projects for the protection and restoration of tributary habitat, and to monitor the effectiveness of 

these efforts. A few of these organizations are described below.

Upper Salmon Basin Watershed Project

The Upper Salmon Basin Watershed Project is a community-driven partnership through which 

landowners work together with local, state, and Federal partners to protect and restore fish 

habitats. The group collaborates to improve habitat for salmon and resident fish while respecting 

and balancing the needs of irrigated agriculture and strengthening the local economy. The 

group’s staff is affiliated with the Idaho Governor’s Office of Species Conservation. It works 

with landowners to develop restoration projects, assists with the permitting process, oversees the 

work, and monitors outcomes. Additionally, the USBWP seeks and manages major funding 

support.

Soil and Water Conservation Districts

Idaho’s soil and water conservation districts assist private landowners and land users in the 

conservation, sustainability, improvement, and enhancement of state natural resources. The 

Custer Soil and Water Conservation District implements projects in Custer County, including the 

Sawtooth lakes area. The SWCDs partner with the BLM, USFS, USFWS, NMFS, NRCS, and 

IDFG and others to evaluate and implement projects needed for fish recovery, including 

improving stream flows, riparian vegetation communities and water quality, and restoring fish 

passage. 

Integration and Coordination

Although there are several funding sources and implementing entities that have prioritization 

processes and elements of adaptive management, there is a need to integrate and coordinate 

adaptive management for tributary habitat restoration associated with the recovery plan. This 

process of integration allows us to track and adjust our efforts effectively. Section 10 describes 

an implementation framework for this recovery plan. The framework is not intended to replace 

the other processes that are currently used. Rather, the framework is meant to improve 

coordination, collaboration, and sharing of information for decision making. Information, 

including successes and failures, will be shared through the framework (see Figure 10-1). This 

will result in the implementation of cost-effective projects throughout the basins.

11.2.2 Hatcheries

The Stanley Basin Sockeye Salmon Oversight Committee coordinates with regional state and 

Federal agencies, tribes and others to provide guidance that directs hatchery programs for Snake 

River Sockeye recovery. The program follows guidance from the Columbia Basin Hatchery 

Scientific Review Group. It works with NMFS through measures defined in a Hatchery and 
ESA Recovery Plan: Snake River Sockeye Salmon | 374

June 2015| NOAA Fisheries 

Genetic Management Plan to minimize risks that could impair recovery of the species under the 

ESA. 

Stanley Basin Sockeye Technical Oversight Committee (SBSTOC)

The Stanley Basin Sockeye Technical Oversight Committee guides new research, coordinates 

ongoing research, and actively participates in all elements of the Snake River Sockeye Salmon

recovery effort. The committee is comprised of technical experts from IDFG, BPA, NMFS, 

ODFW, the University of Idaho, USFS, and the Shoshone-Bannock Tribes. The committee 

continuously reviews the methods and results from monitoring and evaluation projects that guide 

program direction. Based on these findings, it makes yearly recommendations that then direct 

spawning, broodstock sourcing, hatchery releases, and other aspects of program implementation. 

Hatchery Scientific Review Group (HSRG) 

The Hatchery Scientific Review Group, an independent scientific review panel, completed a 

review of the hatchery program for the Redfish Lake Sockeye Salmon population, and provided 

recommendations for the population. The HSRG recommendations were incorporated into the 

hatchery program. Guidance from the HSRG is being used to move the Snake River Sockeye 

Salmon program to an integrated conservation program where the natural environment drives the 

adaptation and fitness of a composite population of fish that spawns both in a hatchery and in the 

wild. 

Hatchery and Genetic Management Plans (HGMPs)

Take prohibitions do not apply to activities associated with artificial propagation programs, 

provided a Hatchery Genetic Management Plan has been approved by NMFS as meeting a list of 

criteria that are specified in the 4(d) rule which only applies to threatened species (NMFS 2000). 

The HGMP must provide adequate monitoring and evaluation to detect and evaluate the success 

of the hatchery program and any risks potentially impairing the recovery of listed ESUs/DPSs. 

An adaptive management processes is needed to provide for the evaluation of the data and 

include the potential to revise the assumptions, management strategies, or objectives of the 

hatchery program. In addition, NMFS is required to evaluate on a regular basis the effectiveness 

of the HGMP in protecting and achieving a level of productivity commensurate with the 

conservation of the listed species. If the HGMP is ineffective, NMFS identifies ways in which 

the program needs to be altered. 

A HGMP has been completed for the Snake River Sockeye Salmon hatchery program. The 

HGMP is a “living document” meant to guide the current and near-term programmatic activities 

associated with Snake River Sockeye Salmon. Program activities and recommendations will 

continue to change as recovery plans and species delisting criterion are established for this 

population.
ESA Recovery Plan: Snake River Sockeye Salmon | 375

June 2015| NOAA Fisheries 

11.2.3 Harvest

Fishery managers use complex management frameworks to restrict annual mortality rates on 

Snake River Sockeye Salmon and other ESA-listed salmon. They manage fisheries in the 

Columbia River estuary and mainstem Columbia and Snake Rivers through a combination of 

laws, policies, and guidelines established to coordinate fisheries and control impacts on ESAlisted Columbia River salmonids. Fisheries in the Salmon River and natal lakes are also designed 

to control impacts on Snake River Sockeye Salmon and other ESA-listed species. The different 

fishery managers coordinate research, monitoring, and evaluation efforts. In the future, fishery 

managers may consider using fisheries to control the number of hatchery-origin spawners 

returning to the natal lakes.

Mainstem Columbia River

Fisheries in the mainstem Columbia River that affect Snake River Sockeye Salmon are managed 

subject to the terms of the U.S. v. Oregon Management Agreement for 2008-2017. The 

management agreement defines harvest limits thought to be sufficiently protective to allow for 

the recovery of ESA-listed species. The strategy also implements research, monitoring, and 

evaluation programs to ensure that fisheries minimize their impacts on the Snake River Sockeye 

Salmon ESU. The objective of monitoring and research is to improve the accuracy and precision 

of harvest management. As identified in the agreement, these data are essential for adaptive 

management. A Technical Advisory Committee, which is comprised of biologists from state, 

Federal, and tribal management agencies, develops, analyzes, and reviews data and provides 

reports and technical recommendations regarding harvest management. The parties to the 

agreement agreed to work together to maintain and seek funding for the research and monitoring 

programs. 

Additional monitoring and adaptive management of harvest in the Columbia River mainstem is 

provided by the ESA Section 7(a)(2) Consultation Biological Opinion and Magnuson-Stevens 

Fishery Conservation and Management Act Essential Fish Habitat Consultation on Treaty Indian 

and Non-Indian Fisheries in the Columbia River Basin subject to the 2008-2017 U.S. v. Oregon

Management Agreement (hereafter Fisheries BiOp) (NMFS 2008e). Several Reasonable and 

Prudent Measures are identified in Section 13.4 of the Fisheries BiOp that emphasize in-season 

management actions, which ensure that incidental take of ESA-listed species remain consistent 

with the Fisheries BiOp. The monitoring of harvest impacts on listed species is an essential 

component of the Fisheries BiOp.

Idaho’s Recreational Fisheries Regulation Process 

Idaho’s Statutes and Rules, Title 36 of the Idaho Code, describe procedures for development and 

implementation of angling regulations. This rule requires the department to continually monitor 

the status of fisheries resources, and report to the Director and Commission any serious or 

abnormal changes in health or abundance of the resource. Currently, no fisheries directly target 

Snake River Sockeye Salmon; however, the fish are occasionally taken in fisheries targeting 
ESA Recovery Plan: Snake River Sockeye Salmon | 376

June 2015| NOAA Fisheries 

other species. State fishery managers conduct substantial monitoring and evaluation during these

fisheries and restrict harvest at times when Sockeye Salmon are present. In the future, fishery 

managers may consider using fisheries to manage the number of hatchery-origin spawners 

returning to natal lakes.

Fisheries Management and Evaluation Plans

Currently no state of Idaho fisheries target Snake River Sockeye Salmon. If the fish population’s 

viability reaches a level that can support harvest, the state would need to complete a NMFSapproved Fisheries Management and Evaluation Plan (FMEP) before implementing a fishery. 

Take prohibitions do not apply to activities associated with fishery harvest activities provided the 

fisheries are managed in accordance with a NMFS-approved FMEP. The FMEP must meet 

several specific criteria described in the 4(d) Rule. 

NMFS developed a template for preparing FMEPs that meet the required criteria. Section 3.5 of 

the template requires the applicant to include a schedule and process for reviewing and 

modifying fisheries management under the FMEP. There are two evaluation review processes 

identified in the FMEP: (1) a regular review of fisheries and (2) a comprehensive assessment of 

the overall effectiveness of the FMEP. The evaluation must assess the effectiveness of the FMEP 

in meeting the stated objectives over a long time and must account for any new information that 

may require revision of assumptions or management strategies.

The FMEP describes the process and schedule that is used on a regular basis (annually) to 

evaluate the fisheries, and, if necessary, revise management assumptions and targets. The FMEP 

also includes a description of the process and schedule that occurs every five years to evaluate 

whether the FMEP is accomplishing the stated objectives. Section 3.5 includes the conditions by 

which revisions to the FMEP will occur and how the revisions will be accomplished.

NMFS also requires that the fisheries managers notify and provide to NMFS any proposed 

fishery regulation changes that affect fisheries within the FMEP. NMFS then evaluates the 

proposed changes to determine if the changes constitute additional negative effects that were not 

contemplated during the review and evaluation of the submitted FMEP. Depending on the 

species and fishery involved, changes in regulations by IDFG can occur annually or in-season.

Tribal Resource Management Plans

Currently no tribal tributary fisheries directly target Snake River Sockeye Salmon. There are 

fisheries targeting hatchery spring/summer Chinook salmon and steelhead, and these fisheries are 

managed to protect Sockeye Salmon. If the fish population’s viability reaches a level that can 

support harvest, the tribes would need to complete a NMFS-approved Tribal Resource 

Management Plan (TRMP) before implementing a fishery. In the future, such a fishery may be 

used to control the number of hatchery-origin spawners returning to natal lakes.
ESA Recovery Plan: Snake River Sockeye Salmon | 377

June 2015| NOAA Fisheries 

11.2.4 Mainstem Hydropower System

The Federal Columbia River Power System Biological Opinion describes steps to integrate

adaptive management with hydrosystem operations. 

Federal Columbia River Power System Biological Opinion

The FCRPS RPA recommends that the Action Agencies (Bonneville Power Administration, U.S. 

Army Corps of Engineers, and U.S. Bureau of Reclamation) collaborate with states and tribes in 

the implementation of the FCRPS RPA actions, progress reporting, and adaptive management 

using regional forums. FCRPS RPA Actions 1 through 3 identify the general requirements 

governing the Action Agencies’ development of implementation plans and reporting 

requirements. The Action Agencies are required to submit implementation plans to NMFS in 

December of 2009, 2013, and 2016 that describe their commitments to implement FCRPS RPA 

actions. The Action Agencies are also required to submit Annual Progress Reports to NMFS for 

the period 2009 through 2018. In addition, in 2013 and 2016, the Action Agencies will submit 

Comprehensive RPA Evaluation Reports to NMFS. These reports will review all implementation 

activities through the end of the previous year and compare them to scheduled completion dates 

in the BiOp, or as modified through the Implementation Plans. The Comprehensive Evaluation 

will also describe the status of the physical and biological factors identified in the FCRPS RPA, 

and compare these with the expected survival improvements identified in the Comprehensive 

Analysis. Included in the Comprehensive Evaluation will be a plan to address any shortcomings 

of current survival improvements as compared to the original survival estimates identified in the 

Comprehensive Analysis.

The FCRPS BiOp includes RPA Actions (50 through 73) for research, monitoring, and 

evaluation. RM&E is required in the following areas: fish population status and trend 

monitoring, hydropower RM&E, tributary habitat RM&E, estuary and ocean RM&E, harvest 

RM&E, hatchery RM&E, and predation management RM&E. Data from RM&E will provide 

information needed to support planning and adaptive management, and to demonstrate 

accountability related to the implementation of hydropower and offsite actions.

A Regional Implementation and Oversight Group (RIOG) provides a high-level policy forum for 

discussing and coordinating the implementation of the FCRPS BiOp and related BiOps. The 

purpose of the RIOG is to inform Federal, state, and tribal agencies engaged in recovery efforts. 

The RIOG will serve as a forum where policy issues and concerns related to the implementation 

of the BiOps will be discussed in a collaborative manner, and to provide a forum for enhanced 

accountability and transparency. The group does not supplant existing Federal, state, or tribal 

decision-making authorities, and no agency or sovereign is required to participate in the group. 

Participation is by interest and choice.

The implementation and oversight group is supported by senior technical teams for hydro, 

habitat, hatcheries, and RM&E integration and by additional technical teams. Technical 

information and recommendations flow from the technical teams to the senior technical teams to 
ESA Recovery Plan: Snake River Sockeye Salmon | 378

June 2015| NOAA Fisheries 

the group. Policy guidance and technical assignments flow from the group to the senior technical 

teams and technical teams. The implementation and oversight group and technical groups ensure 

that actions required by the FCRPS BiOp are implemented effectively, performance standards 

are achieved, disputes are resolved, and other regional processes are considered during the period 

of the BiOp.

11.2.5 Integration of Adaptive Management Processes

Integration of the many adaptive management processes will occur within the implementation 

management framework described in Section10 and illustrated in Figure 10-1. The Sockeye 

Salmon Implementation and Science Team, Stanley Basin Sockeye Technical Oversight 

Committee, and Snake River Science Team will serve key roles in incorporating new knowledge 

into future management guidance and direction. These teams will not only provide input for 

adaptive implementation of hatchery programs and tributary habitat actions, they will also 

provide input into other related regional decision-making forums.
ESA Recovery Plan: Snake River Sockeye Salmon | 379

June 2015| NOAA Fisheries 

12 Literature Cited

Alt, D. D., and D. W. Hyndman. 1989. Roadside geology of Idaho. Mountain Press Publishing, 

Missoula, Montana.

Anderson, P. D. 2009. Irrigation Canal Effects on Copper Levels in Water and Sediment of the MidColumbia and Wenatchee Rivers. Publication No. 09-03-005. February 2009 Washington State 

Department of Ecology, Olympia WA

Anderson, C. W., Rinella, F. A., and S. A. Rounds. 1996. Occurrence and distribution of organic 

pesticides and trace elements in the Willamette River Basin, Oregon: U.S. Geological Survey 

Water-Resources Investigation Report 96-4234, 68 p.

Andrews, J., J. Lloyd, and B. Webster. 1987. Alturas Lake Creek Flow Augmentation. Final Report by 

USDA Forest Service project coordinators, Sawtooth National Forest, Twin Falls, Idaho. Prepared 

for Bonneville Power Administration. Project 83-415, Contract DE-A179-86BP62661. 

Archer, E. K.; R. A. Scully, R. Henderson, B. B. Roper, and J. D. Heitke. 2012. Effectiveness 

monitoring for streams and riparian areas: sampling protocol for stream channel attributes. 

PACFISH/INFISH Biological Opinion Effectiveness Monitoring Program (PIBO-EMP), Multifederal Agency Monitoring Program, Logan, UT. Unpublished paper on file at: 

http://www.fs.fed.us/biology/fishecology/emp.

Arkoosh, M. R., S. A. Strickland, A. L. Van Gaest, G. M. Ylitalo, L. L. Johnson, G. K. Yanagida, T. K. 

Collier, J. P. Dietrich. 2011. Trends in Organic Pollutants in Juvenile Snake River Spring Chinook 

Salmon with Different Outmigrating Histories through the Lower Snake and Middle Columbia 

Rivers. Science of the Total Environment 409:5086-5100.

Arthaud, D. 2012. Snake River sockeye salmon 2012 update. National Marine Fisheries Service, Idaho 

Habitat Office. Boise, Idaho.

Arthaud, D. and J. Morrow. 2007. Survival of Snake River sockeye salmon migrating from Stanley 

basin lakes into the Federal Columbia River Power System. National Marine Fisheries Service, 

Idaho Habitat Office. Boise, Idaho.

Arthaud, D. and J. Morrow. 2013. Improving migration survival estimates of Snake River sockeye 

salmon. National Marine Fisheries Service, Idaho Habitat Office. Boise, Idaho.

Arthaud, D. L., C. M. Greene, K. Guilbault, and J. V. Morrow, Jr.. 2010. Contrasting life-cycle impacts 

of stream flow on two Chinook salmon populations. Hydrobiologia 655:171–188.

Atkinson, C. E., J. H. Rose, and O. T. Duncan. 1967. Salmon of the North Pacific Ocean -- Part IV. 

Spawning populations of North Pacific salmon. 4. Pacific salmon in the United States. Int. North 

Pac. Fish. Comm. Bull. 23:43-223.

Axel, G. A., M. Peterson, B. P. Sandford, E. E. Hockersmith, B. J. Burke, K. E. Frick, J. J. Lamb, M. G. 

Nesbit, and N. D. Dumdei. 2013. Characterizing Migration and Survival between the upper Salmon 

River Basin and Lower Granite Dam for Juvenile Snake River Sockeye Salmon, 2012. Report of 

research by Fish Ecology Division, Northwest Fisheries Science Center National Marine Fisheries 

Service, Seattle, Washington and Idaho Department of Fish and Game, Nampa, Idaho to 

Bonneville Power Administration, Portland, Oregon. Project 2010-076-00.
ESA Recovery Plan: Snake River Sockeye Salmon | 380

June 2015| NOAA Fisheries 

Axel, G. A., M. Peterson, B. P. Sandford, B. J. Burke, K. E. Frick, J. J. Lamb, and M. G. Nesbit, 2014. 

Characterizing Migration and Survival between the upper Salmon River Basin and Lower Granite 

Dam for Juvenile Snake River Sockeye Salmon. March 2014. Report by Fish Ecology Division, 

National Marine Fisheries Service and Idaho Fish and Game. Prepared for the Bonneville Power 

Administration. Project 2010-076-00.

Azuma, T. 1995. Biological mechanisms enabling sympatry between salmonids with special reference 

to sockeye and chum salmon in oceanic waters. Fisheries Research 24 (4):291-300.

Baker, M. J., 1998. Hydrologic and water quality effects of fire. Conference on Effects of Fire 

Management of Southwestern Natural Resources, Krammes, J.S. (Tech Coord.). November 1988, 

15-17, Tucson, AZ. USDA Forest Service, Rocky Mountain Forest and Range Experiment Station: 

Fort Collins, CO; 31-42.

Baker, D. J., T. G. Brown, D. G. Green, and J. A. Heindel. 2011. Snake River sockeye salmon captive 

broodstock program: Hatchery Element. Annual Progress Report: January 1, 2010 – December 31, 

2010. IDFG Report # 11-10. Prepared for the Bonneville Power Administration.

Baker, D. J., T. G. Brown, K. Felty, and J. A. Heindel. 2012. Snake River Sockeye Salmon Captive 

Broodstock Program Hatchery Element Project Progress Report 2011 Annual Report. Idaho 

Department of Fish and Game

Baker, D. J., T. G. Brown, K. Felty, and J. A. Heindel. 2013. Snake River Sockeye Salmon Captive 

Broodstock Program Hatchery Element Project Progress Report 2012 Annual Report. Idaho 

Department of Fish and Game

Baldwin, D. H., C. P. Tatara, N. L. Scholz. 2011. Copper-induced olafactory toxicity in salmon and 

steelhead: extrapolation across species and rearing environments. Aquatic Toxicology, 101(1):295-

297.

Beamish, R. J., and C. Mahnken. 2001. A critical size and period hypothesis to explain natural 

regulation of salmon abundance and linage to climate and climate change. Progress in 

Oceanography 49:423-437.

Beamish, R. J., C. Mahnken, and C. M. Neville. 2004. Evidence that reduced early marine growth is 

associated with lower marine survival of coho salmon. Transactions of the American Fisheries 

Society 1333:26-33.

Beamish, R. J., G. A. McFarlane, J. R. King. 2005. Migratory patterns of pelagic fishes and possible 

linkages between open ocean and coastal ecosystems off the Pacific coast of North America. Deep 

Sea Research (Part II, Topical Studies in Oceanography) 52(5-6):739-755.

Beamsderfer, R. C. and A. A. Nigro. 1989. Status, biology, and alternatives for management of walleye 

in John Day Reservoir: a review. Oregon Department of Fish and Wildlife. Information Reports 

(Fish) 89-2. Portland, Oregon.

Beckvar N., T. M. Dillon, and L. B. Read. 2005. Approaches for linking whole-body fish residues of 

mercury or DDT to biological effects thresholds. Environmental Toxicology and Chemistry 

24:2094-2105. 

Beechie, T. and Bolton, S. 1999. An approach to restoring salmonid habitat-forming processes in Pacific 

Northwest watersheds. Fisheries 24: 6-15.
ESA Recovery Plan: Snake River Sockeye Salmon | 381

June 2015| NOAA Fisheries 

Beechie, T., E. Beamer, L. Wasserman. 1994. Estimating Coho Salmon Rearing Habitat and Smolt 

Production Losses in a Large River Basin, and Implications for Habitat Restoration. North 

American Journal of Fisheries Management. Volume 14 No. 4 P. 797-811, 1/1/1994.

Beechie, T. J., E. A. Steel, P. Roni, and E. Quimby (editors). 2003. Ecosystem recovery planning for 

listed salmon: an integrated assessment approach for salmon habitat. U.S. Dept. of Commerce, 

NOAA Tech. Memo., NMFS-NWFSC-58, December 2003.

Beechie, T. J., E. Buhle, M. H. Ruckelhaus, A. H. Fullerton, and L. Holsinger. 2006. In press. 

Hydrologic regime and the conservation of salmon life history diversity. Biological Conservation., 

1/1/2006.

Beechie, T. J., D. A. Sear, J. D. Olden, G. R. Pess, J. M. Buffington, H. Moir, P. Roni, M. M. Pollock. 

2010. Process-based principles for restoring river ecosystems. BioScience 60:209–222.

Beechie, T., H. Imaki, J. Greene, A. Wade, H. Wu, G. Pess, P. Roni, J. Kimball, J. Stanford, P. Kiffney, 

and N. Mantua. 2012. Restoring salmon habitat for a changing climate. River Research and 

Applications. Online prepublication wileyonlinelibrary.com DOI:10.1002/rra.2590. 

Beiningen, K. T. 1976. Fish runs, section E. Pacific Northwest Regional Commission, Investigative 

Reports of the Columbia River Fisheries Project Vancouver

Bell, M. C. 1991. Fisheries handbook of engineering requirements and biological criteria. U.S. Army 

Corps of Engineers. Fish Passage Development and Evaluation Program. North Pacific Division. 

Portland, Oregon.

Bellerud, B. 2014. Source of information on Sockeye Salmon survival estimates. Communication from 

B. Bellarud (NMFS) to R. Furfey 2014.

Beschta, R. L., 1990. Effects of fire on water quantity and quality. In: Walstad, J.D.; Radosevich, S.R.; 

Sandberg, D.V. (eds.). Natural and prescribed fire in Pacific Northwest forests. Corvallis: Oregon 

State University Press: 219-231.

Bevan, D., J. Harville, P. Bergman, T. Bjornn, J. Crutchfield, P. Klingeman, and J. Litchfield. 1994. 

Snake Salmon Recovery Team: final recommendations to the National Marine Fisheries Service. 

May 1994. Rob Jones, Recovery Plan Coordinator. National Marine Fisheries Service, Portland, 

Oregon. 

Bilton, H. T., D. F. Alderdice, and J. T. Schnute. 1982. Influence of time and size at release of juvenile 

coho salmon (Oncorhynchus kisutch) on returns at maturity. Canadian Journal of Fisheries and 

Aquatic Sciences 39:426-447.

Bjornn, T., D. Craddock, and D. Corley. 1968. Migration and survival of Redfish Lake, Idaho, sockeye 

salmon, Oncorhynchus nerka. Transactions of the American Fisheries Society. 97:360- 375. 

Bottom, D. L., C. A. Simenstad, J. Burke, A. M. Baptista, D. A. Jay, K. K. Jones, E. Casillas, and M. H. 

Schiewe. 2005. Salmon at river's end: The role of the estuary in the decline and recovery of 

Columbia River salmon. U.S. Department of Commerce, NOAA Technical Memorandum NMFSNWFSC-68, 246 p., August 2005.

Bottom, D. L., A. Baptista, J. Burke, L. Campbell, E. Casillas, S. Hinton, D. A. Jay, M. A. Lott, G. 

McCabe, R. McNatt, M. Ramirez, G. C. Roegner, C. A. Simenstad, S. Spilseth, L. Stamatiou, D. 

Teel, and J. E. Zamon. 2011. Estuarine habitat and juvenile salmon: current and historical linkages 
ESA Recovery Plan: Snake River Sockeye Salmon | 382

June 2015| NOAA Fisheries 

in the lower Columbia River and estuary. Final Report 2002–2008. Prepared by Northwest 

Fisheries Science Center for U.S. Army Corps of Engineers, Portland District, Portland, Oregon, 

December 2011.

Bowler, B. 1990. Additional information on the status of the Snake River sockeye salmon. Unpublished 

Report. Idaho Department of Fish and Game, Boise, ID. 23 p. 

Bowles, E. C. and T. Cochnauer 1984. Potential Sockeye Salmon Production in Alturas Lake Creek 

Drainage, Idaho. Prepared for USDA Forest Service Sawtooth National Forest. P.O. No. 40-0267-4-

127. October 1984. 

Boyce, M. S., 1992. Population viability analysis. Annual Review of Ecological Systems. Journal 

Article WWRC-92-18. 

BPA (Bonneville Power Administration). 1995. Draft supplemental environmental assessment: Snake 

River sockeye salmon Sawtooth Valley project conservation and rebuilding program. Bonneville 

Poer Administration, DOE-EA-0934, Portland, Oregon. 

BPA (Bonneville Power Administration). 2013. Draft final report dated July 2013. Supplemental 

biological assessment, Northern Pikeminnow Management Program. On behalf of Bonneville 

Power Administration, prepared for NMFS. Transmitted from John Skidmore (BPA) to Trevor 

Conder (NMFS) via email correspondence, November 1, 2013. 

BPA (Bonneville Power Administration) and USACE (U.S. Army Corps of Engineers). 2012. Columbia 

Estuary Ecosystem Restoration Program, 2013 Strategy Report. Final. Bonneville Power 

Administration and U.S. Army Corps of Engineers, Portland District, Portland, Oregon, November 

2012.

BPA (Bonneville Power Administration) and USACE (U.S. Army Corps of Engineers). 2013. Science 

and the evaluation of habitat restoration projects in the Columbia River Estuary 2012-2017; the 

Expert Regional Technical Group. Bonneville Power Administration, Portland, Oregon, February 

2013.

Brannon, E., A. Setter, T. Welsh, R. Danner, K. Collins, M. Casten, G. Thorgaard, D. Adams and S. 

Cummings. 1994. Genetic analysis of Oncorhynchus nerka: life history and genetic analysis of 

Refish Lake Oncorhynchus nerka. Completion Report, Report to Bonneville Power Administration. 

Contract No. 1990BP12885. BPA Report DOE/BP-12885-2. Portland, Oregon. 

Brett, J. R. Energetic responses of salmon to temperature. A study of some thermal relations in the 

physiology and freshwater ecology of sockeye salmon (Oncorhynchus nerka). American Zoologist. 

1971. 11(1):99-113;doi:10.1093/icb/11.1.99.

Brett, J. R., J. E. Shelboum, and D. T. Shoop. 1969. Growth rate and body composition of fingerling 

sockeye salmon, Oncorhynchus nerka, in relation to temperature and ration size. J. Fish. Res. 

Board Can. 26, 2363-2394.

Brodeur, R. D. 1990. A synthesis of the food habits and feeding ecology of salmonids in the marine 

waters of the North Pacific. University of Washington, Fisheries Research Institute, FRI-UW-9016. 

38pp.
ESA Recovery Plan: Snake River Sockeye Salmon | 383

June 2015| NOAA Fisheries 

Brosnan, I. G., D. W. Welch, E. L. Rechisky, and A. D. Porter. 2014. Evaluating the influence of 

environmental factors on yearling Chinook salmon survival in the Columbia River plume (USA). 

Marine Ecology Progress Series 496:181-196.

Buck, J. A., R. G. Anthony, C. A. Schuler, F. B. Issacs, and D. E. Tillitt. 2005. Changes in productivity 

and contaminants in bald eagles nesting along the lower columbia river, USA. Environ Toxicol 

Chem 2005; 1779-92.

Budy, P., C. Luecke, W. A. Wurtsbaugh, and H. P. Gross. 1995. Limnology of Sawtooth Valley lakes 

with respect to potential growth of juvenile Snake River sockeye salmon. Northwest Science 

69:133–150.

Bugaev, V. F., D. W. Welch, M. M. Selifonov, L. E. Grachev, J. P. Eveson. 2001. Influence of the 

marine abundance of pink (Oncorhynchus gorbuscha) and sockeye salmon(O. nerka) on growth of 

Ozernaya River sockeye. Fisheries Oceanography 10 (1):26-32.

Burgner, R. L. 1987. Factors influencing age and growth of juvenile sockeye salmon (Oncorynchus 

nerka) in lakes. In Sockeye Salmon (Oncorhynchus nerka) Population Biology and Future 

Management. H. D. Smith, L. Margolis, and C. C. Wood editors Canadian special publication of 

fisheries and aquatic science, 96.

Burgner, R. L. 1991. The life history of sockeye salmon (Oncorhynchus nerka). In: C. Groot and L. 

Margolis (eds.), Life history of Pacific salmon. p. 3 -117. Univ. of British Columbia Press. 

Vancouver, B.C.

Burgner, R. L. 1992. Life history of sockeye salmon (Oncorhynchus nerka). Pages 1-117 in C. Groot 

and L. Margolis, editors. Pacific slamon life histories. University of British Columbia Press. 

Vancouver. 

Burke, B. J., W. T. Peterson, B. R. Beckman, C. A. Morgan, E. A. Daly, and M. Litz. 2013. Multivariate 

models of adult Pacific salmon returns. PLoS ONE, 8(1):e54134. 

doi:10.1371/journal.pone.0054134

Cannamela, D. 1993. Hatchery steelhead smolt predation of wild and natural juvenile Chinook salmon 

fry in the upper Salmon River, Idaho. Fisheries Research, Idaho Department of Fish and Game. 

Boise, Idaho.

CBFWA (Columbia Basin Fish & Wildlife Authority). 2008. Status of Fish and Wildlife Resources in 

the Columbia River Basin. Columbia Basin Fish & Wildlife Authority, Portland, Oregon. February 

2008, 142 pp. 

Chang, H., J. Jones, M. Gannett, D. Tullos, H. Moradkhani, K. Vache. 2010. Climate change and 

freshwater resources in oregon. In Oergon Climate Change Research Institute, Oregon Climate 

Assessment Report, KD Dello and PW Mote (Eds.) College of Oceanic and Atmospheric Sciences, 

Oregon State University, Corvallis, OR.

Chapman, D. W. and K. L. Witty. 1993. Habitats of weak salmon stocks of the Snake River basin and 

feasible recovery measures Recovery issues for threatened and endangered Snake River Salmon, 

Technical report 1 of 11. Report to Bonneville Power Administration. Contract Number DE-AM79-

93BP99654. Portland, Oregon. 
ESA Recovery Plan: Snake River Sockeye Salmon | 384

June 2015| NOAA Fisheries 

Chapman, D., W. Platts, D. Park and M. Hill. 1990. Status of Snake River sockeye salmon. Final Report 

to PNUCC. June 26. 

Chatel, J. 2013. Source of information on aquactic species boat inspection station. Communication 

from J. Chatel (USFS) to R. Furfey 2013.

Clark, G. M. and Maret, T. R., 1998. Organochlorine compounds and trace elements in fish tissue and 

bed sediments in the lower Snake River basin, Idaho and Oregon: U.S. Geological Survey WaterResources Investigation Report Report 98-4103, 35 p.

Clark, G. M., T. R. Maret, M. G. Rupert, et al. 1998. Water Quality in the Upper Snake River Basin, 

Idaho and Wyoming, 1992-95. U.S. Geological Survey Circular 1160.

Collis, K. and Roby, D., 2010. Research, monitoring and evaluation of avian predation on salmonid 

smolts in the lower and mid-columbia river. Annual Report to the U.S. Army Corps of Engineers. 

Corvallis, OR.

Coots, R. 2007. Vancouver Lake PCBs, chlorinated pesticides, and dioxins in fish tissue and sediment. 

Washington State Department of Ecology Publication No. 07-03-017. Olympia, WA. 53 pp.

Crozier, L. 2011. Literature review for 2010 citations for BIOP: Biological effects of climate change. In: 

Endangered Species Act Federal Columbia River Power System 2010 Annual ESA Progress 

Report: Section 2, Attachment 1, August 2011. 

Crozier, L. 2012. Literature review for 2011 citations for BIOP: Biological effects of climate change. In: 

Endangered Species Act Federal Columbia River Power System 2011 Annual ESA Progress 

Report: Section 2, Appendix A, July 2012. 

Crozier, L. 2013. Impacts of climate change on Columbia River salmon. Review of the scientific 

literature published in 2012. Prepared by L. Crozier (NMFS) for Bonneville Power Administration, 

Portland, Oregon. Document available in Appendix D.1 in the 2014 Supplemental FCRPS BiOp. 

Crozier, L., M. Scheuerell, and R. Zabel. 2011. Using time series analysis to characterize evolutionary 

and plastic responses to environmental change: a case study of a shift toward earlier migration date 

in sockeye salmon. American Naturalist 178:755–773.

Crozier, L. G., B. J. Burke, B. P. Sanford, G. A. Axel, and B. L, Sanderson. 2014. Adult Snake River 

Sockeye Salmon Passage and Survival Within and Upstream of the FCRPS. Report of research by 

Northwest Fisheries Science Center, NOAA National Marine Fisheries Service, for the U.S. Army 

Corps of Engineers Walla Walla District. July 2014.

Curet, T., B. Esselman, A. Brimmer, M. White, and M. Green. 2009. Fishery management 

investigations, Salmon Region 2007. Idaho Department of Fish and Game, Boise.

Dalton, M. M., P. W. Mote, and A. K. Snover [Eds.]. 2013. Climate change in the 

northwest:implecations for our landscapes, waer and communities. Washington, D.C., Island Press.

Davis, D. A. Johnson, and D. Serdar. 1998. Washington State Pesticide Monitoring Program 1995 

Surface Water Sampling Report. Washington State Department of Ecology Publication No. 98-

300. Olympia, WA. 22 pp. + appendices.
ESA Recovery Plan: Snake River Sockeye Salmon | 385

June 2015| NOAA Fisheries 

Davis, N. D., J. L. Armstrong, and K. W. Myers. 2003. Bering Sea salmon food habits: Diet overlap in 

fall and potential for interactions among salmon. Technical Report. School of Aquatic and Fishery 

Science, Fisheries Research Institute, University of Washington.

DeBano, L.F., D.G. Neary, and P.F. Folliott. 1998. Fire’s effects on ecosystems. New York: John 

Wiley & Sons, Inc. 333 p.

Diefenderfer, H. L., Johnson, G. E., Sather, N. K., Colemna, A. M., Buenau, K. E., Tagestad, J. D., Ke, 

Y., Dawley, E. M., Skalski, J. R., Woodley, C. M. 2012. Evaluation of life history diversity, habitat 

connectivity, and survival benefits associated with habitat restoration action in the lower columbia 

river and estuary. Annual Report 2011 to Pacific Northwest National Lab, Richland, WA.

Dietrich, J. P., M. R. Arkoosh, D. A. Boylen, M. Myers, S. A. Strickland, and A. Van Gaest. 2010. 

Investigation of the toxicity of long-term fire retardants on the survival and health of smolting 

Chinook salmon. Final Report by NOAA Fisheries Northwest Fisheries Science Center to the US 

Forest Service, April 2010. 22 pp. 

Dietrich, J. P., M. S. Myers, S. A. Strickland, A. L. Van Gaest, and M. R. Arkoosh. 2013. Toxicity of 

Forest Fire Retardant Chemicals to Stream-type Chinook Salmon Undergoing Parr-Smolt 

Transformation. Environmental Toxicology and Chemistry, 32(1):326-347. 

Dixon, D. G. and J. B. Sprague. 1981. Acclimation-induced changes in toxicity of arsenic and cyanide 

to rainbow trout Salmo gairdneri Richardson. J. Fish Biol. 18: 579-589.

Duffy, E. J., D. A. Beauchamp, R. M. Sweeting, R. J. Beamish, and J. S. Brennan. 2010. Ontogenetic 

diet shifts of juvenile Chinook salmon in nearshore and offshore habitats of Puget Sound. 

Transactions of the American Fisheries Society 139:803-823.

Elsner, M. M., L. Cuo, N. Voisin, et al. 2009. Implications of 21st century climate change for the 

hydrology of Washington state. Pages 69-106 in: Washington Climate Change Impacts Assessment: 

Evaluating Washington’s future in a changing climate. Climate Impacts Group, University of 

Washington, Seattle, Washington, 6/1/2009.

Emmett, W. 1975. The channels and waters of the upper salmon river area, Idaho. U.S. Geological 

Survey Professional paper 870-A. Washington, D.C.

Erickson R. J., D. R. Mount, T. L. Highland, J. Russell Hockett, and C. T. Jenson. 2011. The relative 

importance of waterborne and dietborne arsenic exposure on survival and growth of juvenile 

rainbow trout. Aquat Toxicol. 104:108-115

Essig, D. A. 2010. Arsenic, Mercury, and Selenium in Fish Tissue and Water from Idaho’s Major 

Rivers: A Statewide Assessment. Idaho Department of Environmental Quality. March 2010. 64 

pp. + appendices.

Essig, D. and M. A. Kosterman. 2008. Arsenic, Mercury, and Selenium in Fish Tissue from Idaho Lakes 

and Reservoirs: A Statewide Assessment. Idaho Department of Environmental Quality, State 

Office. Boise, Idaho. 46p. 

Evermann, B. W. 1895. A preliminary report upon salmon investigations in Idaho in 1894. Bulletin of 

the U.S. Fish Commission 15:253-284.

Evermann, B. W. 1896. A report upon salmon investigations in the headwaters of the Columbia River 

in the state of Idaho in 1895. Bulletin of the U.S. Fish Commission 16:151-202.
ESA Recovery Plan: Snake River Sockeye Salmon | 386

June 2015| NOAA Fisheries 

Faler, J. C. and M. S. Powell. 2003. Genetic analysis of Snake River sockeye salmon (Oncorhynchus 

nerka). Completion Report to Bonneville Power Administration, Contract No. DE-B179-

90BP12885, Project No. 90-93. 

Farley, Jr., E. V., J. H. Moss, and R. J. Beamish. 2007. A review of the critical size, critical period 

hypothesis for juvenile Pacific salmon. North Pacific Anadromous Fish Commission 4:311-317.

Faulkner, J. R., S. G. Smith, W. D. Muir, D. M. Marsh, and J. G. Williams. 2008. Survival estimates 

for the passage of spring-migrating juvenile salmonids through Snake and Columbia River dams 

and resevoirs, 2007. Report of the National Marine Fisheries Service to the Bonneville Power 

Administration, Portland, Oregon.

Faulkner, J. R., S. G. Smith, D. M. Marsh, and R. W. Zabel. 2013. Survival estimates for the passage of 

spring-migrating juvenile salmonids through Snake and Columbia River dams and reservoirs, 2012. 

Prepared by Northwest Fisheries Science Center for Bonneville Power Administration, 4/1/2013.

Ferguson, J. W. 2010. Preliminary survival estimates during the spring migration of juvenile salmonids 

through Snake and Columbia River reservoirs and dams, 2010. Memorandum to B. Suzumoto, 

NMFS. Northwest Fisheries Science Center, Seattle, Washington, September 13, 2010.

Ferguson, J. W., G. M. Matthews, R. L. McComas, R. F. Absolon, D. A. Brege, M. H. Gessel, and L. G. 

Gilbreath. 2005. Passage of adult and juvenile salmonids through Federal Columbia River Power 

System dams. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-64, March 2005.

Fesenmyer, S. 2013. Source of information about introduction of non-native species in lower Salmon 

River. Communication from S. Fesenmyer (NMFS) to R. Furfey RE: NMFS staff comments on 

draft Plan. 2013.

Flagg, T. A., C. V. W. Mahnken, and K. A. Johnson. 1995. Captive broodstocks for recovery of Snake 

River sockeye salmon. Pages 81-90 in H.L. Schramm, Jr. and R.G. Piper, editors. Uses and effects 

of cultured fishes in aquatic ecosystems. American Fisheries Society, Symposium 15, Bethesda, 

Maryland.

Flagg, T. A., C. W. McAuley, P. K. Kline, M. S. Powell, D. Taki, and J. C. Gislason. 2004. Application 

of captive broodstocks to preservation of ESA-listed stocks of Pacific salmon: Redfish Lake 

sockeye salmon case example. American Fisheries Society Symposium 44:387–400. 

Foerster, R. E. 1968. The sockeye salmon. Bulletin of the Fisheries Research Board of Canada. No. 162. 

422 p. 

Ford, M. J. 2002. Selection in captivity during supportive breeding may reduce fitness in the wild. 

Conservation Biology 16(3):815-825, 6/1/2002

Ford, M. J. (ed.). 2011. Status review update for Pacific salmon and steelhead listed under the 

Endangered Species Act: Pacific Northwest. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-113, 281 p.

Ford, J., K. B. Ellis, and M. Graeme. 2006. Selective foraging by fish-eating killer whales Orcinus orca 

in British Columbia. Marine Ecology Progress Series 31:185-199.

Forrest, K. W., J. D. Cave, C. G. Michielsens, M. Haulena, and D. V. Smith. 2009. Evaluation of an 

electric gradient to deter seal predation on salmon caught in gill-net test fisheries. North American 

Journal of Fisheries Management 29(4):885-894.
ESA Recovery Plan: Snake River Sockeye Salmon | 387

June 2015| NOAA Fisheries 

Friedland, K. D., B. R. Ward, D. W. Welch, and S. A. Hayes. 2014. Post-smolt growth and thermal 

regime define the marine survival of steelhead from the Keogh River, British Columbia. Marine and 

Coastal Fisheries: Dynamics, Management, and Ecosystem Science 6:1-11.

Fresh, K. L., E. Casillas, L. L. Johnson, and D. L. Bottom. 2005. Role of the estuary in the recovery of 

Columbia River Basin salmon and steelhead: An evaluation of the effects of selected factors on 

salmonid population viability. U.S. Department of Commerce, NOAA Technical Memorandum 

NMFS-NWFSC-69, September 2005.

Fresh, K. et al. 2014. Module for the Ocean Environment. NMFS Northwest Fisheries Science Center, 

Seattle, WA.

Fritts, A. L. and T. N. Pearsons. 2006. Effects of predation by nonnative smallmouth bass on native 

salmonid prey: the role of predator and prey size. Transactions of the American Fisheries Society 

135:853-860.

Fuhrer, G. J., D. Q. Tanner, J. L. Morace, S. W. McKenzie, W. Stuart, and K. A. Skach. 1996. Water 

quality of the lower Columbia River basin; analysis of current and historical water-quality data 

through 1994. USGS Water-Resources Investigation Report Number 95-4294, Geological Survey 

Portland, OR. Water Resources Div. 157 pp.

Good, T. P., R. S. Waples, and P. Adams (eds.). 2005. Updated status of federally listed ESUs of West 

Coast salmon and steelhead. U.S. Dept. Commerce, NOAA Tech. Memo., NMFS-NWFSC-66, June 

2005.

Graves, R. 2012. Source of information on status of man-made hydraulic controls in the Sawtooth 

Valley lakes. Communication from R. Graves (NMFS) to R. Furfey RE: NMFS input on condition 

of lakes, 2012.

Griswold, R. 2013. Source of information on Sawtooth Valley lakes water elevation. Communication 

from R. Griswold (Consultant to SBT) to R. Furfey RE: SBT input on draft Plan, 2013.

Griswold, R. G., D. Taki, and J. Stockner. 2002. Redfish lake sockeye salmon: nutrient 

supplementation as a means of restoration. American Fisheries Society Symposium 20, Bethesda, 

Maryland.

Griswold, R. G., D. Taki, S. Letzing, and K. Tardy. 2011a. Snake River sockeye salmon habitat and 

limnological research. Annual Progress Report: January 1, 2010 - December 31, 2010. ShoshoneBannock Tribes, Fort Hall, ID and Biolines Environmental Consulting, Ketchum, ID for BPA, 

Portland, OR. Project Number 2007-402-00.

Griswold, R. G., A. E. Kohler, and D. Taki. 2011b. Survival of endangered Snake River sockeye salmon 

smolts from three Idaho Lakes: Relationships with parr size at release, parr growth rate, smolt size, 

discharge and travel time. North American Journal of Fisheries Management 31(5):831-825.

Griswold, K. E., R.G. Griswold, A. E. Kohler, and D. Taki. 2012. Creating a science-based framework 

for restoration of sockeye salmon (Oncorhynchus nerka) in the Sawtooth Valley lakes of Idaho: a 

review of parameters for viable salmon populations. Final report submitted to the ShoshoneBannock Tribes of Ft. Hall, Idaho, 73 pages.

Groot, C., and L. Margolis, editors. 1991. Pacific salmon life histories. University of British Columbia 

Press, Vancouver.
ESA Recovery Plan: Snake River Sockeye Salmon | 388

June 2015| NOAA Fisheries 

Gross, H. P. 1995. Evaluation of lake fertilization as a tool to assist in the recovery of the Snake River 

sockeye salmon. Master's thesis. Utah State University, Logan, 152 pages.

Gross, H. P., W. A. Wurtsbaugh, C. Luecke, and P. Budy. 1992. Nutrient limitation of phytoplankton in 

oligotrophic lakes of the Sawtooth Valley, Idaho. pp. 29-52 in S. Spalding (ed.) Snake River 

sockeye salmon (Uncorhynchus nerka) habitat/limnologic research. Bonneville Power 

Administration, DE-BI79-91BP22548. Portland, OR.

Gross H.P, Wurstbaugh W.A, and Luecke C. 1998. The role of anadromous sockeye salmon in the 

nutrient loading and productivity of Redfish Lake, Idaho. Transactions of the American Fisheries 

Society 127:1–18.

Groves, P. B. and J. A. Chandler. 1999. Spawning habitat used by fall chinook salmon in the snake 

river. North American Journal of Fisheries Management 19:912-922.

Gustafson, R. G., T. C. Wainwright, G. A. Winans, F. W. Waknitz, L. T. Parker, and R. S. Waples.. 

1997. Status review of sockey salmon from Washington and Oregon. NOAA Technical 

Memorandum NMFS-NWFSC-33, Seattle. 

Hamlet, A. F., P. W. Mote, M. P. Clark, and D. P. Lettenmaier. 2005. Effects of temperature and 

precipitation variability on snowpack trends in the western United States, J. Clim., 18, 4545 4561.

Hartman, W. L. and R. L. Burgner. 1972. Limnology and fish ecology of sockeye salmon nursery lakes 

of the world. Journal of the Fisheries Research Board of Canada 29 (6):699-715.

Hauser, D. D. W., C. S. Allen, H. B. Jr. Rich, and T. P. Quinn. 2008. Resident harbor seals (Phoca 

vitulina) in Iliamna Lake, Alaska: Summer diet and partial consumption of adult sockeye salmon 

(Oncorhynchus nerka).

Hebdon, J. L., P. Kline, D. Taki, and T. A. Flagg. 2004. Evaluating reintroduction strategies for Redfish 

Lake sockeye salmon captive broodstock progeny. American Fisheries Society Symposium 44:401–

413.

Hecht, S. A., D. H. Baldwin, C. A. Mebane, T. Hawkes, S. J. Gross, and N. L. Scholz. 2007. An 

overview of sensory effects on juvenile salmonids exposed to dissolved copper: Applying a 

benchmark concentration approach to evaluate sublethal neurobehavioral toxicity. U.S. Dept. of 

Commerce, NOAA Tech. Memo., NMFS-NWFSC-83, 39 p.

Henderson, M. A., and A. J. Cass. 1991. Effect of smolt size on smolt-to-adult survival for Chilko Lake 

sockeye salmon (Oncorhynchus nerka). Canadian Journal of Fisheries and Aquatic Sciences 

48:988-994.

Hicken, C. E., T. L. Linbo, D. W. Baldwin, M. S. Myers, M. L. Willis, L. Holland, M. Larsen, M. S. 

Stekoll, S. D. Rice, T. K. Collier, N. L. Scholz, and J. Incardona. 2011. Sub-Lethal Exposure to 

Crude oil During Development Alters Cardiac Morphology, Swiming Performance and Fitness in 

Adult Fish. PNAS 108:7086-7090

Hinck, J. E., C. J. Schmitt, V. S. Blazer, N. D. Denslow, T. M. Bartish, P. J. Anderson, J. J. Coyle, G. M. 

Dethloff, and D. E. Tillitt. 2006. Environmental contaminants and biomarker responses in fish 

from the Columbia River and its tributaries: Spatial and temporal trends. Science of the Total 

Environment 366:549–578.
ESA Recovery Plan: Snake River Sockeye Salmon | 389

June 2015| NOAA Fisheries 

Hixon, M. A., S. Gregory, and W. D. Robinson. 2010. Oregon's fish and wildlife in a changing climate. 

Chapter 7. In: K. D. Dello and P.W. Mote (eds). Oregon climate assessment report. Oregon Climate 

Change Research Institute, College of Oceanic and Atmospheric Sciences, Oregon State University, 

Corvallis, December 2010. 

Holling, C. S. (ed) 1978. Adaptive environmental assessement and management. John Wiley and Sons. 

London.

Holtby, L. B., B. C. Anderson, and R. K. Kadowski. 1990. Importance of smolt size and early ocean 

growth to interannual variability in marine survival of coho salmon (Oncorhynchus kisutch). 

Canadian Journal of Fisheries and Aquatic Sciences 47:2181-2194.

HSRG (Hatchery Scientific Review Group). 2004. Hatchery Reform: principles and recommendations 

of the Hatchery Scientific Review Group. HSRG, Seattle, Washington, 4/1/2004.

Hutchison, M. J. & Iwata, M. 1997. A comparative analysis of aggression in migratory and nonmigratory salmonids. Environmental Biology of Fishes, 50, 209–215.

Hyatt, K. D. and J. G. Stockner. 1985. Responses of sockeye salmon (Oncorhynchus nerka) to 

fertilization of British Columbia Coastal Lakes. Canadian Journal of Fisheries and Aquatic 

Sciences. 42(2)320-331

ICTRT (Interior Columbia Basin Technical Recovery Team). 2003. Independent Populations of 

Chinook, Steelhead, and Sockeye for Listed Evolutionary Significant Units Within the Interior 

Columbia River Domain. 

ICTRT (Interior Columbia Basin Technical Recovery Team). 2005a. Updated Population Delineation in 

the Interior Columbia Basin. 

ICTRT (Interior Columbia Basin Technical Recovery Team). 2005b. Viability criteria for application to 

interior Columbia basin salmonid ESUs. Northwest Fisheries Science Center, Seattle, Washington, 

July 2005.

ICTRT (Interior Columbia Basin Technical Recovery Team). 2007. Viability criteria for application to 

interior Columbia basin salmonid ESUs. Review draft, 3/1/2007.

ICTRT (Interior Columbia Basin Technical Recovery Team). 2010. Part 5: Status Summary – Snake 

River Fall Chinook Salmon ESU.

IDEQ (Idaho Department of Environmental Quality). 2001. Middle Salmon River-Panther Creek 

Subbasin Assessment and TMDL. Idaho Department of Environmental Quality, Boise, ID. 99 p. + 

Appendices.

IDEQ (Idaho Department of Environmental Quality). 2002. Middle Salmon River-Chamberlain Creek 

Subbasin Assessment and Crooked Creek Total Maximum Daily Load. Idaho Department of 

Environmental Quality, Boise, ID. 99 p. + Appendices.

IDEQ (Idaho Department of Environmental Quality). 2003. Upper Salmon River Subbasin Assessment 

and TMDL. Idaho Department of Environmental Quality, Boise, ID. 99 p. + Appendices.

IDEQ (Idaho Department of Environmental Quality). 2009. Idaho Department of Environmental Quality 

Final 2008 Integrated Report. Boise, ID: Idaho Department of Environmental Quality. 776 p. 
ESA Recovery Plan: Snake River Sockeye Salmon | 390

June 2015| NOAA Fisheries 

IDEQ (Idaho Department of Environmental Quality). 2011. Idaho Department of Environmental Quality 

Final 2010 Integrated Report. Boise, ID: Idaho Department of Environmental Quality. 776 p. 

IDEQ (Idaho Department of Environmental Quality). 2014. Idaho’s 2012 Integrated Report. Boise, ID: 

Idaho Department of Environmental Quality.

IDFG (Idaho Department of Fish and Game). 1959. Fisheries management plan for Stanley, Redfish, 

Little Redfish, Alturas, Perkins, Pettit, and Yellowbelly lakes. Boise, ID. 

IDFG (Idaho Department of Fish and Game). 2010. Springfield sockeye hatchery master plan for the 

snake river sockeye program. Volumes 1 and 2. Boise, ID.

IDFG (Idaho Department of Fish and Game). 2012. Snake river sockeye salmon captive broodstock 

program research element. Annual Progress Report. IDFG Report Number 12-06. Boise, ID.

IDFG (Idaho Department of Fish and Game). 2013a. Map of snake river sockeye salmon spawning 

areas in Redfish Lake prepared by Mike Peterson, IDFG. 

IDFG (Idaho Department of Fish and Game). 2013b. Snake river sockeye slamon step review. Final 

response to ISRP comments identified in document: ISRP 2012-7. Boise, ID.

Peterson, M. K. Plaster, K. Kruse, K. McBaine and C. Kozfkay. In prep. Snake River Sockeye Salmon 

captive broodstock program, research element 2013. IDFG Report. Project No. 200740200. 

Bonneville Power Administration, Annual Report. Portland, OR.

IDWR (Idaho Department of Water Resources). 2013. Water right and adjudication searchable 

database. http://www.idwr.idaho.gov/apps/ExtSearch/WRAJSearch/WRADJSearch.aspx.

Incardona, J., M. G. Carls, H. L. Day, C. A. Sloan, J. L. Bolton, T. K. Collier, and N. L. Scholz. 2009. 

Cardiac arrhythmia is the primary response of embryonic Pacific herring (Clupea pallasi) exposed 

to crude oil during weathering. Environmental Science & Technology, 43(1):201-207.

Irvine, J. R., M. O’Neill, L. Godbout, and J. Schnute. 2013. Effects of smolt release timing and size on 

the survival of hatchery-origin coho salmon in the Strait of Georgia. Progress in Oceanography 

115:111-118.

Isaak, D. J., R. F. Thurow, B. E. Rieman, and J. B. Dunham. 2007. Chinook salmon use of spawning 

patches: relative roles of habitat quality, size, and connectivity. Ecological Applications. 17(2):352-

364.

ISAB (Independent Scientific Advisory Board). 2007. Climate change impacts on columbia river basin 

fish and wildlife. ISAB 2007-2.

ISAB (Independent Scientific Advisory Board). 2008. Non-native species impacts on native salmonids 

in the columbia river basin. ISAB 2007-4.

ISDA (Idaho State Department of Agriculture). 2013. 2012 Sawtooth National Forest Monitoring and 

Evaluation Report, Land and Resource Management Plan. September 2013.

Ishida, Y., T. Azumaya, and M. Fukuwaka, 1999. Summer distribution of fishes and squids caught by 

surface gillnets in the western North Pacific Ocean. Bulletin of Hokkaido National Fisheries 

Research Institute 63:1-18.

ISRP (Independent Scientific Review Panel). 2011. Snake river sockeye springfield hatchery step 2/step 

3 review (Project #200740200). Portland, OR.
ESA Recovery Plan: Snake River Sockeye Salmon | 391

June 2015| NOAA Fisheries 

Jenkins, J. J. 2003. Environmental monitoring of chlorpyrifos and azinphos-methyl dissolved residues in 

Hood River tributaries, Final Report to Hood River Soil and Water Conservation District: Corvallis, 

Oregon State University Agricultural Chemistry Research and Extension, 25 p. 

Jenkins, J. J. and S. Castignoli. 2004. Pesticide Monitoring in Hood River Area Streams. In: Hood River 

Growers and Shippers Association Best Management Practice Areawide II Handbook. 

http://community.gorge.net/hrgsa/table%20of%20contents.htm

Johnson, J. H. 1981. Predation on the eggs of steelhead trout by stream salmonids in a tributary of Lake 

Ontario. Prog. Fish. Cult. 43, 36–37.

Johnson. A., and D. Norton. 2005. Concentrations of 303(d) listed Pesticides, PCBs, and PAHs 

measured with passive samplers deployed in the Lower Columbia River. Washington State 

Department of Ecology Publication No. 05-03-006. Washington Department of Ecology, 

Environmental Assessment Program, Olympia, Washington 98504-7710. 56 pp.

Johnson, J. J., and N. H. Ringler. 1979. Predation on Pacific salmon eggs by salmonids in a tributary of

Lake Ontario. J. Great Lakes Res. 5, 177– 181.

Johnson, L. L., G. M. Ylitalo, C. A. Sloan, B. F. Anulacion, A. N. Kagley, M. R. Arkoosh, T. A. 

Lundrigan, K. Larson, M. D. Siipola, and T. K. Collier. 2007. Persistent organic pollutants in 

outmigrant juvenile chinook salmon from the Lower Columbia Estuary, USA. Science of the Total 

Environment, 374(2007):342-366.

Johnson, L. L., B.A. Anulacion, M. Arkoosh, J. Dietrich, O. P. Olson, C. A. Sloan, S. Y. Sol, J. 

Spromberg, D. Teel, G. Yanagida, and G. M. Ylitalo. 2013. Persistent Organic Pollutants and 

Chinook Salmon Recovery in the Columbia Basin. Trans. Amer. Fish Soc. 142:21-40.

Kalinowski, S. T., D. M. Van Doornik, C. C. Kozfkay, and R. S. Waples. 2012. Genetic diversity in the 

Snake River sockeye salmon captive broodstock program as estimated from broodstock records. 

Conservation Genetics 13:1183–1193.

Kanno, Y. and I. Hamai. 1971. Bull. Fac. Fish., Hokkaido Univ 22(2):107-128.

Karas, N. 1997. Brook Trout. The Lyons Press, New York, New York. 371 pp

Keefer, M. L., C. A. Peery, and M. J. Heinrich. 2008. Temperature-mediated en route migration 

mortality and travel rates of endangered Snake River sockeye salmon. Ecology of Freshwater Fish 

17:136–145.

Killsgaard, T. H., V. Freeman, and J. S. Coffman. 1970. Mineral resources of the Sawtooth Primitive 

Area, Idaho. U.S. Geological Survey, Bulletin 1319-D, Washington, D.C.

Kline, P.A., T. A. Flagg. 2014. Putting the red back in redfish lake, 20 years of progress toward saving 

the pacific northwest’s most endangered salmon population. Fisheries, 39:11, 488-500.

Kohler, A., R. Griswold,and D. Taki. 2000. Snake river sockeye salmon habitat and limnological 

research. Project No. 9107-100, 97 electronic pages, (BPA Report DOE/BP-00004343-3).

Kohler, A., B. Griswold, D. Taki and S. Letzing 2008. Snake River Sockeye Salmon habitat and 

limnological research: 2008 annual progress report. Project no. 199107100. Report to Bonneville 

Power administration. 
ESA Recovery Plan: Snake River Sockeye Salmon | 392

June 2015| NOAA Fisheries 

Kozfkay, C. 2013a. Source of information on native kokanee status in Stanley Lake. Communication 

from C. Kozfkay (IDFG) to R. Furfey RE: IDFG input on Stanley Lake, 2013.

Kozfkay, C. 2013b. Source of information on Alturas Lake adult returns. Communication from C. 

Kozfkay (IDFG) to R. Furfey 2013.

Kozfkay, C. 2013c. Source of information on status of kokanee population in Redfish Lake. 

Communication from C. Kozfkay (IDFG) to R. Furfey RE: IDFG comments on draft Plan. 2013.

Kozfkay C. C., M. R. Campbell, J. A. Heindel, D. J. Baker, P. Kline, M. S. Powell, and T. Flagg. 2007. 

A genetic evaluation of relatedness for broodstock management of captive, endangered Snake River 

sockeye salmon, Oncorhynchus nerka. Conservation Genetics. DOI 10.1007/s10592-007-9466-0

Lance M. M. and W. W. Thompson. 2005. Overlap in diets and foraging of common murres (Uria aalge) 

and rhinocerous auklets (Cerorhinca monocerata) after the breeding season. The Auk 122(3):887-

901.

LCFRB (Lower Columbia Fish Recovery Board). 2004. Lower Columbia Salmon Recovery and Fish & 

Wildlife Subbasin Plan; Volume II – Subbasin Plan, Chapter A – Columbia Estuary Mainstem. 

Watershed Management Plan. Lower Columbia Fish Recovery Board, Longview, Washington, 

December 15, 2004.

LCREP (Lower Columbia River Estuary Partnership). 2006. Lower columbia river plan comprehensive 

conservation and managemnet Plan. Portland, OR. 

LCREP (Lower Columbia River Estuary Partnership). 2007. Lower Columbia River Estuary 

Ecosystem Monitoring: Water Quality and Salmon Sampling Report. Prepared by the Lower 

Columbia River Estuary Partnership, Portland, OR. 76 pp. 

LeBrasseur, R. 1966. Stomach contents of salmon and steelhead trout in the Northeastern Pacific 

Ocean. Journal of the Fisheries Research Board of Canada 23(1):85-100.

Lee, K. N. 1993. Compass and gyroscope: integrating science and politics for the environment. Island 

Press. Washington, D.C.

Lemly, A. D. 1996. Assessing The Toxic Threat Of Selenium To Fish And Aquatic Birds. 

Environmental Monitoring and Assessment 43: 19-35, 1996.

Lemly, A.D. 2002. Selenium Assessment in Aquatic Ecosystems: A Guide for Hazard Evaluation and 

Water Quality Criteria. Springer-Verlag, New York. 161p. 

Lewis, B., D. Taki and R.G. Griswold. 1998. Snake river sockeye salmon habitat and limnological 

research. Annual report 1998. United States Edpartment of Energy, Bonneville Power 

Administration, Enivronment, Fish and Wildlife. Portland, Oregon. Project Number 91-71, 

DOE/BP-22548-7.

Luce, C. H., and Z. A. Holden. 2009. Declining annual streamflow distributions in the Pacific Northwest 

United States, 1948–2006, Geophys. Res. Lett., 36, L16401, doi:10.1029/2009GL039407.

MacFarlane, B. 2010. Energy dynamics and growth of Chinook salmon (Oncorhynchus tshawytscha) 

from the Central Valley of California during the estuarine phase and first ocean year. Canadian 

Journal of Fisheries and Aquatic Sciences 67:1549-1565.
ESA Recovery Plan: Snake River Sockeye Salmon | 393

June 2015| NOAA Fisheries 

Makaryan, S., M. Drews, E. L. Jessup, and K. Casavant. 2005. Waterborne Commerce on the 

Columbia/Snake Waterway: Commodity Movements Up/Down River 1995 – 2003. SFTA Research 

Report # 14, September 2005

Mantua, N., I. Tohver, and A. Hamlet. 2009. Impacts of climate change on key aspects of freshwater 

salmon habitat in Washington State, Chapter 6, pp. 217-254. In: M. McGuire Elsner, J. Littell, and 

L. Whitely Binder (eds.), The Washington Climate Change Impacts Assessment. Center for Science 

in the Earth System, Joint Institute for the Study of the Atmosphere and Oceans, University of 

Washington, Seattle, Washington.

McCarthy, K. A. and R. W. Gale. 2001. Evaluation of persistent hydrophobic organic compounds in 

the Columbia River Basin using semipermeable-membrane devices. Hydrological Processes 

15:1271-1283. 

McClure, M. M., E. E. Holmes, B. L. Sanderson, and C. E. Jordan. 2003. A large-scale, multispecies 

status assessment: anadromous salmonids in the Columbia River basin. Ecological Applications 

13:964–989,

McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C.Wainwright, and E. P. Bjorkstedt. 2000. Viable 

salmonid populations and the recovery of evolutionarily significant units. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-42,156 p.

McKenzie, J. and K. M. Wynne. 2008. Spatial and temporal variation in the diet of Steller sea lions in 

the Kodiak Archipelago, 199 to 2005. Marine Ecology Progress Series Vol 360:265-283.

McMichael, G. A., R. A. Harnish, J. R. Skalski, K. A. Deters, K. D. Ham, R. L. Townsend, P. S. Titzler, 

M. S. Hughes, J. Kim, and D. M. Trott. 2011. Migratory behavior and survival of juvenile 

salmonids in the lower Columbia River, estuary, and plume in 2010. PNNL-20443. Pacific 

Northwest National Laboratory, Richland, Washington, September 2011.

Meador, J. P., T. K. Collier and J. E. Stein. 2002. Use of tissue and sediment-based threshold 

concentrations of polychlorinated biphenyls (PCBs) to protect juvenile salmonids listed under the 

US Endangered Species Act. Aquatic Conservation 12: 493–516.

Meador, J. P., J. Buzms and C. E. Bravo. 2008. Using fluorescent aromatic compounds in bile from 

juvenile salmonids to predict exposure to polycyclic aromatic hydrocarbons. Environmental 

Toxicology and Chemistry 27(4): 845-853.

Mebane, C. A. and D. L. Arthaud. 2010. Extrapolating growth reductions in fish to changes in 

population extinction risks: copper and Chinook salmon. Human and Ecological Risk Assessment 

16: 1026-1065.

Miller, J. A., D. J. Teel, A. M. Baptista, and C. A. Morgan. 2013. Disentangling bottom-up and topdown effects on survival during early ocean residence in a population of Chinook salmon 

(Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 70:617- 629.

Monan, G. 1991. Genetic analysis of O. nerka. Memo to Merritt Tuttle for inclusion in ESA 

Administrative Record for sockeye salmon, February 1991, 8 p. NMFS Environmental and 

Technical Services Division, Portland, Oregon. 
ESA Recovery Plan: Snake River Sockeye Salmon | 394

June 2015| NOAA Fisheries 

Moore, M. E., B. A. Berejikian, and E. P. Tezak. 2010. Early marine survival and behavior of steelhead 

smolts through Hood Canal and the Strait of Juan de Fuca. Transactions of the American Fisheries 

Society 139:41-61.

Morace, J. L. 2006. Water-quality data, Columbia River Estuary, 2004-2005. U.S. Geological Survey 

Data Series 213.

Morace, J. L. 2012. Reconnaissance of contaminants in selected wastewater-treatment-plant effluent 

and stormwater runoff entering the Columbia River, Columbia River Basin, Washington, and 

Oregon, 2008-2010. U.S. Geological Survey Scientific Investigations Reports 2012-5068, 68 pp. 

Mortensen, D., A. Wertheimer, S. Taylor, and J. Landingham. 2000. The relation between early marine 

growth of pink salmon, Oncorhynchus gorbuscha, and marine water temperature, secondary 

production, and survival to adulthood. Fish Bulletin 98:319-335.

Moss J. H., D. A. Beauchamp, A. D. Cross, D. W. Myers, E. V. Farley, et al. 2005. Evidence for sizeselective mortality after the first summer of ocean growth by pink salmon. Transactions of the 

American Fisheries Society 134:1313–1322.

Mote, P. W., and E. P. Salathe, Jr. 2009. Future climate in the Pacific Northwest. In: Washington 

Climate Change Impacts Assessment: Evaluating Washington’s future in a changing climate. 

Climate Impacts Group, University of Washington, Seattle, Washington, 6/1/2009.

Mote, P. W., A. F. Hamlet, M. P. Clark, and D. P. Lettenmaier. 2005. Declining mountain snowpack in 

western North America, Bull. Am. Meteorol. Soc., 86, 39–49.

Mote, P. W., D. Gavin, and A. Huyer. 2010. Climate change in Oregon’s land and marine 

environments.Pages 1–45 in K.D. Dello and P.W. Mote (editors). Oregon climate assessment 

report. Oregon Climate Change Research Institute, College of Oceanic and Atmospheric Sciences, 

Oregon State University, Corvallis, Oregon, December 2010. 

Moulton, Mark. Sawtooth National Recreation Area. Personal communication.

Mueter, F. J., R. M. Peterman, and B. J. Pyper. (2002) Opposite effects of ocean temperature on survival 

rates of 120 stocks of Pacific salmon (Oncorhynchus spp.) in northern and southern areas. Can. J. 

Fish. Aquat. Sci., 59, 456-463.

Munther, G. 1974. Fishery effects of irrigation diversion and related structures in the Sawtooth National 

Recreation Area - progress report 1: U.S. Forest Service, 68 p.

Myers K. W., R. V. Walker, N. D. Davis, K. Y. Aydin, S-Y Hyun, R. W. Hilborn, and R. L. Burgner. 

1999. Migrations, abundance and origins of salmonids in offshore waters of the North Pacific, 

1999. UW, Fisheries Research Institute, FRI-UW-9999. 125pp.

Nagasawa, K. 1998. Predation by salmon sharks (Lamna ditropis) on Pacific salmon (Oncorhynchus 

spp.) in the North Pacific Ocean. Bulletin North Pacific Anadromous Fish commission 1:419-433.

Nelle, R. D. 1999. Smallmouth bass predation on juvenile fall chinook salmon in the hells canyon reach 

of the snake river, ID. Master's Thesis, University of Idaho, Moscow, ID.

NMFS (National Marine Fisheries Service). 1991. Endangered and threatened species; endangered 

status for Snake River sockeye salmon. Federal Register 56(224):58619-58624, 11/20/1991.
ESA Recovery Plan: Snake River Sockeye Salmon | 395

June 2015| NOAA Fisheries 

NMFS (National Marine Fisheries Service). 1993. Designated critical habitat; Snake River sockeye 

salmon, Snake River spring/summer chinook salmon, and Snake River fall chinook salmon. Final 

Rule. Federal Register 58(247):68543-68554, 12/28/1993.

NMFS (National Marine Fisheries Service). 1996. Interim endangered and threatened species recovery 

planning guidance vVersion 1.3. Silver Spring, MD. 

NMFS (National Marine Fisheries Service) 1999a. Endangered and threatened species: threatened status 

for two ESUs of chum salmon in Washington and Oregon, for two ESUs of steelhead in 

Washington and Oregon and for Ozette Lake sockeye salmon in Washington. Federal Register 

64(57):14508-14517, 3/25/1999.

NMFS (National Marine Fisheries Service). 1999b. Designated critical habitat: revision of critical 

habitat for Snake River spring/summer chinook salmon. Federal Register 64(205):57399-57403, 

10/25/1999.

NMFS (National Marine Fisheries Service). 2000. Endangered and Threatened Species: Final Rule 

Governing Take of 14 Threatened Salmon and Steelhead Evolutionarily Significant Units (ESUs). 

Federal Register 65 (132): 42422-42481, 7/10/2000.

NMFS (National Marine Fisheries Service). 2004. Endangered Species Act - Section 7 Consultation, 

Biological Opinion, Consultation on Remand for Operation of the Columbia River Power System 

and 19 Bureau of Reclamation Projects in the Columbia Basin (Revised and reissued pursuant to 

court order, NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon). National Marine Fisheries 

Service, Portland, Oregon, 11/30/2004.

NMFS (National Marine Fisheries Service). 2005. Endangered and Threatened Species: Final Listing 

Determinations for 16 ESUs of West Coast salmon, and Final 4(d) Protective Regulations for 

Threatened Salmonid ESUs. Final Rule. Federal Register 70 (123): 37160-37204, 6/28/2005.

NMFS (National Marine Fisheries Service). 2005b. Endangered and Threatened Species; Designation of 

Critical Habitat for 12 Evolutionarily Significant Units of West Coast Salmon and Steelhead in 

Washington, Oregon, and Idaho. Final Rule. Federal Register 70 (170): 52630-52683, 9/2/2005.

NMFS (National Marine Fisheries Service). 2005c. Policy on the consideration of hatchery-origin fish in 

Endangered Species Act listing determinations for Pacific salmon and steelhead. Federal Register 

70:37204-37216, 6/28/2005.

NMFS (National Marine Fisheries Service). 2006. Endangered and Threatened Species: Final listing 

determinations for 10 Distinct Population Segments of West Coast steelhead. Final rule. Federal 

Register 71(3): 834-862, 1/5/2006.

NMFS (National Marine Fisheries Service). 2008a. Recovery Plan Module: Mainstem Columbia River 

Hydropower Projects. September 24, 2008.

NMFS (National Marine Fisheries Service). 2008b. Supplemental comprehensive analysis of the Federal 

Columbia River Power System and mainstem effects of the Upper Snake and other tributary 

actions. National Marine Fisheries Service, Portland, Oregon, 5/5/2008.

NMFS (National Marine Fisheries Service). 2008c. Endangered Species Act - Section 7(a)(2) 

Consultation, Biological Opinion and Magnuson-Stevens Fishery Conservation and Management 

Act Essential Fish Habitat Consultation. Consultation on remand for operation of the Federal 
ESA Recovery Plan: Snake River Sockeye Salmon | 396

June 2015| NOAA Fisheries 

Columbia River Power System, 11 Bureau of Reclamation Projects in the Columbia Basin and ESA 

Section 10(a)(1)(A) Permit for Juvenile Fish Transportation Program (Revised and reissued 

pursuant to court order, NWF v. NMFS, Civ. No. CV 01-640-RE (D. Oregon)). National Marine 

Fisheries Service, Portland, Oregon, 5/5/2008.

NMFS (National Marine Fisheries Service). 2008d. Endangered Species Act section 7 consultation: 

biological opinion on Environmental Protection Agency registration of pesticides containing 

chlorpyrifos, diazinon, and malathion (Biological Opinion). Silver Spring, Maryland: U.S. 

Department of Commerce.

NMFS (National Marine Fisheries Service). 2008e. Endangered Species Act - Section 7 Consultation 

Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential 

Fish Habitat Consultation: consultation on treaty Indian and non-Indian fisheries in the Columbia 

River basin subject to the 2008-2017 U.S. v. Oregon Management Agreement. NMFS, Portland, 

Oregon, 5/5/2008

NMFS (National Marine Fisheries Service). 2009. NMFS Endangered Species Act Section 7 

Consultation, Biological Opinion: Environmental Protection Agency Registration of Pesticides 

Containing Carbaryl, Carbofuran, and Methomyl. Washington, D.C.: U.S. Department of 

Commerce.

NMFS (National Marine Fisheries Service). 2010a. NMFS Endangered Species Act Section 7 

Consultation, Biological Opinion: Environmental Protection Agency registration of pesticides 

containing azinphos methyl, bensulide, dimethoate, disulfoton, ethoprop, fenamiphos, naled, 

methamidophos, methidathion, methyl parathion, phorate and phosmet. Washington, D.C.: U.S. 

Department of Commerce.

NMFS (National Marine Fisheries Service). 2010b. Endangered Species Act Section 7(a)(2) 

Consultation, Supplemental Biological Opinion on Remand for Operation of the Federal Columbia 

River Power System, 11 Bureau of Reclamation Projects in the Columbia Basin and ESA Section 

10(a)(1)(A) Permit for Juvenile Fish Transportation Program. National Marine Fisheries Service, 

Portland, Oregon, 5/20/2010.

NMFS (National Marine Fisheries Service). 2011a. Columbia River Estuary ESA Recovery Plan 

Module for Salmon and Steelhead. NMFS Northwest Region. Portland, OR. Prepared for NMFS by 

the Lower Columbia River Estuary artnership (contractor) and PC Trask & Associates, Inc. 

(subcontractor). January 2011.

NMFS (National Marine Fisheries Services). 2011b. 5-Year Review: summary & evaluation of Snake 

River sockeye, Snake River spring-summer Chinook, Snake River fall-run Chinook, Snake River 

basin steelhead. National Marine Fisheries Service, Portland, Oregon.

NMFS (National Marine Fisheries Service). 2011c. Endangered Species Act – Section 7 Consultation 

Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential 

Fish Habitat Consultation. Consultation on Fisheries Management and Evaluation Plan for IDFG 

Recreational Fisheries for Spring/Summer Chinook Salmon. October 19, 2011.

NMFS (National Marine Fisheries Service). 2011d. National Marine Fisheries Service Endangered 

Species Act Section 7 Consultation Biological Opinion: Environmental Protection Agency 

Registration of Pesticides 2,4-D, Triclopyr BEE, Diuron, Linuron, Captan, and Chlorothalonil. 

Washington, D.C.: U.S. Department of Commerce.
ESA Recovery Plan: Snake River Sockeye Salmon | 397

June 2015| NOAA Fisheries 

NMFS (National Marine Fisheries Service). 2012a. National Marine Fisheries Service Endangered 

Species Act Section 7 Consultation Final Biological Opinion for the Environmental Protection 

Agency's Proposed Approval of Certain Oregon Administrative Rules Related to Revised Water 

Quality Criteria for Toxic Pollutants. Washington, D.C.: U.S. Department of Commerce.

NMFS (National Marine Fisheries Service). 2012b. Endangered Species Act (ESA) Section 7(a)(2) 

Biological Opinion, Section 7(a)(2) Not Likely to Adversely Affect Determination, and MagnusonStevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation 

Snake River Sockeye Salmon Hatchery Program. NMFS Consultation Number: NWR-2013-10541

NMFS (National Marine Fisheries Service). 2013. Endangered Species Act – Section 7 Consultation 

Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential 

Fish Habitat Consultation. Consultation on the Effects of the Shoshone-Bannock Tribes' Tribal 

Resource Management Plan on Snake River Chinook Salmon and Steelhead Species Listed Under 

the Endangered Species Act.

NMFS (National Marine Fisheries Service). 2014a. Supplemental recovery plan module for snake river 

salmon and steelhead mainstem columbia river hydropower projects. Portland, OR.

NMFS (National Marine Fisheries Service). 2014b. Harvest module for the snake river sockeye 

recovery plan. Portland, OR.

NMFS (National Marine Fisheries Service). 2014c. Endangered Species Act - Section 7(a)(2) 

Consultation, Supplemental Biological Opinion. Consultation on remand for operation of the 

Federal Columbia River Power System. National Marine Fisheries Service, Portland, Oregon, 

January 17, 2014.

NMFS (National Marine Fisheries Service). 2014d. National Marine Fisheries Service Endangered 

Species Act Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and 

Management Act Essential Fish Habitat (EFH) Consultation: Idaho Water Quality Standards for 

Toxic Substances. Washington, D.C.: U.S. Department of Commerce.

NPCC (Northwest Power and Conservation Council). 2004. Salmon Subbasin Management Plan. 

Written by Ecovista, Contracted by Nez Perce Tribe Watershed Division and Shoshone-Bannock 

Tribes 

NPCC (Northwest Power and Conservation Council). 2004. Lower Snake Mainstream Subbasin Plan. 

May 2004 Version,. Submitted by Pomeroy Conservation District. 

NWFSC (Northwest Fishieries Science Center). 2011. ESU and population data. 

Ogi, H. and T. Tsujita. 1973. Preliminary examination of stomach contents of murres (Uria spp.) from 

the eastern Bering Sea and Bristol bay, June-August, 1970 and 1971. J. Ecol. 23(5):201-209.

Paquet, P. J., T. Flagg, A. Appleby, J. Barr, L. Blankenship, D. Campton, M. Delarm, T. Evelyn, D. 

Fast, J. Gislason, P. Kline, D. Maynard, L. Mobrand, G. Nandor, P. Seidel, and S. Smith. 2011. 

Hatcheries, conservation, and sustainable fisheries – achieving multiple goals: results of the 

Hatchery Scientific Review Group’s Columbia River Basin review. Fisheries 36:11, 547-561
ESA Recovery Plan: Snake River Sockeye Salmon | 398

June 2015| NOAA Fisheries 

Pelenev, D., A. Orlov, and N. Klovach. 2008. Predator-prey relations between the Pacific lamprey 

Lampetra tridentate and Pacific salmon (Oncorhynchus spp). NPAFC Doc 1097. 4 pp.

Peterson, M. 2013a. Source of information on trout stocking in Pettit Lake. Communication from M. 

Peterson (IDFG) to R. Furfey RE: IDFG input on status of fish species in Sawtooth Valley lakes, 

2013.

Peterson, M. 2013b. Source of information on introduction of non-native species in the lower Salmon 

River. Communication from M. Peterson (IDFG) to R. Furfey RE: IDFG comments on draft Plan. 

2013.

Peterson, M. 2013c. Source of information about species that prey in sockeye salmon. Communication 

from M. Peterson (IDFG) to R. Furfey RE: IDFG comments on draft Plan. 2013.

Peterson, W. T., R. Brodeur, and W. G. Pearcy. 1982. Diets of juvenile salmon in the Oregon upwelling 

zone in June 1979. Fishery Bulletin U.S. 80:841-851.

Peterson, M. K. Plaster, L. Redfield, and J. Heindel. 2010. Snake River Sockeye Salmon captive 

broodstock program: Research element. Annual Progress Report: January 1 2008-December 31 

2008. IDFG Rept. #10-08. Prepared for Bonneville Power Administration.

Peterson, M., K. Plaster, Z. Klein, K. McBaine, and J. Heindel. 2011. Snake River sockeye salmon 

captive broodstock program: Research Element. Annual Progress Report: January 1, 2010 –

December 31, 2010. IDFG Report # 11-05. Prepared for the Bonneville Power Administration.

Peterson, W. T., C. A. Morgan, J. O. Peterson, J. L. Fisher, B. J. Burke, and K. Fresh. 2012. Ocean 

ecosystem indicators of salmon and marine survival in the Northern California Current. Northwest 

Fisheries Science Center, Seattle, Washington, 12/1/2012.

Peterson, M., K. Plaster, K. Kruse, K. McBaine, and C. Kozfkay. 2013. Snake River Sockeye Salmon 

Captive Broodstock Program: Research Element, 1/1/2011 - 12/31/2011 Annual Report, 2007-402-

00. IDFG, Nampa, ID to BPA, Portland, OR.

Poe, T. P., H. C. Hansel, S. Vigg, D. E. Palmer, and L. A. Prendergast. 1991. Feeding of predaceous 

fishes on out-migrating juvenile salmonids in the John Day Reservoir, Columbia River. 

Transactions of the American Fisheries Society 120:405–420.

Porter, R. 2011. Report on the predation index, predator control fisheries and program evaluation for the 

Columbia River basin experimental northern pikeminnow management program. 2011 Annual 

Report. Prepared by Pacific States Marine Fisheries Commission in Cooperation with Oregon 

Department of Fish and Wildlife Washington Department of Fish and Wildlife for Bonneville 

Power Administration, Portland, Oregon.

Powell, M. S., R. W. Hardy, T. A. Flagg, and P. A. Kline. 2010. Proximate composition of fatty acid 

differences in hatchery-reared and wild Snake River sockeye salmon overwintering in nursery 

lakes. North American Journal of Fisheries Management 30:530-537.

Pyper, B. J., and R. M. Peterman. 1999. Relationship among adult body length, abundance, and ocean 

temperature for British Columbia and Alaska sockeye salmon (Oncorhynchus nerka), 1967-1997. 

Canadian Journal of Fisheries and Aquatic Sciences.56:1716-1720.

Quinn, T. P. 2005. The behavior and ecology of Pacific salmon and trout. American Fisheries Society.
ESA Recovery Plan: Snake River Sockeye Salmon | 399

June 2015| NOAA Fisheries 

Rand, P.S., Berejikian, B.A., Pearsons, T.N., and Noakes, D.L.G. 2012. Ecological interactions between 

wild and hatchery salmonids: an introduction to the special issue. Environmental Biology of 

Fishes 94(1):1-6.

Regonda, S. K., B. Rajagopalan, M. Clark, and J. Pitlick. 2005. Seasonal cycle shifts in 

hydroclimatology over the western United States, J. Clim., 18, 372–384.

Rember, J. 2003. Traplines: Coming Home to Sawtooth Valley. Pantheon Book, New York. 237 pp.

Rich, H. B. , T. P. Quinn, M. Scheuerell, and D. E. Schindler. 2009. Climate and intraspecific 

competition control the growth and life history of juvenile sockeye salmon (Oncorhynchus nerka) 

in Iliamna Lake, Alaska. Canadian Journal of Fisheries and Aquatic Sciences, 66(2):238-246.

Ricker, W. E. 1938. “Residual” and kokanee salmon in Cultus Lake. Journal of the Fisheries Research 

Board of Canada 4:192–217.

Ricker, W. E. 1975. The relation between stock and recruitment, Section 11.5, pp. 280-296. In: 

Computation and interpretation of biological statistics of fish populations. Bulletin 191. Fisheries 

Research Board of Canada, Ottowa, Ontario .

Rieman, B. E. and D. L. Myers. 1992. Influence of fish density and relative productivity on growth of 

Kokanee in Ten Oligotrophic Lakes and Reservoirs in Idaho. Transactions of the American 

Fisheries Society 121. 2:178-191.

Rieman, B. E., D. L. Myers, and R. L. Nielsen. 1994. Use of otolith microchemistry to discriminate 

Oncorhynchus nerka of resident and anadromous origin. Canadian Journal of Fisheries and Aquatic 

Sciences 51: 68-77. 

Robichaud, P.R. 2000. Fire effects on infiltration rates after prescribed fire in Northern Rocky 

Mountain forests, USA. Journal of Hydrology 231-232: 220-229

Roby, D. D., and coauthors. 2012. Research, Monitoring, and Evaluation of Avian Predation on 

Salmonid Smolts in the Lower and Mid-Columbia River Final 2011 Annual Report. Prepared by 

US Geologic Survey - Oregon Cooperative F&W Research Unit, Real Time Research, Oregon State 

University, NWFSC, and PSMFC for BPA, Portland, OR.

Roegner, G. C., R. A. McNatt, D. J. Teel, and D. L. Bottom. 2012. Distribution, size, and origin of 

juvenile Chinook salmon in shallow water habitats of the lower Columbia River and estuary, 2002-

2007. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science, 4(1):450-

472.

Roni, P., T. J. Beechie, R. E. Bilby, F. E. Leonetti, M. M. Pollock, and G. R. Pess. 2002. A review of 

stream restoration techniques and a hierarchical strategy for prioritizing restoration in Pacific 

Northwest watersheds. North American Journal of Fisheries Management 22:1–20.

Roni, P., K. Hanson, T. Beechie, G. Pess, M. Pollock, and D. M. Bartley. 2005. Habitat rehabilitation 

for inland fisheries. Global review of effectiveness and guidance for rehabilitation of freshwater 

ecosystems. FAO Fisheries Technical Paper. No 484, 116 p, Rome, Italy. 

Roni, P., K. Hanson, and T. Beechie. 2008. Global review of the physical and biological effectiveness of 

stream habitat rehabilitation techniques. North American Journal of Fisheries Management 28:856–

890.
ESA Recovery Plan: Snake River Sockeye Salmon | 400

June 2015| NOAA Fisheries 

Rothwell, E. 2009. Consumptive water use of irrigated agriculture in the Lemhi, Salmon, and Snake 

Rivers. National Marine Fisheries Service, Idaho Habitat Office. Boise, Idaho.

Rothwell, E. and M. Moulton. 2001. Influence to stream temperatures from diversions. 2001 

Monitoring Report. Sawtooth National Recreation Area. Ketchum, Idaho.

Ruggerone, G. T. and J. L. Nielsen. 2004. Evidence for competitive dominance of Pink salmon 

(Oncorhynchus gorbuscha) over other Salmonids in the North Pacific Ocean. Reviews in Fish 

Biology and Fisheries 14(3):371-390.

Ruggerone, G. T., E. Farley, J. Nielsen, and P. Hagen. 2005. Seasonal marine growth of Bristol Bay 

sockeye salmon (Oncorhynchus nerka) in relation to competition with Asian pink salmon (O. 

gorbuscha) and the 1077 ocean regime shift. Fishery Bulletin 103(2):355-370.

Salathe, E. P., L. R. Leung, Y. Qian, and Y. Zhang. 2009. Regional climate model projections for the 

state of washington for Chapter 2 in: Littell, J.S., M.M. Elsner, L.C. Whitely and AlL. Snover 

(eds). The Washington Climate Change Impacts Assessment: Evaluating Washington's Future in a 

Changing Climaite. Climate Impacts Group, U. of Washington, Seattle, WA.

Sandahl, J. F., D. H. Baldwin, J. J. Jenkins, and N. L. Scholz. 2007. A sensory system at the interface 

between urban stormwater runnoff and salmon survival. Environmental Science & Technology, 

41:2998-3004.

Sanderson, B. L., K. A. Barnas and A. M. Wargo Rub. 2009. Non-indigenous Species of the Pacific 

Northwest: An Overlooked Risk to Endangered Salmon? Bioscience 59(3): 245-256, 3/1/2009.

Sandvik, P. 2010. Washington State Toxics Monitoring Program: Trends Monitoring for Chlorinated 

Pesticides, PCBs, PAHs, and PBDEs in Washington Rivers and Lakes, 2008. Washington State 

Department of Ecology, Olympia, WA. Publication No. 10-03-027. 

www.ecy.wa.gov/biblio/1003027.html. 

Savinykh, V. F. and I. I. Glebov. 2003. The effects of predation of the daggertooth Anotopterus 

nikparini (Anotopteridae) on Pacific salmons. Journal of Ichthyology. 43(8):625-634.

Seiders, K. and C. Deligeannis. 2009. Washington State Toxics Monitoring Program: Freshwater Fish 

Tissue Component, 2008. Washington State Department of Ecology Publication No. 09-03-055. 

Olympia, Washington. 71 pp.

Seiders, K., C. Deligeannis, and P. Sandvik, 2007. Washington State Toxics Monitoring Program: 

Contaminants in fish tissue from freshwater environments in 2004 and 2005. Environmental 

Assessment Program, Washington State Department of Ecology. Publication No. 07-03-024. 

Olympia, Washington 98504-7710. 35 p. 

Seiders, K., C. Deligeannis, and M. Freise. 2011. Focus on Fish Testing: Snake River Fish Tested for 

Chemicals. Washington State Department of Ecology Publication No. 11-03-067. December 2011. 

Olympia, WA. 6 pp.

Selbie, D. T., B. A. Lewis, J. P. Smol, and B. P. Finney. 2007. Long-Term Population Dynamics of the 

Endangered Snake River Sockeye Salmon: Evidence of Past Influences on Stock Decline and 

Impediments to Recovery. Transactions of the American Fisheries Society 136:800–821.
ESA Recovery Plan: Snake River Sockeye Salmon | 401

June 2015| NOAA Fisheries 

Sethajintanin, D., E. R. Johnson, B. R. Loper, and K. A. Anderson. 2004. Bioaccumulation profiles of 

chemical contaminants in fish from the lower Willamette River, Portland Harbor, Oregon. 

Archives of Environmental Contamination and Toxicology 46:114-123. 

Shively, R. S., R. A. Tabor, R. D. Nelle, D. B. Jepsen, J. H. Petersen, S. T. Sauter, and T. P. Poe. 1991. 

System-wide significance of predation on juvenile salmonids in the Columbia and Snake river 

reservoirs. U. S. Fish and Wildlife Service, National Fishery Research Center, Columbia River 

Field Station. Annual Report for Bonneville Power Administration, Portland, Oregon (Project 

Number 90-078).

Shortreed, K. S., J. M. B. Hume, and J. G. Stockner. 2000. Using photosynthetic rates to estimate the 

juvenile sockeye salmon rearing capacity of British Columbia lakes. Pages 505-521 in: E. E. 

Knudsen, C. R. Steward, D. D. MacDonald, J. E. Williams, and D. W. Reiser, editors. Sustainable 

fisheries management; Pacific salmon. Lewis Publishers, New York, N.Y.

Sigler, W. F. andigler, J. W. 1987. Fishes of the Great Basin. Reno, NV: University of Nevada Press.

Sloan, C. A., B. F. Anulacion, J. L. Bolton, D. Boyd, O. P. Olson, S. Y. Sol, G. M. Ylitalo, and L. L. 

Johnson. 2010. Polybrominated Diphenyl Ethers In Outmigrant Juvenile Chinook Salmon From 

The Lower Columbia River And Estuary And Puget Sound, WA. Archives of Environmental 

Contamination and Toxicology, 58:403-414. 

SNF (Sawtooth National Forest). 2006. Biological Assessment of Effects of Ongoing and Proposed 

Federal Actions on the Sawtooth Valley Subpopulation of listed Snake River Sockeye, Snake River 

Spring/Summer Chinook Salmon, Snake River Steelhead, and Columbia River Bull Trout and 

sensitive Westslope Cutthroat Trout. Sawtooth National Recreation Area. July 26, 2006.

SNF (Sawtooth National Forest). 2012. Biological assessment and biological evaluation of effects from 

noxious and invasive weed management programs on fish, terrestrial wildlife and rare plant species. 

351 pp.

Spaulding, S. 1993. Snake river sockeye salmon (oncorhynchus nerka) Habitat/limnologic research. 

Annual report 1992. Shoshone-Bannock Tribes, Fort Hall, Idaho. Prepared for U.S. Department of 

Energy, Bonneville Power Administration, Division of Fish and Wildlife, Portland, OR, Project # 

91-71, Contract DE-BI79-91BP22548.

Stanley, S., J. Brown, and S. Grigsby. 2005. Protecting Aquatic Ecosystems: A Guide for Puget Sound 

Planners to Understand Watershed Processes. Washington State Department of Ecology. 

Publication #05‐06‐027. Olympia, WA.

Stehr, C. M., T. L. Linbo, D. H. Baldwin, N. L. Scholz, and J. Incardona. 2009. Evaluating the effects of 

forestry herbicides on fish development using rapid phenotypic screens. North American Journal of 

Fisheries Management, 29:975-984.

Steinhart, G.B. and W. Wurtsbaugh. 2003. Winter ecology of kokanee: implications for salmon 

management. Transactions of the American Fisheries Society, Vol 132, Issue 6.

Steinhart, G., H. P.Gross, P. Budy, C. Luecke, and W. Wuttsbaugh. 1993. Limnological investigations 

and hydroacoustic surveys of Sawtooth Valley Lakes. In Snake River Sockeye Salmon Habitat and 

Limnological Research. U.S. Department of Energy, Bonneville Administration, Division of Fish 

and Wildlife, (9 l-7 1).
ESA Recovery Plan: Snake River Sockeye Salmon | 402

June 2015| NOAA Fisheries 

Stewart, I. T., D. R. Cayan, and M. D. Dettinger. 2005. Changes toward earlier streamflow timing across 

western North America, J. Clim., 18, 1136–1155.

Sturdevant, M. V., M. F. Sigler, and J. A. Orsi. 2009. Sablefish predation on juvenile Pacific salmon in 

the coastal marine waters of Southeast Alaska in 1999. Transactions of the American Fisheries 

Society 138(3):675-691.

Sviridov, V.V., I. I. Glebov, M. A. Ocheretyanny, and V. V. Izvestiya. 2004. Traumatization and 

infestation of Pacific salmon in the western Bering Sea and adjacent waters in summer-autumn 

period of 2003. Transactions of the Pacific Research Fisheries Centre 138:84-96.

Taki, D., B. Lewis, and R. Griswold. 1999. Salmon River sockeye salmon habitat and limnological 

research: 1997 annual progress report. U.S. Department of Energy, Bonneville Power 

Administration, Portland, OR. Project number 91-71.

Taki, D., A. E. Kohler, R. G. Griswold, et al. 2006. Snake River sockeye salmon habitat and 

limnological research: 2005 annual progress report. Prepared for Bonneville Power Administration, 

Portland, Oregon, 7/1/2006.

Tear, T. H., P. Kareiva, P. L. Angermeier, P. Comer, B. Czech, R. Kautz, L. Landon, D. Mehlman, K. 

Murphy, M. Ruckelshaus, J. M. Scott, and G. Wilhere. 2005. How much is enough? The recurrent 

problem of setting measurable objectives in conservation. Bioscience 55:835-849.

Temple, W. B. and H. M. Johnson. 2011. Occurrence and distribution of pesticides in surface waters of 

the Hood River basin, Oregon, 1999–2009: U.S. Geological Survey Scientific Investigations Report 

2011–5082, 84 p.

TetraTech Inc. 1996. Lower Columbia River Bi-State Program- The Health of the River, 1990-1996. 

Integrated Technical Report 0253-01. Prepared for Oregon Department of Environmental Quality 

and Washington Department of Ecology.

Teuscher, D. 1999. Federal Aid in Fish Restoration. Grant F-73-R-21, Hatchery trout evaluations, Job 

Performance Report, Subproject #2: Zooplankton Quality Index. Idaho Department of Fish and 

Game, Boise. 

Thackray, G. D., K. A. Lundeen, and J. A. Borgert. 2004. Latest Pleistocene alpine glacier advances in 

the Sawtooth Mountains, Idaho, USA: Reflections of midlatitude moisture transport at the close of 

the last glaciation: Geology, v. 32; no. 3; p. 225-228; doi: 10.1130/G20174.1

Thomson, R. E., R. J. Beamish, T. D. Beacham, M. Trudel, P. H. Whitfield, and R. A. S. Hourston. 

2012. Anomalous ocean conditions may explain the recent extreme variability in Fraser River 

sockeye salmon production. Marine and Coastal Fisheries: Dynamics, Management, and 

Ecosystem Science 4:415-437.

Tinus, E. S. and R. C. Beamesderfer. 1994. An update on the distribution, fisheries, and biology of 

walleye in the lower Columbia River. Oregon Dept. of Fish and Wildlife Information Report 94-3.

Tomaro, L. M., D. J. Teel, W. T. Peterson, and J. M. Miller. 2012. When is bigger better? Early marine 

residence of middle and upper Columbia River spring Chinook salmon. Marine Ecology Progress 

Series 452:237-252.

Tucker, S., M. Trudel, D. W. Welch, J. R. Candy, J.F. T. Morris, M.E. Thiess, C. Wallace, D. J. Teel, 

W. Crawford, E. V. Farley Jr., and T. D. Beacham. 2009. Seasonal stock specific migrations of 
ESA Recovery Plan: Snake River Sockeye Salmon | 403

June 2015| NOAA Fisheries 

juvenile sockeye salmon along the west coast of North America: Implications for growth. 

Transactions of the American Fisheries Society 138:1458-1460.

U.S. v. Oregon Parties. 2008. 2008-2017 United States v. Oregon. Management Agreement. 143p.

URS. 2010. Upland and river operable units remedial investigation report, Bradford Island, Cascade 

Locks, Oregon. Draft final report. Prepared by URS for U.S. Army Corps of Engineers, Portland 

District, Oregon. 11/1/2010.

USBR (United States Bureau of Reclamation). 2007. Assessment of Sockeye Salmon Production 

Potential in the Cle Elum River Basin, Storage Dam Fish Passage Study, Yakima Project, 

Washington, Technical Series No. PN- DFP-008, Bureau of Reclamation, Boise, Idaho, March 

2007.

USBWP (Upper Salmon Basin Watershed Project). 2005. Screening and Habitat Improvement 

Prioritization for the Upper Salmon Subbasin (SHIPUSS). Prepared by the Upper Salmon Basin 

Watershed Project Technical Team, August 2005. 34 p.

USEPA (U.S. Environmental Protection Agency). 2002. Columbia River basin fish contaminant survey 

1996–1998. EPA 910-R-02-006. U.S. Environmental Protection Agency, Seattle, Washington, 

1/1/2002. 

USEPA (U.S. Environmental Protection Agency). 2009. Columbia River Basin: State of the River 

Report for Toxics. USEPA Report EPA 910-R-08-004. U.S. U.S. Environmental Protection 

Agency Region 10, Seattle, WA. 60 pp. 

USFS (U.S. Forest Service). 2001. Environmental assessment Stanley Lake recreation complex 

reconstruction project. Sawtooth National Recreation Area, Sawtooth National Forest. Custer 

County, Idaho. September 2011.

USFS (U. S. Forest Service). 2003. Sawtooth National Forest Land Management Plan. USDA Forest 

Service, Intermountain Region.

USFS (U.S. Forest Service). 2011. Sawtooth National Forest Upper Salmon Watershed Vulnerability 

Assessment Pilot Project.

Ventura-Lima J., D. Fattorini, F. Regoli, and J. M. Monserrat. 2009. Effects of different inorganic 

arsenic species in Cyprinus carpio (Cyprinidae) tissues after short-time exposure: bioaccumulation, 

biotransformation and biological responses. Environ Pollut. 257:3479-3484.

Wagner, R. J., L. M. Frans, and R. L. Huffman. 2006. Occurrence, distribution, and transport of 

pesticides in agricultural irrigation-return flow from four drainage basins in the Columbia Basin 

Project, Washington, 2002-04, and comparison with historical data: U.S. Geological Survey 

Scientific Investigations Report 2006-5005, 54 p.

Walter, M. T., D. S. Wilks, J. Y. Parlange and B. L. Schneider. 2004. Increasing evapotranspiration 

from the conterminous United States. J. Hydrometeorol., 5, 405-408.

Walters, C. J. 1986. Adaptive management of renewable resources. New York, Macmillan.

Waples, R. S., O. W. Johnson, and R. P. Jones, Jr. 1991. Status review for Snake River sockeye salmon. 

NOAA Technical Memorandum NMFS-F/NWC 195. Seattle, WA. 
ESA Recovery Plan: Snake River Sockeye Salmon | 404

June 2015| NOAA Fisheries 

Waples, R.S., P.B. Aebersold, and G.A. Winans. 1997. Population genetic structure and life history 

variability in Oncorhynchus nerka from the Snake River basin. Report to Bonneville Power 

Administration, Contract No.1993BP05326, Project No.199306800. BPA Report DOE/BP-05326-

1. 

Waples, R. S., P. Aebersold, and G. Winans. 2011. Population genetic structure and life history 

variability in Oncorhynchus nerka from the Snake River Basin. Transactions of the American 

Fisheries Society 140:716-733. 

Ward, M. B., P. Nelle, S. M. Walker, and (editors). 2012. CHaMP: 2011 Pilot Year Lessons Learned 

Project Synthesis Report. Prepared for the Bonneville Power Administration by CHaMP. Published 

by Bonneville Power Administration, Portland, OR. 95 pages.

Watson, M., M. Cox, and L. Edmond. 2008. Sediment Quality in the Mid-Columbia River Between 

Vantage, Washington and McNary Dam. EPA 910/R-08-001. U.S. Environmental Protection 

Agency, Office of Environmental Assessment, Region 10, 1200 Sixth Avenue, Suite 900, Seattle, 

Washington.

WCSBRT (West Coast Salmon Biological Review Team). 2003. Updated status of federally listed ESUs 

of West Coast Salmon and steelhead. National Marine Fisheries Service, Northwest Fisheries 

Science Center and Southwest Fisheries Science Center. 

WDFW (Washington Department of Fish and Wildlife). 2012. Winter 2012 Joint Staff Report. 

http://wdfw.wa.gov/publications/01354/wdfw01354.pdf

Weitkamp, L. A., P. J. Bentley, and M. N. C. Litz. 2012. Seasonal and interannual variation in juvenile 

salmonids and associated fish assemblage in open waters of the lower Columbia River estuary. 

Fisheries Bulletin 110:426-550.

Welch, D. W., L. Margolis, M. A. Henderson, and S. McKinnel. 1991. Evidence for attacks by 

bathypelagic fish Anotopterus pharao (Myctophiformes) on Pacific salmon (Oncorhynchus spp.). 

Canadian Journal of Fisheries and Aquatic Sciences. 48(12):2403-2407.

Welch, D. W., M. C. Melnychuk, J. C. Payne, E.L. Rechisky, A. D. Porter, et al. 2011. Measurement of 

coastal ocean movements and survival of juvenile Pacific salmon. Proceedings of the National 

Academy of Sciences 108:8708-8713.

Wells B. K., C. B. Grimes, J. G. Sneva, S. McPherson, and J. B. Waldvogel. 2008. Relationships 

between oceanic conditions and growth of Chinook salmon (Oncorhynchus tshawytscha) from 

California, Washington, and Alaska, USA. Fisheries Oceanography 17: 101–125.

Wentz, D.A., B.A. Bonn, K. D. Carpenter, S.R. Hinkle, M.L. Janet, F. A. Rinella, M.A.Uhrich, I. R. 

Waite, A. Laenen, and K. E. Bencala. 1998. Water quality in the Willamette Basin, Oregon, 1991–

95. U.S. Geological Survey Circular; 1161, 34 pp.

Weston, R. (Roy F. Weston, Inc.). 1998. Portland Harbor sediment investigation report Multnomah 

County, Oregon. EPA 910/R-98-006. USEPA, Seattle

Willette, T. M., R. T. Cooney, V. Patrick, D. M. Mason, G. L. Thomas, and D. Scheel. 2001. Ecological 

processes influencing mortality of juvenile pink salmon (Oncorhynchus gorbuscha) in Prince 

William Sound, Alaska. Fisheries Oceanography 10 (Supplement 1):14–41.
ESA Recovery Plan: Snake River Sockeye Salmon | 405

June 2015| NOAA Fisheries 

Williams, J. G., S. G. Smith, R. W. Zabel, W. D. Muir, M. D. Scheuerell, B. P. Sandford, D. M. Marsh, 

R. A. McNatt, and S. Achord. 2005. Effects of the Federal Columbia River Power System on 

salmonid populations. U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-63, 150 p.

Williamson, A. K., M. D. Munn, S. J. Ryker, R. J. Wagner, J. C. Ebbert, and A. M. Vanderpool. 1998. 

Water quality in the Central Columbia Plateau, Washington and Idaho, 1992–95: U.S. Geological 

Survey Circular 1144, 35 p.

Winans, G. A., P. B. Aebersold, and R. S. Waples. 1996. Allozyme variability of Oncorhynchus nerka in 

the Pacific Northwest, with special consideration to populations of Redfish Lake, Idaho. Trans. Am. 

Fish. Soc. 125:645–663 

Wood, C. C., C. J. Foote, and D. T. Rutherford, 1999. Ecological interactions between juveniles of 

reproductively isolated anadromous and non-anadromous morphs of sockeye salmon, Oncorhyncus 

nerka, sharing the same nursery lake. Environmental Biology of Fishes 54, 2:161-173.Wurtsbaugh, 

W. A., H. P. Gross, C. Luecke, and P. Budy. 1997. Nutrient limitation of oligotrophic sockeye 

salmon lakes of Idaho (USA). Internationale Vereinigung fu ̈r Theoretische und Angewandte 

Limnologie Verhandlungen 26:413–419.

Woodson, L. E., B. K. Wells, P. K. Weber, B. R. MacFarlane, G. E. Whitman, and R. C. Johnson. 2013. 

Size, growth, and origin-dependent mortality of juvenile Chinook salmon Oncorhynchus 

tshawytscha during early ocean residence. Marine Ecology Progress Series 487:163-175.

Wu, H., J. S. Kimball, M. M. Elsner, N. Mantua, R. F. Adler, and J. Stanford. 2012. Projected climate 

change impacts on the hydrology and temperature of Pacific Northwest rivers. Water Resources 

Research 48: W11530 doi:10.1029/2012WR012082.

Wurtsbaugh, W. A., H. P. Gross, C. Luecke and P. Budy. 1997. Nutrient limitation of oligotrophic 

sockeye salmon lakes of Idaho (USA). Verh. Int. Ver. Limnol. 26:413-419.

Yanagida, G. K, B. F. Anulacion, J. L. Bolton, D. Boyd, D. P. Lomax, O. P. Olson, S. Y. Sol, M. J. 

Willis, G. M. Ylitalo, and L. L. Johnson. 2011. Polycyclic aromatic hydrocarbons and risk to 

threatened and endangered Chinook salmon in the Lower Columbia River estuary. Archives of 

Environmental Contamination and Toxicology (in press). 

Zabel, R. W. 2013. Estimation of percentages for listed pacific salmon and steelhead smolts arriving at 

various locations in the Columbia River basin in 2012. Memorandum to J. H. Lecky, NMFS. 

Northwest Fisheries Science Center, Seattle, Washington. January 23, 2013.

Zabel, R. W., S. G. Smith, W. D. Muir, D. M. Marsh, J. G. Williams, and J. R. Skalski. 2001. Survival 

estimates for the passage of spring migrating juvenile salmonids through Snake and Columbia 

River dams and reservoirs, 2000. Report of the National Marine Fisheries Service to the Bonneville 

Power Administration, Portland, Oregon. Available at 

www.nwfsc.noaa.gov/publications/index.cfm (January 2012).

Zaroban, D. 2011. Source of information on water quality. Communication from D. Zaroban (IDEQ) to 

R. Furfey 2011.

Zavolokin, A. V., A. Ya. Efimkin, A. M. Slabinskiy, and N. S. Kosenok. 2007. Food supply and trophic 

relationships of Pacific salmon (Oncorhynchus spp.) and Atka mackerel (Pleurogrammus 

monopterygius) in the western Bering sea in fall 2002-2004. Bulletin North Pacific Anadromous 

Fish Commission 4:127-131.
ESA Recovery Plan: Snake River Sockeye Salmon | 406

June 2015| NOAA Fisheries 
ESA Recovery Plan: Snake River Sockeye Salmon | 407

June 2015| NOAA Fisheries 

Appendix A: Summary of Recovery Measures and Estimated 

Costs
ESA Recovery Plan: Snake River Sockeye Salmon | 408

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 409

June 2015| NOAA Fisheries 

Appendix A. Summary of Recovery Measures and Estimated Costs

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

Recovery Strategy 7.2.1: Conserve population and genetic life history and spatial structure

7.2.1-1 1. Continue to fund 

annual operation of the 

Sockeye Salmon captive 

broodstock propagation 

program.

Sawtooth 

Valley

IDFG, NMFS, 

BPA, ODFW

3,014 3,014 3,014 3,014 3,014

7.2.1-2 2. Fund modifications to 

Sawtooth Hatchery weir 

to improve Sockeye 

Salmon trapping 

efficiency and provide 

adult access to upper 

salmon nursery lakes. 

Sawtooth 

Valley

IDFG

Capital project; 

Could be reduced 

abundance if fish don’t 

enter the trap and stray or 

spawn in other locations

To be 

determined

7.2.1-3 3. Determine additional 

detection needs (e.g., 

PIT-tag detectors) in the 

Salmon River.

Salmon 

River

SBSTOC, 

IDFG

To be 

determined

7.2.1-4 4. Describe conditions 

under which trapping 

would occur at various 

locations, including 

Lower Granite Dam.

Snake River Corps, 

IDFG,SBSTOC

This is currently being 

developed.

To be 

determined

7.2.1-5 5. Determine changes in 

marking/tagging levels 

for increased precision to 

evaluate downstream 

Salmon R.

IDFG, 

ShoshoneBannock Tribes

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 410

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

sources of mortality.

7.2.1-6 6. In the near term at 

Sawtooth Hatchery, 

identify ways to improve 

handling of adults to 

collect genetic data of 

fish returning to Alturas 

Lake, Pettit Lake or 

Redfish Lake.

Sawtooth 

Valley IDFG, USFWS

To be 

determined

7.2.1-7 7. Identify actions to 

improve fish passage at 

Sawtooth Hatchery weir 

to allow fish to return to 

natal lake of origin. 

Sawtooth 

Valley

IDFG, USFWS, 

ShoshoneBannock TribesAlso a predation issue

To be 

determined

7.2.1-8

8. Maintain current 

marking/tagging levels.

Sawtooth 

Valley

IDFG, 

ShoshoneBannock Tribes

7.2.1-9 9. Identify lake of origin 

for adults returning to 

basin collection facilities.

Sawtooth 

Valley

IDFG

To be 

determined

7.2.1-10 10. Mark sufficient 

numbers of outmigrants 

from each lake to enable 

collection of returning 

spawners specific to lake 

Sawtooth 

Valley

IDFG,

ShoshoneBannock Tribes

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 411

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

of origin.

7.2.1-11 11. Continue to sort 

returning adults at basin 

weirs based on marks 

identifying lake of origin.

Sawtooth 

Valley

IDFG

To be 

determined

7.2.1-12 12. Transport returning 

adults to lake of origin or 

to hatchery program 

based on lake of origin or 

allow passage of adults.

Sawtooth 

Valley

IDFG

To be 

determined

7.2.1-13 13. Develop guidance 

and recommendations 

for a preferred recovery 

strategy (ies) for O. 

nerka life history forms of 

Snake River Sockeye 

Salmon. 

Sawtooth 

Valley

NMFS, 

SBSTOC

Technical staff and policy 

action Not Applicable

7.2.1-14 14. Develop long-term 

guidelines to support and 

maintain localized 

adaptations within and 

among populations. 

Sawtooth 

Valley

NMFS Technical staff and policy 

action Not Applicable

Recovery Strategy 7.2.2: Increase naturally spawning Snake River Sockeye Salmon abundance

7.2.2-1 1. Manage Springfield 

Hatchery to meet 

Sockeye Salmon

recovery goals.

Sawtooth 

Valley

IDFG

O&M costs/Springfield 

Hatchery opened in 2013

891 918 964 1,027
ESA Recovery Plan: Snake River Sockeye Salmon | 412

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

7.2.2-2 2. Increase annual 

hatchery smolt releases 

to 1 million through 

funding of additional 

hatchery facility(ies).

Sawtooth 

Valley

IDFG,

BPA

See 7.2.2-1 above

To be 

determined

7.2.2-3 3. Replace Redfish Lake 

weir and trap to allow 

handling and holding of 

larger adult returns.

Redfish 

Lake

IDFG, BPA

To be 

determined

7.2.2-4 4. Modify the Sawtooth 

Hatchery weir to improve 

Sockeye Salmon

trapping efficiency and 

provide adult access to 

upper salmon nursery 

lakes.

Redfish 

Lake

IDFG, BPA

To be 

determined

7.2.2-5 5. Increase adult holding 

capacity at Sawtooth 

Hatchery to provide 

separate holding for 

Sockeye Salmon and 

improve fish passage so 

fish more readily enter 

the trap.

Sawtooth 

Valley

IDFG

To be 

determined

7.2.2-6 6. Develop plan 

describing objectives for 

Pettit Lake IDFG, 

ShoshoneTechnical staff and policy issue. Not applicable
ESA Recovery Plan: Snake River Sockeye Salmon | 413

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

Pettit Lake, e.g., will the 

program use Redfish 

Lake fish in Pettit Lake, 

and what life stage(s) to 

release into Pettit Lake.

Bannock Tribes

7.2.2-7 7. Mark sufficient 

numbers of outmigrants 

from Pettit and Alturas 

Lakes to enable 

collection of returning 

spawners specific to this 

lake.

Pettit Lake

ShoshoneBannock TribesTo be 

determined

7.2.2-8 8. Transport returning 

adults identified as 

originating from Pettit 

and Alturas Lakes to that 

lake, or pass above weir 

for volitional migration, or 

retain as broodstock 

specific for Pettit and 

Alturas Lake releases.

Pettit Lake IDFG

To be 

determined

Recovery Strategy 7.2.3: Improve Sockeye Salmon passage to natal lakes

7.2.3-1 1. In the near term at 

Sawtooth Hatchery, 

identify ways to improve 

adult holding and 

handling of fish returning 

Sawtooth 

Valley

IDFG, USFWS, 

ShoshoneBannock Tribes

Also a viability and 

predation issue; technical 

staff and policy issue

Not applicable
ESA Recovery Plan: Snake River Sockeye Salmon | 414

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

to Alturas Lake, Pettit 

Lake, or Redfish Lake.

7.2.3-2 2. Identify actions to 

improve fish passage at 

Sawtooth Hatchery weir 

to allow fish to enter 

natal lakes.

Sawtooth 

Valley

IDFG, USFWS, 

ShoshoneBannock Tribes

Also a viability and 

predation issue

To be 

determined

7.2.3-3 3. Reestablish adult 

passage at Stanley Lake.

Stanley 

Lake

IDFG, BPA, 

USFS

To be 

determined

7.2.3-4 4. Reconciling lake trout 

management in Stanley 

Lake and remove 

barrier to volitional 

Sockeye Salmon

passage.

Stanley 

Lake

IDFG, USFS,

ShoshoneBannock 

Tribes, NMFS

Technical staff and policy 

issue Not applicable

7.2.3-5 5. Investigating passage 

survival and mortality 

factors during migration 

between natal lakes and 

Lower Granite Dam.

Salmon 

River

Lower 

Snake River

IDFG, NMFS, 

IDEQ

To be 

determined

7.2.3-6 6. Improve instream 

flows in the Salmon 

River above the 

Sawtooth Hatchery to 

Alturas Lake Creek by 

improving irrigation 

efficiencies, using IDWR 

Sawtooth 

Valley

IDFG, IDWR, 

NMFS, USFS, 

Custer/Blaine 

Counties

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 415

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

water bank and other 

conservation tools.

Recovery Strategy 7.2.4: Reestablish a self-sustaining anadromous Sockeye Salmon population in Redfish Lake

7.2.4-1 1. Manage Springfield 

Hatchery to meet 

Sockeye Salmon

recovery goals.

Redfish 

Lake 

IDFG Springfield Hatchery 

opened in 2013

See costs in 

Action 7.2.2-1

7.2.4-2 2. Replace Redfish Lake 

weir and trap to allow 

handling and holding of 

larger adult returns.

Redfish 

Lake

IDFG

To be 

determined

7.2.4-3 3. Once adequate and 

consistent returns of 

anadromous adults are 

achieved, phase out the 

use of Redfish lake 

captive broodstock.

Redfish 

Lake

IDFG, NMFS

To be 

determined

Recovery Strategy 7.2.5:Investigate and develop strategies for future actions to support Sawtooth Valley Sockeye Salmon reintroduction and adaptation for Pettit Lake

7.2.5-1 1. Release adults 

produced through the 

captive broodstock

program into Pettit Lake 

for a defined period.

Pettit Lake IDFG, NMFS

7.2.5.2 2. Refine program as 

needed to reestablish a 

locally adapted 

population in Pettit Lake.

Pettit Lake IDFG, NMFS
ESA Recovery Plan: Snake River Sockeye Salmon | 416

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

Recovery Strategy 7.2.6: Investigate and evaluate the potential for restoring natural production of anadromous Sockeye Salmon from returning residual outplants from Alturas Lake

7.2.6-1 1. Determine appropriate 

strategies and actions for 

restoring natural 

production in Alturas 

Lake. Options may 

include trap and 

transport or establishing 

a new hatchery program. 

Alturas Lake SBSTOC This is a key information 

need that will also be 

included in Section 11 

RM&E. Same as # 14 

above. Not applicable

7.2.6-2 2.Determine whether 

Alturas Lake still 

contains anadromous or 

residual genetic 

resources.

Alturas Lake

NMFS, IDFG, 

SBSTOC Not applicable

Recovery Strategy 7.2.7: As sufficient number of natural-origin adults return, develop integrated approach to manage natural- and hatchery-origin adults in the hatchery program and the wild

7.2.7-1 1. Examine the benefits 

and/or risks of alternative 

strategies for recovering 

extant and/or historical 

life-history patterns in the 

natal lakes.

Sawtooth 

Valley 

SBT, IDFG Technical staff and policy 

issue Not applicable

7.2.7-2 2. Develop long-term 

guidelines to support and 

maintain localized 

adaptations within and 

among populations. 

Sawtooth 

Valley

NMFS Technical staff and policy 

issue Not applicable

7.2.7-3 3. Manage Springfield Redfish IDFG Springfield Hatchery See costs in 
ESA Recovery Plan: Snake River Sockeye Salmon | 417

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

Hatchery to meet 

Sockeye Salmon

recovery goals.

Lake opened in 2013. Action 7.2.2-a

7.2.7-4 4. Once adequate and 

consistent returns of 

anadromous adults are 

achieved, phase out the 

use of Redfish lake 

captive broodstock.

Redfish 

Lake

IDFG, NMFS, 

SBSTOC

To be 

determined

Recovery Strategy 7.2.8: As sufficient numbers of hatchery-origin anadromous adults return to the basin, identify options for future harvest

7.2.8-1 1. Develop a new 

abundance-based 

harvest management 

framework for Snake 

River Sockeye Salmon.

Sawtooth 

Valley 

Salmon 

River

NMFS, IDFG, 

SBT and other 

appropriate comanagers

Recovery Strategy 7.2.9: Continue research and actions to reestablish natural populations in other natal lakes

7.2.9-1 1. Develop plan 

describing objectives for 

Pettit Lake, e.g., whether 

or not the program 

would use Redfish Lake 

fish in Pettit Lake, and 

what life stage(s) to 

release into Pettit Lake.

Pettit Lake

IDFG, 

ShoshoneBannock Tribes

Technical staff and policy 

issue Not applicable

7.2.9-2 2. Mark sufficient 

numbers of outmigrants 

from Pettit Lake to 

Pettit Lake

ShoshoneBannock 

Tribes; IDFG

Same as No. 1 above.

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 418

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

enable collection of 

returning spawners 

specific to this lake.

7.2.9-3 3. Construct 

juvenile/adult trapping 

structure in Alturas Lake 

Creek.

Alturas Lake 

Creek

BPA 

ShoshoneBannock Tribes

To be 

determined

7.2.9-4 4.Improve/replace 

juvenile trapping 

structure in Pettit Lake 

Creek.

Pettit Lake 

Creek

BPA 

ShoshoneBannock Tribes

To be 

determined

7.2.9-5 5. Identify lake of origin 

from adults returning to 

basin collection facilities.

Sawtooth 

Valley

IDFG

To be 

determined

7.2.9-6 6.Continue to sort 

returning adults at 

Sawtooth weir, based on 

marks identifying source 

of outmigrant.

Sawtooth 

Valley

IDFG

To be 

determined

7.2.9-7 7.For returning spawners 

that are to spawn in 

upper basin lakes, pass 

for volitional migration or 

transport to appropriate 

lake.

Sawtooth 

Valley

IDFG, 

ShoshoneBannock Tribes

To be 

determined

7.2.9-8 8. Investigate strategies 

to enhance and support 

Alturas Lake IDFG; 

SBSTOC

Technical staff and policy 

issue Not applicable
ESA Recovery Plan: Snake River Sockeye Salmon | 419

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

anadromy in extant 

Alturas Lake early 

stream spawning 

Sockeye Salmon.

7.2.9-9 9. Continue limnological 

and ecological research 

and evaluations of the 

lakes.

Sawtooth 

Valley lakes

ShoshoneBannock Tribes

467 467 467 467 467

7.2.9-10 10. Address nutrients as 

limiting factors in all 

lakes used for Sockeye 

Salmon recovery and 

study relationship to prey 

base in natal lakes.

Sawtooth 

Valley lakes

ShoshoneBannock TribesTo be 

determined

7.2.9-11 11. Investigate and 

manage risks to native 

kokanee in Stanley Lake: 

i.e., outlet barrier, lake 

trout and non-native 

kokanee

Stanley 

Lake

IDFG, NMFS

To be 

determined

7.2.9-12 12. Research possible 

competition for food 

resources or spawning 

areas in natal lakes.

Sawtooth 

Valley lakes

ShoshoneBannock TribesTo be 

determined

7.2.9-13 13. Determine 

appropriate broodstock 

and strategies for 

Stanley 

Lake

NOAA, 

SBSTOC

This is a key information 

need that will also be 

included in Section 11 

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 420

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

recovery of Sockeye 

Salmon in Stanley Lake .

RM&E

7.2.9-14 14. Identify actions to 

improve fish passage at 

Sawtooth Hatchery weir 

to allow fish to enter 

natal lakes.

Sawtooth 

Valley

IDFG, USFWS, 

ShoshoneBannock Tribes

Also a viability and 

predation issue Not applicable

7.2.9-15 15. Reconciling lake trout 

management in Stanley 

Lake and remove barrier 

to volitional Sockeye 

Salmon passage.

Stanley 

Lake

IDFG, USFS, 

NMFS Not applicable

7.2.9-16 16.Based on resolution 

of lake trout 

management , develop a 

program for Stanley Lake 

to support Sockeye 

Salmon recovery.

Stanley 

Lake

SBSTOC, , 

NMFS

To be 

determined

7.2.9-17 17. Reestablish adult 

passage at Stanley Lake.

Stanley 

Lake

IDFG, BPA, 

USFS

To be 

determined

Recovery Strategy 7.2.10: Continue research on natal lakes’ carrying capacity, nutrients and ecology

7.2.10-1 1. Conduct limnological 

studies to evaluate 

nursery lake habitat 

conditions encountered 

by adult and juvenile 

Sockeye Salmon during 

Sawtooth 

Valley

ShoshoneBannock TribesSee Action 

7.2.9-10
ESA Recovery Plan: Snake River Sockeye Salmon | 421

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

freshwater phase.

7.2.10-2 2. Determine if lake 

fertilization is necessary 

for each lake used for 

Sockeye Salmon

recovery, and, if 

warranted, develop and 

implement a plan to 

fertilize lakes to increase 

rearing habitat 

productivity.

Sawtooth 

Valley

SBSTOC,

ShoshoneBannock Tribes

The selection of lakes to 

fertilize should align with 

the IDFG Master Plan and 

its implementation. 

To be 

determined

7.2.10-3 3. Develop and 

implement a study in 

Yellowbelly Lake to 

evaluate lake carrying 

capacity of Sockeye 

Salmon in the absence 

of resident kokanee.

Yellowbelly 

Lake

ShoshoneBannock TribesTo be 

determined

7.2.10-4 4. Continue limnological 

and ecological research 

and evaluations of the 

lakes reduced population 

structure, distribution, 

abundance, diversity.

Stanley and 

Yellowbelly 

Lakes

ShoshoneBannock TribesSee Action 

7.2.9-10

Recovery Strategy 7.2.11: Protect and conserve natural ecological processes at the watershed scale that support population viability

7.2.11-1 1. Construct and 

maintain NMFSupper Salmon 

NMFS, IDFG,

SWCDs,

Identify costs based on 

each fish screen design 

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 422

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

approved fish screens. River Irrigation 

Districts

and specifications.

7.2.11-2 2. Maintain current 

wilderness protection for 

the ESU in the Sawtooth 

Wilderness area and 

protect the currently 

pristine watershed 

habitat.

Sawtooth 

Wilderness 

area

USFS

To be 

determined

7.2.11-3 3. Continue to implement 

the Sawtooth National 

Recreation Area’s 

Management Plan and 

restoration actions.

Sawtooth 

National 

Recreation 

Area

USFS

To be 

determined

7.2.11-4

4. Implement BMPs to 

protect and conserve 

ecological processes.

Sawtooth 

Valley

USFS, 

SWCDs, 

Counties, 

landowners

To be 

determined

Strategy 7.2.12: Protect, restore and manage spawning and rearing habitat

7.2.12-1 1. Maintain appropriate 

protections to manage 

lakeshore recreation to 

minimize any potential 

disturbance in areas 

where Sockeye Salmon

spawn.

Sawtooth 

Valley

U.S. Forest 

Service, 

IDFG

To be 

determined

7.2.12-2 2. Maintain appropriate Sawtooth U.S. Forest To be 
ESA Recovery Plan: Snake River Sockeye Salmon | 423

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

protections to continue to 

protect, restore and 

maintain spawning and 

rearing habitat.

Valley Service, county determined

7.2.12-3 3. Maintain current 

wilderness protection in 

Sawtooth Wilderness 

Area.

Sawtooth 

Valley 

U.S. Forest 

Service

To be 

determined

7.2.12-4 4. Continue appropriate 

protections to manage 

other human 

development to restore 

or maintain native 

vegetation that provides 

naturally resilient and 

productive shoreline 

habitat.

Sawtooth

Valley

U.S. Forest 

Service, 

IDFG

To be 

determined

7.2.12-5 5. Identify ways to 

maintain current 

protections for Sockeye 

Salmon critical habitat in 

the future, if ESU is 

delisted.

Sawtooth 

Valley

U.S. Forest 

Service, 

IDFG, County

This is important because 

critical habitat protection 

will no longer be 

designated when ESU is 

not listed.

To be 

determined

Recovery Strategy 7.2.13: Maintain unimpaired water quality and improve water quality as needed

7.2.13-1 1. Continue to manage

recreational use and 

motorized boat activity to 

Sawtooth 

Valley

U.S. Forest 

Service, IDFG

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 424

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

minimize the risk of fuel 

spill and introduction of 

wastewater 

contaminants into lakes.

7.2.13-2 2. Implement TMDLs for 

impaired water bodies in 

Salmon River watershed.

Salmon 

River 

watershed

IDEQ

To be 

determined

7.2.13-3 3. Monitor contaminants 

to determine whether 

there is residual 

contamination with 

Toxaphene in three lakes 

or arsenic contamination 

in Alturas Lake.

Sawtooth 

Valley

IDEQ

To be 

determined

7.2.13-4 4. Improve water quality 

(sediment) to maintain, 

enhance and restore fish 

habitat and passage.

Salmon 

River basin SWCDs, USFS

To be 

determined

7.2.13-5 5. Improve water quality 

(sed., temp.) between 

Redfish Lake Creek and 

East Fork Salmon River.

Salmon 

River

SWCDs, IDFG,

ShoshoneBannock Tribes

To be 

determined

7.2.13-6 6. Increase stream flow 

to improve hydrology by 

implementing water 

conservation measures, 

Salmon 

River

(between 

East Fork 

IDFG,

SWCDs,

Irrigation 

Districts,

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 425

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

improved water delivery, 

and improving water 

storage function of 

riparian areas and 

wetlands.

confluence 

and the 

headwaters)

landowners

Recovery Strategy 7.2.14: Investigate and improve conditions in Salmon River and tributaries to support increased survival of migrating Snake River Sockeye Salmon

7.2.14-1 1. Protect and enhance 

stream tributary habitat 

leading from natal lakes 

to the Salmon River in 

the Sawtooth Valley. 

Upper 

Salmon 

River and 

tributaries

USFS

To be 

determined

7.2.14-2 2. Protect and enhance 

watershed habitat to 

promote natural 

processes and 

watershed function.

Salmon and 

Lower 

Snake 

Rivers

USFS

To be 

determined

7.2.14-3

3. Implement existing 

agreements on Federal

lands in the Sawtooth 

Valley and Salmon River 

watersheds.

Upper 

Salmon 

River and 

tributaries; 

Sawtooth 

Valley

USFS Baseline

7.2.14-4 4. Identify specific 

actions and responsible 

parties/entities to 

improve water quantity 

and the quality of 

Especially in 

upper 

reaches of 

the 

mainstem 

USFS

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 426

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

juvenile and adult 

migration corridor 

habitats and monitor the 

actions. 

Salmon 

River and 

mainstem 

lower Snake 

River

7.2.14-5 5. Investigate the 

relatively high losses of 

juvenile and adult 

Sockeye Salmon in the 

Salmon River and 

identify actions that could 

reduce these losses.

Salmon 

River NMFS, IDEQ

To be 

determined

7.2.14-6 6. Continue to implement 

monitoring efforts to 

understand juvenile and 

adult survival in the 

Salmon River.

Salmon 

River IDEQ, NMFS 949

To be 

determined

7.2.14-7 7. Implement TMDLs for 

impaired water bodies in 

Salmon River watershed

Salmon 

River 

watershed

IDEQ

To be 

determined

Recovery Strategy 7.2.15: Monitor and control predation, disease, invasive species and competition and develop actions as needed

7.2.15-1 1. Implement plan for 

collection of returning 

spawners at Lower 

Granite Dam to reduce 

exposure to elevated 

temperatures in the 

Snake River

IDFG,

BPA?

Other?

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 427

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

mainstem Salmon River 

during late July and 

August.

7.2.15-2 2. Implement Idaho 

Department of 

Agriculture, U.S. Forest 

Service and IDFG 

whirling disease 

monitoring and control 

program.

Sawtooth 

Valley, 

upper 

Salmon 

River

IDA, USFWS, 

IDFG

Whirling Disease has 

been detected ....

$29,000 per 

year

29 29 29 29

7.2.15-3 3. Implement Idaho 

Department of 

Agriculture, U.S. Forest 

Service and IDFG 

invasive species 

monitoring and control 

programs.

Sawtooth 

Valley, 

upper 

Salmon 

River

Idaho Dept. of 

Agriculture, 

IDFG, USFS

New Zealand mud snails 

have been detected in 

Salmon River mainstem.

Same as 

7.2.15-2 above

7.2.15-4 4. Reduce non-native 

kokanee in lakes used 

for Sockeye Salmon

recovery.

Redfish 

Lake, Pettit 

Lake, 

Alturas Lake

SBT; IDFG

Only feasible in Alturas 

Lake if genetic structure 

indicates a need

To be 

determined

7.2.15-5 5. Evaluate the effects of 

lake trout on Sockeye 

Salmon, develop an 

eradication strategy, if 

appropriate, and 

implement strategy as 

Stanley 

Lake

IDFG

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 428

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

necessary.

7.2.15-6 6. Develop strategy (ies) 

to prevent lake trout 

movement and 

colonization of additional 

Sockeye Salmon lakes. 

Sawtooth 

Valley

IDFG

To be 

determined

7.2.15-7 7. Evaluate the effects of 

cutthroat trout on 

Sockeye Salmon.

Yellowbelly 

Lake

IDFG

To be 

determined

7.2.15-8 8. Develop and 

implement a study in 

Yellowbelly Lake to 

evaluate lake carrying 

capacity of Sockeye 

Salmon limiting factor in 

the absence of resident 

kokanee.

Yellowbelly 

Lake

SBT

To be 

determined

7.2.15-9 9. Identify criteria for 

transitioning to passing 

selected adults above 

weirs to migrate 

naturally, and for 

opening weirs to allow 

returns to distribute 

themselves naturally.

Sawtooth 

Valley

SBSTOC Technical staff or policy 

issue Not applicable

7.2.15-

10

10. Identify ways to 

address predation at 

Sawtooth 

Valley

IDFG, USFWS

To be 

determined
ESA Recovery Plan: Snake River Sockeye Salmon | 429

June 2015| NOAA Fisheries 

Action 

No. Recovery Actions

Subbasin/

Lake/

Watershed

Potential 

Implementing

Entity

Comments

FY 2014

($K/year)

FY 15 FY 16 FY 17 FY 18

Sawtooth Hatchery weir.

Recovery Strategy 7.2.16: Create an adaptive management feedback loop to track progress toward achieving recovery goals, monitor and evaluate key information needs, assess information 

and refine strategies and actions

7.2.16-1

1. Implement Research, 

Monitoring and Adaptive 

Management Program

Sawtooth 

Valley

IDFG, NMFS, 

BPA, 

ShoshoneBannock Tribes

Key implementation action

To be 

determined

TOTAL FY 14 - FY 19 $20,293,955
ESA Recovery Plan: Snake River Sockeye Salmon | 430

June 2015| NOAA Fisheries 

This page intentionally left blank.
ESA Recovery Plan: Snake River Sockeye Salmon | 431

June 2015| NOAA Fisheries 

Appendix B: Module for Ocean Environment

This appendix can be found at:

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/ocean_module.pdf

Appendix C: Columbia River Estuary ESA Recovery 

Plan Module for Salmon and Steelhead

This appendix can be found at:

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/estuary-mod.pdf

Appendix D: Snake River Harvest Module

This appendix can be found at:

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/harvest_module_062514.pdf

Appendix E: Supplemental Recovery Plan Module 

for Snake River Salmon and Steelhead Mainstem 

Columbia River Hydro System

This appendix can be found at:

http://www.westcoast.fisheries.noaa.gov/publications/recovery_planning/salmon_steelhead/domains/inte

rior_columbia/snake/hydro_supplemental_recovery_plan_module_063014.pdf