NOAA Technical Memorandum NMFS-NWFSC-128

Identifying Historical 

Populations of Steelhead 

within the Puget Sound 

Distinct Population Segment

March 2015

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Northwest Fisheries Science Center
NOAA Technical Memorandum

NMFS-NWFSC Series

The Northwest Fisheries Science Center of NOAA’s

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Memorandum NMFS-NWFSC series continues the NMFSF/NWC series established in 1970 by the Northwest and

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divided into the Northwest Fisheries Science Center and the 

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Reference throughout this document to trade names does not 

imply endorsement by the National Marine Fisheries Service.

Reference this document as follows:

Myers, J.M., J.J. Hard, E.J. Connor, R.A. Hayman, 

R.G. Kope, G. Lucchetti, A.R. Marshall, G.R. Pess, and 

B.E. Thompson. 2015. Identifying historical populations 

of steelhead within the Puget Sound distinct population 

segment. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-128.
NOAA Technical Memorandum NMFS-NWFSC-128

Identifying Historical 

Populations of Steelhead 

within the Puget Sound 

Distinct Population Segment

James M. Myers, Jeffrey J. Hard, Edward J. Connor,1

Robert A. Hayman,2 Robert G. Kope, Gino Lucchetti,3

Anne R. Marshall,

4 George R. Pess, and Bradley E. Thompson5

Northwest Fisheries Science Center

2725 Montlake Boulevard East

Seattle, Washington 98112

1

Seattle City Light

700 Fifth Avenue, Suite 3300

Seattle, Washington 98124

2

Skagit River System Cooperative

11426 Moorage Way

La Conner, Washington 98257

3

King County Department of Natural Resources and Parks

201 South Jackson Street, Suite 600

Seattle, Washington 98104

4

Washington Department of Fish and Wildlife

600 Capitol Way North

Olympia, Washington 98501

5

U.S. Fish and Wildlife Service

Washington Fish and Wildlife Office

510 Desmond Drive Southeast, Suite 102

Lacey, Washington 98503

March 2015

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Most NOAA Technical Memorandums

NMFS-NWFSC are available at the 

Northwest Fisheries Science Center

Web site, http://www.nwfsc.noaa.gov

Copies are also available from the

National Technical Information Service

5285 Port Royal Road 

Springfield, VA 22161 

Phone orders: 1-800-553-6847 

E-mail orders: orders@ntis.fedworld.gov

ii
iii

Table of Contents

List of Figures........................................................................................................................... v

List of Tables...........................................................................................................................vii

Dedication ................................................................................................................................ix

Executive Summary...................................................................................................................xi

Acknowledgments................................................................................................................... xiii

List of Abbreviations.................................................................................................................xv

Introduction .............................................................................................................................. 1

Definition of a Population ....................................................................................................... 1

Structure above the Population Level .................................................................................... 2

Structure below the Population Level .................................................................................... 2

Conceptual Approach to Identifying Populations......................................................................... 3

Migration Rates ................................................................................................................. 4

Genetic Attributes.............................................................................................................. 5

Geography ........................................................................................................................ 6

Patterns of Life History and Phenotypic Characteristics............................................................ 7

Population Dynamics.......................................................................................................... 7

Environmental and Habitat Characteristics............................................................................. 8

Identifying Historical Populations of Salmonids............................................................................10

Criteria for Identifying the Distribution of Historical Populations.................................................10

Tier 1 Criteria ...................................................................................................................10

Tier 2 Criteria ...................................................................................................................11

Sustainability and Independence..........................................................................................12

Ecological Information.......................................................................................................16

Biological Data .................................................................................................................18

Population Boundaries for Fish and Habitat...............................................................................21

Historical Documentation.......................................................................................................21

Taxonomic Descriptions and Observations............................................................................21

Historical Abundance.........................................................................................................23

Puget Sound Steelhead Life History.........................................................................................31

Winter-Run Steelhead........................................................................................................37
iv

Summer-Run Steelhead......................................................................................................37

Juvenile Life History .........................................................................................................40

Ocean Migration ...............................................................................................................41

Genetics..............................................................................................................................41

Previous Studies................................................................................................................41

Recent Studies..................................................................................................................44

Major Population Groups.......................................................................................................46

Major Population Grouping Determinations for Other DPSs and ESUs......................................46

Puget Sound Steelhead MPG Determinations.........................................................................47

Historical Demographically Independent Populations.....................................................................52

Northern Cascades (South Salish Sea) MPG..............................................................................52

Overview.........................................................................................................................52

Proposed DIPs within the MPG (1 through 16) ......................................................................54

Central and South Puget Sound MPG.......................................................................................66

Overview.........................................................................................................................66

Proposed DIPs within the MPG (17 through 24).....................................................................67

Hood Canal and Strait of Juan de Fuca MPG.............................................................................73

Overview.........................................................................................................................73

Proposed DIPs within the MPG (25 through 32).....................................................................74

Puget Sound Steelhead DPS Population Considerations..............................................................80

References...............................................................................................................................81

Appendix A: Comparison of Populations and Management Units.....................................................93

Appendix B: Genetic Analysis of Steelhead from Puget Sound........................................................95

Appendix C: Puget Sound Steelhead TRT Checklist and Gatekeeper Model for Identifying DIPs........ 113

Appendix D: Basin Characteristics and Estimates of Spawners...................................................... 119

Appendix E: Puget Sound Steelhead Hatchery Production from 1900 to 1945 .................................. 123

Appendix F: Puget Sound Steelhead Fisheries Reported Harvest for Years 1895, 1904, and 1909........ 129

Appendix G: Steelhead Smolt Releases into Puget Sound Tributaries from 1965 to 2008................... 131

Appendix H: Steelhead Adult Age-Classes by Sex and Age Structure by Broodyear......................... 141

Appendix I: Catastrophic Risk Categories for Puget Sound Chinook Salmon ................................... 143

Appendix J: Geologic Regions of Washington State..................................................................... 145

Appendix K: Average Monthly Flows for Puget Sound Streams..................................................... 147

Appendix L: Distances between Adjacent Puget Sound River Mouths............................................. 149

Appendix M: Responses to Reviewer Comments......................................................................... 151
v 

Figures

Figure 1. Location of winter-run and summer-run stocks within the Puget Sound Steelhead DPS .........14

Figure 2. Level III and IV ecoregions of the Northwestern United States map ...................................17

Figure 3. Steelhead homing rates................................................................................................19

Figure 4. Harvest of steelhead in Puget Sound, 1889–1925 .............................................................24

Figure 5. Temporal distribution of egg collection for steelhead returning to WDG facilities 

in 1932 and 1938......................................................................................................................34

Figure 6. Standardized distribution of steelhead eggs collection at the Puyallup Hatchery 

from 1932 to 1939 ....................................................................................................................35

Figure 7. Two-dimensional scaling views, based on allozyme analysis, of coastal Washington 

steelhead populations ................................................................................................................44

Figure 8. Geographic regions for Puget Sound Chinook salmon ......................................................48

Figure 9. Major population groupings for the Puget Sound Steelhead DPS........................................51

Figure B-1. Dendrogram of 39 steelhead collections analyzed for 13 microsatellite DNA loci and 

displayed using Cavalli-Sforza and Edwards chord metric and neighbor joining clustering................. 100

Figure B-2. Dendrogram of 39 steelhead collections analyzed for 13 microsatellite DNA loci and 

displayed using Cavalli-Sforza and Edwards chord tree with unweighted pair group method with 

arithmetic averages clustering ................................................................................................... 106

Figure B-3. Relationships between 39 steelhead population samples from Puget Sound based on 

13 microsatellite DNA loci....................................................................................................... 107

Figure B-4. Relationships between 39 steelhead population samples from Puget Sound based on 

13 microsatellite DNA loci....................................................................................................... 108

Figure B-5. Relationships between 25 steelhead population samples from Puget Sound based on 

13 microsatellite DNA loci....................................................................................................... 109

Figure B-6. Relationships between 25 steelhead population samples from Puget Sound based on 

13 microsatellites DNA loci ..................................................................................................... 111

Figure C-1. Schematic of the gatekeeper model used to identify historical demographically 

independent populations .......................................................................................................... 117

Figure C-2. Gower chart of candidate DIP ecological parameters used to distinguish habitat 

characteristics in each basin...................................................................................................... 118

Figure J-1. Geologic map GM-53 of Washington State ................................................................ 145
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Tables

Table 1. Stream habitat rating matrix for Puget Sound steelhead......................................................14

Table 2. Freshwater ages at the time of migration to the ocean........................................................36

Table 3. Puget Sound steelhead freshwater migration and spawning periods......................................38

Table 4. Frequencies of ocean age at the time of first spawning.......................................................42

Table 5. Frequencies of life history patterns.................................................................................42

Table 6. DIPs within the Northern Cascades MPG and their respective categorization by state 

and tribal agencies....................................................................................................................53

Table 7. DIPs within the Central and South Puget Sound MPG and their respective categorization 

by state and tribal agencies.........................................................................................................66

Table 8. DIPs within the Hood Canal and Strait of Juan de Fuca MPG and their respective 

categorization by state and tribal agencies.....................................................................................73

Table A-1. Steelhead populations listed under the 1930 survey were identified as being medium 

to large abundance....................................................................................................................93

Table B-1. Geographic distribution of steelhead genetic samples from the Puget Sound Steelhead 

DPS analyzed for DNA microsatellite variation at 13 loci...............................................................98

Table B-2. Information for collections of steelhead used in the genetic analyses................................99

Table B-3. Cavalli-Sforza and Edwards chord distances for 39 steelhead collections........................101

Table B-4. Information for collections of steelhead used in the genetic analyses..............................110

Table C-1. Data available for DIP evaluation..............................................................................115

Table D-1. Basin geographic, hydrologic, and ecological characteristics with intrinsic potential

estimates of spawners using two smolt-to-adult survival rates........................................................120

Table E-1. Puget Sound steelhead hatchery production from 1900 to 1945......................................124

Table F-1. Steelhead fisheries reported harvest by county for 1895................................................129

Table F-2. Steelhead fisheries reported harvest by county for 1904................................................129

Table F-3. Steelhead fisheries reported harvest by county for 1909................................................130

Table G-1. Releases of winter-run steelhead smolts into tributaries from 1965 to 2008 .....................132

Table G-2. Releases of summer-run steelhead smolts into tributaries from 1965 to 2008...................136

Table H-1. Distribution of steelhead adult age-classes by sex for winter-run steehead captured 

in sport and tribal fisheries for selected Puget Sound rivers...........................................................141

Table H-2. Steelhead age structure by broodyear for selected Puget Sound rivers.............................142

Table I-1. Scores for catastrophic risk categories for Puget Sound Chinook salmon..........................143

Table K-1. Normalized average monthly flows for Puget Sound streams........................................147

Table L-1. Summary of distances to nearest neighbor spawning grounds........................................149
viii
ix

Dedication

Robert August Hayman

27 February 1952–20 December 2011

In the midst of developing and drafting this document, the Puget Sound Steelhead 

Technical Recovery Team was saddened by the death of one of its members, Bob Hayman. His 

contributions to the TRT went beyond his extensive knowledge of the Skagit River basin; it was 

his determination that the TRT process be logical, consistent, and transparent that ensured its 

work would meet the highest standards. Bob’s good-natured and humble manner made him 

likeable even when he was challenging your thinking. He was a tireless worker, and the 

determination he displayed in both his professional endeavors and battling cancer was inspiring. 

We all miss him.
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Executive Summary

The Puget Sound Steelhead Technical Recovery Team (PSS TRT) convened in March 

2008 to review information relevant to the identification of historical demographically 

independent populations (DIPs) of steelhead (Oncorhynchus mykiss) in the Puget Sound 

steelhead distinct population segment (DPS). The PSS TRT identified three major population 

groups (MPGs) containing a total of 32 steelhead DIPs in Puget Sound.

Steelhead in the Puget Sound DPS exhibit two distinct life history strategies: summer-run 

and winter-run migrations. Winter-run steelhead, also known as ocean-maturing steelhead, 

return to freshwater during the winter and early spring months and spawn relatively soon after 

entering freshwater. Alternatively, summer-run (stream-maturing) steelhead return to freshwater 

during late spring and early summer in a relatively immature state and hold there until spawning 

in the following winter/spring. Generally, but not necessarily, summer-run steelhead returntiming is coordinated with river flow patterns that allow access past barriers to headwater 

spawning areas. Presently and historically, winter-run steelhead numerically represent the 

predominant life history type in Puget Sound.

Steelhead exhibit considerable diversity in age at smoltification, age at return or 

maturation, and spawning timing and repeat spawning (iteroparity). Overall, there were few 

clear trends in these life history traits across the Puget Sound DPS. Steelhead in lowland, raindominated streams tended to spawn earlier than fish in upland or headwater, snowfall-dominated 

streams. Information on life history characteristics is limited for all but a few DIPs and 

completely absent for others, especially for summer-run populations. Additionally, there is little 

information available on ocean migratory patterns outside of Puget Sound and, until recently, 

steelhead tagging studies have not been undertaken to any great degree.

The PSS TRT reviewed available information on Puget Sound steelhead, which included 

life history and genetic data. This information was not universally available for all populations 

and, in many cases, ecological information was used to estimate life history characteristics. In 

the absence of historical demographic information (e.g., abundance, spatial structure), the TRT 

also used basin characteristics to estimate the potential historical size and level of interaction 

between prospective populations. The TRT initially utilized an expert panel system to develop 

criteria for establishing DIP criteria, but ultimately incorporated these criteria into a decision 

support system to identify DIPs. DIPs were in turn organized in MPGs. These larger scale units 

delineate DPS-wide spatial structure. The TRT identified MPGs based on the geographic and 

ecological characteristics of the DPS and the genetic clustering of existing steelhead populations 

in Puget Sound.

As a preliminary filter for putative DIPs, the TRT only considered basins with intrinsic 

productivity (based on stream area) equal to or greater than that estimated for Snow Creek, an 

apparently self-sustaining, small, wild population located on the northeastern corner of the 
xii

Olympic Peninsula. The decision support system relied on basin intrinsic potential, basin 

elevation, snow cover, distances between potential DIPs, genetic differences between potential 

DIPs, life history differences between potential DIPs, and the presence of temporal migrational 

barriers between potential DIPs. The decision support system, or gatekeeper model, required 

that the TRT estimate for each factor a threshold value that indicated populations were 

demographically independent with a very high certainty. One of the benefits of this system was 

that missing information did not bias the outcome.

The boundaries for historical DIPs were in part established using information related to 

two isolating mechanisms: homing fidelity and migration timing. Homing fidelity was examined 

to estimate the extent of adult exchange among putative spawning populations. Analysis of the 

terminal recoveries of adult marked hatchery fish indicates that less than 10% of the recoveries 

occur more than 50 km from the mouth of their natal stream (stream of release). Within a basin, 

temporal differences in return migration and spawn timing provided mechanisms for establishing 

demographically and reproductively isolated populations. Adult run and spawn timing are often 

coordinated with stream hydrology and temperature, which in turn are strongly affected by basin 

elevation. Major run-timing (e.g., summer and winter) differences were used as one criterion for 

distinguishing DIPs in the gatekeeper decision support system, especially where temporal 

barriers provided a reproductive barrier between presumptive DIPs.

In the Puget Sound DPS, three MPGs were identified: Northern Cascades, Central and 

South Puget Sound, and Hood Canal and Strait of Juan de Fuca. Within the Northern Cascades 

MPG, 16 DIPs (8 winter run, 3 summer/winter run, 5 summer run) were identified as historically 

present. In the Central and South Puget Sound MPG, 8 winter-run DIPs were historically 

present. There was some discussion regarding the presence of an additional historical summerrun DIP in the Green River or, alternatively, that the Green River winter-run DIP should be 

designated as a mixed summer/winter-run DIP, although the information available was not 

considered compelling. Additionally, while there are no known native-origin summer-run 

steelhead currently in the Green River (i.e., the summer-run steelhead currently released into and 

naturally spawning in the Green River originated from the Skamania Hatchery in the Columbia 

River basin), it is possible that resident O. mykiss above Howard Hansen Dam may contain the 

genetic legacy of a summer run. The Hood Canal and Strait of Juan de Fuca MPG historically 

contained 8 DIPs (1 summer/winter run and 7 winter run, with 2 of these winter runs possibly 

historically including summer-run components).

Where steelhead population information was available, especially genetic information, it 

was possible to identify steelhead DIPs with a relatively high degree of certainty. In other cases, 

ecological information provided a reasonable proxy for population data. The TRT strongly 

recommends further life history and genetics sampling and evaluation, especially in those areas 

currently less well studied. For some populations, basic abundance data are still lacking and 

need to be collected. It is likely that, in the process of collecting additional information on these 

populations, some revision in the DPS population structure will be necessary and should be 

undertaken.
xiii

Acknowledgments

We are grateful to the National Marine Fisheries Service’s West Coast Region for its

support to the Puget Sound Steelhead Technical Recovery Team (PSS TRT) during the 

preparation of this report. Members of the Puget Sound Domain Team, including Elizabeth 

Babcock, Steve Leider, Amilee Wilson, Alison Agness, Samantha Brooke, and Tim Tynan, were 

especially helpful to the PSS TRT’s deliberations. We also acknowledge the advice and 

contributions of Susan Bishop, Bruce Crawford, Bob Donnelly, and Steve Stone, West Coast 

Region; Tristan Peter-Contesse and Jason Mulvihill-Kuntz, Puget Sound Partnership; and Lloyd 

Moody and Sara Laborde, Governor’s Salmon Recovery Office.

Several scientists at the Northwest Fisheries Science Center (NWFSC), including Krista 

Bartz, Barry Berejikian, Shallin Busch, Tom Cooney, Mike Ford, Elizabeth Holmes, Paul 

McElhany, John McMillan, Megan Moore, Mindi Sheer, Robin Waples, and Eric Ward, were 

generous with their time in reviewing particular aspects of the report or in providing technical 

assistance. We are especially grateful to Damon Holzer, NWFSC, for his extensive assistance 

with extracting information from Geographical Information System data layers and producing 

maps. His valuable contributions made much of the TRT’s work possible.

The able assistance and cooperation of several biologists and technicians from various 

agencies were very helpful to the PSS TRT’s efforts. For their help with steelhead 

(Oncorhynchus mykiss) information and comments on aspects of this report, we thank Brett 

Barkdull, the late Steve Foley, Annette Hoffman, Thom Johnson, Robert Leland, and Kris 

Ryding, Washington Department of Fish and Wildlife; Will Beattie, Northwest Indian Fisheries 

Commission; Ned Currence, Nooksack Tribe; Kit Rawson, Tulalip Tribe and the Recovery 

Implementation Technical Team; Alan Chapman, Lummi Tribe; Eric Beamer and Casey Ruff, 

Skagit River System Cooperative; Larry Wasserman, Swinomish Indian Tribal Community; 

Dave Pflug, Seattle City Light; Ian Courter, Cramer and Associates; Frank Thrower, Alaska 

Fisheries Science Center (ret.); Fred Goetz, U.S. Army Corps of Engineers; and Bruce Ward, 

Department of Fisheries and Oceans Canada (ret.).

We also acknowledge several geneticists for help in assembling and interpreting genetic 

data for Puget Sound steelhead: Gary Winans and Don Van Doornik, NWFSC; and Kenneth 

Warheit, Todd Kassler, and Todd Seamons, Washington Department of Fish and Wildlife. 

Furthermore, we are grateful to Megan McPhee, University of Alaska, School of Fisheries and 

Ocean Sciences, Fairbanks; Denise Hawkins, U.S. Fish and Wildlife Service, Abernathy, 

Washington; and several anonymous reviewers for their very helpful comments on this 

document. Finally, we thank Ed Quimby, NWFSC, for technical editing and formatting.
xiv
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Abbreviations

DIP demographically independent population

DPS distinct population segment

EPA U.S. Environmental Protection Agency

ESU evolutionarily significant unit

FCA factorial correspondence analysis

IP intrinsic potential

MPG major population group

NMFS National Marine Fisheries Service

PSS TRT Puget Sound Steelhead Technical Recovery Team

SaSI Salmonid Stock Inventory

SASSI Salmon and Steelhead Stock Inventory

VSP viable salmonid population

WDF Washington Department of Fisheries

WDFG Washington Department of Fish and Game

WDFW Washington Department of Fish and Wildlife

WDG Washington Department of Game
xvi
Introduction

One of the goals of the Puget Sound Steelhead Technical Recovery Team (PSS TRT) is 

to identify historical demographically independent populations (DIPs) of steelhead 

(Oncorhynchus mykiss) in the Puget Sound distinct population segment (DPS). First, we 

consider historical population structure because the historical template is the only known 

sustainable configuration for the DPS. Second, we consider demographic populations as 

fundamental biological units and the smallest units for viability modeling. For each putative 

DIP, where possible, we describe the historical abundance and productivity, life history, 

phenotypic diversity, and spatial distribution of spawning and rearing groups. Understanding 

these population characteristics is critical to viability analyses, recovery planning, and 

conservation assessments. In many cases, the populations we identify will be the same as or 

similar to those identified by state agencies and tribal governments. Washington Department of 

Fisheries (WDF) et al. (1993) identified steelhead populations in their Salmon and Steelhead 

Stock Inventory (SASSI) and further refined them in the Washington Department of Fish and 

Wildlife (WDFW) Salmonid Stock Inventory (SaSI) document (WDFW 2002). Alternatively, 

differences in population structure may occur as a result of inherent differences in the criteria 

used to define populations and the underlying management purpose of some classification 

schemes. In the end, there is likely to be some uncertainty in historical populations presented in 

this document; however, we present a reasonable scenario that can then be used as a template for 

establishing a sustainable DPS. The populations identified in this document are those considered 

when answering the recovery goal question: How many and which populations are necessary for 

persistence of the DPS?

Definition of a Population

The definition of a population that we apply is defined in the National Marine Fisheries 

Service (NMFS) viable salmonid population (VSP) document for use in conservation 

assessments for Pacific salmonids (McElhany et al. 2000). In the VSP context, NMFS defines an 

independent population much along the lines of Ricker’s (1972) definition of a stock. That is, an 

independent population 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 our purposes, not interbreeding to a “substantial degree” means that two 

groups 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 period (McElhany et al. 2000). The exact level of reproductive isolation that is 

required for a population to have substantially independent dynamics is not well understood, but 

some theoretical work suggests that substantial independence will occur when the proportion of a 

population that consists of migrants is less than about 10% (Hastings 1993). Thus independent 

populations are units for which it is biologically meaningful to examine extinction risks that are 

intrinsic factors, such as demographic, genetic, or local environmental stochasticity. In general, 
2

the conditions necessary to maintain demographic independence (isolation) are not as strict as 

the conditions to maintain reproductive or genetic independence at the population level.

Independent populations will generally, but not necessarily, be smaller than a whole DPS 

and will generally inhabit geographic ranges on the scale of whole river basins or major 

subbasins that are relatively isolated from outside migration. Demographically and biologically, 

independent populations are the primary unit for viability assessments and recovery planning.

Structure above the Population Level

Just as there may be substructuring within a population, there may be structure above the 

level of a population. This is explicitly recognized in the designation of a DPS or an 

evolutionarily significant unit (ESU). A DPS or ESU may contain multiple populations that are 

connected by some common element. Thus organisms can be grouped into a hierarchical system 

in which we define the levels from individual to species. Although reproductive isolation forms 

a continuum, it probably is not a smooth continuum, and there is a biological basis for 

designating a hierarchy of levels. The concept of “strata” was developed by the Willamette 

Lower Columbia River TRT to help describe, where necessary, a level of structure intermediate 

between populations and DPSs (McElhany et al. 2003). A similar multiple population unit was 

developed for Chinook salmon (Oncorhynchus tshawytscha) by the Puget Sound TRT 

(geographic regions) and the Interior Columbia River TRT (major population groups). For 

consistency, the term major population groups (MPGs) has been adapted by the TRTs to describe 

these population aggregates. MPGs are generally used to capture major life history differences, 

distinct ecological zones, or geographic structuring. Where specific information was 

unavailable, we considered implied life history differences to exist where populations occupied a 

suitably large geographic region with unique ecological conditions (e.g., hydrology, thermal 

regime, estuarine conditions, etc.). Previous TRTs underscored the importance of MPGs by 

including them in the viability criteria. While criteria for DPS viability vary among the TRTs, 

there is some provision in all TRT viability criteria requiring the viability of all extant MPGs. 

Previous TRTs identified MPGs in conjunction with the development of viability criteria; we 

have elected to concurrently define DIPs and MPGs prior to establishing viability criteria.

Structure below the Population Level

Below the population level, there often will be aggregations of fish that are to some 

degree reproductively isolated from other groups of fish within the population, but that are 

insufficiently isolated to be considered independent by the criteria adopted here. These fish 

groups are referred to as subpopulations. Subpopulations play an important role in the 

sustainability and evolution of populations. However few populations have been studied 

sufficiently in depth to characterize any component subpopulations. The presence of 

subpopulations can have important consequences in the characterization of a VSP. Additionally, 

subpopulations can strongly influence population spatial structure, one of the four key 

parameters (along with abundance, productivity, and diversity) for evaluating the status of a 

population. Where possible, the TRT endeavored to describe internal variability in life history, 

ecological, or geographic structure for each population. For example, in some steelhead 

populations, returning adult winter-run and summer-run fish appear to comingle on the spawning 

grounds. At present there is insufficient information to determine the degree to which these two 
3

life history types are reproductively isolated in basins where they appear to co-occur in spawning 

habitats. As an interim measure, the TRT has identified these life history types as 

subpopulations within those specific populations rather than create separate DIPs. It is important 

to recognize multiple life history forms and the habitats that they rely on. Subsequent recovery 

actions must address this level of diversity in order to ensure the sustainability of the population. 

In many cases, the scale of available information limited the ability of the TRT to distinguish 

between DIPs and subpopulations, and ultimately the size of many DIPs was determined by the 

size of existing census or sampling units. Additionally, in some cases where there was only 

anecdotal information that a distinct population may exist or may have existed, the TRT used the 

subpopulation designation as a placeholder. Ultimately, the extent to which populations and 

subpopulations can be distinguished is determined by the acuity of the information available. 

The TRT thought it likely that future monitoring, especially on a finer scale, could provide 

sufficient new information to designate additional independent populations.

Conceptual Approach to Identifying Populations

To date, several TRTs have identified historical populations, extinct and extant, within 

listed salmonid ESUs and DPSs in the Pacific Northwest and California Recovery domains. 

There are marked differences in the methodologies utilized by the TRTs in identifying 

populations (McClure et al. 2003, Myers et al. 2006, Ruckelshaus et al. 2006, Lawson et al. 

2007), although the underlying definitions for both population and MPGs are similar. These 

differences have evolved in part from the varying quantity and quality of historical and current 

data on listed fish within each of the recovery domains. Differences also reflect biological 

differences among species, ESUs, and DPSs that are in turn related to major geographic and 

ecological differences in recovery domains. For example, ecological conditions in coastal or 

interior areas have a strong influence on life history characteristics, interpopulation interactions, 

and overall metapopulation structure. Additionally, the factors influencing reproductive isolation 

are likely to be different for tributaries to a large river system compared to independent basins 

along the Pacific coastline. As a starting point for this process, we have relied on the work done 

by the SASSI (WDF et al. 1993) and SaSI (WDFW 2002) steelhead stock inventory processes 

(Appendix A).

We also reviewed previous TRT work on Puget Sound Chinook salmon (Ruckelshaus et 

al. 2006). It is likely that, in general, Puget Sound steelhead have responded similarly to the 

ecological and geographic topography that shaped the distribution and discreteness of Chinook 

salmon populations. Given that there is considerably more genetic, life history, migration, and 

abundance information available for Puget Sound Chinook salmon populations than for 

steelhead, the population structure developed for Chinook salmon provided a useful preliminary 

template. However, there are considerable differences in life history strategies and habitat 

utilization between Chinook salmon and steelhead. At a minimum, in contrast to Chinook 

salmon and other Pacific salmon, steelhead are iteroparous, can exist as a resident or anadromous 

form, generally have much longer freshwater juvenile residency, spawn and rear in a wider range 

of stream sizes, and spawn in the spring on a rising thermograph. Spring spawning may also 

diminish the potential for steelhead redds to be scoured by major rain or rain-on-snow events. In 

most cases, the TRT concluded that these life history differences resulted in substantial 

differences in the overall population structure between Chinook salmon and steelhead in Puget 

Sound, with steelhead populations capable of inhabiting smaller watersheds and persisting at 
4

lower abundance levels. Some inferences were also drawn from the Willamette and Lower 

Columbia River TRT’s population document (Myers et al. 2006) that identified populations for 

co-occurring coastal Chinook salmon, coho salmon (O. kisutch), and chum salmon (O. keta) and 

steelhead populations. Ultimately, the TRT relied on both these previous efforts and historical 

and contemporary Puget Sound steelhead information to establish criteria for identifying DIPs 

for the Puget Sound DPS.

Part of the suite of information needed to identify demographically independent 

populations includes interpopulation migration rates and the demographic and genetic 

consequences of those migrations. In practice, information regarding straying of naturally 

produced salmon and steelhead between streams is rarely available. Where population-specific 

information was lacking, our approach for identifying population structure was to use other 

sources of information as proxies for understanding the degree of reproductive isolation between 

fish groups. Each source of information contributes to our understanding of population 

boundaries, but none alone provides us with complete certainty in our conclusion. In the 

following six subsections, we briefly outline the different information sources employed to help 

identify steelhead populations. They are discussed in order of the strength of inference that can 

be made about population structure from each indicator, beginning with relatively high inference 

that can be made with geographic and migration-rate indicators. Depending on the particular 

data quality and the genetic and demographic history of steelhead in different regions, the utility 

of these indicators in any one area can vary.

Migration Rates

The extent to which individuals move between populations determines the demographic 

independence among sites and, to a lesser degree, reproductive isolation among sites. As 

described earlier, demographic independence may exist with migration rates as high as 10% 

(McElhany et al. 2000). Empirical stray rates are particular to the group of fish, season, and 

streams in which they are estimated; thus they provide useful information about straying under 

specific conditions, but should be applied cautiously as a general estimate. Given the limited 

monitoring efforts for steelhead, it is impossible to estimate the magnitude of among-group

migration variation over long time periods (e.g., 100 years) except through estimates of gene 

flow based on population genetic analysis. It should be noted that demographic rates of 

exchange (movement of adults between populations) can be several times greater than the 

genetic rates of exchange (the successful reproduction of adults migrating between populations).

Migration rates usually are estimated using the recovery of tagged adults. Fish are tagged 

using a variety of external tags or internal coded wire tags or passive integrated transponder 

(PIT) tags. Hatchery-origin fish are generally marked for a variety of data needs including 

contribution to fisheries, identifying hatchery fish on natural spawning grounds, and identifying 

broodstock sources for hatcheries. Unfortunately, compared to Chinook or coho salmon, few 

steelhead releases are tagged. Coded wire tags have been utilized for the management of coastal 

mixed stock fisheries and, because the majority of steelhead appear to move quickly offshore,

there are very few inshore recoveries of steelhead, tagged or untagged. Directed steelhead 

fisheries, primarily tribal and sport, are in terminal (e.g., riverine) areas and not in coastal mixedstock areas, thus there has been minimal incentive to tag steelhead other than marking hatcheryorigin fish with a fin clip. In addition, as steelhead are iteroparous, carcass recoveries on or near 
5

the spawning grounds are rare. In contrast, tag recoveries from spawned-out Pacific salmon 

carcasses are a major source of information on straying and the contribution of hatchery fish to 

naturally spawning populations. In addition, the majority of winter-run and summer-run 

steelhead hatchery populations in the Puget Sound DPS are unrepresentative of the native 

populations in basins into which those hatchery fish are released. Finally, hatchery fish are 

readily transferred between hatchery sites for rearing and incubation, factors that would likely 

reduce homing fidelity for hatchery fish to the point of release.

In general, the homing fidelity of steelhead is thought to be at least as finely tuned as that 

of Chinook salmon. For hatchery-origin Chinook and coho salmon, the majority (>95%) of adult 

recoveries occurred within 25 km of the juvenile release sites (Myers et al. 2006, Ruckelshaus et 

al. 2006). In addition to observational mark-recapture data and other direct estimates of straying, 

genetically based estimates of intergroup isolation can be used to estimate straying between fish 

groups integrated over longer time periods. More importantly, genetic monitoring of migration 

between populations provides a measure of successful introgression by migrants, rather than 

simply the physical presence of migrants in a nonnatal watershed.

Some caution should be used in interpreting available data on migration rates. 

Substantial decreases in fish abundance during the past century may have dramatically reduced 

the connectivity between populations. In addition, as population abundance decreases, the rate 

of within-population genetic drift (random changes in allele gene frequencies) increases and 

genetic divergence between populations may arise that was not historically present. 

Alternatively, with the decrease in the size of spawning populations, the genetic influence of 

each successfully reproducing migrant increases. Although interpopulation migration rates are 

useful in identifying independent populations, there was little empirical information available 

that is directly relevant to Puget Sound steelhead.

Genetic Attributes

There are two categories of genetic differences that can be used to distinguish 

populations. Physical or behavioral traits, specifically ones with a genetic basis, and base-pair 

coding variation of specific sequences, are both useful in understanding the distinctiveness of 

populations. Phenotypic (expressed) traits may be under natural selection and reflect different 

environmental pressures. Alternatively, measures of differences in DNA coding can be 

expressed as allozyme variation in the specific sequence variation at specific loci (microsatellite 

DNA and single nucleotide polymorphism) and are generally thought to reflect neutral (random) 

variation in the genome. Neutral genetic markers are useful in identifying salmon and steelhead 

populations because they indicate the extent of reproductive isolation among groups. In contrast, 

genetically influenced phenotypic differences may be useful in distinguishing populations that 

experience different environmental conditions, but cannot readily distinguish reproductively 

isolated populations that share common habitat conditions. However, reliance on phenotypic 

traits may also incorrectly distinguish fish within a population exhibiting variable life history 

strategies.

While genetic variability can provide information on the breeding structure within and 

relationships between provisional populations, neutral marker results can sometimes be difficult 

to interpret, because patterns may reflect hatchery breeding practices or nonequilibrium 
6

conditions such as population bottlenecks or genetic drift. Additionally, DIPs that have only 

recently become isolated may not yet express genetic divergence. For example, the Cedar, 

White, and Green rivers have all experienced dramatic changes in their flow paths within the last 

100 years that created three geographically distinct basins from what was historically a single 

basin. The genetic analysis of steelhead present in these three basins shows very little 

divergence among them, reflecting their shared genetic lineage. While neutral genetic markers 

provide a relatively direct measure of genetic differences, differences in morphology or life 

history characteristics may also be useful as expressions of underlying genetic differences,

depending on the mechanism of expression. Adaptive life history differences between 

presumptive populations are likely reflective of ecological differences in the natal streams and 

are in part indicative of underlying genetic differences. Since the degree of isolation necessary 

to maintain genetic independence is much higher than that for demographic independence, 

genetic information will tend to give a more conservative measure of demographic population 

structure. That is, populations that are genetically significantly different are almost certainly 

demographically independent; alternatively, some populations that do not appear to be 

genetically distinct may still be largely independent demographically.

Our knowledge of steelhead population genetics in Puget Sound is based on a number of 

older allozyme-based studies (e.g., Phelps et al. 1997) and several recent but more 

geographically limited studies using microsatellite DNA markers (e.g., Kassler et al. 2008). In 

some cases, interpretation of results from these studies may be limited by uncertainty in 

estimating the degree of introgression by nonnative hatchery fish into populations. We lack 

genetic data for populations prior to the large, widespread, and sustained releases of hatchery 

stocks. Thus we cannot directly estimate genetic impacts to population structure from hatchery 

fish spawning naturally over the time period of interest. Phelps et al. (1997) suggested that there 

was little evidence for hatchery introgression in most basins sampled. Kassler et al. (2008) 

found evidence of interbreeding between native North Fork Skykomish River steelhead and the 

nonnative summer-run hatchery stock (Columbia Basin origin) released in the Skykomish River. 

A number of steelhead genetics studies are underway throughout Puget Sound and we used 

preliminary results from some of these. Final results from projects are pending. Although the 

state of knowledge of Puget Sound steelhead population genetics is growing, it is clear that much 

more work is needed. The TRT used what genetic data and results were available to best meet 

the requirements of identifying DIPs and MPGs. Analysis of recent genetic collections from 

Puget Sound steelhead populations can be found in Appendix B. As appropriate data become 

available, it will be important to reevaluate population genetic relationships and DIP 

designations.

Geography

The boundaries of a steelhead population are influenced in part by the spatial confines of 

its spawning habitat. Physical features such as a river basin’s topographical, hydrological, and 

temperature characteristics dictate to a large degree where and when steelhead can spawn and 

delimit the spatial area over which a single group of fish can be expected to interact. For 

example, the TRT distinguished between streams draining directly to Puget Sound and those that 

were tributaries to larger river systems in the assessment of population independence because of 

potential differences in homing fidelity. Geographic features such as elevation, geology, and 

precipitation will determine flow distribution, riverbed characteristics (substrate size, stream 
7

width, and depth) and water conditions. Geographic constraints on population boundaries (such 

as distance between streams) can provide a useful starting point, but geographic constraints will 

not generally support strong inferences at a finer scale (e.g., distinguishing separate populations 

within tributaries of a subbasin). In addition, biogeographical characteristics and historical 

connections between river basins on geological time scales can be informative in defining 

population boundaries.

Patterns of Life History and Phenotypic Characteristics

Phenotypic traits based on underlying genetic variation (rather than environmentally 

induced variation) are useful in identifying distinct populations defined on the basis of 

reproductive isolation and demographic independence. Variation in spawning time, fecundity, 

age at juvenile emigration, age at maturation (including repeat spawning), and ocean distribution 

are, to some degree, genetically influenced (Busby et al. 1996, Hard et al. 2007). Differences in 

the expression of those traits that influence fitness are generally thought to be indicative of longterm selection for local conditions, although depending on the trait, a substantial portion of most 

variation observed is still due to purely environmental effects. Hydrological conditions (i.e., 

water temperature, times of peak and low flows, etc.) influence the time of emigration and return 

migration and spawning, and over time (several generations) will influence life history traits best 

adapted to local conditions. While a population may be genetically adapted to general conditions 

in its natal basin, individual fish within the population will still vary in their life history traits due 

to genetic variability and in their individual response to environmental cues. In the face of 

dramatic ecological fluctuations (e.g., El Niños, Pacific decadal oscillations) each population is 

expected to strike a balance between being highly adapted to local conditions and maintaining 

multiple life history strategies (bet hedging).

Observed variation in life history traits can be used to infer genetic variation and may 

indicate similarities in the selective environments experienced by salmonids in different streams. 

In some cases, similarities in phenotype may arise independently in distinct populations, and the 

absence of phenotypic differences does not preclude that populations are distinct. The TRT 

accepted the premise that phenotypic differences in life history traits between populations 

(especially those that have recently diverged) do provide a strong level of support for geographic 

separation and the presence of distinct populations.

Population Dynamics

Abundance data can be used to explore the degree to which demographic trajectories of 

two fish groups are independent of one another. All else being equal, the less correlated two 

time series of abundance are between two fish groups, the less likely they are to be 

demographically interrelated. For steelhead, however, the majority of population abundance 

estimates are based on index area redd counts taken in the winter and spring when periods of 

relatively high flow and poor visibility can result in considerable uncertainty in the accuracy of 

these data. Further complicating the interpretation of correlations in abundance are the 

potentially confounding influences of correlated environmental characteristics, such as shared 

estuarine and ocean conditions or region-wide drought. Harvest effects also may result in 

correlations of abundance when distinct populations share oceanic and inshore migratory routes 

or simply share harvest management goals. However, the majority of Puget Sound steelhead 
8

sport and tribal harvest takes place in freshwater and shared harvest effects would predominantly 

only affect populations within the same river basin. Similarly, hatchery releases can confound 

any correlation between two populations, especially if the magnitude of releases is different and 

the relative contribution of hatchery fish to escapement is unknown or subject to a high degree of 

uncertainty.

When fish groups in close proximity are not correlated in abundance over time, they are 

likely to be demographically independent. Alternatively, as discussed above, when a strong 

positive correlation in abundance between fish groups is detected, it is not necessarily true that 

the two provisional populations are really one population. The TRT considered population 

dynamics as a “one-way” discriminatory character. The lack of a positive correlation between 

populations strongly suggests demographic independence, while the existence of correlated 

trends does not necessarily rule out the existence of distinct populations. Examining trends in 

population abundance offers an intuitively straightforward method of establishing demographic 

independence; however, in practice this criterion was only of limited use in identifying DIPs,

given the relatively poor quality of escapement data. Additionally, most populations in the DPS 

were experiencing substantial declines in abundance.

Environmental and Habitat Characteristics

In identifying demographically independent populations, environmental characteristics 

can influence population structure in two ways. First, environmental characteristics can directly 

isolate populations. Physical structures, falls or cascades, can isolate resident from anadromous 

populations or allow only one-way (downstream) migration, or anadromous populations within a 

basin can be separated by temporal migration barriers (run timing) or simply distance. Thermal 

or flow conditions in a river can create temporal migrational barriers that prevent interactions 

between populations (e.g., the cascades on lower Deer Creek, North Fork Stillaguamish River). 

Second, environmental conditions may exert a selective influence on salmonid populations, 

which in turn over time may influence the expression of life history characteristics, producing 

populations that are highly adapted to local conditions. The strength of the correlation between 

habitat and life history characteristics may be related to homing fidelity and the degree to which 

populations in ecologically different freshwater habitats are effectively reproductively isolated 

(e.g., thermal differences may produce differences in spawn timing). If immigrants from other 

populations are less fit, they will not contribute to the long-term demographics of the receiving 

population. Alternatively, populations from ecologically similar regions that are geographically 

separated will still function as distinct demographic units. Therefore, environmental factors 

alone may have a sufficiently strong effect on the isolation of geographically proximate 

populations (e.g., a higher elevation summer-run population separated from a lowland winter-run 

population by a cascade or falls), justifying their designation as independent populations. 

Alternatively, when life history characteristics are especially plastic, fish migrating between 

populations will effectively “blend in” with the local population with little potential for 

environmental selection.

Classifying basins according to their predominant ecological characteristics was useful in 

comparing presumptive populations. There was some concern however that large river basins 

(e.g., Nooksack, Skagit, and Snohomish rivers) included a wide diversity of ecological 

conditions, from high-gradient snowmelt-dominated streams to lowland rain-dominated streams, 
9

and an overall basin classification system might ignore this. Reproductively isolated populations 

along gradients of environmental conditions might not be evident based only on proximity of 

spawning ground locations. Thus we particularly scrutinized potential effects of environmental 

conditions on population structure within large basins. Lack of population structuring in large 

basins may indicate that steelhead populations are more phenotypically plastic and less locally 

adapted than environmental conditions would suggest. We also acknowledge that there may be 

multiple distinct populations in an environmentally diverse basin, which are undetectable using 

existing data.
10

Identifying Historical Populations of Salmonids

The first goal of the PSS TRT was to identify historical populations of steelhead in the 

Puget Sound DPS. Having established historical DIPs, the second goal of the TRT was to 

provide a historical overview of the diversity of life history characteristics, ecological conditions, 

productivity, and abundance for recovery planning purposes. It is not the TRT’s task to develop 

recovery plans to restore historical conditions completely, but rather to determine in general the 

population structure necessary to restore the needed aspects of life history diversity, population 

distribution, and abundance in order to provide for a sustainable DPS into the foreseeable future. 

Definitions of sustainability and the necessary conditions for achieving sustainability will be 

provided by the TRT in a subsequent technical memorandum: Viability Criteria for Steelhead 

within the Puget Sound Distinct Population Segment (Hard et al. in press).

Criteria for Identifying the Distribution of Historical Populations

Tier 1 Criteria

The task of identifying historical populations in the Puget Sound Steelhead DPS is 

challenging because 1) there are few detailed historical (pre-1900) accounts of steelhead 

populations and 2) anthropogenic factors (hatchery releases, hatchery transfers between 

populations, harvest effects, habitat degradation and elimination) most likely have significantly 

influenced the characteristics and distribution of present-day populations. Additionally, because 

there are relatively few offshore or coastal fisheries for steelhead, there have been only limited 

efforts to collect population-level information useful for managing mixed-stock fisheries. As a 

result, detailed biological profiles are available for only a few contemporary steelhead 

populations in Puget Sound. To compensate for lack of specific information, we used habitatbased productivity models to develop a template for general geographic and ecological 

characteristics of an independent population. A stepwise process (Appendix C) was utilized by 

the TRT to guide the discussion and evaluation of potential DIPs. In general, three primary 

(Tier 1) criteria were used to identify historical DIPs:

1. Documented historical use,

2. Sustainability under historical conditions, and

3. Demographic independence.

For the majority of presumptive DIPs, there was insufficient information to directly 

address the sustainability and demographic independence criteria, and few populations satisfied 

all three Tier 1 criteria. To address the sustainability issue, one would need a historical 

assessment of productivity and abundance. Historical sources can provide some quantitative 

measures of abundance, primarily harvest estimates (commercial, tribal, and sports fisheries) and 

hatchery weir counts. More frequently, historical documents provided qualitative measures, 
11

generally reporting the presence of significant spawning aggregations in reports or surveys. In 

the absence of information on harvest intensity or hatchery collection protocols, any expansion 

of this information to estimate total run size cannot be done with great precision. Anecdotal 

accounts were useful in establishing historical presence, but it was more challenging to quantify 

abundance from notations such as “They were thick as crickets” (Stone 1885). For the purpose 

of identifying DIPs, it is only necessary to establish a minimum threshold for sustainability, 

whereas estimating historical run size is more useful in population viability modeling. At best, 

however, the available historical information is useful for identifying major centers of

abundance, but is less helpful in describing the relationships between populations, especially 

those in smaller independent tributaries.

The TRT discussed at length what a minimum size metric for a sustainable steelhead 

population would be. Based in part on recommendations in Allendorf et al. (1997), the TRT 

concluded that an effective population size (Ne) of 500 per generation was an appropriate 

minimum size for a DIP. The relationship between effective population size and census size (N) 

also was discussed at length. Waples et al. (1993) suggested that, for Interior Columbia Basin 

Chinook salmon populations, this ratio is on the order of 0.20 to 0.25. Ford et al. (2004) found 

similar results for Oregon coastal coho salmon. Steelhead life history characteristics are in many 

ways substantially different from those of Pacific salmon. Overall, the net effect of these 

differences would result in an increase in the ratio between Ne and N. Araki et al. (2007) 

estimated the Ne/N ratio to range from 0.17 to 0.40, depending on the influence of resident O. 

mykiss and hatchery-origin breeders. It is likely that the presence of resident O. mykiss that 

produce anadromous adult offspring, either by interbreeding directly with their anadromous 

counterparts or independently, contributes significantly to abundance dynamics of the 

anadromous population. This contribution may be especially important when ocean conditions 

are poor and the survival of the anadromous component is low. The fact that steelhead are 

iteroparous further increases the number of effective parents in a population and may reduce 

between-year variability. Assuming Puget Sound steelhead have an average generation time of 4 

years, a minimum effective steelhead population size of 500 anadromous fish per generation 

translates to an effective number of breeders (Nb) of 125 fish per year. If the Ne/N ratio for 

steelhead is higher than that for semelparous Pacific salmon, perhaps as high as 0.50, then the 

minimum annual escapement for a population would need to be 250 fish. In other words, with 

250 anadromous spawners in a year, one could expect 125 effective breeders that year. A 

number of TRT members voiced some disagreement about the estimate of 250 fish per year 

being the minimum escapement needed to meet effective size threshold. Alternative escapement 

estimates were roughly balanced at levels below and above the 250 fish estimate. Varying 

escapement estimates were utilized in combination with habitat-based models of productivity to 

establish a relative run size minimum for a sustainable population.

Tier 2 Criteria

Demographic independence can be directly established through an interpopulation 

migration estimate using genetic information or physical tags. However, much of this type of 

information is very limited for steelhead in general and does not exist for many contemporary 

steelhead populations. In lieu of a direct measure, indirect measures of isolation (Tier 2 criteria) 

were employed to gauge the degree of demographic independence. These included:
12

1. Basin size and stream characteristics (length and wetted area);

2. Temporal isolation (different run or spawn timing);

3. Geographic isolation (migration distance between populations1

);

● Relative population size—where population size differentials exist, small migration 

rates from large populations into small populations could preclude independence of 

the small population;

4. Basin-specific information (e.g., barrier falls or cascades);

5. Ecological distinctiveness;

● Ecoregion—geology, rainfall, temperature, elevation;

● Hydrology—rain or snow driven, timing and magnitude of peak and low flows;

● Streambed characteristics (gradient, confined, etc.); and

● Within-basin elevation.

Geographic criteria were developed to infer selective and isolating factors that may be 

instrumental in establishing and maintaining DIPs. This information was used in the absence of 

relevant biological information delineating historical salmonid populations. In some instances, 

presumptive populations that did not meet the criteria for DIPs but exhibited one or more of the 

characteristics of distinct populations were considered subpopulations. Subpopulation 

designations were intended to highlight areas where some level of population structuring may 

exist and where further study should be directed. For example, in the Skagit and Sauk rivers 

summer-run and winter-run steelhead spawning aggregations are temporally but not 

geographically separated, and further data are needed to establish whether these two life histories 

are demographically and genetically distinct. Where present, subpopulations are an important 

diversity component and are considered in the diversity piece of the population viability 

assessment.

Sustainability and Independence

For an independent population to persist in the face of environmental fluctuations and 

other stochastic events, it must maintain a sufficiently large population size. Whether a 

population must contain hundreds or thousands of individuals to be sustainable is the subject of 

considerable debate, but at a minimum, hundreds of individuals are likely necessary. Thus the 

potential for a watershed to sustain a population large enough to be independent will be strongly 

related to the size of the basin, the size of the river, and the productivity of the river. The size of 

a basin and the topography and flow of the river may also influence homing accuracy. The 

presence of a seasonal or complete migration barrier or barriers provides an added if not 

substantial degree of reproductive isolation.

Boundaries between distinct populations could be inferred where rivers diverge into 

distinct tributaries or where sizable areas of poor or absent spawning habitat effectively separate 

 1 Ideally, the distance would be measured between spawning areas, but because that information was not always 

available and subject to year-to-year variability, the TRT opted for tributary mouth-to-mouth distance over water as 

a conservative measure of the distance.
13

spawning areas. If large enough, tributary basins may provide ecologically distinctive habitats 

and characteristic homing (olfactory) cues that reinforce the establishment of independent 

populations. At a minimum, differences in ecology may minimize the “attractiveness” of a 

nonnatal stream type. Lawson et al. (2007) considered distance between mouths of independent 

rivers entering marine waters a very important isolating mechanism.

Steelhead in the Puget Sound DPS spawn in streams from the northwest boundary with 

Canada, through South Puget Sound, in Hood Canal, and throughout the Strait of Juan de Fuca to 

and including the Elwha River (Figure 1). Many of the contemporary spawning distributions are 

well-known (WDF et al. 1993, WDFW 2002), in contrast to information for most basins on the 

location of present day juvenile rearing areas or historical spawning distributions. Disjunct 

spawning areas can suggest discontinuity between populations, especially where ecological 

differences or physical barriers coincide with separations between spawning aggregations. 

Geographic data on spawning reaches were available for only a limited number of rivers; in 

addition, there is considerable annual variability in spawner distribution. Therefore, geographic 

distances (kilometers) separating spawning areas were defined as the shortest nautical distance 

separating river mouths (Appendix D). This measure was considered a conservative estimate of 

the minimum distance between presumptive populations. Distances were calculated using 

network routing tools in ArcMap (Esri, Redlands, California) and 1:100,000 scale National 

Hydrography Dataset (U.S. Geological Survey) streams. The “starting” and “ending” locations 

(such as river mouths) were used to create a network from the National Hydrography Dataset

data.

The theory of island biogeography (MacArthur and Wilson 1967), when applied to 

salmon populations, suggests that a “minimum catchment area” could exist which defines the 

minimum watershed area needed to support a self-sustaining steelhead population. Catchment 

areas for major Puget Sound river basins vary by almost two orders of magnitude. SaSI 

populations (WDFW 2002) range from more than 3,946 km2 for the entire Skagit River basin to 

slightly less than 80 km2 in the Dewatto River basin or Snow Creek. Myers et al. (2006) did not 

establish a minimum catchment area for steelhead in the Lower Columbia River, but speculated 

that it could be smaller than the 25,000 ha/250 km2 threshold utilized for Chinook salmon DIPs 

in the Lower Columbia River.

After reviewing existing run sizes and basin areas, the TRT concluded that 80 km2

may 

be the minimum basin size threshold for a sustainable, demographically independent steelhead 

population in Puget Sound. This threshold was based on the basin size for the Snow/Salmon 

Creek basin (89 km2

), a system that many in the TRT concluded was representative of a selfsustaining population. Setting the threshold basin size slightly below that of the Snow/Salmon 

Creek basin was thought to ensure an inclusive set of potential DIPs to be considered. It was 

also recognized that specific conditions might exist in some basins to significantly raise or lower 

this threshold. For example, basin productivity and hydrology may be positively influenced by 

the presence of a lake (inaccessible or not) in the basin, as is the case with the Snow Creek basin. 

Lakes may act positively by increasing productivity (nutrient input into the stream) or may 

simply attenuate the hydrograph to minimize flooding scour events. Ultimately, it was 

concluded that the use of a 80 km2 basin size or 104,000 m2 high intrinsic potential (IP) (see 

Table 1) criteria was probably not a definitive threshold, but minimized the likelihood of a 
14

Figure 1. Location of winter-run and summer-run stocks within the Puget Sound Steelhead DPS. Stock 

designations are based on WDFW (2002) SaSI designations. Not all SaSI steelhead stocks are 

included in the DPS; specifically not included are South Fork Stillaguamish River (above Granite 

Falls), South Fork Skykomish River (Sunset Falls), and the Deschutes River.

Table 1. Stream habitat rating matrix (below natural barriers) for Puget Sound steelhead. Stream size and 

gradient categories were assigned by TRT members based on consideration of the Interior 

Columbia TRT’s IP model and on expert opinion. The TRT used these basin characteristics to 

calculate the IP of Puget Sound steelhead basins in order to establish whether a large enough 

population could be sustained into the foreseeable future.

Stream gradient

(percent)

Bankfull width

0–3 m 3–20 m >20 m

0.0–0.25 High Moderate Low

0.25–4.0 Moderate High Moderate

>4.0 Low Low Low
15

Type II error (failure to reject a false null hypothesis) and provided a useful first filter for 

prospective DIPs.

We calculated catchment area for each entire basin (based on a topographical Geographic 

Information System [GIS] model) and for accessible portions of each basin for Puget Sound 

streams using both known natural and man-made barriers (Williams et al. 1975, StreamNet 

2012). In large watersheds such as the Skagit River, which contain major tributaries (Appendix 

D), the calculation of catchment area excluded portions of the watershed above major upstream 

confluences (e.g., the lower Skagit River includes the area from the river’s mouth to its 

confluence with the Sauk River). We adopted these estimates as a preliminary step in 

developing a list of prospective steelhead DIPs. Gibbons et al. (1985) directly measured O. 

mykiss juvenile (parr) densities in a number of Puget Sound streams and categorized stream area 

productivity according to stream size and gradient. The TRT generated estimates of stream 

length, stream area (wetted bankfull area), and stream gradient using GIS-based models. 

Gradient was calculated using 100 m reaches. To estimate historical capacity, these data were 

integrated into an IP model adapted from the Interior Columbia TRT’s model based primarily on 

stream size and gradient. For Puget Sound steelhead, we simplified the model to only three 

stream gradient classes, 0–0.25%, 0.25– 4%, and greater than 4% gradient, and to three stream 

widths: 0–3 m, 3–20 m, and greater than 20 m. Stream habitat was initially classified as having 

low, moderate, and high productivity (Table 1).

There are a number of estimates for steelhead freshwater productivity. Chapman (1981) 

estimated freshwater production under pristine conditions at 0.0877 parr/m2 (equivalent to 

0.0263 smolts/m2

). Gibbons et al. (1985) developed a more complex productivity model, based 

on stream gradient and size, with parr productivity for Puget Sound streams varying from 0.05 to 

0.12 parr/m2

, with small independent tributaries having some of the highest productivities. On 

average, western Washington stream productivity was 0.0717 parr/m2 with 0.0265 spawners/parr 

(Gibbons et al. 1985). Similarly, the U.S. Army Corps of Engineers (1988) estimated potential 

steelhead freshwater productivity at 0.067 parr/m2 for streams and 0.041 parr/m2 for rivers. We 

used an average estimate for parr productivity of 0.0754 parr/m2 with the Chapman (1981) parrto-smolt survival of 0.30, to establish a 0.023 smolts/m2 level of productivity. Low productivity 

areas (those with gradients >4%) were not included in the estimate of potential parr numbers. 

There was also considerable discussion on the productivity of large rivers (>50 m wide), because 

much of the bankfull area in larger rivers is not utilized by juvenile salmonids in the absence of 

in-river structures. With the exception of a few river systems, most notably the Skagit, relatively 

little of the IP habitat area considered included larger width rivers.

Overall, our IP estimates were similar to those for the Keogh River, 0.032 smolts/m2

(Tautz et al. 1992). Smolt-to-adult survival was calculated using a range conservatively based on 

Keogh River studies, 10 to 20% (Ward and Wightman 1989), to estimate average precontact 

estuary and ocean productivity. Providing a range of smolt-to-adult survivals helps underscore 

the uncertainties in the productivity estimates and environmental stochasticity.

Given the simplicity of this model, the TRT acknowledges that there is considerable 

uncertainty in the capacity estimates. The TRT used the IP estimate for Snow Creek (274–548 

steelhead for 10–20% smolt-to-adult survival) as a minimum value for identifying candidate 

DIPs. Where independent tributaries did not meet the IP threshold, multiple independent 
16

tributaries were combined to create presumptive DIPs; in some cases multiple iterations of 

independent tributaries were assessed. Collectively, the IP estimates for all of the Puget Sound 

Steelhead DPS represent a total production range of 306,831–613,662 steelhead using the 10–

20% smolt-to-adult survivals, respectively. The high estimate is about one-half to two-thirds of 

the historical estimates put forth by Hard et al. (2007) and Gayeski et al. (2011). Review of IP 

estimates and historical data also suggests that the IP capacity estimates tend to greatly 

underestimate productivity of summer-run steelhead basins with higher gradient stream reaches. 

In cases where IP estimates for summer-run steelhead DIPs were especially low, below threshold 

levels generally thought to represent sustainable populations, minimum abundance levels were 

established (Appendix D). IP estimates of productivity and historical peak escapement estimates 

should not be considered synonymous.

Ecological Information

The fidelity with which salmonids return to their natal streams implies a close association 

between a specific breeding aggregation and its freshwater environment. The selective pressures 

of different freshwater environments may be responsible for differences in life history strategies 

among stocks. Miller and Brannon (1982) hypothesized that local temperature regimes are the 

major factor influencing life history traits. If the boundaries of distinct freshwater habitats

coincide with differences in life histories that have a heritable component, this may indicate that 

conditions promoting reproductive isolation exist. Therefore, identifying distinct freshwater, 

terrestrial, and climatic (ecological) regions may be useful in identifying distinct populations.

The U.S. Environmental Protection Agency (EPA) established the “ecoregion” system of 

hierarchical designations (Figure 2) based on soil content, topography, climate, potential 

vegetation, and land use (Omernik and Gallant 1986, Omernik 1987). On a regional scale (i.e., 

Pacific Northwest), there is a strong relationship between ecoregions and freshwater fish 

assemblages (Hughes et al. 1987). For Puget Sound, ecoregions were largely differentiated 

based on elevation and the associated flora and precipitation. Also included in the ecological 

descriptions are present day river flow, modeled river flows, water temperature information, and 

climate data. Details of this analysis are more comprehensively covered in Appendix D.

Ruckelshaus et al. (2006) identified hydrologic regime (rain-, snow-, or rain/snowdominated precipitation) as a major factor influencing life history characteristics in Chinook 

salmon. It is probable that steelhead life history characteristics are similarly affected, perhaps 

more so because of the longer freshwater residency of steelhead relative to Chinook salmon. In 

reviewing ecological characteristics, the TRT focused on stream hydrology (annual flow pattern 

and flow rate), precipitation, stream temperature, water chemistry (where available), stream size 

(length, area, width), stream confinement, elevation, and gradient in their analysis. Basin 

characteristics were provided to the TRT in a number of different formats, including cluster and 

principle component analyses.

The differences in geography, hydrology, precipitation, vegetation, and geology 

identified among Level III ecoregions probably are substantial enough to differentially select for 

variations in life history strategy and provide a basis for ecological and geographic separation. 

In other words, ecoregions likely indicate separation substantial enough to result in reproductive 

isolation. Ruckelshaus et al. (2002) identified five ecological regions in Puget Sound for 
17

Chinook salmon: Nooksack, Northern Puget Sound (Samish River to Snohomish River), 

Southern Puget Sound, Hood Canal, and Strait of Juan de Fuca. These regions are conceptually 

similar to the ecological zones described for the Lower Columbia and Upper Willamette rivers 

(McElhany et al. 2003). For both Puget Sound Chinook salmon and Lower Columbia River 

Domain ESUs and DPSs, higher level ecological differences were ultimately used in the process 

for identifying MPGs.

Figure 2. Level III and IV ecoregions of the Northwestern United States map were compiled primarily at 

a scale of 1:250,000; it depicts revisions and subdivisions of earlier Level III ecoregions that were 

originally compiled at a smaller scale (Omernik and Gallant 1986, Omernik 1987). Level III 

ecoregions are indicated by a numeric code: 1 = Coast Range, 2 = Puget Lowlands, 4 = Cascades, 

and 77 = North Cascades. Level IV ecoregions are indicated by a lower case letter suffix. (Map 

and supporting documentation online at http://www.epa.gov/wed/pages/ecoregions/level_iv.htm.)
18

Biological Data

While homing fidelity is a major determinant of population structure and plays a key role 

in defining a population’s geographic bounds, estimates of homing fidelity or the rate and 

distance of interpopulation migration (aka straying) are largely unavailable for steelhead in Puget 

Sound. Interpopulation migration rates are most commonly estimated for salmonid species using 

coded wire tag–marked fish releases (primarily from hatcheries). In general, neither naturalorigin nor hatchery-origin steelhead have been marked with coded wire tags or similar originspecific tags to any great extent, hence the lack of data on steelhead stray rates. The results from 

recent experiments with acoustic tags in winter steelhead from Puget Sound will not be available 

in the near term, but will ultimately begin providing information that may or may not confirm the 

assumptions made by the TRT. Additionally, summer steelhead, which have an extended 

freshwater prespawning phase, seek cold water refuges in deep holding pools prior to spawning, 

and often these can be in nonnatal streams (or hatchery holding ponds). Therefore, unless adult 

summer-run steelhead are sampled at the time of spawning, there is little certainty that the 

collection point represents their natal stream. Some straying data exist for hatchery-origin 

steelhead, but many aspects of hatchery rearing and release programs are known to reduce the 

homing fidelity of returning fish. Schroeder et al. (2001) determined that stray hatchery winter 

steelhead comprised an average of 11% of the escapement in coastal Oregon streams. 

Furthermore, hatchery fish that were transported out of their natal stream and released accounted 

for the majority of these strays. Although Schroeder et al. (2001) did not specify the actual 

distances that the steelhead strayed from their point of release, it was apparent that straying rate 

was inversely proportional to the distance from the natal stream. As a conservative measure of 

migration rate, when distances between river mouths were used with the Schroeder et al. (2001) 

data, the rate of exchange dropped to low levels 25 km from the point of release and beyond 50 

km was mostly below 5% (Figure 3). Finally, there is some debate regarding the homing 

accuracy of steelhead relative to Chinook or coho salmon. It is thought that the extended 

duration of freshwater rearing expressed by steelhead should result in better homing accuracy 

than Chinook and possibly coho salmon. Further, the persistence of summer-run steelhead in 

specific small basins around Puget Sound has been suggested as evidence for relatively higher 

fidelity to their natal stream. Overall, while homing is an important consideration in establishing 

independent populations and there is an expectation that steelhead home with high acuity, there 

is little direct information to quantify this. 

Age structure has been used historically to identify steelhead from different freshwater 

environments as a proxy for population identification (Rich 1920, Marr 1943). Analysis of 

scales from naturally spawning adults was utilized to identify similarities in age at marine 

emigration and maturation among proposed populations. This information was used with 

caution because of the unknown origin of unmarked naturally spawning fish, the potential bias of 

fishery gear type or harvest rate on age structure, and the modification or loss of habitats that 

would preclude specific juvenile life history strategies. With a few notable exceptions, age 

structure did not appear to be an important diagnostic for identifying independent populations of 

Puget Sound steelhead.

Historical documentation of fish presence and abundance was based on harvest 

information, stream surveys, and observations reported by the Bureau of Commercial Fisheries 

(the progenitor to NMFS), WDF and Washington Department of Game (WDG, later combined to 
19

Figure 3. Steelhead homing rates. Distance from point of juvenile release (river mouth to river mouth) 

for returning adult steelhead. Proportion recovered is calculated separately for each river release 

group. (Recovery data from Schroeder et al. 2001).

Washington Department of Fish and Game [WDFG], now WDFW), the trade journal Pacific 

Fisherman, tribal accounts, popular sports literature, and various other sources. State and federal 

hatchery records also provided valuable insight into historical abundance and life history 

characteristics. Hatchery operations in Puget Sound were undertaken in nearly every major basin 

in the Puget Sound DPS. Where hatchery records were available, the number of returning adults 

and the timing of their return and maturation were of primary interest. Although studies with 

Pacific salmon species have documented the relative influence of hatchery introductions on local 

populations, the situation is less clear for steelhead. Early hatchery operations stressed the 

release of large numbers of sac fry that provided little benefit to populations they were intended 

to supplement or the fisheries to which they were intended to contribute.

The Pacific Fisherman (June 1914) article on rearing and feeding salmon fry summarized 

this practice:

To the thoughtful person, the system in vogue for many years of depositing 

salmon and other fry in the water as soon as possible after being hatched or after 

the yolk sac had been absorbed, seemed far from an ideal one.... The desire on 

the part of some fish commissions to make a large statistical showing of fry 

deposited at a small cost has also aided in perpetuating this method.

Although there were subsequent changes in hatchery protocols during the 1920s and 

1930s to extend the rearing period prior to release by a few weeks, it is likely that this provided 

little benefit in the survival of steelhead that normally reside in freshwater for 1–3 years. Until 
20

late in the 1940s, the majority of hatchery-propagated steelhead was released as subyearling 

juveniles. Studies by Pautzke and Meigs (1940, 1941) strongly suggested that these releases had 

little or no positive influence on subsequent runs and may have simply served to “mine” the 

natural run. Hatchery broodstock collections prior to 1940 therefore give some insight into the 

size and sustainability of some populations in spite of continuous broodstock mining, which in 

some cases continued for decades.

Some caution should be used in applying historical hatchery production figures to the 

overall analysis. For example, a review of hatchery operations in 1915 (WDFG 1916) 

discovered that “The superintendent supposedly in charge [of the Nisqually Hatchery] was 

discovered to be sojourning in the City of Tacoma with his entire family, although diligently 

maintaining his place on the state’s payroll.” In spite of the likely padding of some production 

numbers, it is clear that for several decades thousands of returning adult steelhead, both natural 

and hatchery-origin, were intercepted annually from streams in Puget Sound in order to sustain 

the very artificial propagation programs that were intended to improve the steelhead runs 

(Appendix E). More recent genetic studies by Phelps et al. (1994, 1997) detected introgression 

by hatchery steelhead stocks primarily in situations where hatchery fish had been introduced into 

relatively small stream basins with numerically few natural-origin steelhead. Additionally, 

hatchery steelhead have been established in some river basins or tributaries following the 

laddering of, or trapping and hauling operations at, falls or cascades that were natural migration 

barriers (e.g., Granite Falls on South Fork Stillaguamish River, Tumwater Falls on the Deschutes 

River, Sunset Falls on South Fork Skykomish River).

Furthermore, because of the magnitude of more recent hatchery releases, similarities or 

differences in abundance trends (especially those based on redd counts) do not necessarily 

indicate demographic independence or lack thereof. Hatchery fish can influence demographic 

data in three ways.

• When present on natural spawning grounds, they inflate the abundance of naturally 

spawning fish.

• Large releases of hatchery fish may reduce the survival of naturally-produced juveniles.

• Hatchery releases reduce estimates of natural productivity by adding more adults to the 

adult-to-spawner relationship. This is especially true if hatchery fish produce redds, but 

subsequent progeny survival is not equivalent to that of naturally produced fish.

For the purpose of population identification, hatchery influence on population 

demographics may not be as important a factor as it is in the estimation of population viability. 

In any event, there are few populations with sufficient information to test the correlation in 

abundance trends between populations. Furthermore, a number of TRT members identified 

ocean conditions as having a major influence on population demographics, enough so to obscure 

freshwater-derived differences.

Genetic analysis of spawning aggregations normally provides a quantitative method for 

establishing population distinctiveness. However, the influence of hatchery fish spawning 

naturally (potential genetic introgression) and the reduced abundance of naturally spawning 

populations has potentially affected the present day genetic structure of steelhead populations in 
21

Puget Sound, although in many cases it is possible to identify and remove hatchery-origin 

individuals from genetic analyses. In the absence of a historical genetic baseline, it is impossible 

to estimate the effects of hatcheries or abundance bottlenecks on steelhead population structure, 

although as more information becomes available, it may be possible to better quantify the effects 

of artificial propagation. These issues underscore the problem of identifying historical 

population structure based on contemporary sampling of existing populations. Despite these 

caveats, genetic information available from contemporary samples provided a useful framework 

for population structure in the Puget Sound Steelhead DPS.

Population Boundaries for Fish and Habitat

In determining population boundaries, both the accessible and inaccessible areas of the 

basin were considered. The accessible area of a basin is directly occupied during spawning, 

initial rearing, and migration, while estimates for the entire basin were based on topography and 

includes portions not occupied by the population (a GIS-based model estimated the boundaries 

of the watershed). By considering the entire basin, one acknowledges that inaccessible portions 

of the basin influence stream conditions in the occupied portion of the basin. It is important to 

consider historical and contemporary conditions in unoccupied headwater areas and their impact 

on the abundance and life history strategies of downstream fish assemblages. This approach 

does not affect the boundaries of the DPS, which include only the anadromous portion of each 

basin (see NMFS 2007).

Historical Documentation

Taxonomic Descriptions and Observations

Specific information on steelhead abundance, distribution, and life history in Puget 

Sound is fairly limited prior to the 1890s. Early confusion in identifying salmon and trout 

species prevented the consolidation of abundance and life history information. The fact that 

steelhead adults return to freshwater in the winter and spring when flows are high and visibility 

is low also limited observations. Furthermore, because steelhead are iteroparous, early settlers 

and naturalists were not confronted by streams lined with steelhead carcasses (in contrast to the 

numerous accounts of rotting salmon carcasses along streams). The Pacific Railroad surveys 

(aka the U.S. Exploring Surveys) conducted during the 1850s provided the first widely available 

descriptions of fish species in the Pacific Northwest, although Walbaum, a naturalist working for 

the Russian Imperial Court, had described the Pacific salmon species some 60 years previously. 

Two of the leading naturalists for the Pacific Railroad surveys, Girard (1858) and Suckley

(1858), compiled species descriptions from their own observations or from a number of other 

sources. Their efforts would later attract considerable criticism. Jordan (1931, p. 157) would 

later comment that, “Girard indeed did all a man could do to make it difficult to determine the 

trout.” Jordan’s opinion of Suckley was equally critical: “He succeeded in carrying the 

confusion to an extreme, making as many as three genera from a single species of salmon, 

founded on differences of age and sex” (Jordan 1931, p. 157). In the appendices to the Pacific 

Railroad surveys, Girard (1858) describes at least four species that could have represented the 

anadromous or resident O. mykiss, steelhead and rainbow trout, respectively: Salmo gairdneri, S. 

gibbsii, S. argyreus and S. truncates. Regardless of their inaccurate taxonomy, the Pacific 
22

Railroad surveys provide a number of important early observations of steelhead in the Pacific

Northwest and specifically the Puget Sound area.

In the Pacific Railroad surveys and other documents of the time, steelhead are commonly 

referred to as salmon-trout, although there is some possibility that the reference could be 

describing sea-run cutthroat trout (O. clarki) or, less likely, sea-run bull trout (Salvelinus 

confluentus) or Dolly Varden (S. malma).

2

 For the Puget Sound region, bull trout would be the 

predominant of the two Salvelinus species. It is generally possible to identify the proper species 

by considering the morphological descriptions and references to run and spawn timing. For 

example, Girard (1858, p. 326–327) quotes Gibbs describing a “salmon” that enters the Puyallup 

at the end of December, holds in the river until the snows begin melting (spring), then ascends 

the stream. These fish were apparently not abundant (relative to salmon at the time) and did not 

travel in schools. The fish weighed between 15 and 18 pounds (6.8 to 8.2 kg) and were silver 

with a bluish-gray dorsal surface.

3

 Girard (1858) also describes a S. truncates caught in the 

Straits of Fuca [sic] in February 1857, noting that this species rarely achieves weights over 12 

pounds and generally less. These fish enter rivers in the beginning of December and continue 

through January. They do not run up the streams in schools, but the run is more “drawn out.” 

The caudal fin is truncated, not forked. The fish was known to the Klallam Tribe as “klutchin” 

and to the Nisqually Tribe as “Skwowl.” Suckley (Girard 1858) described another square-tailed 

salmon, S. gairdneri, captured in the Green River, but which had a later run timing. The fish, 

known to the Skagetts [sic] as “yoo-mitch,” entered freshwater from mid-June to August, a run 

timing that corresponds to existing summer-run steelhead or less likely early returning (springrun or summer-run) Chinook salmon. Another account by Girard (1858) described a S. gairdneri

caught in the Green River as being bright and silvery, 28 inches long (71 cm), and not having a 

forked tail. Another probable steelhead description was provided to Girard by Cooper, but under 

the “scientific name” S. gibbsii (Girard 1858, p. 333). The fish was noted for having a 

“moderately lunated tail at its extremity” and heavily spotted fins. Cooper observed this “salmon 

trout” in the Columbia River basin east of the Cascades. In addition, he observed one caught in 

Puget Sound in March of 1855. There is a strong likelihood that most of these observations were 

of steelhead.

In addition to descriptions of presumptive steelhead, there are a number of observations 

of cutthroat trout. In assessing the historical changes in steelhead/rainbow abundance and habitat 

use, it is useful to understand the relationship between rainbow/steelhead and cutthroat trout. 

Girard (1858) identified Fario stallatus as the predominant trout in the Lower Columbia River 

and Puget Sound tributaries. Girard found this trout to be very abundant and distinguished by a 

patch of vermillion under the chin. This fish is most likely the cutthroat trout, and these 

observations support the contention that cutthroat trout were the primary resident trout in Puget 

Sound and the Lower Columbia River. Lord (1866) also noted that Fario stallatus “lives in all 

streams flowing into Puget’s Sound and away up the western sides of the Cascades.” These 

observations suggest a complex historical relationship between anadromous and resident O. 

mykiss and O. clarki. The presence of large numbers of O. clarki in smaller streams likely 

 2 Dolly Varden and bull trout were not recognized as distinct species until 1980 and most historical references only 

identify Dolly Varden, aka the “red-spotted trout” (Girard 1858). 3 Gibbs’ description generally fits steelhead, although he notes that it has a forked tail and there could be some 

confusion with spring-run Chinook salmon.
23

influenced the distribution and abundance of resident O. mykiss and to a lesser extent steelhead. 

In short, although it is clear that steelhead were historically found throughout Puget Sound, there 

is little basin-specific abundance and distribution information on either anadromous or resident 

O. mykiss to be gleaned from these early accounts.

The taxonomic status of steelhead took on a new importance in the late 1800s when sport 

and commercial fishers debated whether trout or salmon regulations applied to steelhead caught 

in freshwater.

Dr. David Starr Jordan, the renowned piscatorial expert, now at the head of the 

Stanford Jr. University, has declared that these fish belong to the trout family, but 

the fishermen, not those who fish for sport, but those who catch fish for a living, 

have decided that the steelhead is a salmon. Up to 1890 the steelhead was 

regarded as a salmon, but Dr. Jordan, after an exhaustive research, passed 

judgment that the public had been in error (San Francisco Call 1895).

Ultimately, this taxonomic distinction would have considerable consequences on the future 

exploitation of steelhead populations. As a “trout,” the steelhead were regulated by many states 

as a game fish in freshwater fisheries.

Historical Abundance

Analysis of historical abundance can be useful in identifying DIPs, especially where 

populations have experienced severe declines or been extirpated. Estimates of historical 

steelhead abundance in Puget Sound have largely been based on catch records, and it was not 

until the late 1920s that there was an organized effort to survey spawning populations of 

steelhead in Puget Sound (WDFG 1932). There are a number of considerations that need to be 

taken into account in estimating historical run sizes, especially from catch data. First, during the 

late 1800s and early 1900s, Chinook salmon was the preferred species for canning and, whereas 

there is an extensive database of the cannery packs, the fresh fish markets were not extensively 

monitored. Second, steelhead have a protracted run timing relative to Chinook salmon and do 

not tend to travel in large schools, making them less susceptible to harvest in marine waters. 

Finally, winter-run steelhead return from December through April when conditions in Puget 

Sound and the rivers that drain to it are not conducive to some commercial gear types. In the 

absence of standardized fishing effort estimates, it is impossible to report a time series for 

historical run size estimates with great accuracy and approximate harvest estimates must 

generally suffice. We have attempted to expand the peak harvest only in order to present an 

estimate of maximum run size rather than to develop a demographic trend.

Collins (1892) in his review of West Coast fisheries noted that steelhead are found in 

northern Puget Sound, although they are not as numerous as sockeye salmon (O. nerka), and that 

salmon trout4 are common in southern Puget Sound, especially near Olympia and Tacoma. In 

1888, 23,000 kg (50,600 lb) of fresh “salmon-trout” were marketed in the Puget Sound area. 

Catch records from 1889 indicate that 41,168 kg (90,570 lb) of steelhead were caught in the 

Puget Sound District (Rathbun 1900). Rathbun (1900) indicated that steelhead were being 

targeted by fishermen because the winter run occurred at a time when other salmon fisheries 

 4 It is not clear whether he is referring to steelhead, sea-run cutthroat, or both.
24

were at seasonal lows and steelhead could command a premium price, up to $0.04 a pound. In 

converting catch estimates to run size, the PSS TRT used an average fish weight of 4.5 kg, based 

on the size range 3.6 to 5.5 kg (8 to 12 lb) reported by Rathbun 1900. Based on this average, the 

1889 catch (41,118 kg) represents 9,148 steelhead, whereas a more conservative (higher) average 

weight of 5.5 kg (12 lb) would represent only 7,548 steelhead. These estimates do not allow for 

unreported commercial catch, sport catch, cleaning, or wastage. Analysis of the commercial 

catch records from 1889 to 1920 (Figure 4) suggests that the catch peaked at 204,600 steelhead 

in 1895. Sheppard (1972) reported that commercial catches of steelhead in the contiguous 

United States began to decline in 1895 after only a few years of intensive harvest. Using a 

harvest rate range of 30–50%, the estimated peak run size for Puget Sound would range from 

409,200 to 682,000 fish (at 4.5 kg average weight). Alternatively, Gayeski et al. (2011) 

expanded the 1895 harvest data, including estimates of unreported catch and using an average 

fish size of 3.6 kg to approximate historical abundance. Their estimate ranged (90% posterior 

distribution) from 485,000 to 930,000 with a mode of 622,000. In either case, it is clear that the 

historical abundance of steelhead was at least an order or magnitude greater than what is 

observed currently.

Figure 4. Harvest of steelhead in Puget Sound, 1889–1925. The y-axis is total catch in number of fish. 

In years without data points, harvest was reported as a combined salmon/steelhead harvest. (Data 

from Wilcox 1898, Rathbun 1900, WDFG 1902, 1907, 1913, 1916, 1925, Wilcox 1905, and 

Cobb 1911.)

0

50

100

150

200

250

1885 1890 1895 1900 1905 1910 1915 1920 1925 1930

Number of Fish (1,000s)

Year
25

Rathbun (1900) reported that the steelhead fishery occurred mainly in the winter and the 

majority of the harvest occurred in the lakes and rivers. Later reports described the majority of 

the harvest occurring in terminal fisheries (i.e., gill nets or pound nets) in Skagit, Snohomish, 

King, and Pierce counties (Cobb 1911). The county-by-county analysis suggests that the level of 

inclusion of Fraser River steelhead in the catch estimates was fairly low and that the majority of 

steelhead were likely harvested in their natal basins (Appendix F), with the possible exception of 

Clallam and Whatcom counties, where shore-based fish traps or set nets would have had the 

potential to intercept Fraser River–bound fish.

Even by 1898, the Washington State Fish Commissioner noted, “The run of this class of 

fish in the state on the whole has greatly depreciated, and the output for the present season from 

the best information possible is not fifty percent of what it was two or three years ago. Very 

little has been put towards the protection of this class of salmon” (Little 1898). Catches 

continued to decline from 1900 through the 1920s (Figure 2). The rapid decline in the Puget 

Sound steelhead catch after only a few years of intensive fishing is in contrast to other Pacific 

salmonids that sustained high harvest rates for decades before declining. One explanation 

suggests that larger, older, repeat spawners were important in maintaining steelhead productivity. 

High harvest rates would quickly remove existing repeat spawners and reduce the probability 

that returning females would survive to spawn more than once. Repeat spawner rates of around 

30% have been observed in Alaskan (Jones 1976) and British Columbian (Withler 1966) 

streams, levels that may approach those in historical populations.

The management of steelhead was ultimately transferred to the newly formed WDG in 

1921. In 1925 the Washington State Legislature classified steelhead as a game fish, but only 

upstream of the mouth of any river or stream (WDFG 1928), although by that time the Puget 

Sound catch was greatly diminished. Commercial harvest of steelhead in Puget Sound had fallen

to levels generally below 10,000 fish. In 1932 the newly formed Washington State Game 

Commission prohibited the commercial catch, possession, or sale of steelhead (Crawford 1979). 

After 1932, estimates of Puget Sound steelhead abundance were based on sportfishing catch, 

tribal catch, and spawning ground surveys.

Pre-1950 abundance: Basin-specific information

Artificial propagation efforts with steelhead began with the first hatchery releases in 

1900. Initial hatchery releases were primarily smaller fry and subyearling fish. These releases 

had varying degrees of success, although in the absence of marking hatchery-reared fish, it is 

difficult to estimate return rates. Work by Pautzke and Meigs (1941) demonstrated the 

importance of rearing juveniles for at least 1 year prior to release. In light of the likelihood that 

hatchery programs prior to 1950 contributed little to adult steelhead returns, we have used pre1950 abundance levels as estimates of natural productivity. In the early 1970s, artificial 

propagation programs were expanded in both quantity and geographic scope (Appendix G). 

After 1970 and until the widespread use of fin clipping to mark hatchery-origin fish, natural and 

hatchery contributions to spawning escapement cannot be parsed out.
26

Nooksack River

Wilcox (1898) reported that the fishery for steelhead in the Nooksack River was carried 

out up to 18 to 20 miles upstream from the mouth. For the 1895 fishery, Wilcox (1898) noted

that 300,000 kg (660,000 lb) of steelhead were caught in the Nooksack River alone (most other 

sources present harvest on a county basis). This would represent 66,000 fish (at 4.5 kg/fish). On 

a county-wide basis, Whatcom County continued to report a substantial steelhead fishery into the 

early 1900s. It is unclear to what extent Fraser River steelhead were captured by Whatcom 

County fishers, although shoreline fish traps at Point Roberts and along Bellingham Bay and 

Drayton Harbor likely intercepted large numbers of migrating steelhead.

Biological surveys of the North Fork Nooksack River and its tributaries during June and 

July 1921 noted that steelhead spawned in most of the tributaries (Norgore 1921). Surveys 

conducted in 1930 identified several “medium-sized” runs in the north, middle, and south forks

of the Nooksack River (WDFG 1932). Ernst (1950) reported that railway shipments of dressed 

steelhead in the past had averaged 230 kg (500 lb) during the 8-week peak of the run. Sport 

fishery catches in the 1940s and 1950s suggest that abundance had declined considerably and 

only relatively low numbers of steelhead were present, although glacial sediment in the north and 

middle forks of the Nooksack River likely limited observation, fishability, and ultimately sport 

harvest.

Samish River

There is very little information on the early abundance of steelhead in the Samish River 

and Bellingham Bay tributaries. The Samish River Hatchery was built in 1899, but did not begin 

intercepting steelhead for broodstock until 1907. There is no record of steelhead being 

transferred to the hatchery prior to this point, so it is most probable that the original broodstock 

was native to the basin. The Wenatchee Daily World (1906) reported a sport fisher catching a 

near-record steelhead in the Samish River in April (“Lands 30-pound trout”). Production levels 

during the initial years would have required a few hundred female broodstock (Appendix E).

Skagit River

Historical accounts indicate that the run of steelhead in the Skagit River extended from 

November 15 up to the following spring (Wilcox 1895). Only a “scattering” of steelhead were 

reported prior to December and a light run continued through the winter (Wilcox 1902). In 1899

steelhead marketed in La Conner, Washington (Skagit River), averaged 5 kg (11 lb). Little 

(1898) indicated that large numbers of “steel-heads” entered the Baker River and spawned from 

March to April.

Much of the historical information on steelhead in the Skagit River basin comes from 

broodstock collection activities in the early 1900s. In 1900 steelhead were first collected at the 

Baker Lake Hatchery for broodstock. From March 8 to May 9, 81 adults were captured at the 

base of the lake (Ravenel 1901). Of these, only 14 survived to spawn. The high mortality rate 

among the adults and subsequent egg lots was ascribed to maturation difficulties in the net pens. 

It is also possible that if the fish were summer-run steelhead, they would not have matured that 

first spring. Following construction of the Baker River Dam, returning steelhead arrived at the 
27

trap at the base of the dam from March to July (Harisberger 1931). Riseland (1907) reported that 

the Sauk River Hatchery collected steelhead spawn from the first part of February until June 15, 

with more than a million eggs collected in 1906. He commented that the collection would have 

been higher if the hatchery weir gates did not need to continually be raised to allow shingle bolts 

to pass downstream. The Sauk River was characterized as “an excellent spring Chinook and 

steelhead stream and the principal spawning stream of the Skagit” (WDFG 1925). Within the 

Skagit River basin, steelhead eggs were collected from the Baker River, Day Creek, Grandy 

Creek, Illabot Creek, and Phinney (Finney) Creek during the early 1900s. In most cases, these 

egg-taking stations intercepted hundreds of steelhead during their initial years of operation 

(Smith and Anderson 1921a). In 1929 the fish trap at Baker Dam collected 813 steelhead (WDG

no date-a). These fish would have represented the last year of returning “pre-dam” steelhead (4-

year-olds). Subsequent counts at Baker Dam declined to the tens of fish. In the absence of 

specific information related to the operation of weirs or hatchery traps, it is impossible to 

accurately expand the numbers of fish spawned to total escapement.

Stream surveys estimating the extent of natural production were not undertaken until 

some years after the initiation of the first hatchery programs. Additionally by this time, river 

clearing, timber harvest (including splash damming), mining, and land development, in general

had already severely degraded the productivity of a number of streams. Smith and Anderson 

(1921a) provided detailed descriptions of the Skagit River and its tributaries. Steelhead were 

found in “considerable numbers” up to the construction camp for Ross Dam near Nehalem. At 

that time, they identified Goodell Creek as the farthest branch of the Skagit from the mouth that 

contained anadromous fish. Smith and Anderson (1921a) also reported steelhead migrating at 

least as far as Monte Cristo Lake on the Sauk River. It was thought that releases of mining 

wastes had eliminated fish from the headwaters of the South Fork Sauk River, near the mining 

town of Monte Cristo. Through interviews with U.S. Forest Service rangers, Smith and 

Anderson (1921a) also identified a number of tributaries to the Suiattle River that contained runs 

of steelhead. Although the mainstem Suiattle is normally too ladened with glacial sediment to 

provide opportunities to observe or fish for steelhead, a number of the tributaries apparently run 

clear for part of the year. The North Fork Suiattle River, Downey Creek, Buck Creek, and Big 

Creek were all listed as containing steelhead runs. Stream surveys conducted in 1930 indicated 

that “large” aggregations of steelhead were found in Finney, Grandy, and Bacon creeks in the 

mainstem Skagit River and Jordan Creek in the Cascade River (WDFG 1932). Medium 

abundances were observed in the Baker River, Sauk River, and Cascade River. Mainstem Skagit 

River surveys were conducted in May of 1930 and in the Baker, Cascade, Sauk, and Suiattle 

rivers in August of 1930 (WDF 1932). Donaldson (1943) also observed “numerous” steelhead 

fingerlings in Tenas Creek during a stream survey in August 1943. The presence of steelhead, 

often in large numbers, throughout the 1920s and 1930s (despite substantial degradation to the 

freshwater habitat) suggests that the historical (pre-European contact) abundance of steelhead in 

the Skagit Basin was considerable.

Stillaguamish River

The fishery in the lower Stillaguamish River harvested an estimated 81,820 kg of 

steelhead in 1895 (18,200 steelhead at 4.5 kg.), although Wilcox (1898) suggests that the total 

could be considerably higher. WDFG (1916) recommended establishing an egg taking station on 

Canyon Creek, where “many eggs could be secured in Canyon Creek, particularly those of the 
28

steelhead variety, which are very valuable.” An article in the Seattle Daily Times (1918a) on 

September 21 indicated that pools in Canyon Creek contained hundreds of big (7 to 20 pound) 

steelhead (“Fishing Trips out of Seattle, No. 14, Canyon Creek”). Later surveys underscored the 

decline of salmon and steelhead runs, especially in Squire, Boulder, and Deer creeks (Smith and 

Anderson 1921a). Smith and Anderson (1921a) note that the egg-taking station in Canyon Creek 

spawned 245 steelhead in 1916 and the egg-taking station in Jim Creek spawned 173 steelhead in 

1919, the first years for steelhead collection for each site. In 1925 the WDF reported that, “for 

the past four years the station has been operated by the Game Division for the taking of steelhead 

spawn. It is understood that the eggs when eyed were transferred to other parts of the state with 

the result that the steelhead run in Canyon Creek is now about depleted” (WDFG 1925, p. 23). 

The WDFG surveys in 1929 identified large spawning populations in both the main stems of the 

North Fork and South Fork Stillaguamish, as well as Deer Creek and Canyon Creek, with 

medium-sized populations in Boulder, French, Squire, and Jim creeks (WDFG 1932).

Snohomish River

Snohomish River steelhead were reported to return from November 15 and were fished 

throughout the winter (Wilcox 1898). Steelhead harvest levels were estimated at 182,000 kg 

(401,000 lb) or 40,444 steelhead from the Snohomish River alone in 1895 (Wilcox 1898). 

Steelhead were identified as the most plentiful and valuable salmonid (better flesh quality 

allowed longer transportation times). Hatchery records from the Pilchuck River Hatchery 

indicate that 397 females were spawned in 1916 (WDFG 1918). Surveys undertaken by the 

WDFG in 1929 reported large aggregations of steelhead in the Pilchuck, Sultan, Skykomish, and 

Tolt rivers, and medium aggregations in the North Fork Skykomish, South Fork Skykomish, 

Wallace, Snoqualmie, and Raging rivers (WDFG 1932). Spawning at the Sultan River U.S. 

Bureau of Fisheries Hatchery occurred from April 8 to June 4 (Leach 1928). In general, the 

Snohomish River basin was one of the primary producers of steelhead in Puget Sound.

Green River (Duwamish River)

Interpreting historical abundance estimates is more complicated for the Green River due 

to its history of headwater transfers. In 1895 there were 45,900 steelhead (based on average 

weight of 4.5 kg) harvested in King County, with the Duwamish/Green River being the only 

major river in the county (Wilcox 1898). At this time the Duwamish Basin included the Black, 

Green, Cedar, and White rivers, in addition to the entire Lake Washington and Lake Sammamish 

watersheds. In 1906 floodwaters and farmers diverted the White River from the Green River to 

the Puyallup River. Furthermore, construction of the Headworks Dam (RKM 98.1) in 1911 on 

the upper Green River eliminated access to 47.9 km of river habitat. During the first 2 years of 

operation, an egg taking station (White River Eyeing Station) operated by the City of Tacoma 

collected 6,185,000 eggs in 1911 and 11,260,000 eggs in 1912 (WDFG 1913). There were no 

species-specific egg takes given, other than the 1911 production was from coho salmon and 

steelhead and the 1912 production included Chinook salmon and coho salmon in addition to 

steelhead (WDFG 1913). From 1 April 1912 to 31 March 1913, 1,308 steelhead were 

intercepted at the Headworks Dam (Grette and Salo 1986, as cited by Kerwin and Nelson 2000). 

Grette and Salo (1986) further estimated the steelhead escapement above the Headworks Dam 

ranged from 500 to 2,500, although they did not distinguish between summer-run and winter-run 

steelhead.
29

The Lake Washington Ship Canal (first year of operation in 1916) diverted Lake 

Washington and Lake Sammamish, their tributaries, and the Cedar River directly to Puget 

Sound. WDFG surveys in 1930, well after the major modifications to the watershed, identified 

large steelhead populations in the Green River and Soos Creek (WDFG 1932).

Puyallup River

Based on the harvest in 1909, approximately 30,000 steelhead were harvested in rivers in 

Pierce County (Cobb 1911). The WDFG 1930 survey found large steelhead aggregations in the 

Puyallup and Carbon rivers and medium sized aggregations in Voights Creek, South Prairie 

Creek, and the White River (WDFG 1932). In 1942, its second year of operation, nearly 2,000 

steelhead were collected below Mud Mountain Dam and transported to the upper watershed. 

Sport fishery catches for 1946 and 1947 in the Puyallup River averaged 2,846 fish (WDG no 

date-b), all of which were presumed to be of wild origin. During the 1949/1950 tribal harvest, 

2,176 steelhead were caught in the White River during January and February.

Nisqually River

Riseland (1907) described the Nisqually Hatchery as having a steelhead “spawn” that was

equal to that of most of our large hatcheries. In 1905, 962,000 steelhead fry were produced at 

the hatchery, a production level that would have required several hundred female steelhead. 

Hatchery production continued until 1919, when a flood destroyed the hatchery. At its peak in 

1912, the hatchery produced 1,500,000 fry. WDFG (1932) identified the Nisqually and Mashel 

rivers as having medium-sized spawning aggregations. Annual tribal harvest in the Nisqually 

River from 1935 to 1945 averaged approximately 1,500 steelhead, and the reported sport catch in 

the late 1940s varied from a few hundred to a few thousand fish (WDG no date-b).

South Puget Sound tributaries

The presence of steelhead in the South Puget Sound region was noted by Collins (1892): 

“Salmon trout occur about the head of Puget Sound in the vicinity of Olympia. Off Johnson 

Point and near Tacoma are noted fishing grounds for them. Considerable quantities are taken for 

market.” There is relatively little specific quantitative information available on the historical 

abundance or even presence of steelhead in the small independent tributaries draining into South 

Puget Sound. Commercial harvest data from 1909 lists steelhead catches for Thurston, Mason, 

and Kitsap counties that would represent a total escapement of several thousand fish, some of 

which are likely to have originated in the small South Puget Sound tributaries (Appendix F). 

Numerous other references to “salmon trout” fishing in the Olympia area were found in the sport 

literature from the 1800s and early 1900s. For example, an article in the Olympia Record (1909) 

reported that sportsmen were supporting a bill in the state legislature to prohibit netting in 

Olympia Harbor in order to protect salmon trout that were returning to local creeks. Sport 

fishery catch data from the 1940s to 1970s (WDG no date-b) indicate that steelhead catches 

varied annually from the tens to hundreds of fish in Goldsborough Creek, Mill Creek, Sherwood 

Creek, and other smaller creeks. Catch numbers within and among streams varied considerably 

from year to year. It is not clear to what degree this variation is due to true changes in 

abundance or differences in angler effort.
30

Skokomish River

Steelhead were historically present in the Skokomish River; Ells (1887) described 

“salmon-trout” as one of the stable foods of the Twana Tribe. Steelhead were found in both the 

north and south forks of the Skokomish River, although there is some uncertainty regarding the 

accessibility of Lake Cushman to anadromous migration. An article in the Daily Olympian 

newspaper (1897) reported that State Senator McReavey was requesting funds to build a fish 

ladder 3 miles below Lake Cushman to provide anadromous access to the lake. Although the 

ladder was never built, McReavey later testified that he had caught salmon in Big Creek, located 

above the “barrier” falls on the north fork (Olympia Daily Recorder 1921). In 1899 the WDF

established an egg-taking station on the north fork of the Skokomish River below Lake Cushman 

(WDFG 1902). During the first year of operation, the station took an estimated 1,500,000 

steelhead eggs (representing 533 females at 2,812 eggs/female 5

). For unexplained reasons, this 

station was subsequently abandoned 2 years later and the 1899 production figures may be viewed 

with some skepticism. Tribal harvest for winter-run steelhead averaged 351 fish from the 

1934/1935 to 1944/1945 return years, with harvests in the late 1950s averaging more than 2,000 

fish, although there is some hatchery contribution to these later catches. During the late 1940s 

and early 1950s, adjusted punch card–based estimates of the annual sport catch for presumptive 

wild winter-run steelhead averaged 610 fish, with an additional 88 fish caught annually during 

the “summer-run” harvest window (WDG no date-b).

Hood Canal, east side tributaries

There is little detailed information on steelhead abundance in creeks draining from the 

east side of Hood Canal. A number of newspaper accounts from the early 1900s specifically 

mention good steelhead fishing in the Tahuya River. In 1920 an egg-collecting station was 

established on the Tahuya River to intercept returning steelhead. In May and June of 1932, the 

WDF surveyed streams throughout Hood Canal. Of the 26 surveys available for review, all of 

the larger streams and many smaller creeks were reported to have spawning steelhead from 

January through March (WDF 1932). Mission Creek and Dewatto Creek were identified as 

having “good” runs and the Tahuyeh River [sic] contained a small to medium run. Anderson 

Creek, Union River, and Big Beef Creek were all reported to contain small spawning populations 

of steelhead. Smaller stream systems, for example Stavis and Rendsland creeks, all supported 

steelhead spawning, albeit at a low abundance in the 1930s. Additionally, both sea-run and 

resident cutthroat trout were observed throughout Hood Canal.

Hood Canal, west side tributaries

Records for these west side tributaries to Hood Canal are somewhat limited. At varying 

times during the early 1900s, the U.S. Bureau of Fisheries operated egg-collecting stations or 

hatcheries on Quilcene, Dosewallips, and Duckabush rivers. Although the primary objective of 

these operations was the collection of coho salmon and chum salmon eggs, a number of 

steelhead eggs were collected, especially from the Duckabush and Quilcene rivers. It was noted 

that the greater part of the steelhead run ascended by spring high water when the trap could not 

 5 This average steelhead fecundity is based on hatchery averages reported by WDFG (1918).
31

be operated, and many of the fish collected were “too immature to be retained in ponds” (Leach 

1928). Ripe fish were spawned from March 24 to May 1 in 1926.

In the 1932 survey (WDF 1932), the Dosewallips River was specifically mentioned as 

containing a “large run” of steelhead and the Hamma Hamma was reported to have a small to 

medium run of saltwater steelhead and cutthroat trout. Of the remaining creeks surveyed,

Mission, Little Mission, Dabob, Lilliwaup, Waketickeh, Jorsted, Spencer, Jackson, Finch, and 

Eagle creeks were all reported to have small spawning populations of steelhead. The steelhead 

run was observed to begin in January and February, and only a small portion of the steelhead run 

entered the Little Quilcene River before the hatchery weir was put in place in March. Steelhead 

were reported spawning during the late winter and early spring. Notably absent were surveys for 

the Skokomish and Duckabush rivers. Punch card records from the late 1940s to 1960s report 

catches of tens to hundreds of fish from several west side Hood Canal basins.

Dungeness River

In the 1940s, Pautzke (no date) of the WDF described the winter steelhead fishing in the 

Dungeness River as being among the best in the state. In 1903, during its second year of 

operation, the Dungeness Hatchery produced 3,100,840 steelhead. This production represents 

approximately 2,200 females.

6

 Riseland (1907), state fish commissioner, noted that the 

steelhead catch at the hatchery was the largest of any in the state (output in 1905 was 1,384,000 

steelhead), despite of the existence of numerous “irrigation ditches on the Sequin [sic] prairie 

that destroyed large numbers of young salmon.”

Elwha River

Construction of the Elwha Dam in 1912 blocked anadromous access to most of the river. 

There is little information other than anecdotal accounts of fishing in the river to describe the 

pre-dam status of steelhead population(s) in the basin. Rathbun (1900) identified the Elwha and 

Dungeness rivers as supporting both Native American and commercial fisheries. Wilcox (1905) 

reported only that the commercial catch for Clallam County was 52,000 pounds (23,636 kg). It 

is unclear whether these fish were caught in terminal fisheries or in the Strait of Juan de Fuca and 

destined for other basins in the Salish Sea.

Puget Sound Steelhead Life History

Of all the salmonids, O. mykiss arguably exhibits the greatest diversity in life history. In 

part, this diversity is related to the broad geographic range of O. mykiss from Kamchatka, Russia,

to southern California; however, even within the confines of Puget Sound and the Strait of 

Georgia, there is considerable life history variation. Resident O. mykiss, commonly called 

rainbow trout, complete their life cycle in freshwater. Anadromous O. mykiss, steelhead, reside 

in freshwater for their first 1 to 3 years before emigrating to the ocean for 1 to 3 years before 

returning to spawn. Also, in contrast to Pacific salmon, O. mykiss is iteroparous, capable of 

repeat spawning.

 6 This assumes 50% survival from green egg to fry and an average fecundity of 2,812. Also note that these fish 

would all have been natural origin.
32

There are two major life history strategies exhibited by anadromous O. mykiss. In 

general, they are primarily distinguished by the degree of sexual maturation at the time of adult 

freshwater entry (Smith 1969, Burgner et al.1992). Stream-maturing steelhead, or summer-run 

steelhead, enter freshwater at an early stage of maturation, usually from May to October. These 

summer-run steelhead migrate to headwater areas and hold for several months prior to spawning 

in the following spring. Ocean-maturing steelhead, or winter-run steelhead, enter freshwater 

from November to April at an advanced stage of maturation, spawning from February through 

June. Steelhead are somewhat distinctive in exhibiting multiple run times within the same 

watershed (Withler 1966).7

The winter run of steelhead is the predominant run timing in Puget Sound, in part because 

there are relatively few basins in the Puget Sound Steelhead DPS with the geomorphological and 

hydrological characteristics necessary to maintain the summer-run life history. The summer-run 

steelhead’s extended freshwater residence prior to spawning results in higher prespawning 

mortality levels relative to winter-run steelhead. This survival disadvantage may explain why 

winter-run steelhead predominate where there are no seasonal migrational barriers.8

In 1900 a Smithsonian Institution study reported that Puget Sound steelhead begin 

returning to freshwater as early as November, but that the principal river fisheries occurred in 

January, February, and March when “the fish are in excellent condition” (Rathbun 1900). The 

average weight of returning steelhead was 3.6–6.8 kg (8–15 lb), although fish weighing 11.4 kg 

(25 lb) or more were reported. The principal fisheries were in the Skagit River basin, although in 

“nearly all other rivers of any size, the species seems to be taken in greater or less quantities” 

(Rathbun 1900). The spawning season of winter-run steelhead was described as occurring in the 

early spring, but possibly beginning in the latter part of winter.

Information on summer-run steelhead in Puget Sound is very limited. In fact, in its 1898 

report, the Washington State Fish Commission concluded that the Columbia River was “the only 

stream in the world to contain two distinct varieties of steel-heads” (Little 1898). Little (1898) 

did indicate, however, that the winter run of steelhead continued from December through the first 

of May, and overlapping runs of winter and summer steelhead may have been considered a 

single population. Evermann and Meek (1898) reported that B.A. Alexander examined a number 

of steelhead caught near Seattle in January 1897 and the fish were in various stages of 

maturation: “A few fish were spent, but the majority were well advanced and would have 

spawned in a short time.” Returning steelhead were historically harvested from December 

through February, using in-river fish traps rather than trolling in salt water (Gunther 1927).

Much of the life history information taken early in the 1900s comes from the collection 

and spawning of steelhead intercepted at hatchery weirs. The U.S. Fish Commission Hatchery at 

Baker Lake initially collected steelhead returning to Baker Lake using gill nets. Fish were 

collected from March 9 to May 8, few survived to spawn, and no spawning date was given 

(USBF 1900). Later attempts to collect fish from Phinney [Finney] and Grandy creeks in March 

met with limited success; based on a survey of these creeks and the Skagit River, it was 

 7 Other salmonid species, mainly Chinook salmon and to a lesser extent coho salmon, exhibit multiple run times in 

the same watershed.

8 D. Rawding, WDFW, Vancouver, WA. Pers. commun., 12 May 2004.
33

concluded that much of the run entered the rivers in January (Ravenel 1901). During the first 

years of operation of the Baker Dam, 1929–1931, steelhead were passed above the dam from 

April to July. Peak entry to the dam trap occurred during April. Although a relatively large 

number of fish were spawned in May 1931 (51 fish), on 15 June 1931, when spawning 

operations had ceased, 92 “green” (unripe) fish were passed over the dam (Harisberger 1931). It 

is unclear whether these fish would have spawned in late June or July, or whether they would 

have held in freshwater until the next spring (i.e., summer-run steelhead). Riseland (1907) 

reported that the Sauk River Hatchery collected steelhead spawn from the first part of February 

until June 15. Steelhead were spawned at the Quilcene National Fish Hatchery in Hood Canal 

from February 27 to June 7, 1922 (USBF 1923). Stream survey reports for Hood Canal indicated 

that the steelhead spawn during the late winter and early spring (WDF 1932). It should be noted 

that this spawning time was only noted for tributaries on the east side of Hood Canal (Dewatto 

Creek, Tahuyeh [sic] River, Big Beef Creek) or smaller tributaries on the west side of Hood 

Canal (Jorsted Creek, Little Quilcene River, Little Lilliwaup Creek); larger tributaries were 

generally too turbid to survey. These larger rivers (primarily Dosewallips and Duckabush) 

originate in the glacial fields of the Olympic Mountains and it is likely that the temperature and 

flow regimes in these rivers would produce a different run timing from the lowland, raindominated rivers on the east side of Hood Canal.

Pautzke and Meigs (1941) indicated that the run arrived in two phases: “In the early run 

the fish are small, averaging 8 or 9 pounds. The later run is composed of fish as large as 16 or 18 

pounds.” It is unclear whether these phases were distinct runs or different segments of the same 

run. In general, summer-run fish run later in the spring than winter-run fish, and the former also 

tend to be physically smaller than the latter, although historically this may not have been the 

case. Scale analysis indicates that the majority of first-time spawning summer-run fish have 

spent only 1 year in the ocean. WDG records from the 1930s indicate a north-south differential 

in spawn timing (Figure 5), although the timing of egg collection in the hatcheries may not be 

fully representative of natural spawning timing. The egg collection time for the Dungeness 

River appears to be especially late. A Seattle Daily Times column (1923) also notes that the 

Dungeness River steelhead run is much later than those found in Hood Canal. Pautzke (no date) 

stated that, “During the summer and fall this river [Dungeness] is the conductor of large runs of 

Chinook and humpback [aka pink, O. gorbuscha] salmon, also the steelhead trout.” This would 

suggest the presence of a summer run in the Dungeness River. Pautzke further stated that the 

winter steelhead fishing in the Dungeness River was one of the best in the state. A Port Angeles 

resident9 reported that the Dungeness River produced both winter-run and summer-run steelhead 

in the 1940s. Summer-run fishing extended up into the Gray Wolf River and there was some 

overlap between the two run times, with the summer-run fish appearing in May. A Seattle Times 

article reported summer-run steelhead caught in the Grey Wolf River in August (Bradner 1945). 

Alternatively, in the southern tributaries to Puget Sound, the steelhead spawning/egg-take data 

for the Puyallup Hatchery indicated that this stock of fish spawned earlier than those at other 

hatcheries (Figure 6). In some years, the majority of the spawning took place prior to March 15, 

the date presently used to distinguish naturally spawning Chambers Creek Hatchery fish from 

“native” fish. Similarities in spawn timing between the steelhead captured at the Puyallup 

Hatchery and the widely used Chambers Creek winter-run hatchery stocks may be related to the 

close geographic proximity of the two basins.

 9 D. Goin, Port Angeles, WA. Pers. commun., 21 November 2011.
34

Figure 5. Temporal distribution (proportion of total egg take) of egg collection for steelhead returning to 

WDG facilities in 1932 and 1938. Egg collection dates may not be representative of natural 

spawn timing. There was no egg collection at the Green River Hatchery in 1932. (Data from 

Washington State Archives no date).

Nooksack

Samish

Skykomish

Green River

Puyallup

Dungeness

0

0.1

0.2

0.3

0.4

0.5

0.6

Proportion of Egg Take

Date

1932

Nooksack Samish Skykomish Green River Puyallup Dungeness

Nooksack

Samish

Skykomish

Green River

Puyallup

Dungeness

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Proportion of Egg Take

Date

1938

Nooksack Samish Skykomish Green River Puyallup Dungeness
35

Figure 6. Standardized distribution of steelhead eggs collection at the Puyallup Hatchery from 1932 to 

1939, 1933 and 1934 not included. (Data from Washington State Archives no date.)
36

Certainly given the variations in spawning times between 1932 and 1938, some caution 

should be used in associating peak spawning timing at the hatchery with peak timing for natural 

spawning. Despite the obvious caveats, historical hatchery spawning records provide important 

information on within-population and between-population differences in spawn timing.

There is only limited documentation on the age structure of Puget Sound steelhead from 

historical (pre-1950) sources. Work by Pautzke and Meigs (1941) indicated that the majority of 

steelhead from the Green River emigrated to estuary and marine habitats in their second year 

(third spring), then remained at sea for 2 years. Scales from returning adults indicated a minority 

of the fish had been 1-year-old or 3-year-old smolts. Although the historical record is sparse,

there appears to be little difference in age structure to first spawning between samples from the 

1940s and present day collections (Table 2).

Within the Puget Sound Steelhead DPS, both major steelhead life history strategies are 

exhibited: summer-run timing (stream maturing) and winter-run timing (ocean maturing). Each 

strategy includes a suite of associated traits that ultimately provide a high degree of local 

adaptation to the specific environmental conditions experienced by the population. In some 

cases, there is a clear geographic distinction between spawning areas containing winter-run or 

summer-run steelhead; for example, in short, rain-dominated streams or above partially 

impassable barriers, respectively. In other areas, winter-run and summer-run steelhead can be 

found utilizing the same holding and spawning habitat, and it may appear that there is a 

continuum of returning adults. In cases where both runs comingle on spawning grounds, it is 

unclear whether these two life history types exist as discrete populations, a diverse single 

population, or a population in transition. Pending further genetic and life history studies, the 

TRT will treat these populations as single, mixed-run DIPs.

Table 2. Freshwater ages at the time of migration to the ocean. The two populations in italics are 

representative populations outside the Puget Sound Steelhead DPS. W = winter-run steelhead 

and S = summer-run steelhead. The frequency in boldface indicates the most common age. 

(Includes data from Busby et al. 1996).

Population Run

Freshwater age at ocean migration

1 2 3 4 Reference

Chilliwack River W 0.02 0.62 0.36 <0.01 Maher and Larkin 1955

Skagit River W <0.01 0.82 0.18 <0.01 WDFW 1994

Skagit River (fishery) W <0.01 0.56 0.27 0.067 Hayman 2005

Deer Creek S — 0.95 0.05 — WDF et al. 1993

Snohomish River W 0.01 0.84 0.15 <0.01 WDFW 1994

Green River W 0.16 0.75 0.09 — Pautzke and Meigs 1941

Puyallup River W 0.05 0.89 0.06 — WDFW 1994

White River W 0.20 0.72 0.08 0.00 Smith 2008*

Nisqually River W 0.19 0.80 0.01 — WDFW 1994

Minter Creek W 0.03 0.85 0.12 — Gudjonsson 1946

Snow Creek W 0.09 0.85 0.06 — Johnson and Cooper 1993

Elwha River W 0.08 0.77 0.15 0.00 Morrill 1994

Hoh River W 0.03 0.91 0.06 — Larson and Ward 1955

* B. Smith, Fisheries, Puyallup Tribe of Indians, Puyallup, WA. Pers. commun., 5 August 2008.
37

Winter-Run Steelhead

In general, winter-run (ocean maturing) steelhead return as adults to the tributaries of 

Puget Sound from December to April (WDF et al. 1993). This period of freshwater entry can 

vary considerably, depending on the characteristics of each specific basin or annual climatic 

variation in temperature and precipitation. Spawning occurs from January to mid-June, with 

peak spawning occurring from mid-April through May (Table 3). Prior to spawning, maturing 

adults reside in pools or in side channels to avoid high winter flows during the relatively short 

prespawning period.

Steelhead generally spawn in moderate gradient sections of streams. In contrast to 

semelparous Pacific salmon, steelhead females do not guard their redds, but return to the ocean 

following spawning, although they may dig several redds in the course of a spawning season 

(Burgner et al. 1992). Spawned-out fish that return to the sea are referred to as kelts. Adult male 

steelhead may be relatively less abundant among fish returning to the ocean after spawning, and 

males usually form a small proportion of repeat (multiyear) spawning fish, based on scale pattern 

analyses (McGregor 1986, McMillan et al. 2007, Appendix H). If there is lower postspawning 

survival of winter-run males overall, it may be due to the tendency of males to remain on the 

spawning ground for longer periods than individual females in an effort to spawn with multiple 

females, or fighting in defense of prime spawning areas or mates (Withler 1966).

In Puget Sound, winter steelhead are found both in smaller independent streams that drain 

directly into Puget Sound and the Strait of Juan de Fuca and in larger rivers and their tributaries. 

The smaller drainages generally experience rain-dominated hydrological and thermal regimes 

(with the exception of smaller streams draining the Olympic Mountains), while the larger rivers 

are influenced by rain-and-snow-transitional or snow-dominated hydrological regimes. It is 

likely that differences in habitat conditions are reflected in the life history characteristics (i.e., 

migration and spawn timing) of winter steelhead inhabiting these two types of basins. For 

example, it appears that steelhead spawn earlier in smaller lowland streams where water 

temperatures are generally warmer than in larger rivers with higher elevation headwaters.

Summer-Run Steelhead

In many cases, the summer migration timing is associated with barrier falls or cascades. 

These barriers may temporally limit passage in different ways. Some are velocity barriers that 

prevent passage in the winter during high flows, but are passable during low summer flows, 

while others are passable only during high flows when plunge pools are full or side channels 

emerge (Withler 1966). In Puget Sound, winter-run steelhead predominate, in part because there 

are relatively few basins with the geomorphological (e.g., basalt rock strata) and hydrological 

characteristics necessary to create the temporal barrier features that establish and sustain the 

summer-run life history. In general, summer-run steelhead return to freshwater from May or 

June to October, with spawning taking place from January to April. During the summer-run 

steelhead’s extended freshwater residence prior to spawning, the fish normally hold in deep 

pools, which exposes the fish to prolonged predation risk and seasonal environmental extremes, 

likely resulting in higher prespawning mortality relative to winter-run steelhead. This potential 

survival disadvantage may explain why winter-run steelhead predominate where there are no 
38 

Table 3. Puget Sound steelhead freshwater migration and spawning periods.* WR-W = winter run, wild; SR-W = summer run, wild; and WRH/W = winter run, hatchery/wild. The letter s indicates months of observed spawning and the letter P indicates the peak spawning period. 

Shaded months indicate observed freshwater migration (entry) in recent years.

Run Years River, tributary, or area (basin) May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr

Undescribed MPG

WR-W 1973 Puget Sound tributaries s s s s s s

WR-W 2007 Puget Sound small tributaries s s s

Northern Cascades MPG

WR-W 1931–1937 Nooksack River s s

WR-W 1937–1938 Nooksack River s

WR-W 2007 Nooksack River P s s s s

WR-W 1931–1940 Samish River s s s

WR-W 2007 Samish River s s s s P

WR-W 1907 Sauk River (Skagit River) s s s s s

WR-W 2007–2013 Skagit River P s s s

WR-W 1931–1932 Skykomish River (Snohomish River) s s s s s

WR-W 1935–1940 Skykomish River (Snohomish River) s s

WR-W 2007 Snohomish River s s s P

WR-W 2007 Stillaguamish River P s s s

Central and South Puget Sound MPG

WR-W 1897 Central Puget Sound tributaries s

WR-W 2007 Lake Washington tributaries s s s P

WR-W 1940 Issaquah Creek (Lake Washington/Lake 

Sammamish)

s s

WR-W 1935–1937 Green River s s

WR-W 1937–1938 Green River s s s

WR-W 1940 Green River s s

WR-W 2007 Green River s s s P

WR-W 1931–1932 Puyallup River s s s s

WR-W 1935–1936 Puyallup River s s s

WR-W 1936–1938 Puyallup River s s s s s s

WR-W 1940 Puyallup River s s

WR-W 2007 Puyallup River s s s P

WR-W 2007 Nisqually River s s s P

WR-W 2007 Deschutes River s P s s

WR-W 2000s South Puget Sound tributaries s P P
39 

Table 3 continued. Puget Sound steelhead freshwater migration and spawning periods.* WR-W = winter run, wild; SR-W = summer run, wild; 

and WR-H/W = winter run, hatchery/wild. The letter s indicates months of observed spawning and the letter P indicates the peak 

spawning period. Shaded months indicate observed freshwater migration (entry) in recent years.

Run Years River, tributary, or area (basin) May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr

Hood Canal and Strait of Juan de Fuca MPG

WR-W 2007 Skokomish River s s s s P

WR-W 2007 Tahuya River s s s P

WR-W 2007 Dewatto River s s s P

WR-W 2007 Discovery Bay tributaries s s s s P

WR-W 2007 Morse Creek s s s s P

WR-W 1931–1932, 

1937, 1940 

Dungeness River s s s s

WR-W 1935–1936 Dungeness River s s s s

WR-W 1937–1938 Dungeness River s s

WR-W 2007 Dungeness River P s s s

WR-W 2012 Elwha River tributaries s s s

Northern Cascades MPG

SR-W 2007 Cascade River (Skagit River) s s s s

SR-W 2007 Sauk River (Skagit River) s s

SR-W 2007 S. F. Stillaguamish River s s s s

SR-W 2007 Deer Creek (Stillaguamish River) s s s

SR-W 2000s N. F. Skykomish River (Snohomish River)

Northern Cascades MPG

WR-H/W 2008–2013 Five small Skagit River tributaries s s s s s

WR-H/W 2005–2013 Finney Creek (Skagit River) s s s s s s

WR-H/W 2010 Cascade River (Skagit River) s s s

WR-H/W 1997–2011 Upper Skagit River s s s s

WR-H/W 1998–2008 Sauk River (Skagit River) s s s s s

Hood Canal and Strait of Juan de Fuca MPG

WR-H/W 1984–1991 Morse Creek s s s s s s

* Data compiled from historical and current literature or raw spawning surveys:Abernethy 1886, Barin 1886, Birtchet and Meekin 1962, WDFW 2002, Pflug et 

al. 2013, and McMillan unpubl. data. 
40

migrational barriers.10 In at least two or possibly three Puget Sound river systems lacking 

obvious migration barriers, the Skagit, Sauk, and Dungeness rivers, there appear to be cooccurring winter-run and summer-run steelhead. The circumstances in each river are somewhat 

different and further discussion is provided in the specific population descriptions.

The life history of summer-run steelhead is highly adapted to specific environmental 

conditions. Because these conditions are not commonly found in Puget Sound, the relative 

incidence of summer-run steelhead populations is substantially less than that for winter-run 

steelhead. Summer-run steelhead have not been widely monitored, in part because of their small 

population size and the difficulties in monitoring fish in their headwater holding areas. Much of 

our general understanding of the summer-run life history comes from studies of Interior 

Columbia River populations that undergo substantial freshwater migrations to reach their natal 

streams. Sufficient information exists for only 4 of the 16 Puget Sound summer-run steelhead 

populations identified in the 2002 SaSI (WDFW 2002) to determine their population status. 

There is considerable disagreement on the existence of many of the SaSI-designated summer-run 

steelhead populations. This is due in part to the use of sport and tribal catch data in establishing 

the presence of summer-run steelhead. Steelhead caught after May were thought to be summerrun fish; however, in many basins with colder, glacial-origin rivers, adult return and spawning 

times for winter-run fish can extend well into June (e.g., the Dosewallips River). Additionally, 

kelts may reside in freshwater for several weeks after spawning and appear in catch records 

through July. In the absence of a substantial database on summer-run steelhead in Puget Sound,

considerable reliance was placed on observations by local biologists in substantiating the 

presence of summer-run steelhead.

In contrast to the classical scenario where summer-run steelhead populations are present 

only above temporally passable barriers, the PSS TRT considered a number of situations where 

summer-run and winter-run steelhead were observed holding and spawning in the same river 

reach, primarily in the Skagit River basin. Based on the information available, there appears to 

be some temporal separation between the two runs in spawning times, although genetic 

information is not available to establish whether there is complete reproductive isolation. 

Furthermore, this occurrence is not sporadic and has occurred regularly each year. It was unclear 

how the two run times could persist with overlapping niches. One suggestion was that the 

summer-run fish might represent anadromous progeny from resident O. mykiss above nearby 

impassable barriers and that the summer-run fish are not self-sustaining, but maintained by 

regular infusions of migrants from above barriers. In the absence of empirical data, such as 

genetic analysis of winter-run and summer-run steelhead and resident O. mykiss to establish 

whether two co-occurring runs in a basin are indeed DIPs, the TRT opted to include both run 

times as components of an inclusive DIP. Further investigation is warranted to ensure proper 

management for these fish.

Juvenile Life History

The majority of naturally produced steelhead juveniles reside in freshwater for 2 years 

prior to emigrating to marine habitats (Table 2 through Table 5), with limited numbers 

emigrating as 1-year-old or 3-year-old smolts. Additional age-class distributions are in 

 10 See footnote 8.
41

Appendix H. Smoltification and seaward migration occurs principally from April to mid-May 

(WDF et al. 1993). Smolt size varies according to age and location. Wydoski and Whitney 

(1979) and Burgner et al. (1992) give an average length for 2-year-old naturally produced smolts 

as 140–160 mm. Alternatively, steelhead smolts from the Keogh River averaged 171 mm in 

2002 (McCubbing 2002). Unmarked steelhead smolts from the Dungeness averaged 170 mm

with a range of 109–215 mm, and similarly, smolts from the Green River averaged 153 mm with 

a range of 120–195 mm (Volkhardt et al. 2006). Moore et al. (2010) reported that smolts from 

Hood Canal streams ranged 159–235 mm. The inshore migration pattern of steelhead in Puget 

Sound is not well-known, and it was generally thought that steelhead smolts moved offshore 

within a few weeks (Hartt and Dell 1986). Recent acoustic tagging studies (Moore et al. 2010) 

have shown that smolts migrate from rivers to the Strait of Juan de Fuca from 1 to 3 weeks.

Ocean Migration

Steelhead oceanic migration patterns are largely unknown. Evidence from tagging and 

genetic studies indicates that Puget Sound steelhead travel to the central North Pacific Ocean 

(French et al. 1975, Hartt and Dell 1986, Burgner et al. 1992), although these conclusions are 

based on a very limited number of recoveries in the open ocean.

Puget Sound steelhead feed in the ocean for 1 to 3 years before returning to their natal 

stream to spawn. Typically, Puget Sound steelhead spend 2 years in the ocean obtaining weights 

of 2.3–4.6 kg (Wydoski and Whitney 1979), although notably, Deer Creek summer-run steelhead 

only spend a single year in the ocean before spawning (Table 4 and Table 5).

11 Tipping (1991) 

demonstrated that age at maturity (ocean age) was heritable in steelhead. Additionally, the return 

rate was similar for fish that spent either 2 or 3 years at sea, and Tipping (1991) concluded that 

the majority of ocean mortality occurred during the first year at sea. Acoustic tagging studies are 

currently underway to better understand the use of inshore and offshore habitats by steelhead. 

Additional population age structure distributions are in Appendix H.

Genetics

Previous Studies

Busby et al. (1996) presented a compilation of results from a number of genetic studies 

that described the population structure of O. mykiss throughout the Pacific Northwest. 

Collectively, these studies provided the genetic evidence for the establishment of the 16 

steelhead DPSs that have been identified to date. The following summary focuses on those 

studies that are relevant to the delineation of the Puget Sound Steelhead DPS.

Work by Allendorf (1975) with allozymes (protein products of genes) identified two 

major O. mykiss lineages in Washington, inland and coastal, that are separated by the Cascade 

Crest. This pattern also exists in British Columbia (Utter and Allendorf 1977, Okazaki 1984, 

Reisenbichler et al. 1992). Reisenbichler and Phelps (1989) analyzed genetic variation from nine 

populations in northwestern Washington using 19 allozyme gene loci. Their analysis indicated

 11 Steelhead are typically aged from scales or otoliths based on the number of years spend in freshwater and salt 

water. For example a 2/2-aged steelhead spent 2 years in freshwater prior to emigrating to the ocean, where after 2 

years in the ocean the fish returned to spawn.
42

Table 4. Frequencies of ocean age at the time of first spawning. The two populations in italics are 

representative of adjacent DPSs. W = winter-run steelhead and S = summer-run steelhead. The 

frequency in bold indicates the most common age. (Includes data from Busby et al. 1996.)

Population Run

Ocean age at first spawning

0 1 2 3 4 Reference

Chilliwack River W — <0.01 0.50 0.49 <0.01 Maher and Larkin 1955

Skagit River W — — 0.57 0.42 0.01 WDFW 1994

Deer Creek S — 1.00 — — — WDF et al. 1993

Snohomish River W — — 0.57 0.42 0.01 WDFW 1994

Green River W 0.02 0.07 0.66 0.25 — Pautzke and Meigs 1941

White River W — 0.03 0.67 0.30 — Smith 2008*

Puyallup River W — — 0.70 0.30 — WDFW 1994

Nisqually River W — — 0.63 0.36 0.01 WDFW 1994

Elwha River W — 0.03 0.51 0.46 — Morrill 1994

Hoh River W — 0.02 0.81 0.17 — Larson and Ward 1955

* B. Smith, Fisheries, Puyallup Tribe of Indians, Puyallup, WA. Pers. commun., 5 August 2008.

Table 5. Frequencies of life history patterns. Age structure indicates freshwater age/ocean age. The two 

populations in italics are representative of adjacent DPSs. (Includes data from Busby et al. 1996.)

Population Run

Life history (frequency)

Primary Secondary Reference

Chilliwack River W 2/2 0.31 2/3 0.31 Maher and Larkin 1955

Skagit River W 2/2 0.48 2/3 0.33 WDFW 1994

Skagit River (fishery) W 2/2 0.30 2/3 0.18 Hayman 2005

Deer Creek S 2/1 0.95 3/1 0.05 WDF et al. 1993

Snohomish River W 2/2 0.47 2/3 0.36 WDFW 1994

Green River W 2/2 0.52 2/3 0.17 Pautzke and Meigs 1941

Puyallup River W 2/2 0.61 2/3 0.28 WDFW 1994

White River W 2/2 0.50 2/3 0.21 Smith 2008*

Nisqually River W 2/2 0.51 2/3 0.28 WDFW 1994

Hoh River W 2/2 0.74 2/3 0.14 Larson and Ward 1955

* B. Smith, Fisheries, Puyallup Tribe of Indians, Puyallup, WA. Pers. commun., 5 August 2008.

that there was relatively little between-basin genetic variability, which they suggested might 

have been due to the extensive introduction of hatchery steelhead throughout the area. 

Alternatively, Hatch (1990) suggested that the level of variability detected by Reisenbichler and 

Phelps (1989) may be related more to the geographical proximity of the nine populations rather 

than the influence of hatchery fish.

The number and morphology of chromosomes in a fish offers an alternative indicator of 

differences in major lineages. Analysis of chromosomal karyotypes from anadromous and 

resident O. mykiss by Thorgaard (1977, 1983) indicated that fish from Puget Sound and the Strait 

of Georgia had a distinctive karyotype. In general, O. mykiss have 58 chromosomes; however, 

fish from Puget Sound had 60 chromosomes. Further study by Ostberg and Thorgaard (1994) 

verified this pattern through more extensive testing of native-origin populations. While 
43

suggesting that steelhead populations in Puget Sound share a common founding source, this 

methodology does not offer much potential for identifying finer scale genetic differences within 

Puget Sound.

Genetic analysis of Skagit Basin O. mykiss in 1980 using allozymes found little 

distinction between the major subbasins (i.e., lower Skagit, Sauk, and upper Skagit rivers), in 

part because of the variation between sample sites within each of the subbasins (USFWS and 

WDG 1981). The Cascade River was specifically identified as being distinct from other samples 

in the upper Skagit Basin. Although the electrophoretic detection of allozyme variation is not as 

sensitive to genetic variation as present day microsatellite DNA analysis and only seven loci 

were analyzed, the report suggested that there was considerable structure within basins (the study 

sampled O. mykiss juveniles at 57 different locations in the Skagit River basin):

There was a highly significant difference (P < 0.0001) between allele frequencies 

when comparing one stream to another within each sub-area. This statistical 

difference made by far the greatest contribution to the total genetic difference 

among steelhead trout samples within the Skagit River drainage. The magnitude 

of these differences among tributary creeks can be seen by examining Figures 5 

through 11 where allele frequencies were plotted for each creek and mainstem 

sample site (USFWS and WDG 1981, p. 82).

Phelps et al. (1994) and Leider et al. (1995) reported results from an extensive genetic 

survey of Washington state anadromous and resident O. mykiss populations using allozymes. 

Populations from Puget Sound and the Strait of Juan de Fuca were grouped into three clusters of 

genetically similar populations: 1) North Puget Sound (including the Stillaguamish River and 

basins to the north, 2) South Puget Sound, and 3) the Olympic Peninsula (Leider et al. 1995). 

Additionally, populations in the Nooksack River basin and the Tahuya River (Hood Canal) were 

identified as genetic outliers. Leider et al. (1995) also reported on the relationship between the 

life history forms of O. mykiss. They found a close genetic association between anadromous and 

resident fish in the Cedar and Elwha rivers. Phelps et al. (1994) indicated that there were 

substantial genetic similarities between hatchery populations that had exchanged substantial 

numbers of fish during their operation. Within Puget Sound, hatchery populations of winter-run 

steelhead in the Skykomish River, Chambers Creek, Tokul River, and Bogachiel River showed a 

high degree of genetic similarity (Phelps et al. 1994). There was also a close genetic association 

between natural and hatchery populations in the Green, Pilchuck, Raging, mainstem Skykomish, 

and Tolt rivers, suggesting a high level of genetic exchange (Phelps et al. 1994). Because these 

results were based on juvenile collections, there is some uncertainty regarding the origin of the 

fish collected at different sites. Specifically, it is unclear whether the sample included naturally 

produced hatchery fish, hatchery by wild hybrids, migrating juvenile steelhead from another 

population, or potentially distinct resident O. mykiss. Overall, however, there were several 

distinct, naturally sustained steelhead populations in Puget Sound (Cedar River, Deer Creek, 

North Fork Skykomish River, and North Fork Stillaguamish River) that appeared to have 

undergone minimal hatchery introgression (Phelps et al.1994).

A subsequent study by Phelps et al. (1997) with additional population samples found 

little evidence for hatchery influence in Puget Sound steelhead populations. Among the North 

Puget Sound populations sampled in that study, four genetic clusters were detected: Nooksack, 
44

Skagit (Sauk), Stillaguamish River winter run, and Stillaguamish River summer run, while 

Tahuya River and Pilchuck River samples were distinct from other geographically proximate 

steelhead populations (Figure 7). In general, early allozyme studies on Puget Sound O. mykiss

did provide substantial evidence for population distinctiveness on a large (basin-wide) scale, but 

did not provide much resolution on finer level population structure.

Recent Studies

There have been a number of genetic studies in the 14 years since the Coast-wide 

Steelhead Biological Review Team (Busby et al. 1996) reviewed the genetic structure of 

steelhead populations in Puget Sound. In general, these more recent studies have focused on the 

analysis of microsatellite DNA variation among populations within specific river basins.

Figure 7. Two-dimensional scaling views, based on allozyme analysis, of coastal Washington steelhead 

populations. (Reprinted from Phelps et al. 1997.)
45

Van Doornik et al. (2007) assessed differences between presumptive steelhead 

populations in the Puyallup River basin. These results indicated that significant genetic 

differences exist between winter steelhead in the White River and the Puyallup River. Although 

the White River is a tributary to the Puyallup River, differences between steelhead in these two 

basins is not surprising, given that the White River formerly flowed into the Green 

River/Duwamish River basin (Williams et al. 1975). Floodwaters in 1906 diverted the White 

River into the Puyallup Basin. Additionally, the steelhead sampled from the Puyallup and White 

rivers were distinct from hatchery-origin fish (derivatives of the Chambers Creek winter 

steelhead broodstock) that have been released into the Puyallup Basin over the last 50 years (Van 

Doornik et al. 2007). More importantly, in the 100 years since the White and Puyallup rivers 

were merged, there has not been sufficient straying between the populations to eliminate genetic 

differences. This further underscores the presumed homing fidelity of steelhead.

Genetic analysis (microsatellite DNA) of winter steelhead from the Green and Cedar 

rivers suggested a close affinity between fish from the two basins (Marshall et al. 2006). In 

contrast to the situation with the White and Puyallup rivers, the Cedar and Green rivers 

historically flowed together via the Black River, which also drained Lake Washington 

(Chrastowski 1983). The Cedar River was diverted into Lake Washington initially as a flood 

control measure in 1912, but this new channel was later expanded to provide adequate flows for 

the Hiram M. Chittenden Locks in 1916 (Bogue 1911, Williams et al. 1975, Klingle 2005). 

Furthermore, Marshall et al. (2006) concluded that the Green River and Cedar River steelhead 

populations were genetically distinct from hatchery-origin winter steelhead (Chambers Creek 

origin) and summer steelhead (Skamania National Fish Hatchery origin), which have been 

released in the Green River for many years.

Preliminary results from the genetic analysis of Hood Canal steelhead (Van Doornik and 

Berejikian 2015) indicated that steelhead from western tributaries, Olympic Peninsula to Hood 

Canal, are distinct from steelhead in eastern tributaries, Kitsap Peninsula. Tributaries that enter 

the eastern side of Hood Canal drain lowland hills and are characterized by low to moderate 

stream gradients, while western Hood Canal tributaries are generally larger, higher gradient

rivers that are dominated by snow melt. In general, parr, smolt, and resident O. mykiss samples 

from the same river were genetically more similar to each other than to the same life history 

stages in other rivers, with the exception of those residents sampled above barriers (Van Doornik 

et al. 2013, Van Doornik and Berejikian 2015). Hood Canal steelhead were distinct from 

hatchery (Chambers Creek–origin) winter-run steelhead and resident rainbow trout in area lakes, 

and were distinct from Snow Creek (Strait of Juan de Fuca tributary) steelhead (Van Doornik et 

al. 2013).

During the course of the TRT’s review of Puget Sound steelhead population information,

the preliminary results from a number of genetic studies were released. Microsatellite DNA 

analyses were carried out by WDFW and NMFS’s Northwest Fisheries Science Center. In many 

cases, the analysis of existing samples was undertaken in response to TRT requests for specific 

information. This new information was incorporated into the existing Puget Sound steelhead 

genetic database (Appendix B). Given that this new information for presumptive populations 

usually includes limited numbers of fish samples taken from a single return year, or in some 

cases from smolt traps downstream of multiple tributaries, some caution was advised in drawing 

strong conclusions from the genetic results.
46

Major Population Groups

The concept of the MPG, a biologically and ecologically based unit that includes one or 

more DIPs within the DPS or ESU, was developed by previous TRTs (Ruckelshaus et al. 2002, 

McElhany et al. 2003, Cooney et al. 2007). Rather than simply setting a fixed number or 

proportion of populations to be fully recovered across the DPS, the TRTs used MPGs to establish 

guidelines ensuring that populations representative of major life history traits (e.g., summer-run

and winter-run steelhead), major genetic lineages, or existing in ecologically or geographically 

distinct regions, are viable at the time of delisting. Ultimately, if a DPS contains viable 

populations in each MPG, it will have a relatively lower extinction risk from catastrophic events, 

correlated environmental effects, and loss of diversity (McElhany et al. 2003). Good et al. 

(2008) demonstrated that recovered populations dispersed across multiple MPGs in the Puget 

Sound Chinook Salmon ESU were less susceptible to catastrophic risks than populations 

randomly dispersed (Appendix I). The linkage between sustainable MPGs (strata) and DPS 

viability was further underscored in Waples et al. (2007), who suggest that MPGs are useful 

elements for evaluating whether a species is threatened or endangered under the “significant 

portion of its range” consideration in the U.S. Endangered Species Act. Therefore, MPGs should 

be designated based on the premise that the loss of any one MPG within a DPS may put the 

entire DPS at a heightened risk of extinction. Establishing guidelines for population assignment 

into MPGs has generally been done in the viability documents produced by the TRTs; however, 

because the basis for designating MPGs is biologically based, it was convenient to 

simultaneously identify MPGs and DIPs for the Puget Sound Steelhead DPS within this 

document.

Major Population Grouping Determinations for Other DPSs and ESUs

For steelhead in the Lower Columbia River Steelhead DPS, two major life history types 

were recognized by the Lower Columbia River TRT: winter run and summer run (McElhany et 

al. 2003). Additionally, the TRT recognized that there was substantial ecological diversity 

within the DPS. Within the Lower Columbia River, the TRT recognized three ecological zones 

from the mouth of the Columbia River to the historical location of Celilo Falls. The Lower 

Columbia River Steelhead DPS included two of these three ecological zones: Cascade and 

Gorge. These ecological zones were based on the EPA’s Level III ecoregions (Omernik 1987) 

and the Pacific Northwest River Basins Commission physiographic provinces (PNRBC 1969). 

The TRT designated the ecologically based MPGs as follows (McElhany et al. 2003).

MPG Ecological zone Run timing Historical populations

1 Cascade Summer 4

2 Cascade Winter 14

3 Columbia Gorge Summer 2

4 Columbia Gorge Winter 3

They reflect the homing fidelity exhibited by steelhead and the likely degree to which 

populations will be locally adapted to marine and nearshore migratory corridors and freshwater 

spawning and rearing conditions. These MPGs are intended to assist in coordinating watershed 

planning, ensuring that recovery efforts are spread adequately across the distribution of distinct 

life history and ecological diversity categories.
47

The Interior Columbia TRT also established MPGs for ESUs and DPSs within their 

recovery domain (Cooney et al. 2007). The determination of MPGs was primarily established 

using geographic and ecological criteria. Interior populations of salmonids do not exhibit the 

same range of life history traits within an ESU or DPS as is observed among coastal populations. 

Within the Snake River Steelhead DPS, six MPGs were identified, each associated with a major 

tributary or mainstem section. Similarly, four MPGs were identified within the Middle 

Columbia River Steelhead DPS, but only one MPG in the Upper Columbia River Steelhead DPS. 

The situation in the Upper Columbia River Steelhead DPS was complicated by the loss of 

spawning habitat due to the construction of the Grand Coulee and Chief Joseph dams and the 

potential influence of the Grand Coulee Fish Maintenance Project on contemporary steelhead 

population structure (Cooney et al. 2007).

The North-Central California Coast TRT identified both historical populations and 

diversity MPGs for steelhead (Bjorkstadt et al. 2005). Geographically, the situation along the 

California coast is somewhat similar to that of Puget Sound. River basins drain separately into 

marine waters, providing geographic and environmental isolation (nonmigratory juveniles are 

restricted to their natal basin for an extended period). Based on observed genetic differences 

between populations in the river basins, coastal geography (e.g., coastal headlands), ecology, and 

life history differences, the North-Central California Coast TRT recognized seven diversity 

MPGs (two summer run and five winter run) within the North California Steelhead DPS and five 

diversity MPGs (winter run only) within the Central California Coast Steelhead DPS (Bjorkstedt 

et al. 2005).

The Puget Sound Chinook Salmon TRT established five “geographic regions” (Figure 8) 

within the ESU (Ruckelshaus et al. 2002). These geographic regions were established to provide 

population spatial distribution “based on similarities in hydrographic, biogeographic, and 

geologic characteristics of the Puget Sound basin and freshwater catchments, which also 

correspond to regions where groups of populations could be affected similarly by catastrophes 

(volcanic events, earthquakes, oil spills, etc.) and regions where groups of populations have 

evolved in common” (Ruckelshaus et al. 2002). In doing so, the TRT created de facto MPG 

subdivisions by requiring for future viability that one of each life history type (e.g., spring run

and fall run) be represented in each geographic region where they currently exist.

Puget Sound Steelhead MPG Determinations

The geographic region template developed for Puget Sound Chinook salmon (Figure 8) 

provided a foundation for developing the configuration of steelhead MPGs. In contrast to 

Chinook salmon that spawn predominately in the main stem and major tributaries of most river 

basins in Puget Sound, steelhead utilize a variety of stream types, from the larger streams 

(similar to Chinook salmon) to smaller tributaries and drainages (more similar to coho salmon). 

In addition, resident O. mykiss occupy a variety of small tributaries in anadromous zones. The 

TRT identified a number of major basins that contain multiple habitat types, all of them 

containing O. mykiss. Although the TRT considered that freshwater habitat was an important 

factor in establishing steelhead life history phenotypes, larger scale geographic factors were 

identified as the primary factor in establishing substructuring within the DPS (i.e., MPGs).
48

Figure 8. Geographic regions for Chinook salmon as developed by the Puget Sound Chinook Salmon 

TRT (Ruckelshaus et al. 2002).

Geomorphology was evaluated as a structuring factor because of its influence on stream 

morphology, streambed composition, precipitation, stream hydrology, and water temperature. In 

Puget Sound, unconsolidated glacial deposits dominate much of the lowland habitat (Appendix 

J). The geologic composition of the upper basins of Puget Sound streams varied from volcanic 
49

depositions along western Hood Canal, the Strait of Juan de Fuca, and Mt. Rainier to a mix of 

sedimentary, metamorphic, and igneous formations in the North Cascades. The presence of 

erosion-resilient basalt formations in the North Cascades was often associated with waterfalls or 

cascades and the potential conditions for a summer-run steelhead life history strategy. The 

geomorphology of marine areas in association with land masses was also considered in 

identifying MPGs boundaries. Submarine sills, terminal moraines from glacial recession, may 

provide oceanographic substructure in Puget Sound. For example, there is a sill at Admiralty 

Inlet separating central Puget Sound from the Strait of Juan de Fuca and Strait of Georgia, and an

additional sill at the entrance to Hood Canal. A sill at the Tacoma Narrows was considered a 

potential biogeographic barrier dividing south Puget Sound from northern areas.

The EPA ecoregion designations were useful in identifying ecologically distinct areas in 

Puget Sound, Hood Canal, and the Strait of Juan de Fuca. Portions of four Level III ecoregions 

are found within the Puget Sound DPS (Figure 2): the Coast Range (covering the western side of 

the Hood Canal), the Puget Lowlands, the Cascades (covering the headwater regions of the 

Cedar River and south), and the North Cascades (encompassing the higher elevation areas of the 

Olympic Mountains and the Cascades north of the Cedar River).

The North Cascades Ecoregion differs from the Cascades Ecoregion in geology and 

glacial coverage. Currently the North Cascades Ecoregion contains the highest concentration of 

glacial coverage in the continuous United States. Glacially influenced streams exhibit an 

“inverse” hydrology relative to the precipitation-driven flow patterns observed in lowland 

streams (Appendix K). River flows in glacial-source streams peak during warmer summer 

months and stream temperatures are universally cooler in glacially driven relative to rain-driven 

streams. As a result, the timing of most major steelhead life history events is different in 

glacial/snow-dominated vs. rain-dominated systems. Substantial differences in the timing of 

stream flow events provide a strong isolating mechanism via spawn timing differences or 

through some fitness/selection mechanism in the timing of development, hatch, emigration, and 

adult return migration.

Seasonal stream flow differences were also evident among rain-driven streams, with 

smaller lowland streams having summer low flows that were less than 10% of the peak winter 

flows, while larger rain-driven streams have more sustained groundwater-driven summer flows, 

normally 20–40% of winter peak flows. Summer flows in turn likely have a strong influence on 

the life history of juvenile O. mykiss. Thus major hydrological differences between basins 

provide a useful proxy for steelhead life history diversity and the delineation of both DIPs and 

MPGs when life history data are not available.

Life history and genetic characteristics, ecological diversity, and geographic distribution 

were important factors influencing the designation of MPGs. Although, many TRT members 

emphasized the importance of freshwater hydrology and ecology, it was recognized that a wide 

range of conditions exist across subbasins within individual basins. Ultimately, rather than 

divide basins or create of patchwork of populations within an MPG, it was decided that MPGs 

would be primarily based on geographic proximity, marine migrational corridors, and genetics 

(Figure 9). Finally, genetic analysis of steelhead populations suggested a clustering of 

populations similar to some of the geographic regions developed by the Puget Sound Chinook 

Salmon TRT (Appendix B). Genetic analysis suggested a further split in the Northern Cascades, 
50

with Drayton Harbor, Nooksack Basin, and Samish River as a possible MPG; however, the 

ecological and geographic characteristics were not considered distinct enough. In contrast, the 

placement of the Snohomish Basin was based solely on ecological data in the absence of genetic 

data (other than South Fork Tolt River summer-run fish). Using these criteria to establish MPGs 

ensures that there would be broad spatial and genetic representation in the DPS that is ultimately 

recovered. Each MPG in turn contains populations with a variety of habitats and associated life 

history traits. It is the TRT’s intention to create viability criteria for each MPG to ensure that 

among-population diversity and spatial structure is preserved.
51

Figure 9. Major population groupings for the Puget Sound Steelhead DPS: Northern Cascades, Central 

and South Puget Sound, and Hood Canal and Strait of Juan de Fuca MPGs. Note that the 

Deschutes, South Fork Stillaguamish, and South Fork Skykomish River basins are not included in 

the DPS and have not been assigned to DIPs. We are unaware of historical or current information 

on steelhead presence in the islands in North Puget Sound (Whidbey, San Juan, etc.) and these 

areas remain unassigned.
52

Historical Demographically Independent 

Populations

The PSS TRT ultimately utilized two parallel methodologies to identify DIPs. An expert 

panel system was employed, with each TRT member evaluating the likelihood that presumptive 

populations met the criteria for being DIPs. The process focused on several data categories, 

including: genetic distance, geographic distance (Appendix L), basin size, abundance, life 

history, habitat type, hydrology, demographic trends, and spawn timing. These categories were 

selected for their relevance to the question of sustainability and independence and the quantity 

and quality of the data for most populations. TRT members evaluated the information categories 

for each population and determined whether the information for that category was a factor 

“contributing to independence,” a factor “contributing to amalgamating,” or “not informative.” 

The TRT then reviewed the combined category scores and any additional information not 

specifically covered by the categories before deciding the status of the presumptive DIP.

In a parallel effort, the TRT employed a number of decision support systems to identify 

DIPs. The decision support system provides a more quantitative and transparent methodology 

than the panel system, although the selection of categories and thresholds are still assigned by the 

TRT via an expert panel system. Most of the decision support systems reviewed by the TRT 

required a considerable amount of information on each population or utilized default values that 

introduced considerable uncertainty into the system conclusions. Ultimately, the TRT developed 

a simplified linear decision model that used independence threshold values derived in part from 

the truth membership functions generated by the TRT. Discussion of this model and the truth 

membership functions it relied on is in Appendix B. The linear decision (aka gatekeeper) model 

identified a set of provisional DIPs that was nearly identical to that arrived at via the expert panel 

system. Where the two systems differed, the TRT debated the specifics of the DIP, but generally 

endorsed the outcome of the gatekeeper model.

The following subsections list the MPGs and DIPs identified by the TRT and provide 

some detail on those factors that were especially relevant in that determination. Where 

appropriate, we have noted where there were substantial uncertainties among the TRT members 

in the DIP determination.

Northern Cascades (South Salish Sea) MPG

Overview

The Northern Cascades MPG includes populations of steelhead from the Canadian border 

to and including the Snohomish River basin (Table 6). This MPG was established based on the 

geologic distinctiveness, ecological differences, geographic separation between it and the MPGs 

to the south and west, and genetic relatedness of populations within the MPG boundary. The 
53

Table 6. DIPs within the Northern Cascades MPG and their respective categorization by state and tribal 

agencies. WRIA = Water Resource Inventory Area and SASSI/SaSI = Salmon and Steelhead 

Stock Inventory/Salmonid Stock Inventory.

WRIA 1992 SASSI/2002 SaSI TRT DIP

1 Dakota Creek winter 1. Drayton Harbor Tributaries Winter Run

1 N. F. Nooksack River winter 2. Nooksack River Winter Run

1 M. F. Nooksack River winter

1 S. F. Nooksack River summer

S. F. Nooksack River winter

3. S. F. Nooksack River Summer Run

3 Samish River winter 4. Samish R. and Bellingham Bay Winter Run

4 Mainstem Skagit River winter 5. Skagit River Summer Run and Winter Run 

4 Finney Creek summer

4 Cascade River summer

Cascade River winter

4 — 6. Nookachamps Creek Winter Run

4 — 7. Baker River Summer Run and Winter Run

4 Sauk River summer

Sauk River winter

8. Sauk River Summer Run and Winter Run

5 Stillaguamish River winter 9. Stillaguamish River Winter Run

5 Deer Creek summer 10. Deer Creek Summer Run

5 S. F. Stillaguamish River summer Out of DPS

5 Canyon Creek summer 11. Canyon Creek Summer Run

7 Snohomish/Skykomish R. winter 12. Snohomish/Skykomish Rivers Winter Run

7 Pilchuck River winter 13. Pilchuck River Winter Run

7 S. F. Skykomish River summer Out of DPS

7 N. F. Skykomish River summer 14. N. F. Skykomish River Summer Run

7 Snoqualmie River winter 15. Snoqualmie River Winter Run

7 Tolt River summer 16. Tolt River Summer Run

boundary between this MPG and the South Central Cascades MPG to the south largely 

corresponds with the ecoregion boundary between the North Cascades and Cascades ecoregions 

in headwater areas. Glaciers dominate many of the mountain areas. In some areas the rock 

substrate is highly erosible, while in others it is relatively stable, resulting in a number of 

cascades and falls that may serve as isolating mechanisms for steelhead run times (Appendix J).

This geology is likely responsible for the relatively large number of summer-run 

populations. In fact, this MPG currently contains the majority of existing steelhead summer 

runs, although there is some uncertainty about the historical presence or present day persistence 

of summer-run steelhead in rivers elsewhere in the DPS. The Snohomish River, the most 

southern population in this MPG, is geographically separated from the nearest populations in the 

other MPGs by 50–100 km. A recent microsatellite analyses indicated that populations in the 

North Cascades MPG represented a major genetic cluster, although it should be noted that 

samples from the Snohomish Basin were unavailable.12 Alternatively, Phelps et al. (1997), using 

allozyme genetic analysis, indicated that the genetic diversity unit boundary between major 

 12 Additional genetic analyses have been made of Snohomish River basin populations, but have not been integrated 

into the DPS-wide database at the time of this publication.
54

genetic groups lies between the Stillaguamish and Snohomish basins, farther to the north. 

Notwithstanding concerns about the samples used in the Phelps et al. (1997) study, all agreed 

that further steelhead genetic studies were necessary to address these critical uncertainties.

The Puget Sound Chinook Salmon TRT (Ruckleshaus et al. 2006) identified a similar 

MPG (originally termed a “geographic region”), although within the boundaries of the steelhead 

Northern Cascades MPG, they also identified the Nooksack River basin as a major geographic 

unit. Based on available information, primarily limited genetic analysis, and life history 

information, the PSS TRT concluded that the Nooksack River basin steelhead populations did 

not constitute a distinct MPG.

Proposed DIPs within the MPG

1. Drayton Harbor Tributaries Winter Run

This population includes steelhead that spawn in tributaries from the Canadian border to 

Sandy Point, Washington, primarily in Dakota and California creeks (Smith 2002). It was 

identified based on geographic isolation from the Nooksack and Fraser rivers, the most 

proximate steelhead populations. Although genetic analysis is unavailable for this population, it

is thought that it is sufficiently geographically isolated from the nearby larger basins, Nooksack 

and Fraser. Spawning and rearing habitat in these smaller, low-gradient, rain-dominated systems 

is very different from the glacially influenced conditions in the North Fork Nooksack River. 

Dakota Creek steelhead have an earlier spawn timing than fish in the Fraser or Nooksack rivers

and are morphologically distinct, being generally smaller and looking “more like cutthroat” than 

Nooksack River fish.13

The tributaries supporting this population are wholly contained within the EPA Level III 

Puget Lowlands Ecoregion, with 89 m maximum elevation in the basin. The basin size for 

Dakota Creek is 139 km2

, although this does not include some other minor tributaries (e.g., 

Terrell Creek). Historical information indicates that this population was of medium abundance; 

however, observations were only reported in Dakota Creek and not California or Terrill creeks 

(WDFG 1932). Habitat-based IP run size was estimated to be 2,426–4,930 fish14 (Appendix D). 

Sportfishing punch card records indicate a maximum catch (adjusted)15 of 67 fish in 1957, with 

an average catch of 18 fish annually from 1946 to 1970. Steelhead and presumptive steelhead 

redds have been observed recently, but in low numbers, although monitoring is intermittent.

2. Nooksack River Winter Run

This population includes winter-run steelhead in the north, middle, and south forks of the 

Nooksack River. While the entire TRT agreed that winter-run steelhead in the Nooksack 

constituted at least one DIP, some members suggested the presence of multiple winter-run DIPs 

within the basin, including making each of the three forks a DIP. SaSI (WDFW 2002) reported 

that the Middle Fork Nooksack River may have supported a summer run of steelhead prior to the 

 13 B. Barkdull, WDFW, La Conner, WA. Pers. commun., October 2008. 14 IP estimates of basin capacity are presented as a range using smolt survivals varying from 10 to 20%. 15 Sport catch estimates were adjusted by 0.60 from numbers published in WDG (no date-b), basedon a personal 

communication (P. K. Hahn, WDFW, Olympia,WA. Pers. commun., 18 November 2009).
55

construction of the impassable diversion dam at RKM 11. Genetic analysis (based on allozymes) 

indicated that North Fork and South Fork Nooksack rivers steelhead were genetically distinct 

(Phelps et al. 1997), although the south fork samples may have included some summer-run fish. 

Preliminary microsatellite DNA analysis indicated that: 1) Nooksack River steelhead were 

distinct from Samish River winter-run steelhead and 2) genetic differences among samples 

within the Nooksack River basin did not suggest a high degree of differentiation (although 

sample sizes were relatively small).

Winter-run steelhead from the north, middle, and south forks of the Nooksack River were 

combined based on the geographic proximity of the basins and the apparent continuum of 

spawning grounds. The lower reaches of the mainstem Nooksack River are located in the Puget 

Lowlands Ecoregion and upstream tributary areas are located in the North Cascades Ecoregion. 

Currently, there is considerable spawning area in low elevation, low gradient tributaries, such as 

Fishtrap and Bertrand creeks.

16 There is considerable ecological variability among the major 

tributaries. The North Fork Nooksack River has a glacial, snowmelt-driven hydrology, the 

Middle Fork Nooksack River has a rain and snow–driven hydrology, and the South Fork 

Nooksack River is a lower gradient, primarily rain-driven river. Conditions specifically related 

to glacial sediment in the North Fork and Middle Fork Nooksack rivers prevent visual estimation 

of escapement (e.g., redd counts) or life history characteristics (e.g., spawn timing). Local 

biologists for the state and tribes suggested that winter-run steelhead spawning has a continuous 

distribution throughout the basin, with little opportunity for spatial or temporal isolation.17

Historical estimates from in-river harvest suggest that there was a substantial run 

(10,000s) of steelhead into the Nooksack Basin in the early 1900s. The habitat-based IP capacity 

estimate was 22,045–44,091 steelhead. Spawner surveys of the North Fork and Middle Fork 

Nooksack rivers in 1930 identified a number of tributaries that supported steelhead. Ernst (1950) 

reported that the South Fork Nooksack River was the major producer in the basin, and that most 

of these fish spawned in the main stem. Adjusted punch card catch estimates (1946–1972) 

peaked in 1953 at 2,114 winter-run steelhead. Additionally, there are reports of summer-run 

steelhead present in the North Fork and Middle Fork Nooksack rivers; however, it was unclear 

whether these were fish from the South Fork Nooksack Summer-Run DIP, a distinct North Fork

or Middle Fork Nooksack River summer run, or a diversity component within this population. 

The TRT recommends that further genetic sampling be carried out in order to verify the 

proposed DIP boundaries.

3. South Fork Nooksack River Summer Run

The TRT identified a DIP in the upper portion of the South Fork Nooksack River based 

in part on geographic separation between winter-run and summer-run steelhead in the Nooksack 

Basin. According to WDFW (2002), summer-run steelhead spawn in the mainstem South Fork 

Nooksack above the series of cascades and falls at RKM 40 and in upper watershed tributaries, 

Hutchinson and Wanlick creeks (RKM 16.3 and 54.9, respectively). Smith (2002) suggested that 

the summer run of steelhead in the South Fork Nooksack has always been relatively small 

compared to the winter run, although the potential run size, based on habitat above the cascades 

 16 N. Currence, Nooksack Tribe, Natural Resource Department, Deming, WA. Pers. commun., October 2008. 17 See footnote 16.
56

(IP range), was estimated at 1,137–2,273 steelhead. WDFW (2002) suggested that summer-run 

spawning extends from February to April, while winter-run steelhead exhibit a more protracted 

spawning interval, mid-February to mid-June. Genetic analysis by Phelps et al. (1997) indicated 

that winter-run and summer-run steelhead were significantly different from each other in the 

South Fork Nooksack River. Preliminary microsatellite DNA analysis of steelhead from there

did not suggest the presence of multiple populations, although the sample size was relatively 

small. Additional sampling, especially of adults in the holding pools below the falls at RKM 40

or above the falls, was identified by the TRT as a priority for future sampling.

The South Fork Nooksack River basin above the falls covers 480 km2 and lies within the 

EPA Level III North Cascades Ecoregion. The South Fork Nooksack River is categorized 

hydrologically as a rain and snow–driven system and experiences relatively high late summer 

water temperatures in the lower reaches (>20°C). Under these conditions, summer-run steelhead 

holding habitat in the lower river would be limited by the availability of cold water seeps, deep 

resting holes, or access to headwater areas. Surveys during 1930 identified steelhead spawning 

aggregations in Hutchinson and Skookum creeks (WDFG 1932), although no distinction was 

made between winter-run and summer-run fish in these surveys. Ernst (1950) reported that 

steelhead migrated as far as 5.6 km above Howard Creek.

4. Samish River and Bellingham Bay Tributaries Winter Run

This DIP exists in a series of independent tributaries to Puget Sound; the Samish River 

and associated nearby creeks drain into Samish and Bellingham bays. In contrast to the adjacent 

DIP areas, the Samish River exhibits a largely rain-dominated flow pattern. The entire basin is

located within the Puget Lowlands Ecoregion with relatively low elevation headwaters. Average 

elevation in the basin is only 192 m. Only winter-run steelhead are present in this basin, with the 

majority of spawning occurring in Friday Creek and the Samish River from mid-February to 

mid-June (WDFW 2002). This run was noted as being especially early relative to other 

populations in the area (Seattle Daily Times 1923). The present day run has maintained that 

early timing.

18 The Samish River Hatchery was originally constructed in 1899 primarily as a 

coho salmon hatchery, but substantial numbers of steelhead eggs were obtained, 2.1 million eggs 

in 1910 (Cobb 1911, WDFG 1913). Although the basin is relatively small, the basin averaged 

617 steelhead over the most recent 5-year period.

19 Peak catch based on adjusted punch cards 

was 1,934 winter-run steelhead in 1951. The IP-based estimated range of capacity for the 

Samish Basin was 3,193–6,386 steelhead (Appendix D). Furthermore, while the adjacent 

Nooksack River and Skagit River steelhead populations appear to be steadily declining, the 

Samish River steelhead escapement trend has been stable or increasing at times during recent 

years, indicating that it is demographically independent of the other populations.

Genetic analysis using microsatellite DNA indicated samples from the Samish River 

winter run are more closely related to Nooksack River fish than to Skagit River or Stillaguamish 

River steelhead. There was a general consensus among the TRT members that genetically the 

Samish and Nooksack steelhead were part of a larger MPG that included rivers to the south.

 18 B. Barkdull, WDFW, La Conner, WA. Pers. commun., August 2012. 19 Data from B. Leland, WDFW, Olympia, WA. Pers. commun., 14 February 2012.
57

The TRT included in the Samish River DIP a number of independent tributaries draining 

into Bellingham Bay: Squalicum, Whatcom, Padden, Chuckanut, Oyster, and Colony creeks. 

Smith (2002) reported steelhead spawning in these creeks. Punch card records (WDG no date-b) 

indicate a peak catch of 23 fish in Chuckanut Creek (1958), 8 in Squalicum Creek (1970), and 34 

in Whatcom Creek (1953). The IP estimate indicates that annual production would be 185 fish 

annually for Chuckanut Creek alone. These creeks are lowland, rain-driven systems, very 

distinct from the nearby, glacially influenced Nooksack River. Although there was some 

discussion that these creeks might constitute a DIP, the distances between these streams and both 

the Nooksack and Samish rivers were not considered large enough to warrant independence. 

The TRT concluded that ecological conditions in these creeks were more similar to those in the 

Samish River than in the Nooksack River and supported grouping them with Samish steelhead to 

form a DIP.

5. Skagit River Summer Run and Winter Run

There was considerable discussion by the TRT on the structure of populations within the 

Skagit River basin. Abundance, life history, and genetic information were limited, especially at 

the subbasin level. At the time of this review, an extensive genetics sampling program was being 

undertaken in the Skagit River basin. Results from the analysis of the first 2 years of sampling 

(2010 and 2011) did not provide evidence for much divergence among fish sampled in 

anadromous zones within the basin, but did show high divergence between steelhead and O. 

mykiss that resided upstream of anadromous barriers. Given the recent decline in steelhead 

abundance in the Skagit River, especially in the tributaries, it is unclear how informative 

contemporary genetic sampling will be regarding the potential historical population structure of 

the basin. As with all DIP determinations, information may become available that initiates a 

review of one or more DIPs. In the case of the Skagit River basin, there is a clear timeline for 

the availability of new genetic information.

The Skagit River Summer-Run and Winter-Run DIP includes all steelhead spawning in 

the mainstem Skagit River and its tributaries, excluding the Baker and Sauk rivers, from the 

mouth to the historical location of a series of cascades located near the Gorge Dam (Smith and 

Anderson 1921b). Based on abundance, Skagit River steelhead represent one of the predominant 

steelhead populations in Puget Sound, accounting annually for several thousand spawning 

steelhead. WDFW (2002) notes that, although they consider winter-run steelhead in the main

stem and tributaries to be distinct stocks, there is no apparent break in the spawning distribution 

between the Skagit, Sauk, and Cascade rivers. In the recent genetic analysis (Appendix B), the 

Cascade River and Goodell Creek juvenile samples from the anadromous zone accessible 

reaches were distinct from some of the other Skagit Basin samples. In the case of the Cascade 

River juvenile fish sampled that did not genetically resemble resident O. mykiss from above a 

series of inaccessible falls, it is still unclear whether they represent the progeny of anadromous 

steelhead. The population status of the Cascade River steelhead and steelhead from other 

tributaries may need to be reassessed as new information becomes available.

Winter-run steelhead predominate in the main stem and lower tributaries, with summerrun steelhead reported in Day and Finney creeks and the Cascade River (Donaldson 1943, WDG 

no date-a). In the case of these three summer-run steelhead–bearing tributaries, cascades or falls 

may present a migrational barrier to winter-run fish but not summer-run fish. Some members of 
58

the TRT concluded that these barriers were sufficient to maintain independent summer runs in 

each of these tributaries, while others were unsure whether there was sufficient habitat above the 

barriers to sustain a population. Of these summer-run aggregates, the Cascade River came the 

closest to meeting DIP criteria, although there was limited information available. For example, 

peak adjusted punch card catch was 58 summer-run fish in 1970 (WDG no date-b), although 

accessibility to fishers likely limited the sport catch. Further sampling efforts in these basins 

were recommended. At a minimum, winter-run and summer-run life histories are somewhat 

reproductively isolated (temporal separation) from each other; however, it is unclear whether any 

of these summer-run aggregates was historically large enough to persist as a DIP. In evaluating 

the viability of this DIP, both life histories were recognized as important diversity components.

In a previous genetic analysis, samples from the Skagit, Sauk, and North Fork 

Stillaguamish rivers formed a cluster within the greater Puget Sound grouping (Phelps et al. 

1997) (Figure 7). Steelhead samples (possibly containing summer-run fish) from Finney Creek 

and the Cascade River clustered with samples from Deer Creek and the Nooksack River (Phelps 

et al. 1997), although the number of fish sampled from Finney Creek was relatively small. 

Interestingly, the headwaters of Deer Creek (Stillaguamish River) and Finney Creek (Skagit 

River) are adjacent to each other. While there is considerable information that summer-run 

steelhead existed in the Skagit River tributaries, recent surveys suggest that the summer-run 

component is at a critically low level. While the abundance of winter-run steelhead is also 

depressed, there is not as marked a decline as with the summer-run steelhead. Given the large 

size of this DIP relative to other populations, there is the potential for considerable withinpopulation ecological, spatial, and genetic (life history) diversity. Preliminary results from the 

recent genetic analysis indicated that Skagit River steelhead have remained relatively distinct 

from steelhead broodstock (Chambers Creek–origin) used at Marblemount Hatchery,

20 near the 

confluence of the Cascade and Skagit rivers.

This DIP includes the entire Skagit River except for the Sauk and Baker river subbasins. 

In total, this DIP covers 3,327 km2

, the largest of the DIPs within the DPS. Estimated historical 

capacity, based on IP estimates, ranges from 64,775 to 129,551 steelhead (Appendix D). 

Spawning occurs from early March to early June. The majority of this population spawns within 

the North Cascades Ecoregion. Given the size of the DIP, it is not surprising that tributaries 

exhibit a variety of hydrologies, from lowland rain-driven to snowmelt-dominated streams, many 

with heavy glacial sediment loads. Landslides and volcanic activity pose some of the greatest 

catastrophic risks.

6. Nookachamps Creek Winter Run

Nookachamps Creek, was identified as a potential DIP for winter-run steelhead. This 

basin met the criteria for basin size and IP production. In contrast to much of the Skagit Basin, 

this lowland subbasin exhibits a rain-driven hydrology, with peak flows in December and 

January and low flows in August and September. Given the lowland ecology, it is thought that 

Nookachamps Creek only supported winter-run steelhead and that there may have been a 

difference in run timing between these steelhead and other steelhead returning to snowdominated tributaries higher in the Skagit Basin, similar to the situation between the Drayton 

 20 T. Kassler, WDFW, Olympia. Pers. commun., 26 May 2010.
59

Harbor Tributaries Winter-Run DIP and the Nooksack River Winter-Run DIP. However, it was 

unclear how geographically separated spawning areas in Nookachamps Creek would be from 

other Skagit tributaries. In the absence of specific information on steelhead characteristics, 

ecological information provided the majority of information for designating a DIP.

WDF (1932) identified steelhead as being “very scarce,” while notations on the 1940 

steelhead map of the Skagit River basin (WDG no date-a) suggested that a fair number of fish 

spawned in Lake Creek up to the swamps below Lake McMurray. Additionally, a fairly 

extensive run was noted in East Fork Nookachamps Creek. Given the lowland nature of this 

subbasin and its proximity to Mt. Vernon, Washington, it is thought that significant habitat 

alterations had likely occurred by the time of the 1932 and 1940 surveys. Juvenile O. mykiss, 

presumptive steelhead, were sampled from both forks of Nookachamps Creek and from Lake 

Creek in 1980 (USFWS and WDG 1981). Juvenile surveys in the 1980s observed some of the 

highest juvenile densities in the Skagit River basin in Nookachamps Creek (Phillips et al. 1981).

There was little information available on the characteristics of historical or contemporary 

steelhead in the Nookachamps Creek basin. Potential abundance was estimated at 1,231 to 2,462 

using the IP method. Although identifying this as a historical DIP, the TRT agreed that 

additional information and monitoring was needed to address critical uncertainties.

7. Baker River Summer Run and Winter Run

Historically, the Baker River was likely a major contributor to Skagit River basin 

steelhead runs. The Baker River is the second largest tributary to the Skagit River, with a basin 

size of 771 km2

. The Baker Lake Hatchery began operation in 1896, initially managed by the 

State of Washington and subsequently transferred to the U.S. Bureau of Commercial Fisheries. 

Steelhead were not the primary species cultured (only a few thousand eggs were taken annually)

and the number of spawned fish recorded might have been limited by the available incubation 

space. Hatchery reports strongly suggest that this population included a summer-run life history 

element. In any event, the construction of the lower Baker Dam in 1927 eliminated access to 

nearly all of the Baker River and necessitated the initiation of a trap and haul program. During 

the first year of operation (1929), 830 steelhead were transported to the upper basin from April to 

July. Upper Baker Dam, constructed in 1958, inundated the lower reaches of the upper Baker 

River tributaries. During those years when adults were transported to the upper Baker River (the 

practice was terminated some years ago) the origin of steelhead collected was unknown. Recent 

analysis of genetics samples from Baker Lake resident O. mykiss showed that they were 

genetically similar to Skagit River anadromous steelhead; however, it is unclear whether O. 

mykiss currently spawning in Baker Lake/River retain any genetic association with the historical 

population.21 Many of the TRT members and reviewers considered the Baker River SummerRun and Winter-Run DIP to have been extirpated, although resident O. mykiss in the Baker River 

basin may retain some of the historical genetic legacy of this population. In the absence of 

anadromous adults being transported above the dams, the resident O. mykiss population

continues to produce smolts, with a few hundred collected in the bypass system annually. 

Marking outmigrating smolts to see if there is any contribution to returning adults would be 

 21 Presentation by D.Pflug, Seattle City Light, to the PSS TRT, Seattle, WA., 25 January 2012.
60

informative. Finally, while it is clear that steelhead historically occupied the Baker River basin, 

there is considerable uncertainty regarding the characteristics of that population.

The majority of this population historically spawned within the North Cascades 

Ecoregion and the river exhibits a glacial snowmelt–dominated hydrograph. Habitat-based 

abundance estimates (IP) suggest a capacity of 5,028 to 10,056 steelhead (Appendix D). 

Historically, canyon areas in the lower river below Baker Lake (corresponding with the present 

locations of Lower Baker and Upper Baker dams) may have represented migrational barriers 

normally corresponding to the presence of summer-run fish. This basin is one of the highest 

elevation DIPs in the DPS, with an average elevation of 1,014 m, and drains the slopes of Mt. 

Baker. Landslides and volcanic activity pose some of the greatest catastrophic risks.

8. Sauk River Summer Run and Winter Run

The identification of this DIP followed extensive discussions by the TRT. These 

discussions focused on the separation of Sauk River steelhead from those in the mainstem Skagit 

River and the distinctiveness of diversity components within the Sauk River basin itself. 

Summer-run and winter-run steelhead are present in the Sauk River, but they were not assigned 

to separate DIPs. No migrational barriers (falls or cascades) have been identified that would 

provide a reproductive isolating mechanism between the two run times, yet they likely maintain 

some reproductive isolation through spawn timing differences (WDF et al. 1993). Current 

abundance of summer-run fish is relatively low and is thought to have historically been a minor 

contributor to total abundance (WDFW 2002). Historical surveys suggest that the winter run of 

steelhead in the Sauk River basin was significantly earlier than that in the mainstem Skagit

River, specifically in the Suiattle River: “Of considerable biological importance is the persistent 

report that the early run of steelhead in the Skagit River system proceed up the Sauk River” 

(WDG no date-a). It was suggested that the early run timing allowed fish to access spawning 

grounds while stream conditions were good and prior to the spring glacial runoff. During 1906, 

the WDFG hatchery on the Sauk River collected more than a million steelhead eggs from early 

February to June 15 (WDFG 1907). The wide temporal window for collecting eggs suggests that 

they were collected from both summer and winter runs. For summer-run and winter-run 

steelhead in the Sauk River basin, there does not appear to be any geographic separation on the 

spawning grounds. WDFW (2002) reported that summer-run fish spawn from mid-April to early 

June and winter-run fish spawn from mid-March to mid-July.

Samples from Sauk River steelhead were genetically similar to winter-run steelhead 

sampled from the mainstem Skagit River, especially those downstream of the Skagit/Sauk River 

confluence (Phelps et al. 1997). Steelhead from the Suiattle River were distinct from mainstem 

Skagit River steelhead and Sauk River steelhead (Figure 8 in Phelps et al. 1997). Sauk River 

flows are strongly influenced by snow melt and, as mentioned earlier, are subject to considerable 

glacial turbidity for most of the year (except during winter low flow periods), depending on the 

tributary. The Suiattle and Whitechuck rivers were specifically noted as containing high levels 

of glacial debris (WDG no date-a). There was some discussion regarding additional populations 

within the Sauk River. However, although many tributaries to the Sauk are capable of sustaining 

independent populations (based solely on basin size), there was little information available to 

support such a conclusion. Genetic sampling efforts are underway in the Skagit River basin. 

Preliminary results from recent genetic sampling indicated that O. mykiss from anadromous-
61

accessible areas of the Skagit Basin were genetically similar, with samples from the Suiattle 

River and Goodell Creek being slightly more distinct, and those from the Cascade River being 

considerably more distinct (Figure 2 through Figure 5 and Appendix B). Pooling samples within 

the Upper Skagit and Lower Skagit basins and Sauk Basin reduces the genetic distance between 

the Skagit and Sauk sample aggregates, but this may be because of variability within subbasins. 

As more genetic information becomes available, it may be necessary to revisit the TRT’s DIP 

conclusions.

The entire Sauk River basin is contained within the North Cascades Ecoregion. Given 

the large size of the Sauk River basin, 1,898 km2

, and the number of larger tributaries within the 

basin, it is possible that other DIPs exist within the basin. Recent escapement (2006) to the Sauk 

River was estimated to be 3,068. The IP estimate of basin capacity ranged from 23,230 to 

46,460 steelhead (Appendix D). At a minimum, there is likely to be some population 

substructure that should be considered in maintaining within-population diversity.

9. Stillaguamish River Winter Run

Winter-run steelhead spawn in the mainstem north and south forks of the Stillaguamish 

River and in numerous tributaries. Winter-run steelhead were identified by the TRT as distinct 

from summer-run steelhead in Deer Creek and Canyon Creek because of the likely geographic 

and temporal separation of spawners. Nonnative summer-run fish (Skamania Hatchery, 

Columbia River origin) and their progeny spawning above Granite Falls (South Fork 

Stillaguamish River) are not part of the DPS and were not considered. It is not known whether

any native steelhead spawn above the falls (an area historically inaccessible prior to the 

construction of a fish ladder). Genetic analysis indicated that there was some reproductive 

isolation between the native winter-run (North Fork Stillaguamish River) and summer-run (Deer 

Creek) spawners (Phelps et al.1997). Stillaguamish River winter-run steelhead clustered with 

winter-run and summer-run Sauk River steelhead and other Skagit River steelhead (Phelps et al. 

1997). Recent genetic analysis using microsatellite loci also indicated a close affinity between 

the Stillaguamish River steelhead and Sauk/Suiattle River steelhead collections (Appendix B). 

This genetic relationship is thought to be related to the Sauk River’s historical drainage to the 

North Fork Stillaguamish River prior to a series of lahars (volcanic mudflows) diverting the flow 

of the Upper Sauk River to the Skagit River more than 10,000 years BP. WDFW (2002) 

reported that winter-run steelhead spawn from mid-March to mid-June, and summer-run fish 

spawn from early April to early June in Deer Creek and February to April in Canyon Creek.

The Stillaguamish River basin, not including the Deer Creek and Canyon Creek SummerRun DIPs, covers 1,282 km2

. The IP-based capacity ranged from 19,118 to 38,236 steelhead 

(Appendix D). There are no basin-wide estimates of escapements. Current escapement surveys 

only cover index areas and these estimates have averaged in the low hundreds of adult fish in 

recent years.

The lower Stillaguamish River is located in the Puget Lowlands Ecoregion and the upper 

North Fork and South Fork Stillaguamish are located in the North Cascades Ecoregion. 

Historically, the Sauk River flowed into the North Fork Stillaguamish River and, as a result, the 

North Fork Stillaguamish River valley is much broader than might be expected based on current 
62

river size and flow. Flow in the Stillaguamish River is considered rain-and-snow transitional. 

The river is subject to moderate risks from volcanic, landslide, and earthquake events.

10. Deer Creek Summer Run

The Deer Creek summer-run steelhead population spawns and rears in the upper portion 

of Deer Creek. Steep canyons and cascades from RKM 2.5 to 8 may present a temporal barrier 

to winter-run fish, but Deer Creek is accessible to summer-run steelhead up to approximately 

RKM 32. Deer Creek summer-run steelhead were most famously observed by Zane Grey in 

August 1918, during a fishing trip (Grey 1928). Smith and Anderson (1921a) surveyed the basin 

in August 1921, but observed only summer-run coho salmon and reported that a few steelhead 

run in the stream. Even under pristine conditions, the steelhead run into Deer Creek may not

have been very large, potentially 1,000 to 2,000 adults (WSCC 1999), although the 1929 survey 

classified Deer Creek as a large population (WDFG 1932). The IP estimate range for Deer 

Creek is 1,572 to 3,144 adults (Appendix D). There are no recent estimates of escapement; the 

last adult census was conducted in October 1994 and resulted in an estimate of 460 steelhead 

(Kraemer 1994). The supporting basin is relatively small, 172 km2

, and freshwater productivity 

varied from 0.059 to 0.609 parr/m2 (Kraemer 1994).

Deer Creek steelhead were genetically distinct from winter-run fish in the Stillaguamish 

River and Skagit River (Phelps et al. 1997). Reanalysis of one of the same Deer Creek samples 

from 1995 using microsatellite DNA variation indicated that Deer Creek steelhead were outliers,

loosely clustering with the South Fork Tolt River steelhead and steelhead derived from Skamania 

Hatchery broodstock in dendrogram presentations; however, principal component analysis 

placed the Deer Creek collection more closely with collections from the Skagit and 

Stillaguamish rivers (Appendix B). In general, this analysis supports the contention that the 

summer-run life history has evolved independently in different basins, as initially described by 

Phelps et al. (1997). Deer Creek steelhead also have distinct 2/1 age structure (2 years in fresh 

water and 1 year in the ocean before returning to spawn) (Kraemer 1994), although the writings 

and photographs of Zane Grey would suggest that previously larger, likely repeat spawners were 

more common (Grey 1928). Deer Creek is located in the North Cascades Ecoregion and is 

categorized as a rain-and-snow transitional river.

11. Canyon Creek Summer Run

There is relatively little information available on the present-day summer run of steelhead 

in the Canyon Creek basin. Information provided by local biologists indicates that a summer run 

is still present in the basin. Historically, Canyon Creek was identified as having a relatively 

good-sized run of steelhead. Newspaper accounts listed Canyon Creek as a good summer-run 

steelhead stream (Seattle Daily Times 1935). There is no genetic information available on this 

run. A series of cascades and falls at RKM 2 is thought to be a partial temporal barrier to most 

adult salmon (Williams et al. 1975) and may provide a barrier to separate winter-run and 

summer-run steelhead. Above the cascades, there are approximately 26 km of accessible 

mainstem and tributary habitat (Appendix D). These conditions may provide a sufficiently 

strong isolating mechanism to justify designating this population as a DIP. Similar to Deer 

Creek, the Canyon Creek basin is small, 163 km2

, with an IP-based capacity of 121 to 243; this 

low estimate highlights the likely use of higher gradient stream reaches by summer-run steelhead 
63

(a factor not currently included in the model). Alternatively, summer-run steelhead may rear in 

the lower reaches of the basin, below the cascades that demark the winter-run and summer-run 

spawning habitat. The upper reaches of Canyon Creek lie in the North Cascades Ecoregion.

12. Snohomish/Skykomish Rivers Winter Run

This population includes winter-run steelhead in the mainstem Snohomish, Sultan, and 

Wallace rivers, and in the North Fork Skykomish River below Bear Creek Falls and the South 

Fork Skykomish River below Sunset Falls. WDFW (2002) identified three winter-run 

populations in the Snohomish Basin based on geographic discreteness. There is no recent 

genetic information available (e.g., microsatellite DNA analysis). Based on the work of Phelps 

et al. (1997), winter-run steelhead in the Tolt, Skykomish, and Snoqualmie rivers were most 

similar genetically, forming a cluster along with winter-run steelhead from the Green River. 

Spawn timing for winter-run steelhead through the Snohomish Basin extends from early-March 

to mid-June, similar to neighboring steelhead populations.

Historically, a number of mainstem and tributary areas of this population were identified 

as supporting medium and large “populations” of steelhead that may have constituted some of 

the most productive in Puget Sound (WDFG 1932). Furthermore, harvests recorded for 

Snohomish County in the late 1800s and early 1900s indicated that runs likely exceeded 100,000 

fish (Appendix D). Basin area is 2,185 km2 and the IP estimates suggest a run size of 

approximately 21,389 to 42,779 fish (Appendix D).

The lower reaches of the Snohomish River are in the Puget Lowlands Ecoregion, while 

the upper portions of the Skykomish and Snoqualmie rivers are in the Northern Cascades 

Ecoregion. The boundary between the Northern Cascades and Cascades ecoregions lies between 

the Snohomish River and the Lake Washington basin. The Pilchuck River is predominantly a 

rainfall-driven system, whereas the Snohomish, Snoqualmie, and Skykomish rivers are classified 

as rain-and-snow transitional. The Snohomish River is subject to relatively high earthquake 

catastrophic risks, but low volcanic risks.

13. Pilchuck River Winter Run

In 1876 Ranche provided the following description: “The Pill Chuck (or red water as it 

means in English)—the water is always clear and cold as any mountain spring. In salmon season 

it abounds with these delicious fish, also trout” (Ranche 1876). The Pilchuck River flows 

through the Northern Cascades and Puget Lowlands ecoregions. The basin is relatively low 

gradient and low altitude and has a rainfall-dominated flow pattern. There is sufficient habitat 

(366 km2

) to support a population as defined by the TRT. The IP-based estimate of capacity is 

5,193 to 10,386 steelhead (Appendix D). The last escapement estimate (2011) was 552 

steelhead. The Pilchuck River was historically reported to be a good producer of winter-run 

steelhead (WDFG 1932) and an egg collecting station was operated on the Pilchuck for a number 

of years in the early 1900s. The Pilchuck River is mentioned in numerous newspaper articles on 

steelhead fishing, including a notable catch of two steelhead, each weighing 10 kg (Seattle Daily 

Times 1918b). Although genetic samples from Pilchuck River steelhead were most similar to 

those from other Snohomish Basin samples, the Pilchuck River was an outlier from other 

Snohomish River and central Puget Sound samples (Phelps et al. 1997). More recent genetic 
64

sampling indicated that there were significant differences between steelhead from the Pilchuck 

River and other samples; however, the sample size was small (<25) and no other Snohomish 

River basin samples were available. In identifying steelhead from the Pilchuck River as a DIP, 

the TRT deviated from the findings of the gatekeeper model. In this case, the TRT considered 

additional information not included in the model. Pilchuck River steelhead have an earlier run 

timing than other Snohomish River basin winter-run steelhead, and there appears to a 

discontinuous spawning distribution between the lower Pilchuck River and mainstem Snohomish 

River.

22 WDF et al. (1993) reported that the Pilchuck River age structure may include a higher

proportion of 3-year ocean fish than found in other Snohomish Basin populations.

14. North Fork Skykomish River Summer Run

Summer-run steelhead in the North Fork Skykomish River primarily spawn upstream of 

Bear Creek Falls (RKM 21) (WDFW 2002). There is limited spawning habitat above these falls, 

and accessible habitat may terminate at RKM 31 (Williams et al. 1975). Falls and cascades may 

provide some level of reproductive isolation from winter-run steelhead in the Skykomish River, 

but probably also limit population abundance. The basin size above the falls is relatively small, 

381 km2

, but still large enough to sustain an estimated 663 to 1,325 fish, based on the IP estimate 

(Appendix D). Again, the IP estimate appears to underestimate the summer-run population’s 

possible abundance. Genetic analysis by Phelps et al. (1997) indicated that a North Fork 

Skykomish River sample, presumably summer-run fish, was very distinct from winter-run fish in 

the Snohomish Basin and from summer-run fish in the Tolt River; however, the fact that the 

north fork sample clustered with Columbia River steelhead may be indicative of some 

introgression or natural spawning by introduced Skamania Hatchery summer-run steelhead. 

Alternatively, the analysis by Phelps et al. (1997) relied on juvenile samples collected in 1993 

and 1994 and may have contained both winter-run and summer-run fish, as well as the progeny 

of feral hatchery fish. More recent analysis by Kassler et al. (2008) suggested that North Fork 

Skykomish River summer-run steelhead are distinct from Skamania Hatchery summer-run 

steelhead, although some introgression appears to have occurred. The Kassler et al. (2008) study 

did not include samples from other Puget Sound basins, so no comparisons could be made 

among North Fork Skykomish River summer-run steelhead and other summer-run steelhead.

The North Fork Skykomish River is located in the North Cascades Ecoregion. 

Geologically, much of the North Fork Basin consists of volcanic and igneous rock formations. 

Hydrologically, the river exhibits more of a snow-dominated pattern than the rest of the 

Skykomish River.

15. Snoqualmie River Winter Run

This DIP includes steelhead in the mainstem Snoqualmie River and those in its 

tributaries, particularly the Tolt River, Raging River, and Tokul Creek. There are numerous 

historical references indicating that this basin sustained large runs of steelhead. The lower 

Snoqualmie River, downstream of the Tolt River, is rarely used by steelhead as a spawning area 

and provides some geographic separation from other Snohomish Basin areas. Similarly, a series 

of falls and cascades creates temporal migrational barriers on the North Fork Tolt and South 

 22 G. Pess, NWFSC, Seattle, WA. Field observation, October 2008.
65

Fork Tolt rivers. Genetic analysis by Phelps et al. (1997) indicated that Snoqualmie River 

winter-run steelhead generally clustered with other central Puget Sound steelhead, but were most 

closely associated with Green River winter-run rather than steelhead from the Tolt or Skykomish 

rivers. The presence of offspring from hatchery-origin fish may have confounded the analysis. 

The Snohomish River basin is one of the largest basins in Puget Sound that have yet to be 

comprehensively assessed using microsatellite DNA analysis. Kassler and Bell (2011) analyzed 

genetic variation in juvenile O. mykiss from the lower South Fork Tolt River and found that these 

fish most closely resembled unmarked winter-run steelhead from the Skagit River, rather than 

presumptive summer-run steelhead from the upper South Fork Tolt River.

The Snoqualmie River Winter-Run DIP includes nearly 1,100 km of stream in a 

relatively large basin, 1,534 km2

. The IP-based historical capacity is estimated in the range of 

16,740 to 33,479 steelhead (Appendix D). In contrast, the most recent escapement estimate 

(2010) for the Snoqualmie River is 732 steelhead. Much of the accessible portion of the 

Snoqualmie River is contained within the Puget Lowlands Ecoregion, although stream flows are 

heavily influenced by flows from inaccessible headwater subbasins in the Cascades Ecoregion, 

primarily above Snoqualmie Falls. As a result, the Snoqualmie River exhibits a rain/snow 

hydrograph with relatively sustained summer flows.

16. Tolt River Summer Run

The majority of the TRT concluded that summer-run steelhead in the Tolt River basin 

constituted a DIP. Summer-run steelhead are found in the North Fork Tolt and South Fork Tolt 

rivers. Both forks are typical of summer-run steelhead habitat and contain a number of falls and 

cascades, although the North Fork Tolt is higher gradient with steeply sloped canyon walls 

(Williams et al. 1975). Genetically, Tolt River steelhead were similar to other Snohomish Basin 

steelhead samples (Phelps et al. 1997), but the samples were comprised of juveniles, and the 

progeny of naturally spawning native, hatchery, or native-by-hatchery hybrid winter-run or 

summer-run steelhead would not be phenotypically distinguished (the possibility of resident 

juvenile O. mykiss being included would further confuse the issue). Thus genetic relationships 

among Tolt River summer-run steelhead and other populations are not clear. Recent genetic 

analysis identifies the South Fork Tolt River fish as being distinct, but most closely associated 

with Skamania Hatchery–derived summer-run steelhead (Appendix B). This association may be 

related to introgression by Skamania-origin fish released into the Tolt River summer-run 

population; because of the distinct (Columbia River origin) genetic composition of Skamania 

Hatchery steelhead, even low levels of introgression would influence clustering outcomes. 

Principal component analysis suggested that the South Fork Tolt River collection is intermediate 

between Skamania Hatchery and populations from the western Cascades (no other Snohomish 

Basin collections were available). Spawn timing for Tolt River summer-run fish is from January 

to May, somewhat earlier than other summer-run steelhead populations in Puget Sound 

(Campbell et al. 2008). Additionally, there appear to be two peaks in spawning activity, one in 

February and the other in mid-April, the earlier peak possibly representing hatchery-origin fish 

(Campbell et al. 2008).

The Tolt River basin is similar to other Puget Sound basins supporting summer-run 

steelhead; it is relatively small, 255 km2

, and contains geologic formations (basalt shelves) that 

create falls which act as temporal migratory barriers. The IP-based estimate of capacity ranges
66

from 321 to 641 steelhead (Appendix D), while the most recent (2010) escapement estimate was 

116 steelhead. Much of the Tolt Basin contains glacial sediments, with the exception of harder 

volcanic formations in the canyons (Haring 2002). The basin straddles the Puget Lowlands and 

North Cascades ecoregions. Tolt River flows are generally rain-and-snow transitional.

Central and South Puget Sound MPG

Overview

The Central and South Puget Sound MPG includes populations in the Lake Washington 

and Cedar River basins, in the Green, Puyallup, and Nisqually rivers, and in South Puget Sound 

and East Kitsap Peninsula tributaries (Table 7). This MPG includes portions of the Cascades 

(higher elevation) and Puget Lowlands ecoregions. The TRT identified this MPG based on the 

geographic discreteness of central and south Puget Sound from the other MPGs. There is a 

geographic break of 50 to 100 km between the nearest populations in the three MPGs. Genetic 

information was quite extensive for steelhead in the major basins draining the Cascades, but 

there is little information on neighboring smaller, lowland rivers. Recent genetic analysis 

indicates that sampled populations in this MPG clustered together on a scale similar to those in 

the other MPGs. This MPG contains only winter-run steelhead populations, although there is 

some anecdotal information that summer-run steelhead populations may have existed in

headwater areas of some rivers. Geologically, the headwater areas of this region are different 

from those in the Northern Cascades (South Salish Sea) MPG. Although the large river systems 

Table 7. DIPs within the Central and South Puget Sound MPG and their respective categorization by 

state and tribal agencies. WRIA = Water Resource Inventory Area and SASSI/SaSI = Salmon 

and Steelhead Stock Inventory/Salmonid Stock Inventory.

WRIA 1992 SASSI/2002 SaSI TRT DIP

8 Lake Washington winter 17. Cedar River Winter Run

18. North Lake Washington and Lake 

Sammamish Winter Run

9 Green River summera

Green River winter

19. Green River Winter Run

10 Mainstem Puyallup R. winter 20. Puyallup/Carbon Rivers Winter Run

10 Carbon River winter

10 White River winter 21. White River Winter Run

11 Nisqually River winter 22. Nisqually River Winter Run

13 Deschutes River winterb 23. South Puget Sound Tributaries Winter Run

13,14 Eld Inlet winter

14 Totten Inlet winter

14 Hammersley Inlet winter

14,15 Case/Carr Inlet winter

15 East Kitsap winter 24. East Kitsap Peninsula Tributaries Winter Run

a The existing Green River summer-run steelhead population is descended from nonnative summer-run steelhead 

(Skamania Hatchery origin) and any native historical population (anadromous component) was likely extirpated, but 

may persist above Howard Hanson Damin a resident life history form. b Historically, Tumwater Falls on the Deschutes River was impassable; therefore, the Deschutes River was not 

included as part of the Puget Sound DPS.
67

have their headwaters in higher elevation areas, most of these river basins also have extensive 

alluvial plains that are ecologically similar to smaller lowland steams. Geographically, this MPG 

is identical to a Chinook salmon MPG established by the Puget Sound Chinook Salmon TRT.

Areas of South Puget Sound and Kitsap Peninsula contain predominately smaller, raindominated, low-elevation tributaries. Little is known of the steelhead populations that existed or 

exist in these basins. The Nisqually River basin is the only large river system in the southern 

portion of this MPG with a historically documented steelhead run (or runs). The Deschutes 

River was historically impassable to anadromous fish at Tumwater Falls.

Proposed DIPs within the MPG

17. Cedar River Winter Run

This DIP includes the Cedar River basin and major tributaries to the southern portion of 

Lake Washington, primarily Kelsey Creek, May Creek, and Coal Creek. Dramatic changes in 

the Lake Washington/Green River basin in the early 1900s resulted in the Cedar River being 

artificially rerouted from the Green/Black River confluence into Lake Washington. The 

concurrent construction of the Lake Washington ship canal established a new outflow for the 

Cedar River watershed into Puget Sound rather than through the Black River. Although the 

current Cedar River/Lake Washington relationship does not reflect historical conditions, it is 

unlikely that there will be a return to a prior-to-ship-canal environment, thus the TRT evaluated 

the contemporary hydrological/biological unit. Winter-run steelhead in the Cedar River adapted 

to the changes in their migration routes, but in turn increased their level of isolation from 

steelhead in the Green River. The historical relationship between the Cedar River and Lake 

Washington has been influenced by alterations in the course of the Cedar River, which has 

alternatively drained to Lake Washington or the Black River for various lengths of time 

following the last glacial recession (≈10,000 years BP). Recent data may be influenced by the 

numerous attempts by state and county agencies to establish steelhead runs in the creeks draining 

into Lake Washington and Lake Sammamish. A substantial resident O. mykiss population exists 

in the Cedar River. The relationship between the existing resident population and the historical 

anadromous population remains unclear, and underscores the complexities of interactions 

between rainbow trout and steelhead. Marshall et al. (2006) provide a genetic analysis of 

contemporary Cedar River smolts, and nonanadromous O. mykiss downstream and upstream of 

Landsburg Dam, which until 2003 was impassable to anadromous fish.

Genetically, Cedar River steelhead are very similar to native Green River winter-run 

steelhead (Phelps et al. 1997, Marshall et al. 2004). Based on spawning ground surveys 

currently conducted in the Cedar river and previous fish ladder counts, the abundance of 

steelhead has been critically low for at least a decade, with some years when few or no fish were 

observed at the Hiram M. Chittenden (aka Ballard) Locks fish ladder (although fish can pass 

undetected through the locks). The IP estimate of abundance ranges from 5,949 to 11,899 

steelhead (Appendix D). The Lake Washington basin is mostly contained in the Puget Lowlands 

Ecoregion, with the headwaters of the Cedar River and Issaquah Creek extending into the 

Cascades Ecoregion. The Cedar River has a rain-and-snow-transitional flow pattern, which is 

very distinct from most of the tributaries to Lake Washington, although flows have been 
68

modified by Seattle Public Utilities municipal water withdrawals. Earthquake and flood events 

constitute the most likely catastrophic risks.

18. North Lake Washington and Lake Sammamish Winter Run

This DIP includes tributaries draining the northern end of Lake Washington 

(approximately north of Lake Union and Evergreen Point) and the Sammamish River/Lake 

Sammamish basin. Dramatic changes in the Lake Washington/Green River basin in the early 

1900s resulted in the lowering of Lake Washington and the dewatering of the Black River, the 

historical outlet of Lake Washington. The concurrent construction of the Lake Washington ship 

canal established a new outflow for the Lake Washington/Cedar River watershed into Puget 

Sound. Although the current Cedar River/Lake Washington relationship does not reflect 

historical conditions, it is unlikely that there will be a return to a prior-to-ship-canal 

environment; therefore, the TRT evaluated the existing hydrological/biological unit. Winter-run 

steelhead adapted to the changes in their migration routes, but in turn increased their level of 

isolation from steelhead in the Green River. It is not clear to what degree steelhead historically 

utilized tributaries other than the Cedar River in the Lake Washington basin. Evermann and 

Meek (1898) suggested that small numbers of steelhead migrated up the Sammamish River into 

Lake Sammamish, although they did not observe any in their sampling. Analysis of recent data 

may be influenced by the numerous attempts by state and county agencies to establish steelhead 

runs in the creeks draining into Lake Washington and Lake Sammamish. WDFW (2002) listed a 

number of tributaries (e.g., Swamp Creek, Bear Creek, Issaquah Creek) to Lake Washington and 

Lake Sammamish as supporting steelhead, although given the very low steelhead counts at the 

Chittenden Locks, it is unlikely that there is much of a current steelhead presence in these 

tributaries. Cutthroat trout appear to be the predominant resident species in many of the smaller 

Lake Washington tributaries. In recent years the abundance of cutthroat trout exhibiting an 

anadromous life history has dramatically declined, but it is not clear whether O. mykiss in Lake 

Washington tributaries have undergone a similar shift in life history expression. The relationship 

between the existing resident population and the historical anadromous population remains 

unclear, and underscore the complexities of interactions between rainbow trout and steelhead.

Steelhead passing through the Chittenden Locks fish ladder are destined for either of two 

DIPs (Lake Washington or the Cedar River). Based on fish ladder counts, the abundance of 

steelhead has been critically low for at least a decade, with several years when few or no fish 

were observed at the fish ladder (although fish can pass undetected through the locks). The Lake 

Washington basin is mostly contained in the Puget Lowlands Ecoregion, with the headwaters of 

Issaquah Creek extending into the Cascades Ecoregion. Tributaries to Lake Washington exhibit 

rain-dominated flow patterns (high fall and winter flows with low summer flows), which 

distinguishes them from the Cedar River, whose flow is more snowmelt dominated. The IPestimated range is 5,268 to 10,536 steelhead (Appendix D). Earthquake and flood events 

constitute the most likely catastrophic risks.

19. Green River Winter Run

The TRT determined that a single winter-run DIP is present in the Green River basin. 

Winter-run steelhead were historically present in considerable numbers in the Green River, 

although until the early 1900s, the current population existed as part of a larger metapopulation 
69

that included steelhead in the Cedar, Black, and White rivers. Genetic analysis (Phelps et al. 

1997, Marshall et al. 2006) confirms the close genetic affinity that these populations have with 

one another. WDFW (2002) reports that winter-run steelhead spawn from mid-March through 

early June. The presence of early returning, hatchery-origin, winter-run steelhead (Chambers 

Creek stock) may confound the identification of early spawning (February to March) native 

steelhead. Kerwin and Nelson (2000) suggest that a native summer-run steelhead existed in the 

Green River, likely passing upstream of the Headworks Diversion Dam (RKM 98.1). This dam 

blocked migratory access to the upper basin in 1913.

A minority of TRT members indicated that a native steelhead summer run likely occurred 

in the Green River in upstream basin areas. A 1907 newspaper article (Seattle Daily Times) 

describes how a man nearly drowned landing a 4.5 kg steelhead in the Green River above 

Auburn in July. The upper basin of the Green River is characteristic of summer-run steelhead 

habitat, with numerous cascades and falls. Major tributaries such as the North Fork Green River, 

May Creek, and Sunday Creek would have provided additional spawning and rearing habitat. A 

historical summer run in the Green River should not be confused with the existing Skamania 

Hatchery–origin, summer-run steelhead. Native O. mykiss currently exist above Howard Hanson 

Dam and it is unclear to what degree these fish represent some portion of the historical 

anadromous population. The majority of the TRT concluded that a summer-run life history 

should not be considered a diversity component of the Green River steelhead DIP.

Native-origin winter-run steelhead currently spawn throughout the Green River up to the 

Headworks Diversion Dam, although historically steelhead could have had access up to RKM

149. Efforts are underway to provide passage via a trap and haul program to the upper river.

The Green River basin covers 1,191 km2

, with Soos and Newaukum creeks constituting 

the major tributaries. The lower portion of the Green River is in the Puget Lowlands Ecoregion, 

while the upper basin is in the Cascades Ecoregion. The IP-estimated range for this DIP is 

19,768 to 39,537 steelhead (Appendix D); however, the recent 5-year average has only been 770 

fish. Much of the lower portion of this basin has been highly modified through channelization 

and land development. Flow gauge information indicates that the Green River is a raindominated system, although this may be due to the effects of Howard Hanson Dam (RKM 104), 

a flood control dam. Historically, it is more likely that the Green River was a rain-and-snowtransitional system.

20. Puyallup/Carbon Rivers Winter Run

This population includes winter-run steelhead in the Puyallup River and one of its major 

tributaries, the Carbon River. Steelhead in the Puyallup Basin’s other major tributary, the White 

River, were designated in a separate DIP. The TRT determined that the mainstem Puyallup 

River below the confluence of the Puyallup and White rivers was more closely associated with 

the Carbon River than with the White River. Historically, the White River drained to the Green 

River rather than the Puyallup River and the Puyallup/Carbon was a separate basin. The 

Puyallup/Carbon River DIP covers 1,277 km2 and, although recent escapements have averaged 

410 steelhead (between 2007 and 2011), the IP-based capacity estimate is 14,716 to 29,432 

steelhead (Appendix D). There is little life history information available on these stocks other 

than spawn timing, which extends from early March to mid-June (WDFW 2002). Phelps et al. 
70

(1997) reported that steelhead genetic samples from the Green, White, and Puyallup rivers 

clustered together, with Puyallup River steelhead being slightly more distinct. Van Doornik et 

al. (2007) found that samples from the White and Carbon rivers were genetically significantly 

different from each other, although genetic divergence (FST) between samples from the two 

locations was only 0.015, a relatively low degree of differentiation.

The Puyallup River drains the slopes of Mt. Rainer and exhibits a generally transitional 

hydrograph, although the Carbon River is not as glacially influenced (i.e., glacial flour) as the 

White River. Much of the basin is located in the Cascades Ecoregion. The dominance of Mt. 

Rainer in this basin greatly increases the risk of a catastrophic event, especially from volcanic, 

earthquake, and flood sources.

21. White River Winter Run

The TRT determined the White River steelhead population begins at the confluence of 

the White and Puyallup rivers. Differences in the hydrologies of the White and Puyallup/Carbon

rivers were cited as distinguishing ecological factors between the two basins. It also appears that 

steelhead returning to the White River have a somewhat later migration and spawning time than 

those in the Carbon River, in part due to the colder stream temperatures in the White River. 

There is no evidence that native summer-run steelhead exist or existed in the White River basin. 

Phelps et al. (1997) reported that steelhead genetic samples from the Green, White, and Puyallup 

rivers clustered together, with Puyallup River steelhead being slightly more distinct. Genetic 

analysis found that samples from the White and Carbon rivers were statistically different from 

each other, with the genetic distance (Cavalli-Sforza and Edwards chord distance, a measure of 

genetic distinction) between samples of 0.23, above the 0.20 threshold set by the TRT. The 

course of the White River has changed considerably over time; in the 1800s, the White River 

drained to the Green River rather than the Puyallup River, which likely explains some of the 

underlying genetic differences among steelhead in the existing Puyallup Basin.

The basin is located in the Cascades Ecoregion and covers 1,287 km2

. Recent run size 

was 516 winter-run steelhead fish in 2011 (based on Mud Mountain Dam counts); however the 

IP estimate is considerably higher at 17,490 to 34,981 fish (Appendix D). The dominance of Mt. 

Rainer in this basin greatly increases the risk of a catastrophic event, especially from volcanic, 

earthquake, and flood sources.

22. Nisqually River Winter Run

Winter-run steelhead in the Nisqually River are presently restricted to the lower gradient 

reaches, with the exception of the Mashel River. The LaGrande and Alder dams (RKM 63.5 and 

66.0, respectively) have eliminated access to higher gradient reaches in the mainstem Nisqually 

River and numerous tributaries that drain the southern slopes of Mt. Rainier. These areas may 

have also historically supported summer runs of steelhead, although the information on summerrun steelhead presence is less definitive. Historically a series of cascades near the present site of 

the La Grande and Alder dams may have been a seasonal barrier, but also could have been a 

complete barrier to fish passage. Based on topography and river morphology, it is possible that a 

summer run of steelhead historically existed in the upper basin of the Nisqually River. There is 

little documentation to reconstruct the characteristics of this population.
71

Presently, winter-run steelhead spawn from mid-March to early June (WDFW 2002), 

although as mentioned in earlier subsections, the harvest targeting early returning hatchery-origin 

fish may have truncated the early portion of the native-origin spawn timing range. Phelps et al. 

(1997) reported that Nisqually River steelhead did not cluster genetically with steelhead in 

nearby rivers such as the Puyallup or Green rivers, but instead clustered with steelhead in small 

rivers draining to the Strait of Juan de Fuca. More recently, microsatellite DNA analysis 

suggested that the Nisqually River steelhead are somewhat distinct from other central Puget 

Sound populations, including the steelhead originating from the adjacent Chambers Creek basin 

(Appendix B), and they are more closely associated with north and south Puget Sound steelhead 

than with steelhead from Hood Canal and the Olympic Peninsula. There are few data regarding 

relationships among steelhead in the Nisqually River and those in the smaller watersheds 

throughout southern Puget Sound south of the Tacoma Narrows.

Much of the accessible river habitat is located in the Puget Lowlands Ecoregion, while 

the upper basin (above the existing dams) is located in the Cascades Ecoregion. The basin 

covers 1,842 km2

, making it one of the largest DIPs in Puget Sound. Although much of the 

accessible habitat is in the lowlands, the highest identified potential spawning habitat is at 749 m. 

The IP estimate ranges from 15,330 to 30,660 steelhead (Appendix D). In the late 1980s, run 

size estimates for “wild” Nisqually River steelhead were in excess of 6,000 fish, although recent 

estimates (2007–2011) have averaged only 402 steelhead. Currently, the Nisqually River 

exhibits a rain-dominated flow pattern, which is most likely heavily influenced by the two dams 

present that moderate snowmelt and rain runoff from Mt. Rainier. This population is most likely 

at risk from catastrophic volcanic, earthquake, and flood events.

23. South Puget Sound Tributaries Winter Run

This population includes winter-run steelhead in rivers and streams that drain to Eld Inlet, 

Totten Inlet, Hammersley Inlet and Case/Carr Inlet—effectively all of the lowland tributaries 

entering South Puget Sound (south of the Tacoma Narrows). There is little definitive 

information on their abundance, life history characteristics, or genetic variation. Commercial 

harvest data from the early 1900s indicates that several thousand steelhead were caught in 

Thurston County (Cobb 1911), which effectively covers much of the South Puget Sound. Sport 

fishery catch records (punch cards) indicate that steelhead were caught in a number of

independent tributaries to the South Puget Sound area: Coulter, Goldsborough, Kennedy, Mill, 

Percival, and Sherwood creeks. The average reported sport harvest was 85 steelhead through the 

1950 and 1960s (WDG no date-b). Overall, while some streams have long histories of hatchery 

introductions, others would appear to represent natural production. The Chambers Creek basin 

historically supported winter steelhead, although presently steelhead are no longer thought to be 

present in the basin. There is little historical information available on the abundance of steelhead 

in the basin. Beginning in 1935, steelhead returning to Chambers Creek were used to establish a 

hatchery stock that was subsequently released throughout much of western Washington and the 

Lower Columbia River (Crawford 1979).

In total, this DIP covers 1,914 km2

. There is no one dominant stream in this DIP and 

demographic connectivity is likely through a “stepping stone” interaction process. The 

tributaries all lie within the Puget Lowlands Ecoregion and are generally rain-dominated short 

river systems, with the exception of the Deschutes River, which was not historically accessible to 
72

steelhead above Tumwater Falls (RKM 3.2). The only South Puget Sound sample available for 

genetic analysis (other than Chambers Creek Hatchery origin broodstocks) was from Minter 

Creek, although this sample included only 13 fish. In general, the Minter Creek collection was 

closely related to, but still distinct from, the Chambers Creek Hatchery samples and the 

Nisqually River samples (Appendix B). The IP-estimated range is 9,854–19,709 steelhead 

(Appendix D). There are no recent estimates of escapement and no genetic samples are available 

for analysis. There has been no concerted effort to survey streams in this area and, until these are 

undertaken, this DIP is something of a placeholder for the one or more populations it may 

contain. StreamNet (no date) distribution maps do, however, indicate steelhead spawning in a 

number of tributaries throughout the DIP.

This DIP has been the subject of considerable discussion by the TRT. A plurality of TRT 

members proposed the DIP structure described above, and alternate variations included distinct 

Chamber’s Creek, and Case/Carr Inlet DIPs in addition to a combined Eld, Totten, and 

Hammersley Inlet (southwest Puget Sound) DIP. Much of the uncertainty in DIP structure was 

related to historical abundances in the streams throughout the DIP and whether those numbers 

were sufficient to sustain one or more DIPs. Some TRT members were concerned that the DIP 

straddles the Nisqually River DIP; however, stark differences in hydrology and water quality 

between the lowland stream tributaries and the rain-and-snow-fed Nisqually River likely 

produced historical differences in life history traits between steelhead in the two DIPs and 

provided some level of isolation.

24. East Kitsap Peninsula Tributaries Winter Run

This population includes small independent tributaries on the east side of the Kitsap 

Peninsula. There is limited information, other than presence, for East Kitsap steelhead with the 

exception of Curley Creek, which had an average annual sport catch of 15.4 fish (range 0–68)

from 1959 to 1970 (WDG no date-b). Numerous other smaller tributaries have been identified as 

containing spawning steelhead via redd surveys in the 1980s, although there are no specific 

estimates of production. Redds were observed in various streams from February to April 

(Zischke 2011). IP estimates for this DIP are relatively low, 1,557 to 3,115 steelhead, especially 

given the relatively large basin size of 678 km2 (Appendix D). The streams in this DIP all 

display rain-dominated flow patterns. Currently, many streams have critically low summer 

flows, although this may be an artifact of land use patterns over the last century. There is no one 

dominant stream in this DIP and demographic connectivity is through a “stepping stone” 

interaction process. Marine biogeographic barriers at Point No Point and the Tacoma Narrows 

may influence the demographic isolation of this DIP.

Spawn timing extends from February to mid-June, with some slight differences between 

river systems (WDFW 2002). The entire population lies within the Puget Lowlands Ecoregion, 

with headwater areas that drain low hills. Although some TRT members were concerned that the 

estimated historical abundance within this DIP was relatively low for sustainability, a majority of 

the TRT considered that the geographic isolation of this area was complete enough to ensure 

demographic independence.
73

Hood Canal and Strait of Juan de Fuca MPG

Overview

This MPG includes steelhead from rivers draining into the Strait of Juan de Fuca, either 

directly or via Hood Canal (Table 8). Larger rivers share a common headwater source in the 

Olympic Mountain Range and are largely glacially influenced. With the exception of streams in 

Sequim and Discovery bays, most of these systems are dominated by relatively constrained,

high-gradient reaches. In addition, there are numerous small tributaries and those draining 

lowland areas are rain dominated or rely on groundwater.

Winter-run steelhead currently are and historically were the predominant run in this 

MPG. There is some uncertainty regarding the historical or current presence of summer-run 

steelhead in a number of rivers, although if present, none of these summer-run populations 

(subpopulations) was thought to be very large. There is considerable genetic information 

available for many of the populations in this MPG. In general, genetic analysis indicates that the 

steelhead populations from this MPG cluster together, with three genetic subgroups: eastern 

Hood Canal, western Hood Canal, and the Strait of Juan de Fuca. The TRT was influenced in its 

designation by the geographic discreteness of this region. From the eastern-most edge 

(Foulweather Bluff) to the nearest population in either of the other MPGs, there was substantial 

separation (more than 50 km) between major spawning regions. The Puget Lowlands and 

Table 8. DIPs within the Hood Canal and Strait of Juan de Fuca MPG and their respective categorization 

by state and tribal agencies. WRIA = Water Resource Inventory Area and SASSI/SaSI = Salmon 

and Steelhead Stock Inventory/Salmonid Stock Inventory.

WRIA 1992 SASSI/2002 SaSI TRT DIP

15 Dewatto River winter 25. East Hood Canal Tributaries Winter Run

15 Tahuya River winter 26. South Hood Canal Tributaries Winter Run

15 Union River winter

16 Skokomish River summer

Skokomish River winter

27. Skokomish River Winter Run

16 Hamma Hamma River winter 28. West Hood Canal Tributaries Winter Run

16 Duckabush River summer

Duckabush River winter

16 Dosewallips River summer

Dosewallips River winter

17 Quilcene/Dabob Bays winter

17 Discovery Bay winter 29. Sequim/Discovery Bays Tributaries Winter Run

17 Sequim Bay winter

18 Dungeness River summer

Dungeness River winter

30. Dungeness River Summer Run and Winter Run

18 Morse Creek winter 31. Strait of Juan de Fuca Tributaries Winter Run

18 Elwha River summer

Elwha River winter

32. Elwha River Winter Run (summer)*

* Native summer run in the Elwha River basin may no longer be present. Further work is needed to distinguish 

whether existing,feral,summer-run steelhead are derived from introduced Skamania Hatchery (Columbia River) 

summer-run steehead.
74

Coastal Range ecoregions dominate the low elevation areas of the MPG, while high elevation 

areas are located in the North Cascades Ecoregion. This MPG corresponds to the amalgamation 

of the Puget Sound Chinook Salmon TRT’s Strait of Juan de Fuca and Hood Canal geographic 

regions (MPGs).

Proposed DIPs within the MPG

25. East Hood Canal Tributaries Winter Run

This DIP includes winter-run steelhead spawning in small independent tributaries on the 

west side of the Kitsap Peninsula (eastern shore of Hood Canal) from Foulweather Bluff to the 

Great Bend of southern Hood Canal. The primary tributaries in this DIP include: Big Beef 

Creek, Anderson Creek, and the Dewatto River. Stream surveys conducted in 1932 provide very 

general estimates of abundance; small runs of steelhead were identified in Anderson, Big Beef, 

and Stavis creeks, with larger runs in the Dewatto River (WDFG 1932). Maximum harvest 

(adjusted) in the Dewatto was 232 steelhead in 1952 and 242 in 1963 in Big Beef Creek (WDG 

no date-b). Historical and contemporary estimates of abundance for this DIP underscore the 

significant contribution of smaller lowland streams to overall DPS abundance. The IP estimate

ranges from 1,270 to 2,540 steelhead (Appendix D).

The streams in this DIP share a Puget Sound lowland ecology with rain-dominated flow 

patterns. Elevations are relatively low throughout the DIP. Currently, many streams have high 

winter flows and critically low summer flows, although this may be an artifact of land 

development and water withdrawals.

There was considerable discussion regarding the composition of this DIP, with a minority 

considering the East Hood Canal and South Hood Canal DIPs as one unit. There were numerous 

other variations, each grouping four main components (northwest Kitsap Peninsula, Dewatto 

River, Tahuya River, and Union River) into different combinations. Although many of these 

components exhibited abundance and habitat characteristics above the population thresholds, the 

proximity of the streams to one another was thought to allow a higher rate of exchange than is 

generally considered for a demographically independent population. However, genetic data 

indicated that, despite their relative proximity, steelhead populations in the Dewatto, Tahuya, and 

Union rivers were genetically distinct, although these differences were smaller than those 

observed in comparisons between the East Hood Canal and West Hood Canal DIPs (Appendix 

B). Ongoing research on steelhead populations in Hood Canal should provide additional 

information on the rate of straying and further boundary adjustments may be necessary.

26. South Hood Canal Tributaries Winter Run

This DIP includes winter-run steelhead spawning in independent tributaries on the 

southwest side of the Kitsap Peninsula (eastern shore of Hood Canal) that drain into the “hook” 

of southern Hood Canal. The streams in this DIP include the Tahuya and Union rivers (the 

primary streams) and streams to the southern end of Hood Canal (including Alderbrook and 

Twanoh creeks). Stream surveys conducted in 1932 give very general estimates of abundance,

with larger runs of steelhead in the Tahuya and Union rivers (WDFG 1932). Maximum harvest 

(adjusted) was 640 steelhead in 1952 (WDG no date-b). Overall, the IP estimate ranges from 
75

2,985 to 5,970 fish (Appendix D), which is somewhat high for the basin size, 641 km2, relative to 

adjacent DIPs.

The streams in this DIP share a Puget Sound lowland ecology with rain-dominated flow 

patterns. Elevations are relatively low throughout the DIP. Currently, many streams have 

critically low summer flows, although this may be an artifact of land use patterns over the last 

century. There is no one dominant stream in this DIP and demographic connectivity is likely 

maintained through a “stepping stone” process. Genetically, there was very good coverage of 

steelhead spawning aggregations throughout Hood Canal. In general, samples from within this 

DIP clustered together relative to samples from the Skokomish and west side of Hood Canal.

While there was considerable disagreement regarding the composition of this DIP, a 

plurality of members considered it as a single unit. There were numerous other variations, 

grouping four main components (northwest Kitsap Peninsula, Dewatto River, Tahuya River, and 

Union River) in different arrangements. Although many of these components exhibited 

abundance and habitat characteristics above the population thresholds, the proximity of the 

streams to one another (<20 km) was thought to allow a higher rate of exchange than is 

allowable for a DIP. Ongoing research on steelhead populations in Hood Canal should provide 

further information on the rate of straying and life history characteristics, and further adjustments 

may be necessary.

27. Skokomish River Winter Run

This population contains native winter-run steelhead in the north fork and south fork of 

the Skokomish River. Much of the North Fork Skokomish River is currently inaccessible 

beyond Cushman Dam No. 2 (RKM 27.8). There has been considerable debate as to whether 

winter-run steelhead had access beyond the series of falls in the lower North Fork Skokomish 

River; steelhead may have had access at least to the Staircase Rapids, RKM 48.1 (Williams et al. 

1975). In all, the Skokomish River basin occupies 635 km2

. Currently, winter-run steelhead 

spawn in the mainstem Skokomish, the South Fork Skokomish, and the lower North Fork 

Skokomish rivers from mid-February to mid-June (WDFW 2002). Genetically, Skokomish 

River steelhead are distinct from other populations in the region, but most similar to other West 

Hood Canal steelhead populations (Phelps et al. 1997, Van Doornik and Berejikian 2015).

A summer run of steelhead was identified in SaSI (WDFW 2002), but there is no 

information on this presumptive population. WDFW (2002) reported that summer-run steelhead 

spawn in the upper reaches of the South Fork Skokomish River from February to April. 

Anadromous access may extend as far as Steel Creek (RKM 36.8) and the upper 10 km is 

characterized by very high-gradient reaches that would be suitable for summer-run steelhead 

(Williams et al. 1975, Correa 2003). No genetic analysis has been specifically done for 

Skokomish River summer-run steelhead, although juvenile samples collected in the river’s

winter-run section (n = 23) may include summer-run steelhead. Fish classified as summer run 

based on harvest after May 30 were caught in the sport fishery from 2000 to 2004, with 50 fish 

recorded in 2003 (WDFW et al. 2004). Based on available information, the TRT was unable to 

establish whether a self-sustaining run was historically or is currently present. Furthermore, 

additional monitoring would be needed to assess any differences among winter-run steelhead in 

the North Fork Skokomish and South Fork Skokomish rivers.
76

The Skokomish River exhibits a rain-dominated flow regime, although this may be 

because the majority of the flow from the more mountainous north fork is diverted for 

hydropower and discharges directly into Hood Canal. The entire basin covers approximately 628 

km2

, with the north fork and south fork basins roughly equal size. The habitat-based IP estimate

for this basin is 10,030 to 20,060 steelhead (Appendix D). The Skokomish River basin lies in the 

Coast Range and Puget Lowlands ecoregions. Earthquake, landslide, and flood events pose a 

relatively high catastrophic risk to the Skokomish River basin.

28. West Hood Canal Tributaries Winter Run

This population combines winter-run steelhead from four former SaSI stocks (WDFW 

2002): Hamma Hamma, Duckabush, and Dosewallips rivers, and QuilceneRiver/Dabob Bay. 

WDFW (2002) identified these as distinct stocks based on their geographic separation. 

However, resident, parr, and smolt O. mykiss from the Duckabush and Dosewallips rivers 

clustered together genetically relative to steelhead populations on the east side of Hood Canal 

(Van Doornik and Berejikian 2015). In an initial genetic analysis, Hamma Hamma River O. 

mykiss samples were genetic outliers relative to samples from other rivers in this DIP, although 

that appears to be related to the small total spawning escapement (less than 20 fish in some 

recent years) and a potentially biased sample in one year. In any event, a Hamma Hamma River 

population would not be large enough to be sustainable (and thus not independent). Spawn 

timing for winter-run steelhead in these rivers is similar, occurring from mid-February to midJune. This population lies mostly in the Coast Range Ecoregion, with the exception of 

headwater areas that lie in the North Cascades Ecoregion and parts of Dabob Bay that lie in the 

Puget Lowlands Ecoregion. Much of the area is in the rain shadow of the Olympic Mountain 

Range. River flows in the Dosewallips River are strongly influenced by glacial runoff, while the 

Duckabush, Hamma Hamma and Quilcene rivers exhibit more transitional rain-and-snowdominated flow patterns. Although SaSI identified summer-run steelhead in the Dosewallips and 

Duckabush rivers, the TRT did not find any evidence to establish that native summer-run 

steelhead existed. SaSI designations may have been based on run timing indicated by punch card 

catch records. Summer-run steelhead harvest (based on fish caught after May 30) from 2000 to 

2004 has been at or near zero in the Duckabush, Dosewallips, and Quilcene rivers (WDFW et al. 

2004). It was thought that the glacially influenced (e.g., colder) rivers in this DIP may have a 

much later winter-run timing, resulting in fish being misclassified as summer run.

Total watershed area is 1,423 km2

, although the topography of the area creates 

impassable barrier falls on a number of the streams. The IP estimate in this DIP ranges from 

3,608 to 7,217 fish (Appendix D). Stream surveys conducted in 1932 identified a “large” run of 

steelhead on the Dosewallips River, with steelhead runs reported in almost every stream (WDFG

1932). Punch card records indicate a maximum (adjusted) catch of 982 fish in 1952, although 

this estimate does include some hatchery returns. In recent years, stream surveys have been 

intermittent on many of the rivers. Overall, total escapement to this DIP likely consists of a few 

hundred fish, with the most recent (2011) estimate of 227 adults.

23

There was considerable discussion among the TRT members regarding this DIP; based 

on basin size and IP estimates, some members reasoned that this DIP should be split into 

 23 See footnote 19.
77

multiple DIPs. Alternatively, because the two largest steelhead rivers (Dosewallips and 

Duckabush) in this area are so geographically close to one another (12 km), and are highly 

similar environmentally to one another, they should be considered demographically linked. The 

other rivers along the western shore of the Hood Canal were too small to exist as DIPs, so they 

were included in a single DIP. These considerations, in addition to the general clustering of 

steelhead genetic samples from western Hood Canal streams, resulted in a majority of the TRT 

concluding that there was a single west Hood Canal population.

29. Sequim/Discovery Bays Tributaries Winter Run

This population combines two former SaSI stocks, Sequim Bay and Discovery Bay, and 

includes winter-run steelhead that occupy streams in the Quimper Peninsula (Port Townsend) 

that were not included in the WDFW (2002) stock list. The entire population is located within 

the Puget Lowlands Ecoregion. Stream flows are rain dominated with many streams lacking 

surface flow during summer. Although the 802 km2 basin size for this DIP is well above the 

minimum, the majority of the area contains relatively small, independent streams. Steelhead in 

one tributary, Snow Creek, have been intensively monitored since 1976; they provided most of 

the abundance and life history data available for this DIP and provided the TRT with an 

understanding of the potential productivity of small, independent steelhead populations. 

Steelhead in this DIP spawn from early-February to mid-May, with the majority of smolts 

emigrating as 2-year-olds. Combined recorded sport catch for these tributaries averaged more 

than 60 steelhead annually during the 1950s and 1960s, with an adjusted peak catch of 200 

steelhead in 1962 (WDG no date-b). The IP estimate is 512 to 1,024 steelhead (Appendix D). 

Genetically, Snow Creek steelhead are distinct from neighboring Dungeness River and Hood 

Canal steelhead. Many streams in the western portion of this DIP are relatively near the 

Dungeness River. However, substantial differences in basin character and river hydrology 

(glacial vs. rain driven) were thought to produce differences in run timing and thus provide an 

isolating mechanism to minimize interpopulation migration.

30. Dungeness River Summer Run and Winter Run

This population includes steelhead spawning in the mainstem Dungeness and Greywolf 

rivers. Winter-run steelhead in the Dungeness River spawn from mid-March to early June 

(WDFW 2002). Haring (1999) and Goin24 indicate that summer-run steelhead were present in 

the early 1940s, prior to the introduction of Skamania Hatchery steelhead. It is unclear whether 

native summer-run steelhead are still present in the basin. The Dungeness River is accessible to 

RKM 30, where a waterfall above Gold Creek prevents passage. Greywolf River, the major 

tributary to the Dungeness River, is accessible to RKM 15.5, above where the three forks of the 

Greywolf River meet. River conditions in the glacially influenced Dungeness River were 

thought to be different enough from the rain-driven, lower elevation streams in the adjacent DIPs 

to provide some level of demographic isolation between the DIPs.

The Dungeness River basin area is approximately 560 km2

, with headwaters in the 

Olympic Mountains. The upper basin is glacially influenced and the flow regime in the 

Dungeness River is snowmelt dominated. Geologically, the basin consists of volcanic bedrock 

 24 See footnote 9.
78

and unstable glacial deposits that produce a high sediment load (Haring 1999). Genetically, the 

Dungeness River steelhead most closely cluster with other collections from the Strait of Juan de 

Fuca, Snow Creek (Sequim/Discovery Bays Tributaries DIP) and the Elwha River, but are also 

part of a large clusters of populations belonging to rivers draining the Olympic Peninsula 

(Appendix B). Each year a few hundred steelhead spawn in the Dungeness River, although high 

flows, particularly during the spring snowmelt, limits the accuracy of redd surveys. The last 

escapement estimate for the year 2000/2001 was 183 steelhead based on index area counts. 

Punch card returns from sport harvest (adjusted) averaged 348 steelhead from 1946 to 1953 prior 

to the introduction of large numbers of hatchery fish. The IP estimate is 2,465 to 4,930 steelhead 

(Appendix D).

A majority of the TRT agreed that a winter-run population existed as a DIP in the 

Dungeness River basin. A minority of the TRT concluded that summer-run steelhead likely 

existed in the upper accessible reaches of the mainstem Dungeness and Greywolf rivers. The 

relatively late timing of winter steelhead in the Dungeness River may have resulted in identifying 

some winter-run steelhead as summer-run fish, as likely occurred in the Dosewallips and 

Duckabush rivers. Historically, Native Americans harvested steelhead using fish traps or lines 

(Gunther 1927) from December through February, although in-river conditions may not have 

been amenable for harvesting summer-run fish. Haring (1999) indicated that summer-run fish 

were present, although conditions in the river limited direct observation. The TRT strongly 

encourages further monitoring to establish whether native summer-run fish are still present and,

if so, determine whether they are part of a combined summer/winter DIP or represent an 

independent population.

31. Strait of Juan de Fuca Tributaries Winter Run

This population consists of steelhead spawning in independent tributaries to the Strait of 

Juan de Fuca between the Dungeness and Elwha rivers, including: Ennis, White, Morse, Siebert, 

and McDonald creeks. Each of the tributaries is relatively small and collectively the creeks 

contain a 410 km2 watershed. Sports catch (punch card) data for Morse, Siebert, and McDonald 

creeks indicate that well over 100 wild fish were caught annually through the 1950s and 1960s, 

with a peak catch of 258 in 1958 (WDG no date-b). The IP estimate is 728 to 1,456 fish 

(Appendix D), with the most recent (2010) abundance estimate, 245 steelhead, based on index 

counts in just Morse and McDonald creeks. The headwaters of these creeks extend into the 

Olympic Mountains and flows can be considerable, especially following lowland rain events 

(Haring 1999). Summer-run steelhead have been reported caught in Morse Creek, although it is 

unclear whether these fish were native or strays from the Elwha or Dungeness rivers (Haring

1999). Further investigation is warranted to confirm the presence and identify the source of 

summer-run fish in Morse Creek (as well as in the Dungeness River and Elwha River DIPs).

The TRT concluded that it was unlikely that any one of the streams within this DIP was 

large enough to persist as a DIP. In any case, their proximity to one another in addition to their 

environmental similarity limited the likelihood of their demographic independence. Distances 

between streams in this DIP and the Dungeness and Elwha rivers to the east and west, 

respectively, were at their closest less than 20 km. The TRT concluded that while the distances 

between the Elwha and Dungeness rivers and the smaller independent tributaries were somewhat 

small for a DIP, ecological differences between the smaller creeks and larger river systems 
79

would reduce the likelihood of interaction between these DIPs, while not limiting demographic 

connectivity between Ennis, McDonald, Morse, Siebert, and White creeks.

32. Elwha River Winter Run

Winter-run steelhead were historically present in the Elwha River basin, although little is 

known of their life history diversity prior to the construction of the two Elwha River dams in the 

early 1900s. Currently, there are two known populations of winter-run steelhead in Elwha River, 

one presumptive native, late-winter run and one early winter, hatchery-origin run (Chambers 

Creek origin). Natural spawning occurs throughout the main stem and tributaries below the 

(former, now removed) Elwha Dam (RKM 7.9), with early returning steelhead spawning prior to 

mid-March and late returning steelhead spawning from April to June. Genetic analysis indicated 

that the early timed portion of the steelhead run is largely derived from Chambers Creek 

Hatchery stock, while the later returning component is significantly different from the early, 

hatchery-origin, component, but also different from some collections of resident O. mykiss in the 

upper Elwha River (Winans et al. 2008). However, Phelps et al. (2001) suggested that some 

residualized populations (above the dams) of O. mykiss were similar to anadromous steelhead 

below the dam. It is unclear whether existing resident O. mykiss populations contain an 

anadromous legacy. If so, it may take several years following the removal of the (former, now 

removed) Elwha and Glines Canyon dams for these populations to reestablish themselves as 

anadromous and reach some equilibrium with steelhead that are currently spawning below the 

Elwha Dam site. Additionally, it is unclear whether summer-run steelhead were historically 

present and still persist, either as anadromous fish below the dams or above the dams as resident 

O. mykiss.

The Elwha River basin is 832 km2 with its headwaters in the Olympic Mountains. Much 

of the upper basin is in the North Cascades Ecoregion with the lower reaches in the Puget 

Lowlands Ecoregion. The Elwha River exhibits a rain-and-snow-transitional flow pattern. 

Historically, the mainstem Elwha River was accessible to RKM 62.8, with additional habitat in 

tributaries in the lower and middle reaches. The IP estimate for steelhead abundance in the 

Elwha River is 7,116–14,231 (Appendix D), based on unrestricted access to the basin (without 

the dams). Estimates of native-origin spawner escapement have not been done on a 

comprehensive basis in recent years. For the last complete year, 1996/1997, escapement was 

only 153 fish (anadromous access was limited to the lower river).

Historically, a summer run may have been present in the Elwha River; however, it is 

possible that the run was extirpated or residualized when the Elwha and Glines Canyon dams 

were constructed in the early 1900s at RKM 7.9 and RKM 21.6, respectively. Although 

summer-run steelhead have been observed in the pools below the Elwha Dam in recent years, it 

is most probable that these fish are the product of nonnative, Skamania Hatchery, summer-run 

steelhead releases into the Elwha River (see Appendix G for summer-run releases). Summer 

temperatures in the lower Elwha River, in addition to frequent outbreaks of Dermocystidium, 

greatly reduce survival of returning adult salmonids. Thus it is likely that the native summer

steelhead run was (or runs were) extirpated follow the construction of the Elwha River dams. 

Alternatively, summer or winter steelhead runs may have residualized in tributaries to the Elwha

River above the dams. The historical distribution of summer-run steelhead in the Elwha River is 

unknown, but it is possible that rapids and cascades in canyon areas may have provided an
80

isolating mechanism for migrating winter-run and summer-run steelhead (especially during high 

spring flows). Alternatively, the two run times could have occupied similar spawning habitat 

with temporal isolation in spawning. Although there was general agreement regarding the 

presence of winter-run steelhead in the Elwha River DIP, there was no consensus regarding the 

historical existence of summer-run steelhead in the Elwha River. At present, the majority 

conclusion was that summer-run steelhead were absent. Further study is required to establish 

whether there is any legacy of a native summer run above or below the recently removed dams.

Puget Sound Steelhead DPS Population Considerations

The TRT conclusions presented are based on available information. Responses to 

reviewer comments are in Appendix M. It is likely that in the future (during the course of 

subsequent monitoring efforts, historical document review, etc.) new information will become 

available that may support the need for reconsidering the DIPs identified in this document, 

including the addition, deletion, or redelineation of DIPs. Where possible, we have identified 

areas where there was uncertainty in the designation of DIPs to stimulate further research and 

assessment. As with any biological unit, DIPs represent part of a continuum of population 

structure and there is some potential for between-TRT-member differences in the criteria for 

DIPs and MPGs. For example, the process of identifying components for truth membership 

functions in the decision support system was very informative in identifying variation in DIP 

thresholds among the individual members within the TRT. We have utilized both the 

conclusions of the TRT members and the results of the gatekeeper model to identify the 

historical DIPs and MPGs within the Puget Sound Steelhead DPS. In developing our 

reconstruction of the structure of the historical DIPs of steelhead in Puget Sound, we are 

providing a general template for the restoration of a sustainable DPS. Our descriptions of the 

individual populations and major population groups are intended to convey a sense of the 

diversity and dispersal of demographic units and their environment. It is the restoration of these 

essential elements that will ensure the sustainability of this DPS into the foreseeable future. A 

companionate technical memorandum (Hard et al. in press) focuses on viability criteria for this 

DPS.
81

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92
93

Appendix A: Comparison of Populations and 

Management Units

Table A-1. Steelhead (Oncorhynchus mykiss) populations listed under the 1930 survey were identified as 

being medium to large abundance (WDFG 1932). Genetic analysis indicates populations in 

genetic diversity units (GDUs) (Phelps et al. 1997). State and tribal comanagers identified 

populations in their 1992 SASSI (WDF et al. 1993) and 2002 SaSI (WDFW 2002) steelhead 

inventories.

1930 survey Genetic analysis 1997 1992 SASSI / 2002 SaSI WRIAa

Dakota Creek Dakota Creek winter 1

Nooksack River 1

North Fork North Puget Sound GDU 8 N. F. Nooksack River winter 1

Middle Fork North Puget Sound GDU 8 M. F. Nooksack River winter 1

South Fork S. F. Nooksack River summer

S. F. Nooksack River winter

1

Samish River winter 3

Skagit River North Puget Sound GDU 8 Mainstem Skagit River winter 4

Finney Creek North Puget Sound GDU 8 Finney Creek summer 4

Grandy Creek 4

Bacon Creek 4

Baker River 4

Cascade River North Puget Sound GDU 8 Cascade River summer

Cascade River winter

4

Sauk River North Puget Sound GDU 8 Sauk River summer

Sauk River winter

4

Dan Creek 4

Stillaguamish River Stillaguamish River winter 5

N. F. Stillaguamish North Puget Sound GDU 8 5

Pilchuck River North Puget Sound GDU8 5

Deer Creek North Puget Sound GDU 8 Deer Creek summer 5

Boulder Creek 5

French Creek 5

Squire Creek 5

S. F. Stillaguamish S. F. Stillaguamish R. summerb 5

Jim Creek 5

Canyon Creek Canyon Creek summer 5

Snohomish River Snohomish River winter 7

Pilchuck River South Puget Sound GDU 2 Pilchuck River winter 7

Skykomish River South Puget Sound GDU 2 7

Woods Creek 7

Elwell Creek 7

Wallace River 7

S. F. Skykomish R. S. F. Skykomish River summerc 7
94

Table A-1 continued. Steelhead populations listed under the 1930 survey were identified as being 

medium to large abundance (WDFG 1932). Genetic analysis indicates populations in genetic 

diversity units (GDUs) (Phelps et al. 1997). State and tribal comanagers identified populations in 

their 1992 SASSI (WDF et al. 1993) and 2002 SaSI (WDFW 2002) steelhead inventories.

1930 survey Genetic analysis 1997 1992 SASSI / 2002 SaSI WRIAa

N. F. Skykomish R. South Puget Sound GDU 2 N. F. Skykomish River summer 7

Snoqualmie River Snoqualmie River winter 7

Tolt River South Puget Sound GDU 2 Tolt River summer 7

Raging River South Puget Sound GDU 2 7

Cedar Riverd South Puget Sound GDU 2 Lake Washington winter 8

Duwamish River 9

Green River South Puget Sound GDU 2 Green River summere

Green River winter

9

Soos Creek 9

Puyallup River South Puget Sound GDU 2 Mainstem Puyallup River winter 10

Carbon River Carbon River winter 10

Voight Creek 10

S. Prairie Creek 10

White River South Puget Sound GDU 2 White River winter 10

Nisqually River South Puget Sound GDU 2 Nisqually River winter 11

Mashel River 11

Not Surveyed Deschutes River winter 13

Not Surveyed Eld Inlet winter 13,14

Not Surveyed Totten Inlet winter 14

Not Surveyed Hammersley Inlet winter 14

Not Surveyed Case/Carr Inlet winter 14,15

Not Surveyed East Kitsap winter 15

Not Surveyed Dewatto River winter 15

Not Surveyed South Puget Sound GDU 2 Tahuya River winter 15

Not Surveyed Union River winter 15

Not Surveyed South Puget Sound GDU 2 Skokomish River summer

Skokomish River winter

16

Not Surveyed South Puget Sound GDU 2 Hamma Hamma River winter 16

Not Surveyed Duckabush River summer

Duckabush River winter

16

Not Surveyed South Puget Sound GDU 2 Dosewallips River summer

Dosewallips River winter

16

Not Surveyed Quilcene/Dabob bays winter 17

Not Surveyed South Puget Sound GDU 2 Discovery Bay winter 17

Not Surveyed Sequim Bay winter 17

Not Surveyed South Puget Sound GDU 2 Dungeness River summer

Dungeness River winter

18

Not Surveyed South Puget Sound GDU 2 Morse Creek winter 18

Not Surveyed North Coast GDU 9 Elwha River summer

Elwha River winter

18

a WRIA = Water Resource Inventory Area.

b South Fork Stillaguamish River steelhead were considered nonnative.

c South Fork Skykomish River steelhead were considered nonnative.

d Cedar River steelhead were considered “scarce.”

e Green River summer-run steelhead were considered nonnative (the historical population was extirpated).
95

Appendix B: Genetic Analysis of Steelhead 

from Puget Sound

A number of studies have analyzed genetic variation among steelhead (Oncorhynchus 

mykiss) populations in Puget Sound; however, the majority of these have focused on specific 

river basins or geographic areas within the Puget Sound distinct population segment (DPS). The 

last comprehensive genetic assessment of Puget Sound steelhead was undertaken by Phelps et al. 

(1997). This appendix reports on microsatellite DNA variation for 21 of the 32 proposed 

demographically independent populations (DIPs) within the Puget Sound Steelhead DPS (Table 

B-1).

Samples representing all three major population groups (MPGs) and the majority of DIPs 

within those MPGs were obtained on an as available basis (Table B-1). Data were analyzed for 

13 microsatellite DNA loci for 4,563 fish from 39 collections available from published and 

unpublished sources (Table B-2). Collections generally consisted of more than 48 fish. The 

Minter Creek collection was the smallest (n = 13), but was retained in the analysis as a distinct 

sample because it was thought to be representative of South Puget Sound steelhead and distinct 

from the Nisqually River collection. The majority of the samples were acquired subsequent to 

the study by Phelps et al. (1997). Laboratory conditions are given in Winans et al. (2008).

We evaluated Hardy-Weinberg equilibrium with FSTAT version 2.9.3.

25 The 

significance of FIS estimates was determined with permutation over alleles by 468,000 

randomizations. Differences among collections were illustrated in a dendrogram using the 

Cavalli-Sforza and Edwards chord metric (Cavalli-Sforza and Edwards 1967) calculated with 

Populations version 1.2.30.

26 Precision of branching patterns was evaluated by bootstrapping 

over loci 1,000 times. The tree was printed with TreeView.

27 An additional independent 

assessment of among-collection variability was done using a factorial correspondence analysis 

(FCA) with GENETIX 4.05.2.28 It was believed that some collections (e.g., Snow Creek and 

Samish River) contained fish with Chambers Creek ancestry. To identify these fish and 

eliminate them from the subsequent analyses, we implemented Structure 2.229 (burn-in of 50,000 

iterations and a run of 500,000 iterations) (Pritchard et al. 2000), using the selected collections 

and two Chambers Creek stocks—Soos Creek Hatchery (adults, 2008) and Lower Elwha 

 25 A software program developed by Jerome Goudet to estimate and test gene diversities and fixation indices, online 

at http://www2.unil.ch/popgen/softwares/fstat.htm.

26 A population genetics software program (individuals or population distance, phylogenetic trees) developed by 

Olivier Langella, online at http://bioinformatics.org/~tryphon/populations.

27 A tree drawing software program, online at http://rana.lbl.gov/EisenSoftware.htm and http://www.treeview.net/tv

/download.asp.

28 Population genetics software, online at http://kimura.univ-montp2.fr/genetix. 29 The program implements a model-based clustering method for inferring population structure, online at 

http://pritchardlab.stanford.edu/software/structure2_2.html.
96

Klallam Hatchery (juveniles, 2005 and 2006). Fish assigned a Chambers Creek contribution to 

genetic composition of more than 50% were removed from further analyses.

Of the 4,363 samples analyzed, five fish from Snow Creek and five from the Samish 

River were identified with substantial Chambers Creek ancestry. A total of 4,353 fish were used 

in the remaining analyses. Significant departures from Hardy-Weinberg equilibrium were 

detected at Duckabush, Skokomish, and Green River samples where FIS values were significantly 

positive in each case (indicating heterozygote deficiency, Table B-2). Heterozygote deficiency 

(Wahlund effect) may indicate a pooling of dissimilar gene pools.

In the 39-collection dendrogram (Cavalli-Sforza and Edwards chord metric and neighbor 

joining clustering, Figure B-1), seven groups are apparent:

• Samish and Nooksack River collections,

• Skagit River and tributaries collections (six Skagit River samples and Stillaguamish, 

Sauk, and Suiattle rivers),

• East Hood Canal collections (Big Beef Creek and Dewatto River) that are joined by 

Tahuya River,

• Four Chambers Creek–based hatcheries that are joined by Minter Creek,

• Three Olympic Peninsula collections (Elwha and Dungeness rivers and Snow Creek) that 

join to the Skokomish River and three West Hood Canal collections (Hamma Hamma, 

Duckabush, and Dosewallips rivers),

• Five collections from South Puget Sound and Central Puget Sound, and

• Skamania stock joined with South Fork Tolt River and loosely with Deer Creek.

In a Cavalli-Sforza and Edwards chord tree with unweighted pair group method with 

arithmetic mean clustering (Table B-3 and Figure B-2), several collections or collection groups 

are distinctive: Minter, Deer, East Hood Canal, Tahuya, Nooksack, and Skamania-Tolt. Two 

broad groups are seen, the Chambers Creek collections, Samish, West Hood Canal, and Olympic 

Peninsula populations, and the South/Central Puget Sound, Stillaguamish, and Skagit collections. 

The Puyallup River sample is distinctive.

The first three FCA components explained 30.6% of the total variance in the 39-

collection data set. Along the first axis, the East Hood Canal and West Hood Canal, Chambers 

Creek stocks, and Olympic Peninsula collections (including single locales Tahuya River and 

Minter Creek) were broadly different from Nooksack/Samish, Skagit, and Stillaguamish rivers, 

in addition to summer-run fish (Skamania Hatchery, South Fork Tolt River, and Deer Creek), 

and South/Central Puget Sound collections (except Minter Creek, Figure B-3). Along FCA1 and 

FCA2, collections grouped by DIP. Noticeably similar are Skagit and Nooksack/Samish rivers,

and particularly distinctive are Tahuya and Skokomish rivers. Along FCA3, the Skagit 

collections are more different from Nooksack/Samish River collections, as are the summer-run 

fish compared to their variability along FCA1 and FCA2. Nisqually is distinctive from the other 

South/Central Puget Sound collections along FCA3 (Figure B-4). Collections from Big Beef 

Creek and Dewatto River are highly divergent along FCA3.
97

In general, there was a close correspondence between geographic proximity and genetic 

similarity. From a Puget Sound–wide prospective, it was surprising that collections from Hood 

Canal accounted for considerable between-collection variability (Figure B-5 and Figure B-6). Of 

the summer-run samples, FCA results suggested a closer affinity of Deer Creek steelhead with 

winter-run steelhead in the Stillaguamish River basin. In contrast, the close affinity of South 

Fork Tolt River summer-run steelhead to Skamania Hatchery summer-run steelhead is likely the 

result of the presence of offspring from hatchery strays or introgression between native and 

introduced fish in the Tolt River basin. The Skamania Hatchery steelhead that originated from 

the Columbia River are genetically distinctive; it is safe to say that populations in the Puget 

Sound that are genetically similar have probably experienced introgression with the nonnative 

summer-run fish. In contrast, because Chambers Creek Hatchery winter-run steelhead were 

developed from native South Puget Sound fish, there is likely some level of statistically inferred 

Chambers Creek Hatchery introgression that is simply the result of shared alleles between Puget 

Sound–origin populations.
98

Table B-1. Geographic distribution of steelhead genetic samples from the Puget Sound Steelhead DPS 

analyzed for DNA microsatellite variation at 13 loci. Additional sample information can be 

found in subsequent tables.

TRT MPG TRT DIP

Genetics sample(s)

25 sample no. 39 sample no.

North Cascades Drayton Harbor Tributaries Winter Run — —

Nooksack River Winter Run 1, 2 (3, 4?) 1, 2, 5 (3, 4?)

South Fork Nooksack River Summer Run (3, 4?) (3, 4?)

Samish River and Bellingham Bay Tributaries 

Winter Run

5 6,7

Skagit River Summer Run and Winter Run 6 8, 9, 10, 13, 

15, 16

Nookachamps Creek Winter Run — —

Baker River Summer Run and Winter Run — —

Sauk River Summer Run and Winter Run 7 11, 12

Stillaguamish River Winter Run 8 18

Deer Creek Summer Run 9 17

Canyon Creek Summer Run — —

Snohomish/Skykomish Rivers Winter Run — —

Pilchuck River Winter Run — —

North Fork Skykomish River Summer Run — —

Snoqualmie River Winter Run — —

Tolt River Summer Run 10 21

Central and 

South Puget 

Sound 

Cedar River Winter Run 11 22

North Lake Washington and Lake Sammamish 

Winter Run

— —

Green River Winter Run 12 24

Puyallup/Carbon Rivers Winter Run 14 26

White River Winter Run 12 25

Nisqually River Winter Run 15 27

South Puget Sound Tributaries Winter Run 16 28

East Kitsap Peninsula Tributaries Winter Run — —

Olympic 

Peninsula 

East Hood Canal Tributaries Winter Run 17 29, 30

South Hood Canal Tributaries Winter Run 18 31

Skokomish River Winter Run 19 32

West Hood Canal Tributaries Winter Run 20 33, 34, 35

Sequim/Discovery Bays Tributaries Winter Run 21 36

Dungeness River Summer Run and Winter Run 22 37

Strait of Juan de Fuca Tributaries Winter Run — —

Elwha River Winter Run 23 39
99

Table B-2. Information for collections of steelhead used in the genetic analyses. A significant positive 

value for FIS within samples indicates a significant departure from Hardy-Weinberg. Based on 

468,000 randomizations, the adjusted nominal level of P (5%) for FIS is 0.00011. 

Pop Sample Source Fish sampled N FIS

P

values

1 Nooksack R. 1 NMFS/Nooksack Tribe Mix, 2008–2009 25 0.086 0.0020

2 Nooksack R. 2 NMFS Not available 37 0.045 0.0210

3 S.F. Nooksack A WDFW unpublished Adults, 2007–2010 38 0.040 0.0310

4 S.F. Nooksack J WDFW unpublished Juveniles, 2009 26 0.018 0.2340

5 Main Nooksack WDFW unpublished Juveniles, 2009 47 0.020 0.1510

6 Samish R. 2009 WDFW unpublished Adults, 2009 37 0.025 0.1410

7 Samish R. 2008 WDFW unpublished Adults, 2008 41 0.000 0.4800

8 Skagit/Manser WDFW unpublished Parr, 2007 235 0.019 0.0090

9 Upper Skagit R. WDFW unpublished Adults, 2008–2011 81 0.014 0.1590

10 Cascade River WDFW unpublished Juveniles, 2009–10 98 0.006 0.3270

11 Suiattle River WDFW unpublished Adults, 2010–2011 51 0.010 0.2790

12 Sauk River WDFW unpublished Adults, 2008–2011 81 0.021 0.0720

13 Finney Creek WDFW unpublished Juveniles, 2009–10 105 0.000 0.5110

14 Marblemount H. WDFW unpublished Adults, 2008–2010 151 0.020 0.0240

15 Mid Skagit R. WDFW unpublished Adults, 2009–2010 42 0.035 0.0340

16 Goodell Creek WDFW unpublished Juveniles, 2010–11 88 0.008 0.2800

17 Deer Creek WDFW unpublished Juveniles, 1995 31 0.020 0.2050

18 Stillaguamish R. WDFW unpublished Smolts, 2006 109 0.036 0.0010

19 Tokul Creek H. WDFW unpublished Adults, 2001 95 −0.008 0.7391

20 Skamania H. WDFW unpublished N/A, 2008 95 −0.033 0.9900

21 S.F. Tolt (above) WDFW unpublished Juveniles, 2010 75 0.005 0.3820

22 Cedar River Marshall et al. 2004 Mix, 2007 144 0.033 0.0010

23 Soos Creek H. Winans et al. 2010 Adults, 2008 48 0.038 0.0211

24 Green River Winans et al. 2010 Adults, 2006 43 0.076 0.0000

25 White River Van Doornik et al. 2007 Mix, 2002, 2004–06 438 0.015 0.0060

26 Pulyallup River Van Doornik et al. 2007 Mix, 2002, 2004–06 70 0.008 0.2870

27 Nisqually River NMFS-NWFSC Juv., 2006–2008 151 0.018 0.0480

28 Minter Creek WDFW unpublished Mix, 2006–2007 13 0.039 0.1600

29 Big Beef Creek NWFSC-Manchester Mix, 2006–2007 264 0.023 0.0020

30 Dewatto River NWFSC-Manchester Parr, smolts, 2006–7 295 0.000 0.5100

31 Tahuya River NWFSC-Manchester Smolts, 2006–2007 179 0.014 0.0720

32 Skokomish R. NWFSC-Manchester Parr, smolts, 2006–7 299 0.041 0.0000

33 Hamma Hamma NWFSC-Manchester Smolts, 2006, 2007 64 0.049 0.0010

34 Duckabush R. NWFSC-Manchester Parr, smolts, 2006–7 228 0.040 0.0000

35 Dosewallips R. NWFSC-Manchester Parr, smolts, 2006–7 169 0.033 0.0000

36 Snow Creek NWFSC-Manchest./WDFW Smolts, 2006–2007 129 0.011 0.1710

37 Dungeness River WDFW unpublished Parr, smolts, 2006–7 251 0.017 0.0130

38 L. Elwha Kla. H. Winans et al. 2008 Juv., 2005–2006 142 0.029 0.0070

39 Elwha River Winans et al. 2008 Juveniles, 2005 48 0.032 0.9690

Total: 4563
100

Central Puget Sound

East and South Hood Canal

Skagit and Stillaguamish rivers

Nooksack and Samish rivers

Olympic Peninsula

Chambers Creek H.

Figure B-1. Dendrogram of 39 Puget Sound steelhead collections analyzed for 13 microsatellite DNA 

loci and displayed using Cavalli-Sforza and Edwards chord metric and neighbor joining 

clustering. Numbers at the branches of the tree are representative of bootstrap values (percent).
101

Table B-3. Cavalli-Sforza and Edwards chord distances for 39 steelhead collections from Puget Sound. 

The gatekeeper model (Appendix C) used a Cavalli-Sforza and Edwards chord distance of 0.200 

as a threshold for population independence. Numbers shaded in gray have distances less than 

0.20. Numbers framed within lined boxes represent intra-Skagit River basin collections.

Population Pop. no.

Population number

1 2 3 4 5 6 7 8

Big Beef 1 0 0.262116 0.241455 0.262637 0.279043 0.290157 0.214851 0.332614

Dewatto 2 0.262116 0 0.286243 0.293168 0.315803 0.318019 0.239286 0.359593

Dosewallips 3 0.241455 0.286243 0 0.175085 0.228511 0.268656 0.243821 0.293635

Duckabush 4 0.262637 0.293168 0.175085 0 0.237968 0.266607 0.258463 0.301843

Skokomish 5 0.279043 0.315803 0.228511 0.237968 0 0.281614 0.282103 0.303785

Snow 6 0.290157 0.318019 0.268656 0.266607 0.281614 0 0.282242 0.345242

Tahuya 7 0.214851 0.239286 0.243821 0.258463 0.282103 0.282242 0 0.341022

Puyallup 8 0.332614 0.359593 0.293635 0.301843 0.303785 0.345242 0.341022 0 

White 9 0.265447 0.307553 0.227053 0.236120 0.258416 0.283369 0.270277 0.230843

Nisqually 10 0.287926 0.325270 0.265088 0.274664 0.313629 0.321052 0.286171 0.294474

Elwha 11 0.297039 0.316219 0.236469 0.266258 0.285213 0.291876 0.291943 0.319542

Green 12 0.299120 0.325930 0.258079 0.261443 0.294091 0.319159 0.299414 0.289932

Skamania H. 13 0.409008 0.445069 0.380190 0.378980 0.394588 0.446388 0.437625 0.408210

Dungeness 14 0.260616 0.289429 0.191793 0.195368 0.249072 0.251927 0.239008 0.285152

Minter 15 0.421685 0.441543 0.406143 0.400416 0.436430 0.438207 0.431098 0.455574

Cedar 16 0.333143 0.352983 0.293839 0.289460 0.316655 0.334837 0.318299 0.295857

Stillaguamish 17 0.262464 0.291450 0.214412 0.222831 0.259532 0.281870 0.270271 0.276437

Skagit Manser 18 0.257255 0.284414 0.209617 0.215832 0.261767 0.272643 0.255704 0.274446

Nooksack 1 19 0.336913 0.341797 0.308496 0.318860 0.343484 0.354178 0.325958 0.343759

Nooksack 2 20 0.311230 0.324536 0.290164 0.293473 0.319683 0.334226 0.301917 0.342053

Upper Skagit 21 0.270676 0.294632 0.224910 0.228140 0.263425 0.289793 0.255529 0.289025

Mid Skagit 22 0.276755 0.314458 0.247853 0.257809 0.280300 0.288480 0.276764 0.307629

Cascade 23 0.288620 0.312604 0.259065 0.263651 0.270060 0.302447 0.287364 0.302185

Suiattle 24 0.286295 0.301935 0.255646 0.267996 0.283659 0.301296 0.283013 0.291080

Sauk 25 0.270891 0.307891 0.243761 0.254745 0.267928 0.284099 0.266308 0.294726

Finney 26 0.270903 0.299876 0.236840 0.236662 0.261582 0.293311 0.265983 0.296803

Goodell 27 0.293439 0.301672 0.279179 0.291768 0.302318 0.321544 0.279469 0.329600

Marblemount H. 28 0.268846 0.293805 0.242732 0.259085 0.305934 0.293909 0.259775 0.333254

Deer 29 0.370476 0.366557 0.345459 0.364302 0.370736 0.396580 0.364632 0.363295

S. F. Tolt 30 0.324545 0.364875 0.291886 0.289282 0.319169 0.346591 0.343278 0.331715

S. F. Nooksack 31 0.314759 0.344220 0.300838 0.309086 0.324501 0.346640 0.322223 0.336414

S. F. Nooksack j 32 0.337109 0.351399 0.293936 0.311733 0.334160 0.353473 0.331402 0.341541

Mainstem N’sack 33 0.336429 0.369378 0.322172 0.325020 0.338686 0.358526 0.336260 0.360462

Samish 08 34 0.292386 0.314068 0.248982 0.261353 0.298857 0.310697 0.281388 0.337938

Samish 09 35 0.297191 0.332507 0.286921 0.284363 0.303490 0.315319 0.298967 0.350057

Lower Elwha H. 36 0.307446 0.315650 0.277532 0.283882 0.304858 0.296743 0.282911 0.358379

Tokul Hatchery 37 0.279919 0.296422 0.247468 0.260761 0.307233 0.282423 0.267917 0.331927

Hamma Hamma 38 0.299071 0.342052 0.233147 0.241947 0.278394 0.300938 0.295151 0.335092

Soos Creek H. 39 0.296569 0.313922 0.276336 0.288313 0.317479 0.302252 0.291281 0.337560
102

Table B-3 continued horizontally. Cavalli-Sforza and Edwards chord distances for 39 steelhead 

collections from Puget Sound. The gatekeeper model (Appendix C) used a Cavalli-Sforza and 

Edwards chord distance of 0.200 as a threshold for population independence. Numbers shaded in 

gray have distances less than 0.20. Numbers framed within lined boxes represent intra-Skagit 

River basin collections.

Population Pop. no.

Population number

9 10 11 12 13 14 15 16

Big Beef 1 0.265447 0.287926 0.297039 0.299120 0.409008 0.260616 0.421685 0.333143

Dewatto 2 0.307553 0.325270 0.316219 0.325930 0.445069 0.289429 0.441543 0.352983

Dosewallips 3 0.227053 0.265088 0.236469 0.258079 0.380190 0.191793 0.406143 0.293839

Duckabush 4 0.236120 0.274664 0.266258 0.261443 0.378980 0.195368 0.400416 0.289460

Skokomish 5 0.258416 0.313629 0.285213 0.294091 0.394588 0.249072 0.436430 0.316655

Snow 6 0.283369 0.321052 0.291876 0.319159 0.446388 0.251927 0.438207 0.334837

Tahuya 7 0.270277 0.286171 0.291943 0.299414 0.437625 0.239008 0.431098 0.318299

Puyallup 8 0.230843 0.294474 0.319542 0.289932 0.408210 0.285152 0.455574 0.295857

White 9 0 0.258035 0.286888 0.216689 0.382943 0.228604 0.424696 0.243325

Nisqually 10 0.258035 0 0.306498 0.297183 0.399713 0.274427 0.443317 0.320326

Elwha 11 0.286888 0.306498 0 0.308999 0.418636 0.220238 0.428818 0.334763

Green 12 0.216689 0.297183 0.308999 0 0.416368 0.264104 0.448291 0.248451

Skamania H. 13 0.382943 0.399713 0.418636 0.416368 0 0.389832 0.501450 0.439181

Dungeness 14 0.228604 0.274427 0.220238 0.264104 0.389832 0 0.397546 0.286452

Minter 15 0.424696 0.443317 0.428818 0.448291 0.501450 0.397546 0 0.445248

Cedar 16 0.243325 0.320326 0.334763 0.248451 0.439181 0.286452 0.445248 0

Stillaguamish 17 0.197018 0.272815 0.258143 0.242932 0.346478 0.207397 0.410468 0.284919

Skagit Manser 18 0.180758 0.267719 0.264860 0.221565 0.381906 0.195191 0.405612 0.262210

Nooksack 1 19 0.269087 0.329307 0.342332 0.306815 0.404724 0.304009 0.441800 0.328132

Nooksack 2 20 0.271969 0.316956 0.319534 0.297634 0.398205 0.270711 0.423518 0.317118

Upper Skagit 21 0.202947 0.278837 0.276714 0.236125 0.404531 0.217505 0.409157 0.284095

Mid Skagit 22 0.210108 0.296812 0.300449 0.245891 0.398347 0.242066 0.412304 0.291643

Cascade 23 0.238197 0.308837 0.308239 0.263302 0.381994 0.260985 0.423223 0.294278

Suiattle 24 0.195495 0.284790 0.294026 0.234859 0.401148 0.248012 0.432298 0.270615

Sauk 25 0.209449 0.288656 0.284461 0.240422 0.408236 0.229248 0.420127 0.282860

Finney 26 0.205955 0.277488 0.284488 0.241039 0.390311 0.232278 0.420708 0.283001

Goodell 27 0.251493 0.310393 0.311858 0.274439 0.414342 0.275331 0.421917 0.300480

Marblemount H. 28 0.270701 0.285184 0.284894 0.291091 0.418600 0.225636 0.400976 0.312430

Deer 29 0.348754 0.381735 0.358883 0.330676 0.420397 0.354510 0.506952 0.374539

S. F. Tolt 30 0.282519 0.321114 0.324569 0.303572 0.270701 0.302472 0.466584 0.333043

S. F. Nooksack 31 0.285603 0.331376 0.322516 0.313397 0.395930 0.280491 0.425616 0.334013

S. F. Nooksack j 32 0.299376 0.322761 0.331165 0.327285 0.391858 0.291844 0.431605 0.341644

Mainstem N’sack 33 0.313057 0.347254 0.329620 0.321460 0.434785 0.311412 0.442822 0.342884

Samish 08 34 0.269045 0.288837 0.283959 0.305436 0.402356 0.240810 0.421185 0.315321

Samish 09 35 0.296533 0.324683 0.306425 0.315900 0.402566 0.252417 0.403525 0.340730

Lower Elwha H. 36 0.304343 0.323565 0.323403 0.317216 0.446427 0.265550 0.413726 0.333218

Tokul Hatchery 37 0.269091 0.278677 0.301051 0.288881 0.428447 0.238966 0.405815 0.313088

Hamma Hamma 38 0.284766 0.297010 0.301290 0.303257 0.399595 0.244495 0.421153 0.335307

Soos Creek H. 39 0.267050 0.281003 0.321389 0.296117 0.418930 0.260958 0.402961 0.326066
103

Table B-3 continued horizontally. Cavalli-Sforza and Edwards chord distances for 39 steelhead 

collections from Puget Sound. The gatekeeper model (Appendix C) used a Cavalli-Sforza and 

Edwards chord distance of 0.200 as a threshold for population independence. Numbers shaded in 

gray have distances less than 0.20. Numbers framed within lined boxes represent intra-Skagit 

River basin collections.

Population Pop. no.

Population number

17 18 19 20 21 22 23 24

Big Beef 1 0.262464 0.257255 0.336913 0.311230 0.270676 0.276755 0.288620 0.286295

Dewatto 2 0.291450 0.284414 0.341797 0.324536 0.294632 0.314458 0.312604 0.301935

Dosewallips 3 0.214412 0.209617 0.308496 0.290164 0.224910 0.247853 0.259065 0.255646

Duckabush 4 0.222831 0.215832 0.318860 0.293473 0.228140 0.257809 0.263651 0.267996

Skokomish 5 0.259532 0.261767 0.343484 0.319683 0.263425 0.280300 0.270060 0.283659

Snow 6 0.281870 0.272643 0.354178 0.334226 0.289793 0.288480 0.302447 0.301296

Tahuya 7 0.270271 0.255704 0.325958 0.301917 0.255529 0.276764 0.287364 0.283013

Puyallup 8 0.276437 0.274446 0.343759 0.342053 0.289025 0.307629 0.302185 0.291080

White 9 0.197018 0.180758 0.269087 0.271969 0.202947 0.210108 0.238197 0.195495

Nisqually 10 0.272815 0.267719 0.329307 0.316956 0.278837 0.296812 0.308837 0.284790

Elwha 11 0.258143 0.264860 0.342332 0.319534 0.276714 0.300449 0.308239 0.294026

Green 12 0.242932 0.221565 0.306815 0.297634 0.236125 0.245891 0.263302 0.234859

Skamania H. 13 0.346478 0.381906 0.404724 0.398205 0.404531 0.398347 0.381994 0.401148

Dungeness 14 0.207397 0.195191 0.304009 0.270711 0.217505 0.242066 0.260985 0.248012

Minter 15 0.410468 0.405612 0.441800 0.423518 0.409157 0.412304 0.423223 0.432298

Cedar 16 0.284919 0.262210 0.328132 0.317118 0.284095 0.291643 0.294278 0.270615

Stillaguamish 17 0 0.137383 0.264259 0.252405 0.170106 0.204741 0.203564 0.191996

Skagit Manser 18 0.137383 0 0.252524 0.227307 0.131883 0.165032 0.174665 0.153392

Nooksack 1 19 0.264259 0.252524 0 0.232230 0.246735 0.252575 0.283602 0.252331

Nooksack 2 20 0.252405 0.227307 0.232230 0 0.240708 0.254176 0.250281 0.249163

Upper Skagit 21 0.170106 0.131883 0.246735 0.240708 0 0.184463 0.176769 0.172175

Mid Skagit 22 0.204741 0.165032 0.252575 0.254176 0.184463 0 0.209389 0.189032

Cascade 23 0.203564 0.174665 0.283602 0.250281 0.176769 0.209389 0 0.206946

Suiattle 24 0.191996 0.153392 0.252331 0.249163 0.172175 0.189032 0.206946 0 

Sauk 25 0.187856 0.150035 0.257765 0.257406 0.154893 0.174744 0.178446 0.168374

Finney 26 0.180195 0.152284 0.252271 0.252109 0.163960 0.186015 0.193578 0.183244

Goodell 27 0.216016 0.188604 0.273522 0.241893 0.177206 0.219964 0.205820 0.208057

Marblemount H. 28 0.259171 0.251124 0.313982 0.313714 0.260332 0.276910 0.298777 0.281571

Deer 29 0.306421 0.303290 0.335933 0.310287 0.314434 0.317836 0.304327 0.310301

S. F. Tolt 30 0.255692 0.284347 0.334152 0.333401 0.300263 0.302139 0.295647 0.303513

S. F. Nooksack 31 0.262809 0.242951 0.231305 0.225257 0.247637 0.256454 0.262545 0.256778

S. F. Nooksack j 32 0.270677 0.241158 0.258098 0.244985 0.254225 0.264854 0.260629 0.255716

Mainstem N’sack 33 0.298489 0.284110 0.282598 0.273990 0.299856 0.295220 0.330380 0.300496

Samish 08 34 0.245746 0.236540 0.276470 0.257450 0.243389 0.263980 0.275314 0.263400

Samish 09 35 0.252544 0.253471 0.274514 0.258904 0.250606 0.263898 0.290250 0.275237

Lower Elwha H. 36 0.292708 0.278425 0.349498 0.327139 0.291563 0.302241 0.313606 0.318323

Tokul Hatchery 37 0.271132 0.256791 0.324349 0.317552 0.268008 0.281089 0.292854 0.282040

Hamma Hamma 38 0.271388 0.268114 0.323223 0.311459 0.283746 0.305176 0.301793 0.301037

Soos Creek H. 39 0.274657 0.279389 0.333105 0.326814 0.291879 0.295808 0.304853 0.297502
104

Table B-3 continued horizontally. Cavalli-Sforza and Edwards chord distances for 39 steelhead 

collections from Puget Sound. The gatekeeper model (Appendix C) used a Cavalli-Sforza and 

Edwards chord distance of 0.200 as a threshold for population independence. Numbers shaded in 

gray have distances less than 0.20. Numbers framed within lined boxes represent intra-Skagit 

River basin collections.

Population Pop. no.

Population number

25 26 27 28 29 30 31 32

Big Beef 1 0.270891 0.270903 0.293439 0.268846 0.370476 0.324545 0.314759 0.337109

Dewatto 2 0.307891 0.299876 0.301672 0.293805 0.366557 0.364875 0.344220 0.351399

Dosewallips 3 0.243761 0.236840 0.279179 0.242732 0.345459 0.291886 0.300838 0.293936

Duckabush 4 0.254745 0.236662 0.291768 0.259085 0.364302 0.289282 0.309086 0.311733

Skokomish 5 0.267928 0.261582 0.302318 0.305934 0.370736 0.319169 0.324501 0.334160

Snow 6 0.284099 0.293311 0.321544 0.293909 0.396580 0.346591 0.346640 0.353473

Tahuya 7 0.266308 0.265983 0.279469 0.259775 0.364632 0.343278 0.322223 0.331402

Puyallup 8 0.294726 0.296803 0.329600 0.333254 0.363295 0.331715 0.336414 0.341541

White 9 0.209449 0.205955 0.251493 0.270701 0.348754 0.282519 0.285603 0.299376

Nisqually 10 0.288656 0.277488 0.310393 0.285184 0.381735 0.321114 0.331376 0.322761

Elwha 11 0.284461 0.284488 0.311858 0.284894 0.358883 0.324569 0.322516 0.331165

Green 12 0.240422 0.241039 0.274439 0.291091 0.330676 0.303572 0.313397 0.327285

Skamania H. 13 0.408236 0.390311 0.414342 0.418600 0.420397 0.270701 0.395930 0.391858

Dungeness 14 0.229248 0.232278 0.275331 0.225636 0.354510 0.302472 0.280491 0.291844

Minter 15 0.420127 0.420708 0.421917 0.400976 0.506952 0.466584 0.425616 0.431605

Cedar 16 0.282860 0.283001 0.300480 0.312430 0.374539 0.333043 0.334013 0.341644

Stillaguamish 17 0.187856 0.180195 0.216016 0.259171 0.306421 0.255692 0.262809 0.270677

Skagit Manser 18 0.150035 0.152284 0.188604 0.251124 0.303290 0.284347 0.242951 0.241158

Nooksack 1 19 0.257765 0.252271 0.273522 0.313982 0.335933 0.334152 0.231305 0.258098

Nooksack 2 20 0.257406 0.252109 0.241893 0.313714 0.310287 0.333401 0.225257 0.244985

Upper Skagit 21 0.154893 0.163960 0.177206 0.260332 0.314434 0.300263 0.247637 0.254225

Mid Skagit 22 0.174744 0.186015 0.219964 0.276910 0.317836 0.302139 0.256454 0.264854

Cascade 23 0.178446 0.193578 0.205820 0.298777 0.304327 0.295647 0.262545 0.260629

Suiattle 24 0.168374 0.183244 0.208057 0.281571 0.310301 0.303513 0.256778 0.255716

Sauk 25 0 0.171487 0.206453 0.275394 0.307677 0.303311 0.249819 0.249106

Finney 26 0.171487 0 0.212237 0.267714 0.308050 0.283384 0.248863 0.252053

Goodell 27 0.206453 0.212237 0 0.302677 0.313351 0.328118 0.262411 0.267763

Marblemount H. 28 0.275394 0.267714 0.302677 0 0.371994 0.336912 0.318152 0.331069

Deer 29 0.307677 0.308050 0.313351 0.371994 0 0.362203 0.317951 0.323598

S. F. Tolt 30 0.303311 0.283384 0.328118 0.336912 0.362203 0 0.330266 0.330302

S. F. Nooksack 31 0.249819 0.248863 0.262411 0.318152 0.317951 0.330266 0 0.251182

S. F. Nooksack j 32 0.249106 0.252053 0.267763 0.331069 0.323598 0.330302 0.251182 0 

Mainstem N’sack 33 0.293090 0.287072 0.295110 0.315008 0.376250 0.365296 0.273840 0.313267

Samish 08 34 0.249145 0.255524 0.283847 0.262116 0.359234 0.325833 0.261897 0.274127

Samish 09 35 0.261353 0.254635 0.277195 0.295466 0.355830 0.332953 0.264236 0.286343

Lower Elwha H. 36 0.301161 0.285637 0.317065 0.231527 0.387189 0.359809 0.340588 0.351923

Tokul Hatchery 37 0.276532 0.262379 0.313843 0.159131 0.374250 0.337070 0.320555 0.335666

Hamma Hamma 38 0.292387 0.285257 0.319196 0.284200 0.388456 0.314794 0.320264 0.334894

Soos Creek H. 39 0.297475 0.299291 0.327031 0.209113 0.395013 0.334958 0.334033 0.341975
105

Table B-3 continued horizontally. Cavalli-Sforza and Edwards chord distances for 39 steelhead 

collections from Puget Sound. The gatekeeper model (Appendix C) used a Cavalli-Sforza and 

Edwards chord distance of 0.200 as a threshold for population independence. Numbers shaded in 

gray have distances less than 0.20. Numbers framed within lined boxes represent intra-Skagit 

River basin collections.

Population Pop. no.

Population number

33 34 35 36 37 38 39

Big Beef 1 0.336429 0.292386 0.297191 0.307446 0.279919 0.299071 0.296569

Dewatto 2 0.369378 0.314068 0.332507 0.315650 0.296422 0.342052 0.313922

Dosewallips 3 0.322172 0.248982 0.286921 0.277532 0.247468 0.233147 0.276336

Duckabush 4 0.325020 0.261353 0.284363 0.283882 0.260761 0.241947 0.288313

Skokomish 5 0.338686 0.298857 0.303490 0.304858 0.307233 0.278394 0.317479

Snow 6 0.358526 0.310697 0.315319 0.296743 0.282423 0.300938 0.302252

Tahuya 7 0.336260 0.281388 0.298967 0.282911 0.267917 0.295151 0.291281

Puyallup 8 0.360462 0.337938 0.350057 0.358379 0.331927 0.335092 0.337560

White 9 0.313057 0.269045 0.296533 0.304343 0.269091 0.284766 0.267050

Nisqually 10 0.347254 0.288837 0.324683 0.323565 0.278677 0.297010 0.281003

Elwha 11 0.329620 0.283959 0.306425 0.323403 0.301051 0.301290 0.321389

Green 12 0.321460 0.305436 0.315900 0.317216 0.288881 0.303257 0.296117

Skamania H. 13 0.434785 0.402356 0.402566 0.446427 0.428447 0.399595 0.418930

Dungeness 14 0.311412 0.240810 0.252417 0.265550 0.238966 0.244495 0.260958

Minter 15 0.442822 0.421185 0.403525 0.413726 0.405815 0.421153 0.402961

Cedar 16 0.342884 0.315321 0.340730 0.333218 0.313088 0.335307 0.326066

Stillaguamish 17 0.298489 0.245746 0.252544 0.292708 0.271132 0.271388 0.274657

Skagit Manser 18 0.284110 0.236540 0.253471 0.278425 0.256791 0.268114 0.279389

Nooksack 1 19 0.282598 0.276470 0.274514 0.349498 0.324349 0.323223 0.333105

Nooksack 2 20 0.273990 0.257450 0.258904 0.327139 0.317552 0.311459 0.326814

Upper Skagit 21 0.299856 0.243389 0.250606 0.291563 0.268008 0.283746 0.291879

Mid Skagit 22 0.295220 0.263980 0.263898 0.302241 0.281089 0.305176 0.295808

Cascade 23 0.330380 0.275314 0.290250 0.313606 0.292854 0.301793 0.304853

Suiattle 24 0.300496 0.263400 0.275237 0.318323 0.282040 0.301037 0.297502

Sauk 25 0.293090 0.249145 0.261353 0.301161 0.276532 0.292387 0.297475

Finney 26 0.287072 0.255524 0.254635 0.285637 0.262379 0.285257 0.299291

Goodell 27 0.295110 0.283847 0.277195 0.317065 0.313843 0.319196 0.327031

Marblemount H. 28 0.315008 0.262116 0.295466 0.231527 0.159131 0.284200 0.209113

Deer 29 0.376250 0.359234 0.355830 0.387189 0.374250 0.388456 0.395013

S. F. Tolt 30 0.365296 0.325833 0.332953 0.359809 0.337070 0.314794 0.334958

S. F. Nooksack 31 0.273840 0.261897 0.264236 0.340588 0.320555 0.320264 0.334033

S. F. Nooksack j 32 0.313267 0.274127 0.286343 0.351923 0.335666 0.334894 0.341975

Mainstem N’sack 33 0 0.286991 0.268826 0.344762 0.330004 0.336249 0.361875

Samish 08 34 0.286991 0 0.225735 0.303091 0.275504 0.304365 0.291041

Samish 09 35 0.268826 0.225735 0 0.307622 0.304091 0.312427 0.320300

Lower Elwha H. 36 0.344762 0.303091 0.307622 0 0.215918 0.318801 0.261522

Tokul Hatchery 37 0.330004 0.275504 0.304091 0.215918 0 0.293326 0.189651

Hamma Hamma 38 0.336249 0.304365 0.312427 0.318801 0.293326 0 0.301092

Soos Creek H. 39 0.361875 0.291041 0.320300 0.261522 0.189651 0.301092 0
106

Figure B-2. Dendrogram of 39 Puget Sound steelhead collections analyzed for 13 microsatellite DNA 

loci and displayed using Cavalli-Sforza and Edwards chord tree with unweighted pair group 

method with arithmetic averages clustering. Numbers at the branches of the tree are 

representative of bootstrap values (percent).
107

 Figure B-3. Relationships between 39 steelhead population samples from Puget Sound based on 13 

microsatellite DNA loci. The x-axis corresponds to the primary principal component variable 

(FCA1) and the y-axis corresponds to the secondary principal component variable (FCA2). 

Numbers correspond to samples listed in Table B-2. Colors indicate the general geographic 

location of the samples.
108

 Figure B-4. Relationships between 39 steelhead population samples from Puget Sound based on 13 

microsatellite DNA loci. The x-axis corresponds to the primary principal component variable 

(FCA1) and the z-axis corresponds to the tertiary principal component variable (FCA3). 

Numbers correspond to samples listed in Table B-2. Colors indicate the general geographic 

location of the samples.
109

 Figure B-5. Relationships between 25 steelhead population samples from Puget Sound based on 13 

microsatellite DNA loci. The x-axis corresponds to the primary principal component variable 

(FCA1) and the y-axis corresponds to the secondary principal component variable (FCA2). 

Numbers correspond to samples listed in Table B-4. Colors indicate the general geographic 

location of the samples.
110

Table B-4. Information for collections of steelhead used in the genetic analyses. Presumptive 

populations were created by pooling samples from Table B-2 by basin, with the exception of the 

Nooksack River basin samples.

Pop Sample Fish sampled N

Sample no. from 

Table B-2

1 Main Nooksack Juveniles, 2009 47 5

2 Nooksack1 and 2 Mix, 2008–2009 62 1 and 2

3 S. F. Nooksack A Adults, 2007–2010 38 3

4 S. F. Nooksack J Juveniles, 2009 26 4

5 Samish River Adults, 2008–2009 78 6 and 7

6 Skagit River Mix, 2008–2011 551 8, 9, 10, 13, 15, and 16

7 Sauk River Adults, 2008–2011 132 11 and 12

8 Stillaguamish River Smolts, 2006 109 18

9 Deer Creek Juveniles, 1995 31 17

10 S. F. Tolt (above falls) Juveniles, 2010 75 21

11 Cedar River Mix, 2007 144 22

12 Green River Adults, 2006 43 24

13 White River Mix, 2002, 2004–2006 438 25

14 Puyallup River Mix, 2002, 2004–2006 70 26

15 Nisqually River Juv., 2006–2008 151 27

16 Minter Creek Mix, 2006–2007 13 28

17 East Hood Canal Mix, 2006–2007 558 29 and 30

18 Tahuya/South Hood Canal Smolts, 2006–2007 179 31

19 Skokomish River Parr, smolts, 2006–2007 299 32

20 West Hood Canal Smolts, 2006, 2007 461 33, 34, and 35

21 Snow Creek Smolts, 2006–2007 129 36

22 Dungeness River Parr, smolts, 2006–2007 251 37

23 Elwha River Juveniles, 2005 48 39

24 Chambers Creek Hatcheries Juveniles, 2005, 2006 436 14, 19, 23, and 38

25 Skamania Hatchery Not available, 2008 95 20

Total: 4,563
111

Figure B-6. Relationships between 25 steelhead population samples from Puget Sound based on 13 

microsatellites DNA loci. The x- axis corresponds to the primary principal component variable 

(FCA1) and the z-axis corresponds to the tertiary principal component variable (FCA3). 

Numbers correspond to samples listed in Table B-4. Colors indicate the general geographic 

location of the samples.
112
113

Appendix C: Puget Sound Steelhead TRT 

Checklist and Gatekeeper Model 

for Identifying DIPs

Demographically Independent Population Checklist

The Puget Sound Steelhead Technical Recovery Team (PSS TRT) developed a layered 

checklist (Table C-1) to assist in identification of historical demographically independent 

populations (DIPs). This checklist provided a conceptual framework for establishing prospective 

DIPs and identifying the supporting evidence available and level of certainty for each DIP. 

Essentially, if one can show that a presumptive population was historically present and sufficient 

evidence exists that the population is (or was) large enough to be sustainable and is not 

substantially demographically influenced by other populations (via migration), it qualifies as a 

DIP. There was some discussion regarding how large is large enough. Work by Allendorf et al. 

(1997) suggests that an “effective population size, Ne,” of 500 or more would be sufficient to 

ensure a less than 5% risk of extinction in the near future (100 years). Converting Ne to a census 

population size (N) is somewhat challenging. Waples suggests that Ne/N is 0.2–0.25 for 

Chinook salmon (Oncorhynchus tshawytscha); this number should be somewhat larger 

(approximately 0.50) for iteroparous steelhead (O. mykiss), giving a target N of possibly 1,000 

spawners per generation (this adjusted Ne/N ratio roughly accounts for an unknown number of 

resident fish contributing to the anadromous DPS and the presence of a small proportion of 

repeat spawners), or about 250 spawners annually (at a mean generation length of 4 years). 

Demographic independence was most clearly demonstrated when the abundance trajectory of a 

presumptive population is clearly distinct from its neighboring populations. The PSS TRT also 

considered empirical evidence for identifying DIPs. Specifically, the TRT selected the smallest 

independent spawning aggregation for which a long-term data set exists (establishing 

sustainability); for Puget Sound steelhead this was Snow Creek. Historical abundance was 

estimated using historical estimates, harvest expansions, or a habitat-based intrinsic potential (IP) 

model, with the amount of habitat in each presumptive DIP compared to that in Snow Creek.

Tier 1 Checklist

 Historically present

 Abundance (actual or IP-estimated)

 Demographic independence

If all three conditions are met, the presumptive population is considered a DIP; for that 

population, the only further discussion necessary is to discern whether there are additional DIPs 

within the population in question.
114

For Puget Sound steelhead, it is more likely that there will be insufficient information to 

establish whether the conditions in the first box or third box are met. In these cases it will 

become necessary to use proxies, more indirect measures of abundance and demographic 

independence. As stated earlier, the habitat-based IP model was used as the abundance proxy for 

historical abundance. For the demographic independence measure, there are a number of 

possible proxies, all of which provide some indicator of the degree of isolation.

For the Tier 2 Checklist, geographic isolation is the distance between presumptive 

population spawning locations. Isolation barriers normally are falls and cascades, velocity 

barriers that may provide temporal windows to upstream access. Genetic distinctiveness, a 

measure of genetic differences, indicates the degree to which populations interbreed (gene flow 

rates and time of isolation). Ecological differences are differences between natal streams that 

may result in local adaptation by presumptive populations. Strong freshwater adaptation would 

reinforce homing fidelity. Temporal isolation indicates that run timing differences may result in 

fish spawning in the same or nearby stream reaches, but at different times of the year with 

minimum chance for introgression.

Tier 2 Checklist

 Abundance proxy—IP or other habitat-based estimate of potential productivity

 Basin size—a very simple proxy for abundance (potential productivity)

Drainage area (80 km2

)—adjusted for gradient

 Geographic isolation—beyond 50 km independent, bays and shoreline morphology

 Genetic distance (FST) 

 Barriers—physical (seasonal, flow [high or low], substrate)

 Temporal isolation—run or spawn timing

While there is no minimum number of Tier 2 boxes that need to be checked, it is assumed that 

meeting just one of the above conditions would not necessarily be sufficient to establish a DIP. 

There are also gradations to many of the check boxes; for example, where temporal isolation is 

considered as a factor, it is possible that the spawn timing of presumptive populations is 

separated by days, weeks, or months.

Where there is a marginal degree of support for designating a presumptive population as 

a DIP, it may be useful to identify additional measures within the Tier 3 Checklist. Essentially, it

utilizes a number of the categories from Tier 2, but the information is related to population 

independence by an additional level of inference.

Tier 3 Checklist

 Ecological separation (geology, flow regime, elevation, ecoregion)—in the absence of life 

history information, the TRT concluded that ecological differences between basins would 

result in life history differences in the steelhead that reared and spawned in those basins.
115

Table C-1. Data available for DIP evaluation. A check mark indicates that information was available for 

consideration by the TRT. A star indicates that information was available and that it was 

definitive in identifying the DIP.

DIP criteria

––––Tier 1–––– ––––Tier 2 and Tier 3–––– VSP data

Population name

Historical presenceSustainability (abundance)Demographic independenceBasin size (IP)Temporal isolationGeographic isolationLife history (except run type)GeneticsHabitat typeAbundance*GeneticsAgePunch card

Baker River ✔ ✔ — ✔ — — — — — — ✔ — —

Canyon Creek ✔ — — — ★ — — — — — — — ✔

Cedar River ✔ — — ✔ — ★ — — ★ ✔ ✔ — ✔

Deer Creek ✔ ✔ — ✔ ★ — — ✔ — — ✔ ✔ ✔

Drayton Harbor Tributaries ✔ — — ✔ — ★ ✔ — ★ — — — ✔

Dungeness River ✔ — — ✔ — — — ★ ★ — ✔ — ✔

East Hood Canal Tributaries ✔ — ✔ ✔ — — — ★ ★ ✔ ✔ — ✔

East Kitsap Peninsula Tributaries ✔ — — ✔ — — — — ✔ — — — ✔

Elwha River ✔ — — ✔ — — — ✔ — ✔ ✔ — ✔

Green River ✔ ✔ — ✔ — ★ — ✔ — ✔ ✔ ✔ ✔

Nisqually River ✔ — — ✔ — — — ★ ★ ✔ ✔ ✔ ✔

Nookachamps Creek ✔ — — ✔ — — — — ★ — — — —

Nooksack River ✔ ✔ — ✔ — — — ★ ★ — ✔ ✔ ✔

North Fork Skykomish River ✔ — — ✔ ★ — — ★ — — ✔ — ✔

N. Lake Wash. & Lake Sammam. ✔ — — ✔ — ★ — — ★ — — — —

Pilchuck River ✔ ✔ — ✔ — — ★ — ✔ ✔ — ✔ ✔

Puyallup/Carbon Rivers ✔ — — ✔ — — — ★ — ✔ ✔ ✔ ✔

Samish R.&Bellingham Bay Tribs. ✔ ✔ ★ ✔ — — — ★ ★ ✔ ✔ — ✔

Sauk River ✔ ✔ — ✔ — — ★ ✔ — — ✔ ✔ ✔

Sequim/Discovery Bays Tribs. — — — ✔ — — — ✔ ★ ✔ ✔ ✔ ✔

Skagit River ✔ ✔ — ✔ — — — ✔ ✔ ✔ ✔ ✔ ✔

Skokomish River ✔ ✔ — ✔ — — — ✔ ★ ✔ ✔ — ✔

Snohomish/Skykomish Rivers ✔ ✔ — ✔ — — — — — ✔ — ✔ ✔

Snoqualmie River ✔ ✔ — ✔ ★ ★ — — — ✔ — ✔ ✔

South Fork Nooksack River ✔ — — ✔ ★ — — — — — — — ✔

South Hood Canal Tributaries ✔ ✔ ✔ ✔ — — — ★ ✔ ✔ ✔ — ✔

South Puget Sound Tributaries ✔ — — ✔ — ★ — ✔ ★ — — — ✔

Stillaguamish River ✔ ✔ — ✔ ★ — — — — ✔ ✔ ✔ ✔

Strait of Juan de Fuca Tributaries ✔ — — ✔ — — — ✔ ★ ✔ ✔ — ✔

Tolt River ✔ — — — ★ — — ✔ — ✔ ✔ — ✔

West Hood Canal Tributaries ✔ — — ✔ — — — ★ ✔ ✔ ✔ — ✔

White River ✔ ✔ — ✔ — — — ★ — ✔ ✔ — ✔

* Abundance information available for 5 of the last 10 years.
116

Gatekeeper Model

In an effort to develop a simplified methodology for identifying historical DIPs, the PSS 

TRT established a number of DIP threshold values related to the biological and geographic 

characteristics of the provisional population (Figure C-1). These threshold values were set such 

that if any pair-wise comparison of DIPs exceeded the value, there was a very high degree of 

certainty that the two populations were independent. Because information on many provisional 

DIPs was limited or lacking, the number of characteristics considered was constrained to only 

those that were available for nearly all populations.

The initial set of candidate populations was established by identifying those hydrological 

units or combinations of hydrological units with IP production levels greater than that estimated 

for Snow Creek in the Strait of Juan de Fuca. Snow Creek was selected as a minimum size for 

consideration because long-term monitoring of juvenile and adult steelhead suggests that this 

natural population is self-sustaining.

Presumptive DIPs were compared in a pair-wise manner according to five characteristic 

categories: geographic distance, presence of a temporal barrier, genetic distance (Cavalli-Sforza 

and Edwards chord distance), run timing/life history, and river flow hydrographs (standardized 

across months). For geographic distance, a river mouth to river mouth distance of 50 km was 

established as a threshold, beyond which the TRT concluded it was highly unlikely for there to 

be demographic interaction between populations. The presence of a substantial temporal barrier 

(low flow or velocity) was considered to provide a mechanism for reproductively isolating two 

populations. A Cavalli-Sforza and Edwards chord distance of 0.20, based on the microsatellite 

DNA analysis of contemporary Puget Sound steelhead populations, was considered to be 

representative of a significant genetic (reproductive) isolation between populations. Where 

substantial life history differences exist or existed, the populations were considered to be 

reproductively isolated. These life history characteristics most commonly included run timing, 

spawn timing, and age structure. Since variation in these traits is partially influenced by genetic 

effects, differences in trait expression indicate genetic differences and some degree of 

reproductive isolation. Lastly, where the annual hydrographs for two populations were 

substantially different (primarily distinguishing between snow-dominated and rain-dominated 

systems), it was inferred that the major life history characteristics would be adapted to local 

conditions and parallel these differences. In the case of river hydrology, flow types were 

distinguished via cluster analysis, based on the Gower similarity coefficient (Gower 1971)

(Figure C-2). A substantial difference in river hydrograph was inferred by differences in 

clustering based solely on the first bifurcation (a distinction that accounted for the majority of the 

variability).

In the gatekeeper model, each population characteristic is evaluated independently of the 

others. Therefore, neither order nor missing data affected the outcome of the analysis.
117

Figure C-1. Schematic of the gatekeeper model used to identify historical DIPs. If differences between 

presumptive populations exceeded the threshold for any of the gatekeeper criteria, those 

populations were considered independent of each other. CSE > 0.200 50 km apart River flow Barrier Life history Yes Yes Yes Yes

Nonindependent 

population pairs

Independent 

population pairs

No No No No 

No 
118

Figure C-2. Gower chart of candidate DIP ecological parameters used to distinguish habitat 

characteristics in each basin. The Gower index (Gower 1971) includes information on permanent 

snow cover, elevation, and basin size. Groups that clustered below the 0.2 height thresholds were 

considered to have similar habitat types.
119 

Appendix D: Basin Characteristics and Estimates of Spawners

This appendix contains a two-page table, continued horizontally.
120 

Table D-1. Basin geographic, hydrologic, and ecological characteristics with intrinsic potential (IP) estimates of spawners using two smolt-toadult survival (SAS) rates. Capacity is the number of returning adults.

Population name

Basin dimensions

Basin climate

Mean max. 

temp.

Mean min. 

temp.

Mean precipitation 

(mm) Hydrograph type (%)

Area 

(km2)

Mean 

elev. 

(m)

Total 

stream 

len. (m) Jan. July Jan. July Jan. July Year

HighlandLowland

Rain 

dominated

R/S 

dominated

Snow 

dominated

Baker River 770.68 999 421,859 186 2,041 -457 817 408 80 3,017 0.46 0.00 0.19 0.12 0.22

Canyon Creek 99.84 864 47,716 311 2,054 -271 937 527 106 3,610 0.10 0.00 0.10 0.36 0.44

Cedar River 649.93 461 402,349 472 2,252 -112 1,001 263 49 1,867 0.06 0.48 0.15 0.13 0.17

Deer Creek 180.44 761 105,313 367 2,129 -246 939 472 91 3,322 0.06 0.00 0.21 0.28 0.44

Drayton Harbor Tributaries 223.07 37 206,057 569 2,238 -35 1,102 150 41 1,168 0.00 1.00 0.00 0.00 0.00

Dungeness River 564.16 978 306,740 311 1,912 -309 855 218 34 1,493 0.16 0.20 0.12 0.33 0.20

East Hood Canal Tributaries 341.99 99 174,736 694 2,412 85 1,132 207 25 1,446 0.00 1.00 0.00 0.00 0.00

East Kitsap Peninsula Tributaries 703.00 75 259,413 723 2,384 132 1,175 169 23 1,194 0.00 0.99 0.01 0.00 0.00

Elwha River 832.87 1,021 472,871 309 1,899 -301 850 380 41 2,574 0.11 0.05 0.09 0.36 0.39

Green River 1,443.92 463 834,472 470 2,280 -135 989 227 41 1,621 0.06 0.51 0.10 0.17 0.17

Nisqually River 1,991.50 524 1,030,771 528 2,306 -147 952 228 38 1,610 0.08 0.47 0.13 0.16 0.15

Nookachamps Creek 182.95 252 159,503 556 2,264 -52 1,048 185 57 1,553 0.00 0.45 0.40 0.09 0.06

Nooksack River 1,982.16 619 1,257,480 362 2,164 -266 956 278 64 2,133 0.22 0.31 0.15 0.15 0.17

North Fork Skykomish River 156.19 1,195 117,602 -17 2,124 -636 768 432 63 2,825 0.61 0.00 0.01 0.12 0.27

N. Lake Wash. & Lake Sammam. 977.61 119 441,887 677 2,360 79 1,142 152 31 1,151 0.00 0.90 0.07 0.02 0.00

Pilchuck River 355.62 253 242,383 567 2,314 -21 1,068 246 51 1,863 0.00 0.56 0.35 0.06 0.03

Puyallup River 1,394.77 672 803,817 459 2,194 -216 904 218 49 1,635 0.20 0.35 0.16 0.16 0.12

Samish R. and Bellingham Bay 661.49 203 453,694 561 2,290 -58 1,083 191 52 1,500 0.00 0.50 0.41 0.08 0.02

Sauk River 1,896.68 1,132 1,079,263 42 2,083 -611 822 406 63 2,758 0.54 0.00 0.13 0.12 0.21

Sequim/Discovery Bays Tribs. 557.46 197 234,042 628 2,237 48 1,102 98 28 771 0.00 0.74 0.17 0.08 0.00

Skagit River 5,542.66 1,098 2,815,113 98 2,052 -567 810 311 57 2,148 0.47 0.12 0.10 0.13 0.18

Skokomish River 634.47 570 411,699 485 2,192 -120 1,000 428 46 2,969 0.02 0.21 0.25 0.40 0.12

Snohomish/Skykomish Rivers 1,595.49 420 1,021,690 481 2,249 -112 1,026 308 60 2,222 0.09 0.45 0.21 0.13 0.12

Snoqualmie River 1,615.45 620 1,134,038 358 2,195 -210 924 334 65 2,408 0.18 0.24 0.28 0.14 0.16

South Fork Nooksack River 172.44 926 99,347 324 2,059 -339 903 499 86 3,516 0.30 0.00 0.06 0.23 0.41

South Hood Canal Tributaries 294.73 126 216,935 683 2,473 56 1,117 238 27 1,649 0.00 0.92 0.08 0.00 0.00

South Puget Sound Tributaries 1,859.99 84 582,451 702 2,454 66 1,107 205 24 1,432 0.00 0.98 0.02 0.00 0.00

Stillaguamish River 1,230.17 398 927,234 508 2,248 -96 1,038 303 62 2,201 0.05 0.33 0.35 0.14 0.13

Strait of Juan de Fuca Tributaries 403.06 611 246,441 431 2,081 -130 1,007 196 24 1,300 0.04 0.37 0.24 0.23 0.12

Tolt River 181.79 784 117,732 264 2,094 -268 882 419 91 3,055 0.12 0.00 0.26 0.31 0.31

West Hood Canal Tributaries 1,433.45 715 842,382 417 2,075 -193 962 276 37 1,986 0.09 0.31 0.13 0.31 0.16

White River 1,284.83 1,061 863,251 173 2,035 -447 751 262 43 1,767 0.41 0.15 0.07 0.15 0.23
121 

Table D-1 continued horizontally. Basin geographic, hydrologic, and ecological characteristics with intrinsic potential (IP) estimates of spawners 

using two smolt-to-adult survival (SAS) rates. Capacity is the number of returning adults.

Population name

Low IP Moderate IP High IP Total IP 

area

Total IP 

Area (m length 10% SAS 20% SAS 2) Length (m) Area (m2) Length (m) Area (m2) Length (m)

Baker River 664,185 33,456 756,160 13,600 1,429,939 48,977 2,850,284 96,033 5,028 10,056

Canyon Creek 38,897 1,198 0 0 52,800 1,600 91,697 2,798 121 243

Cedar River 194,567 19,704 26,506 12,431 2,560,148 98,155 2,781,221 130,290 5,949 11,899

Deer Creek 892,062 29,791 0 0 683,535 19,998 1,575,597 49,789 1,572 3,144

Drayton Harbor Tributaries 27,173 4,712 1,108 426 1,053,755 144,565 1,082,036 149,703 2,426 4,852

Dungeness River 377,935 16,488 17,732 27,031 1,053,909 25,799 1,449,576 69,318 2,465 4,930

East Hood Canal Tributaries 316,861 48,602 13,725 21,355 538,539 61,704 869,125 131,661 1,270 2,540

East Kitsap Peninsula Tributaries 137,480 40,273 63,470 41,482 613,683 105,698 814,633 187,453 1,557 3,115

Elwha River 821,470 26,380 1,609,610 29,113 1,484,141 44,188 3,915,221 99,681 7,116 14,231

Green River 1,575,485 105,150 5,378,593 142,598 3,216,399 195,118 10,170,477 442,866 19,768 39,537

Nisqually River 403,936 22,106 4,666,086 97,995 1,999,147 185,214 7,069,169 305,315 15,330 30,660

Nookachamps Creek 335,222 38,171 16,113 7,896 519,131 42,745 870,466 88,812 1,231 2,462

Nooksack River 1,049,951 62,533 5,066,204 125,680 4,518,781 263,717 10,634,936 451,930 22,045 44,091

North Fork Skykomish River 126,531 3,798 0 0 288,151 7,598 414,682 11,396 663 1,325

N. Lake Wash. & Lake Sammam. 314,181 60,580 71,368 44,554 2,219,024 196,643 2,604,573 301,777 5,268 10,536

Pilchuck River 188,570 16,504 37,520 16,026 2,220,396 144,372 2,446,486 176,902 5,193 10,386

Puyallup River 1,381,684 64,725 2,092,459 60,899 4,305,737 179,856 7,779,880 305,480 14,716 29,432

Samish R. & Bellingham Bay 227,796 27,173 64,002 29,465 1,324,222 128,158 1,616,020 184,796 3,193 6,386

Sauk River 2,768,556 93,608 7,235,046 101,598 2,864,886 94,149 12,868,488 289,355 23,230 46,460

Sequim/Discovery Bays Tribs. 112,707 36,528 12,661 41,573 209,957 27,463 335,325 105,564 512 1,024

Skagit River 1,875,151 99,753 24,639,163 168,235 3,524,068 185,443 30,038,382 453,431 64,775 129,551

Skokomish River 1,680,590 47,530 535,705 8,616 3,825,158 94,030 6,041,453 150,176 10,030 20,060

Snohomish/Skykomish Rivers 1,875,442 88,275 4,921,478 94,072 4,378,288 257,393 11,175,208 439,740 21,389 42,779

Snoqualmie River 460,438 34,104 5,335,600 62,000 1,942,496 142,803 7,738,534 238,907 16,740 33,479

South Fork Nooksack River 301,160 13,085 0 0 494,222 18,399 795,382 31,484 1,137 2,273

South Hood Canal Tributaries 277,401 34,043 0 0 1,297,905 117,841 1,575,306 151,884 2,985 5,970

South Puget Sound Tributaries 622,873 61,652 15,051 6,153 4,269,429 390,014 4,907,353 457,819 9,854 19,709

Stillaguamish River 1,502,178 93,530 4,207,466 103,583 4,104,756 229,107 9,814,400 426,220 19,118 38,236

Strait of Juan de Fuca Tributaries 351,837 45,542 11,281 7,669 305,255 20,930 668,373 74,141 728 1,456

Tolt River 92,503 3,799 0 0 139,380 5,600 231,883 9,399 321 641

West Hood Canal Tributaries 487,392 57,002 48,234 51,748 1,520,652 61,586 2,056,278 170,336 3,608 7,217

White River 1,465,480 77,561 4,784,282 71,150 2,820,242 126,362 9,070,004 275,073 17,490 34,981
122 
123 

Appendix E: Puget Sound Steelhead Hatchery Production 

from 1900 to 1945

This appendix contains a five-page table, continued horizontally by year.
124 

Table E-1. Puget Sound steelhead (Oncorhynchus mykiss) hatchery production from 1900 to 1945. Release numbers represent fry or fingerlings 

(subyearlings). E = egg production (in addition to fish listed) and out = transfers of eggs or fish from the hatchery. Data for 1900–1911 

are incomplete.

Basin Hatchery 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909

Nooksack Kendall — — — — — — 55,000 E

Kendall (out)

Samish Samish

Samish (out)

Skagit Baker 26,000 — 110,000* 80,000 E 

663,815

255,000 E 

70,000

— 103,000 E 

540,000

Birdsview — — — — — 400,000 E

Birdsview (out)

Darrington

Day Creek

Illabott Creek

Sauk River — — — — — — 1,027,000 E

Skagit River

Stillaguamish Stillaguamish

Snohomish Snohomish — — — 369,000 E — 435,000 577,820 E

Pilchuck

Pichuck (out)

Skykomish (Startup)

Skykomish (out)

Sultan

Green Green/White — — — 96,800 E — 84,426 417,000

Green/White (out)

Puyallup Puyallup

Puyallup (out)

South Sound Chambers Creek

Chambers Creek (out)

Nisqually Nisqually — — — 265,000 E — 962,000 218,000 E

Hood Canal Skokomish 1,500,000

Tahuya Station

Dungeness (Brinnon)

Duckabush

Quilcene

Dungeness Dungeness — — 1,500,000 3,100,000 E — 1,384,000 1,168,000

Elwha Elwha

Elwha (out)

WDF est.: — — — — 2,395,150 2,886,926 3,463,970 4,429,575 3,681,450 4,855,000

USBF est.: Fry 1,572,560 1,398,476 2,591,371 3,107,891 3,518,476 1,329,940 3,162,174 3,964,308 4,566,491 4,499,141

Total: Fingerling — — — 218,200 — — 15,000

* Egg-collection source was Finney Creek and Grandy Creek. 
125 

Table E-1 continued horizontally. Puget Sound steelhead hatchery production from 1900 to 1945. Release numbers represent subyearlings. 

E = egg production (in addition to fish listed) and out = transfers of eggs or fish from the hatchery. Data for 1900–1911 are incomplete.

Basin Hatchery 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919

Nooksack Kendall — — 50,000 203,400 98,705 74,176 — 52,826 — 61,000

Kendall (out) — — — — — — — — 40,000

Samish Samish — — 2,310,000 994,000 1,406,252 1,311,149 — 1,639,777 980,600 129,700

Samish (out)

Skagit Baker 1,368,000 — — 12,400

Birdsview — — 733,000 E 

2,001,650

780,000 E 

409,000

579,000 E 

752,225

1,848,365 529,000 E

1,207,000

240,000 1,589,500 198,865

Birdsview (out) — — 125,000 E 350,000 E 150,000 E 125,000 E

Darrington — — — 114,000

Day Creek 769,000 — — — — 47,500 — — 43,000

Illabott Creek — — 255,665 347,500 187,755 60,000 277,000 451,000

Sauk River

Skagit River — — 95,000 E 38,920 27,849

Stillaguamish Stillaguamish — — 205,400 20,600 E 29,575 577,570 — 139,765

Snohomish Snohomish — — — — 66,740 119,225

Pilchuck — — — — — — — 644,100 480,000 838,000

Pichuck (out) — — — — — — — — — 100,000

Skykomish (Startup) — — 524,000 E 578,685 232,046 182,712 — 395,540 227,490 359,200

Skykomish (out)

Sultan — — — 486,700 112,000 292,425 34,000 — 50,000 E 

60,000

92,500

Green Green/White — — 315,200 516,500 505,150 558,750 — 198,600 42,600 277,500

Green/White (out)

Puyallup Puyallup — — — — — — — — 390,200 153,200

Puyallup (out)

South Sound Chambers Creek — — — — — — — 119,300 395,000 160,000

Chambers Creek (out) — — — — — — — — — 10,000

Nisqually Nisqually 1,500,000 740,365 305,932 981,402 123,220 112,200 Floods

Hood Canal Skokomish — — — — — — — — 114,825 56,560

Tahuya Station

Dungeness (Brinnon) — — — — — 35,000 E 100,000 — 129,000

Duckabush — — — 200,00 E 

258,000

603,000 — 91,000 689,700 446,840

Quilcene — — 47,000 E 

27,000

34,000 37,700 101,400 — 626,500 284,000 50,000 E 

170,000

Dungeness Dungeness — — 912,456 — — 589,850 — 633,000 189,537 784,800

Elwha Elwha — — — — — — — 395,200 38,000 24,600

Elwha (out)

WDF est.: 5,234,240 5,912,656 11,059,000 3,462,639 4,975,460 5,545,652 5,545,653 567,625 3,551,830 3,764,450

USBF est.: Fry 6,292,338 4,841,330 3,732,805 9,731,400 4,444,271 4,922,555 5,102,566 1,979,010 4,851,092 3,152,452

Total: Fingerling — — 1,000 — — — 891,000 1,420,500 352,420
126 

Table E-1 continued horizontally. Puget Sound steelhead (Oncorhynchus mykiss) hatchery production from 1900 to 1945. Release numbers 

represent fry or fingerlings (subyearlings). E = egg production (in addition to fish listed) and out = transfers of eggs or fish from the 

hatchery. Data for 1900–1911 are incomplete.

Basin Hatchery 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929

Nooksack Kendall 80,200 19,425 — — — 122,500 105,600 — 141,775 122,250

Kendall (out) — — — — — — — 122,975

Samish Samish 9,575 661,783 273,955 271,316 1,789,790 141,655 842,100 963,550 499,905 923,840

Samish (out) — 279,500 667,000 E 

167,000

751,000 250,000 — 800,000 400,000 375,000 400,000

Skagit Baker

Birdsview 255,000 128,250 78,000 93,305 550,000 418,000 346,500 200,000 E

715,600

1,585,000 750,000

Birdsview (out) — 85,000 55,000 — — 100,000 — — 25,000

Darrington

Day Creek

Illabott Creek

Sauk River

Skagit River

Stillaguamish Stillaguamish

Snohomish Snohomish

Pilchuck 229,900 335,200 — — — — — — — 2,071,000

Pichuck (out) 100,000 200,000 — — — — — — — 600,000

Skykomish (Startup) 151,200 264,855 287,509 486,408 609,730 348,915 334,390 482,950 684,760 664,894

Skykomish (out) — 100,000 25,000 250,000 50,000 — 250,000 200,000 100,000 200,000

Sultan 92,000 76,800 104,400 207,800 216,000 83,000 64,000 474,500 247,500

Green Green/White 70,100 41,300 32,000 — 450,500 204,500 65,000 50,000 221,000 335,000

Green/White (out) 490,000 44,000 E 

226,000

— — 20,000 — 283,000

Puyallup Puyallup 273,237 — — — — — — — — 138,250

Puyallup (out)

South Sound Chambers Creek 273,000 385,000

Chambers Creek (out) 105,000 109,600

Nisqually Nisqually

Hood Canal Skokomish

Tahuya Station 2,000

Dungeness (Brinnon) — 100,000

Duckabush 405,000 1,095,000 90,300 139,445 209,110 90,400 34,200 60,100

Quilcene 460,000 303,500 83,400 545,555 658,400 50,000 100,000 44,000 190,500 540,000

Dungeness Dungeness 1,068,100 144,350 253,000 939,000 839,000 223,000 470,000 331,000 — 304,000

Elwha Elwha 150,500 121,000

Elwha (out) — — 22,000

WDF est.: 3,784,050

USBF est.: Fry

Total: Fingerling
127 

Table E-1 continued horizontally. Puget Sound steelhead (Oncorhynchus mykiss) hatchery production from 1900 to 1945. Release numbers 

represent fry or fingerlings (subyearlings). E = egg production (in addition to fish listed) and out = transfers of eggs or fish from the 

hatchery. Data for 1900–1911 are incomplete.

Basin Hatchery 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939

Nooksack Kendall 65,175 — — — — — 268,500 128,000 88,000 36,579

Kendall (out) 250,000

Samish Samish 1,040,170 — — — — 1,116,900 2,725,700 1,392,800 2,196,100 799,511

Samish (out) 50,000

Skagit Baker

Birdsview 535,000 E 

462,000

90,000 E 

281,680

616,000 113,000 E 

672,000

1,145,000 603,000 289,000 184,000 666,500 813,700

Birdsview (out) — — 143,000 — 110,000 — — 375,000 — 35,000

Darrington

Day Creek

Illabott Creek

Sauk River

Skagit River

Stillaguamish Stillaguamish

Snohomish Snohomish

Pilchuck 984,700

Pichuck (out)

Skykomish (Startup) 848,500 — — — — 50,000 71,500 93,000 60,000 51,110

Skykomish (out)

Sultan 431,000 73,800 270,660

Green Green/White 87,000 — — — — 5,000 40,000 48,000 107,000 95,197

Green/White (out)

Puyallup Puyallup 430,000 — — — — 674,000 585,000 628,000 597,000 86,670

Puyallup (out) 33,827

South Sound Chambers Creek

Chambers Creek (out)

Nisqually Nisqually

Hood Canal Skokomish

Tahuya Station

Dungeness (Brinnon)

Duckabush 206,000 — 19,000 108,000 53,500

Quilcene 578,000 50,000 E 

204,000

50,000 E 

380,000

283,319 290,500 185,500 153,000 259,115 322,305 39,020

Dungeness Dungeness 771,000 683,000 394,000 968,500 806,500 1,265,000 1,080,000 978,000 712,000 995,414

Elwha Elwha

Elwha (out)

WDF est.: — — 413,000 1,076,500 860,000 3,105,900 4,462,200 3,091,800 3,565,100 1,932,705

USBF est.: Fry

Total: Fingerling — — 996,000 955,319 1,435,500 788,500 442,000 443,115 988,805 852,720
128 

Table E-1 continued horizontally. Puget Sound steelhead (Oncorhynchus mykiss) hatchery production from 1900 to 1945. Release numbers 

represent fry or fingerlings (subyearlings). E = egg production (in addition to fish listed) and out = transfers of eggs or fish from the 

hatchery. Data for 1900–1911 are incomplete.

Basin Hatchery 1940 1941 1942 1943 1944 1945

Nooksack Kendall

Kendall (out)

Samish Samish 456,24 555,485 486,267 219,152 118,315 502,947

Samish (out)

Skagit Baker

Birdsview 810,000

Birdsview (out) 38,500

Darrington

Day Creek

Illabott Creek

Sauk River

Skagit River

Stillaguamish Stillaguamish

Snohomish Snohomish

Pilchuck

Pichuck (out)

Skykomish (Startup) 10,814

Skykomish (out)

Sultan

Green Green/White 25,488

Green/White (out)

Puyallup Puyallup 167,223

Puyallup (out)

South Sound Chambers Creek

Chambers Creek (out)

Nisqually Nisqually

Hood Canal Skokomish

Tahuya Station

Dungeness (Brinnon)

Duckabush

Quilcene 509,285

Dungeness Dungeness 405,701 189,050 1,014,568 — 221,763 121,659

Elwha Elwha

Elwha (out)

WDF est.: 1,039,986 744,535 1,500,835 219,152 340,078 624,606

USBF est.: Fry

Total: Fingerling 1,319,285
129

Appendix F: Puget Sound Steelhead Fisheries 

Reported Harvest for Years 1895, 1904, and 1909

Table F-1. Steelhead (Oncorhynchus mykiss) fisheries reported harvest by county for 1895 

(Wilcox 1898).

County

Gear (catch kg)

Total (kg)

Count

(@ 4.5 kg)

Run (40% 

Gill net Seine net harvest)

Clallam — — 0 0 0

Jefferson — — 0 0 0

Pierce — — 0 0 0

King 204,704 — 204,704 45,490 113,725

Snohomish 264,372 — 264,372 58,749 146,873

Skagit 93,268 — 93,268 20,726 51.815

Whatcom 347,856 10,503 358,359 79,635 199,088

Total: 920,703 204,600 511,500

Table F-2. Steelhead fisheries reported harvest by county for 1904 (Wilcox 1905).

County River Total (kg)

Count 

(@ 4.5 kg)

Run (40% 

harvest)

Clallam Hoh, Elwha 23,636 5,253 13,132

Jefferson Coast/Hood Canal 11,363 2,525 6,313

Kitsap — 11,363 2,525 6,313

Mason Skokomish 11,363 2,525 6313

Thurston — 0 0 0

Pierce — 0 0 0

King Green 82,020 18,237 45,566

Snohomish Snohomish 53,409 11,868 29,671

Skagit Skagit 18,181 4,040 10,100

Whatcom Nooksack 130,754 29,056 72,641

Total: 342,089 76,029 190,049
130

Table F-3. Steelhead fisheries reported harvest by county for 1909 (Cobb 1911).

County River Total (kg)

Count 

(@ 4.5 kg)

Run (40% 

harvest)

Clallam Hoh, Elwha 21,470 4,771 11,927

Jefferson Coast/Hood Canal 6,334 1,408 3,520

Kitsap — 11,036 2,453 6,133

Mason Skokomish 3,455 768 1,920

Thurston South Sound 13,818 3,070 7,675

Pierce Puyallup/Nisqually 50,182 11,152 27,880

King Green 99,591 22,131 55,327

Snohomish Snohomish 76,929 17,095 74,178

Skagit Skagit 60,285 27,402 68,505

Whatcom Nooksack 3,181 707 1,768

Total: 346,281 90,957 258,833
131 

Appendix G: Steelhead Smolt Releases into Puget Sound 

Tributaries from 1965 to 2008

This appendix contains a four-page table for winter-run steelhead (Oncorhynchus mykiss) and a four-page table for summerrun steelhead. Both are continued horizontally by year.
132 

Table G-1. Releases of winter-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977

Dakota Creek — — — — — — — 10,000

Nooksack River — — — — — — — 35,261 62,600 34,219 10,000 20,019 87,680

Whatcom Creek/Squalicum — — — — — — — — — 8,650 — 10,075 9,702

Samish River 42,900 48,667 38,604 43,151 55,440 62,708 60,642 41,960 43,477 24,492 40,013 77,860 75,375

Skagit River System 183,669 250,297 201,308 278,327 360,963 307,107 349,579 155,202 289,608 147,503 124,710 261,943 358,839

Skagit River main stem 143,570 179,454 113,659 187,370 270,761 227,079 297,050 125,600 214,309 86,889 66,075 145,780 328,521

Nookachamps/Big Lake — — — — — — — — — 20,900 — 55,120

Baker River

Sauk River 40,099 68,893 75,786 58,863 59,712 47,022 52,529 29,602 64,695 29,120 38,235 45,300 30,318

Cascade River — 1,950 11,863 32,094 30,490 33,006 — — 10,604 10,594 20,400 15,743

Stillaguamish River System 87,416 116,946 107,190 126,580 141,569 105,405 100,989 115,728 110,630 87,808 106,009 217,296 139,513

Stillaguamish main stem — — — — 36,000 — — — — — — 89,202

Canyon Creek — — — — — 18,058 5,468 — — — — 10,123 12,104

Pilchuck Creek (Still.) 17,440 19,970 18,240 20,055 15,218 16,664 2,895 14,532 8,105 9,606 10,547 28,769 33,564

North Fork 69,976 68,080 88,950 55,475 67,873 50,748 70,991 71,047 72,480 58,937 70,188 68,915 72,536

South Fork — 28,896 — 51,050 22,478 19,935 21,635 30,149 30,045 19,265 25,274 20,287 21,309

Snohomish River System 303,073 252,032 212,53 266,588 469,136 332,843 332,428 364,406 389,579 417,714 345,894 583,717 664,396

Skykomish River 64,635 58,411 19,920 55,045 100,202 54,717 37,790 58,768 65,230 59,245 60,951 89,139 149,148

Pilchuck River (Snoho.) 19,500 28,162 25,691 25,060 42,826 23,486 44,538 35,260 36,362 47,191 40,002 40,247 34,797

Snoqualmie River 44,000 42,240 31,006 51,334 59,993 47,886 59,903 60,242 65,152 52,298 41,786 133,948 139,691

Tolt River 42,712 20,000 10,005 19,710 34,163 26,985 16,733 17,221 20,084 26,968 24,535 32,190 41,540

Raging River

Sultan River — — — — — — 15,062 10,001 10,160 25,010 13,206 — 21,063

Wallace River 10,000 8,260 16,920 20,005 15,578 — 15,132 9,976 — 25,024 — 20,138 15,010

N. F. Skykomish River 26,200 — 9,867 9,992 20,076 60,224 — 25,652 14,956 15,000 15,272 30,437

Lake Wash. System 28,696 15,120 22,975 — 41,393 19,964 30,047 20,261 24,216 91,920 59,800 56,610 62,191

Green River (King Co.) 67,330 79,839 76,151 85,442 154,905 99,581 113,223 127,025 153,419 75,058 90,342 181,008 200,956

Puyallup River System 65,129 99,803 66,516 99,617 127,676 167,271 122,418 107,441 105,449 91,338 145,630 38,682 113,422

Puyallup River 65,129 81,804 66,516 87,536 101,909 137,133 101,767 89,314 75,419 71,618 125,454 15,330 83,310

White (Stuck) River — 17,999 — 12,081 25,767 30,138 20,651 18,127 30,030 19,720 20,176 23,352 30,112

Carbon River (Voight Cr.) w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall. w/Puyall.

Nisqually River — 26,334 20,312 19,630 30,492 17,170 26,547 24,841 23,136 14,974 16,030 10,000 9,950

Deschutes River 10,200 24,480 20,131 7,800 40,435 14,779 12,175 39,661 38,721 29,055 24,868 39,592 41,400

Kennedy Creek — — — — — — — — — 10,001 10,200 10,000 15,005

Burley Creek — — — — — — — — — — — — 10,025

Goldsborough Creek 5,082 4,290 — 4,410 — 11,872 — — 5,025 14,649 5,100 10,165 15,000

Curley Creek/Kitsap — — — — — — — — — — — — 5,025

Dewatto River — — — — 10,020 3,600 — 10,060 8,640 10,014 10,013 10,000

Tahuyha River — 4,971 5,055 5,022 9,860 9,967 10,107 10,229 10,328 1,003 10,040 10,295 10,000

Union River — 5,012 — 5,084 10,330 9,998 10,112 10,126 10,068 10,000 9,993 17,850 10,066

Skokomish River 14,730 21,000 5,257 15,431 39,389 43,640 20,022 20,010 15,090 13,847 18,775 — 35,759

Hamma Hamma

Duckabush River — — — — — 19,987 19,017 20,010 19,825 20,119 15,000 35,477 20,005

Dosewallips River — — — — — 20,160 20,025 20,015 19,800 20,007 44,180 25,033 40,046

Quilcene River — — — — — 10,260 10,350 10,356 10,046 20,849 10,547 15,000 15,080

Dungeness River 12,535 15,017 14,125 10,516 25,841 24,300 20,355 17,680 13,942 25,137 20,050 30,004 40,067

Morse Creek 3,544 — — — — — — — — — — 4,174 10,032

Elwha River 24,000 15,000 14,694 12,306 38,998 15,022 15,347 17,180 20,076 20,100 20,075 20,02 30,374

Total for year: 0.85 0.98 0.80 0.98 1.56 1.30 1.27 1.17 1.37 1.19 1.14 1.68 2.00
133 

Table G-1 continued horizontally. Releases of winter-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990

Dakota Creek

Nooksack River 69,572 57,759 55,795 70,470 65,900 81,485 130,900 110,100 123,800 131,000 111,000 109,400 100,100

Whatcom Creek/Squalicum 10,032 9,900 8,000 103,000 7,000 10,000 10,000 14,300 7,600 6,400 6,600 11,200 13,500

Samish River 80,200 80,007 90,600 41,100 40,100 46,951 45,138 30,100 27,800 29,900 40,900 39,000 50,100

Skagit River System 275,847 372,227 283,417 171,700 236,700 237,300 258,200 336,400 298,400 136,000 228,300 286,800 172,200

Skagit River main stem 244,467 273,385 166,678 5,247 — 167,100 197,000 276,000 269,200 112,400 203,300 251,800 163,000

Nookachamps/Big Lake

Baker River

Sauk River 31,380 98,842 78,758 20,953 30,278 20,700 61,200 60,400 29,200 16,100 25,000 35,000 9,200

Cascade River — — 37,981 27,192 25,471 49,500

Stillaguamish River System 103,726 56,881 83,897 111,554 91,241 127,542 110,000 114,600 117,500 128,900 116,100 145,300 122,000

Stillaguamish main stem — — — — 29,498 33,944

Canyon Creek 9,983 — — 7,498 6,300 11,998 12,300 12,700 10,100 9,300 11,900 10,600 9,800

Pilchuck Creek (Still.) — 13,159 31,842 29,068 25,172 10,000 15,500 10,000 10,300 5,000 15,000 15,000 10,100

North Fork 77,659 20,494 26,851 52,466 20,248 49,600 64,900 71,800 77,100 90,800 63,800 101,200 102,100

South Fork 16,084 23,228 25,204 22,522 10,023 22,000 17,300 20,100 20,000 23,800 25,400 18,500

Snohomish River System 593,274 481,599 501,886 521,995 437,934 335,200 227,300 359,900 353,100 230,000 436,800 424,900 350,200

Skykomish River 141,801 108,873 118,522 84,796 80,496 170,500 29,600 125,800 151,100 90,200 155,200 159,600 139,100

Pilchuck River (Snoho.) 39,915 — — — — 21,000 19,600 28,800 24,300 19,100 26,700 30,400 5,700

Snoqualmie River 94,265 99,539 91,299 105,002 100,650 65,200 89,800 119,400 93,600 62,000 129,700 122,500 117,400

Tolt River 37,915 6,666 40,714 28,400 16,664 16,700 20,000 20,100 14,800 10,900 47,600 35,000 40,900

Raging River — — — — — 12,000 14,600 15,000 16,000 9,800 13,900 10,200 10,300

Sultan River 18,239 17,727 16,927 38,451 20,000 15,300 20,300 10,500 10,500 10,800 23,000 19,800 15,400

Wallace River 7,840 20,894 20,224 20,246 15,024 20,000 20,400 20,100 20,700 12,100 7,800 25,000

N. F. Skykomish River 25,199 — — — — 14,500 13,000 20,200 22,100 15,100 32,900 22,400 21,400

Lake Wash. System 33,600 39,200 52,600 56,800 38,500 45,000 64,900 66,400 50,300 75,200 76,800 48,900 50,160

Green River (King Co.) 194,500 188,700 161,600 188,300 166,600 164,600 221,100 223,500 151,100 140,000 186,100 231,300 225,800

Puyallup River System 174,449 67,265 92,516 88,605 86,213 106,844 149,800 167,100 186,078 132,517 165,800 138,700 169,400

Puyallup River 101,449 54,265 92,516 73,539 81,171 85,900 139,800 157,100 176,100 132,500 140,700 123,500 149,400

White (Stuck) River 73,000 13,000 — 15,066 5,042 10,444

Carbon River (Voight Cr.) w/Puyall. 14,000 — 6,270 17,228 10,500 10,000 10,000 10,000 — 25,100 15,200 20,000

Nisqually River 10,000 10,000 30,200 10,000 35,400

Deschutes River 40,800 32,600 40,300 30,000 19,100 32,100 32,000 24,500 25,100 9,500 35,000 49,300 22,300

Kennedy Creek 15,000 15,000 10,100 15,200 6,400 18,000 18,100 11,300 15,000 4,900 15,500 15,000 10,000

Burley Creek 10,080

Goldsborough Creek 17,400 15,000 15,200 15,000 3,100 13,000 13,000 4,900 10,100 5,200 10,100 15,000 10,100

Curley Creek/Kitsap 10,080

Dewatto River 10,000 10,010 10,254 12,400 9,996 12,000 12,000 11,000 9,900 3,000 10,100 14,800 10,000

Tahuyha River 9,900 10,100 10,500 10,700 8,400 15,100 10,300 10,000 10,000 10,000 10,000 15,000

Union River 10,000 10,100 10,300 9,900 10,010 10,000 10,000 9,400 10,000 10,000 15,000 14,850 10,035

Skokomish River 18,700 10,500 17,000 27,200 14,800 27,082 29,600 23,100 20,900 20,000 44,800 39,975 39,000

Hamma Hamma

Duckabush River 26,400 15,100 15,000 17,800 18,100 20,000 20,000 20,100 22,300 5,000 20,000 20,000 15,000

Dosewallips River 30,000 25,200 23,200 23,700 18,200 20,000 25,100 20,800 19,600 15,000 25,400 25,000 15,100

Quilcene River 15,000 15,300 9,585 15,043 13,060 11,900 10,300 10,200 10,200 5,300 5,100 10,160 10,100

Dungeness River 30,300 24,800 20,000 20,100 17,000 18,600 14,800 15,900 15,400 15,545 20,100 20,123 20,300

Morse Creek 15,000 12,900 12,300 18,000 15,400 16,400 15,500 15,900 18,800 15,200 15,000 15,514 10,100

Elwha River 45,200 60,400 51,000 66,400 63,600 86,300 95,600 90,000 118,800 73,600 88,200 118,600 46,100

Total for year: 1.83 1.62 1.61 1.67 1.43 1.46 1.52 1.69 1.62 1.20 1.68 1.81 1.47
134 

Table G-1 continued horizontally. Releases of winter-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003

Dakota Creek

Nooksack River 55,000 47,400 81,800 70,500 75,900 89,300 43,300 63,900 33,900 35,000 56,500 34,800 160,000

Whatcom Creek/Squalicum 10,000 7,200 5,500 6,500 5,100 9,700 5,400 20,000 20,100 — 5,000 — 5,370

Samish River 13,900 27,000 19,600 6,600 32,100 31,200 22,900 47,900 12,100 25,000 31,000

Skagit River System 205,800 166,300 364,200 446,400 354,100 289,000 328,400 562,700 414,400 417,600 463,500 241,200 513,330

Skagit River main stem 183,100 145,900 332,600 415,800 239,200 202,900 194,300 400,600 238,300 214,300 242,000 20,000 225,000

Nookachamps/Big Lake

Baker River — — — — — — — — 49,000 60,000 93,000 — 68,000

Sauk River 22,700 20,400 31,600 30,600 30,200 25,900 21,600 30,800 26,800 20,900 21,800 21,200 20,000

Cascade River — — — — 84,700 60,200 112,500 131,300 100,300 122,400 106,700 200,000 200,330

Stillaguamish River System 137,900 106,800 133,200 140,600 122,900 130,900 100,175 162,700 106,500 98,600 129,800 138,600 161,662

Stillaguamish main stem — 19,100 — — — — — 8,000 — — — 15,700

Canyon Creek 10,100 10,000 10,200 10,300 5,000 15,000 9,975 10,200 9,100 10,000 — 4,700 15,225

Pilchuck Creek (Still.) 15,800 4,700 10,000 4,000 4,900 10,700 — 10,000

North Fork 96,000 73,000 113,000 119,200 113,000 105,200 90,200 132,500 97,400 88,600 121,400 118,200 146,437

South Fork 16,000 — — 7,100 — — — 2,000 — — 8,400

Snohomish River System 345,000 343,200 436,200 326,600 288,600 414,900 196,200 474,000 442,700 402,300 418,000 418,650 433,552

Skykomish River 128,300 129,100 161,000 110,200 111,300 173,000 44,200 132,600 161,200 119,700 112,600 133,400 143,584

Pilchuck River (Snoho.) 21,400 14,900 28,400 7,500 25,000 21,900 14,800 20,700 31,200 34,200 29,000 25,500 35,295

Snoqualmie River 114,000 153,500 150,000 113,800 100,300 117,200 93,400 184,400 151,900 145,400 180,900 165,500 161,661

Tolt River 23,400 10,700 39,300 35,700 17,400 35,300 9,100 30,900 24,800 20,900 21,200 20,000 20,017

Raging River 4,000 4,100 10,900 8,600 10,100 14,900 9,000 14,100 10,000 10,400 11,700 10,000 11,795

Sultan River 16,200 5,800 8,500 20,300 12,400 17,200 7,700 43,600 45,000 35,900 17,700 29,100 24,575

Wallace River 19,100 15,000 18,800 20,200 12,100 20,200 13,000 5,200 14,800 15,800 20,000 20,000 19,700

N. F. Skykomish River 18,600 10,100 19,300 10,300 — 15,200 5,000 42,500 3,800 20,000 24,900 15,150 16,925

Lake Wash. System 38,000 — — — — — — — 12,400 14,300

Green River (King Co.) 212,400 137,000 197,400 231,200 237,700 210,900 262,300 220,100 285,800 274,600 280,000 102,200 155,432

Puyallup River System 182,800 123,600 336,500 317,000 221,500 252,900 235,550 223,500 240,300 305,600 207,300 211,300 200,000

Puyallup River 162,900 98,500 287,700 238,600 152,300 179,300 157,700 14,800 42,100 107,000 10,000

White (Stuck) River — 41,300 24,900 19,700 24,900 24,000 18,600 19,600 18,200 20,000 21,000 20,000

Carbon River (Voight Cr.) 19,900 25,100 23,900 58,700 44,300 49,600 59,250 189,100 180,000 178,600 176,300 191,300 200,000

Nisqually River

Deschutes River 10,100 15,000 20,000 15,600 — 95,900 18,000 29,400 26,900 — 24,400 25,000 27,000

Kennedy Creek 5,000 10,200 7,900 7,000 — 10,000

Burley Creek

Goldsborough Creek 5,000 9,300 9,100 14,200

Curley Creek/Kitsap

Dewatto River

Tahuyha River — — 9,800 14,976

Union River 5,000 10,000 11,500 15,028

Skokomish River 19,900 28,500 20,000 39,130 39,296 53,684 14,688 53,495 46,700 62,300 63,000 68,400 55,803

Hamma Hamma — — — — — — — — 1,524 1,336 489 1,454 877

Duckabush River 15,100 17,000 15,142 5,000 10,080 — 10,032 10,638 10,200 10,000 10,000 10,032

Dosewallips River 5,600 15,000 20,100 14,742 5,000 12,648 — 12,500 12,300 12,500 12,600 12,500 12,533

Quilcene River

Dungeness River 15,000 15,100 15,300 18,800 9,900 10,000 9,800 9,000 11,000 10,500 12,200 10,250 13,715

Morse Creek 14,700 15,200 15,400 15,338 15,029 5,100 5,000 5,000 5,000 5,000 5,000 5,000 5,000

Elwha River 91,000 83,500 229,100 92,400 94,000 170,100 59,600 61,300 182,200 225,200 120,000 151,700 99,600

Total for year: 1.37 1.18 1.95 1.81 1.51 1.80 1.30 1.96 1.86 1.90 1.84 1.43 1.85
135 

Table G-1 continued horizontally. Releases of winter-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 2004 2005 2006 2007 2008 21-yr avg 10-yr avg

Dakota Creek

Nooksack River — — — — — 83,099 66,310

Whatcom Creek/Squalicum — — — — — 8,546 7,717

Samish River — — — — — 27,580 20,880

Skagit River System 529,821 466,100 517,000 511,560 235,010 329,561 403,063

Skagit River main stem 243,500 200,000 210,000 185,000 20,000 223,514 239,240

Nookachamps/Big Lake

Baker River 70,000 30,000 30,000 30,000 30,000 12,857 27,000

Sauk River 20,000 20,000 30,000 30,000 10 27,681 24,980

Cascade River 196,321 216,100 247,000 266,560 185,000 55,973 111,843

Stillaguamish River System 150,027 152,427 148,760 153,937 145,734 127,378 129,244

Stillaguamish main stem — — — — — 4,039 2,633

Canyon Creek — — — — — 9,928 8,950

Pilchuck Creek (Still.) 5,226 10,000 10,004 10,018 1,080 7,190 2,960

North Fork 144,801 142,427 138,756 143,919 144,654 96,926 113,214

South Fork — — — — — 8,600 1,750

Snohomish River System 442,790 444,677 442,308 436,224 439,326 368,186 381,550

Skykomish River 173,500 160,025 184,324 181,536 150,740 127,680 124,178

Pilchuck River (Snoho.) 33,314 25,108 28,014 35,025 25,314 23,114 24,510

Snoqualmie River 156,333 188,573 160,437 177,712 166,585 125,312 141,446

Tolt River 22,160 — — — 24,970 24,510 23,532

Raging River 4,650 15,117 20,273 — 24,998 11,019 11,060

Sultan River 19,906 20,270 15,660 15,073 25,014 19,504 25,348

Wallace River 18,500 22,000 22,000 26,878 21,705 16,190 16,100

N. F. Skykomish River 14,427 13,584 11,600 — — 17,304 15,378

Lake Wash. System — — — — — 25,827 2,670

Green River (King Co.) 76,895 253,318 243,246 254,669 281,430 207,168 226,023

Puyallup River System 231,859 207,400 211,900 128,000 218,353 203,031 241,495

Puyallup River — — — — — 134,521 112,725

White (Stuck) River — — — — 56,378 21,887 20,667

Carbon River (Voight Cr.) 231,859 207,400 211,900 128,000 161,975 74,843 132,715

Nisqually River

Deschutes River 30,400 24,550 — — — 28,268 32,775

Kennedy Creek — — — — — 11,377 8,500

Burley Creek

Goldsborough Creek — — — — — 9,917 14,200

Curley Creek/Kitsap

Dewatto River — — — — — 10,350

Tahuyha River — — — — — 11,686 14,976

Union River — — — — — 10,901 15,028

Skokomish River 49,946 — — — 4,091 38,541 49,650

Hamma Hamma 965 — — 131 1,136 1,136

Duckabush River — — — — — 13,980 10,125

Dosewallips River — — — — — 15,701 11,925

Quilcene River — — — — — 9,158

Dungeness River 10,500 — 10,900 10,700 10,200 14,349 11,517

Morse Creek 5,000 — — — — 11,342 7,047

Elwha River 59,500 — 38,850 29,150 267,899 113,186 125,610

Total for year: 1.59 1.55 1.61 1.52 1.60 1.63 1.73
136 

Table G-2. Releases of summer-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976

Nooksack River — — — — — — — — — — 20,028

Whatcom Creek

Skagit River System

Skagit River main stem — — — — — — 132,726 141,503 92,187 69,432 50,413 36,470

Sauk River

Cascade River — — — — — — 48,815 — 11,380 30,656 26,775 15,369

Stillaguamish R.System

Stillag. main stem

Canyon Creek — — — — — — — — 26,678 11,358 9,900 12,815

South Fork 12,462 — 43,000 28,170 26,164 21,627 17,139 20,934 24,610 52,732 21,466 17,034

North Fork 26,902 33,050 32,020 33,240 36,264 91,944 46,288 44,981 48,888 55,893 43,902 28,169

Snohomish River System

Skykomish River 24,350 11,520 35,110 — — — — 9,240 — — 76,374 74,975

Pilchuck River (Snoho.)

Snohomish River

Snoqualmie River — — 20,005 31,967 — — 23,088 25,622 19,764 30,854 41,300 20,988

Tolt River 22,200 14,130 — — — 43,505 25,787 15,886 35,993 47,901 34,799 17,297

Raging River

Sultan River

Wallace River

N. F. Skykomish River 9,900 39,635 32,860 40,005 39,322 5,783 37,183 18,518 57,045 66,720 20,662 10,923

S. F. Skykomish River 11,121 10,278

Green River (King Co.) — — — — — 49,713 64,440 58,532 68,921 58,328 94,477 63,840

Puyallup River System

White (Stuck) River

Carbon R. (Voight Cr.)

Nisqually River

Deschutes River

East Hood Canal — — — — — 17,450

Skokomish River — — — — — — — 20,130 20,430 21,588 20,085

West Hood Canal

Dungeness River — — — — — — — — — 20,025 20,136 19,430

Morse Creek

Elwha River — — — 20,127 22,747 21,180 20,940 20,010 20,195 20,080 30,600 19,926

Total for year: 120,814 138,335 192,995 178,593 124,497 289,227 427,456 382,265 453,071 514,995 551,248 347,514
137 

Table G-2 continued horizontally. Releases of summer-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988

Nooksack River — 63,000 — 3,078 10,818

Whatcom Creek

Skagit River System — — — — — — — — — — 0 30,900

Skagit River main stem 63,962 59,731 23,306 53,559 73,322 — 30,958 — 10,022 10,089

Sauk River — — — — 7,463

Cascade River 15,930 22,345 60,966 16,279 29,081 — — 34,897 10,104 25,030 — 30,900

Stillaguamish R.System — — — — — — — — — — 73,111 82,800

Stillag. main stem — — — — — — — — — — 3,500

Canyon Creek 13,616 12,699 — 5,121 5,217 — — 2,475 10,877 10,243 9,711 9,700

South Fork 24,097 24,236 25,018 — 33,071 — — 34,143 15,806 26,342 — 18,500

North Fork 47,260 53,413 53,184 121,543 39,160 27,704 24,530 42,167 33,014 63,172 59,900 54,600

Snohomish River System — — — — — — — — — — 63,100 233,000

Skykomish River 62,629 64,307 61,478 59,409 24,960 54,598 65,760 112,063 36,744 95,235 63,100 76,400

Pilchuck River (Snoho.)

Snohomish River

Snoqualmie River 35,956 16,951 16,951 17,955 7,655 16,650 — 16,650 27,376 68,381 — 72,700

Tolt River 37,055 30,337 11,598 32,498 23,651 15,952 11,763 7,854 11,013 14,175 — 15,800

Raging River — — — — — — — 5,050 5,785 5,600 — 4,100

Sultan River 7,623 — — — — — — 18,677 20,378 9,800 — 19,400

Wallace River

N. F. Skykomish River 42,460 35,530 32,500 41,290 — 13,342 19,147 26,935 16,322 18,092 — 24,700

S. F. Skykomish River 10,236 4,930 52,833 18,469 25,485 15,000 8,165 32,132 11,665 20,287 — 19,900

Green River (King Co.) 93,872 90,016 140,044 118,666 54,096 76,633 76,398 72,208 69,304 114,085 — 74,800

Puyallup River System — — — — — — — — — — 0 0

White (Stuck) River

Carbon R. (Voight Cr.)

Nisqually River 29,120 19,500 47,640 19,355 11,250 20,243 34,390 42,646 19,952 26,028 — 22,200

Deschutes River 689 — — — — — — — — — 115,011

East Hood Canal

Skokomish River — — 20,215 17,010 10,107

West Hood Canal — — — — 15,043

Dungeness River 19,530 18,300 20,025 10,010 5,141 4,530 4,150 5,000 10,371 5,150 10,200 10,100

Morse Creek

Elwha River 20,776 27,100 20,007 20,020 26,115 17,820 15,175 20,285 20,747 18,949 19,800 25,400

Total for year: 524,811 542,395 585,765 554,262 401,635 262,472 290,436 473,182 329,480 530,658 281,222 479,200
138 

Table G-2 continued horizontally. Releases of summer-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000

Nooksack River

Whatcom Creek

Skagit River System 0 24,100 18,700 19,800 32,300 27,000 25,200 25,000 0 21,000 0 0

Skagit River main stem — 24,100 18,700 19,800 27,300 27,000 25,200 25,000 — 21,000

Sauk River — — — — 5,000

Cascade River

Stillaguamish R.System 59,500 100,000 80,600 85,100 81,300 87,100 74,000 85,100 38,600 74,700 17,600 70,000

Stillag. main stem — — — — — — — — — 31,300 17,600 21,800

Canyon Creek — 7,500 9,200 9,600 7,900 9,700 5,300 13,500

South Fork — 23,300 8,100 15,500 15,300 18,500 20,100 21,000

North Fork 59,500 69,200 63,300 60,000 58,100 58,900 48,600 50,600 38,600 43,400 — 48,200

Snohomish River System 137,700 184,300 179,900 235,100 127,100 230,500 180,900 226,400 168,631 265,300 266,300 167,200

Skykomish River 101,600 91,800 104,500 111,500 72,800 146,200 120,000 127,400 93,700 175,000 185,700 117,400

Pilchuck River (Snoho.)

Snohomish River — — — 26,900 0 0 0 0 0 0 0 0

Snoqualmie River 30,800 38,300 44,900 46,200 30,500 56,500 48,700 73,500 45,221 41,600 27,800 22,000

Tolt River 5,300 8,700 0 0 8,000 0 0 0 0 0 0 0

Raging River — — — — — — — — — — 21,700 9,200

Sultan River — 15,000 0 10,100 8,200 8,200 5,500 9,700 15,100 15,400 13,300 14,000

Wallace River

N. F. Skykomish River — 14,600 15,300 20,400 7,600 19,600 6,700 15,800 14,610 33,300 17,800 4,600

S. F. Skykomish River — 15,900 15,200 20,000 0 0 0 0 0 0 0 0

Green River (King Co.) 5,200 71,300 23,700 79,600 83,700 81,300 83,600 100,100 36,000 86,300 67,300 65,300

Puyallup River System 0 0 0 0 0 0 0 0 0 0 0 0

White (Stuck) River

Carbon R. (Voight Cr.)

Nisqually River — 13,400 0 24,800 23,700 12,800

Deschutes River — — 3,300 3,000

East Hood Canal

Skokomish River

West Hood Canal

Dungeness River 10,100 6,100 0 15,100 16,100 10,500

Morse Creek

Elwha River 19,800 15,000 0 23,600 25,100 0 25,100 20,200 10,000 10,000 10,100 10,000

Total for year: 232,300 414,200 306,200 486,100 389,300 449,200 388,800 456,800 253,231 457,300 361,300 312,500
139 

Table G-2 continued horizontally. Releases of summer-run steelhead smolts into Puget Sound tributaries from 1965 to 2008

Name of stream 2001 2002 2003 2004 2005 2006 2007 2008 10-yr avg

Nooksack River

Whatcom Creek

Skagit River System 0 0 0 0 0 0 0 0 0

Skagit River main stem

Sauk River

Cascade River

Stillaguamish R.System 106,900 90,600 45,633 77,776 73,633 105,575 97,000 96,858 78,158

Stillag. main stem — 61,800 — — — — — — 33,733

Canyon Creek — — — — — — 7,020 5,100 6,060

South Fork 46,900 28,800 — — — 29,321 13,052 15,330 26,681

North Fork 60,000 — 45,633 77,776 73,633 76,254 76,928 76,428 66,857

Snohomish River System 223,400 221,200 177,849 248,268 261,770 234,006 245,057 271,686 231,674

Skykomish River 136,500 0 107,217 165,000 168,800 149,440 160,135 178,361 136,855

Pilchuck River (Snoho.)

Snohomish River 0 0 0

Snoqualmie River 28,300 0 44,901 18,885 52,470 50,838 28,840 62,763 33,680

Tolt River 0 0 0

Raging River 21,700 51,500 0 23,786 — — 27,720 — 22,229

Sultan River 20,600 14,900 10,449 20,447 20,340 20,330 28,362 30,562 19,329

Wallace River

N. F. Skykomish River 16,300 154,800 15,282 20,150 20,160 13,398 — — 32,811

S. F. Skykomish River 0 0 0 — — — — — 0

Green River (King Co.) 39,600 101,100 59,833 74,605 164,463 96,841 96,564 54,400 82,001

Puyallup River System 0 0 0 0 0 0 0 0 0

White (Stuck) River

Carbon R. (Voight Cr.)

Nisqually River

Deschutes River

East Hood Canal

Skokomish River

West Hood Canal

Dungeness River

Morse Creek

Elwha River — — — — — — — — 10,050

Total for year: 369,900 412,900 283,315 400,649 499,866 436,422 438,621 422,944 393,842
140 
141 

Appendix H: Steelhead Adult Age-Classes by Sex (Table H-1) 

and Age Structure by Broodyear (Table H-2)

Table H-1. Distribution of steelhead (Oncorhynchus mykiss) adult age-classes (including multiple spawner information) by sex for winter-run 

steehead captured in sport and tribal fisheries for selected Puget Sound rivers. All fish were identified as naturally produced based on 

scale growth patterns. The letter S indicates a “spawn check” in the scale growth pattern (e.g., repeat spawner). (Data from R. F. Leland, 

Fish Program, WDFW, Olympia. Pers. commun., 16 April 2009.)

River basin 

(all tribs.) Year

1.1+ 1.2+ 2.1+ 2.2+ 2.3+ 2.1+S+ 2.1+S+S 2.2+S+ 2.3+S+ 3.1+ 3.2+ 3.1+S+

M F M F M F M F M F M F M F M F M F M F M F M F

Stillaguamish 1982/83 0 1 0 0 11 8 14 34 0 0 3 11 0 3 0 3 0 1 0 0 0 0 0 0

Green 1982/83 0 1 0 2 9 4 10 18 1 0 1 1 0 0 0 1 0 0 1 2 0 0 0 0

Skagit 1984/85 0 0 0 0 51 51 11 30 0 0 2 7 0 1 0 3 0 0 11 6 1 0 0 1

Skagit 1982/83 0 0 0 0 11 9 14 23 0 0 1 8 0 0 1 4 0 0 3 1 0 0 0 3

Puyallup 1983/84 2 1 10 6 0 0 3 2 0 0 0 0 0 1 0 3 0 0 0 1 0 0 0 1

Puyallup 1979/80 3 1 0 1 24 24 2 11 0 0 0 5 0 0 0 0 0 0 4 5 0 0 0 0

Puyallup 1978/79 1 2 0 1 18 16 7 14 0 0 0 1 0 1 0 1 0 0 0 1 0 1 0 1
142 

Table H-2. Steelhead age structure by broodyear for selected Puget Sound rivers. Age structure (freshwater/ salt water)is based on scales 

collected from steelhead captured in tribal net fisheries and sport fisheries (sp). All fish were identified as naturally produced based on 

scale growth patterns. The notation “all” indicates that samples came from all fisheries. Skykomish numbers 1 and 2 indicate 

management zones. Decimal numbers are percentages and numbers in bold indicate the most common age-class. (Data from R. F. 

Leland, Fish Program, WDFW, Olympia. Pers. commun., 16 April 2009.) 

River Broodyear 1.1+ 1.2+ 2.1+ 1.3+ 2.2+ 3.1+ 2.3+ 3.2+ 4.1+

Nooksack 1978/80 0.00 0.00 78.72 0.00 13.18 7.09 0.00 1.01 0.00

Skagit 1979/86 0.29 0.06 45.85 0.00 30.42 13.60 1.06 8.57 0.15

Sauk 1983 0.00 0.00 29.47 0.00 43.16 5.26 0.00 22.11 0.00

Snohomish (all) 1978/86 1.07 0.27 47.40 0.00 37.27 5.69 0.84 7.46 0.00

Snohomish (sp) 1980/86 0.86 0.32 48.82 0.00 31.69 8.40 0.92 9.00 0.00

Pilchuck 1983/85 1.90 0.68 46.70 0.00 36.60 8.19 3.49 2.44 0.00

Skykomish (1) 1985/86 0.36 1.49 62.22 0.00 34.19 0.00 0.00 1.74 0.00

Skykomish (sp) (1+2) 1979/81 0.58 0.00 61.39 0.00 27.96 2.16 1.24 6.67 0.00

Tolt 1984 0.00 48.98 0.00 0.00 51.02 0.00 0.00 0.00 0.00

Snoqualmie 1979/85 0.61 0.90 58.33 0.00 36.04 1.60 0.00 2.51 0.00

Green 1981/86 6.14 2.37 42.82 0.00 40.72 3.52 1.90 2.53 0.00

Puyallup 1976/77 7.57 0.58 62.98 0.00 20.57 8.31 0.00 0.00 0.00

Nisqually 1978/80 10.49 3.86 66.61 0.00 17.41 1.49 0.05 0.08 0.00
143

Appendix I: Catastrophic Risk Categories for 

Puget Sound Chinook Salmon

Table I-1. Scores for catastrophic risk categories for Puget Sound Chinook salmon (Oncorhynchus 

tshawytscha). (Modified from Good et al. 2008.)

Risk source

Georegion Basin/population

VolcanoaEarthquakebLandslidec FlooddToxic 

leake

Toxic 

spillf

HatcherygDam 

breachh

NE N. F. Nooksack 70.6 34.9 18.8 20 0.20 0.19 0.0 0.0

NE S. F. Nooksack 4.2 33.6 20.2 20 0.04 0.14 0.0 0.0

CE Lower Skagit 70.3 34.8 20.6 20 0.20 0.15 0.0 55.8

CE Upper Skagit 3.5 20.7 32.2 20 0.10 0.61 11.6 51.5

CE Cascade 0.0 20.0 34.0 20 0.10 0.00 0.0 0.0 

CE Lower Sauk 98.9 30.0 19.4 22 0.10 0.25 0.0 6.8

CE Upper Sauk 100 29.9 31.0 25 0.00 0.00 0.0 0.0

CE Suiattle 99.2 25.7 31.0 23 0.01 0.03 0.0 0.0

CE N. F. Stillaguamish 79.7 34.0 21.3 25 0.02 0.26 9.0 0.0

CE S. F. Stillaguamish 52.5 40.0 16.5 25 0.20 0.28 0.0 25.2

CE Skykomish 0.0 40.0 19.7 26 0.30 0.39 3.0 17.9

CE Snoqualmie 0.0 48.3 19.8 33 0.20 0.28 0.0 25.2

S Sammamish 0.0 51.4 4.5 31 1.60 0.62 12.2 0.0

S Cedar 0.0 52.3 10.7 33 0.80 0.74 0.0 45.0

S Green 37.3 45.5 9.2 33 0.90 0.39 14.6 42.2

S White 92.1 39.9 14.4 27 0.30 0.28 1.9 31.2

S Puyallup 98.6 44.6 10.4 25 0.20 0.31 8.4 7.0

S Nisqually 92.9 42.3 5.1 28 0.10 0.16 33.1 52.9

CW Skokomish 0.0 50.0 23.3 25 0.03 0.08 28.0 35.5

CW Mid-Hood Canal 0.0 50.0 32.2 21 0.10 0.06 5.4 0.0

NW Dungeness 0.0 50.0 30.2 14 0.10 0.02 41.1 0.0

NW Elwha 0.0 50.0 36.6 15 0.04 0.16 46.8 20.4

a

Chinook salmon distribution overlapping with volcanic hazard zones (%).

b

Chinook salmon distributionfalling under earthquake risk; weighted mean amount of the distribution under each 

contour value (%).

c

Chinook salmon distribution under high landslide risk (%)

d

Mean chance of annual flood occurrence (%).

e

Potential point source pollution facilities per kilometer of Chinook salmon reaches (no./km). f

Major transportation routes per kilometer of Chinook salmon reaches (km/km).

g

Releases of hatchery Chinook salmon per kilometer of Chinook salmon reaches (no./km). h

Chinook salmon distribution impacted by unplanned dam breaches (%).
144
145

Appendix J: Geologic Regions of 

Washington State

Figure J-1. Geologic map GM-53 of Washington State. (Reprinted from Schuster 2005.)
146
147 

Appendix K: Average Monthly Flows for Puget Sound Streams

Table K-1. Normalized average monthly flows for Puget Sound streams. Peak monthly flows for each river are set to 100 in boldface.

River Year Jan. Feb. March April May June July Aug. Sept. Oct. Nov. Dec.

Baker River Concrete 1990–2006 79.8 68.9 52.0 48.5 62.0 81.1 69.9 56.9 50.0 65.8 100.0 74.5

Big Beef Creek 1990–2006 100.0 73.1 53.8 28.6 14.3 8.4 4.9 3.5 3.8 12.6 39.5 84.9

Cascade RiverMarblemount 1990–2006 32.5 29.1 27.6 39.4 76.0 100.0 78.8 42.6 31.0 34.0 40.2 38.7

Cedar River Landsberg 1990–2006 100.0 91.9 74.1 72.8 61.1 57.4 41.0 31.9 31.9 45.9 86.1 98.5

Duckabush River 1990–2006 100.0 71.8 65.4 63.5 76.2 73.4 43.8 24.6 17.4 38.4 84.0 94.4

Dungeness River 1990–2006 79.7 65.0 53.0 54.5 82.5 100.0 70.9 39.8 24.1 32.2 67.0 73.9

Elwha River (above Mills) 1994–2007 100.0 75.8 62.1 52.5 76.7 73.1 48.9 23.2 19.2 34.3 76.3 93.6

Green River Auburn 1990–2006 100.0 92.6 71.3 71.3 61.7 43.0 22.3 12.6 15.0 30.3 79.6 87.8

Hoko River 1962–2007 100.0 70.1 61.9 36.2 18.6 11.6 8.7 4.8 8.0 33.9 87.8 92.7

Huge Creek (Kitsap) 1990–2006 100.0 84.0 64.0 44.0 29.2 24.0 19.6 17.6 17.2 22.8 44.0 76.0

Issaquah Creek 1990–2006 100.0 82.0 71.2 56.0 36.8 29.6 17.6 10.8 10.8 21.6 69.2 87.2

Leach Creek 1990–2006 100.0 71.0 62.0 55.0 38.0 35.0 27.0 29.0 31.0 55.0 91.0 87.0

Mercer Creek 1990–2006 100.0 76.2 66.7 54.8 38.1 31.0 22.6 22.4 26.2 47.6 85.7 90.5

M. Fork Snoqualmie Tanner 1990–2006 84.8 66.0 56.5 71.2 88.5 83.2 41.6 18.4 21.8 53.4 100.0 75.9

N. Fork Snoqualmie near falls 1990–2006 90.6 68.1 59.7 72.1 78.4 68.6 33.5 14.7 23.1 56.0 100.0 80.2

Nisqually McKenna 1990–2006 97.8 93.8 66.4 57.5 46.9 36.8 28.5 21.9 24.6 32.7 65.0 100.0

Nooksack Rivermain stem 1990–2006 95.9 76.4 67.2 69.5 76.4 79.8 58.0 37.8 31.7 54.1 100.0 92.6

North ForkNooksack River 1990–2006 46.4 37.1 34.1 45.6 76.6 100.0 86.9 55.2 37.9 49.1 61.1 45.9

South ForkNooksack River 1990–2006 93.8 55.8 64.3 68.2 71.7 57.9 29.5 15.7 18.8 51.2 100.0 82.9

Pilchuck River 1992–2007 100.0 76.3 76.5 60.3 43.3 31.3 18.1 10.8 12.9 36.1 80.0 98.5

Puyallup River Boise 1990–2006 100.0 93.0 75.4 66.7 52.6 45.6 26.3 16.5 14.9 26.3 77.2 86.0

Puyallup/Carbon rivers 1990–2006 91.8 71.6 57.4 64.4 92.8 100.0 73.4 51.4 40.4 55.3 92.3 88.0

Puyallup RiverElectron Dam 1990–2006 85.4 67.6 57.9 66.7 88.0 100.0 91.6 78.1 57.5 58.3 88.6 82.1

Puyallup R. Greenwater River 1990–2006 73.9 70.1 55.8 74.5 100.0 79.9 33.8 16.5 12.4 20.1 52.2 65.1

Puyallup River main stem 1990–2006 100.0 92.6 73.6 75.7 78.8 89.0 64.2 44.8 34.0 46.2 83.1 95.5

South Prairie Creek 1990–2006 100.0 89.4 72.0 71.2 66.7 53.7 28.0 15.9 15.6 31.0 78.8 88.1

Samish River 1990–2006 100.0 71.9 68.9 54.5 32.8 24.7 14.0 8.0 8.5 27.5 73.2 88.8

Sauk River Whitechuck 1990–2006 66.3 54.4 47.7 62.4 95.0 100.0 63.0 27.9 21.3 48.7 83.4 61.3
148 

Table K-1 continued. Normalized average monthly flows for Puget Sound streams. Peak monthly flows for each river are set to 100 in boldface.

River Year Jan. Feb. March April May June July Aug. Sept. Oct. Nov. Dec.

South ForkTolt 1990–2006 100.0 85.1 64.5 58.9 67.4 64.5 46.1 42.6 42.6 45.4 83.7 90.1

Skagit River Marblemount 1990–2006 92.8 90.9 78.1 73.4 78.5 83.9 89.6 59.5 48.2 60.9 100.0 75.7

Skagit River Mount Vernon 1990–2006 93.0 84.2 71.6 71.6 86.5 96.3 81.9 52.6 42.1 59.1 100.0 86.0

Skokomish River 1990–2006 100.0 74.8 57.2 41.4 25.3 18.0 11.2 9.6 9.9 27.8 77.2 97.9

Skykomish RiverGold Bar 1990–2006 80.8 64.9 57.7 74.4 100.0 92.2 46.6 18.9 18.4 49.3 99.2 72.5

Snohomish River Monroe 1990–2006 95.1 78.2 66.3 75.4 85.2 78.2 41.2 19.5 20.6 49.6 100.0 88.0

Snoqualmie River Tolt River 1990–2006 100.0 78.2 66.4 67.6 63.8 53.5 31.0 19.9 22.5 44.5 88.7 90.9

Stillaguamish River Arlington 1990–2006 98.4 75.5 68.0 64.0 57.5 44.7 21.7 13.6 17.6 49.1 100.0 94.4

Stillaguamish R.Granite Falls 1990–2006 87.4 71.4 62.9 61.7 78.3 64.6 36.9 21.0 30.6 50.4 79.4 100.0

Tulalip Creek 2000–2006 100.0 88.9 88.9 88.9 55.0 41.1 30.6 29.4 32.2 49.4 61.1 83.3
149

Appendix L: Distances between Adjacent Puget 

Sound River Mouths

Table L-1. Summary of distances to nearest neighbor spawning grounds. Distances are determined by 

water-based migration.

Spawning area Nearest neighbor(s)

Distance 

(km) Next nearest

Distance 

(km)

Boundary tributaries Mainstem Nooksack 25.5c Samish 39.8

Mainstem Nooksack North Fork, Middle Fork, 

and South Fork Nooksack

0.0a Boundary tributaries 25.5

North Fork Nooksack Mainstem and Middle 

Fork Nooksack

0.0a South Fork Nooksack 5.6

Middle Fork Nooksack Mainstem and North Fork

Nooksack

0.0a South Fork Nooksack 5.6

South Fork Nooksack Mainstem Nooksack 0.0a N. Fork and Middle 

Fork Nooksack

5.6

Samish Boundary tributaries 39.8d Mainstem Nooksack 61.3

Lower Skagit Middle Skagit and Finney 

and Sauk

0.0a Baker 26.1

Middle Skagit Lower Skagit and

Cascade and Sauk

0.0a Finney 14.5

Sauk Middle Skagit 0.0a Lower Skagit 19.1

Skagit–Finney Lower Skagit 0.0a Middle Skagit 14.5

Skagit–Baker River Lower Skagit 26.1c Finney 40.5

Skagit–Cascade Middle Skagit 0.0a Sauk 19.5

Stillaguamish North Fork and South 

Fork Stillaguamish

0.0a Deer Creek 37.6

North Fork Stillaguamish Stillaguamish and South 

Fork Stillaguamish

0.0a Deer Creek 14.7

South Fork Stillaguamish Stillaguamish and North 

Fork Stillaguamish

0.0a Deer Creek 37.7

Stillaguamish–Deer Cr. North Fork Stillaguamish 14.7b Stillaguamish 37.6

Snohomish Skykomish 1.2a Snoqualmie 4.2

Snohomish–Pilchuck R. Snohomish 8.3a Skykomish 11.4

North Fork Skykomish Skykomish 0.0a Snohomish 47.6

N. F. and S. F. Skykomish North Fork Skykomish 0.0a Snohomish 1.2

Snoqualmie Skykomish 3.6a Tolt 3.9

Snoqualmie–Tolt River Snoqualmie 3.9a Skykomish 39.5

Sammamish Cedar 68.3d East Kitsap 81.2

Cedar River East Kitsap 51.0d Sammamish 68.3

Green River East Kitsap 66.3d Cedar 89.0
150 

Table L-1 continued. Summary of distances to nearest neighbor spawning grounds. Distances are 

determined by water-based migration.

Spawning area Nearest neighbor(s)

Distance 

(km) Next nearest

Distance 

(km)

Puyallup–entire basin Carbon 0.0a White 7.5

Puyallup–White Puyallup 7.5a Carbon 19.6

Puyallup–Carbon Puyallup 0.0a White 19.6

Nisqually South Sound inlets 35.7d Puyallup 61.0

South Sound inlets Nisqually 35.7d East Kitsap 79.5

Kitsap–East/Curley Cedar 51.0d Puyallup 56.2

Hood Canal East Dosewallips 13.2b Hamma Hamma 15.8

Tahuya Skokomish 10.1b East Hood Canal 18.9

Skokomish–entire basin N. F. and S. F. Skokomish 0.0a Tahuya 10.1

North Fork Skokomish Skokomish and South 

Fork Skokomish

0.0a Tahuya 24.1

South Fork Skokomish Skokomish and North 

Fork Skokomish

0.0a Tahuya 24.1

Hamma Hamma East Hood Canal 15.8b Duckabush 18.8

Duckabush Dosewallips 12.0b Hamma Hamma 18.8

Dosewallips Duckabush 12.0b Hamma Hamma 24.7

Big Quilcene Dabob Bay 20.9b Dosewallips 27.5

Sequim/Discovery/

Dabob bays

Big Quilcene 20.9b Dungeness 21.8

Dungeness Strait of Juan de Fuca

tributaries

21.6b Sequim/Discovery/

Dabob bays

21.8

Strait of J. de Fuca tribs. Elwha 18.5b Dungeness 21.6

Elwha Strait of J.. de Fuca tribs. 18.5b Dungeness 44.7

a Separation <10 km.

b Separation 10 to 25 km.

c Separation 25 to 35 km.

d Separation >35 km.
151

Appendix M: Responses to Reviewer Comments

This appendix includes comments and concerns provided by two peer reviewers as well 

as by other interested parties. Not included here are editorial comments; we have addressed 

those issues directly in the text. There have been a number of requests for comments. 

Comanagers and interested parties were contacted by letter (17 October 2011), and electronic 

and paper copies of a draft document were provided prior to a 30 May 2013 workshop at 

NOAA’s Western Regional Office (7600 Sand Point Way Northeast, Seattle) that discussed both 

this population identification document and the viability criteria document (Hard et al. in press) 

for the Puget Sound steelhead (Oncorhynchus mykiss) distinct population segment (DPS). 

Following the workshop, a revised population identification document was made electronically 

available for review.

Peer Reviewer 1

Review

The reviewer was concerned about “a lack of clarity about the nature of phenotypic 

variation,” and specifically how that variation or lack thereof would be used in the identification 

of demographically independent populations (DIPs).

Response

The reviewer correctly identified a section on local adaptation and plasticity that did not 

clearly discuss their application to identifying populations. Where ecological conditions differ, 

there is a potential for selection in life history or morphological traits. Over time this selection 

will confer a fitness advantage to “native” individuals over strays from other populations and 

increase the level of genetic isolation between populations. Alternatively, where these traits are 

highly plastic, allowing for a wide range of phenotypic expression, the selective advantage of 

“native” fish is decreased and the potential for genetic introgression between populations 

increases.

Interestingly, in the case of steelhead populations in the Puget Sound DPS and elsewhere, 

there is little phenotypic or life history variation on a regional basis other than in run timing

(winter run or summer run); yet we find there is genetic differentiation between proximate 

populations. This may indicate a strong homing fidelity or the presence of locally adapted traits 

that are not readily detectable.
152

Review

The reviewer also commented that the P value for Hardy-Weinberg was especially 

stringent. In the case of Table 3-2 (appendix Table B-2 herein), the threshold was FIS = 0.00011 

for an overall experiment-wise error of P = 0.05.

Response

The large number of total individuals sampled generates a very low FIS threshold for an 

experiment-wise error rate of P = 0.05; however, the values in the table reflect within sample 

(population level) deviations from Hardy-Weinberg. In most cases where there was a significant 

deviation, the FIS value was positive, indicating a deficiency of heterozygotes and the possibility 

that multiple populations were represented, or where populations are numerically small this 

deviation can be due to family effects within a population.

Peer Reviewer 2

Review

The reviewer suggested that in those cases where both summer-run and winter-run 

steelhead were found to hold and spawn in the same river reaches (i.e., mainstem Skagit River) a 

more conservative approach would have been to designate the two run times as independent 

populations.

Response

In identifying criteria for establishing DIPs, the Puget Sound Steelhead Technical 

Recovery Team (PSS TRT) focused on widely accepted factors influencing the degree of 

reproductive isolation between populations. In contrast to summer-run steelhead in Deer Creek 

or the North Fork Skykomish River, summer-run steelhead in the mainstem Skagit and Sauk 

rivers are not separated by obvious migration barriers, but spawn in the same river reaches 

without a clear temporal separation. In the case of Finney Creek (Skagit River), comanagers 

argued that the summer-run spawning aggregation was too small to be a DIP and was likely 

extirpated. In addition, some reviewers suggest that these presumptive summer-run fish were 

resident fish from nearby tributaries. In the absence of genetic information on summer-run and 

winter-run steelhead to establish reproductive isolation (and thereby demographic independence) 

in the rivers in question, the PSS TRT decided that making a DIP distinction was too tenuous. A 

further consideration in not identifying distinct DIPs was the absence of abundance information 

indicating that historical and present abundance was sufficient for a sustainable summer-run 

population. The TRT did not discount the potential presence of summer-run populations cooccurring with winter-run steelhead, but suggested that data were currently lacking to support 

such a conclusion. In the case of the Dungeness, Elwha, and Green rivers, there were potential 

migration barriers, but historical and current documentation was deficient. The TRT strongly 

encourages the comanagers to undertake the necessary studies to resolve this issue.
153

Additional Reviewer Comments

Review

One of the concerns put forward was that the 50 km distance threshold for 

demographically independent populations was not clearly defined; specifically questioning 

whether it focused on the distance mouth-to-mouth for tributaries or between spawning sites, etc. 

Specific examples were provided of hatchery-run steelhead straying from the Stillaguamish 

River to the Skagit River.

Response

The TRT took a conservative approach and established the 50 km distance as mouth-tomouth. There was some discussion that the distance could be measured between spawning areas; 

however, there were insufficient data to attempt this calculation for most rivers. Additionally, 

much of the steelhead straying data analyzed was presented using the mouth-to-mouth distance.

The examples provide by the commentator underscore a number of issues. Firstly, under 

the criteria establish by the TRT, the mouth-to-mouth distance would be less than 50 km. 

Secondly, the return migration of summer-run steelhead often includes extended freshwater 

holding periods in nonnatal stream, making it difficult to distinguish between true strays and “dip 

ins.” Thirdly, they highlight the potential for hatchery fish to stray more widely than their 

naturally born counterparts. Straying may be further affected by rearing and release strategies, 

specifically off-site releases.

Review

There was considerable concern that the level of gene flow between the populations 

identified by the TRT was more substantial than the 10% level set forth in defining DIPs. The 

commentator interpreted the relatively low (below threshold) genetic distances between several 

populations as being indicative of a much higher gene flow. Creating such artificial populations, 

it was argued, would limit the efficacy of any management actions.

Response

It is important to consider that demographic independence is different from reproductive 

independence. The level of demographic influence from other populations (straying) is thought 

to be about 10% and still maintain independence. Reproductive independence is related to the 

proportion of straying individuals that successfully reproduce. Therefore, the level of 

reproductive independence will be lower than the level of demographic independence.

The threshold set for independence based on genetic differences, Cavalli-Sforza and 

Edwards chord distances, was set large enough that there was a very high level of certainty for 

independence. This reflects the TRT’s desire for multiple types of evidence to establish 

independence. In addition, analysis of the genetic data suggests a deviation from HardyWeinberg proposing that there may be some mixing of populations in the sample. This mixing 

may not necessarily be between the two populations in question, but could suggest additional 
154

populations may be present within a sample. If multiple populations were included in a 

presumptive single population sample, the increase in variation could reduce the betweenpopulation Cavalli-Sforza and Edwards chord distances presented in Figure 3-7 (appendix Table 

B-3 herein).

Review

There were a number of comments from biologists with the comanaging agencies that 

questioned the inclusion of collections of several smaller independent streams or smaller 

tributaries as DIPs; for example, the Nookachamps Basin (small tributary to the Skagit River), 

several clusters of independent tributaries in Hood Canal, and independent tributaries in South 

Puget Sound and the East Kitsap Peninsula. Another area that generated a number of comments 

was the Strait of Juan de Fuca and variations of combinations of smaller independent tributaries 

with the two large rivers, Dungeness and Elwha.

Commentators questioned whether some of these provisional DIPs ever historically 

contained sufficient numbers of steelhead to be considered self-sustaining, and if they did 

historically, they had been effectively extirpated in the recent past. In other cases, there was a 

preference voiced to combine smaller independent tributaries with geographically proximate 

larger rivers.

Response

Firstly, it is important to remember that a primary criterion for establishing DIPs is 

evidence of historical presence, and therefore even if fish were no long present in large numbers,

the capacity of the basin may be sufficient to support a DIP. There was sufficient historical data 

(primarily historical catch records from the 1940s and 1950s) to establish that steelhead were 

naturally produced in the streams in question. This information comported with intrinsic 

potential (IP) estimates of steelhead productivity. Secondly, analysis of steelhead populations in 

Hood Canal, one the most data-rich regions in Puget Sound, validated the premise that 

genetically distinct populations of steelhead can be sustained in close geographic proximity to 

one another. This geographic template was very useful in areas where information was much 

more limiting, especially in the South Puget Sound area. Finally, regarding the combination of 

smaller independent tributaries with larger rivers, it was observed that the run and spawn timing 

for winter steelhead in smaller, rain-driven tributaries was much earlier than in the larger, colder, 

snow-driven rivers. This provided some temporal spawning separation between steelhead in the 

two stream types.

The TRT debated a number of scenarios for South Puget Sound, with as many as six 

DIPs being present. In addition to the Nisqually River, where there is considerable historical and 

contemporary information available, historical catch records indicate that there were winter-run 

steelhead in a number of independent tributaries throughout the area. Also, the rain-driven 

hydrology of these tributaries was distinct from the larger, snowmelt-driven Nisqually River. 

Furthermore, these smaller tributaries were distributed across a large geographic area, providing 

the potential for geographic isolation. Ultimately, the majority of the TRT agreed that the minor 

tributaries constituted one or more DIPs, but were unable to agree upon an exact number, nor 

identify where the boundaries might lie. In creating one South Sound DIP, the TRT confirmed 
155

the historic importance of this region, but left further subdivision to the acquisition of additional 

information.

In contrast to the comments received disputing the inclusion of small independent 

tributaries in DIPs, the TRT received a number of responses that included redd counts and adult 

sightings from many of the tributaries being discussed (especially in Bellingham Bay and the 

East Kitsap Peninsula). These responses reinforced the TRT’s understanding that steelhead 

utilized a wide range of stream habitats and that many spawning aggregations thought to be 

extirpated continued to persist at low abundance levels. It also underscored the need for more 

extensive monitoring to more accurately evaluate the status of steelhead populations.

Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center

NOAA Technical Memorandum NMFS-NWFSC127 Roni, P., G.R. Pess, T.J. Beechie, and K.M. Hanson. 2014. Fish-habitat relationships and the 

effectiveness of habit restoration. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-127, 

154 p. NTIS number PB2014-108836.

126 Russell, S., and M.S. Ruff. 2014. The U.S. whale watching industry of Greater Puget Sound: A 

description and baseline analysis. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-126, 

171 p. NTIS number PB2014-105939.

125 Sloan, C.A., B.F. Anulacion, K.A. Baugh, J.L. Bolton, D. Boyd, R.H. Boyer, D.G. Burrows, D.P. 

Herman, R.W. Pearce, and G.M. Ylitalo. 2014. Northwest Fisheries Science Center’s analyses of 

tissue, sediment, and water samples for organic contaminants by gas chromatography/mass spectrometry 

and analyses of tissue for lipid classes by thin layer chromatography/flame ionization detection. U.S. 

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-125, 61 p. NTIS number PB2014-104055.

124 Anderson, L.E., and S.T. Lee. 2013. Washington and Oregon saltwater sportfishing surveys: 

Methodology and results. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-124, 61 p. NTIS 

number PB2014-101405.

123 Ward, E.J., M.J. Ford, R.G. Kope, J.K.B. Ford, L.A. Velez-Espino, C.K. Parken, L.W. LaVoy, 

M.B. Hanson, and K.C. Balcomb. 2013. Estimating the impacts of Chinook salmon abundance and 

prey removal by ocean fishing on Southern Resident killer whale population dynamics. U.S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-123, 71 p. NTIS number PB2013-110079.

122 Frame, E., and K. Lefebvre. 2013. ELISA methods for domoic acid quantification in multiple marine 

mammal species and sample matrices. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-122, 

20 p. NTIS number PB2013-109341.

121 Lian, C.E. 2012. West Coast limited entry groundfish cost earnings survey: Protocol and results for 

2008. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-121, 62 p. NTIS number PB2013-

104899.

120 Pollock, M.M., J.M. Wheaton, N. Bouwes, C. Volk, N. Weber, and C.E. Jordan. 2012. Working 

with beaver to restore salmon habitat in the Bridge Creek intensively monitored watershed: Design 

rationale and hypotheses. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-120, 47 p. NTIS 

number PB2013-101722.

Most NOAA Technical Memorandums NMFS-NWFSC are available at the

Northwest Fisheries Science Center Web site, http://www.nwfsc.noaa.gov