Preliminary conclusions regarding the updated status of listed 

ESUs of West Coast salmon and steelhead 

A. Chinook salmon 

February 2003 

Co-manager review draft 

This section deals specifically with chinook salmon It is part of a larger report, the 

remaining sections of which can be accessed from the same website used to access this 

section (http://www.nwfsc.noaa.gov/). The main body of the report (Background and 

Introduction) contains background information and a description of the methods used in 

the risk analyses. 
Draft Report 2/20/2003 

A. CHINOOK 1 

A. CHINOOK 

A.1 BACKGROUND AND HISTORY OF LISTINGS 

Chinook salmon (Oncorhynchus tshawytscha Walbaum), also commonly referred to as 

king, spring, quinnat, Sacramento, California, or tyee salmon, is the largest of the Pacific salmon 

(Myers et al. 1998). The species historically ranged from the Ventura River in California to 

Point Hope, AK in North America, and in northeastern Asia from Hokkaido, Japan to the Anadyr 

River in Russia (Healey 1991). Additionally, chinook salmon have been reported in the 

Mackenzie River area of Northern Canada (McPhail and Lindsey 1970). Of the Pacific salmon, 

chinook salmon exhibit arguably the most diverse and complex life history strategies Healey 

(1986) described 16 age categories for chinook salmon, seven total ages with three possible 

freshwater ages. This level of complexity is roughly comparable to sockeye salmon (O. nerka), 

although sockeye salmon have a more extended freshwater residence period and utilize different 

freshwater habitats (Miller and Brannon 1982, Burgner 1991). Two generalized freshwater lifehistory types were initially described by Gilbert (1912): “stream-type” chinook salmon reside in 

freshwater for a year or more following emergence, whereas “ocean-type” chinook salmon 

migrate to the ocean predominately within their first year. Healey (1983, 1991) has promoted 

the use of broader definitions for “ocean-type” and “stream-type” to describe two distinct races 

of chinook salmon. This racial approach incorporates life history traits, geographic distribution, 

and genetic differentiation and provides a valuable frame of reference for comparisons of 

chinook salmon populations. For this reason, the BRT has adopted the broader “racial” 

definitions of ocean- and stream-type for this review. 

Of the two life history types, ocean-type chinook salmon exhibit the most varied and plastic 

life history trajectories. Ocean-type chinook salmon juveniles emigrate to the ocean as fry, 

subyearling juveniles (during their first spring or fall), or as yearling juveniles (during their 

second spring), depending on environmental conditions. Ocean-type chinook salmon also 

undertake distinct, coastally oriented, ocean migrations. The timing of the return to freshwater 

and spawning is closely related to the ecological characteristics of a population’s spawning 

habitat. Five different run times are expressed by different ocean-type chinook salmon 

populations: spring, summer, fall, late-fall, and winter. In general, early run times (spring and 

summer) are exhibited by populations that use high spring flows to access headwater or interior 

regions. Ocean-type populations within a basin that express different runs times appear to have 

evolved from a common source population. Stream-type populations appear to be nearly 

obligate yearling outmigrants (some 2-year-old smolts have been identified), they undertake 

extensive off-shore ocean migrations, and generally return to freshwater as spring- or summerrun fish. Stream-type populations are found in northern British Columbia and Alaska, and in the 

headwater regions of the Fraser River and Columbia River interior tributaries. 

Prior to development of the ESU policy (Waples 1991), the NMFS recognized Sacramento 

River winter chinook salmon as a “distinct population segment” under the ESA (NMFS 1987). 

Subsequently, in reviewing the biological and ecological information concerning West Coast 

chinook salmon, Biological Review Teams (BRTs) have identified additional ESUs for chinook 

salmon from Washington, Oregon, and California: Snake River fall-run (Waples et al. 1991), 
Draft Report 2/20/2003 

A. CHINOOK 2 

Snake River spring- and summer-run (Matthews and Waples 1991), and Upper Columbia River 

summer- and fall-run chinook salmon (originally designated as the mid-Columbia River 

summer- and fall-run chinook salmon, Waknitz et al. 1995), Puget Sound chinook salmon, 

Washington Coast chinook salmon, Lower Columbia River chinook salmon, Upper Willamette 

River chinook salmon, Middle Columbia River spring-run chinook salmon, Upper Columbia 

River spring-run chinook salmon, Oregon Coast chinook salmon, Upper Klamath and Trinity 

rivers chinook salmon, Central Valley fall and late-fall-run chinook salmon, and Central Valley 

spring-run chinook salmon (Myers et al. 1998), the Southern Oregon and Northern California 

chinook salmon, California Coastal chinook salmon, and Deschutes River (NMFS 1999). 

Of the 17 chinook salmon ESUs identified by the NMFS, eight are not listed under the 

United States ESA, seven are listed as threatened (Snake River spring- and summer-run chinook 

salmon, and Snake River fall-run chinook salmon [Federal Register, Vol. 57, No. 78, April 22, 

1992, p. 14653]; Puget Sound chinook salmon, Lower Columbia River chinook salmon, and 

Upper Willamette River chinook salmon [Federal Register, Vol. 64, No. 56, March 24, 1999, p. 

14308]; Central Valley fall-run, and California Coastal chinook salmon [Federal Register, Vol. 

64, No. 179, September 16, 1999, p. 5039]), and two are listed as endangered (Sacramento River 

winter-run chinook salmon [Federal Register, Vol. 59, No. 2, January 4, 1994, p. 440], and 

Upper Columbia River spring-run chinook salmon [Federal Register, Vol. 64, No. 56, March 24, 

1999, p. 14308]). 

The NMFS convened a BRT to update the status of listed chinook salmon ESUs in 

Washington, Oregon, California, and Idaho. The chinook salmon BRT1

 met in January of 2003 

in Seattle, WA to review updated information on each of the ESUs under consideration. 

 

1

 The Biological Review Team (BRT) for the updated chinook salmon status review included, from the NMFS 

Northwest Fisheries Science Center: Thomas Cooney, Dr. Robert Iwamoto, Dr. Robert Kope, Gene Matthews, Dr. 

Paul McElhaney, Dr. James Myers, Dr. Mary Ruckelshaus, Dr. Thomas Wainwright, Dr. Robin Waples, and Dr. 

John Williams; from the NMFS Southwest Fisheries Science Center: Dr. Peter Adams, Dr. Eric Bjorkstedt, and Dr. 

Steve Lindley; from the NMFS Alaska Fisheries Science Center (Auke Bay Laboratory): Alex Wertheimer; and 

from the USGS Biological Resource Division: Dr. Reginald Reisenbichler. 
Draft Report 2/20/2003 

A. CHINOOK 3 

A.2.1 SNAKE RIVER FALL CHINOOK 

Snake River fall chinook spawn above Lower Granite Dam in the mainstem Snake River 

and in the lower reaches of major tributaries entering below Hells Canyon Dam. Adult fall 

chinook enter the Columbia River in July and August. The Snake River component of the fall 

chinook run migrates past the Lower Snake river mainstem dams in September and October. 

Spawning occurs from October through November. Juveniles emerge from the gravels in March 

and April of the following year. Snake River fall chinook are subyearling migrants, moving 

downstream from natal spawning and early rearing areas from June through early fall. 

Fall chinook returns to the Snake River generally declined through the first half of this 

century (Irving and Bjornn 1981). In spite of the declines, the Snake River basin remained the 

largest single natural production area for fall chinook in the Columbia drainage into the early 

1960s (Fulton 1968). Spawning and rearing habitat for Snake River fall chinook was 

significantly reduced by the construction of a series of Snake River mainstem dams. 

Historically, the primary spawning fall chinook spawning areas were located on the upper 

mainstem Snake River. Currently, natural spawning is limited to the area from the upper end of 

Lower Granite Reservoir to Hells Canyon dam and the lower reaches of the Imnaha , Grande 

Ronde, Clearwater and Tucannon Rivers. 

Adult counts at Snake River dams are an index of the annual return of Snake River fall 

chinook to spawning grounds. Lower Granite Dam is the uppermost of the mainstem Snake 

River dams that allow for passage of anadromous salmonids. Adult traps at Lower Granite Dam 

have allowed for sampling of the adult run as well as for removal of non-local hatchery returns. 

Lyons Ferry Hatchery was established as one of the hatchery programs under the Lower 

Snake Compensation Plan administered through the USFWS. Snake River fall chinook 

production is a major program for Lyons Ferry Hatchery, which is operated by the Washington 

Department of Fish and Wildlife and is located along the Snake mainstem between Little Goose 

Dam and Lower Monumental Dam. WDFW began developing a Snake River fall chinook 

broodstock in the early 1970s through a trapping program at Ice Harbor Dam and Lower Granite 

Dam. The Lyons Ferry facility became operational in the mid-1980s and took over incubation 

and rearing for the Snake River egg bank program. 

A.2.1.1 Previous BRT Conclusions 

Previous chinook status reviews (Myers et al. 1998, Waples et al. 1991) identified several 

concerns regarding Snake River fall chinook status including: steady and severe decline in 

abundance since the early 1970s; loss of the primary spawning and rearing areas upstream of the 

Hells Canyon Dam complex; increase in non-local hatchery contribution to adult escapement 

over Lower Granite Dam, and relatively high aggregate harvest impacts in ocean and in-river 

fisheries. 
Draft Report 2/20/2003 

A. CHINOOK 4 

A.2.1.2 New Data and Updated Analyses 

A major Snake River fall chinook supplementation effort based upon the Lyons Ferry 

Snake River fall chinook broodstock has been implemented in recent years (references??). 

Acclimation facilities adjacent to major natural spawning areas have been used to acclimate 

release groups of yearling smolts. Additional releases of sub-yearlings have been made, 

depending on the availability of sufficient broodstock to maintain the on-station program and the 

off-station yearling releases. Returns in 2000 and 2001 reflect increases in the off-station plants 

in recent years as well as improved survival after release. 

Abundance 

The 1999 NMFS Status Review Update noted increases in the Lower Granite Dam counts 

in the mid-1990s (Figure A.2.1.1), and the upward trend in returns--the 2001 count over Lower 

Granite Dam exceeded 8,700 adult fall chinook--has continued. The 1997 through 2001 

escapements were the highest on record since the count of 1,000 in 1975. Wild chinook returns 

and hatchery returns from increased production in the Lyons Ferry Hatchery Snake River egg 

bank stock have provided the bulk of the increase in returns. Returns classified as natural origin 

exceeded 2,600 in 2001. The 1997-2001 geometric mean natural origin count over Lower 

Granite Dam was 871 fish. The largest increase in fall chinook returns to the Snake River 

spawning area was from the Lyons Ferry Snake River stock component. Returns increased from 

under 200 per year prior to 1998 to over 1,200 and 5,300 adults in 2000 and 2001, respectively. 

The increase includes returns from the on-station release program as well as returns from large 

supplementation releases above Lower Granite Dam. 

Snake Fall Chinook

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

1970 1975 1980 1985 1990 1995 2000

Year

Abundance

TLC NatOrigSpawners

Figure A.2.1.1. Estimated spawning escapement of Lower Granite Dam. 
Draft Report 2/20/2003 

A. CHINOOK 5 

Snake River Fall Chinook

0.1

1.0

10.0

100.0

1970 1975 1980 1985 1990 1995 2000

Brood Year

Return (Esc) /Spawner 

(Esc)

All Spawners Natural Spawners

Productivity 

Both the long-term and short-term trends in natural returns are positive (1.013, 1.188). The 

short-term (1990-2001) estimates of the median population growth rate λ are 0.98 with a 

hatchery spawning effectiveness of 1.0 (equivalent to that of wild spawners) and 1.137 with a 

hatchery spawning effectiveness of 0. The estimated long-term growth rate for the Snake River 

fall chinook population is strongly influenced by the hatchery effectiveness assumption. If 

hatchery spawners have been equally as effective as natural-origin spawners in contributing to 

brood year returns, the long-term λ estimate is 0.899 and the associated probability that λ is less 

than 1.0 is estimated as 98.7%. If hatchery returns over Lower Granite Dam are not contributing 

at all to natural production, the long-term estimate of λ is 1.024. The associated probability that 

λ is greater than 1.0 is 25.7%, under the assumption that hatchery effectiveness is 0. 

Broodyear return-per-spawner (r/s) estimates were low for three or more consecutive years 

in the mid-1980s and the early 1990s (Figure A.2.1.2). The large increase in natural abundance 

in 2000 and 2001 is reflected in the 1996 and 1997 return-per-spawner estimates (1997 r/s based 

on 4-year-old component only). 

Harvest impacts 

Snake River fall chinook are subject to harvest in a wide range of fisheries due to their 

patterns of ocean distribution and the timing of their spawning run up the Columbia River. 

Coded-wire tag studies using Lyons Ferry Hatchery fish of Snake River origin indicate that 

Snake River fall chinook have a broad distribution. Recoveries of Snake River tagged fish have 

been reported from coastal fisheries from California, Oregon, Washington, British Columbia and 

Southeast Alaska. The timing of the return and upriver spawning migration of Snake River fall 

Figure A.2.1.2. Return/spawner escapements for Snake River fall-run chinook. 
Draft Report 2/20/2003 

A. CHINOOK 6 

Figure A.2.1.3. Aggregate (ocean and in-river fisheries) exploitation rate index for Snake 

River fall chinook. 

Snake River Fall Chinook

0

0.2

0.4

0.6

0.8

1

1970 1975 1980 1985 1990 1995 2000 2005

Run Year

Exploitation Rate Index

chinook overlaps with the Hanford Reach up-river bright returns as well as with several large 

hatchery runs returning to lower river release areas or to the major hatcheries adjacent to the 

lower mainstem Columbia River. 

Harvest impacts on Snake River fall chinook declined after listing and have remained 

relatively constant in recent years (Figure A.2.1.3). The decline and subsequent listing of Snake 

River fall chinook prompted major restrictions on U. S. fisheries impacting this stock. In-river 

gillnet and sport fisheries are ‘shaped’ in time and space to maximize the catch of harvestable 

hatchery and natural (Hanford Reach) stocks while minimizing impacts on the intermingled 

Snake River fall chinook. Reductions in ocean fishery impacts on Snake River fall chinook 

resulted from management measures in ocean fisheries that were designed to protect weakened 

or declining stocks specific to each set of fisheries. 

Mainstem hydropower impacts 

Migration conditions for subyearling chinook migrants from the Snake River have 

generally improved since the early 1990s (FCRPS 2000 Biological Opinion). The lack of 

baseline data prior to the mid-1990s precludes quantifying the changes. 

Habitat 

There have been no major changes in available habitat for Snake River Fall chinook since 

the previous status review.

A.2.1.5 New Hatchery/ESU Information 

Hatchery/natural composition 
Draft Report 2/20/2003 

A. CHINOOK 7 

The composition of the run at Lower Granite is determined by sampling marked returns. 

Since the early 1980s, the run has consisted of three major components: unmarked returns of 

natural origin, marked returns from the Lyons Ferry Hatchery program, and strays from hatchery 

programs outside of the mainstem Snake River. While all three components of the run have 

increased in recent years, returns of Snake River origin have increased disproportionately to 

outside hatchery strays. Prior to the 1998/99 status reviews, the five-year average contribution of 

outside stocks to the escapement over Lower Granite Dam exceeded 26.2%. The most recent 

five-year average (1997-2001) was 12.4%, with the contribution in 2001 being just over 8%. 

The drop in relative contribution by outside stocks reflects the disproportionate increase in 

returns of the Lyons Ferry component, the systematic removal of marked hatchery fish at the 

Lower Granite trap, and modifications to the Umatilla program to increase homing of fall 

chinook release groups intended to return to the Umatilla River. 

Categorizations of Snake River hatchery stocks (SSHAG 2003) can be found in Appendix 

A.5.1. 
Draft Report 2/20/2003 

A. CHINOOK 8 

A.2.2 SNAKE RIVER SPRING/SUMMER CHINOOK 

Spring and summer chinook salmon runs returning to the major tributaries of the Snake 

River were classified as an Evolutionarily Significant Unit (ESU) by NMFS (Matthews and 

Waples 1991). This ESU includes production areas that are characterized by spring-timed 

returns, summer-timed returns, and combinations from the two adult timing patterns. Runs 

classified as spring chinook are counted at Bonneville Dam beginning in early March and ending 

the first week of June; runs classified as summer chinook return to the Columbia River from June 

through August. Returning fish hold in deep mainstem and tributary pools until late summer, 

when they emigrate up into tributary areas and spawn. In general, spring type chinook tend to 

spawn in higher elevation reaches of major Snake River tributaries in mid- through late August, 

and summer run Snake River chinook spawn approximately 1 month later than spring-run fish. 

Many of the Snake River tributaries used by spring and summer chinook runs exhibit two 

major features: extensive meanders through high elevation meadowlands and relatively steep 

lower sections joining the drainages to the mainstem Salmon (Matthews and Waples 1991). The 

combination of relatively high summer temperatures and the upland meadow habitat creates the 

potential for high juvenile salmonid productivity. Historically, the Salmon River system may 

have supported more than 40% of the total return of spring and summer chinook to the Columbia 

system (e.g., Fulton 1968) 

The Snake River spring/summer chinook ESU includes current runs to the Tucannon River, 

the Grand Ronde River system, the Imnaha River and the Salmon River (Matthews and Waples 

1991). The Salmon River system contains a range of habitats used by spring/summer chinook. 

The South Fork and Middle Fork tributaries to the Salmon currently support the bulk of natural 

production in the drainage. Two large tributaries entering above the confluence of the Middle 

Fork, the Lemhi and Pahimeroi Rivers, both drain broad alluvial valleys and are believed to have 

supported substantial, relatively productive anadromous fish runs. Returns into the upper 

Salmon River tributaries have re-established following the opening of passage around Sunbeam 

Dam on the mainstem Salmon River downstream of Stanley, ID. Sunbeam Dam was completed 

around 1910 as a power source for mining activities in the region. The dam was impassable to 

anadromous fish until the 1930s. 

Current runs returning to the Clearwater River drainages were specifically not included in 

the Snake River spring/summer chinook ESU. Lewiston Dam in the lower mainstem of the 

Clearwater River was constructed in 1927 and functioned as an anadromous block until the early 

1940s (Matthews and Waples 1991). Spring and summer chinook runs into the Clearwater 

system were reintroduced via hatchery outplants beginning in the late 1940s. As a result, 

Matthews and Waples (1991) concluded that “...the massive outplantings of nonindigenous 

stocks presumably substantially altered, if not eliminated, the original gene pool.” 

Spring and summer chinook from the Snake River basin exhibit stream type life history 

characteristics (Healey 1983). Eggs are deposited in late summer and early fall, incubate over 

the following winter and hatch in late winter/early spring of the following year. Juveniles rear 

through the summer, overwinter and migrate to sea in the spring of their second year of life. 

Depending on the tributary and the specific habitat conditions, juveniles may migrate extensively 

from natal reaches into alternative summer rearing and/or overwintering areas. Snake River 
Draft Report 2/20/2003 

A. CHINOOK 9 

spring/summer chinook return from the ocean to spawn primarily as 4 and 5 year old fish, after 2 

to 3 years in the ocean. A small fraction of the fish return as 3-year-old ‘jacks’, heavily 

predominated by males. 

A.2.2.1 Previous BRT Conclusions

The 1991 ESA status review (Mathews and Waples, 1991) of the Snake River 

spring/summer chinook ESU concluded that the ESU was at risk based on a set of key factors. 

Aggregate abundance of naturally produced Snake River spring/summer chinook runs had 

dropped to a small fraction of historical levels. Short-term projections (including jack counts, 

habitat/flow conditions in the brood years producing the next generation of returns) were for a 

continued downward trend in abundance. Risk modeling indicated that if the historical trend in 

abundance continued, the ESU as a whole was at risk of extinction within 100 years. The review 

identified related concerns at the population level within the ESU. Given the large number of 

potential production areas in the Snake basin and the low levels of annual abundance, risks to 

individual subpopulations may be greater than the extinction risk for the ESU as a whole. The 

1998 chinook status review (Myers et al. 1998) summarized and updated these concerns. Both 

short and long-term abundance trends had continued downward. The report identified 

continuing disruption due to the impact of mainstem hydroelectric development including altered 

flow regimes and impacts on estuarine habitats. The 1998 review also identified regional habitat 

degradation and risks associated with the use of outside hatchery stocks in particular areas—

specifically including major sections of the Grande Ronde River basin. 

A.2.2.2 New Data and Analyses 

Abundance 

Direct estimates of annual runs of historical spring/summer chinook to the Snake River are 

not available. Chapman (1986) estimated that the Columbia River produced 2.5 million to 3.0 

million spring and summer chinook per year in the late 1800s. Total spring and summer chinook 

production from the Snake Basin contributed a substantial proportion of those returns; the total 

annual production of Snake River spring and summer chinook may have been in excess of 1.5 

million adult returns per year (Matthews and Waples 1991). Returns to Snake River tributaries 

had dropped to roughly 100,000 adults per year by the late 1960s (Fulton 1968). Increasing 

hatchery production contributed to subsequent years returns, masking a continued decline in 

natural production. 

Aggregate returns of spring-run chinook (as measured at Lower Granite Dam) showed a 

large increase over recent year abundances (Figure A.2.2.1). The 1997-2001 geometric mean 

return of natural-origin chinook exceeded 3,700. The increase was largely driven by the 2001 

return—estimated to have exceeded 17,000 naturally produced spring chinook—however, a large 

proportion of the run in 2001 was estimated to be of hatchery origin (98.4%). The summer run 

over Lower Granite Dam has increased as well (Figure A.2.2.2). The 1997-2001 geometric 

mean total return was slightly more than 6,000. The geometric mean return for the broodyears 

for the recent returns (1987-96) was 3,076 (Note: does not address hatchery/wild breakdowns of 

the aggregate run). 

 
Draft Report 2/20/2003 

A. CHINOOK 10 

Returns in other production areas are shown in Figures A.2.2.3-A.2.2.16. The lowest fiveyear geometric mean returns for almost all of the individual Snake River spring/summer chinook 

production areas were in the 1990s. Sulphur Creek and Poverty Flats production areas had low 

five-year geometric mean returns in the early 1980s. Many, but not all, production areas had 

large increases in return year 2001. 

Productivity 

Long-term trend and long-term λ estimates were below 1 for all natural production data 

sets, reflecting the large declines since the 1960s. Short-term trends and λ estimates were 

generally positive with relatively large confidence intervals (Figure A.2.2.17). Grande Ronde 

and Imnaha data sets had the highest short-term growth rate estimates. Tucannon River, Poverty 

Flat (did not have 2000 and 2001 included) and Sulphur Creek index areas had the lowest shortterm λ estimates in the series. Patterns in returns per spawners for stocks with complete age 

information (e.g. Minam River) show a series of extremely low return rates in the 1990s 

followed by increases in the 1995-97 brood years (Figure A.2.2.18). 

Hydropower impacts 

Snake River spring/summer chinook must migrate past a series of mainstem Snake and 

Columbia River hydroelectric dams on their migrations to and from the ocean. The Tucannon 

River population must migrate through six dams; all other major Snake River drainages 

supporting spring/summer chinook production are above eight dams. Earlier status reviews 

concluded that mainstem Columbia and Snake River hydroelectric projects have resulted in a 

major disruption of migration corridors and affected flow regimes and estuarine habitat. 

Harvest 

Harvest impacts on Snake River spring chinook are generally low. Ocean harvest rates are 

also low. Historical harvest estimates reflect the impact of mainstem and tributary in-river 

fisheries. In response to initial declines in returns, in-river harvests of both spring and summer 

chinook were restricted beginning in the early 1970s. Fishery impacts were further reduced 

following listing in 1991, with lower harvest rates from 1991-1999. In response to the large 

increase in returns of spring chinook runs, additional impacts were allowed beginning in 2000. 

The management agreement providing for increased impacts as a function of abundance also 

calls for additional reductions if and when runs drop back down below prescribed thresholds.
Draft Report 2/20/2003 

A. CHINOOK 11 

Habitat 

Tributary habitat conditions vary widely among the various drainages of the Snake River 

basin. There is habitat degradation in many areas of the basin reflecting the impacts of forest, 

grazing and mining practices. Impacts relative to anadromous fish include lack of pools, 

increased water temperatures, low flows, poor overwintering conditions, and high sediment 

loads. Substantial portions of the Salmon River drainage, particularly in the Middle Fork, are 

protected in wilderness areas. 

A.2.2.5 New Hatchery/ESU Information 

Hatchery production 

Spring and summer chinook are produced from a number of artificial production facilities 

in the Snake River Basin. Much of the production was initiated under the Lower Snake River 

Compensation Plan. Lyons Ferry Hatchery serves as a rearing station for Tucannon spring 

chinook broodstock. Rapid River Hatchery and McCall Hatchery provide rearing support for a 

regionally derived summer chinook broodstock released into lower Salmon River areas. Two 

major hatchery programs have operated in the upper Salmon basin—the Pahsimeroi and 

Sawtooth facilities. Since the mid-1990s, small-scale natural stock supplementation studies and 

captive breeding efforts have been initiated in the Snake River basin. 

Historically, releases from broodstock originating outside of the basin have constituted a 

relatively small fraction of the total release into the basin. The 1998 chinook status review 

(Myers et al. 1998) identified concerns regarding the use of the Rapid River Hatchery stock 

reared at Lookingglass Hatchery in the Grande Ronde basin. The Rapid River stock was 

originally developed from broodstock collected from the spring chinook returns to historical 

production areas above the Hells Canyon complex. 

Use of the Rapid River stock in Grande Ronde drainage hatchery programs has been 

actively phased out since the early 1990s. In addition, a substantial proportion of marked returns 

of Rapid River stock released in the Grande Ronde have been intercepted and removed at the 

Lower Granite Dam ladder and at some tributary level weirs. Carcass survey data indicate 

significant declines in hatchery contributions to natural spawning in areas previously subject to 

Rapid River stock strays. 

Concerns for the high incidence of BKD disease in Snake Basin hatchery facilities were 

also identified (Myers et al. 1998). 

Categorization for Snake River spring/summer chinook hatchery stocks (SSHAG 2003) can 

be found in Appendix A.5.1. 
Draft Report 2/20/2003 

A. CHINOOK 12 

Wenaha R Spring Chinoo

0

500

1000150020002500

1960 1965 1970 1975 1980 

Abundance

Estimated Total Spawners 

Snake R Spring

0

20000400006000080000

100000120000140000160000

1975 1980 1985 1990 1995 2000 2005

Abundance

Total Escapement over LGR Natural Origin 

Snake R Summer Chinook

0

5000

10000150002000025000

1975 1980 1985 1990 

Abundance

Total Escapement over LGR 

T u c a n n o n R S p rin g C h in o o k

0

200400600800

10001200

1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Abundance

E s tim a te d T o ta l E s c a p e m e n t N a tO rig S p a w n e rs

Figure A.2.2.1. Snake River spring chinook spawning escapement. Figure A.2.2.2. Snake River summer chino

Figure A.2.2.4. Wenaha River spring chino

Figure A.2.2.3. Tucannon River spring chinook spawning escapement. 
Draft Report 2/20/2003 

A. CHINOOK 13 

Im n a h a R

0

500

1000150020002500300035004000

1950 1960 1970 1980 

Abundance

E s t. T o ta l S p a w n e rs 

Minam R

0

100200300400500600700800

1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Abundance

Estimated Total Spawners NatOrigSpawners

Lostine Spring Chino

0

20406080

100120140160

1960 1965 1970 1975 1980 198

Count

Total Counts 

Upper Grande Ronde Spring Chinook

0

50

100150200250300350

1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Redd Count

Natural Origin Redd Count

Figure A.2.2.5. Minam River chinook spawning escapements. Figure A.2.2.6. Lostine River spring ch

Figure A.2.2.7. Upper Grande Ronde River spring chinook redd counts. Figure A.2.2.8. Imnaha River chinook spaw
Draft Report 2/20/2003 

A. CHINOOK 14 

Johnson Cr

0

200400600800

10001200

1950 1955 1960 1965 1970 1975 1980 19

Abundance

Estimated Total Spawners N

Sulphur Cr Spring Chinook

0

100200300400500600700800900

1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Abundance

Estimated Total Spawners NatOrigSpawners

B e a r V a lle y/E lk C r

0

500

1000150020002500

1960 1965 1970 1975 1980 1985 

Abundance

T o ta l E s tim a te d E s c a p e m e n t 

Poverty Flat

0

500

1000150020002500300035004000

1950 1960 1970 1980 1990 2000 2010

Abundance

Estimated Total Spawners NatOrigSpawners

Figure A.2.2.9. Poverty Flat chinook spawning escapement. Figure A.2.2.10. Johnson Creek chinoo

Figure A.2.2.11. Sulphur Creek spring chinook spawning escapement. Figure A.2.2.12. Bear Valley/Elk Creek 
Draft Report 2/20/2003 

A. CHINOOK 15 

Marsh Cr

0

200400600800

100012001400

1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Abundance

Total Estimated Escapement NatOrigSpawners

Lemhi RC

0

200400600800

100012001400160018002000

1950 1955 1960 1965 1970 1975 1980 

Redds

Figure A.2.2.13. Marsh Creek chinook spawning escapement. Figure A.2.2.14. Lemhi redd counts.Figure A.2.2.15. Upper Vallry Creek spring chinook redd counts. Figure A.2.2.16. East Fork Salmon sum

Upper Valley Cr Spring Chinook

0

50

100150200250300350

1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

Redd Count

East Fk Salmon Summer C

05

1015202530354045

1950 1955 1960 1965 1970 1975 1980 

Redds per Mile
Draft Report 2/20/2003 

A. CHINOOK 16 

Short - term Trends

1990-2001

0.00.10.20.30.40.50.60.70.80.91.01.11.21.31.41.51.61.71.8

Tucannon

Lostine

Upper

Imnaha

Johnson

Camas

Marsh

East Fk

Snake River Spring Chinook

Annual Rate of Change

Minam River

0.01

0.1

1

10

100

1960 1965 1970 1975 1980 19

Brood Year

Return per Spawner

Figure A.2.2.18. Short-term trends of Snake River 

spring/summer production areas. 

Figure A.2.2.19. Snake River spring/summer c
Draft Report 2/20/2003 

A. CHINOOK 17 

A.2.3 UPPER COLUMBIA RIVER SPRING-RUN CHINOOK

There are no estimates of historical abundance specific to this ESU prior to the 1930s. The 

drainages supporting this ESU are all above Rock Island Dam on the upper Columbia River. 

Rock Island Dam is the oldest major hydroelectric project on the Columbia River; it began 

operations in 1933. Counts of returning chinook have been made since the 1930s. Annual 

estimates of the aggregate return of spring chinook to the upper Columbia are derived from the 

dam counts based on the nadir between spring and summer return peaks. Spring chinook salmon 

currently spawn in three major drainages above Rock Island Dam--Wenatchee, Methow and 

Entiat Rivers. Historically, spring chinook may have also used portions of the Okanogan River. 

Grand Coulee Dam, completed in 1938, formed an impassable block to the upstream 

migration of anadromous fish. Chief Joseph Dam was constructed on the mainstem Columbia 

River downstream from Grand Coulee Dam and is also an anadromous block. There are no 

specific estimates of historical production of spring chinook from mainstem tributaries above 

Grand Coulee Dam. Habitat typical of that used by spring chinook salmon in accessible portions 

of the Columbia basin is found in the middle/upper reaches of mainstem tributaries above Grand 

Coulee Dam. It is likely that the historical range of this ESU included these areas. 

Artificial production efforts in the area occupied by the Upper Columbia spring chinook 

ESU extend back to the 1890s. Hatchery efforts were initiated in the Wenatchee and Methow 

systems to augment catches in response to declining natural production (e.g., Craig and Soumela 

1941). While there are no direct estimates of adult production from early efforts, it is likely 

contributions were small. 

In the late 1930s, the Grand Coulee Fish Maintenance Program (GCFMP) was initiated to 

address the fact that the completion of the Grand Coulee dam cut off anadromous access above 

site of the dam. Returning salmonids, including spring chinook, were trapped at Rock Island 

Dam and either transplanted as adults or released as juveniles into selected production areas 

within the accessible drainages below Grand Coulee Dam. Nason Creek in the Wenatchee 

system was a primary adult transplantation area in this effort. The program was conducted 

annually from 1938 until the mid-1940s. 

A.2.3.1 Previous BRT Conclusions 

Previous BRT Review 

The Upper Columbia spring chinook ESU was reviewed by the BRT in late 1998 (BRT 

1998b). “The BRT was mostly concerned about risks falling under the abundance/distribution 

and trends/productivity risk categories for the ESU...average recent escapements to the ESU has 

been less than 5,000 hatchery plus wild chinook salmon, and individual populations all consist of 

less than 100 fish. The BRT was concerned that at these population sizes, negative effects of 

demographic and genetic stochastic processes are likely to occur. Furthermore, both long- and 

short-term trends in abundance are declining, many strongly so.” The BRT noted that the 

implemetation of emergency natural broodstocking and captive broodstocking efforts for the 

ESU “...indicate(s) the severity of the population declines to critically small sizes.” The BRT 
Draft Report 2/20/2003 

A. CHINOOK 18 

recognized that “(h)abitat degradation, blockages and hydrosystem passage mortality all have 

contributed to the significant declines in this ESU.” 

A.2.3.2 New Data and Updated Analyses 

WDFW, the Yakima Tribe and the Fish and Wildlife Service conduct annual redd count 

surveys in nine selected production areas within the geographical area encompassed by this ESU 

(Mosey and Murphy 2002, Hubble and Crampton 2000, Carie 2000). Prior to 1987, redd count 

estimates were single-survey peak counts. From 1987 on, annual redd counts are generated from 

a series of on-the-ground counts and represent the total number of redds constructed in any 

particular year. The agencies use annual dam counts from the mainstem Mid-Columbia dams as 

the basis for expanding redd counts to estimates of total spring chinook returns. Returns to 

hatchery facilities are subtracted from the dam counts prior to the expansion. Updated returns 

are summarized in Table A.2.3.1 and in Figures (A.2.3.1-A.2.3.6). 

An initial set of population definitions for Upper Columbia spring chinook ESU along with 

basic criteria for evaluating the status of each population were developed using the Viable 

Salmonid Population (VSP) guidelines described in McElhany et al. (2000). The definitions and 

criteria are described in Ford et al. (2000) and have been used in the development and review of 

Mid-Columbia PUD plans and the FCRPS Biological Opinion. The interim definitions and 

criteria are being reviewed as recommendations by the Interior Columbia Technical Recovery 

Team. Briefly, the joint technical team recommended that the Wenatchee River, the Entiat River 

and the Methow River be considered as separate populations within the Upper Columbia 

Steelhead ESU. The historical status of spring chinook production in the Okanogan River is 

uncertain. The committee deferred a decision on the Okanogan to the Technical Recovery Team. 

Abundance, productivity and spatial structure criteria for each of the populations in the ESU 

were developed and are described in Ford et al. (2001). 

A.2.3.3 New Hatchery/ESU Information 

Three national fish hatcheries operated by the U. S. Fish and Wildlife Service are located 

within the geographic area associated with this ESU. These hatchery programs were established 

as mitigation programs. Leavenworth National Fish Hatchery, located on Icicle Creek in the 

Wenatchee River system, has released chinook salmon since 1940. Entiat National Fish 

Hatchery is located on the Entiat River, approximately 10 km upstream of the confluence with 

the Columbia River mainstem. Spring chinook have been released from this facility since 1974. 

Winthrop National Fish Hatchery is on the Methow River mainstem, approximately 72 km 

upstream of the confluence with the Columbia River. Spring chinook were released from 1941-

1961, and from 1974 to the present. Initial spring chinook releases from these facilities were for 

the GCFMP project. Leavenworth Hatchery returns served as the principle stock source for all 

three facilities until recently. Production was augmented with eggs transferred into the programs 

from facilities outside of the ESU, primarily Carson Hatchery. Broodstocking for each hatchery 

program has been switched to emphasize locally adapted broodstocks. Carcass surveys and 

broodstocking efforts in the upstream natural spawning areas of the Wenatchee River and the 

Entiat River support the assumption that the stray rate from the downstream hatchery facilities is 

low—on the order of 1%-5%. Significantly higher contribution rates have been observed in 

mainstem Methow natural spawning areas, possibly due to the close proximity of the hatchery.
Draft Report 2/20/2003 

A. CHINOOK 19 

Additional spring chinook hatchery production efforts were initiated in the 1980s as 

mitigation for smolt losses at the five mainstem mid-Columbia River projects operated by public 

utility districts. This program is aimed at directly supplementing targeted natural production 

areas in the Wenatchee and Methow River systems. In the Wenatchee River drainage, this 

program has targeted the Chiwawa River production area. Broodstock are collected at a weir 

located just upstream of the mouth of the Chiwawa River. Release groups are returned to this 

site for final acclimation and release. In the Methow River, the program is operated in 

conjunction with Winthrop Hatchery. Juveniles are reared at the Winthrop Facility and moved to 

acclimation sites on the Twisp, Chewuch, and Methow mainstem shortly before the spring 

migration period. The Methow program was initiated with Winthrop Hatchery stock and is 

being converted to local broodstock. These supplementation programs have had two major 

impacts on natural production areas. Returns to natural spawning areas have included increasing 

numbers of supplementation fish in recent years, especially in the Methow mainstem spawning 

areas adjacent to the hatchery. In addition, following the major drop in returns in the mid-1990s, 

a major portion of the natural return was taken as broodstock for supplementation. In 2 years 

(1995 and 1997) virtually the entire adult run to Wells Dam were taken. 

The WDFW SASSI report identified nine stocks of spring chinook within the upper 

Columbia spring chinook ESU. Ford et al. (2001) describes the results of applying the 

population definition and criteria provided in McElhany et al. (2000) to current upper Columbia 

spring chinook production. The conclusions of the effort were that “...there are (or historically 

were) three or four independent viable populations of spring chinook salmon in the upper 

Columbia River basin, inhabiting the Wenatchee, Entiat, Methow and (possibly) the Okanogan 

River basins. There appears to be considerable population substructure within the Wenatchee 

and Methow basins, however, this substructure should be considered when evaluating recovery 

goals and management actions.”2

 

Hatchery impacts 

Hatchery impacts vary among the production areas. Large on-station production programs 

in the Wenatchee and Entiat River drainages are located in the lower reaches, some distance 

downstream of natural spawning areas. In the Methow River, Winthrop National Fish Hatchery 

is located upstream, adjacent to a portion of the mainstem spawning reach for spring chinook and 

steelhead. Straying of returning hatchery origin adults into the natural production areas is 

thought to be low for the Wenatchee River and Entiat River. In years when the return of 

naturally produced adults is extremely low, the proportion of hatchery adults on the spawning 

grounds can be high, even if the dispersal rate of the returning hatchery fish is low. It is likely 

that returning hatchery fish contribute to spawning in natural production areas in the Methow at a 

higher rate. Carcass sampling data are available for a limited number of year/area combinations 

for the upper Columbia drainages (e.g., WDF 1992). 

 2

Spring chinook spawning in Icicle Creek and the Leavenworth Hatchery are considered an independent, 

hatchery-derived population that is not part of the ESU (NMFS 1999). 
Draft Report 2/20/2003 

A. CHINOOK 20 

Spring chinook returns to the Wenatchee and the Methow River systems have included 

relatively large numbers of supplementation program fish in recent years. The total return to 

natural spawning areas in the Wenatchee River system for 2001 is estimated to be approximately 

4,000-1,200 returning from natural spawning and 2,800 from the hatchery-based 

supplementation program. The return to spawning areas for the Methow in 2001 is estimated at 

well over 9,000. Carcass surveys indicate that returning supplementation adults accounted for 

approximately 80% of the 2001 run to the Methow spawning areas. Supplemenation programs 

have contributed substantially to getting fish on the spawning grounds in recent years. Little 

information is available to assess the long-term impact of high levels of supplementation on 

productivity. Categorization for Upper Columbia River spring chinook hatchery stocks (SSHAG 

2003) can be found in Appendix A.5.1. 

A.2.3.4 Comparison with Previous Data 

All three of the existing upper Columbia River spring chinook populations have exhibited 

similar trends and patterns in abundance over the past 40 years. The 1998 Chinook Status 

Review (Myers et al. 1998) reported that long-term trends in abundance for upper Columbia 

spring chinook populations were generally negative, ranging from -5% to +1%. Analyses of the 

data series, updated to include 1996-2001 returns, indicate that those trends have continued. The 

long-term trend in spawning escapement is downward for all three systems. The Wenatchee 

River spawning escapements have declined an average of 5.6% per year, the Entiat River 

population at an average of 4.8%, and the Methow River population an average rate of 6.3% per 

year since 1958. These rates of decline were calculated from the redd count data series3

. 

Mainstem spring chinook fisheries harvested chinook at rates between 30%-40% per year 

through the early1970s. Harvest was substantially reduced by restricting mainstem commercial 

fisheries and sport harvest in the mid-1970s. The calculated downward trend in abundance for 

the upper Columbia stocks would be higher if the early redd counts had been revised to reflect 

the potential ‘transfer’ from harvest to escapement for the early years in the series. 

In the 1960s and 1970s, spawning escapement estimates were relatively high with 

substantial year-to-year variability. Escapements declined in the early 1980s, then peaked at 

relatively high levels in the mid 1980s. Returns declined sharply in the late 1980s and early 

1990s. Returns between 1990-94 were at the lowest levels observed in the 40-plus years of the 

data sets. The Upper Columbia Biological Requirements Workgroup (Ford et al. 2001) 

recommended interim delisting levels of 3,750, 500, and 2,200 spawners for the populations 

returning to the Wenatchee, Entiat, and Methow drainages, respectively. The most recent 5-year 

geometric mean spawning escapements (1997-2001) were at 8%-15% of these levels. Target 

levels have not been exceeded since 1985 for the Methow run and the early 1970s for the 

Wenatchee and Entiat populations. 

 3

Prior to 1987, annual redd counts were obtained from single surveys and reported as peak counts. From 

1987 on, redd counts were derived from multiple surveys and are reported as annual total counts. An adjustment 

factor of 1.7 was used to expand the pre-1987 redd counts for comparison with the more recent total counts. 

(Beamsesderfer et al. 1997). 
Draft Report 2/20/2003 

A. CHINOOK 21 

Short-term rates for the aggregate population areas reported in the 1998 Status Review 

(Myers et al. 1998) ranged from a -15.3% (Methow R.) to a -37.4% (Wenatchee R.). The 

Escapements from 1996-1999 reflected that downward trend. Escapements increased 

substantially in 2000 and 2001 in all three systems. Returns to the Methow River and the 

Wenatchee River reflected the higher return rate on natural production as well as a large increase 

in contributions from supplementation programs. Short-term trends (1990-2001) in natural 

returns remain negative for all three upper Columbia spring chinook populations. Natural returns 

to the spawning grounds for the Entiat, Methow, and Wenatchee River populations continued 

downward at average rates of 3%, 10%, and 16% respectively. 

Short- and long-term trends in natural returns to the individual subpopulations within the 

Wenatchee and Methow systems were consistent with the aggregate population level trends. 

Long-term and short-term trends for Upper Columbia spring chinook populations are shown in 

Figures A.2.3.7-A.2.3.8. 

McClure et al. (in press) reported standardized quantitative risk assessment results for 152 

listed salmon stocks in the Columbia basin, including representative data sets (1980-2000 return 

years) for upper Columbia spring chinook. Average annual growth rate (λ) for the upper spring 

chinook population was estimated as 0.85, the lowest average reported for any of the Columbia 

River ESUs analyzed in the study. Assuming that population growth rates were to continue at 

the 1980-2000 levels, upper Columbia spring chinook populations are projected to have a very 

high probability of a 90% decline within 50 years (0.87 for the Methow River population, 1.0 for 

the Wenatchee and Entiat runs). 

The major harvest impacts on upper Columbia River spring chinook have been in mainstem 

fisheries below McNary Dam and in sport fisheries in each tributary. There are no specific 

estimates of historical harvest impacts on upper Columbia spring chinook runs. Assuming that 

upper Columbia spring chinook runs were equally available to mainstem commercial fisheries as 

were the runs to other areas of the Snake and Columbia rivers, harvest rates in the lower river 

commercial fisheries were likely on the order of 20%-40% of the in-river run. Lower river 

harvest rates on up-river spring chinook stocks were sharply curtailed beginning in 1980 and 

were again reduced after the listing of Snake River spring/summer chinook in the early 1990s. 

Sport fishery impacts were also curtailed. Harvest impacts are currently being managed under a 

harvest management schedule—harvest rates are curtailed even further if the average return 

drops below a predefined level, increases area allowed at high run sizes. 

Mainstem hydropower impacts 

Upper Columbia spring chinook runs are subject to passage mortalities associated with 

mainstem hydroelectric projects. Production from all of these drainages passes through the four 

lower river federal projects and a varying number of Mid-Columbia River Public Utility District 

projects. The Wenatchee River enters the Columbia River above seven mainstem dams, the 

Entiat above eight dams; the Methow River and Okanogan Rivers above nine dams. Since the 

Early 1990s, the draft Mid-Columbia Habitat Conservation Plan establishes salmonid survival 

objectives for Wells, Rocky Reach, and Rock Island dams. Interim operating guidelines apply to 

Wanapum and Priest Rapids dam. Operational improvements have been made to increase 

outmigrant survival through the mainstem Mid-Columbia Public Utility hydroelectric dams 

(Cooney 2001, FCRPS Biological Opinion 2000). 
Draft Report 2/20/2003 

A. CHINOOK 22 

Each of the upper Columbia River spring chinook areas has a particular set of habitat 

problems. In general, tributary habitat problems affecting this ESU include the effects of 

increasing urbanization on the lower reaches, irrigation/flow diversions in up-river sections of 

the major drainage, and the impacts of grazing on middle reaches. 

Previous assessments of stocks within this ESU have identified several as being at risk or 

of concern. WDF et al. (1993) considered nine stocks within this ESU, of which eight were 

considered to be of native origin and predominately natural production. The status of all nine 

stocks was considered as depressed. 

Nehlsen et al. (1991) listed six additional stocks from the upper Columbia as extinct. All 

of those stocks were associated with drainages entering the Columbia River mainstem above 

Chief Joseph and Grand Coulee Dams. Those projects blocked off access by adult anadromous 

fish to the upper basin. 

Table A.2.3.1. Summary of recent population status information. 

5 Year Geometric 

Mean 

Long-Term Trend Short-Term Trend 

Production Area 

1989-95 1990-2001 1998 

Assessment

1960-2001 1998 

Assessment 

1990-2001

 

Methow River 355 282 

 

-5.4 -9.7 

Methow Mainstem 1.1 -5.9 -15.3 -5.5 

Twisp -4.1 -7.7 -2.1 -12.1 

Chewuch -2.1 -7.2 -22.5 -9.0 

Lost/Early Winters -2.2 -6.8 -16.1 -14.1 

Entiat River 89 65 -18.5 -5.7 -19.4 -6.2 

Wenatchee River 328 273 -11.5 -6.9 -37.4 -7.4 

Chiwawa 

 

-3.1 -5.3 -35.1 -8.4 

Nason Cr. 

 

-4.1 -6.2 -20.9 -6.8 

Upper Wenatchee 

 

-2.1 -5.3 -36.6 -11.7 

White 

 

0.9 -3 -25.0 -8.0 

Little Wenatchee 

 

-0.7 -4.6 -26.5 -16.5 
Draft Report 2/20/2003 

A. CHINOOK 23 

Wenatchee

0

1000

2000

3000

4000

5000

6000

7000

8000

1950 1960 1970 1980 1990 2000 2010

Year

Estimated Spawning Escapement

Total Estimated Spawners NatOrigSpawners

Figure A.2.3.1. Wenatchee Spring chinook: Estimated spawning escapement. Expanded 

from redd counts (Beamesderfer et al. 1997, Cooney 2001). Recent year data from 

Mosey & Murphy (2002). 

Entiat

0

200

400

600

800

1000

1200

1400

1950 1960 1970 1980 1990 2000 2010

Year

Abundance

Total Estimated Spawners NatOrigSpawners

Figure A.2.3.2. Entiat Spring chinook: Estimated spawning escapement. Expanded from redd 

counts (Beamesderfer et al. 1997, Cooney 2001). Recent-year data from Carie (2002). 
Draft Report 2/20/2003 

A. CHINOOK 24 

Methow

0

2000

4000

6000

8000

10000

12000

1950 1960 1970 1980 1990 2000 2010

Year

Abundance

Total Estimated Spawners NatOrigSpawners

Figure A.2.3.3. Methow Spring chinook: Estimated spawning escapement. Expanded from redd 

counts (Beamesderfer et al. 1997, Cooney 2001). Recent year data from Yakima Indian 

Nation Fisheries (J. Hubbell, pers. comm.). 

Wenatchee Spring Chinook

0.01

0.10

1.00

10.00

1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

Brood Year

Return(Spwner)/Spawner

Figure A.2.3.4. Wenatchee Spring chinook Return per spawner by brood year (returns to 

spawning grounds). 
Draft Report 2/20/2003 

A. CHINOOK 25 

Methow Spring Chinook

0.01

0.1

1

10

1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

Brood Year

Return(Spwner)/Spawner

Spawning Escapement Harvest Adj

Figure A.2.3.5. Methow spring chinook return/spawner by brood year (returns to spawning grounds).

E ntiat S pring C hinook

0.1

1

1 0

1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

Brood Year

Return/Spawner

S paw ning E scapement Harvest Adj

Figure A.2.3.6. Entiat spring chinook return/spawner by brood year (returns to spawning grounds).
Draft Report 2/20/2003 

A. CHINOOK 26 

S hort Term Trends

1990-2001

0.7

0.8

0.9

1.0

1.1

1.2

1.3

WEN ww+hENT ww+hMET w

Lambda

Long Term Trends

1960-2001

0.7

0.8

0.9

1.0

1.1

1.2

1.3

WEN ww+hENT ww+hMET w

Lambda

Figure A.2.3.7. Long-term annual growth rates (λ) for upper Columbia Spring chinook populations. 

Figure A.2.3.8. Short-term (1990-2001) annual growth rates (λ) for upper Columbia Spring chinook populations. 
Draft Report 2/20/2003 

A. CHINOOK 27 

A.2.4 PUGET SOUND CHINOOK SALMON 

A.2.4.1 Previous BRT conclusions 

Status and trends 

The BRT concluded in 1999 that the Puget Sound chinook ESU was likely to become 

endangered in the foreseeable future. The estimated total run size of chinook salmon to Puget 

Sound in the early 1990s was 240,000 chinook, down from an estimated 690,000 historic run 

size. The 5-year geometric mean of spawning escapement of natural chinook salmon runs in 

North Puget Sound during the period from 1992-1996 was approximately 13,000. Both longand short-term trends for these runs were negative, with few exceptions. In south Puget Sound, 

spawning escapement of the natural runs averaged 11,000 spawners at the time of the last status 

review update. In this area, both long- and short-term trends were predominantly positive. In 

Hood Canal, spawning populations in six streams were considered a single stock by the comanagers because of extensive transfers of hatchery fish (WDF et al. 1993). Fisheries in the area 

were managed primarily for hatchery production and secondarily for natural escapement; high 

harvest rates directed at hatchery stocks resulted in failure to meet natural escapement goals in 

most years (USFWS 1997a). The 5-year geometric mean natural spawning escapement at the 

time of the last update was 1,100, with negative short- and long-term trends (except in the 

Dosewallips River). The ESU also included the Dungeness and Elwha Rivers, which had natural 

chinook salmon runs as well as hatcheries. The Dungeness River had a run of spring/summerrun chinook salmon with a 5-year geometric mean natural escapement of 105 fish at the time of 

the last status review update. The Elwha River has a 5-year geometric mean escapement of 

1,800 fish during the mid-1990s, which included a large, but unknown fraction of naturally 

spawning hatchery fish. Both the Elwha and Dungeness populations exhibited downward trends 

in abundance in the 1990s. 

Threats 

 Habitat throughout the ESU has been blocked or degraded. In general, upper tributaries 

have been impacted by forest practices and lower tributaries and mainstem rivers have been 

impacted by agriculture and/or urbanization. Diking for flood control, draining and filling of 

freshwater and estuarine wetlands, and sedimentation due to forest practices and urban 

development are cited as problems throughout the ESU (WDF et al. 1993). Blockages by dams, 

water diversions, and shifts in flow regime due to hydroelectric development and flood control 

projects are major habitat problems in several basins. Bishop and Morgan (1996) identified a 

variety of critical habitat issues for streams in the range of this ESU, including changes in flow 

regime (all basins), sedimentation (all basins), high temperatures (Dungeness, Elwha, 

Green/Duwamish, Skagit, Snohomish, and Stillaguamish Rivers), streambed instability (most 

basins), estuarine loss (most basins), loss of large woody debris (Elwha, Snohomish, and White 

Rivers), loss of pool habitat (Nooksack, Snohomish, and Stillaguamish Rivers), and blockage or 

passage problems associated with dams or other structures (Cedar, Elwha, Green/Duwamish, 

Snohomish, and White Rivers). The Puget Sound Salmon Stock Review Group (PFMC 1997a) 

provided an extensive review of habitat conditions for several of the stocks in this ESU. It 
Draft Report 2/20/2003 

A. CHINOOK 28 

concluded that reductions in habitat capacity and quality have contributed to escapement 

problems for Puget Sound chinook, citing evidence of direct losses of tributary and mainstem 

habitat due to dams, and of slough and side-channel habitat due to diking, dredging, and 

hydromodification. It also cited reductions in habitat quality due to land management activities. 

 WDF et al. (1993) classified 11 out of 29 stocks in this ESU as being sustained, in part, 

through artificial propagation. Nearly 2 billion fish have been released into Puget Sound 

tributaries since the 1950s (Myers et al. 1998). The vast majority of these have been derived 

from local returning fall-run adults. Returns to hatcheries have accounted for 57% of the total 

spawning escapement, although the hatchery contribution to spawner escapement is probably 

much higher than that, due to hatchery-derived strays on the spawning grounds. Almost all of 

the releases into this ESU have come from stocks within this ESU, with the majority of within 

ESU transfers coming from the Green River Hatchery or hatchery broodstocks that have been 

derived from Green River stock (Marshall et al. 1995). The electrophoretic similarity between 

Green River fall-run chinook salmon and several other fall-run stocks in Puget Sound (Marshall 

et al. 1995) suggests that there may have been a significant effect from some hatchery 

transplants. Overall, the pervasive use of Green River stock throughout much of the extensive 

hatchery network that exists in this ESU may reduce the genetic diversity and fitness of naturally 

spawning populations. 

 Harvest impacts on Puget Sound chinook salmon stocks were quite high. Ocean 

exploitation rates on natural stocks averaged 56%-59%; total exploitation rates averaged 68%-

83% (1982-89 brood years) (PSC 1994). Total exploitation rates on some stocks have exceeded 

90% (PSC 1994). 

Previous assessments of stocks within this ESU have identified several stocks as being at 

risk or of concern (reviewed in Myers et al. 1998). 

A.2.4.2 New Data 

ESU status at a glance 

Historical peak run size ~690,000 

Historical populations 31 

Extant populations 22 

5-year geometric mean natural 

spawners per population 42 – 7,000 

Long-term λ per population 0.89 – 1.2 (H0); 0.7 – 1.1 (H1) 

Recent λ per population 0.90 – 1.2 (H0); 0.65 – 1.2 (H1)

Listing status Threatened 
Draft Report 2/20/2003 

A. CHINOOK 29 

Table A.2.4.1. Number of populations in the ESU of each life history type. Populations with “some 

current natural production” have some natural origin recruits present but are not necessarily 

considered naturally self-sustaining (“viable”). (Evidence for presumed historical population 

structure for the ESU is summarized in Myers et al. [1998]; and estimates of “viable” populations 

are based on preliminary analyses conducted by the Puget Sound TRT.) 

Life-History Type 

Late run Early run Total 

Historical 17 14 31 

Some current natural 

production 16 6 22 

Currently “viable” 

populations 2-4 0-2 2-6 

ESU structure 

The Puget Sound ESU is comprised of 31 historically quasi-independent populations of 

chinook, 22 of which are believed to be extant currently (PSTRT 2001 and 2002) (Table 

A.2.4.1). The populations that are presumed to be extinct are mostly of early-returning fish, and 

most of these are in the mid- to southern parts of the Puget Sound or in Hood Canal/Strait of 

Juan de Fuca (Table A.2.4.2). The populations in the ESU with the greatest estimated fractions 

of hatchery fish tend to be in the mid- to southern parts of Puget Sound, in Hood Canal, and in 

the Strait of Juan de Fuca (Table A.2.4.3). 
Draft Report 2/20/2003 

A. CHINOOK 30 

Table A.2.4.2. Historical populations of chinook salmon in the Puget Sound ESU. Run-timing types for 

each population and the biogeographic region within which each population occurs also are noted 

(Puget Sound TRT 2001 and 2002). 

Population Status Run-Timing Bio-Geographic 

Region Reference 

North Fork 

Nooksack Extant early Strait of Georgia 

South Fork 

Nooksack Extant early Strait of Georgia 

Nooksack late Extinct late Strait of Georgia PS TRT 2001 

Lower Skagit Extant late Whidbey Basin 

Upper Skagit Extant late Whidbey Basin 

Lower Sauk Extant late Whidbey Basin 

Upper Sauk Extant early Whidbey Basin 

Suiattle Extant early Whidbey Basin 

Upper Cascade Extant early Whidbey Basin 

North Fork 

Stillaguamish Extant late Whidbey Basin 

South Fork 

Stillaguamish Extant late Whidbey Basin 

Stillaguamish early Extinct early Whidbey Basin Nehlsen et al. 1991; 

WDF et al. 1993 

Skykomish Extant late Whidbey Basin 

Snoqualmie Extant late Whidbey Basin 

Snohomish early Extinct early Whidbey Basin Nehlsen et al. 1991; 

WDF et al. 1993 

Cedar Extant late Main Basin/ 

South Basin 

North Lake 

Washington Extant late Main Basin/ South Basin 

Green/Duwamish Extant late Main Basin/ 

South Basin 

Green/Duwamish 

early Extinct early Main Basin/ South Basin 

Nehlsen et al. 1991; 

WDF et al. 1993 

Puyallup Extant late Main Basin/ 

South Basin 

White Extant early Main Basin/ 

South Basin 

Puyallup early Extinct early Main Basin/ 

South Basin 

Nehlsen et al. 1991 

Nisqually Extant late Main Basin/ 

South Basin 

Nisqually early Extinct early Main Basin/ 

South Basin 

Nehlsen et al. 1991; 

ONRC 1995 

Skokomish Extant late Hood Canal 

Skokomish early Extinct early Hood Canal 

Deschamps 1954; 

Nehlsen et al. 1991; 

WDF et al. 1993 

Table A.2.4.2 continued
Draft Report 2/20/2003 

A. CHINOOK 31 

Dosewallips Extant late Hood Canal 

Dosewallips early Extinct early Hood Canal Nehlsen et al. 1991; 

ONRC 1995 

Dungeness Extant late Strait of Juan de 

Fuca 

Elwha Extant late Strait of Juan de 

Fuca 

Elwha early Extinct early Strait of Juan de 

Fuca 

Nehlsen et al. 1991; 

WDF et al. 1993 
Draft Report 2/20/2003 

A. CHINOOK 32 

A.2.4.3. Updated Analyses 

Abundance of natural spawners 

The most recent 5-year geometric mean natural spawner numbers in populations of Puget 

Sound chinook ranges from 42 (in the Dosewallips) to just over 7,000 fish (in the upper Skagit 

population). Most populations contain natural spawners numbering in the hundreds (median 

recent natural escapement = 481); and of the six populations with greater than 1,000 natural 

spawners, only two are thought to have a low fraction of hatchery fish (Table A.2.4.3; Figure 

A.2.4.1). Estimates of the fraction of natural spawners that are of hatchery origin are sparse—

data are available for only seven of the 22 populations in the ESU, and such information is 

available for only the most recent 5 years or so. Estimates of the hatchery fraction of natural 

spawners come from counts of otolith-marked local hatchery fish sampled from carcasses 

(Nooksack River Basin, Snohomish River Basin), adipose fin clip counts from redd count 

surveys (Skagit River Basin), and coded-wire tag sampling (NF Stillaguamish and Green River). 

In general, populations in the Skagit river basin are the only ones with presumed low estimates 

of naturally spawning hatchery fish. The Stillaguamish and Snohomish populations have 

moderate estimates of naturally spawning hatchery fish. Estimates of historical equilibrium 

abundance from predicted pre-European settlement habitat conditions range from 1,700 to 

51,000 potential chinook spawners per population. The historical estimates of spawner capacity 

are several orders of magnitude higher than realized spawner abundances currently observed 

throughout the ESU. 
Draft Report 2/20/2003 

A. CHINOOK 33 

Table A.2.4.3. Abundance of natural spawners, estimates of the fraction of hatchery fish in natural 

escapements, and estimates of historical capacity of Puget Sound streams (Puget Sound TRT, 

unpublished data and Puget Sound co-managers). 

Population 

Geometric 

mean natural 

spawners 

(recent 5 y) 

% hatchery in 

escapement 

(mean, min, 

max) 

Chinook hatcheries 

in basin? 

Hatchery 

fraction 

data? 

EDT 

estimate of 

historical 

capacity3

NF Nooksack 64 19 (3 –57) Kendall (NF; rm 45) yes 26,000 

SF Nooksack 148 25 (0 - 43) Kendall (NF; rm 45) yes 13,000 

Lower Skagit 1,537 0 Marblemount (mouth 

of Cascade)1 none 22,000 

Upper Skagit 7,332 2(0 - 3) Marblemount (mouth 

of Cascade) 1 yes 35,000 

Upper Cascade 268 0 Marblemount (mouth 

of Cascade) 1 none 1,700 

Lower Sauk 480 0 Marblemount (mouth 

of Cascade) 1 none 7,800 

Upper Sauk 298 0 Marblemount (mouth 

of Cascade) 1 none 4,200 

Suiattle 401 0 Marblemount (mouth 

of Cascade) 1 none 830 

NF Stillaguamish 483 27 (0 – 52) Tribal (NF) yes 24,000 

SF Stillaguamish 250 NA Tribal (NF) none 20,000 

Skykomish 1,662 36 (10 - 66) Wallace R. yes 51,000 

Snoqualmie 1,467 21 (2 – 72) Wallace R. yes 33,000 

NL Washington 251 NA Lake Wash, Issaquah, 

UW none NA 

Cedar 244 NA Lake Wash, Issaquah, 

UW none NA 

Green 547 70 (0 -100) Soos, Icy and Keta Cr. yes NA 

White2 735 NA 

White R (rm 23); 

Voights Cr. (Carbon 

R), Diru (rm 5) 

none NA 

Puyallup 2,039 NA Voights Cr. (Carbon 

R), Diru (rm 5) none 33,000 

Nisqually 883 NA Kalama, Clear Cr none 18,000 
Draft Report 2/20/2003 

A. CHINOOK 34 

Table A.2.4.3 continued

Skokomish 1,105 NA George Adams (Purdy 

Cr., lower Skok) none NA 

Dosewallips 42 NA none none 4,700 

Dungeness2 132 NA Dungeness 

(and Hurd Cr) none 8,100 

Elwha 821 NA Tribal (rm 1) and 

State (rm 3.2) none NA 

1

Summer-run chinook hatchery program discontinued; last returns in 1996. 

2

Captive broodstock program in place. 

3 Estimates of historical habitat capacity based on an EDT analysis conducted by the co-managers in Puget 

Sound (PSTRT 2002). 
Draft Report 2/20/2003 

A. CHINOOK 35 

Trends in natural spawners 

Long-term trends in abundance and median population growth rates for naturally spawning 

populations of chinook in Puget Sound both indicate that approximately half of the populations 

are declining and half are increasing in abundance over the length of available time series (Table 

A.2.4.4; Fig. A.2.4.2). Long-term population growth rates (λ) were calculated under two 

assumptions about the reproductive success of naturally spawning hatchery fish: the reproductive 

success was 0 (i.e., HO), or the reproductive success was equivalent to that of wild fish (i.e., H1). 

Calculations of long-term λ for Puget Sound chinook populations were not greatly affected by 

the assumptions about the reproductive success of hatchery fish because of the dearth of 

information on the fraction of hatchery fish in time series (Table A.2.4.4). The median over all 

populations of long-term population growth rates is λ = 1.001 (regardless of assumptions about 

hatchery fish reproduction), indicating that most populations are just replacing themselves. 

Similarly, the probability that the long-term trend (median across populations = 0.8, mean = 0.6) 

or long-term λ (median across populations = 0.4, mean = 0.52-0.58) are less than one indicate 

that on average, populations have declining trends and stable growth rates (Table A.2.4.5). In 

those cases where hatchery information is available (e.g., North Fork Nooksack, Green River), 

the effect of the reproductive success of hatchery fish assumption on estimates of λ is dramatic. 

The most extreme declines in natural spawning abundance have occurred in the North Fork 

Nooksack, North Fork Stillaguamish, Green, and Elwha populations over the long term. All of 

those populations likely have a moderate to high fraction of naturally spawning hatchery fish. 

Those populations with the greatest long-term population growth rates are the Upper Cascade, 

White, Puyallup, and Dosewallips; all of which likely have a high fraction of naturally spawning 

hatchery fish except for the Upper Cascade. 

The number of populations with declining abundance over the short term is similar to longterm trends--8 of 22 (short-term trend) and 11-12 of 22 (short-term λ) populations in the ESU are 

declining. The median short-term λ over all populations is similar to long-term estimates of λ, 

except when the reproductive success of hatchery fish is assumed to be 1 (median short term λH0 = 1.003; median short-term λ−Η1 = 0.995). The probability that the short-term trend 

(median across populations = 0.4, mean = 0.5) or short-term λ (median across populations = 0.5, 

mean = 0.48-0.57) are less than one indicate that on average, populations have stable to slightly 

increasing trends and mixed positive and negative growth rates (Table A.2.4.5). The most 

extreme short-term declines in natural spawner abundance have occurred in the North Fork 

Nooksack, Green River, and Elwha populations. All of these populations are likely to have high 

fractions of hatchery fish—the Green River population has one of the highest estimated fractions 

of hatchery fish spawning naturally in the Puget Sound area. The populations with the most 

positive short-term trends and population growth rates are the Upper Skagit, White River, and 

Dosewallips populations. Of this group, only the Upper Skagit population is thought to have a 

low fraction of naturally spawning hatchery fish. 
Draft Report 2/20/2003 

A. CHINOOK 36 Table A.2.4.4. Estimates of long- and short-term trend, median population growth rate (

λ), and their 95% confidence interv

Puget Sound chinook populations (data are from the Puget Sound TRT, unpublished data). “H0” and “H1” indicat

calculated assuming the reproductive success of naturally spawning hatchery fish is 0 or equivalent to that of wild 

Population Data years LT Trend (CI) LT 

λ (H0) (CI) LT λ (Η1) (CI) ST Trend (CI) ST 

λ (H

NF Nooksack 1984-2001 0.95 (0.852-1.058) 0.942 (0.804-1.103) 0.804 (0.651-0.9) 1.003 (0.791-1.271) 0.8

(0.766

SF Nooksack 1984-2001 0.964 (0.913-1.018) 0.972 (0.83-1.138) 0.922 (0.784-1.084) 1.016 (0.918-1.124) 0.9

(0.853

Lower Skagit 1952-2001 0.983 (0.972-0.994) 1.005 (0.921-1.096) 1.004 (0.921-1.102) 1.016 (0.893-1.156) 1.0

(0.942

Upper Skagit 1952-2001 0.998 (0.991-1.006) 1.005 (0.921-1.097) 1.001 (0.922-1.231) 1.041 (0.951-1.14) 1.0

(0.965

Upper Cascade 1984-2001 1.038 (0.992-1.086) 1.036 (0.885-1.213) 1.035 (0.89-1.093) 1.051 (0.959-1.151) 1.0

(0.911

Lower Sauk 1952-2001 0.991 (0.978-1.005) 1.001 (0.918-1.092) 1.001 (0.914-1.06) 1.009 (0.869-1.171) 0.9

(0.908

Upper Sauk 1984-2001 0.969 (0.955-0.984) 0.975 (0.894-1.064) 0.975 (0.886-1.094) 0.95 (0.861-1.047) 0.9

(0.857

Suiattle 1952-2001 0.986 (0.976-0.995) 1 (0.915-1.092) 1 (0.915-1.033) 1.011 (0.925-1.106) 1.0

(0.92

NF Stillaguamish 1974-2001 0.969 (0.951-0.988) 0.962 (0.852-1.085) 0.923 (0.807-1.127) 0.985 (0.928-1.046) 0.

(0.869

SF Stillaguamish 1974-2001 1.018 (0.999-1.038) 1.001 (0.887-1.129) 1.001 (0.879-0.999) 0.984 (0.963-1.006) 0.

(0.89

Skykomish 1965-2001 0.984 (0.973-0.996) 0.987 (0.89-1.094) 0.911 (0.809-1.109) 0.995 (0.945-1.047) 0.9

(0.933

Snoqualmie 1965-2001 1.017 (0.998-1.037) 1.028 (0.927-1.139) 1.001 (0.898-1.196) 1.08 (0.925-1.261) 1.0

(0.924

NL Washington 1983-2001 0.964 (0.901-1.03) 0.995 (0.854-1.159) 0.995 (0.874-1.08) 1.037 (0.882-1.219) 1.0

(0.831

Cedar 1971-2001 0.964 (0.943-0.986) 0.966 (0.861-1.085) 0.966 (0.852-0.773) 0.913 (0.822-1.014) 0.9

(0.843
Draft Report 2/20/2003 

A. CHINOOK 37 Table A.2.4.4 continued 

Green 1971-2001 1.075 (0.995-1.162) 1.023 (0.913-1.146) 0.698 (0.612-1.226) 0.89 (0.661-1.199) 0.9

(1.034

White 1974-2001 1.094 (1.029-1.162) 1.057 (0.937-1.192) 1.057 (0.957-1.144) 1.155 (1.065-1.254) 1.1

(0.891

Puyallup 1971-2001 1.03 (1.01-1.051) 1.024 (0.914-1.148) 1.024 (0.906-1.163) 0.966 (0.9-1.038) 0.9

(0.896

Nisqually 1979-2001 1.022 (0.961-1.088) 1.006 (0.878-1.152) 1.006 (0.881-1.213) 1.046 (0.901-1.213) 1.0

(0.872

Skokomish 1987-2001 0.978 (0.916-1.044) 0.988 0.826-1.18) 0.988 (0.842-1.429) 1.038 (0.954-1.129) 1.0

(1.014

Dosewallips 1981-2001 1.076 (0.862-1.344) 1.174 (0.982-1.403) 1.174 (.991-1.429) 1.177 (0.828-1.675) 1.2

(0.869

Dungeness 1986-2001 0.991 (0.912-1.076) 1.01 (0.851-1.198) 1.01 (0.851-1.198) 1.02 (0.887-1.173) 1.

(0.797

Elwha 1986-2001 0.918 (0.839-1.003) 0.894 (0.754-1.06) 0.894 (0.767-1.089) 0.974 (0.856-1.108) 0.9

(.797-
Draft Report 2/20/2003 

A. CHINOOK 38 Table A.2.4.5. Estimates of the probability that short- and long-term trends and 

λ are less than one for populations of chino

ESU. “H0” and “H1” indicate whether 

λ is calculated assuming the reproductive success of naturally spawning hatc

equivalent to that of wild fish. 

Population P (LT Trend > 1) P (LT 

λ-H0 <1) P (LT 

λ-H1 <1) P (ST Trend < 1) P (ST 

λ-H0 

NF Nooksack 0.837 0.888 0.998 0.491 0.967 SF Nooksack 0.914 0.723 0.958 0.367 0.506 Lower Skagit 0.998 0.433 0.393 0.396 0.397 Upper Skagit 0.655 0.406 0.358 0.172 0.230 Upper Cascade 0.049 0.162 0.106 0.127 0.122 Lower Sauk 0.898 0.486 0.505 0.449 0.528 Upper Sauk 1.000 0.742 0.791 0.866 0.831 Suiattle 0.998 0.504 0.489 0.393 0.464 NF Stillaguamish 0.999 0.884 0.995 0.707 0.657 SF Stillaguamish 0.034 0.493 0.560 0.930 0.836 Skykomish 0.996 0.718 1.000 0.583 0.579 Snoqualmie 0.038 0.170 0.533 0.148 0.268 NL Washington 0.870 0.536 0.351 0.315 0.198 Cedar 0.999 0.866 0.911 0.959 0.887 Green 0.034 0.361 1.000 0.798 0.751 White 0.003 0.268 0.186 0.001 0.023 Puyallup 0.002 0.221 0.281 0.845 0.518 Nisqually 0.232 0.473 0.446 0.259 0.372 Skokomish 0.766 0.597 0.418 0.176 0.199 Dosewallips 0.243 0.189 0.170 0.163 0.222 Dungeness 0.593 0.448 0.448 0.381 0.394 Elwha 0.971 0.884 0.834 0.673 0.686 
Draft Report 2/20/2003 

A. CHINOOK 39 

A.2.4.4 Updated Threats Information 

The Puget Sound TRT (unpublished data) has estimated adult equivalent fishing rates 

for each population of chinook in the ESU (Table A.2.4.6). Fishing rates are estimated as the 

proportion of the available population caught in the ocean (often in mixed fisheries) or in 

terminal fisheries at each age. These estimates include sport and commercial fishing, and 

they should include incidental mortalities. Fishing rates are a function of catch and 

escapement estimates, and usually are based on CWT recoveries and estimates of incidental 

mortalities and natural mortality constants provided by the CTC. 

Harvest rates on Puget Sound chinook populations averaged 75% (median = 85%; range 

31-92%) in the earliest 5 years of data availability and have dropped to an average of 44% 

(median = 45; range 26-63%) in the most recent 5-year period. 

Table A.2.4.6. Estimated brood-year harvest rates on populations of Puget Sound chinook (Puget 

Sound TRT unpublished data). 

Population Data years (broodyear) 

Earliest 5-year 

mean fishing rate 

(%) 

Most recent 5-year 

mean fishing rate 

(%) 

NF Nooksack 1982 – present 43 26 

SF Nooksack 1982 – present 44 26 

Lower Skagit 1969 – present 81 61 

Upper Skagit 1969 - present 88 63 

Upper Cascade 1982 - present 89 56 

Lower Sauk 1969 - present 88 63 

Upper Sauk 1979 - present 84 55 

Suiattle 1979 - present 84 30 

NF Stillaguamish 1972 - present 89 52 

SF Stillaguamish 1972 - present 89 52 

Skykomish 1973 - present 86 49 

Snoqualmie 1973 - present 85 45 

NL Washington 1981 - present 41 27 

Cedar 1969 - present 52 31 

Green 1969 - present 82 57 

White 1972 - present 90 26 

Puyallup 1969 - present 51 30 

Nisqually 1977 - present 92 62 

Skokomish 1985 - present 92 41 

Dosewallips 1985 - present 92 45 

Dungeness 1984 - present 31 31 

Elwha 1984 - present 64 45 

The Puget Sound TRT (unpublished data) has amassed estimates of the total number of 

hatchery-born chinook salmon returning to streams (Table A.2.4.7). These estimates for each 

population include the total return—returns to natural spawning grounds and to hatchery racks 

within a population’s geographic boundaries. These estimates do not account for possible 

strays of hatchery fish from outside the population’s boundaries. It is apparent from Table 
Draft Report 2/20/2003 

A. CHINOOK 40 

A.2.4.7 that even populations of chinook in northern Puget Sound (not a hatchery production 

management area for co-managers) receive significant numbers of hatchery fish returning 

each year. The Dungeness and White populations are undergoing captive broodstock 

programs as part of co-manager re-building plans, and so it is likely that a large fraction of the 

escapements reported in Table A.2.4.3. are hatchery fish. 

Table A.2.4.7. Total estimated recent annual average returns of hatchery-born chinook salmon and 

most recent total releases in streams containing independent populations of chinook in Puget 

Sound (Puget Sound TRT and B. Waknitz, unpublished data). 

Population 

Average annual hatchery

return to stream 1997 – 

present (min, max) 

Most recent (1990-2001) total 

releases of chinook hatchery juveniles, 

by life-stage (in millions) 

NF Nooksack 1,734 (0 – 9,169) 

SF Nooksack 1,287 (0 – 5,515) 54 (41 fall, 13 spring/summer) 

Lower Skagit see Upper Skagit 

Upper Skagit 1,031 (0 – 4,028) 

Upper Cascade see Upper Skagit 

Lower Sauk see Upper Skagit 

Upper Sauk see Upper Skagit 

Suiattle see Upper Skagit 

12 (3 fall, 5 spring, 4 summer) 

NF Stillaguamish 318 (0 – 777) 

SF Stillaguamish see NF Stillaguamish 1 summer (plus additional marine releases) 

Skykomish 3,666 (824 – 8,530) 

Snoqualmie 2,921 (19 – 6,514) 22 (11 fall, 11 summer) 

NL Washington NA 

Cedar NA 26 fall 

Green 13,565 (3,211 – 23,744) 48 fall 

White NA 

Puyallup 2,048 (248 – 3,484) 

24.1 (20 fall, 4.1 

spring—net pens) 

Nisqually 2,559 (0 – 13,481) 10 fall 

70 fall in South 

Sound general 

Skokomish 3,621 (294 – 8,816) 

Dosewallips NA 89 (71 fall, 18 spring) 

Dungeness NA 6 spring 

Elwha 1,332 (663 – 2,595) 27 fall 
Draft Report 2/20/2003 

A. CHINOOK 41 

Table A.2.4.8 lists hatchery stocks of chinook in Puget Sound and provides the scores 

from the SSHAG (2003) categorizations of hatchery populations. 

Table A.2.4.8. Preliminary SSHAG (2003) categorizations of hatchery populations of the Puget 

Sound chinook salmon ESU. See “Artificial Propagation” in General Introduction for 

explanation of the categories. 

Stock Run Basin SSHAG Category 

Kendall Creek Spring Nooksack 2 

Lummi Bay Fall Nooksack 3 

Samish River Fall Samish 3 

Marblemount Spring Skagit 2 

Marblemount Spring Skagit 1 

Marblemount Fall Skagit 1 

Tulalip Spring Tulalip Bay 3 

Tulalip Summer Tulalip Bay 3 

Tulalip Fall Tulalip Bay 3 

N. Fork Stillaguamish Summer Stilliguamish 1 

Wallace River Summer Snohomish 2 

Issaquah Hatchery Fall Lake Washington 3 

UW Portage Bay Fall Lake Washington 3 

Soos Creek Fall Green 1 or 2 

Keta Creek Fall Green 1 or 2 

Grover's Creek Fall East Kitsap 3 

Garrison Springs Fall Chambers Creek 3 

Voights Creek Fall Puyallup 3 

Diru Creek Fall Puyallup 3 

White River Spring Puyallup 2 

Clear/Kalama Creeks Fall Nisqually 3 

Minter Creek Fall S. Sound 3 

Tumwater Falls Fall Deschutes 3 

George Adams Fall Skokomish 3 

WSC Hood Canal Fall Skokomish 3 

Finch Creek Fall S. Hood Canal 3 

Hamma Hamma Fall S. Hood Canal 3 

Big Beef Creek Fall N. Hood Canal 3 

Dungeness Spring Dungeness 1 

Elwha Fall Elwha 1 or 2 

Glenwood Springs Fall San Juan Islands 3 
Draft Report 2/20/2003 

A. CHINOOK 42 

A.2.4.5 Comparison with Previous Data 

Overall, the natural spawning escapement estimates for Puget Sound chinook 

populations are very similar to those at the time of the previous status review of Puget Sound 

chinook conducted with data through 1997. The differences between population escapement 

estimates between the previous status assessments using data from 1997 and the present 

assessment using data through 2001 could be due to (1) revised pre-1997 data, (2) differences 

in which fish are counted as part of a population, (3) new information on the fraction of 

natural spawners that are hatchery fish, or (4) true differences reflected in new data on natural 

spawners obtained over the most recent 4 years. The median across populations of the most 

recent 5-year geometric mean natural escapement for the same 22 populations through 1997 

was N = 438 (compared to N = 481 through 2001), and the range was 1-5,400. A few more 

populations increased (n = 13) in their geometric mean escapements as decreased (n = 9) over 

the past 4 years. The most dramatic change in recent natural escapement estimates from the 

previous status assessment was in the Green River—the recent natural escapement estimate is 

lower than the previous one by almost 5,000 spawners. This apparent drop in natural 

escapement is due primarily to new information about the fraction of hatchery fish that are 

spawning naturally. 

Throughout the ESU, the estimates of trends in natural spawning escapements for Puget 

Sound chinook populations are similar to the previous status review of Puget Sound chinook 

conducted with data through 1997. As stated above for escapement estimates, the differences 

in trend estimates between the previous status assessments using data from 1997 and the 

present assessment using data through 2001 could be due to (1) revised pre-1997 data, (2) 

differences in which fish are counted as part of a population, (3) new information on the 

fraction of natural spawners that are hatchery fish, or (4) true differences reflected in new data 

on natural spawners obtained over the most recent 4 years. The median across populations of 

the long-term trend in natural spawners was a 1.1% decline per year through 1997, compared 

to a median 1.2% decline per year through 2001. Twelve populations had declining long-term 

trends through 1997, and 14 populations have declining long-term trends through 2001. 

Short-term trends are generally less negative in more recent years—the median trend across 

22 populations through 1997 was a -4% decline per year, and the median trend through 2001 

was a 1.4% increase per year. Fourteen populations showed declining short-term trends at the 

time of the previous status reviews, and only eight populations exhibit declining short-term 

trends in recent years.
Draft Report 2/20/2003 

A. CHINOOK 43 

-----*----- Spawners □----- NatOrigSpawners 

NF Nooksack

0

200

400

600

800

1000

1200

1400

1600

1970 1975 1980 1985 1990 1995 2000 2005

SF Nooksack

0

100

200

300

400

500

600

700

1970 1975 1980 1985 1990 1995 2000 2005

Lower Skagit

0

1000

2000

3000

4000

5000

6000

1970 1975 1980 1985 1990 1995 2000 2005

Upper Skagit

0

2000

4000

6000

8000

10000

12000

14000

16000

1970 1975 1980 1985 1990 1995 2000 2005

Figure A.2.4.1. Abundance of spawning chinook in Puget Sound. Where available, the fraction of 

natural spawners that are hatchery-origin fish also are reported.
Draft Report 2/20/2003 

A. CHINOOK 44 

Upper Cascade

0

50

100

150

200

250

300

350

1970 1975 1980 1985 1990 1995 2000 2005

Lower Sauk

0

500

1000

1500

2000

2500

3000

1970 1975 1980 1985 1990 1995 2000

Upper Sauk

0

200

400

600

800

1000

1200

1400

1600

1800

2000

1970 1975 1980 1985 1990 1995 2000 2005

Suiattle

0

100

200

300

400

500

600

700

800

900

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 45 

NF Stillaguamish

0

200

400

600

800

1000

1200

1400

1970 1975 1980 1985 1990 1995 2000 2005

SF Stillaguamish

0

50

100

150

200

250

300

350

400

1970 1975 1980 1985 1990 1995 2000 2005

Skykomish

0

1000

2000

3000

4000

5000

6000

7000

1970 1975 1980 1985 1990 1995 2000 2005

Snoqualmie

0

500

1000

1500

2000

2500

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 46 

Lake Washington

0

100

200

300

400

500

600

1970 1975 1980 1985 1990 1995 2000 2005

Cedar

0

200

400

600

800

1000

1200

1400

1600

1800

1970 1975 1980 1985 1990 1995 2000 2005

White

0

200

400

600

800

1000

1200

1400

1600

1970 1975 1980 1985 1990 1995 2000 2005

Green

0

2000

4000

6000

8000

10000

12000

14000

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 47 

 

Puyallup

0

1000

2000

3000

4000

5000

6000

1970 1975 1980 1985 1990 1995 2000 2005

Nisqually

0

500

1000

1500

2000

2500

1970 1975 1980 1985 1990 1995 2000 2005

Skokomish

0

200

400

600

800

1000

1200

1400

1600

1800

2000

1970 1975 1980 1985 1990 1995 2000 2005

Dosewallips

0

50

100

150

200

250

300

350

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 48 

Dungeness

0

50

100

150

200

250

300

350

1970 1975 1980 1985 1990 1995 2000 2005

Elwha

0

500

1000

1500

2000

2500

3000

3500

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 49 

NF Nooksack

0

200

400

600

800

1000

1200

1400

1600

1970 1975 1980 1985 1990 1995 2000 2005

SF Nooksack

0

100

200

300

400

500

600

700

800

1970 1975 1980 1985 1990 1995 2000 2005

Lower Skagit

0

5000

10000

15000

20000

25000

30000

35000

40000

45000

1970 1975 1980 1985 1990 1995 2000 2005

Upper Skagit

0

20000

40000

60000

80000

100000

120000

1970 1975 1980 1985 1990 1995 2000 2005

----*---- Pre-Harvest Recruits □---- Spawners

Figure A.2.4.2. Abundance of spawners and pre-harvest recruits to chinook populations in Puget Sound.
Draft Report 2/20/2003 

A. CHINOOK 50 

Upper Cascade

0

100

200

300

400

500

600

700

800

1970 1975 1980 1985 1990 1995 2000 2005

Lower Sauk

0

5000

10000

15000

20000

25000

1970 1975 1980 1985 1990 1995 2000 2005

Upper Sauk

0

500

1000

1500

2000

2500

3000

3500

4000

4500

5000

1970 1975 1980 1985 1990 1995 2000 2005

Suiattle

0

500

1000

1500

2000

2500

3000

3500

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 51 

NF Stillaguamish

0

1000

2000

3000

4000

5000

6000

7000

8000

9000

10000

1970 1975 1980 1985 1990 1995 2000 2005

SF Stillaguamish

0

500

1000

1500

2000

2500

1970 1975 1980 1985 1990 1995 2000

Skykomish

0

5000

10000

15000

20000

25000

30000

35000

40000

45000

50000

1970 1975 1980 1985 1990 1995 2000 2005

Snoqualmie

0

5000

10000

15000

20000

25000

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 52 

Lake Washington

0

100

200

300

400

500

600

700

800

900

1000

1970 1975 1980 1985 1990 1995 2000 2005

Cedar

0

500

1000

1500

2000

2500

3000

3500

1970 1975 1980 1985 1990 1995 2000 2005

Green

0

10000

20000

30000

40000

50000

60000

1970 1975 1980 1985 1990 1995 2000 2005

White

0

500

1000

1500

2000

2500

3000

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 53 

Puyallup

0

1000

2000

3000

4000

5000

6000

7000

8000

1970 1975 1980 1985 1990 1995 2000 2005

Nisqually

0

2000

4000

6000

8000

10000

12000

14000

16000

18000

20000

1970 1975 1980 1985 1990 1995 2000 2005

Skokomish

0

500

1000

1500

2000

2500

3000

3500

1970 1975 1980 1985 1990 1995 2000 2005

Dosewallips

0

100

200

300

400

500

600

700

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 54 

Dungeness

0

50

100

150

200

250

300

350

1970 1975 1980 1985 1990 1995 2000 2005

Elwha

0

500

1000

1500

2000

2500

3000

3500

1970 1975 1980 1985 1990 1995 2000 2005
Draft Report 2/20/2003 

A. CHINOOK 55

A.2.5 LOWER COLUMBIA CHINOOK

A.2.5.1 Previous BRT Conclusions 

• A majority of the previous BRT concluded that the Lower Columbia River ESU is 

likely to become endangered in the foreseeable future. A minority felt that 

chinook salmon in this ESU were not presently in danger of extinction, nor were 

they likely to become so in the foreseeable future. 

• LCR Chinook ESU was listed as Threatened in 1999. 

• The previous BRT was concerned that there were very few naturally selfsustaining populations of native chinook salmon remaining in the lower Columbia 

River ESU. 

• Naturally reproducing (but not necessarily self-sustaining) populations included 

the Lewis and Sandy River “bright” fall runs and the “tule” fall runs in the 

Clackamas, East Fork Lewis and Coweeman Rivers. These populations were 

identified as the only bright spots in the ESU. 

• The few remaining populations of spring chinook salmon in the ESU were not 

considered to be naturally self-sustaining because of either small size, extensive 

hatchery influence, or both. The previous BRT felt that the dramatic declines and 

losses of spring-run chinook salmon populations in the Lower Columbia River 

ESU represented a serious reduction in life-history diversity in the region. 

• The previous BRT felt that the presence of hatchery chinook salmon in this ESU 

posed an important threat to the persistence of the ESU and also obscured trends 

in abundance of native fish. 

• The previous BRT noted that habitat degradation and loss due to extensive 

hydropower development projects, urbanization, logging and agriculture 

threatened the chinook salmon spawning and rearing habitat in the lower 

Columbia River. 

• Currently listed as threatened. 

A.2.5.2. New Data 

New Data include: 

• Spawner abundance through 2000 or 2001. 

• new estimates of the fraction of hatchery spawners and harvest estimates. 

• EDT based estimates of historical abundance. 

• Information on recent hatchery releases. 

A.2.5.3 New Updated Analyses 

New analyses include 

• Designation of relatively demographically independent populations. 

• Recalculation of previous BRT metrics with additional years data. 

• Estimates of median annual growth rate (λ) under different assumptions about the 

reproductive success of hatchery fish. 

• Estimates of current and historically available kilometers of stream. 
Draft Report 2/20/2003 

A. CHINOOK 56

Historical population structure—As part of its effort to develop viability criteria for 

LCR chinook, The Willamette/Lower Columbia Technical Recovery Team (WLC-TRT) 

has identified historically demographically independent populations (Myers et al. 2002). 

Population boundaries are based on an application of Viable Salmonid Populations 

definition (McElhany et al. 2000). Myers et al. hypothesized that the ESU historically 

consisted of 20 fall-run populations (“tules”), two late fall-run populations (“brights”) 

and nine spring-run populations for a total of 31 populations (Figures A.2.5.1 and 

A.2.5.2). The populations identified in Myers et al. are used as the units for the new 

analyses in this report. 

The WLC-TRT partitioned LCR Chinook populations into a number of “strata” 

based on major life-history characteristics and ecological zones (McElhany et al. 2002). 

The WLC-TRT argues that a viable ESU would need a number of viable populations in 

each of these strata. The strata and associated populations are identified in Table 1. 

Abundance and trends 

Data sources for abundance time series and related data are in Appendix A.5.2. The 

recent abundance of natural origin spawners, recent fraction of hatchery origin spawners, 

and recent harvest rates for LCR Chinook populations are summarized in Table A.2.5.1. 

Natural origin fish had parents that spawned in the wild as opposed to hatchery origin 

fish whose parents were spawned in a hatchery. The abundances of natural origin 

spawners range from completely extirpated for most of the spring run populations to over 

6,500 for the Lewis River bright population. The majority of the fall run tule populations 

have a substantial fraction of hatchery origin spawners in the spawning areas and are 

hypothesized to be sustained largely by hatchery production. Exceptions are the 

Coweeman and the Sandy fall run populations which have few hatchery fish spawning on 

the natural spawning areas. These populations have recent mean abundance estimates of 

348 and 183 spawners respectively. The majority of the spring run populations have 

been extirpated largely as the result of dams blocking access to their high elevation 

habitat. The two bright chinook populations (i.e. Lewis and Sandy) have relatively high 

abundances, particularly the Lewis. 

Where data are available, the abundance time series information for each of the 

populations is presented in Figures A.2.5.3-A.2.5.32. Three types of time series figures 

are presented. The first type of figure plots abundance against time (Figures A.2.5.3-

A.2.5.19). Where possible, two lines are presented on the abundance figure, where one 

line is the total number of spawners (or total count at a dam) and the other line is the 

number of fish of natural origin. In many cases, data were not available to distinguish 

between natural and hatchery origin spawners, so only total spawner (or dam count) 

information is presented. This type of figure can give a sense of the levels of abundance, 

overall trend, patterns of variability, and the fraction of hatchery origin spawners. A high 

fraction of hatchery origin spawners indicates that the population may potentially be 

sustained by hatchery production and not the natural environment. It is important to note 

that estimates of the fraction of hatchery origin fish are highly uncertain since the 

hatchery marking rate for LCR fall chinook is generally only a few percent and expansion 

to population hatchery fraction is based on only a handful of recovered marked fish 

(unpublished analysis, McElhany, Rawding, and Sydor).
Draft Report 2/20/2003 

A. CHINOOK 57

The second type of time series figure displays fish per mile data. For three 

populations of fall run chinook in Oregon watersheds total abundance estimates are not 

available, but fish per mile time series exists (Figures A.2.5.20-A.2.5.22). There are no 

estimates of the fraction of hatchery origin spanwers in these fish/mile time series, but 

may be high given the large number of hatchery fish released and the high fraction of 

hatchery origin spawners estimated in Washington watersheds directly across the 

Columbia River. The lack of information on hatchery fraction reduces the value of these 

time series for evaluating extinction risk. 

The third type of time series figure presents the total number of spawners (natural 

and hatchery origin) and the number of preharvest recruits produced by those spawners 

against time (Figures A.2.5.23-A.2.5.32). Dividing the number of preharvest recruits by 

the number of spawners for the same time period would yield an estimate of the 

preharvest recruits per spawner. This type of figure requires harvest and age structure 

information and therefore could be produced for only a limited number of populations. 

This type of figure can indicate if there have been changes in preharvest recruitment and 

the degree to which harvest management has the potential to recover populations. If the 

preharvest recruitment line is consistently below the spawner line, it indicates that the 

population would not be replacing itself, even in the absence of all harvest. 

Summary statistics on population trends and growth rate are presented in Tables 

A.2.5.2-A.2.5.3 and in Figures A.2.5.33-A.2.5.35. The methods for estimating trends and 

growth rate (λ) are described in the general method section. Because trends are only 

calculated for time series where the fraction of hatchery origin spawners is known, most 

of the long-term trend estimates use data starting in 1980, even though the abundance 

time series of total spawners may extend earlier than 1980. The majority of populations 

have a long-term trend less than one, indicating the population is in decline. In addition, 

there is a high probability for most populations that the true trend/growth rate is less than 

one (Table A.2.5.3). When growth rate is estimated, assuming that hatchery origin 

spawners have a reproductive success equal to that of natural origin spawners, all of the 

population have a negative growth rate except the Coweeman fall run, which had very 

few hatchery origin spawners (Figure A.2.5.35). The potential reasons for these declines 

have been cataloged in previous status reviews and include habitat degradation, 

deleterious hatchery practices, and climate-driven changes in marine survival. 

The Lewis River bright population is considered the healthiest in the ESU. The 

population is significantly larger than any other population in the ESU, and, in fact, it is 

larger than any population of salmon in the Columbia Basin except the Hanford Reach 

chinook. The Lewis bright chinook harvest has been managed to an escapement target of 

5,700 and this target has been met every year for which data are available (Figure 

A.2.5.16). The preharvest recruits have exceeded spanwers in all years for which data are 

available except one (Figure A.2.5.32). There is a hatchery program for Lewis River 

brights, but hatchery origin spawners have generally comprised less than 10% of the 

spawning population over the time series. These indicators all suggest a relatively 

healthy population. However, the long-term population trend estimate is negative (Figure 

A.2.5.33), and it is not clear the extent to which this reflects management decisions to 

harvest closer to the escapement goal as compared to declining productivity over the time 

series. The population is also geographically confined to a reach that is only a few 
Draft Report 2/20/2003 

A. CHINOOK 58

kilometers in length and is immediately below Merwin Dam, where it is affected by the 

flow management of the hydrosystem. This limited spatial distribution is a potential risk 

factor. 

EDT-based estimates of historical abundance—The Washington Department of 

Fish and Wildlife (WDFW) has conducted analyses of the LCR chinook populations 

using the Ecosystem Diagnosis and Treatment (EDT) model (in McElhany et al 2002). 

The EDT model attempts to predict fish population performance based on input 

information about reach-specific habitat attributes (http://www.olympus.net/community/ 

dungenesswc/EDT-primer.pdf). WDFW populated this model with estimates of 

historical habitat condition which produced the estimates of average historical abundance 

shown in Table A.2.5.1. There is a great deal of unquantified uncertainty in the EDT 

historical abundance estimates that should be taken into consideration when interpreting 

these data. In addition, the habitat scenarios evaluated as “historical” may not reflect 

historical distributions, since some areas are historically accessible but currently blocked 

by large dams are omitted from the analyses and some areas that were historically 

inaccessible but recently passable because of human intervention are included. The EDT 

outputs are provided here to give a sense of the historical abundance of populations 

relative to each other and an estimate of the historical abundance relative to the current 

abundance. 

Loss of habitat from barriers—An analysis was conducted by Steel and Sheer 

(2002) to assess the number of stream km historically and currently available to salmon 

populations in the LCR (Table A.2.5.4). Stream km usable by salmon are determined 

based on simple gradient cut offs and on the presence of impassable barriers. This 

approach will over estimate the number of usable stream km as it does not take into 

consideration habitat quality (other than gradient). However, the analysis does indicate 

that for some populations (particularly spring run) the number of stream habitat km 

currently accessible is greatly reduced from the historical condition. 

A.2.5.4 New Hatchery/ESU Information 

Recent Hatchery Releases 

Updated information on chinook hatchery releases in the ESU is provided in Tables 

A.2.5.6- A.2.5.10. 

Categorizations of Lower Columbia River hatchery stocks (SSHAG 2003) can be 

found in Appendix A.5.1. 

A.2.5.5 Comparison with Previous Data 

ESU Summary 

The ESU exhibits three major life history types: fall run (“tules”), late fall run 

(“brights”), and spring run. The ESU spans three ecological zones: Coastal (rain driven 

hydrograph), Western Cascade (snow or glacial driven hydrograph), and Gorge 

(transitioning to drier interior Columbia ecological zones). The fall chinook populations 

are currently dominated by large scale hatchery production, relatively high harvest and 
Draft Report 2/20/2003 

A. CHINOOK 59

extensive habitat degradation. The Lewis River late fall chinook population is the 

healthiest in the ESU and has a reasonable probability of being self-sustaining. The 

spring-run populations are largely extirpated as the result of dams which block access to 

their high elevation habitat. Abundances have largely declined since the last status 

review update (1998) and trend indicators for most all populations are negative, 

especially if hatchery fish are assumed to have a reproductive success equivalent to that 

of natural origin fish 

Based on professional judgment synthesis of the updated information provided in 

this report plus the information contained in previous LCR status reviews, we have 

tentatively identified the number of historical and currently viable populations (Table 

A.2.5.5). This summary indicates that the ESU is substantially modified from historical 

population structure. Most tule fall chinook populations are potentially at risk of 

extinction and no populations of the spring run life-history type are currently considered 

self-sustaining. The Lewis River late fall bright population has the highest likelihood of 

being self-sustaining under current conditions. 
Draft Report 2/20/2003 

A. CHINOOK 60

Table A.2.5.1. Population structure and status information on LCR Chinook. The life history 

divisions are based on run timing and other correlated characters. The ecological zone is 

based on ecological community and hydro dynamic patterns. Every lifehistory/ecological zone combination constitutes a “stratum” (McElhany et al. 2002). The 

recent abundance is the geometric mean of natural origin spawners of the last five years 

of available data and the min-max are the lowest and highest five year geometric means 

in the time series. The data years are the data years used for the abundance min-max 

estimates, the extinction risk estimate and the trends (Figure 3). Longer time series may 

be available for spawners only (see figures) but hatchery fraction information was 

required to estimate means, extinction risk and trends. The fraction hatchery is the 

average percent of spawners of hatchery origin over the last four years. The harvest rate 

is the percent of adults harvested. The EDT estimate of historical abundance is based on 

analysis by WDFW of equilibrium abundance under historical habitat conditions. The 

quasi-extinction metric is the probability of declining from the current abundance to a 

four year average of 50 spawners/year within 100 years based on stochastic projection. 

Life 

History 

Ecological 

Zone Population 

Recent 

Abundance 

(min-max) 

Data 

Years 

Hatchery 

Fraction 

(%) 

Harves

t Rate 

(%) 

EDT 

Estimate of 

Historical 

Abundance 

Youngs Bay 

Fall Run 

1970- 

2001 

Grays River 

Fall Run 

61 

(33-627) 

1980-

2000 37 57 2,477 

Big Creek Fall 

Run 

1970-

2001 

Elochoman 

River Fall Run

154 

(78-349) 

1980-

2000 69 49 

Clatskanie 

River Fall Run

1970-

2001 

Mill, 

Abernathy, 

Germany Fall 

Run 

248 

(248-1604) 

1980-

2000 47 40 

coastal 

Scappoose 

Creek Fall 

Run 

 

Coweeman 348 

(64-849) 

1980-

2000 0 31 4,973 

Lower 

Cowlitz River 

Fall Run 

463 

(20-1014) 

1980-

2000 67 24 53,956 

Upper Cowlitz 

River Fall Run Extirpated 

Toutle River 

Fall Run 25,392 

Kalama River 

Fall Run 

848 

(848-4511) 

1980-

2000 67 30 2,455 

Fall 

Run 

cascade 

Salmon Creek, 

Lewis River 

Fall Run 

230 

(213-360) 
Draft Report 2/20/2003 

A. CHINOOK 61

Clackamas 

River Fall Run 

Washougal 

River Fall Run

903 

(580-1840) 

1980-

2000 57 26 7,518 

Sandy River 

Fall Run 183 1988-2001 3 

Lower Gorge 

Tributaries 

Fall Run 

 

Upper Gorge 

Tributaries 

Fall Run 

90 

(11-390) 

1980-

2000 17 2,363 

Hood River 

Fall Run <50 

gorge 

Big White 

Salmon Fall 

Run 

98 

(98-747) 

1980-

2000 22 65 

Sandy Late 504 

(504-1213) 

1984-

2001 3 Late 

Fall 

(bright) 

cascade N.F. Lewis 

(bright) 

6797 

(6797-

15903) 

1980-

2000 13 34 

Upper Cowlitz 

Spring Run 

225 

(169-334) 

1980-

2000 0 

Cispus River 

Spring Run Extirpated 

Tilton River 

Spring Run Extirpated 

Toutle River 

Spring Run Extirpated 2,901 

Kalama River 

Spring Run 

138 

(91-663) 

1980-

2000 4,178 

Lewis River 

Spring Run 

320 

(320-3287) 

1980-

2000 1,728 

cascade 

Sandy River 

Spring Run Extirpated 

Big White 

Salmon Spring 

Run 

Extirpated 

Spring 

Run 

gorge 

Hood River 

Spring Run Extirpated 

 Total 11,720 107,941 

 Average 31 40 
Draft Report 2/20/2003 

A. CHINOOK Table A.2.5.2. Trend and growth rate for subset of Lower Columbia Chinook populations. 95% confidence intervals are in pa

analysis used the entire data set (see table 2 for years). The criteria for the short term data set is defined in the metho

“Hatchery = 0” columns, the hatchery fish are assumed to have zero reproductive success. In the “Hatchery = Wild” are assumed to have the same relative reproductive success as natural origin fish. 

Long Term Analysis Short Term 

Lambda (C.I.) 

Population Trend (C.I.) Hatchery = 0 Hatchery = 

Wild 

Trend (C.I.) Hatcher

Grays River Fall Run 

0.882 

(0.806-0.965) 

0.919 

(0.718-1.177) 

0.824 

(0.648-1.07) 

1.002 

(0.759-1.323) 

0.9

(0.742-1

Elochoman River Fall Run 

1.012 

(0.933-1.097) 

0.991 

(0.774-1.269) 

0.776 

(0.613-1.013) 

1.067 

(0.86-1.323) 

1.01

(0.793-1

Mill, Abernathy, Germany Fall 

0.944 

(0.885-1.007) 

0.919 

(0.718-0.891) 

0.778 

(0.588-0.971) 

0.874 

(0.756-1.011) 

0.66

(1.087-0

Coweeman 

1.104 

(1.022-1.192) 

1.131 

(0.883-1.448) 

1.13 

(0.86-1.421) 

0.953 

(0.762-1.192) 

1.04

(0.818-1

Lower Cowlitz River Fall Run 

0.931 

(0.799-1.085) 

0.998 

(0.779-1.278) 

0.651 

(0.533-0.882) 

1.467 

(0.906-2.375) 

1.23

(0.962-1

Kalama River Fall Run 

0.951 

(0.876-1.033) 

0.973 

(0.76-1.246) 

0.821 

(0.635-1.049) 

0.843 

(0.669-1.062) 

0.9

(0.734-1

Salmon Creek, Lewis River Fall 

0.971 

(0.94-1.003) 

0.972 

(0.759-1.245) 

0.968 

(0.761-1.257) 

0.983 

(0.893-1.083) 

1.00

(0.784-1

Washougal River Fall Run 

1.028 

(0.978-1.082) 

1.016 

(0.793-1.3) 

0.81 

(0.616-1.018) 

0.962 

(0.845-1.094) 

0.95

(0.749-1

Upper Gorge Tributaries Fall 

0.876 

(0.793-0.968) 

0.942 

(0.736-1.206) 

0.94 

(0.792-1.308) 

1.103 

(0.802-1.516) 

1.23

(0.967-1

Big White Salmon Fall Run 

0.905 

(0.849-0.964) 

0.89 

(0.695-1.139) 

0.879 

(0.679-1.122) 

0.94 

(0.767-1.154) 

0.88

(0.69-1

Sandy Late 

.946 

(0.883-1.014) 

.943 

(0.836-1.063) 

.935 

(0.829-1.054) 

0.915 

(0.796-1.052) 

0.91

(0.815-1

N.F. Lewis (bright) 

0.962 

(0.932-0.993) 

0.957 

(0.747-1.225) 

0.937 

(0.725-1.198) 

0.927 

(0.842-1.022) 

0.93

(0.732-
Draft Report 2/20/2003 

A. CHINOOK 

Upper Cowlitz Spring Run 

0.987 

(0.924-1.054) 

0.957 

(0.755-1.259) 

0.975 

(0.76-1.271) 

0.989 

(0.818-1.196) 

1.00

(0.776-1

Kalama River Spring Run 

0.933 

(0.812-1.072) 

0.872 

(0.675-1.126) 

0.872 

(0.718-1.201) 

1.097 

(0.848-1.419) 

1.09

(0.85-1

Lewis River Spring Run 

0.935 

(0.867-1.009) 

0.949 

(0.735-1.226) 

0.947 

(0.695-1.163) 

0.792 

(0.72-0.87) 

0.78

(0.611-1
Draft Report 2/20/2003 

A. CHINOOK Table A.2.5.3. Probability the trend or growth rate is less than one. In the “Hatchery = 0” columns, the hatchery fish are assu

reproductive success. In the “Hatchery = Wild” columns, hatchery fish are assumed to have the same relative reprod

origin fish. 

Long Term Analysis Short Term Analysis 

Population Lambda Lambda 

Trend Hatchery = 0 Hatchery = Wild Trend Hatchery = 0 Hatche

Grays River Fall Run 0.996 0.789 0.955 0.493 0.594 0Elochoman River Fall Run 0.380 0.531 0.972 0.258 0.467 0Mill, Abernathy, Germany Fall 0.961 0.849 1.000 0.967 0.912 0Coweeman 0.007 0.113 0.160 0.680 0.395 0Lower Cowlitz River Fall Run 0.830 0.507 0.998 0.053 0.165 0Kalama River Fall Run 0.890 0.606 0.970 0.936 0.692 0Salmon Creek, Lewis River Fall 0.965 0.765 0.712 0.651 0.474 0Washougal River Fall Run 0.130 0.391 1.000 0.746 0.639 0Upper Gorge Tributaries Fall 0.994 0.649 0.455 0.249 0.177 0Big White Salmon Fall Run 0.998 0.888 0.925 0.743 0.778 0Sandy Late 0.944 0.833 0.863 0.906 0.827 0N.F. Lewis (bright) 0.991 0.847 0.964 0.944 0.877 0Upper Cowlitz Spring Run 0.659 0.624 0.588 0.553 0.491 0Kalama River Spring Run 0.847 0.866 0.729 0.216 0.303 0Lewis River Spring Run 0.960 0.731 0.890 1.000 0.997 0
Draft Report 2/20/2003 

A. CHINOOK 65

Table A.2.5.4. Loss of habitat from barriers. The potential current habitat is the kilometers of 

stream below all currently impassible barriers between a gradient of 0.5% and 4%. . The 

potential historical habitat is the kilometers of stream below historically impassible barriers 

between a gradient of 0.5% and 4%. The current to historical habitat ratio is the percent of 

the historical habitat that is currently available. 

Population 

Potential 

Current 

Habitat 

(km) 

Potential 

Historical 

Habitat 

(km) 

Current 

to 

Historical 

Habitat 

Ratio 

(%) 

Youngs Bay 

Fall Run 178 195 91 

Grays River 

Fall Run 133 133 100 

Big Creek 

Fall Run 92 129 71 

Elochoman River 

Fall Run 85 116 74 

Clatskanie River 

Fall Run 159 159 100 

Mill, Abernathy, 

Germany Fall Run 117 123 96 

Scappoose Creek 

Fall Run 122 157 78 

Coweeman 61 71 86 

Lower Cowlitz 

River Fall Run 418 919 45 

Upper Cowlitz 

River Fall Run 

Toutle River 

Fall Run 217 313 69 

Kalama River 

 Fall Run 78 83 94 

Salmon Creek, 

Lewis River 

Fall Run 

438 598 73 

Clackamas River 

Fall Run 568 613 93 

Washougal River 

Fall Run 84 164 51 

Sandy River Fall 

Run 227 286 79 

Lower Gorge 

Tributaries 

Fall Run 

34 35 99 

Upper Gorge 

Tributaries 

Fall Run 

23 27 84 

Hood River 35 35 100 
Draft Report 2/20/2003 

A. CHINOOK 66

Fall Run 

Big White Salmon 

Fall Run 0 71 0 

Sandy Late 217 225 96 

N.F. Lewis 

(bright) 87 166 52 

Upper Cowlitz 

Spring Run 4 276 1 

Cispus River 

Spring Run 0 76 0 

Tilton River 

Spring Run 0 93 0 

Toutle River 

Spring Run 217 313 69 

Kalama River 

Spring Run 78 83 94 

Lewis River 

Spring Run 87 365 24 

Sandy River 

Spring Run 167 218 77 

Big White Salmon 

Spring Run 0 232 0 

Hood River 

Spring Run 150 150 99 

Total 4,075 6,421 63 

Average 

Table A.2.5.5. Number of populations in the ESU of each life history type. Populations with 

“some current natural production” have some natural origin recruits present but are not 

necessarily considered self-sustaining (“viable”). The determination of the number of 

populations potentially currently viable is based on professional judgment analysis of 

abundance, growth rate/trends and other extinction risk metrics. 

Life-History Type 

Fall Late-Fall 

(“bright”) Spring Total 

Historical 20 2 9 31 

Some current natural 

production 17-19 2 2 21-23 

Currently “viable” 

populations 0-1 1-2 0 1-3 
Draft Report 2/20/2003 

A. CHINOOK 67

Table A.2.5.6. Washington Fall LCR Chinook hatchery releases. 

Watershed Years Hatchery Stock Release Site Total 

1990-1994 Sea Resources 

Chinook 

River Chinook R 2,598,400

1990 Sea Resources Washougal Chinook R 629,500 Chinook 

River 

1997-2000 Sea Resources 

Chinook 

River Chinook R 820,627

Deep River 1993 

Lower 

Columbia Kalama Falls Deep R 49,400

1990-1994 Grays River Grays River Grays R 2,767,900

1991, 1993 Grays River Kalama Falls Grays R 1,332,380

1992 Grays River Spring Creek Grays R 1,107,000

1995-1997 Grays River Kalama Grays R 764,550

Grays 

River 

1996, 1997 Grays River Washougal Grays R 1,745,500

1990-1994 Elokomin Elochomin Elochomin R 17,809,719

1991 Elokomin Kalama Falls Elochomin R 1,046,700

1995 Beaver Creek Abernathy Beaver Cr 377,252

1997 Beaver Creek Big Creek Beaver Cr 1,096,198

1996-1999 Beaver Creek Elochoman Elochoman R 2,081,670

1995 Beaver Creek Kalama Beaver Cr 760,039

1995-2001 Elochoman Elochoman Elochoman R 15,280,038

1999 Elochoman Grays River Elochoman R 174,500

Elochomin 

River 

1997-1998 Elochoman Washougal Elochoman R 1,633,200

L Columbia 

River 1996-1998 Cathlamet Ffa Washougal Columbia R 1,132,500

Cowlitz 1990-1994 Cowlitz Cowlitz Cowlitz R 28,757,600

River 1995-2001 Cowlitz Cowlitz Cowlitz R 42,322,920

1990-1993 Toutle Kalama Falls Green R 5,718,000

1991-1993 Toutle Toutle Green R 2,941,000

1994 Toutle Tule Green R 2,044,500

1990-1993 Toutle Washougal Green R 2,693,400

2000 North Toutle Elochoman Green R 618,266

1996 North Toutle Kalama Green R 1,588,937

1996-2001 North Toutle Toutle Green R 10,584,543

Toutle 

River 

1996 North Toutle Washougal Green R 633,414

1991-1994 Lower Kalama Kalama Kalama 10,701,203

1990-1994 Kalama Falls Kalama Falls Kalama 17,600,800

1996-2001 Fallert Cr Kalama Fallert Cr 13,998,602

Kalama 

River 

1995-2001 Kalama Falls Kalama Kalama R 20,198,653

1994 Washougal Kalama Falls Washougal R 2,443,100

1992 Washougal Spring Creek Washougal R 1,409,300

1991-1994 Washougal Washougal Washougal R 27,002,103

2000 Washougal Elochoman Washougal R 1,312,680

Washougal 

River 

1995-2001 Washougal Washougal Washougal R 32,878,694

Spring 

Creek 1992 Ringold 

L White 

Salmon Spring Creek 82,511
Draft Report 2/20/2003 

A. CHINOOK 68

Table A.2.5.7. Oregon Fall LCR Chinook hatchery releases. 

Watershed Years Hatchery Stock Release Site Total 

1991-1995 Astoria H.S. Big Creek Youngs Bay 15,500 

1991-1994 Cedc Rogue River Youngs Bay 394,382 

1991, 1992 Step Big Creek Youngs Bay 13,758 

1992, 1993 Step Klaskanine Youngs Bay 15,700 

1996-1998 Step Big Creek Youngs Bay 63,050 

1997, 1998 Step Unknown Youngs Bay 16,500 

1995-2002 Youngs Bay Rogue River Youngs Bay 4,248,147 

Youngs Bay 

1996-1998 Youngs Bay Urb Youngs Bay 828,884 

1991 Step Unknown 

L Columbia 

River 25,000 

1996, 1997 Tongue Pt Rogue River Tongue Point 54,274 

1996, 1997 Tongue Pt Urb Tongue Point 299,715 

L Columbia 

River 

1995-1997 Blind Slough Rogue River Blind Slough 54,793 

1992-1993 Step Klaskanine Skipanon R 3,550 Skipanon River 1996-1999 Step Big Creek Skipanon R 15,193 

Plympton 

Creek 1991 Big Creek Big Creek Plympton Cr 50,278 

1991-1994 Big Creek Big Creek Big Cr 34,675,446 

1991-1994 Big Creek Rogue River Big Cr 2,798,710 

1993 Big Creek Kalama Falls Big Cr 886,471 

1995-2002 Big Creek Big Creek Big Cr 40,633,091 

Big Creek 

1995-1996 Big Creek Rogue River Big Cr 1,530,550 

Klaskanine 1995 Cedc Rogue River Klaskanine R 15,758 

River 1996-1999 Klaskanine Rogue River Klaskanine R 3,694,245 

Wahkeena Pd 1991-1993 Bonneville Urb Columbia River 1,183,764 

Johnson Cr 1994, 1995 Step Tanner Creek Johnson Creek 99,008 

1991 Bonneville Big Creek Tanner Creek 2,580,763 

1991-1994 Bonneville Tanner Creek Tanner Creek 32,862,338 

1991 Bonneville Wa Tule Tanner Creek 1,534,122 

1991-1994 Bonneville Urb Tanner Creek 26,877,822 

1993 Bonneville Kalama Falls Tanner Creek 1,505,421 

1995-1996 Bonneville Tanner Creek Tanner Creek 15,369,642 

1995-1996 Bonneville Wa Tule Tanner Creek 10,922,745 

1995-2002 Bonneville Urb Tanner Creek 43,729,497 

Tanner Cr 

2000-2001 Bonneville Wa Urb Tanner Cr 328,426 
Draft Report 2/20/2003 

A. CHINOOK 69

Table A.2.5.8. Washington LCR spring Chinook hatchery releases. 

Watershed Years Hatchery Stock Release Site Total 

Deep River 1999-2001 Deep R Cowlitz Deep R 255,657 

Abernathy 1991-1996 Abernathy Nfh Abernathy Cr Abernathy Cr 6,853,504 

Creek 1997-1999 Abernathy Nfh Abernathy Cr Abernathy Cr 1,223,647 

1990-1994 Cowlitz Cowlitz Cowlitz R 9,016,451 

1992-1994 Friends Of Cow Cowlitz Cowlitz R 115,800 

1995-2001 Cowlitz Cowlitz Cowlitz R 8,870,002 

1995, 

1997 Cowlitz Cowlitz Tilton R 

3,074 

Adults 

Cowlitz 

River 

1996, 

1999 

Friends Of 

Cowlitz Cowlitz Cowlitz R 53,800 

1991, 

1993 Toutle Cowlitz Green R 641,382 

1995 North Toutle Toutle Green R 1,412,100 

1995 North Toutle Washougal Green R 1,086,100 

Toutle 

River 

1995-2001 North Toutle Cowlitz Green R 766,740 

1990-1993 Speelyai Lewis Lewis R 1,229,262 

1994 Lewis River Kalama N F Lewis R 975,700 

1991, 

1992 Lewis River Lewis Lewis R 1,885,900 

1990-1994 Lewis River N F Lewis N F Lewis R 1,801,800 

1996 Fish First Np Lewis Lewis R 55,872 

1997-2000 Fish First Np Lewis Lewis R 570,857 

1996, 

1998 Lewis River Lewis Lewis R 2,074,841 

2001 Lewis River Lewis Lewis R 34 Adults 

1995-2001 Lewis River Lewis Lewis R 4,692,781 

Lewis 

River 

2001 Speelyai Lewis Lewis R 566,373 

1990-1994 Lower Kalama Kalama Hatchery Cr 2,455,252 

1995-2001 Fallert Cr Kalama Fallert Cr 2,129,550 

1998, 

2000 Fallert Cr Lewis Fallert Cr 615,463 

1999 Gobar Pond Kalama Gobar Cr 87,500 

Kalama 

River 

1997, 

2001 Kalama Falls Kalama Gobar Cr 332,281 

1993 Ringold Carson Spring Cr 68,900 

1993 Ringold Kalama Spring Cr 462,700 

1990 Ringold Klickitat Spring Cr 40,264 

1994 Ringold 

L White 

Salm Spring Cr 336,268 

1993-1994 Ringold Ringold Spring Cr 596,274 

Spring 

Creek 

1992-1994 Ringold Wind River Spring Cr 2,250,000 

Wind 1991-1996 Carson Nfh Carson Wind R 13,350,658 

River 1997-2001 Carson Nfh Carson Wind R 7,096,346 

1991-1994 

L White Salmon 

Nfh Spring Creek 

L White 

Salmon R 2,757,539 

L White 

Salmon 

River 

1992 Willard Nfh Carson 

L White 

Salmon R 869,952 
Draft Report 2/20/2003 

A. CHINOOK 70

1991-1994 

L White Salmon 

Nfh Carson 

L White 

Salmon R 4,780,148 

1997 

L White Salmon 

Nfh Carson 

L White 

Salmon R 2,835,741 

1998-2001 

L White Salmon 

Nfh 

L White 

Salmon 

L White 

Salmon R 4,272,833 

1998-2001 

L White Salmon 

Nfh Urb-Mixed 

L White 

Salmon R 8,057,188 

Drano 

Lake Abernathy Nfh Spring Creek Dranos Lake 40,756 

1991 

Spring Creek 

Nfh 

Urb-Bonn 

Dam Spring Cr 14,348,604 

1991 

Spring Creek 

Nfh Clackamas Spring Cr 3,292,304 

1992-1996 

Spring Creek 

Nfh Spring Creek Spring Cr 89,083,822 

Spring 

Creek 

1997-2001 

Spring Creek 

Nfh Spring Creek Spring Cr 70,435,986 

1991-1996 

Big White 

Salmon Nfh Carson 

B White 

Salmon R 3,581,536 

1997-1999 

Big White 

Salmon Nfh Carson 

B White 

Salmon R 2,795,464 

2001 

Big White 

Salmon Nfh Methow 

B White 

Salmon R 1,238,764 

B White 

Salmon 

River 

1997 

Spring Creek 

Nfh Carson 

B White 

Salmon R 543,270 

Deep River 1999-2001 Deep R Cowlitz Deep R 255,657 

Abernathy 1991-1996 Abernathy Nfh Abernathy Cr Abernathy Cr 6,853,504 

Creek 1997-1999 Abernathy Nfh Abernathy Cr Abernathy Cr 1,223,647 

1990-1994 Cowlitz Cowlitz Cowlitz R 9,016,451 

1992-1994 Friends Of Cow Cowlitz Cowlitz R 115,800 

1995-2001 Cowlitz Cowlitz Cowlitz R 8,870,002 

1995, 

1997 Cowlitz Cowlitz Tilton R 

3,074 

Adults 

Cowlitz 

River 

1996, 

1999 

Friends Of 

Cowlitz Cowlitz Cowlitz R 53,800 

1991, 

1993 Toutle Cowlitz Green R 641,382 

1995 North Toutle Toutle Green R 1,412,100 

1995 North Toutle Washougal Green R 1,086,100 

Toutle 

River 

1995-2001 North Toutle Cowlitz Green R 766,740 

1990-1993 Speelyai Lewis Lewis R 1,229,262 

1994 Lewis River Kalama N F Lewis R 975,700 

1991, 

1992 Lewis River Lewis Lewis R 1,885,900 

1990-1994 Lewis River N F Lewis N F Lewis R 1,801,800 

1996 Fish First Np Lewis Lewis R 55,872 

1997-2000 Fish First Np Lewis Lewis R 570,857 

1996, 

1998 Lewis River Lewis Lewis R 2,074,841 

Lewis 

River 

2001 Lewis River Lewis Lewis R 34 Adults 
Draft Report 2/20/2003 

A. CHINOOK 71

1995-2001 Lewis River Lewis Lewis R 4,692,781 

2001 Speelyai Lewis Lewis R 566,373 

1990-1994 Lower Kalama Kalama Hatchery Cr 2,455,252 

1995-2001 Fallert Cr Kalama Fallert Cr 2,129,550 

1998, 

2000 Fallert Cr Lewis Fallert Cr 615,463 

1999 Gobar Pond Kalama Gobar Cr 87,500 

Kalama 

River 

1997, 

2001 Kalama Falls Kalama Gobar Cr 332,281 

1993 Ringold Carson Spring Cr 68,900 

1993 Ringold Kalama Spring Cr 462,700 

1990 Ringold Klickitat Spring Cr 40,264 

1994 Ringold 

L White 

Salm Spring Cr 336,268 

1993-1994 Ringold Ringold Spring Cr 596,274 

Spring 

Creek 

1992-1994 Ringold Wind River Spring Cr 2,250,000 

Wind 1991-1996 Carson Nfh Carson Wind R 13,350,658 

River 1997-2001 Carson Nfh Carson Wind R 7,096,346 

1991-1994 

L White Salmon 

Nfh Spring Creek 

L White 

Salmon R 2,757,539 

1992 Willard Nfh Carson 

L White 

Salmon R 869,952 

1991-1994 

L White Salmon 

Nfh Carson 

L White 

Salmon R 4,780,148 

1997 

L White Salmon 

Nfh Carson 

L White 

Salmon R 2,835,741 

1998-2001 

L White Salmon 

Nfh 

L White 

Salmon 

L White 

Salmon R 4,272,833 

L White 

Salmon 

River 

1998-2001 

L White Salmon 

Nfh Urb-Mixed 

L White 

Salmon R 8,057,188 

Drano 

Lake Abernathy Nfh Spring Creek Dranos Lake 40,756 

1991 

Spring Creek 

Nfh 

Urb-Bonn 

Dam Spring Cr 14,348,604 

1991 

Spring Creek 

Nfh Clackamas Spring Cr 3,292,304 

1992-1996 

Spring Creek 

Nfh Spring Creek Spring Cr 89,083,822 

Spring 

Creek 

1997-2001 

Spring Creek 

Nfh Spring Creek Spring Cr 70,435,986 

1991-1996 

Big White 

Salmon Nfh Carson 

B White 

Salmon R 3,581,536 

1997-1999 

Big White 

Salmon Nfh Carson 

B White 

Salmon R 2,795,464 

2001 

Big White 

Salmon Nfh Methow 

B White 

Salmon R 1,238,764 

B White 

Salmon 

River 

1997 

Spring Creek 

Nfh Carson 

B White 

Salmon R 543,270 
Draft Report 2/20/2003 

A. CHINOOK 72

Table A.2.5.9. Oregon LCR spring Chinook hatchery releases. 

Watershed Years Hatchery Stock Release Site Total 

1991-1992 Cedc Clackamas Youngs Bay 242,534 

1994 Cedc N Santiam Youngs Bay 301,361 

1992 Cedc Willamette Youngs Bay 301,786 

1996 Youngs Bay Clackamas Youngs Bay 97,945 

1995-1999 Youngs Bay Willamette Youngs Bay 3,114,060 

Youngs Bay 

1996 Youngs Bay S Santiam Youngs Bay 276,493 

1996 

Blind 

Slough S Santiam Blind Slough 199,389 

1995-2002 

Blind 

Slough Willamette Blind Slough 1,457,655 

1996 Tongue Pt S Santiam Tongue Point 242,319 

L Columbia 

River 

1997-2000 Tongue Pt Willamette Tongue Point 1,029,850 

1991 Cedc Clackamas 

Sf Klaskanine 

R 119,627 

1994 Cedc N Santiam 

Sf Klaskanine 

R 109,974 

1992, 

1997 Cedc Willamette 

Sf Klaskanine 

R 238,316 

Klaskanine 

River 

1996 Cedc S Santiam 

Sf Klaskanine 

R 76,618 

Multnomah 

Channel 1997-1998 Step Mckenzie 

L Willamette 

R 123,134 

1991-1994 Clackamas Clackamas Sandy R 1,316,973 

Sandy R 1991-1993 Clackamas Clackamas Salmon R 594,656 

1995-2002 Clackamas Clackamas Sandy R 3,539,458 

1991-1992 Bonneville Lookingglass Hood R 288,727 

1993-1995 Bonneville Deschutes Hood R 245,209 

1996-2001 Various (3) Deschutes Hood R 677,652 

2000-2002 Parkdale Wild Origin Hood R 101,883 

Hood River 

2000 Parkdale Hood River Hood R 4,126 

Table A.2.5.10. Washington up river bright hatchery releases. (Note “up river bright” chinook 

are not in the LCR chinook ESU. 

Watershed Years Hatchery Stock Release Site Total 

1991-1993 

L White 

Salmon Nfh 

UrbEggbank L White 

Salmon R 8,758,842 

1994-1996 

L White 

Salmon Nfh Carson 

L White 

Salmon R 8,453,502 

L White 

Salmon River 

1994-1996 

L White 

Salmon Nfh Carson 

L White 

Salmon R 1,225Adults 

Spring Creek 1994 Ringold 

Urb-Bonn 

Dam Spring Cr 4,217,491 
Draft Report 2/20/2003 

A. CHINOOK 73

. 

Figure A.2.5.1. Historical independent LCR early and late fall Chinook populations (Myers et al. 2002).

Figure A.2.5.2. Historical independent LCR spring Chinook populations (Myers et al. 2002).
Draft Report 2/20/2003 

A. CHINOOK 

Coweeman Fall

0

500

1000150020002500

1960 1970 1980 1990 2000 2010

Year

Abundance 

Figure A.2.5.3. Grays River fall Chinook 

population abundance. 

Figure A.2.5.4. Elochoman fall chinook popu

abundance. 

Figure A.2.5.5. Mill, Germany Abernathy fall 

chinook population abundance. 

Grays Fall

0

500

10001500200025003000

1960 1970 1980 1990 2000 2010

Year

Abundance Spawners Natural Origin

Elochoman Fall

0

500

10001500200025003000

1960 1970 1980 1990 2000 2010

Year

Abundance 

Mill Fall

0

1000200030004000500060007000

1975 1980 1985 1990 1995 2000 2005

Year

Abundance Spawners NatOrigSpawners

Figure A.2.5.6. Coweeman fall chinook popu
Draft Report 2/20/2003 

A. CHINOOK 

Figure A.2.5.7. Lower Cowlitz fall chinook population abundance. Figure A.2.5.8. Kalama fall chinook population Figure A.2.5.9. E.F Lewis fall chinook abundance. The E.F. Lewis is a 

component of the Salmon/Lewis fall Chinook population. 

Figure A.2.5.10. Clackamas fall chinook popu

Lower Cowlitz Fall

0

5000

10000150002000025000

1960 1970 1980 1990 2000 2010

Year

Abundance Spawners Natural Spawners

Kalama Fall Graph

0

5000

1000015000200002500030000

1960 1970 1980 1990 2000 

Year

Abundance 

EF Lewis Fall

0

100200300400500600700

1975 1980 1985 1990 1995 2000 2005

Year

Abundance Spawners NatOrigSpawners

Clackamas Fall

0

200400600800

1000120014001600

1960 1970 1980 1990 2000 2

Year

Abundance 
Draft Report 2/20/2003 

A. CHINOOK 

Figure A.2.5.11. Washougal fall chinook population abundance. 

Figure A.2.5.12. Sandy fall chinook population 

Figure A.2.5.13. Wind fall chinook abundance. The Wind is a component of 

the Upper Gorge fall Chinook population. 

Washougal Fall

0

10002000300040005000

1960 1970 1980 1990 2000 2010

Year

Abundance Spawners Natural Spawners

Wind Fall

0

500

100015002000

1960 1970 1980 1990 2000 2010

Year

Abundance Spawners Natural Spanwers

Big White Salmon

0

500

100015002000250030003500

1960 1970 1980 1990 2000 

Year

Abundance 

Sandy Early Fall Chinook

0

500

1000150020002500

1986 1988 1990 1992 1994 1996 19

Year

Figure A.2.5.14. Big White Salmon fall chinook popu
Draft Report 2/20/2003 

A. CHINOOK 

Figure A.2.5.15. Sandy late fall (“bright”) chinook population abundance. 

Figure A.2.5.17. Upper Cowlitz spring chinook population abundance. Figure A.2.5.18. Kalama spring chinook popula

Lewis Brights

0

5000

10000150002000025000

1960 1970 1980 1990 2000 

Year

Abundance 

Upper Cowlitz Spring

0

200400600800

10001200

1975 1980 1985 1990 1995 2000

Year

Abundance Spawners NatOrigSpawners

Kalama Sprin

0

500

100015002000250030003500

1975 1980 1985 1990 1

Year

Abundance 

Sandy Late Fall

0

500

1000150020002500

1980 1985 1990 1995 2000 2005

Year

Abundance Spawners Natural Origin

Figure A.2.5.16. Lewis late fall (“bright”) chinook po
Draft Report 2/20/2003 

A. CHINOOK 

Clatskanie

0

200400600800

1000

1960 1970 1980 1990 

Year

Fish per Mile

Figure A.2.5.19. Lewis spring chinook population abundance. Figure A.2.5.20. Youngs Bay f

Figure A.2.5.21. Big Creek population fish per mile. Figure A.2.5.22. Clatskanie population 

Lewis Spring

0

10002000300040005000600070008000

1975 1980 1985 1990 1995 2000

Year

Abundance Spawners NatOrigSpawners

Youngs Bay Fall Chinoo

0

20406080

100120

1970 1975 1980 1985 1990 

Year

Fish per Mile

Big Creek Population

0

200400600800

100012001400

1960 1970 1980 1990 2000 2010

Year

Fish per Mile
Draft Report 2/20/2003 

A. CHINOOK 

Figure A.2.5.23. Preharvest recruits and spawners for 

Grays River fall Chinook population. 

Figure A.2.5.24. Preharvest rec

Elochoman fall Chinoo

Figure A.2.5.26. Preharvest recruits 

Coweeman fall Chinook po

Figure A.2.5.25. Preharvest recruits and spawners for Mill, 

Germany, Abernathy fall Chinook population. 

Grays

0

500

1000150020002500

1975 1980 1985 1990 1995 2000 2005

Year

Abundance

Pre-Harvest Recruits Spawners

Mill Cr

0

10002000300040005000600070008000

1975 1980 1985 1990 1995 2000 2005

Year

Abundance

Pre-Harvest Recruits Spawners

Coweeman

0

500

10001500200025003000

1975 1980 1985 1990 

Year

Abundance

Pre-Harvest Recruits 

Elochoman

0

500

10001500200025003000

1975 1980 1985 1990 

Year

Abundance

Pre-Harvest Recruits 
Draft Report 2/20/2003 

A. CHINOOK 

Figure A.2.5.28. Preharvest recruit

Kalama fall chinook popul

Figure A.2.5.27. Preharvest recruits and spawners for 

Lower Cowlitz River fall chinook population. 

EF Lewis (Tule)

0

200400600800

100012001400

1975 1980 1985 1990 1995 2000 2005

Year

Abundance

Pre-Harvest Recruits Spawners

Cowlitz

0

100020003000400050006000

1975 1980 1985 1990 1995 2000 2005

Year

Abundance

Pre-Harvest Recruits Spawners

Kalama

0

5000

1000015000200002500030000

1975 1980 1985 1990 

Year

Abundance

Pre-Harvest Recruits 

Washougal

0

10002000300040005000600070008000

1975 1980 1985 1990 

Year

Abundance

Pre-Harvest Recruits 

Figure A.2.5.30. Preharvest rec

Washougal fall Chinoo

Figure A.2.5.29. Preharvest recruits and spawners for East Fork Lewis River fall population. The East Fork Lewis is a component of the 

Salmon/Lewis fall chinook 

p

o

pulation.
Draft Report 2/20/2003 

A. CHINOOK 

Lewis R Fall (brights)

0

5000

100001500020000250003000035000

1975 1980 1985 1990 

Year

Abundance

Pre-Harvest Recruits 

Big White Salmon

0

500

1000150020002500300035004000

1975 1980 1985 1990 1995 2000 2005

Year

Abundance

Pre-Harvest Recruits Spawners

Figure A.2.5.31. Preharvest recruits and spawners for 

Big White Salmon fall chinook population. 

Figure A.2.5.32. Preharvest recruits and 

River late fall (“bright”) chinoo
Draft Report 2/20/2003 

A. CHINOOK 82

Figure A.2.5.34. Long-term lambda vs. recent abundance. Lambda calculated assuming hatchery

fish have a reproductive success of zero. NOTE LOG SCALE OF X-AXIS. 

Figure A.2.5.35. Long-term lambda vs. recent abundance. Lambda calculated assuming hatchery fish have a 

reproductive success equivalent to that of natural origin fish. NOTE LOG SCALE OF X-AXIS. 

Lower Columbia Chinook 

Hatchery Reproductive Sucess = 0

Big White Salmon

Coweeman

Cowlitz

EF Lewis

Elochoman

Grays

Kalama

Lewis

Mill

Sandy

Sandy Washougal

Wind

Cowlitz

Kalama

Lewis

0.85

0.90

0.95

1.00

1.05

1.10

1.15

10 100 1,000 10,000

Recent Abundance

λ

▲ = Fall

■ = Late Fall

● = Spring

Lower Columbia Chinook 

Hatchery Reproductive Sucess = 0

Big White Salmon

Coweeman

Cowlitz

EF Lewis

Elochoman

Grays

Kalama

Lewis

M ill

Sandy

Sandy Washougal

Wind

Cowlitz

Kalama

Lewis

0.85

0.90

0.95

1.00

1.05

1.10

1.15

10 100 1,000 10,000

Recent Abundance

Median Annual Growth Rate 

(λ)

▲ = Fall

■ = Late Fall

● = Spring

Lower Columbia Hatchery 

Reproductive Success = Wild

Big White Salmon

Coweeman

Cowlitz

EF Lewis

Elochoman

Grays Kalama

Lewis

M ill

Sandy Early

Sandy

Washougal

Wind

Cowlitz

Kalama

Lewis

0.6

0.7

0.8

0.9

1.0

1.1

10 100 1,000 10,000

Recent Abundance

Median Anual Growth Rate 

(l)

▲ = Fall

■ = Late Fall

● = Spring

Figure A.2.5.33. Long-term trend vs. recent abundance. NOTE LOG SCALE OF X-AXIS.
Draft Report 2/20/2003 

A. CHINOOK 83

A.2.6 UPPER WILLAMETTE CHINOOK 

A.2.6.1 Previous BRT Conclusions 

• A majority of the previous BRT concluded that the Lower Columbia River ESU is likely 

to become endangered in the foreseeable future. A minority felt that chinook salmon in 

this ESU were not presently in danger of extinction, nor were they likely to become so in 

the foreseeable future. 

• The BRT was concerned about the few remaining populations of spring chinook salmon 

in the Upper Willamette River ESU, and the high proportion of hatchery fish in the 

remaining runs. 

• The BRT noted with concern that ODFW was able to identify only one remaining 

naturally-reproducing population in this ESU–the spring chinook salmon in the 

McKenzie River. 

• Severe declines in short-term abundance had occurred throughout the ESU, and the 

McKenzie River population continued to decline precipitously, indicating that it may not 

be self-sustaining. 

• The potential for interactions between native spring-run and introduced fall-run chinook 

salmon had increased relative to historical times due to fall-run chinook salmon hatchery 

programs and the laddering of Willamette Falls. 

• The declines in spring chinook salmon in the Upper Willamette River ESU can be 

attributed in large part to the extensive habitat blockages caused by dam construction. 

• The BRT was encouraged by efforts to reduce harvest pressure on naturally-produced 

spring chinook salmon in Upper Willamette River tributaries, and the increased focus on 

selective marking of hatchery fish should help managers targeting specific populations of 

wild or hatchery chinook salmon. 

• Currently listed as threatened. 

A.2.6.2 New Data and Analyses 

New Data include: 

• Spawner abundance through 2002 in Clackamas, 2001 in McKenzie and 2001 at 

Willamette Falls. 

• Updated redd surveys in the basin. 

• New estimates of the fraction of hatchery origin spawners in McKenzie and North 

Santiam from otolith marking study. 

• First estimate of hatchery fraction in Clackamas (2002 data). 

• Information on recent hatchery releases. 

New analyses include: 

• Designation of relatively demographically independent populations. 

• Recalculation of previous BRT metrics in McKenzie with additional years data. 

• Estimates of current and historically available kilometers of stream. 

• Update on current hatchery releases. 
Draft Report 2/20/2003 

A. CHINOOK 84

Historical population structure—As part of its effort to develop viability criteria for UW 

chinook, The Willamette/Lower Columbia Technical Recovery Team (WLC-TRT) has identified 

historically demographically independent populations (Myers et al. 2002). Population 

boundaries are based on an application of Viable Salmonid Populations definition (McElhany et 

al. 2000). Myers et al. hypothesized that the ESU historically consisted of 7 spring run 

populations (Figure A.2.6.1). The populations identified in Myers et al. (2002) are used as the 

units for the new analyses in this report. 

Abundance and trends 

References for abundance time series and related data are in Appendix A.5.3. Recent 

abundance of natural-origin spawners, recent fraction of hatchery-origin spawners, and recent 

harvest rates for UW Chinook populations are summarized in Table A.2.6.1. The total number 

of spring chinook spawners passing Willamette Falls from 1953 to 2001 is shown in Figure 

A.2.6.2. All spring chinook in the ESU, except those entering the Clackamas River, must pass 

Willamette Falls. There is no assessment of the ratio of hatchery-origin to wild-origin chinook 

passing the falls, but the majority of fish are undoubtedly of hatchery origin. (Natural-origin fish 

are defined has having had parents that spawned in the wild as opposed to hatchery -origin fish 

whose parents spawned in a hatchery.) Individual population’s status is discussed below. 

Clackamas—The count of spring chinook passing the North Fork dam on the Clackamas 

from 1958 to 2002 are shown in Figure A.2.6.3 (Cramer 2002). The total number of chinook 

passing above the dam has exceeded 1,000 in most years since 1980 and the last several year 

show large increases. However, the majority of these fish are likely of hatchery origin. The only 

year for which hatchery origin estimates are available is 2002 and the estimate is 64% of 

hatchery origin. Although the majority of spring chinook spawning habitat is above North Fork 

Dam, spawning is observed below the dam. The majority of spawning below the dam is also 

considered to be by hatchery origin spawners. The population has shown substantial increases in 

total abundance (mixed hatchery and natural origin) in the last couple of years. 

Molalla—A 2002 survey of 16.3 miles of stream in the Molalla found 52 redds. However, 

93% of the carcasses recovered in the Molalla in 2002 were fin-clipped and of hatchery origin 

(Schroeder et al 2002). Fin-clip recovery fractions for spring chinook in the Willamette tend to 

underestimate the proportion of hatchery origin spawners, so the true fraction is likely in excess 

of 93 % (i.e. near 100%). The Molalla natural spring chinook population is believed to be 

extirpated, or nearly so. 

North Santiam—Survey estimates of redds per mile in the North Santiam are shown in 

Figure A.2.6.4 (from Schroeder et al 2002). The number of stream miles surveyed varies 

between 26.8 and 43.5. The total redds counted in a year varies between 116 and 310. 

Schroeder et al. (2002) estimate an escapement of 94 natural origin spawners above Bennett 

Dam in 2000 and 151 in 2001. These natural-origin spawners were greatly outnumbered by 

hatchery origin spawners (2,192 and 6,635 in 2000 and 2001 respectively). This resulted in 

estimated 94% hatchery origin spawners in 2000 and 98% in 2001. This population is not 

considered self-sustaining. 
Draft Report 2/20/2003 

A. CHINOOK 85

South Santiam—A 2002 survey of 50.8 miles of stream in the South Santiam found 982 

redds. However, 84% of the carcasses recovered in the Molalla in 2002 were fin-clipped and of 

hatchery origin (Schroeder et al 2002). Fin-clip recovery fractions for spring chinook in the 

Willamette tend to underestimate the proportion of hatchery origin spawners, so the true fraction 

is likely in excess of 84 %. This population is not considered self-sustaining. 

Calapooia—A 2002 survey of 11.1 miles of stream in the Calapooia above Brownsville 

found 16 redds (Schroeder et al 2002). The carcasses recovered in the Calapooia in 2002 were 

too decomposed to determine the presence or absence of fin clips. However, it was assumed that 

all the fish were surplus hatchery fish outplanted from the South Santiam hatchery. (Schroeder et 

al. 2002). The Calapooia natural spring chinook population is believed to be extirpated, or 

nearly so. 

McKenzie—The time series of total spring chinook counts and natural origin fish passing 

Leaburg dam on the McKenzie is shown in Figure A.2.6.5. The average fraction of hatcheryorigin fish passed above the dam from 1998 to 2001 was estimated at 26%. Redds are observed 

below Leaburg Dam, but the fraction of hatchery-origin fish is higher (Schroeder et al 2002). 

The fraction of fin-clipped spring chinook carcasses recovered below Leaburg was 72% in 2000 

and 67% in 2001. Again, fin clip recoveries tend to underestimate the fraction of hatchery-origin 

spawners. The spring chinook population above Leaburg Dam in the McKenzie is considered 

the best in the ESU, but with over 20% of the fish of hatchery origin, it is difficult to determine if 

this population would be naturally self sustaining. The population has shown substantial 

increases in total abundance (mixed hatchery and natural origin) in the last couple of years. 

Middle Fork Willamette—A 2002 survey of 17 miles of the mainstem Middle Fork found 

64 redds. However, 77% of the carcasses recovered in the Middle Fork in 2002 were fin-clipped 

and of hatchery origin (Schroeder et al 2002). In Fall Creek, a tributary of the Middle Fork, 171 

redds in 13.3 miles were found in 2002. The 2002 carcass survey found 39% of fish fin-clipped. 

Fin-clip recovery fractions for spring chinook in the Willamette tend to underestimate the 

proportion of hatchery origin spawners. This population is not considered self-sustaining. 

No formal trend analyses were conducted on any of the UW chinook populations. The two 

populations with long time series of abundance (Clackamas and McKenzie) have insufficient 

information on the fraction of hatchery-origin spawners to permit a meaningful analysis. 

Loss of habitat from barriers—An analysis was conducted by Steel and Sheer (2002) to assess 

the number of stream km historically and currently available to salmon populations in the UW 

(Table A.2.6.1). Stream km usable by salmon are determined based on simple gradient cut offs 

and on the presence of impassable barriers. This approach will over estimate the number of 

usable stream km, as it does not take into consideration habitat quality (other than gradient). 

However, the analysis does indicate that for some populations the number of stream habitat km 

currently accessible is significantly reduced from the historical condition. 
Draft Report 2/20/2003 

A. CHINOOK 86

Hatchery releases 

A large number of spring chinook are released in the Upper Willamette as mitigation for 

the loss of habitat above federal hydroprojects (Table A.2.6.2). This hatchery production is 

considered a potential risk, because it masks the productivity of natural population, interbreed of 

hatchery and natural fish poses potential genetic risks and the incidental take from the fishery 

promoted by the hatchery production can increase adult mortality. Harvest retention is only 

allowed for hatchery marked fish, but take from hooking mortality and non-compliance is still a 

potential issue. 

Fall chinook are not native to the upper Willamette and are not part of the Upper 

Willamette chinook ESU. Fall chinook hatchery fish are no longer released into the upper 

Willamette, though there have been substantial releases in the past (Figure A.2.6.6). 

A.2.6.3 New ESU Information 

Based on the updated information provided in this report, the information contained in 

previous LCR status reviews, and preliminary analysis by the WLC-TRT, we have tentatively 

identified the number of historical and currently viable populations (Table A.2.6.3). This 

summary indicates that the ESU is substantially modified from historical population structure. 

Most populations would are considered extirpated or nearly so. The only population considered 

potentially self-sustaining is the McKenzie. However, its abundance has been relatively low 

(low thousands) with a substantial number of these fish being of hatchery origin. The population 

has shown a substantial increase in the last couple of years, hypothesized to be a result of 

increase ocean survival. It is unknown what ocean survivals will be in the future and the longterm sustainability of this population in uncertain. 
Draft Report 2/20/2003 

A. CHINOOK 87

Table A.2.6.1. Historical populations of Upper Willamette spring chinook. The recent abundance is the 

geometric mean of natural origin spawners of the last five years of available data and the minmax are the lowest and highest five-year geometric means in the time series. Natural origin fish 

had parents that spawned in the wild as opposed to hatchery origin fish whose parents were 

spawned in a hatchery. The data years are the data years used for the abundance min-max 

estimates, the extinction risk estimate and the trends (see Figures). Longer time series may be 

available for spawners only (see figures) but hatchery fraction information was required to 

estimate means, extinction risk and trends. For McKenzie population, the fraction hatchery is the 

average percent of spawners of hatchery origin over the last four years. For Clackamas only one 

hatchery fraction estimate is available (2002). Hatchery fraction in the Molalla, South Santiam 

and Middle Fork and minimum estimates based on the ratio of adipose marked verses unmarked 

fish recovered in 2001 (Schroeder et al 2002). 

Population Recent 

Abundance 

Data 

Years 

Hatcher

y 

Fraction 

(%) 

Potential 

Current 

Habitat 

(%) 

Potential 

Historical 

Habitat 

(km) 

Current to 

Historical 

Habitat 

Ratio 

Clackamas 

River 830 1958-2002 64 369 475 78 

Molalla River 

Extirpated (or 

nearly so) >93 432 688 63 

North Santiam 

River 

119 (above 

Bennett Dam) 

2000-

2001 97 173 269 64 

South Santiam 

River >84 445 658 68 

Calapooia 

River 

Extirpated (or 

nearly so) 163 253 65 

McKenzie 

1664 

(824-1664) 

1970-

2001 26 283 382 74 

Middle Fork 

Willamette 

River 

 >77 197 425 46 

Total 1,787 2,063 3,150 65 

Average 26 
Draft Report 2/20/2003 

A. CHINOOK 88

Table A.2.6.2. Upper Willamette spring chinook hatchery releases (compiled by Waknitz 2002). 

Watershed Years Hatchery Stock Release Site Total 

1994 Dexter Pd Mckenzie L Willamette R 73,028 

1995 Dexter Pd Willamette L Willamette R 137,573 

1995 Lone Star Clackamas L Willamette R 59,654 

1995 Marion Forks N Santiam L Willamette R 40,320 

1993, 1994 Mckenzie Mckenzie L Willamette R 344,089 

1992, 1993 Step Clackamas L Willamette R 70,193 

1993, 1994 Step Mckenzie L Willamette R 331,446 

1993-1995 Mckenzie Clackamas L Willamette R 125,585 

1996-1999 Willamette Mckenzie L Willamette R 225,122 

1995-1996 Willamette N Santiam L Willamette R 81,513 

Willamette R 

1995-1999 Mckenzie Mckenzie L Willamette R 574,117 

1991-1994 Clackamas Clackamas Clackamas R 4,358,092

1995-2002 Clackamas Clackamas Clackamas R 9,182,916

1996-2001 Mckenzie Mckenzie Clackamas R 1,332,542 Clackamas R 

1991 Eagle Creek Nfh Clackamas Eagle Cr 556,814 

Table A.2.6.3. Number of populations in the ESU. Populations with “some current natural production” 

have some natural origin recruits present but are not necessarily considered self-sustaining 

(“viable”). 

Total 

Historical 7 

Some current natural 

production 5-6 

Currently “viable” 0-1 
Draft Report 2/20/2003 

A. CHINOOK 89

Figure A.2.6.1. Historical populations of spring chinook in the Willamette ESU (Myers et al. 2002). 
Draft Report 2/20/2003 

A. CHINOOK 90

Figure A.2.6.2. Counts of spring chinook passing Willamette Falls.

Figure A.2.6.3. Counts of Spring Chinook passing North Fork Dam on the Clackamas River (Cramer 

2002). The total count is all fish passing above the dam. There is only one estimate (in 2002) of 

the number of fish passing above the dam that are of natural origin. 

Spring Chinook (Willamette Fall Count)

0

10,000

20,000

30,000

40,000

50,000

60,000

70,000

80,000

1950 1960 1970 1980 1990 2000 2010

Year

Abundance

Clackamas

0

1000

2000

3000

4000

5000

6000

7000

1950 1960 1970 1980 1990 2000 2010

Year

Abundance

Total Count Natural Origin
Draft Report 2/20/2003 

A. CHINOOK 91 

Figure A.2.6.4. North Santiam redds per mile (data from Schroeder et al. 2002). The number of stream 

miles surveyed varies between 26.8 and 43.5 miles. The total redds count in a year varies 

between 116 and 310. Over 95% of the spawners are estimated of hatchery origin 

Figure A.2.6.5. Counts of spring chinook at Leaburg Dam. 

McKenzie

0

1000

2000

3000

4000

5000

6000

7000

8000

1965 1970 1975 1980 1985 1990 1995 2000 2005

Year

Abundance

Total Count Natural Origin

North Santiam

0

2

4

6

8

10

12

1995 1996 1997 1998 1999 2000 2001 2002 2003

Year

Redds/Mile
Draft Report 2/20/2003 

A. CHINOOK 92 

Figure A.2.6.6. Counts of fall chinook at Willamette Falls. Fall chinook are not native in the Upper 

Willamette and are not in the in the Upper Willamette Chinook ESU. 

Fall Chinook- Not in ESU (Willamette Falls Count)

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

1950 1960 1970 1980 1990 2000 2010

Year

Abundance
Draft Report 2/20/2003 

A. CHINOOK 93 

A.2.7 CALIFORNIA COASTAL CHINOOK 

A.2.7.1 Previous BRT Conclusions 

The status of chinook salmon throughout California and the Pacific Northwest was 

formally assessed in 1998 (Myers, et al. 1998). Substantial scientific disagreement about the 

biological data and its interpretation persisted for some Evolutionarily Significant Units (ESUs); 

these ESUs were reconsidered in a subsequent status review update (NMFS 1999). Information 

from those reviews regarding ESU structure, analysis of extinction risk, risk factors, and 

hatchery influences is summarized in the following sections. 

ESU structure 

The initial status review proposed a single ESU of chinook salmon inhabiting coastal 

basins south of Cape Blanco and the tributaries to the Klamath River downstream of its 

confluence with the Trinity River (Myers et al 1998). Subsequent review of an augmented 

genetic data set and further consideration of ecological and environmental information led to the 

division of the originally proposed ESU into the Southern Oregon and Northern California 

Coastal Chinook Salmon ESU and the California Coastal Chinook Salmon ESU (NMFS 1999). 

The California Coastal Chinook Salmon ESU currently includes chinook salmon from Redwood 

Creek to the Russian River (inclusive). 

Summary of risk factors and status 

The California Coastal Chinook Salmon ESU is listed as Threatened. Primary causes for 

concern were low abundance, reduced distribution (particularly in the southern portion of the 

ESU’s range), and generally negative trends in abundance; all of these concerns were especially 

strong for spring-run chinook salmon in this ESU (Myers et al. 1998). Data for this ESU are 

sparse and, in general of limited quality, which contributes to substantial uncertainty in estimates 

of abundance and distribution. Degradation of the genetic integrity of the ESU was considered 

to be of minor concern and to present less risk for this ESU than for other ESUs. 

Previous reviews of conservation status for chinook salmon in this area exist. Nehlsen et 

al. (1991) identified three putative populations (Humboldt Bay Tributaries, Mattole River, and 

Russian River) as being at high risk of extinction and three other populations (Redwood Creek, 

Mad River, and Lower Eel River) as being at moderate risk of extinction. Higgins et al. (1992) 

identified seven “stocks of concern,” of which two populations (tributaries to Humboldt Bay and 

the Mattole River) were considered to be at high risk of extinction. Some reviewers indicate that 

chinook salmon native to the Russian River have been extirpated. 

Historical estimates of escapement are presented in Table A.2.7.1. These estimates are 

based on professional opinion and evaluation of habitat conditions, and thus do not represent 

rigorous estimates based on field sampling. Historical time series of counts of upstream 

migrating adults are available for Benbow Dam (South Fork Eel River; 1938-1975), Sweasy 

Dam (Mad River; 1938-1964), and Cape Horn Dam (Van Arsdale Fish Station, Eel River); the 
Draft Report 2/20/2003 

A. CHINOOK 94 

Table A.2.7.1. Historical estimates of abundance of chinook salmon in the California Coastal Chinook 

Salmon ESU. 

Selected Watersheds CDFG 

1965 

Wahle & 

Pearson 1987 

Redwood Creek 5,000 1,000 

Mad River 5,000 1,000 

Eel River 55,000 17,000 

Mainstem Eel1 13,000 

Van Duzen River1 2,500 

Middle Fork Eel1 13,000 

South Fork Eel1 27,000 

Bear River 100 

Small Humboldt County 

Rivers 1,500 

Miscellaneous Rivers 

North of Mattole 600 

Mattole River 5,000 1,000 

Noyo River 50 

Russian River 500 50 

Total 72,550 20,750 

1

Entries for subbasins of the Eel River Basin are not included separately in the total. 

latter represent a small, unknown and presumably variable fraction of the total run to the Eel 

River. Data from cursory, nonsystematic stream surveys of two tributaries to the Eel River 

(Tomki and Sprowl Creeks) and one tributary to the Mad River (Canon Creek) were also 

available; these data provide crude indices of abundance. 

Previous status reviews considered the following to pose significant risks to the California 

Coastal Chinook Salmon ESU: degradation of freshwater habitats due to a variety of agricultural 

and forestry practices, water diversions, urbanization, mining, and severe recent flood events 

(exacerbated by land use practices). Special concern was noted regarding the more precipitous 

declines in distribution and abundance in spring-run chinook salmon. Many of these factors are 

particularly acute in the southern portion of the ESU range and were compounded by uncertainty 

stemming from the general lack of population monitoring in California (Myers et al. 1998). 

In previous status reviews, the effects of hatcheries and transplants on the genetic integrity 

of the ESU elicited less concern than other risk factors for this ESU, and were less of a concern 

for this ESU in comparison to other ESUs. 

Listing status 

The California Coastal Chinook Salmon ESU is currently listed as “Threatened.” 
Draft Report 2/20/2003 

A. CHINOOK 95 

A.2.7.2 New Data and Analysis 

The Technical Recovery Team for the North-Central California Coast Recovery 

Domain has proposed a set of plausible hypotheses, based largely on geography, regarding 

the population structure of the California Coast Chinook Salmon ESU (Table A.2.7.2), but 

has concluded that insufficient information exists to discriminate among these hypotheses 

(NCCC-TRT, in preparation). Data are not available for all of the potential populations; 

only those for which data are available are considered below. 

New or updated time series for chinook salmon in this ESU include (1) counts of 

adults reaching Van Arsdale Fish Station near the effective headwater terminus of the Eel 

River; (2) cursory, quasi-systematic spawner surveys on Canon Creek (tributary to the Mad 

River), Tomki Creek (tributary to the Eel River), and Sprowl Creek (tributary to the Eel 

River); (3) counts of returning spawners at a weir on Freshwater Creek (tributary to 

Table A.2.7.2. Plausible hypotheses for independent populations considered by the North Central 

California Coast Technical Recovery Team. This information is summarized from a working 

draft report, and should be considered as preliminary and subject to revision. 

“Lumped” “Split” 

Redwood Creek 

Mad River 

Humboldt Bay Tributaries 

Eel River1 

 South Fork Eel River 

 Van Duzen River 

 Middle Fork Eel River 

 North Fork Eel River 

 Upper Eel River 

Bear River 

Mattole River 

Tenmile to Gualala2 

Russian River 

1

Plausible hypotheses regarding the population structure of chinook salmon in the Eel River basin include scenarios 

ranging from five independent populations (South Fork Eel River, Van Duzen River, Upper Eel River, Middle Fork 

Eel River, and North Fork Eel River) to a single, strongly structured independent population.

2

This stretch of the coast comprises numerous smaller basins that drain directly into the Pacific Ocean, some of 

which appear sufficiently large to support independent populations of chinook salmon. The following hypotheses 

span much of the range of plausible scenarios: (1) independent populations exist in all basins that exceed a minimum 

size; (2) independent populations exist only in basins between the Tenmile River and Big River, inclusive, that 

exceed a minimum size; (3) chinook salmon inhabiting basins along this stretch of coastline exhibit patchy 

population or metapopulation dynamics in which the occupancy of any given basin is dependent on migrants from 

other basins, and possibly from larger basins to the north and south; and (4) chinook salmon inhabiting basins 

between the Tenmile River and Big River, inclusive, exhibit patchy population or metapopulation dynamics in 

which the occupancy of any given basin is dependent on migrants from other basins in this region and possibly to 

the north while other basins to the south only sporadically harbor chinook salmon. 
Draft Report 2/20/2003 

A. CHINOOK 96 

Table A.2.7.3. Geometric means, estimated lambda, and long- and short-term trends for abundance time 

series in the California Coastal Chinook Salmon ESU. 

5 year Geometric Mean Trend 

Rec Min Max Long Short 

Freshwater Creek 22 13 22 0.137 

(-0.405, 0.678) 

0.137 

 (-0.405, 0.678) 

Mad River 

Canon Creek 73 19 103 0.0102 

(-0.106, 0.127) 

0.155 

(-0.069, 0.379) 

Eel River 

Sprowl Creek 43 43 497 -0.096 

(-0.157, -0.0336) 

-0.183 

(-0.356, -0.0096) 

Tomki Creek 61 13 2,233 -0.199 

 (-0.351, -0.0464) 

0.294 

 (0.0547, 0.533) 

Humboldt Bay). None of these time series is especially suitable for analysis of trends or 

estimation of population growth rates. For this reason, we have presented the data 

graphically, and restricted analysis to estimation of long- and short-term trends, rather than 

pursue more sophisticated analysis. 

Freshwater Creek—Counts of chinook salmon passing the weir near the mouth of 

Freshwater Creek, a tributary to Humboldt Bay, provide a proper census of a small (N ~ 

20) population of naturally and hatchery-spawned chinook (Figure A.2.7.1). Chinook 

salmon occupying this watershed may be part of a larger “population” that uses tributaries 

of Humboldt Bay (NCCC-TRT, in preparation). The time series comprises only 8 years of 

observations, which is too few to draw strong inferences regarding trends. Clearly, the 

trend is positive, although the role of hatchery production in producing this signal may be 

significant (Table A.2.7.3; Figure A.2.7.1) 

Mad River—Data for naturally spawning fish are available from spawner surveys on 

Canon Creek, and to a lesser extent on the North Fork Mad River. Only the counts from 

Canon Creek extend continuously to the present (Figure A.2.7.2a). Due to high variability 

in these counts, short-term and long-term trends do not differ significantly from zero, 

although the tendency is towards a positive trend. Due to a hypothesized, but 

unquantified, effect of interannual variation in water availability on distribution of 

spawners in the basin, it is not clear whether these data provide any useful information for 

the population as a whole; however, more sporadic counts from the mainstem Mad River 

suggest that the estimates from Canon Creek capture gross signals, and support the 

hypothesis of a recent positive trend in abundance (Figure A.2.7.2b). 

Eel River—The Eel River plausibly harbors anywhere from one to five independent 

populations (NCCC-TRT, in preparation, Table A.2.7.2). Three current time series provide 

information for the population(s) that occupy this basin: (1) counts of adults reaching Van 

Arsdale Fish Station near the effective headwater terminus of the Eel River (Figure 

A.2.7.3a); (2) spawner surveys on Sprowl Creek (tributary to the Eel River) (Figure 

A.2.7.3b); and (3) spawner surveys on Tomki Creek (tributary to the Eel River) (Figure 
Draft Report 2/20/2003 

A. CHINOOK 97 

1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 0

20406080

100120140160

totalclipped

Figure A.2.7.1. Counts of chinook salmon at the weir on Freshwater Creek.

a b 

1980 1985 1990 1995 2000 0

100200300400500600

Canon Creek (Mad River): Spaw ner Survey Estim ates

1980 1985 1990 1995 

0

100200300400500600

Mad River: Spawner Counts

Figure A.2.7.2. Abundance time series for chinook salmon in portions of the Mad River 

basin. (a) spawner 

counts on Canon Creek; and (b) spawner counts on portions of the mainstem Mad River.
Draft Report 2/20/2003 

A. CHINOOK 98 

a b 

1940 1950 1960 1970 1980 1990 2000 0

200

400

600

800

1000

1200

1400

1600

1800

VanArsdale Fish Station Counts

total

clipped

1965 1970 1975 1980 1985 1990 1995 2000 0

500

1000

1500

2000

2500

Sprowl Creek (Eel River); Spawner Survey Estimates

c 

1965 1970 1975 1980 1985 1990 1995 2000 0

500

1000

1500

2000

2500

3000

3500

4000

Tomki Creek (Eel River); Spawner Survey Estimates

Figure A.2.7.3. Abundance time series for chinook salmon in portions of the Eel River basin. (a) counts of 

chinook salmon at Van Arsdale Fish Station at the upstream terminus of anadromous access on the 

mainstem Eel River; (b) estimates of spawner abundance based on spawner surveys and additional data 

from Sprowl Creek; and (c) estimates of spawner abundance based on spawner surveys and additional data 

from Tomki Creek.
Draft Report 2/20/2003 

A. CHINOOK 99 

A.2.7.3c). These data are not especially suited to rigorous analysis of population status for 

a number of reasons, and sophisticated analyses were not pursued. 

Inferences regarding population status drawn from the time series of counts of adult 

chinook salmon reaching Van Arsdale Fish Station (VAFS) are weakened by two 

characteristics of the data. First, adult salmon reaching VAFS include both naturally and 

hatchery spawned fish, yet the long-term contribution of hatchery production to the 

spawner population is unknown and may be quite variable due to sporadic operation of the 

egg-take and release programs since the mid-1970’s. Second, and perhaps more 

importantly, it is not clear what counts of natural spawners at VAFS indicate about the 

population or populations of chinook salmon in the Eel River. As a weir count, 

measurement error is expected to be small for these counts. However, very little spawning 

habitat exists above VAFS, which sits just below the Cape Horn dam on the Eel River, 

which suggests that counts made at VAFS represent the upper edge of the spawners’ 

distribution in the upper Eel River. Spawner access to VAFS and other headwater habitats 

in the Eel River basin is likely to depend strongly on the timing and persistence of suitable 

river flow, which suggests that a substantial component of the process error in these counts 

is not due to population dynamics. For these reasons, no statistical analysis of these data 

was pursued. 

Additional data for the Eel River population or populations are available from 

spawner surveys from Tomki and Sprowl Creeks, which yield estimates of abundance 

based on (1) quasi-systematic index site spawner surveys that incorporate mark-recapture 

of carcasses and (2) additional so-called “compatible” data from other surveys. Analysis 

for Sprowl Creek indicates negative long-term and short-term trends; similar analysis 

indicates a long-term decline and short-term increase for Tomki Creek (Table 3). Caution 

in interpreting these results is warranted, particularly given the quasi-systematic collection 

of these data, and the likelihood that these data include unquantified variability due to 

flow-related changes in spawners’ use of mainstem and tributary habitats. In particular, 

inferences regarding population status based on extrapolations from these data to basinwide estimates of abundance are expected to be weak and perhaps not warranted. 

Mattole River—Recent spawner and redd surveys on the Mattole River and 

tributaries have been conducted by the Mattole Salmon Group since 1994. The surveys 

provide useful information on the distribution of salmon and spawning activity throughout 

the basin. Local experts have used these and ancillary data to develop rough “index” 

estimates of spawner escapement to the Mattole; however, the intensity and coverage of 

these surveys has not been consistent, and the resulting data are not suitable for rigorous 

estimation of abundance (e.g., through area-under-the-curve analysis). 

Russian River—No long-term, continuous time series are available for sites in the 

Russian River basin, but sporadic estimates based on spawner surveys are available for 

some tributaries. Video-based counts of upstream migrating adult chinook salmon passing 

a temporary dam near Mirabel on the Russian River are available for 2000-2002. Counts 

are incomplete, due to technical difficulties with the video apparatus, occasional periods of 

poor water clarity, occasional overwhelming numbers of fish, and disparities between 
Draft Report 2/20/2003 

A. CHINOOK 100 

counting and migration periods; thus, these data represent a minimum count of adult 

chinook. Counts have exceeded 1,300 fish in each of the last three years (5,465 in 2002); 

and a rigorous mark-recapture estimate of outmigrant abundance in 2002 exceeded 200,000 

(Shawn Chase, Sonoma County Water Agency, personal communication). Since chinook 

salmon have not been produced at the Don Clausen Hatchery since 1997, so these counts 

represent natural production or straying from other systems. No data were available to 

assess the genetic relationship of these fish to others in this or other ESUs. 

Summary—Historical and current information indicates that abundance in putatively 

independent populations of chinook salmon is depressed in many of those basins where 

they have been monitored. The relevance of recent strong returns to the Russian River to 

ESU status are not clear as the genetic composition of these fish is unknown. Reduction in 

geographic distribution, particularly for spring-run chinook salmon and for basins in the 

southern portion of the range, continues to present substantial risk. Genetic concerns are 

reviewed below (Hatchery Information). As for previous status reviews, uncertainty 

continues to contribute substantially to assessments of risk facing this ESU. 

A.2.7.3 Hatchery Information 

Hatchery stocks that are being considered for inclusion in this ESU are: (1) Mad 

River Hatchery, (2) hatchery activities of the Humboldt Fish Action Council on Freshwater 

Creek; (3) Yager Creek Hatchery operated by Pacific Lumber Company; (4) Redwood 

Creek Hatchery; (5) Hollow Tree Creek Hatchery; (6) Van Arsdale Fish Station; and (6) 

hatchery activities of the Mattole Salmon Group. Chinook salmon are no longer produced 

at the Don Clausen hatchery on Warm Springs Creek (Russian River). In general, hatchery 

programs in this ESU are not oriented towards large-scale production, but rather are smallscale operations oriented at supplementing depressed populations. 

Freshwater Creek—This hatchery is operated by Humboldt Fish Action Council and 

CDFG to supplement and restore natural production in Freshwater Creek. All spawners are 

from Freshwater Creek; juveniles are marked and hatchery fish are excluded from use as 

broodstock. Weir counts provide good estimates of the proportion of hatchery- and 

naturally produced fish returning to Freshwater Creek (30-70% hatchery from 1997-2001); 

the contribution of HFAC production to spawning runs in other streams tributary to 

Humboldt Bay is unknown. 

Mad River—Recent production from this hatchery has been based on small numbers 

of spawners returning to the hatchery. There are no estimates of naturally spawning 

chinook salmon abundance available for the Mad River to determine the contribution of 

hatchery production to chinook salmon in the basin as a whole. Broodstock has generally 

been drawn from chinook salmon returning to the Mad River; however, releases in the 

1970s and 1980s have included substantial releases of fish from out-of-basin (Freshwater 

Creek) and out-of-ESU (Klamath-Trinity and Puget Sound). 

Eel River—Four hatcheries, none of which are major production hatcheries, 

contribute to production of chinook salmon in the Eel River Basin: hatcheries on Yager 

Creek (recent effort: ~12 females spawned per year), Redwood Creek (~12 females), 
Draft Report 2/20/2003 

A. CHINOOK 101 

Hollow Tree Creek, and the Van Arsdale Fish Station (VAFS) (~60 males and females 

spawned). At the first three hatcheries, broodstock is selected from adults of non-hatchery 

origin; at VAFS, broodstock includes both natural and hatchery origin fish. In all cases, 

however, insufficient data on naturally spawning chinook salmon are available to estimate 

the effect of hatchery fish on production or other characteristics of naturally spawning 

chinook salmon in the Eel River basin. Since 1996, all fish released from VAFS have been 

marked. Subsequent returns indicate that approximately 30% of the adult chinook salmon 

trapped at VAFS are of hatchery origin. It is not clear what these numbers indicate about 

hatchery contributions to the population of fish spawning below VAFS. 

Mattole River—The Mattole Salmon Group has operated a small hatchbox program 

since 1980 (current effort: ~40,000 eggs from ~10 females) to supplement and restore 

chinook salmon and other salmonids in the Mattole River. All fish are marked, but no 

rigorous estimate of hatchery contributions to adult escapement is possible. Hatcheryproduced outmigrants comprised approximately 17.3% (weighted average) of outmigrants 

trapped during 1997, 1998 and 2000 (Mattole Salmon Group 2000, Five Year Management 

Plan for Salmon Stock Rescue Operations 2000-2001 through 2004-2005 Seasons). 

Trapping efforts did not fully span the period of natural outmigration so this figure may 

overerestimate the contribution of hatch-box production to total production in the basin. 

Russian River—Production of chinook salmon at the Don Clausen (Warm Springs 

Hatchery) ceased in 1997 and had been largely ineffective for a number of years prior to 

that. Recent returns of chinook salmon to the Russian River stem from natural production, 

and possibly from fish straying from other basins, including perhaps Central Valley stocks. 

Summary 

Artificial propagation of chinook salmon in this ESU remains at relatively low levels. 

No putatively independent populations of chinook salmon in this ESU appear to be entirely 

dominated by hatchery production, although proportions of hatchery fish can be quite high 

where natural escapement is small and hatchery production appears to be successful (e.g., 

Freshwater Creek). It is not clear whether current hatcheries pose a risk or offer a benefit 

to naturally spawning populations. Extant hatchery programs are operated under guidelines 

designed to minimize genetic risks associated with artificial propagation, and save for 

historical inputs to the Mad River Hatchery stock, do not appear to be at substantial risk of 

incorporating out-of-basin or out-of-ESU fish. Thus, it is likely that artificial propagation 

and degradation of genetic integrity continue do not represent a substantial conservation 

risk to the ESU. Categorizations of hatchery stocks in the California Coastal chinook ESU 

(SSHAG 2003) can be found in Appendix A.5.1. 

A.2.7.4 Comparison with Previous Data 

Few new data, and few new datasets were available for consideration, and none of the 

recent data contradict the conclusions of previous status reviews. Chinook salmon in the 

Coastal California ESU continue to exhibit depressed population sizes relative to historical 

abundances; this is particularly true for spring-run chinook, which may no longer be extant 

anywhere within the range of the ESU. Evaluation of the significance of recent potential 
Draft Report 2/20/2003 

A. CHINOOK 102 

increases in abundance of chinook salmon in the Russian River must weigh the substantial 

uncertainty regarding the genetic relatedness of these fish to others in the northern part of 

the ESU. 

Harvest rates are not explicitly estimated for this ESU; however, it is likely that 

current restrictions on harvest of Klamath River fall chinook maintain low ocean harvest of 

chinook salmon from the California Coastal ESU (PFMC 2002a, b). Potential changes in 

age-structure of chinook salmon populations (e.g., Hankin et al. 1993) and associated risk 

has not been evaluated for this ESU. 

No information exists to suggest new risk factors, or substantial effective 

amelioration of risk factors noted in the previous status reviews save for recent changes in 

ocean conditions. Recent favorable ocean conditions have contributed to apparent 

increases in abundance and distribution for a number of anadromous salmonids, but the 

expected persistence of this trend is unclear. 
Draft Report 2/20/2003 

A. CHINOOK 103 

A.2.8. SACRAMENTO RIVER WINTER-RUN CHINOOK 

A.2.8.1. Previous BRT Conclusions 

Summary of major risk factors and status indicators 

Historically, winter chinook were dependent on access to spring-fed tributaries to the upper 

Sacramento River that stayed cool during the summer and early fall. Adults enter freshwater in 

early winter and spawn in the spring and summer. Juveniles rear near the spawning location 

until at least the fall, when water temperatures in lower reaches are be suitable for migration. 

Winter chinook were abundant and comprised populations in the McCloud, Pit, and Little 

Sacramento, with perhaps smaller populations in Battle Creek and the Calaveras River. On the 

basis of commercial fishery landings in the 1870s, Fisher (1994) estimated that the total run size 

of winter chinook may have been 200,000 fish. 

The most obvious challenge to winter chinook was the construction of Shasta Dam, which 

blocked access to the entire historic spawning habitat. It was not expected that winter chinook 

would survive this habitat alteration (Moffett 1949). Cold-water releases from Shasta, however, 

created conditions suitable for winter chinook for roughly 100 km downstream from the dam. 

Presumably, there were several independent populations of winter chinook in the Pitt, McCloud, 

Little Sacramento Rivers and various tributaries to these rivers such as Hat Creek and the Fall 

River, and these populations merged to form the present single population. If there ever were 

populations in Battle Creek and the Calaveras River, they have been extirpated. 

In addition to having only a single extant population dependent on artificially-created 

conditions, winter chinook face numerous other threats. Chief among these is small population 

size: escapement fell below 200 fish in the 1980s. Population size declined monotonically from 

highs of near 100,000 fish in the late 1960s, indicating a sustained period of poor survival. There 

are questions of genetic integrity due to winter chinook having passed through several 

bottlenecks in the 20th century. Other threats include inadequately screened water diversions, 

predation at artificial structures and by nonnative species, overfishing, pollution from Iron 

Mountain mine (among other sources), adverse flow conditions, high summer water 

temperatures, unsustainable harvest rates, passage problems at various structures (especially, 

until recently, Red Bluff Diversion Dam), and vulnerability to drought. 

BRT conclusions 

The chinook BRT spent little time considering the status of winter chinook, because winter 

chinook were already listed as endangered at the time of previous BRT meetings. 

Listing status 

Winter chinook were listed as Threatened in 1990 and reclassified as Endangered 1994. 
Draft Report 2/20/2003 

A. CHINOOK 104 

A.2.8.2 Summary of New Information 

Viability assessments 

Two studies have been done on the population viability of Sacramento River winter 

chinook. Botsford and Brittnacher, (1998), in a paper that is part of the draft recovery plan, 

developed de-listing criteria using a simple age-structured, density-independent model of 

spawning escapement. They concluded, on the basis of the 1967-1995 data, that winter chinook 

were certain to fall below the quasi-extinction threshold of 3 consecutive spawning runs with less 

than 50 females. 

Lindley and Mohr, (in press) developed a slightly more complex Bayesian model of winter 

chinook spawning escapement that allowed for density dependence and a change in population 

growth rate in response to conservation measures initiated in 1989. This model, due to its 

allowance for the growth rate change, its accounting for parameter uncertainty, and use of newer 

data (through 1998), suggested a lower but still biologically significant expected quasi-extinction 

probability of 28%. 

Draft recovery plan 

The draft recovery plan for winter chinook (NMFS 1997) provides a comprehensive review 

of the status, life history, habitat requirements, and risk factors of winter chinook. It also 

provides a recovery goal: an average of 10,000 females spawners per year and a λ ≥ 1.0 

calculated over 13 years of data (assuming a certain level of precision in spawning escapement 

estimates). 

New abundance data 

The winter chinook spawning run has been counted at Red Bluff Diversion Dam (RBDD) 

fish ladders since 1967. Escapement has been estimated with a carcass survey since 1997. 

Through the mid-1980s, the RBDD counts were very reliable. At that time, changes to the dam 

operation were made to alleviate juvenile and adult passage problems. Now, only the tail end of 

the run (about 15% on average) is forced over the ladders, greatly reducing the accuracy of the 

RBDD counts. The carcass mark-recapture surveys were initiated to improve escapement 

estimates. The two measures are in very rough agreement, and there are substantial problems 

with both estimates, making it difficult to choose one as more reliable than the other. It does 

appear that the RBDD count is an underestimate, since the carcass survey crews have handled 

more carcasses than the RBDD estimate in some years, and only a fraction of the carcasses are 

available for capture. The problem with the carcass-based estimate is the estimation of this 

fraction—it appears that the probability of initial carcass recovery depends strongly on the sex of 

the fish and possibly on whether it has been previously recovered. In spite of these problems, 

both abundance measures suggest that the abundance of winter chinook is increasing. Based on 

the RBDD counts, the winter chinook population has been growing rapidly since the early 1990s 

(Figure A.2.8.1), with a short-term trend of 0.26 (Table A.2.8.1). On the population growth ratepopulation size space, the winter chinook population has a somewhat low population growth and 

moderate size compared to other Central Valley salmonid populations (Figure A.2.8.2). 
Draft Report 2/20/2003 

A. CHINOOK 105 

Table A.2.8.1. Summary statistics for trend analyses. Numbers in parentheses are 0.90 confidence 

intervals 

Population 5-yr 

mean 

5-yr 

min 

5-yr 

max λ μ LT trend ST trend 

Sac. R. winter 

chinook 2,191 364 65,683 

0.97 

(0.87, 

1.09) 

-0.10 

(-0.21, 

0.01) 

-0.14 

(-0.19, -

0.09) 

0.26 

(0.04, 0.48) 

Butte Cr. spring 

chinook 4,513 67 4,513 

1.30 

(1.09, 

1.60) 

0.11 

(-0.05, 

0.28) 

0.11 

(0.03, 0.19) 

0.36 

(0.03, 0.70) 

Deer Cr. spring 

chinook 1,076 243 1,076 

1.17 

(1.04, 

1.35) 

0.12 

(-0.02, 

0.25) 

0.11 

(0.02, 0.21) 

0.16 

(-0.01, 0.33) 

Mill Cr. spring 

chinook 491 203 491 

1.19 

(1.00, 

1.47) 

0.09 

(-0.07, 

0.26) 

0.06 

(-0.04, 0.16) 

0.13 

(-0.07, 0.34) 

Sac. R. steelhead 1,952 1,425 12,320 

0.95 

(0.90, 

1.02) 

-0.07 

(-0.13, 

0.00) 

-0.09 

(-0.13, -

0.06) 

-0.06 

(-0.26, 0.15) 

Winter chinook may be responding to a number of factors, including wetter-than-normal 

winters, reduced harvest, changes in RBDD operation, installation of a cold-water release device 

on Shasta Dam, changes in operations of the state and federal water projects, and a variety of 

other habitat improvements. While the status of winter chinook is improving, there is only one 

winter chinook population and it is dependent on cold-water releases of Shasta Dam, which 

could be vulnerable to a prolonged drought. The recent 5-year geometric mean is only 3% of the 

maximum post-1967 5-year geometric mean. 

The RBDD counts are suitable for modeling as a random-walk-with-drift (also known as 

the “Dennis model” [Dennis et al., 1991]). In the RWWD model, population growth is described 

by exponential growth or decline: 

Nt+1 = Nt exp(μ+ ηt), (1)

where Nt is the population size at time t, μ is the mean population growth rate, and ηt is a normal 

random variable with mean=0 and variance = σ

2

p. 
Draft Report 2/20/2003 

A. CHINOOK 106 

Table A.2.8.2. Parameter estimates for the constant-growth and step-change models applied to winter 

chinook. Numbers in parentheses indicate 90% confidence intervals. 

 model 

parameter constant  step change  

μ 0.085 0.214 

0.181,0.016 (0.322,0.113) 

δ NA 0.389 

 NA (0.210, 0.574) 

σ

2

p 0.105 0.056 

 (0.0945, 0.122) (0.046, 0.091) 

σ

2

m 0.0025 0.011 

 (2.45×106, 0.0126) (3.92×106, 0.022) 

P100(ext)[a] 0.40 0.003 

 (0.00, 0.99) (0.0, 0.0)

[a] Probability of extinction (pop. size < 1 fish) within 100 years. 

The RWWD model, as written in Equation 1, ignores measurement error. Observations (yt) 

can be modeled separately, 

yt = Nt exp(εt), (2)

where εt is a normal random variable with mean = 0 and variance = σ

2

m. Equations 1 and 2 

together define a state-space model that, after linearizing by taking logarithms, can be estimated 

using the Kalman filter (Lindley, in press). 

A recent analysis of the RBDD data (Lindley and Mohr, in press) indicated that the 

population growth since 1989 was higher than in the preceding period. For this reason, I fit two 

forms of the RWWD model- one with a fixed growth rate (constant-growth model) and another 

with a growth rate with a step-change in 1989, when conservation actions began (step-change 

model, μt = μ for t < 1989, μt = μ+ δ for t ≥ 1989). In both cases, a 4-year running sum was 

applied to the spawning escapement data to form a total population estimate (Holmes, 2001). 

Results of model fitting are shown in Table A.2.8.2. The constant-growth model satisfies all 

model diagnostics, although visual inspection of the residuals shows a strong tendency to underpredict abundance in the most recent 10 years. The residuals of the step-change model fail the 

Shapiro-Wilks test for normality; the residuals look truncated on the positive side, meaning that 

good years are not as extreme as bad years. Winter chinook growth rate might be better modeled 

as a mixture between a normal distribution and another distribution reflecting near-catastrophic 

population declines caused by episodic droughts. 
Draft Report 2/20/2003 

A. CHINOOK 107 

According to Akaike’s information criterion (AIC), the step-change model is a much better 

approximation to the data than the constant population growth rate model, with an AIC 

difference of 9.61 between the two models (indicating that the data provide almost no support for 

the constant-growth model). The step-change model suggests the winter chinook population 

currently has a λ of 1.21, while for the constant population growth rate model, λ = 0.974

. The 

extinction risks predicted by the two models are extremely different: winter chinook have almost 

no risk of extinction if the apparent recent increase in λ holds in the future, but are certain to go 

extinct if the population grows at its average rate, with a most likely time of extinction being 100 

years. While it would be dangerous to assume that recent population growth will hold 

indefinitely, it does appear that the status of winter chinook is improving. 

Harvest impacts 

Substantial changes in ocean fisheries off central and northern California have occurred 

since the last status review (PFMC 2002a, b). Ocean harvest rate of winter chinook is thought to 

be a function of the Central Valley chinook ocean harvest index (CVI), which is defined as the 

ratio of ocean catch south of Point Arena to the sum of this catch and the escapement of chinook 

to Central Valley streams and hatcheries. Note that other stocks (e.g., Klamath chinook) 

contribute to the catch south of Point Arena. This harvest index ranged from 0.55 to nearly 0.80 

from 1970 to 1995, when harvest regimes were adjusted to protect winter chinook. In 2001, the 

CVI fell to 0.27. The reduction in harvest is presumably at least partly responsible for the record 

spawning escapement of fall chinook (≈ 540,000 fish in 2001). 

Because they mature before the onset of the ocean fishing season, winter chinook should 

have lower harvest rates than fall chinook. At the time of the last status review, the only 

information of the harvest rate of winter chinook came from a study conducted in the 1970s. The 

impact rate (direct and indirect effects of harvest) of ocean fisheries on winter chinook was 

estimated to be 0.54, and the river sport fishery at that time was thought to have an impact rate of 

0.08. 

The recent release of significant numbers of ad-clipped winter chinook provides new, but 

limited, information on the harvest of winter chinook in coastal recreational and troll fisheries. 

The 1998 brood year was the first brood to have sufficient tag releases. Dan Viele (Sustainable 

Fisheries, SWR) conducted a cohort reconstruction of the 1998 broodyear. Winter chinook are 

mainly vulnerable to ocean fisheries as 3-year olds. Viele calculated, on the basis of 123 codedwire-tag recoveries, that the ocean fishery impact rate on 3-year-olds is 0.21 and the in-river 

sport fishery impact rate is 0.24. For a given year, these fisheries combine to reduce spawning 

escapement by about 43%. The high estimated rate of harvest in the river sport fishery, which 

arises from the recovery of 8 coded-wire tags, was a surprise, because salmon fishing is closed 

from January 15 to July 31 to protect winter-run chinook. The tags were recovered in late 

December/early January, at the tail end of the fishery for late-fall chinook. The estimate of river 

sport fishery impact is much less certain than the ocean fishery impact estimate because of the 

lower number of tag recoveries, less rigorous tag sampling, and larger expansion factors. Never 

the less, in response to this information, the California Fish and Game Commission is moving 

 

4

In this section of the document is defined as exp(μ + σ2

p / 2), the mean annual population growth rate. 
Draft Report 2/20/2003 

A. CHINOOK 108 

forward with an emergency action to amend sport fishing regulations to ban retention of salmon 

caught in river sport fisheries on January 1 rather than January 15. Had such regulations been in 

place in 1999/2000, the harvest rate would have been 20% of that observed. 

New hatchery information 

Livingston Stone National Fish Hatchery (LSNFH) was constructed at the base of Shasta 

Dam in 1997, with the sole purpose of helping to restore natural production of winter chinook. 

LSNFH was designed as a conservation hatchery with features intended to overcome the 

problems of CNFH (better summer water quality, natal water source). All production is adclipped. Each individual considered for use as broodstock is genotyped to ensure that it is a 

winter chinook. No more than 10% of the broodstock is composed of hatchery origin fish, and no 

more than 15% of the run is taken for broodstock, with a maximum of 120 fish. Figure 3 shows 

the number of winter chinook released by CNFH/LSNFH; Figure 4 shows the returns to these 

hatcheries. 

A.2.8.3 New Comments 

The California State Water Contractors, the San Luis and Delta-Mendota Water Authority, 

and the Westlands Water District recommend that the listing status of winter chinook be changed 

from endangered to threatened. They base this proposal on the recent upturn of adult abundance, 

recently initiated conservation actions (restoration of Battle Creek, ocean harvest reductions, 

screening of water diversions, remediation of Iron Mountain Mine, and improved temperature 

control), and a putative shift in ocean climate in 1999. 
Draft Report 2/20/2003 

A. CHINOOK 109 

1965 1970 1975 1980 1985 1990 1995 2000 2005

0

2

4

6

8

10

12 x 104

Year

Escapement

 

2 2.5 3 3.5 4 4.5 5

0. 4

0. 3

0. 2

0. 1

0

0.1

0.2

0.3

0.4

Log10(5-year mean pop. size)

μ

1955 1960 1965 1970 1975 1980 1985 1990 1995 2000

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

0.16

Year

Releases (Millions)

1988 1990 1992 1994 1996 1998 2000

20

40

60

80

100

120

140

160

180

200

Year

Returns

Figure A.2.8.1. Estimated winter chinook spawner 

abundance as determined by RBDD fish 

ladder (solid line) and carcass markrecapture (dashed line). 

Figure A.2.8.2. Abundance and growth rate of Central 

Valley salmonid populations. Open circlesteelhead; open squares- spring chinook; filled 

triangle- winter chinook; small black dots- other 

chinook stocks. Error bars represent central 0.90 

probability intervals for μ estimates. (Note: as 

defined in other sections of the status reviews, μ

≈ log(λ).)

Figure A.2.8.3. Number of juvenile winter-run chinook 

released by Coleman and Livingston Stone 

National Fish Hatcheries. 

Figure A.2.8.4. Number of adult winter-run 

chinook captured by Coleman and 

Livingston Stone National Fish 

Hatcheries. 
Draft Report 2/20/2003 

A. CHINOOK 110 

A.2.9. CENTRAL VALLEY SPRING-RUN CHINOOK

A.2.9.1. Previous BRT Conclusions 

Summary of major risk factors and status indicators 

Threats to Central Valley (CV) spring chinook fall into three broad categories: loss of most 

historic spawning habitat, degradation of remaining habitat, and genetic threats from the Feather 

River Hatchery spring chinook program. Like most spring chinook, CV spring chinook require 

cool water while they mature in freshwater over the summer. In the Central Valley, summer 

water temperatures are suitable for chinook salmon only above 150-500m elevation, and most 

such habitat in the CV is now behind impassable dams (Figure A.2.9.1). Only three selfsustaining wild populations of spring chinook (on Mill, Deer and Butte creeks, tributaries to the 

lower Sacramento River draining out of the southern Cascades) are extant. These populations 

reached quite low abundance levels during the late 1980s (5-year mean population sizes of 67-

243 spawners), compared to a historic peak abundance of perhaps 700,000 spawners for the ESU 

(estimate of Fisher [1994], based on catches in the early gill-net fishery). Of the numerous 

populations once inhabiting Sierra Nevada streams, only the Feather River and Yuba River 

populations remain, and these are apparently dependent on the Feather River Hatchery. 

In addition to outright loss of habitat, CV spring chinook must contend with the widespread 

habitat degradation and modification of their rearing and migration habitats in the natal stream, 

the Sacramento River, and the Delta. The natal tributaries do not have large impassable dams 

like many Central Valley Streams, but they do have many small hydropower dams and water 

diversions that, in some years, have greatly reduced or eliminated in-stream flows during springrun migration periods. Problems in the migration corridor include unscreened or inadequately 

screened water diversions, predation by non-native species, and excessively high water 

temperatures. 

The Feather and Yuba Rivers contain populations thought to be significantly influenced by 

the Feather River Hatchery (FRH) spring chinook stock. The FRH spring chinook program 

releases its production far downstream of the hatchery, causing high rates of straying (CDFG 

2001). There is concern that fall and spring chinook have hybridized in the hatchery. The BRT 

viewed FRH as a major threat to the genetic integrity of the remaining wild spring chinook 

populations. 

BRT conclusions 

In the original chinook status review, a majority of BRT concluded that the CV spring 

chinook ESU was in danger of extinction (Myers et al. 1998). Listing of this ESU was deferred, 

and in the status review update, the BRT majority shifted to the view that this ESU was not in 

danger of extinction, but was likely to become endangered in the foreseeable future (NMFS 

1999). A major reason for this shift was data indicating that a large run of spring chinook on 

Butte Creek in 1998 was naturally produced, rather than strays from FRH. 
Draft Report 2/20/2003 

A. CHINOOK 111 

Elevation

<VALUE>

-5 - 150

150.0000001 - 500

500.0000001 - 1,000

1,000.000001 - 4,411

Current spring chinook streams

Keystone dams

.

0 100 200 50 Kilometers

Figure A.2.9.1. Map of Central Valley showing the locations of self-sustaining spring chinook populations. These 

populations are found in the only watersheds with substantial accessible habitat above 500 m elevation.
Draft Report 2/20/2003 

A. CHINOOK 112 

Listing status 

Central Valley spring chinook were listed as threatened in 1999. Naturally spawning 

spring chinook in the Feather River were included in the listing, but the Feather River Hatchery 

stock of spring chinook was excluded. 

A.2.9.2 New Data 

Status assessments 

In 1998, CDFG reviewed the status of spring-run chinook in the Sacramento River 

drainage in response to a petition to list these fish under the California Endangered Species Act 

(CESA) (CDFG 1998). CDFG concluded that spring chinook formed an interbreeding 

population segment distinct from other chinook salmon runs in the Central Valley. CDFG 

estimated that peak run sizes might have exceeded 600,000 fish in the 1880s, after substantial 

habitat degradation had already occurred. They blame the decline of spring chinook on the early 

commercial gillnet fishery, water development that blocked access to headwater areas, and 

habitat degradation. Current risks to the remaining populations include continued habitat 

degradation related to water development and use, and the operation of FRH. CDFG 

recommended that Sacramento River spring-run chinook be listed as threatened under the CESA. 

Population structure 

There are preliminary results for two studies of spring chinook population structure. Two 

important insights are provided by these data sets. First, CV spring chinook do not appear to be 

monophyletic, yet wild CV spring chinook populations from different basins are more closely 

related to each other than to fall chinook from the same basin. Second, neither Feather River 

natural (FR) or Feather River Hatchery (FRH) spring chinook are closely related to any of the 

three wild populations although they are closely related to each other and to CV fall chinook. 

David Teel of the NWFSC used allozymes to show that Butte and Deer creek spring 

chinook are not closely related to sympatric fall chinook populations or the FRH spring chinook 

stock (Figure A.2.9.2). FRH spring chinook, putative Feather River natural spring chinook, and 

Yuba River spring chinook fell into a large cluster composed mostly of natural and hatchery fall 

chinook. 

Dennis Hedgecock and colleagues, using 12 microsatellite markers, showed that there are 

two distinct populations of chinook in the Feather River (Hedgecock 2002). One population is 

formed by early-running (“spring”) chinook, the other by late running fish (“fall run”). Once run 

timing was accounted for, hatchery and naturally spawning fish appear to form a homogeneous 

population. The Feather River spring population is most closely related to FR fall (Fst=0.010) 

and to Central Valley Fall chinook (Fst=0.008) and is distinct from spring chinook in Deer, Mill 

(Fst=0.016) and Butte (Fst=0.034) creeks. Figure A.2.9.3 shows the neighbor-joining tree with 

Cavalli-Sforza and Edwards chord distances and unweighted pair-group method arithmetic 

averaging. 
Draft Report 2/20/2003 

A. CHINOOK 113 

Figure A.2.9.2. Neighbor joining tree (Cavalli-Sforza and Edwards chord distances) for Central Valley chinook popula

polymorphic allozyme loci (unpublished data from D. Teel, NWFSC). Populations labeled with only a number 

chinook populations.
Draft Report 2/20/2003 

A. CHINOOK 114 

At least two hypotheses could explain the Feather River observations: 

1. an ancestral Mill/Deer/Butte-type spring chinook was forced to hybridize with the fall 

chinook, producing an intermediate form. 

2. the ancestral Feather River spring chinook had a common ancestor with the Feather River 

fall chinook, following the pattern seen in Klamath chinook but different from the pattern 

seen in Deer, Butte and Mill creeks. The FR and FRH populations have merged. 

Hedgecock argues against the first hypothesis. Feather River fish cluster well within 

Central Valley fall chinook rather than between Mill/Deer/Butte spring chinook and Central 

Valley fall chinook, as would be expected under hypothesis 1. Furthermore, there is no evidence 

from linkage disequilibria that FR spring and FR fall populations are hybridizing, i.e., these 

populations are reproductively isolated. It is perhaps not surprising that Feather River spring 

chinook might have a different ancestry than spring chinook in Mill, Deer and Butte creek, since 

the Feather River is in a different ecoregion. 

Regardless of the cause of the genetic patterns described above, these new data do not 

support the current configuration of the CV spring chinook ESU. Feather River spring chinook 

do not appear to share a common ancestry or evolutionary trajectory with other spring chinook 

populations in the Central Valley. They share the designation of “spring” chinook, and indeed, 

the Feather River and FRH have a chinook spawning run that starts much earlier than other 

Sacramento basin rivers. There is no longer a distinct bimodal distribution to run timing, 

however, and substantial fractions of fish released as FRH spring chinook have returned during 

the fall chinook period (and vice versa) (CDFG 1998). If FR and FRH spring chinook are 

retained in the CV spring chinook ESU, then the ESU configuration of the CV fall-late fall 

chinook ESU (among several others) should be reconsidered for the sake of consistency, because 

late-fall chinook are more distinct genetically and arguably as distinct in terms of life history as 

FRH spring chinook. 

L Fall

FR Sp Fall

BC Sp

D&M Sp

Winter

900

998

1000

994

Figure A.2.9.3. Neighbor joining tree (Cavalli-Sforza and Edwards chord distances) for Central Valley 

chinook populations, based on 12 microsatellite loci. D&M = Deer and Mill Creek; BC = Butte 

Creek; FR = Feather River; Sp= spring chinook; L Fall = late-fall chinook; Winter = winter chinook. 

The tree was constructed using Cavalli-Sforza and Edwards measure of genetic distance and the 

unweighted pair-group method arithmetic averaging. Figure from Hedgecock (2002).
Draft Report 2/20/2003 

A. CHINOOK 115 

Historic habitat loss 

Yoshiyama and colleagues detailed the historic distribution of Central Valley spring 

chinook. Yoshiyama et al. (2001) estimated that 72% of salmon spawning and rearing habitat 

has been lost in the Central Valley. This figure is for fall as well as spring chinook, so the 

amount of spring chinook habitat lost is presumably higher, because spring chinook spawn and 

rear in higher elevations, areas more likely to be behind impassable dams. They deem the 95% 

loss estimate of CDFG (Reynolds et al. 1993) as “perhaps somewhat high but probably roughly 

accurate.” 

Life history 

CDFG recently began intensive studies of Butte Creek spring chinook (Ward et al. 2002). 

One of the more interesting observations is that while most spring chinook leave Butte Creek as 

young-of-the-year, yearling outmigrants make up roughly 25% of the ocean catch of Butte Creek 

spring chinook. 

New harvest information 

Coded-wire tagging of juvenile spring chinook in Butte Creek provides some limited 

information on current harvest rates of this population. Based on eight CWT recoveries in the 

ocean fisheries and 15 CWT recoveries in Butte Creek, the harvest rate on age 3 Butte Creek 

spring chinook is 0.44 (Ward et al. 2002). 

Substantial changes in ocean fisheries off central and northern California have occurred 

since the last status review (PFMC 2002a, b). Ocean harvest rate of Central Valley spring 

chinook is thought to be a function of the Central Valley chinook ocean harvest index (CVI), 

which is defined as the ratio of ocean catch south of Point Arena to the sum of this catch and the 

escapement of chinook to Central Valley streams and hatcheries. Note that other stocks (e.g., 

Klamath chinook) contribute to the catch south of Point Arena. This harvest index ranged from 

0.55 to nearly 0.80 from 1970 to 1995, when harvest regimes were adjusted to protect winter 

chinook. In 2001, the CVI fell to 0.27. The reduction in harvest is presumably at least partly 

responsible for the record spawning escapement of fall chinook ( ≈ 540,000 fish in 2001). 

A.2.9.3 New Comments 

The State Water Contractors (SWC) submitted several documents, one of them relevant to 

the status review for CV spring chinook. The document, “Reconsideration of the listing status of 

spring-run chinook salmon within the Feather River portion of the Central Valley ESU,” argues 

that Feather River spring chinook should not be included in the Central Valley spring chinook 

ESU and do not otherwise warrant protection under the ESA. SWC also suggested that NOAA 

Fisheries conduct a series of evaluations of the following topics: 

1. impact of hatchery operations on the population dynamics and the genetic integrity of 

natural stocks 

2. hatcheries as conservation 
Draft Report 2/20/2003 

A. CHINOOK 116 

Figure A.2.9.4. Abundance and growth rate of Central Valley salmonid populations. Open circlesteelhead; filled squares- spring chinook; open triangle- winter chinook; small black dots- other 

chinook stocks (mostly fall runs). Error bars represent central 0.90 probability intervals for μ

estimates. (Note: as defined in other sections of the status reviews, μ ≈ log [λ].)

3. effects of mixed-stock fisheries 

4. assessment of the relative roles of different mortality factors 

5. experimental assessment of the effects of river operations 

6. efficacy of various habitat improvements 

7. stock identification for salvage and ocean fishery management 

8. constant fractional marking 

The California Farm Bureau Federation (CFBF) submitted comments with several 

attachments calling for the removal of most salmonid ESUs from the endangered species list. 

The attachments included (1) an analysis by B.J. Miller showing that significant and expensive 

changes to water operations in the Delta provide fairly modest benefits to chinook populations; 

(2) “Reconsideration of the listing status of spring-run chinook salmon within the Feather River 

portion of the Central Valley ESU,” discussed in the preceding paragraph; (3) a memo from J. F. 

Palmisano to C.H. Burley arguing that because changes in marine climate have been shown to 

influence salmon stocks, other putative causes for declines of salmonid populations must be 

over-rated. CFBF reviews Alsea Valley Alliance v. Evans and argues that hatchery fish must be 

included in risk analyses. 

New abundance data 

The time series of abundance for Mill, Deer, Butte, and Big Chico creek spring chinook 

have been updated through 2001, and show that the increases in population that started in the 

early 1990s has continued (Figure A.2.9.4). During this period, there have been significant 

2 2.5 3 3.5 4 4.5 5

0. 4

0. 3

0. 2

0. 1

0

0.1

0.2

0.3

0.4

Log10(5-year mean pop. size)

μ
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A. CHINOOK 117 

Table A.2.9.1. Summary statistics for trend analyses. Numbers in parentheses are 0.90 confidence 

intervals. 

Population 5-yr 

mean 

5-yr 

min 

5-yr 

max λ μ LT trend ST trend 

Sac. R. winter chinook 2,191 364 65,683 

0.97 

(0.87, 

1.09) 

-0.10 

(-0.21, 0.01) 

-0.14 

(-0.19, -

0.09) 

0.26 

(0.04, 0.48) 

Butte Cr. spring chinook 4,513 67 4,513 

1.30 

(1.09, 

1.60) 

0.11 

(-0.05, 0.28) 

0.11 

(0.03, 0.19) 

0.36 

(0.03, 0.70) 

Deer Cr. spring chinook 1,076 243 1,076 

1.17 

(1.04, 

1.35) 

0.12 

(-0.02, 0.25) 

0.11 

(0.02, 0.21) 

0.16 

(-0.01, 0.33)

Mill Cr. spring chinook 491 203 491 

1.19 

(1.00, 

1.47) 

0.09 

(-0.07, 0.26) 

0.06 

(-0.04, 0.16) 

0.13 

(-0.07, 0.34)

habitat improvements (including the removal of several small dams and increases in summer 

flows) in these watersheds, as well as reduced ocean fisheries and a favorable terrestrial climate. 

The time series for Butte, Deer and Mill Creeks are barely amenable to simple analysis 

with the random walk-wth-drift model (Homes 2001, Lindley in press). The data series are 

short, and inconsistent methods were used until 1992, when a consistent snorkel survey was 

initiated on Butte and Deer Creeks. The full records for these three systems are analysed with 

the knowledge that there may be significant errors in pre-1992 observations. Table A.2.9.1 

summarizes the analyses of these time series. 

It appears that the three spring chinook populations in the Central Valley are growing. The 

current five-year geometric means for all three populations are also the maximum 5-year means. 

All three spring chinook populations have long and short-term λ > 1 (λ is defined as exp(μ+ σ

2

p / 

2)--the mean annual population growth rate in this document), with lower bounds of 

 90% confidence intervals generally > 1. Long- and short-term trends are also positive, although 

some confidence interval lower bounds are negative. Central Valley spring chinook have some 

of the highest population growth rates in the Central Valley, but other than Butte Creek and the 

hatchery-influenced Feather River, population sizes are relatively small compared to fall chinook 

populations (Figure A.2.9.5). 

A.2.9.4 New Hatchery Information 

FRH currently aims to release 5 million spring chinook smolts per year although actual 

releases have been mostly lower than this goal (Figure A.2.9.5). Returns to the hatchery appear 

to be directly proportional to the releases (Figure A.2.9.6). 
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A. CHINOOK 118 

A.2.9.5 Comparison with Previous Data 

The upward trends in abundance of the Mill, Deer and Butte creek populations noted in the 

previous status review have apparently continued. New population genetics information 

confirms previous suspicions that Feather River hatchery and Feather River spring chinook are 

not closely related to the Mill, Deer and Butte creek spring chinook populations. 

1965 1970 1975 1980 1985 1990 1995 2000

0.00

1.00

2.00

3.00

4.00

5.00

6.00

Year

Releases (Millions)

Figure A.2.9.5. Number of spring-run chinook released by Feather River Hatchery. 

1960 1965 1970 1975 1980 1985 1990 1995 2000

0

1000

2000

3000

4000

5000

6000

7000

Year

Returns

Figure A.2.9.6. Number of spring-run chinook returning to Feather River Hatchery.
Draft Report 2/20/2003 

A. CHINOOK 119 

A.3 PRELIMINARY CHINOOK BRT CONCLUSIONS 

Snake River fall chinook 

 A majority of the BRT votes for this ESU fell in the “likely to become endangered” 

category, with minorities falling in the “danger of extinction,” and “not likely to become 

endangered” categories. This represented a somewhat more optimistic assessment of the 

status of this ESU than was the case at the time of the original status review, when the 

BRT concluded that Snake River fall chinook salmon “face a substantial risk of 

extinction if present conditions continue” (Waples et al. 1991). The BRT found 

moderately high risks in all VSP elements, with mean risk matrix scores ranging from 3.0 

for growth rate/productivity to 3.6 for spatial structure (Table A.3.1). 

 On the positive side, the number of natural-origin spawners in 2001 was well in 

excess of 1,000 for the first time since counts at Lower Granite Dam began in 1975. 

Management actions have reduced (but not eliminated) the fraction of fish passing Lower 

Granite Dam that are strays from out-of-ESU hatchery programs. Returns in the last 2 

years also reflect an increasing contribution from supplementation programs based on the 

native Lyons Ferry Broodstock. With the exception of the increase in 2001, the ESU has 

fluctuated between approximately 500-1,000 adults, suggesting a somewhat higher 

degree of stability in growth rate and trends than is seen in other salmon populations. 

 In spite of the recent increases, however, the recent geometric mean number of 

naturally produced spawners is still less than 1,000, a very low number for an entire ESU. 

Because of the large fraction of naturally spawning hatchery fish, it is difficult to assess 

the productivity of the natural population. The relatively high risk matrix scores for 

spatial structure and diversity (3.5-3.6) reflect the concerns of the BRT that a large 

fraction of historic habitat for this ESU is inaccessible, diversity associated with those 

populations has been lost, the single remaining population is vulnerable to variable 

environmental conditions or catastrophes, and continuing immigration from outside the 

ESU at levels that are higher than occurred historically. Some BRT members were 

concerned that the efforts to remove stray, out-of-ESU hatchery fish only occur at Lower 

Granite Dam, well upstream of the geographic boundary of this ESU. Specific concerns 

are that natural spawners in lower river areas will be heavily affected by strays from 

Columbia River hatchery programs, and that this approach effectively removes the 

natural buffer zone between the Snake River ESU and Columbia River ocean-type 

chinook salmon. The effects of these factors on ESU viability are not known, as the 

extent of natural spawning in areas below Lower Granite Dam is not well understood, 

except in the lower Tucannon River. 

Snake River spring/summer 

 The majority of BRT votes for this ESU fell in the “likely to become endangered” 

category, with minorities falling in the “danger of extinction,” and “not likely to become 

endangered” categories. As indicated by mean risk matrix scores, the BRT had much 
Draft Report 2/20/2003 

A. CHINOOK 120 

higher concerns about abundance (3.6) and growth rate/productivity (3.5) than for spatial 

structure (2.2) and diversity (2.3) (Table A.3.1). 

Although there are concerns about loss of an unquantified number of spawning 

aggregations that historically may have provided connectivity between headwater 

populations, natural spawning in this ESU still occurs in a wide range of locations and 

habitat types. 

 Like many others, this ESU saw a large increase in escapement in many (but not 

all) populations in 2001. The BRT considered this an encouraging sign, particularly 

given the record low returns seen in many of these populations in the mid 1990s. 

However, recent abundance in this ESU is still short of the levels that the proposed 

recovery plan for Snake River salmon indicated should be met over at least an 8-year 

period (NMFS 1995). The BRT considered it a positive sign that the non-native Rapid 

River broodstock has been phased out of the Grande Ronde system, but the relatively 

high level of both production/mitigation and supplementation hatcheries in this ESU 

leads to ongoing risks to natural populations and makes it difficult to assess trends in 

natural productivity and growth rate. 

Upper Columbia spring chinook 

 Assessments by the BRT of the overall risks faced by this ESU were divided, with a 

slight majority of the votes being cast in the “danger of extinction” category, and a 

substantial minority in the “likely to be endangered” category. The mean risk matrix 

scores reflect strong ongoing concerns regarding abundance (4.4) and growth 

rate/productivity (4.5) in this ESU, and somewhat less (but still significant) concerns for 

spatial structure (2.9) and diversity (3.5) (Table A.3.1). 

 Many populations in this ESU have rebounded somewhat from the critically low 

levels that immediately preceded the last status review evaluation, and this was reflected 

in the substantial minority of BRT votes cast that were not cast in the “danger of 

extinction” category. Although this was considered an encouraging sign by the BRT, the 

last year or two of higher returns come on the heels of a decade or more of steep declines 

to all-time record low escapements. In addition, this ESU continues to have a very large 

influence by hatchery production, both from production/mitigation and supplementation 

programs. The extreme management measures taken in an effort to maintain populations 

in this ESU during some years in the late 1990s (collecting all adults from major basins at 

downstream dams) are a strong indication of the ongoing risks to this ESU, although the 

associated hatchery programs may ultimately play a role in helping to restore selfsustaining natural populations. 

Lower Columbia River chinook 

 A majority of the BRT votes for this ESU fell in the “likely to become endangered” 

category, with minorities falling in the “danger of extinction,” and “not likely to become 

endangered” categories. Moderately high concerns for all VSP elements are indicated by 
Draft Report 2/20/2003 

A. CHINOOK 121 

mean risk matrix scores ranging from 3.2 for abundance to 3.9 for diversity (Table 

A.3.1). 

All of the risk factors identified in previous reviews were still considered important 

by the BRT. The Willamette/Lower Columbia River TRT has estimated that eight to 10 

historic populations in this ESU have been extirpated, most of them spring run. Near loss 

of that important life history type remains an important BRT concern. Although some 

natural production currently occurs in 20 or so populations, only one exceeds 1,000 

spawners. High hatchery production continues to pose genetic and ecological risks to 

natural populations and to mask their performance. Most populations in this ESU have 

not seen pronounced increases in recent years as occurred in other geographic areas. 

Upper Willamette River chinook 

A majority of the BRT votes for this ESU fell in the “likely to become endangered” 

category, with minorities falling in the “danger of extinction,” and “not likely to become 

endangered” categories. The BRT found moderately high risks in all VSP elements 

(mean risk matrix scores ranged from 3.1 for growth rate/productivity to 3.6 for spatial 

structure) (Table A.3.1). 

Although the number of adult spring chinook salmon crossing Willamette Falls is in 

the same range (about 20,000–70,000) it has been for the last 50 years, a large fraction of 

these are hatchery produced. The score for spatial structure reflects concern by the BRT 

that perhaps a third of the historic habitat used by fish in this ESU is currently 

inaccessible behind dams, and the BRT remained concerned that natural production in 

this ESU is restricted to a very few areas. Increases in the last 3-4 years in natural 

production in the largest remaining population (the McKenzie) were considered 

encouraging by the BRT. With the relatively large incidence of hatchery fish, it is 

difficult to determine trends in natural production. 

Puget Sound chinook 

A majority of the BRT votes for this ESU fell in the “likely to become endangered” 

category, with minorities falling in the “danger of extinction,” and “not likely to become 

endangered” categories. The BRT found moderately high risks in all VSP elements, with 

mean risk matrix scores ranging from 2.9 for spatial structure to 3.6 for growth 

rate/productivity (Table A.3.1). 

Population indices have not changed dramatically since the last BRT assessment. 

The Puget Sound TRT has identified approximately 31 historic populations, of which 

nine are believed to be extinct, with most of the populations that have been lost being 

early run. Other concerns noted by the BRT are the concentration of the majority of 

natural production in just two basins, high levels of hatchery production in many areas of 

the ESU, and widespread loss of estuary and lower floodplain habitat diversity (and, 

likely, associated life history types). Although populations in this ESU have not 

experienced the sharp increases in the last 2-3 years seen in many other ESUs, more 
Draft Report 2/20/2003 

A. CHINOOK 122 

populations have increased than decreased over the 4 years since the last BRT 

assessment. After adjusting for changes in harvest rates, however, trends in productivity 

are less favorable. Most populations are relatively small, and recent abundance within 

the ESU is only a small fraction of estimated historic run size. 

California Coastal chinook 

A majority of the BRT votes for this ESU fell in the “likely to become endangered” 

category, with minorities falling in the “danger of extinction” and “not warranted” 

categories. The BRT found moderately high risks in all VSP elements, with mean risk 

matrix scores ranging from 3.1 for diversity to 3.9 for abundance (Table A.3.1). 

The BRT was concerned by continued evidence of low population sizes relative to 

historical abundance and mixed trends in the few time series of abundance indices 

available for analysis, and by the low abundances and potential extirpations of 

populations in the southern part of the ESU. The BRT’s concerns regarding genetic 

integrity of this ESU were moderate or low relative to similar issues for other ESUs 

because 1) hatchery production in this ESU is on a minor scale, and 2) current hatchery 

programs are largely focused on supplementing and restoring local populations. 

However, the BRT did have concerns with respect to diversity that were based largely on 

the loss of spring-run chinook in the Eel River basin and elsewhere in the ESU, and to a 

lesser degree on the potential loss of diversity concurrent with low abundance or 

extirpation of populations in the southern portion of the ESU. Overall, the BRT was 

strongly concerned by the paucity of information and resultant uncertainty associated 

with estimates of abundance, natural productivity and distribution of chinook salmon in 

this ESU. 

Sacramento River winter chinook 

 A majority of the BRT votes fell into the “in danger of extinction” category, with 

minorities falling in the “likely to become endangered,” and “not warranted” categories. 

The main VSP concerns were in the spatial structure (4.8) and diversity (4.2) categories, 

although there was significant concern in the abundance and productivity categories (3.7 

and 3.5, respectively) (Table A.3.1). 

 The main concerns of the BRT relate to the lack of diversity within this ESU. The 

BRT was very troubled by the fact that this ESU is represented by a single population 

that has been displaced from its historic spawning habitat into an artificial habitat created 

and maintained by a dam. The BRT presumed that several independent populations of 

winter chinook were merged into a single population, with the potential for a significant 

loss of life history and genetic diversity. Furthermore, the population has passed through 

at least two recent bottlenecks—one when Shasta Dam was filled and another in the late 

1980s-early 1990s—that probably further reduced genetic diversity. The population has 

been removed from the environment where it evolved, dimming its long-term prospects 

for survival. The BRT was modestly heartened by the increase in abundance since the 

lows of the late 1980s and early 1990s. 
Draft Report 2/20/2003 

A. CHINOOK 123 

Central Valley spring chinook 

A majority of the BRT votes fell into the “likely to become endangered” category, 

with minorities falling in the “in danger of extinction,” and “not warranted” categories. 

There was roughly equal concern about abundance, spatial structure and diversity (3.5-

3.8), and less concern about productivity (2.8) (Table A.3.1). 

 A major concern of the BRT was the loss of diversity caused by the extirpation of 

spring chinook populations from most of the Central Valley, including all San Joaquin 

tributaries. The only populations left in the Sierra Nevada ecoregion are supported by the 

Feather River hatchery. Another major concern of the BRT was the small number and 

location of extant spring chinook populations—only three streams, originating in the 

southern Cascades, support self-sustaining runs of spring chinook, and these three 

streams are close together, increasing their vulnerability to catastrophe. Two of the three 

extant populations are fairly small, and all were recently quite small. The BRT was also 

concerned about the Feather River spring chinook hatchery population, which is not in 

the ESU but does produce fish that potentially could interact with other spring chinook 

populations, especially given the off-site release of the production. 

Table A.3.1. Summary of risk scores (1 = low to 5 = high) for four VSP categories (see section “Factors 

Considered in Status Assessments” for a description of the risk categories) for the nine chinook 

ESUs reviewed. Data presented are means (range). 

ESU Abundance Growth Rate/ 

Productivity 

Spatial Structure 

and Connectivity Diversity 

Snake River Fall 3.4 (2-5) 3.0 (2-5) 3.6 (2-5) 3.5 (2-5) 

Snake River Spring/Summer 3.6 (2-5) 3.5 (3-5) 2.2 (1-3) 2.3 (1-3) 

Upper Columbia Spring 4.4 (3-5) 4.5 (3-5) 2.9 (2-4) 3.5 (2-5) 

Puget Sound 3.3 (2-4) 3.6 (3-4) 2.9 (2-4) 3.2 (2-4) 

Lower Columbia 3.2 (2-4) 3.7 (3-5) 3.5 (3-4) 3.9 (3-5) 

Upper Willamette 3.7 (2-5) 3.1 (2-5) 3.6 (3-4) 3.2 (2-4) 

California Coastal 3.9 (3-5) 3.3 (3-4) 3.2 (2-4) 3.1 (2-4) 

Sacramento Winter 3.7 (3-5) 3.5 (2-5) 4.8 (4-5) 4.2 (3-5) 

Central Valley Spring 3.5 (3-4) 2.8 (2-4) 3.8 (3-5) 3.8 (3-5) 
Draft Report 2/20/2003 

A. CHINOOK 124 

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A. CHINOOK 131 

A.5 APPENDICES 

Appendix A.5.1. Preliminary SSHAG (2003) categorizations of hatchery populations of the nine chinook salmon 

See “Artificial Propagation” in General Introduction for explanation of the categories. 

 Stock Run Basin SSHAG Categ

Snake River fall Lyons Ferry Fall Snake River 1 and 2 

Snake River spring/summer McCall (supplementation) Spring Salmon 1 

 McCall (production) Spring Salmon 1 or 2  Rapid River Spring Little Salmon 3  Sawtooth Spring Salmon 2  Pahsimeroi Summer Salmon 1 or 2  Captive Broodstock  Catherine Creek Summer Grande Ronde 1  Upper Grande Ronde Summer Grande Ronde 1  Lostine River Summer Grande Ronde 1  Clearwater Spring Clearwater 3  Imnaha (# 29) Spr/Sum Imnaha 1  Dworshak Spring Clearwater 3  Kooskia Spring Clearwater 3  Tucannon Spring Tucannon 1 or 2 

Upper Columbia River spring Leavenworth NFH Spring Wenatchee 3 or 4 

 Entiat NFH Spring Entiat 3 or 4  Winthrop NFH Spring Methow 3 or 4  Chiwawa Spring Wenatchee 1  Methow Composite  Twisp Spring Methow 1  Chewuch Spring Methow 1  Methow Spring Methow 3 or 4  U. Columbia River Captive  Nason Spring Wenatchee 1  White River Spring Wenatchee 1 
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A. CHINOOK 132 

 Twisp Spring Methow 1  Methow Spring Methow 1  Ringold Hatchery Spring U. Col. River 3 or 4  Carson Hatchery Spring Wind 3 or 4 

Puget Sound Kendall Creek Spring Nooksack 2 

 Lummi Bay Fall Nooksack 3  Samish River Fall Samish 3  Marblemount Spring Skagit 2  Marblemount Spring Skagit 1  Marblemount Fall Skagit 1  Tulalip Spring Tulalip Bay 3  Tulalip Summer Tulalip Bay 3  Tulalip Fall Tulalip Bay 3  N. Fork Stillaguamish Summer Stillaguamish 1  Wallace River Summer Snohomish 2  Issaquah Hatchery Fall Lake Washington 3  UW Portage Bay Fall Lake Washington 3  Soos Creek Fall Green 1 or 2  Keta Creek Fall Green 1 or 2  Grover's Creek Fall East Kitsap 3  Garrison Springs Fall Chambers Creek 3  Voights Creek Fall Puyallup 3  Diru Creek Fall Puyallup 3  White River Spring Puyallup 2  Clear/Kalama Creeks Fall Nisqually 3  Minter Creek Fall S. Sound 3  Tumwater Falls Fall Deschutes 3  George Adams Fall Skokomish 3  WSC Hood Canal Fall Skokomish 3  Finch Creek Fall S. Hood Canal 3  Hamma Hamma Fall S. Hood Canal 3  Big Beef Creek Fall N. Hood Canal 3  Dungeness Spring Dungeness 1 
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A. CHINOOK 133 

 Elwha Fall Elwha 1 or 2  Glenwood Springs Fall San Juan Islands 3 

Lower Columbia River Sea Resources Fall Chinook River 3 

 Abernathy NFH Fall Abernathy Creek 3  Grays River Fall Grays 3  Elochoman Fall Elochoman 3  Cowlitz Fall Cowlitz 2  Cowlitz Spring Cowlitz 2  Toutle Spring Cowlitz 3  Kalama Fall Kalama 2  Kalama Spring Kalama 3  Lewis Spring Lewis 3  Washougal Fall Washougal 2  Carson Spring Wind 4  LWS NFH Fall Little White 4  Spring Creek NFH Fall Spring Creek 3 (or 2?)  Klickitat Fall Klickitat 4  Willamette Spring Youngs Bay 4  Big Creek Fall Big Creek 3  Rogue River (#52) Fall Youngs Bay 4  Klaskanine (# 15) Fall Klaskanine 3  Willamette Spring Klaskanine 4  Bonneville (#14) Fall Gorge 3  Bonneville (#95) Fall Gorge 4  Hood River Spring Hood 4 

Upper Willamette River N. Fork Santiam (#21) Spring Santiam 3 

 Willamette Hatchery (#22) Spring M. Fork Willamette 3  McKenzie (#24) Spring McKenzie 2 or 3  S. Fork Santiam (#23) Spring Santiam 3  Clackamas (# 19) Spring Clackamas 3 

California Coastal Mad River Fall Mad River 3 

 Freshwater Creek Fall Humboldt Bay 1 
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A. CHINOOK 134 

 Yaeger Creek Fall Van Duzen 1  Redwood Creek Fall Redwood Creek 1  Hollow Tree Creek Fall Eel River 1  Van Arsdale Fall Eel River 1  Mattole Fall Mattole River 1 

Sacramento River winter chinook Feather River Spring Feather River 4 

California Central Valley spring Feather River Spring Feather River 4 
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A. CHINOOK 135 Appendix A.5.2. Lower Columbia Chinook Time Series References Population Big White Salmon River Fall Chinook Years of Data, Length of Series 1964 - 2000, 37 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a; Norman, G. 1982. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 1980-200 data from Rawdingfrom streamnet reference (Norman) 

Hatchery Reference Rawding, Dan (WDFW). 2001a 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference Stock Spring Creek 

Harvest Reference Pacific Salmon Commission 2002 Harvest Notes Estimated exploitation rate on hatchery stocks applied to natural stocks. 

Age Reference Rawding, Dan (WDFW).2001a. 

Age Notes Age distribution for 1982-1990 based on an average of 1991-2000. Population Clackamas River Fall Chinook Years of Data, Length of Series 1967 - 2001, 35 years Abundance Type Peak Count Abundance References Oregon Dept of Fish and Wildlife. 1998. Hatchery Reference No Hatchery Data Hatchery Notes No Hatchery Data Harvest Reference No Harvest Data Available Age Reference Myers, et al.1998. Age Notes Generic fall age structure Population Coweeman River Fall Chinook Years of Data, Length of Series 1964 - 2000, 37 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a; Kreitman, G.. 1981. Abundance Notes Abundance data are for adults and jacks. Estimates extrapolated from peak 

marking rate. 1964-1979 spawning data from Kreitman; 1980-2000 from R
Draft Report 2/20/2003 

A. CHINOOK 136 Hatchery Reference Rawding, Dan (WDFW). 2001a. Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference Stock Coweeman 

Harvest Reference Pacific Salmon Commission 2002. Harvest Notes Harvest data based on PFMC models provided by Dell Simmons. Age Reference Rawding, Dan (WDFW) 2001a. Age Notes Age distribution for 1980-1990 and estimate based on average from 1991-2Population East Fork Lewis River Fall Chinook Years of Data, Length of Series 1980 - 2000, 21 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Harvest Reference Stock Lewis Wild 

Harvest Reference Rawding, Dan (WDFW). 2001a. Harvest Notes AEQ ER for Lewis River from Dell Simmons Age Reference Rawding, Dan (WDFW).2001a. Age Notes Age distribution for 1980-1983 based on an average of 1984-2000 Population Lewis River (Brights) Fall Chinook Years of Data, Length of Series 1964 - 2000, 37 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a. Kreitman, G.. 1981. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 1964-1979 spawning data fro2000 from Rawding. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference Stock Lewis Wild 
Draft Report 2/20/2003 

A. CHINOOK 137 Harvest Reference Pacific Salmon Commission. 2002. Harvest Notes AEQ provided by Dell Simmons Age Reference Rawding, Dan (WDFW).2001a. Age Notes Age distribution for 1980-1990 and estimate based on average from 1991-2Population Middle Gorge Tributaries Fall Chinook Years of Data, Length of Series 1964 - 2000, 37 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a; Norman, G. 1982. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 1980-200 data from Rawdingfrom streamnet reference (Norman) 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference No Harvest Data Available. . . 

Age Reference Rawding, Dan (WDFW).2001a. Age Notes Age distribution for 1980-1990 and estimate based on average from 1991-2

data missing for 1993 

Population Mill Creek Fall Chinook Years of Data, Length of Series 1980 - 2000, 21 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference Stock Coweeman 

Harvest Reference Pacific Salmon Commission. 2002 Age Reference Rawding, Dan (WDFW).2001a. Age Notes Age distribution for 1982-1990 based on an average of 1991-2000. Population Sandy River Fall Chinook 
Draft Report 2/20/2003 

A. CHINOOK 138 Years of Data, Length of Series 1988 - 2001, 14 years Abundance Type Total from redd count Abundance References Oregon Dept of Fish and Wildlife. 1998; Abundance Notes The estimate of spawning abundance is based on a one time peak count of l

River. The index area is 10 miles from the mouth of Gordon Cr. To Lewis & number of fish is then multiplied by 2.5 to get the estimate (Streamnet ref # are provided in Streamnet trend # 57517. Surveys were not conducted prior 

Hatchery Reference Oregon Dept of Fish and Wildlife. 1998. Hatchery Notes Michelle McClure (NOAA Fisheries) references ODFW for proportion of n

Harvest Reference No Harvest Data Available 

Age Reference Myers, et al.1998. Age Notes Generic fall age structurePopulation Sandy River Late Fall Chinook Years of Data, Length of Series 1984 - 2001, 18 years Abundance Type Total from redd count Abundance References Oregon Dept of Fish and Wildlife. 2002; Oregon Dept of Fish and Wildlife

Massey, J.; Bennett, D.E. 1997. 

Hatchery Reference Oregon Dept of Fish and Wildlife. 1998. Hatchery Notes Michelle McClure (NOAA Fisheries) references ODFW for proportion of n

Harvest Reference No Harvest Data Available. 

Age Reference Myers, et al.1998. Age Notes Generic fall age structure Population Washougal River Fall Chinook Years of Data, Length of Series 1964 - 2000, 37 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a; Kreitman, G.. 1981. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 1964-1979 spawning data fro2000 from Rawding. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 
Draft Report 2/20/2003 

A. CHINOOK 139 Harvest Reference Stock Cowlitz Hatchery Harvest Reference Pacific Salmon Commission 2002. Harvest Notes AEQ provided by Dell Simmons Age Reference Rawding, Dan (WDFW).2001a. Age Notes Age distribution for 1982-1990 based on an average of 1991-2000. Population Kalama River Spring Chinook Years of Data, Length of Series 1980 - 1999, 20 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference No Harvest Data Available. 

Age Reference No Age Data Available. Population Lewis River Spring Chinook Years of Data, Length of Series 1980 - 1999, 20 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a. Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference No Harvest Data Available. 

Age Reference No Age Data Available. Population Upper Cowlitz River Spring Chinook Years of Data, Length of Series 1980 - 1999, 20 years Abundance Type Peak Count Abundance References Rawding, Dan (WDFW). 2001a. 
Draft Report 2/20/2003 

A. CHINOOK 140 Abundance Notes Abundance data are for adults and jacks. Estimates of spawner abundance a

made using peak count data and marking rate. 

Hatchery Reference Rawding, Dan (WDFW). 2001a. 

Hatchery Notes Hatchery data are part of the escapement data from Dan Rawding, WDFW. 

Harvest Reference No Harvest Data Available. 

Age Reference Myers, et al. 1998.Population Youngs Bay Fall Chinook Years of Data, Length of Series 1950 - 2001, 52 years Abundance Type Fish/Mile Abundance References ODFW. 9999a. Population Big Creek Fall Chinook Years of Data, Length of Series 1970 - 2001, 32 years Abundance Type Fish/Mile Abundance References ODFW. 9999a. Population Clatskanie River Fall Chinook Years of Data, Length of Series 1970 - 2001, 32 years Abundance Type Fish/Mile Abundance References ODFW. 9999a. 
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A. CHINOOK 141 Appendix A.5.3. Upper Willamette Chinook Time Series References Population Clackamas River Spring Chinook Years of Data, Length of Series 1958 - 2002, 45 years Abundance Type Dam/weir count Abundance References Cramer, Doug. 2002e. Abundance Notes Data are dam counts for NF Dam; adults only, production is mixed 

Hatchery Reference Cramer, Doug. 2002e. 

Hatchery Notes Counts of hatchery vs wild done only for 2001-2002 (Doug Cramer). Doug 

the number of marked hatchery fish to be 50%. 

Harvest Reference No Harvest Data Available. Age Reference McClure, Michelle.2002. Age Notes Age distribution is taken from the Upper Willamette Chinook totals, not sp

Spring Chinook. 

Population Mckenzie River Spring Chinook Years of Data, Length of Series 1970 - 2001, 32 years Abundance Type Dam/weir count Abundance References Kostow, Kathryn (ODFW). 2002b. Abundance Notes Data come from dam counts at Leaburg Dam. Spawning also occurs below Hatchery Reference Kostow, Kathryn (ODFW). 2002b.Hatchery Notes Hatchery fish have only been 100% marked in recent years. The hatchery m

detectable at the dam because a portion of the hatchery fish are double inde

the fishery impact to wild fish. Double index markes mean that the hatchery wire tag but it is not externally marked (that is, no fin clip). Therefore, the fto the fisherman (who must release the fish) and in the raw dam count. The managers therefore do several expansions to deal with these issues.

Harvest Reference No Harvest Data Available. Age Reference McClure, Michelle.2002. Age Notes Age distribution is taken from the Upper Willamette Chinook totals, not sp

Spring Chinook. 
Draft Report 2/20/2003 

A. CHINOOK 142 Population Sandy River Spring Chinook Years of Data, Length of Series 1977 - 2001, 25 years Abundance Type Dam/weir count Abundance References Cramer, Doug. 2002d. Abundance Notes Abundance estimates only Hatchery Reference No Hatchery Data. Harvest Reference No Harvest Data Available. Age Reference No Age Data Available. Population Willamette Falls Fall Chinook Years of Data, Length of Series 1946 - 2001, 56 years Abundance Type Dam/weir count Abundance References Howell, P.J.. 1986; Bennett, D.E.. 1986; Bennett, D.E. and C.A. Foster. 199

Foster, C.A.. 1994; Bennett, D.E. and C.A. Foster. 1995; Foster, C.A.. 1998

Abundance Notes 2 additional references: Foster 2000 and Foster 2002. Data are for adults anPopulation Willamette Falls Spring Chinook Years of Data, Length of Series 1946 - 2001, 56 years Abundance Type Dam/weir count Abundance References Anonymous. 1998; Foster, C.A.. 1998; Foster, C.A.. 2000. Abundance Notes Data are for adults and jacks.