U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

NOAA Technical Memorandum NMFS-NWFSC-69

Role of the Estuary in the Recovery

of Columbia River Basin

Salmon and Steelhead:

An Evaluation of the Effects of Selected

Factors on Salmonid Population Viability

September 2005
NOAA Technical Memorandum

NMFS Series

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Marine Fisheries Service, NOAA, uses the NOAA

Technical Memorandum NMFS series to issue informal scientific and technical publications when complete formal review and editorial processing are not

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The NMFS-NWFSC Technical Memorandum series of

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has since been split into the Northwest Fisheries

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series is now being used by the Alaska Fisheries

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Reference throughout this document to trade names

does not imply endorsement by the National Marine

Fisheries Service, NOAA.

This document should be cited as follows:

Fresh, K.L., E. Casillas, L.L. Johnson, and D.L.

Bottom. 2005. Role of the estuary in the recovery of

Columbia River basin salmon and steelhead: an

evaluation of the effects of selected factors on salmonid population viability. U.S. Dept. Commer., NOAA

Tech. Memo. NMFS-NWFSC-69, 105 p.
NOAA Technical Memorandum NMFS-NWFSC-69

Role of the Estuary in the Recovery

of Columbia River Basin

Salmon and Steelhead:

An Evaluation of the Effects of Selected

Factors on Salmonid Population Viability

Kurt L. Fresh, Edmundo Casillas,

Lyndal L. Johnson, and Daniel L. Bottom

Northwest Fisheries Science Center

2725 Montlake Boulevard East

Seattle, Washington 98112

September 2005

U.S. DEPARTMENT OF COMMERCE

Carlos M. Gutierrez, Secretary

National Oceanic and Atmospheric Administration

Vice Admiral Conrad C. Lautenbacher, Jr. USN (Ret), Administrator

National Marine Fisheries Service

William T. Hogarth, Assistant Administrator for Fisheries
Most NOAA Technical Memorandums NMFS-NWFSC

are available online at the Northwest Fisheries Science

Center web site (http://www.nwfsc.noaa.gov)

Copies are also available from:

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phone orders (1-800-553-6847)

e-mail orders (orders@ntis.fedworld.gov)

ii
Table of Contents 

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

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

Executive Summary ........................................................................................................................ix 

Acknowledgments..........................................................................................................................xv 

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

Columbia River Estuary...................................................................................................................3 

Use of Estuarine Habitats by Columbia River Salmonids...............................................................6 

River Mouth to Bonneville Dam ...............................................................................................6 

Columbia River Plume ..............................................................................................................7 

Role of the Estuary in the Recovery and Management of Salmon Populations ............................12 

Historical Views of the Role of the Estuary............................................................................12 

Current Views of the Role of the Estuary: Population Perspective.........................................13 

The Estuary and Viability of Anadromous Salmonid Populations and ESUs.........................14 

Analyzing Effects of Factors on Population Viability ...................................................................19 

Defining Life History Type and Life History Strategy ...........................................................19 

Selection of Estuarine Factors for Analysis ............................................................................23 

Analyzing and Rating the Relative Importance of Estuarine Factors......................................26 

Level 1: Is the Factor Likely a Concern for the ESU?......................................................26 

Level 2: How Does the Factor Affect the ESU?...............................................................27 

Analyses of the Effects of Estuarine Factors on Columbia River Basin Salmonids......................29 

Water Flow..............................................................................................................................29 

Effects of Climate on Flow...............................................................................................29 

What Changes Have Occurred in Flow Attributes............................................................30 

Factors Causing Changes in Flow Attributes....................................................................33 

Flow Effects on Sediment Transport ................................................................................34 

Impacts of Water Flow Changes on Salmonid Habitat in the Estuary..............................36 

Summary of Flow Effects.................................................................................................39 

Habitat .....................................................................................................................................39 

Estuarine Habitat and its Use by Juvenile Salmon ...........................................................39 

How Have Estuarine Habitats Changed............................................................................44 

iii
Habitat Summary ..............................................................................................................52 

Toxics......................................................................................................................................52 

Caspian Tern Predation of Juvenile Salmon ...........................................................................66 

Effects of Estuarine Factors on Recovery Potential of ESUs........................................................72 

Other Considerations in Evaluating the Role of the Estuary in Recovery 

of Anadromous Salmonids.............................................................................................................80 

Data Gaps................................................................................................................................80 

Hatchery Fish Effects..............................................................................................................81 

Northern Pikeminnow Predation on Juvenile Salmonids........................................................81 

Direct Affects of the Hydropower System on the Estuary ......................................................83 

How Much Change Is Necessary to Affect Population Status................................................83 

References......................................................................................................................................85 

iv
List of Figures 

Figure 1. The Columbia River estuary extends from the upper extent of tidal influence 

at Bonneville Dam through the oligohaline zone of the river mouth into the coastal zone. .........................4 

Figure 2. Historical and contemporary early life history types for one broodyear of Chinook 

salmon in the Columbia River estuary..........................................................................................................8 

Figure 3. Relationship between average river flow registered at Bonneville Dam for 10 days 

prior to sampling in the Columbia River plume in May, and the maximum distance offshore 

juvenile Chinook and coho salmon were captured. ......................................................................................9 

Figure 4. Biomass of megalopae (Cancer magister) captured in May 2001 and 2002 in the ocean, 

front, and plume habitats using a neuston net.............................................................................................10 

Figure 5. Abundance of yearling coho salmon, yearling Chinook, juvenile chum salmon, and 

juvenile steelhead captured in ocean, front, and plume habitats using a Nordic rope trawl. ......................11 

Figure 6. Comparison of the monthly averaged Columbia River interior subbasin virgin, adjusted, 

and observed river-flow estimates from 1970 to 1999................................................................................31 

Figure 7. Changes in the annual Columbia River flow cycle at Beaver Army Terminal, 

near Quincy, Oregon, 1878–1903 versus 1970–1999.................................................................................32 

Figure 8. Peak freshet day versus year suggests that the freshet is now about two weeks earlier 

than in the 19th century in the Columbia River basin.................................................................................32 

Figure 9. The incidence of flows above 18,000 m3s

-1 (the pre-1900 estimated bankfull flow level) 

and above 24,000 m3

s

-1 (the present bankfull flow level)...........................................................................33 

Figure 10. Monthly average flows at Beaver Army Terminal present and historical bankfull flow 

levels, and warm and cold PDO cycles, 1878–1999...................................................................................34 

Figure 11. Hindcast total sediment load for the Columbia River interior basin associated with the 

observed flow and estimated virgin flow....................................................................................................35 

Figure 12. Habitat opportunity in Cathlamet Bay as a function of stream flow. .......................................36 

Figure 13. The change in availability of shallow water habitat in the tidally influenced region between 

RM 50 and RM 90 on the Columbia River under unmodified and modified flow conditions only. ..........37 

Figure 14. Catch per unit effort for juvenile Chinook salmon for 2002 and 2003 at several sites in 

the mouth of the Columbia River estuary, in the mixing zone, or in the tidal freshwater zone..................41 

Figure 15. Mean fork length of juvenile Chinook salmon for 2002 and 2003 at several sites in 

the mouth of the Columbia River estuary, in the mixing zone, or in the tidal freshwater zone..................41 

Figure 16. Box plots of size of juvenile salmon captured in peripheral habitats (trapnets) 

and near the main channels (beach seine) of the Columbia River estuary..................................................42 

Figure 17. Proportion of Chinook salmon ESUs originating from various parts of the basin 

identified in samples taken from marsh, forested, and shrub habitat of the lower Columbia River 

estuary during 2002 from April to August..................................................................................................43 

v
Figure 18. Stock composition of subyearling Chinook salmon in Columbia River plume 

study area June 1998–2001.........................................................................................................................44 

Figure 19. Catch of naturally and hatchery produced juvenile Chinook salmon over time 

in Skagit Bay, Washington. ........................................................................................................................45 

Figure 20. Shifts in distribution of juvenile Chinook salmon in the Skagit River estuary system. ...........45 

Figure 21. The relationship between freshwater wild Chinook smolt population size 

and density of juvenile wild Skagit Chinook in Skagit River delta habitat, 1992–2002. ...........................46 

Figure 22. Change in acreage of various habitat types used by juvenile salmon in the 

Columbia River estuary (to approximately RM 42) from 1870 to 1980....................................................47 

Figure 23. Daily shallow water habitat area from 1974 to 1998 for virgin and observed 

river flows without dikes, and for virgin and observed flows with dikes. ..................................................51 

Figure 24. Mean concentrations of total PCBs (ng/g wet wt) in whole bodies of juvenile 

fall Chinook salmon sampled from Pacific Northwest estuaries. ...............................................................56 

Figure 25. Mean concentrations of DDTs (ng/g wet wt) in whole bodies of juvenile 

fall Chinook salmon sampled from Pacific Northwest estuaries. ...............................................................56 

Figure 26. Mean concentrations of PCBs and DDTs (ng/g wet wt) in stomach contents 

of juvenile fall Chinook salmon sampled from Pacific Northwest estuaries. .............................................57 

Figure 27. Mean concentrations of high molecular weight polycyclic hydrocarbons (PAHs) 

in stomach contents, and metabolites of PAHs in bile, of juvenile fall Chinook salmon sampled 

from Pacific Northwest estuaries. ...............................................................................................................57 

Figure 28. Mean concentrations of PCBs (ng/g lipid) in juvenile fall Chinook salmon sampled 

from the Columbia River estuary as compared to the 2,400 ng/g lipid biological effects threshold..........59 

Figure 29. The leucocyte primary and secondary in vitro plaque forming cell response per 

culture against an antigen. The mean PFC response was analyzed in Chinook salmon from the 

Green/Duwamish system (urban) and the Nisqually system (nonurban)....................................................61 

Figure 30. Cumulative mortality of juvenile Chinook salmon collected from the Duwamish 

Waterway (urban) and the associated hatchery-estuary system, and the Nisqually hatchery estuary 

system (nonurban) following disease challenge with the marine bacterium Vibrio anguillarum...............62 

Figure 31. Foraging activity in the presence of olfactory signals of a potential predator in juvenile 

Chinook salmon exposed to diazinon. ........................................................................................................64 

Figure 32. Dose-response curves and threshold determinations for sublethal copper neurotoxicity.........65 

Figure 33. Estimated predation rates on all steelhead in the Columbia River estuary by Caspian 

terns, 1999–2002, using bioenergetics modeling and recovery of PIT tags. ..............................................69 

Figure 34. Per capita smolt consumption by Columbia River estuary Caspian terns on all salmonids, 

1997–2003. .................................................................................................................................................70 

vi
List of Tables 

Table 1. Major types of estuarine habitats and some of their important attributes in the 

Columbia River below RM 46......................................................................................................................5 

Table 2. A summary of the juvenile characteristics of stream and ocean life history types. .....................20 

Table 3. Some general attributes of life history strategies associated with Columbia River 

anadromous salmon populations based upon historical use of the system. ................................................22 

Table 4. Linkage between anadromous salmonid ESU, life history type (ocean-type or stream-type), 

and dominant life history strategies of juvenile salmon in the Columbia River. ........................................24 

Table 5. Linkages between limiting factors associated with the estuary upstream of the river’s 

mouth, life history strategies, life history type (ocean-type and stream-type), and ESU............................73 

Table 6. Linkages between limiting factors associated with the plume, life history strategies, 

life history type (ocean-type and stream-type), and ESU. ..........................................................................74 

Table 7. Summary rating table for listed Columbia River basin ESUs for estuary factors........................75 

Table 8. Level 1 ratings of estuary factors for stream-type ESUs. ............................................................76 

Table 9. Level 2 ratings of estuary factors for stream-type ESUs. ............................................................77 

Table 10. Level 1 ratings of estuary factors for ocean-type ESUs.............................................................78 

Table 11. Level 2 ratings of estuary factors for ocean-type ESUs.............................................................79 

vii
viii
Executive Summary 

The primary purpose of this technical memorandum is to evaluate the potential of 

selected factors associated with the Columbia River estuary to improve viability of listed 

anadromous salmonids in the Columbia River basin. We examine how the estuary supports 

viability of anadromous salmonid populations, review what is known about juvenile salmon in 

the Columbia River estuary, examine how changes in selected factors associated with the estuary 

have potentially affected salmon, and describe an approach to value the contribution to salmon 

population viability derived from potentially reducing a factor’s impact. This evaluation was 

conducted in support of efforts by NOAA Fisheries Service to revise deficiencies identified by 

Judge J. A. Redden in the 2000 Biological Opinion on the effects of the federal Columbia River 

Power System (FCRPS) on listed anadromous populations in the basin. 

For this review, we defined the Columbia River estuary broadly to encompass the entire 

continuum where tidal forces and river flows interact. The upstream extent of the estuary is 

Bonneville Dam and the downstream extent includes the plume. Geomorphic features, 

ecological functions, and physical characteristics vary broadly within this area and give rise to a 

mix of habitats that juvenile salmon can potentially occupy. The importance or function of any 

unit of estuarine habitat depends on site specific or patch scale attributes such as vegetation type, 

substrate type, and salinity regime. In addition, habitat functions depend on the landscape 

context of that habitat, such as its size, shape, location in the estuary, the composition of 

surrounding habitat, and connectivity with other habitats. Throughout the entire estuary, the 

distribution and quality of habitats has been affected (and continues to be affected) by a variety 

of anthropogenic (e.g., urbanization) and natural (e.g., climate) factors. 

Our understanding of the role of the estuary in the life history and ecology of salmonid 

populations has changed considerably over the past century. Initial perspectives about the 

estuary were that it was unimportant or irrelevant because the estuary (and ocean) was 

considered to be limitless in its ability to support salmon. Thus the major factors affecting 

salmon were considered to be density-dependent factors occurring in freshwater. Eventually, 

scientists became aware that nonfreshwater factors had an important influence on numbers of 

returning adult salmon and began to consider the role that the estuary and ocean played in 

salmon population fluctuations. The estuary was viewed as a bottleneck or limiting factor to the 

numbers of adults that could be produced. Attempts to remove or bypass the bottleneck (e.g., by 

releasing juveniles from hatcheries or transporting fish rapidly through the estuary) proved 

unsatisfying at increasing abundance of adults. In more recent years, the estuary has come to be 

regarded as part of the continuum of ecosystems that salmon need to utilize in order to complete 

their life cycle, rather than a place that salmon need to avoid. 

Fundamental to the view that estuaries are an important part of the life history of salmon 

is the concept that anadromous salmonids are comprised of populations, or discrete breeding 

units, that vary with respect to their spatial and temporal use of habitats. Variability in climate, 

ix
instream flow conditions, harvest practices, hatchery operations, and accessibility of habitats by 

adults and juveniles help define how populations use estuarine habitats, including arrival timing 

in the estuary, duration of estuarine residence, and fish size at the time of estuarine entry. 

NOAA Fisheries Service defines the status of anadromous salmonids based on the 

viability of populations or groups of populations (evolutionarily significant units or ESUs) over 

long time-frames. For populations and ESUs to recover, the risk that they will go extinct needs 

to decline. Four viable salmonid population (VSP) performance criteria are used to define 

viability: abundance, productivity, spatial structure, and diversity. Levels of these attributes in 

aggregate define extinction risk or persistence of the population; all four VSP criteria are critical 

to recovery and are interrelated. This approach to evaluating population status differs from 

traditional salmon management, which assessed the status of anadromous salmonids from a 

production perspective using primarily numbers of harvested fish, numbers of reproducing 

adults, or survival. Estuarine habitats clearly contribute to the viability and persistence of 

salmon populations in a number of ways. The amount of estuarine habitat that is accessible 

affects the abundance and productivity of a population. The distribution, connectivity, number, 

sizes, and shapes of estuarine habitats affect both the life history diversity and the spatial 

structure of a population. Attributes of estuarine habitats (e.g., temperature and salinity regimes, 

food web relationships) affect diversity and productivity of populations as life-stage specific 

survivals vary with habitat characteristics. 

Ideally, we would like to be able to link factors in the estuary to their potential to affect 

the viability of each listed population or ESU. However, because we do not have specific, 

empirical information describing estuarine habitat use at the population level, we used an 

alternate approach. We evaluated effects of candidate factors on the main life history type 

expressed by an ESU and the range of life history strategies utilized by each ESU. As each ESU 

is comprised of a number of populations, we then inferred responses of the populations based on 

what we predict will occur for the ESU. 

Each listed ESU in the Columbia River basin—the lower Columbia River coho salmon 

(Oncorhynchus kisutch) ESU was also included—was classified as expressing either a streamtype or ocean-type behavior based on when juveniles arrive in the estuary and their size at 

arrival. When viewed over long time-scales, most members of ocean-type populations migrate 

to sea early in their first year of life after spending only a short period (or no time) rearing in 

freshwater. Most members of stream-type fish migrate to sea after rearing for more extended 

periods in freshwater, usually at least a year. Thus ocean-type fish tend to spend longer periods 

in ocean habitats compared to stream-type populations. 

Individual members within each population employ a variety of alternative life history 

strategies or approaches to using available habitat. A life history strategy describes if, how, 

when, and for how long individual salmon use various habitats throughout the freshwater, 

estuarine, and ocean landscape. We used two attributes associated with use of estuarine 

habitats—size of fish at estuarine entry and time of estuarine entry—to define six general life 

history strategies that can potentially be expressed by all anadromous populations: 1) early fry, 

2) late fry, 3) early fingerling, 4) late fingerling, 5) subyearling, and 6) yearling. Although each 

life history type can produce members that use each strategy, the relative proportion of members 

associated with each strategy varies by life history type. Ocean-type populations are dominated 

x
by the fry and fingerling strategies while stream-type populations are dominated by the yearling 

strategy. 

Of the possible estuarine factors that could potentially affect viability, we considered the 

effects of four on salmon in the Columbia River estuary: flow, predation, habitat, and 

contaminants/toxics. These four were selected from a larger list of factors affecting salmon in 

the estuary based on whether: 1) a significant change in the factor from historical conditions was 

evident, 2) the factor could potentially affect population viability, 3) there was quantitative data 

available that could be used to analyze effects of the factor, and 4) the factor could be linked to 

hydropower operations in the Columbia River basin. The selection of factors relied primarily on 

the first three criteria. We did not use the fourth criteria to exclude evaluation of any factor. 

A brief evaluation of changes in each factor and how the factor could affect population 

viability was conducted based on existing data and analyses. We only considered impacts on 

juvenile life stages and did not include potential impacts on adults during their return migration. 

From these overviews, we developed a series of hypotheses or assumptions about each factor 

that helped guide how we rated their relative importance for each ESU. 

It is important to note that our analyses were not inclusive of all factors that may have a 

significant affect on salmon population viability. For example, we expect that water 

temperatures have warmed from historical levels, which could exclude some habitats from use 

by juveniles during part of the year and affect metabolic processes of both salmon and their 

predators. These changes in water temperature could alter mortality rates. The intent of our 

evaluation was to lay out a framework for future consideration of other factors that may affect 

juvenile salmon use and benefits from estuarine habitat as more comprehensive information 

becomes available. 

River flow is a fundamental factor affecting characteristics of juvenile salmon and their 

habitat in the estuary and plume. The interaction of flow and tides with the land creates and 

maintains estuarine habitat. Large-scale changes in flow occur as a result of spatially explicit 

interactions of short- and long-term climate cycles—El Niño-Southern Oscillation (ENSO) and 

Pacific Decadal Oscillation (PDO), respectively—with the watershed. Operations of the Federal 

Hydropower system (e.g., generation of electricity, flood control, and irrigation) have had 

significant affects on attributes of flow, including reducing the mean annual flow, reducing the 

size of spring freshets, almost completely eliminating overbank flows, and changing the timing 

of ecologically important flow events. The hydrological changes, along with floodplain diking, 

represent a fundamental shift in the physical state of the Columbia River estuarine ecosystem. 

Major changes in the estuary resulting from flow alterations that are especially relevant to 

salmon include a loss of vegetated, shallow water habitats and changes in the size, seasonality, 

and behavior of the plume. Such changes potentially have significant consequences for both 

expression of salmonid diversity and productivity. In particular, because the changes in habitat 

are most pronounced in shallow water areas, we predict that effects on the ESUs and life history 

strategies (the fry and fingerling strategies) that make the most extensive use of these shallow 

water areas will be especially significant. Further, we predict that altering and reducing plume 

size, shape, and intensity will also affect ESUs expressing the yearling life history strategy. 

xi
The location and types of habitats present in the Columbia River estuary have been 

substantially altered from historical conditions. Although the entire estuary has not yet been 

surveyed, the main changes that have been identified to date have been a major loss of emergent 

marsh, tidal swamp, and forested wetlands; shifts in organic matter important to estuarine food 

webs; and changes in features of the plume. Shallow water-dependent life history strategies (fry 

and fingerlings) have been most affected by the loss of shallow water-vegetated habitat types in 

the estuary, while larger life history strategies have been most affected by changes in the plume. 

Alterations in attributes of flow and the construction of dikes and levees have caused these 

changes. Diking is an especially significant change because it severs the connection of the 

habitat with the river, eliminating any direct (use) or indirect (export of organic matter for food 

webs) benefit to the fish. 

Exposure to waterborne and sediment-associated chemical contaminants has the potential 

to affect survival and productivity of both ocean- and stream-type stocks in the estuary. Streamtype ESUs are likely to be most affected by short-term exposure to waterborne contaminants 

such as current use pesticides and dissolved metals. These chemicals can disrupt olfactory 

function and interfere with such behaviors as capturing prey, avoiding predators, imprinting, and 

homing. Ocean-type ESUs may also be exposed to these types of contaminants, but will also be 

affected by persistent, bioaccumulative toxicants such as poly chlorinated biphenyls (PCBs) and 

DDTs, which they may absorb during their more extended estuarine residence. Consequently, 

we expect that the impact of contaminants on ESUs exhibiting the ocean life history type will be 

more significant. 

Predation is a major source of mortality of all salmonid populations. Although many 

predator-prey interactions in the Columbia River estuary appear to have changed from historical 

conditions, we have little quantitative data on most predators. One exception is Caspian tern 

(Sterna caspia) predation, which has significantly increased recently due to a change in nesting 

habits of the birds in the Columbia River estuary. The main impact of tern predation is on ESUs 

with stream-type life history types, especially steelhead (Oncorhynchus mykiss). This is 

primarily because the dominant migratory periods employed by salmonids with a stream-type 

life history most overlap with the nesting period of the terns. Improvements to productivity of 

populations by managing terns would be expected to especially benefit stream-type ESUs, 

although lesser benefits to other salmonid ESUs in the basin should also occur. 

To evaluate effects of factors on population viability, we developed a rating system that 

ranked each factor as having a high, medium, or low ability to improve the status of anadromous 

salmon populations if the impact of the factor was substantially reduced. We drew inferences 

about how a factor affects an ESU based on the life history type of the ESU and how the factor 

would affect the different life history strategies that characterized that life history type. Because 

the currently available information regarding use of the estuary does not allow resolution at the 

level of a population, limiting factors for all stream-type ESUs were ranked similarly while those 

for ocean-type ESUs were ranked similarly. Ratings were developed by considering each factor 

relative to other estuarine factors within an ESU; we did not consider the effect of factors relative 

to other nonestuary factors. 

The rating system used to evaluate effects of factors on population viability consisted of 

two screening levels; each level addressed two major issues. The level 1 screen evaluated 

xii
whether the factor was likely of concern to an ESU based on its affects on VSP and change in the 

factor relative to historical conditions. The level 2 screens asked how the factor affected an ESU 

based on where the affects occurred. Each question was evaluated for each factor for each ESU 

based on whether the ESU was ocean-type or stream-types. Scoring was done using guidance 

from the principles/hypotheses developed in the analyses of the limiting factors. Because of 

limitations in our knowledge base, we aggregated the estuary into two zones—river mouth to 

Bonneville Dam and the plume. From the river mouth to Bonneville Dam, we only 

differentiated two habitat types—shallow and deep. 

For ocean-type ESUs, for example, Columbia River chum salmon (Oncorhynchus keta) 

and Snake River fall Chinook salmon (O. tshawytscha), flow and habitat were rated as having a 

high ability to affect population viability. As noted above, flow changes in the basin are 

primarily a result of dam operations, whereas habitat changes are a function of both hydropower 

operations and other, nonhydro issues, notably the construction of dikes and levees in the 

estuary. The combined affect of flow and habitat changes on estuarine habitat has been to reduce 

the amount of shallow water habitat (especially vegetated habitat such as swamps and marshes) 

and disrupt organic matter inputs from these vegetated habitats. The dominant life history 

strategies of ocean-type Chinook salmon extensively use shallow water habitat, which is where 

the main flow and habitat changes have occurred. Moreover, the beneficial use of shallow water 

habitat by each ESU is likely a function of location in the estuary. Whereas all estuarinedependent life history strategies expressed by each ESU will use the lower portion of the estuary 

(mouth of the Columbia River to RM 40), upriver ESUs (e.g. Snake River fall Chinook salmon) 

will be more dependent on tidally influenced shallow freshwater habitats between Bonneville 

Dam (their point of entry to the Columbia River estuarine system) and approximately RM 40. 

Tern predation was considered to have a low affect on the ocean life history type because terns 

do not prey significantly on fry and fingerling-sized fish (the dominant ones associated with this 

life history type). Contaminants received a medium score. Both waterborne and sediment 

contaminants can affect fry and fingerling life history strategies in shallow water areas. 

For stream type ESUs (e.g., Snake River spring/summer Chinook salmon and midColumbia River steelhead), the primary estuarine factors affecting population viability were tern 

predation and flow; both of these factors were ranked as medium. Tern predation was ranked in 

the medium category because it is primarily directed at subyearling and yearling size fish, which 

are the dominant strategies in stream-type ESUs. In addition, these larger fish occur in deeper 

water channel habitats where they are most vulnerable to the terns and migrate at a time when 

they are most susceptible to tern predation. Flow changes were ranked medium for stream-type 

ESUs because both abundance and productivity were affected by changes in plume habitat. In 

addition, the main life history strategies for these ESUs are most abundant in plume habitats 

where they would be expected to be most vulnerable to flow-related changes in plume habitat. 

From the perspective of the estuary, we conclude that population viability of stream-type 

ESUs is most affected by tern predation and flow, while flow and habitat most affect ocean-type 

ESUs. At this time, we do not know how much of a change in each factor is required to affect 

improvements in population responses of relevant ESUs. Based on available information, we 

hypothesize that the greatest opportunity to affect ESUs in the Columbia River basin by the 

manipulation of estuarine factors is with restoration of shallow water habitat. These actions will 

primarily affect ocean-type ESUs and the shallow water-dependent strategies of stream-type 

xiii
ESUs. This is because there is a strong linkage between the fry and fingerling life history 

strategies, which dominate ocean-type ESUs, and shallow water habitat. Thus the main affect on 

ocean-type ESUs of making changes in habitat and flow will be realized as gains in abundance 

and productivity. The main affect on stream-type ESUs of reducing tern predation and altering 

flow will also be realized as gains in abundance and productivity. 

There is a large amount of vegetated shallow water habitat that has been lost due to the 

combined effects of flow changes and diking. These two factors must be considered in concert 

in considering restoration approaches because of the strong effects of flow on functions of 

shallow water habitat. Restoration of shallow water habitat can be done without changing 

hydropower operations (which can have other, unintended consequences, such as an increase in 

gas bubble disease). However, we expect that studies now underway will provide greater insight 

into how much change and where such change in shallow water is both possible and needed to 

affect population viability. 

xiv
Acknowledgments 

We thank Jennifer Burke for her insights and discussions on many aspects of salmon use 

of the Columbia River estuary. Critical reviews of this document were provided by Jennifer 

Burke, Si Simenstad, Joyce Howard, Mary Ruckelshaus, Tim Beechie, Lynne Krasnow, John 

Ferguson, and Cathy Tortorici. We thank Casey Rice, Eric Beamer, Curtis Roegner, A. D. 

Robertis, and Paul Moran for sharing unpublished data sets. Our thanks to Dave Ward for 

helping with the subsection on northern pikeminnow predation. 

xv
xvi
Introduction 

Since 1991, 12 different groupings or evolutionarily significant units (ESUs) of 

anadromous salmonids that reproduce in the Columbia River basin have been listed as threatened 

or endangered under the Endangered Species Act (ESA) of the United States. These include 

steelhead (Oncorhynchus mykiss), chum salmon (O. keta), Chinook salmon (O. tshawytscha), 

and sockeye salmon (O. nerka) populations that spawn from the upper Snake River basin to 

tributaries of the lower river below Bonneville Dam. Every subbasin of the Columbia that is 

currently accessible to anadromous salmonids contains at least one threatened or endangered 

population. The Federal Columbia River Power System (FCRPS) has had a variety of well 

documented impacts on anadromous salmonids in the basin, including the loss and degradation 

of spawning and rearing habitat and increased mortality of upstream and downstream migrating 

fish during passage at hydroelectric facilities (ISG 2000, Williams et al. 2005). As a result, 

efforts to recover these populations at risk have focused almost exclusively on identifying and 

modifying risk factors directly associated with the large hydroelectric dams constructed 

throughout the basin. 

In recent years, increasing attention has been directed at the role of other hydropower 

related issues and nonhydropower-related issues in the decline and recovery of salmonids in the 

basin. One such issue is changes in the condition and availability of habitats in the estuary. The 

growing recognition that the estuary has a role in the recovery of Columbia Basin salmonids 

represents a significant departure from previous management efforts in the system. Several 

developments appear to be responsible for this change. First, legislation Congress passed in 

1996 amended the Power Act and required the Northwest Power Planning Council (NWPPC) to 

consider the effect of ocean conditions on fish and wildlife populations when recommending 

hydropower mitigation projects for the Columbia River basin. This legislation focused new 

attention on the estuary, plume, and coastal ocean habitats. 

Second, life stage risk and sensitivity modeling analyses of Columbia River salmon 

populations by Kareiva et al. (2000) and McClure et al. (2003) suggested that additional actions 

beyond passage improvements were needed to recover salmonid populations. Two life stages 

identified as sensitive to perturbations included the first years spent rearing in the river, estuary, 

and ocean. Kareiva et al. (2000) used a matrix population model to conclude that the maximum 

potential to contribute to anadromous salmonid recovery was associated with these life stages. 

However, they could not discriminate between these life stages nor could they determine how 

much of a change in survival was possible. 

Third, scientific perspectives of the life history and ecology of anadromous salmonids 

have shifted in recent years (Bottom et al. 2005). Previously, habitats and life stages important 

to salmon were considered in isolation with the goal of identifying single limiting factors 

restricting salmon production. We now recognize that marine, estuarine, and riverine 

environments are each components of an extended salmon ecosystem that cannot be treated 

independently (NRC 1996, Bisbal and McConnaha 1998, ISG 2000). Thus the estuary, which 

includes the plume, is part of the continuum of landscapes all juvenile and adult anadromous 
salmonids use that originate from the Columbia River basin. They connect freshwater and 

marine habitats and are used by all life stages to some degree for feeding, refugia from predators, 

and physiological transition (McCabe et al. 1983, 1986, Bottom and Jones 1990). 

Finally, our understanding of the relationships between habitats and the persistence of 

salmon populations has evolved in recent years. It is clear that habitats cannot be valued simply 

on the basis of their role in producing fish biomass or numbers (Bottom 1997). Instead, diverse 

habitats and the expression of life history strategies based on use of these habitats are directly 

linked to salmon population viability (i.e., persistence) over long time scales (McElhany et al. 

2000). These linkages were explicitly recognized by the Independent Scientific Group (ISG) for 

the NWPPC, which concluded that estuary and ocean dynamics help to control salmon 

productivity (Beamish and Bouillon 1993, Beamish et al. 1999) and that salmon biodiversity 

(including the diversity of estuarine life histories) helps to reduce the effects of fluctuations in 

ocean, and presumably freshwater, conditions (ISG 2000). Alterations and loss of estuarine 

habitats thus has direct implications for salmonid population viability. 

The challenges of identifying, designing, implementing, and evaluating recovery actions 

in the estuary are significant, in part because we know little about the estuary and the salmon that 

use the estuary. While ongoing research efforts will significantly upgrade our knowledge base in 

upcoming years, much of what we now know is conceptual or based on research from other 

areas, such as Puget Sound. Estuary restoration at any scale is a challenge and in the Columbia 

River estuary it is an especially daunting challenge because of the massive size of this system. 

Further, the estuary is among the most heavily modified portions of the basin (Thomas 1983) due 

to the long history of coastal development and the cumulative effects of flow regulation, habitat 

modification in the estuary, and other changes upriver which have altered sediment transport and 

salinity regimes in the system (Simenstad et al. 1992, Weitkamp 1994). In the last 100 years, 

these and other changes have decreased the amount of some types of wetland habitats in this 

region by as much as 70% from historical levels (LCREP 1999). 

The primary purpose of this technical memorandum is to evaluate the potential of 

selected factors associated with the estuary to improve viability of listed anadromous salmonids 

in the Columbia River basin. Accordingly, we: 

1) examine how the estuary supports viability of anadromous salmonid populations, 

2) review what is known about juvenile salmon in the Columbia River estuary (which 

includes the plume), 

3) examine how changes in selected factors associated with the estuary have potentially 

affected salmon populations, and 

4) describe an approach to value the contribution to salmon population viability resulting 

from reducing the impact of a factor. 

These analyses were conducted in support of efforts by NOAA Fisheries Service to address 

deficiencies identified by Judge J. A. Redden in the 2000 Biological Opinion on the effects of the 

Federal Columbia River Power System (FCRPS) on listed anadromous populations in the basin. 

2
Columbia River Estuary 

An estuary is generally defined as a semienclosed coastal body of water with a free 

connection to the open ocean in which salt water is diluted with runoff from the land (Pritchard 

1967). For this review, however, we define the Columbia River estuary more broadly to 

encompass the entire continuum where tidal forces and river flows interact, regardless of the 

extent of saltwater intrusion. Thus the upstream boundary of the estuary is Bonneville Dam, 

which is the extent of tidal influence, while the downstream boundary includes the plume 

(Figure 1). 

The estuary can be divided into different zones based on a variety of attributes, such as 

geomorphic features, ecological functions, tidal conditions, salinity regimes, and physical 

characteristics. A number of approaches have been employed to describe and classify the 

different zones of the estuary (e.g., Johnson et al. 2003). In this report, we consider only two 

zones of the estuary, primarily because our information on use of the estuary by juvenile salmon 

does not yet allow us to discriminate use at a finer scale. The first zone extends from the mouth 

upstream to Bonneville Dam and includes conditions ranging from the tidally influenced 

freshwater in the upper estuary to higher salinities and higher wave energies near the river’s 

mouth. The second zone is the river plume, which is generally defined by a reduced-salinity 

contour near the ocean surface of 31 parts per thousand. During high flows, the plume front is 

readily visible as a sharp interface between sediment-laden river water and the clear ocean. Its 

geographic position varies greatly with seasonal changes in river discharge, prevailing nearshore 

winds, and ocean currents. During summer months, the plume extends far to the south and 

offshore along the Oregon coast; during the winter it shifts northward and inshore along the 

Washington coast. Strong density gradients between ocean and plume waters create relatively 

stable habitat features where organic matter and organisms can be concentrated. 

Throughout the estuary is a mix of habitats that the juvenile salmon can occupy. Habitat 

is the physical, biological, and chemical characteristics of a specific unit of the environment 

occupied by a specific plant or animal. Thus habitat is unique to specific organisms and 

encompasses all the physiochemical and biological requirements of that organism within a 

spatial unit. The function of any estuarine habitat for juvenile salmon depends on site specific or 

patch scale attributes such as vegetation type, substrate type, and salinity regime (Simenstad and 

Cordell 2000). In addition, habitat functions depend on the landscape context of that habitat 

(Simenstad 2000). Landscape context refers to the spatial arrangement of habitat, including its 

size and shape; location of the habitat within the estuary; the composition of surrounding habitat; 

and connectivity with other habitats (Turner 1989). A variety of systems have been employed 

(and others continue to be developed) to classify and describe the diverse array of habitats 

present in the estuary that vary in their basic philosophical approaches, information that is used, 

scope, complexity, and application. Table 1 presents a general classification of major habitat 

types within the estuary below RM 46, after Thomas (1983) and Johnson et al. (2003); habitat 

classification systems have not yet been developed for other parts of the estuary. 

3
Figure 1. The Columbia River estuary extends from the upper extent of tidal influence at Bonneville Dam 

(RKm 235), through the oligohaline zone of the river mouth, into the coastal zone including the 

plume in the Pacific Ocean. (Reprinted from Bottom et al. 2005.) 

4
Table 1. Major types of estuarine habitats and some of their important attributes in the Columbia River 

below RM 46. (Adapted from Thomas 1983 and Johnson et al. 2003.) 

Major habitat types Important attributes 

Tidal swamps Vegetation is mostly shrub and woody species. Higher 

elevations. Low water velocities. 

Tidal marshes Dominant vegetation varies. Includes emergent marshes. 

Tidal channels often present. Depths generally range 

from mean lower low water (MLLW) to above mean higher 

high water (MHHW). Low water velocities. 

Tidal flats Depths range between MLLW and 6 ft below MLLW. 

Usually not vegetated. 

Medium deep Depths range from 3–18 ft below MLLW. Mostly associated 

with medium sized and larger channels. Higher water 

velocities. 

Deep Depths >18 ft. Mostly associated with the main channel. 

Higher water velocities. 

5
Use of Estuarine Habitats by Columbia River 

Salmonids 

There have been few studies of habitat use of the Columbia River estuary by wild 

juvenile salmon and steelhead, and most of this work has been conducted downstream of Puget 

Island. Research recently initiated by NOAA Fisheries Service in the middle and lower estuary 

and plume will significantly upgrade our knowledge about how juvenile salmon, specific 

populations, and ESUs use the estuary. Most of our knowledge about how juvenile salmon use 

estuaries has come relatively recently from studies in Puget Sound, British Columbia, and Alaska 

(e.g., Parker 1971, Stober and Salo 1973, Kaczynski et al. 1973, Reimers 1973, Mason 1974, 

Bailey et al. 1975, Fresh et al. 1979, Salo et al. 1980, Healey 1979, 1980, 1982, Simenstad et al. 

1982). It is remarkable that given the overall importance of Columbia River for salmon in the 

Pacific Northwest and the large size and diversity of this estuarine system, empirical knowledge 

about how salmon use this estuary is distinctly lacking compared to other estuarine systems in 

the Pacific Northwest. 

An important factor that needs to be considered in any analysis of estuarine habitat use by 

wild salmon and steelhead is the occurrence of hatchery fish. Because our ability to separate 

wild and hatchery fish captured in the estuary has been limited and remains so even at present, 

many of the spatial and temporal patterns observed in previous data sets may apply to hatchery 

fish rather than wild fish (e.g., Dawley et al. 1985, 1986). 

River Mouth to Bonneville Dam 

In the portion of the estuary between Bonneville Dam and the river’s mouth, one study 

that provided enough information to distinguish use of different estuarine habitats by juvenile 

salmonids was by Columbia River Estuary Data Development Program (CREDDP); however, 

sampling in this program was limited to the lower estuary (to the upstream end of Puget Island). 

In general, McCabe et al. (1986) found that subyearling Chinook in shallow intertidal habitats of 

the Columbia River were smaller than subyearlings captured in deeper pelagic areas. Larger 

yearling migrants spent little time in shallow estuarine habitats and more time in deeper channel 

areas (Bottom et al. 1984, McCabe et al. 1986). 

Most of what is known about juvenile salmon use of the estuary concerns timing of fish 

passage through the estuary and was derived from seining studies conducted to recapture coded 

wire tagged (CWT) fish below Bonneville Dam. In the late 1970s and early 1980s, subyearling 

Chinook salmon (these are all nonyearling fish combined) were present year round in the estuary 

(Bottom et al. 1984, Dawley et al. 1986, McCabe et al. 1986). While in many of the years 

studied overall peak abundance occurred from May to September, there were years when a 

bimodal distribution was observed (Dawley et al. 1985, 1986). There was also evidence of 

specific patterns in seasonal timing that particular populations exhibited (e.g., Lewis River) that 

6
were different than the patterns for all populations considered in aggregate (Dawley et al. 1985). 

Peak catches at Jones Beach, where much of the estuary timing work has been conducted, often 

were highly correlated with the timing of hatchery releases. 

Since 2001 NOAA Fisheries Service has investigated habitat relationships of juvenile 

salmon in the area upstream of the river mouth. Similar to the work by Dawley et al. (1985), 

juvenile salmon were present in the estuary year round. However, the number of size classes of 

juvenile salmon passing through the estuary is considerably reduced from historical levels 

(Figure 2). 

Although knowledge of habitat use in the Columbia River estuary is limited, the 

information that does exist, in combination with studies in other estuaries of the Pacific 

Northwest, provides insight into how juvenile salmonids use habitats in this large estuary. 

Estuarine research has demonstrated that juvenile salmon are generally distributed based on 

water depth (e.g., Healey 1980, Levy and Northcote 1982, Simenstad et al. 1982, Bottom et al. 

1984, Levings et al. 1986, McCabe et al. 1986, Miller and Sadro 2003). The smallest size 

classes tend to be the most closely associated with shallow water. As fish size increases, fish use 

a broader array of depths; fish size can change as a result of growth that occurs in the estuary, 

growth in freshwater, or some combination of rearing in the two environments. Habitat shifts by 

the juvenile salmon do not necessarily occur continuously as fish size increases, but may occur at 

specific size thresholds. For example, Simenstad et al. (1980) suggested that juvenile chum 

salmon shifted from use of littoral to offshore habitats at a size threshold of about 50 mm. Based 

on this size based model, the smallest juvenile salmon in the Columbia River estuary (fry and 

fingerlings) will be primarily associated with the shallowest, most peripheral, wetland type of 

habitat, while the larger subyearlings and yearlings will be found in deeper pelagic areas. 

Coincident with the fish size/depth relationship, smaller salmon tend to spend longer in the 

estuary and larger yearling migrants spend less time. 

Columbia River Plume 

Studies of use of the Columbia River plume were initiated in 1998 by NOAA Fisheries 

Service. In general, the plume is primarily used by yearlings and less so by subyearlings which 

appear to stay closer to shore (Emmett et al. 2004). Thus far, because sampling has been 

conducted in late spring and early summer, the distribution of fish in summer is unknown. 

Although they were not specifically studying use of the plume, Fisher and Pearcy (1995) found 

relatively few yearlings near the mouth of the Columbia River in summer. The evidence 

obtained to date suggests the plume serves juvenile salmon in multiple ways. Pearcy (1992) 

hypothesized that one function of the plume was to distribute juvenile salmon offshore, away 

from predation pressure closer to the shore. Findings by NOAA Fisheries Service are consistent 

with the hypothesis proposed by Pearcy (1992). In May and June when flows are higher, 

juveniles are found further offshore, in the low saline waters, than when flows are lower (Figure 

3). During years when river flow out of the Columbia River during the freshet period is reduced, 

salmon are more localized around the mouth of the Columbia River. 

In addition, the plume appears to provide a place for juvenile salmon to feed and grow 

(Schabetsberger et al. 2003). It may support juvenile salmon foraging by facilitating primary 

production during the spring freshet period. During low-flow years, such as observed in 2001, 

7
January

February

March

April

May

June

July

August

September

October

November

December

January

February

March

April

May

June

July

Relative abundance 

Fry (<60 mm)

Fingerling - recent arrivals

Fingerling - riverine rearing

Fingerling - estuarine rearing

Fingerling - riverine and additional rearing

Yearling

a

b

January

February

March

April

May

June

July

August

September

October

November

December

January

February

March

April

May

June

July

Relative abundance

Fry

Fingerling - natal / riverine rearing

Yearling

Figure 2. Historical and contemporary early life history types for one broodyear of Chinook salmon in 

the Columbia River estuary. Historical timing and relative abundance (top) inferred from 

historical sampling throughout the lower estuary (Rich 1920). Contemporary timing and relative 

abundance (bottom) derived from Dawley et al. (1985) sampling at Jones Beach. (Adapted from 

Burke 2005.) 

8
Outflow at Bonneville Dam (kcf s-1)

0 100 200 300

Distance offshore (nautical miles)

0

10

20

30

40

50

Coho yearling

Chinook yearling

2001

2000

1999

2002

2003

Figure 3. Relationship between average river flow (thousand cubic feet per second) registered at 

Bonneville Dam for 10 days prior to sampling in the Columbia River plume in May, and the 

maximum distance offshore juvenile Chinook and coho salmon were captured in surface trawls 

along a transect extending east along latitude 46.15, just south of the mouth of the Columbia 

River. (From B. Peterson, NWFSC.) 

the amount of chlorophyll evident off of the Oregon and Washington coast affiliated with the 

plume, as characterized with satellite observations by SeaWifs, was much lower than that 

observed when more normal flows occurred, such as observed in 1999 (Thomas et al. 2003). 

Zooplankton biomass is also highly associated with frontal features at the plume margins (Figure 

4) and less so either within the plume or oceanic zones. 

Some of the ongoing plume research being conducted by NOAA Fisheries Service has 

focused on identifying attributes of the plume that can be used to define habitat important to 

juvenile salmon. Features such as the surface area of the plume, the volume of the plume waters, 

the extent and intensity of frontal features, and the extent and distance offshore of plume waters 

are considered physical attributes defining habitat important to salmon. One hypothesis that has 

been studied is that juvenile salmon would preferentially utilize frontal features; this, however, 

has not been validated. Juvenile salmon abundance was not higher exclusively around frontal 

features. Studies did suggest that smaller juvenile salmon showed a significant preference for 

the plume and front habitats as compared to the more marine, oceanic habitats (Figure 5). 

NOAA Fisheries Service has also found that salmon continue their preference for the low saline 

environment of the plume as they retain their orientation to the surface region (Emmett et al. in 

press). The higher turbidity associated with the low salinity plume waters may provide a refuge 

from predators. 

9
Ocean Front Ocean Front Plume

2001

0

50

100

150

200

250

300

p<0.0001

17x

Carbon (mg m-3)

2001

Plume

0

50

100

150

200

250

300

p<0.0001

17x

2235

2002

0

50

100

150

200

250

300

p<0.0001

71x

2002

0

50

100

150

200

250

300

p<0.0001

71x

Figure 4. Biomass (milligrams carbon per cubic meter) of megalopae (Cancer magister) captured in May 

2001 and 2002 in the ocean, front, and plume habitats using a neuston net. Box plots demarcate 

the 10th, 25th, 50th, 75th, and 90th percentiles. An analysis of variance (ANOVA) (blocked) was 

used to identify significant differences. Biomass of this species was 17 and 71 times higher in the 

front habitat compared to the average of the ocean and plume habitats (Morgan et al. in press).

10
Y

Figure 5. Abundance of A) yearling coho salmon, B) yearling Chinook, C) juvenile chum salmon, and D) 

juvenile steelhead captured in ocean (O), front (F), and plume (P) habitats using a Nordic rope 

trawl. Box plots demarcate the 10th, 25th, 50th, 75th, and 90th percentiles of densities. (From A. D. 

Robertis, NWFSC.)

2001 2002 2001 2002

earling coho

O F P O F P 

Year

No. km-2

0

2000

4000

6000

8000

ling Chinook

O F P O F P 

0

1000

2000

3000

4000

Juvenile chum

O F P O F P 

No. km -2

0

1000

2000

3000

4000

Juvenile steelhead

O F P O F P 

0

100

200

300

400

2001 2002 2001 2002

A B

C D

11
Role of the Estuary in the Recovery and 

Management of Salmon Populations 

The following section describes our conceptual framework of the role of the estuary in 

the life history of anadromous salmonids and how this perspective has evolved. It is intended to 

help structure our evaluation of the potential of selected factors to affect salmonids in the 

Columbia River basin and to help facilitate recovery and management of anadromous salmonids. 

The framework describes and organizes our current understanding of how the estuary supports 

anadromous salmonid species and integrates information on the life history and ecology of 

salmon, conservation biology, and how estuarine ecosystems function. We incorporated 

elements of the model that Bottom et al. (2005) developed to guide research on juvenile 

salmonids in the Columbia River estuary. Because of the lack of knowledge specifically about 

juvenile salmon in the Columbia River estuary, we used relevant information from throughout 

the Pacific Northwest to help develop the framework. We recognize that the estuary is much 

larger than most systems on the Pacific coast where juvenile salmon use of estuaries has been 

studied, so information from other systems needs to be applied carefully. But, because the 

salmon are using the estuary for the same fundamental purposes and estuaries have many of the 

same attributes regardless of size, we believe that principles of estuarine use can be developed 

from these other systems and applied in the Columbia River estuary. 

Historical Views of the Role of the Estuary 

Our understanding of the role of the estuary in the life history and ecology of salmon has 

evolved as we have learned more about how juvenile salmon use estuarine habitats. Initially, the 

estuarine and ocean environments were considered limitless in their ability to support salmon 

and so were believed to be unimportant or irrelevant. At this time, freshwater, density dependent 

factors were assumed to regulate salmon species (Bottom 1997, Bottom et al. 2005), with more 

adults expected simply as a result of an increase in the number of eggs and fry. A major goal of 

early salmon research and management was to understand freshwater sources of mortality so that 

they could be more easily manipulated and more adults could be produced (Bottom 1997). 

Salmon were viewed primarily from a production perspective as simply another agricultural 

product or crop to be managed for the benefit of people (Bottom 1997). The output of this crop 

was defined as short term changes in the numbers of harvestable or reproducing adults. 

One outgrowth of the production approach to salmon management has been the use of 

hatchery fish throughout the Pacific Northwest. Because of habitat destruction and alteration, 

the high demand for salmon, overharvest, and the expanding human population, there has never 

been enough harvestable salmon to go around (Lichatowitch and McIntyre 1987). Hatcheries 

evolved as a way to increase salmon abundance and were based on the freshwater-centric, 

density-dependent philosophy that more adults would result in direct proportion to the additional 

number of eggs that survived (Lichatowitch 1999). Hatcheries focused on bypassing as much of 

12
the freshwater life of salmon as possible, where the most significant sources of mortality were 

believed to occur. 

The continued failure of hatchery production to increase or even maintain salmon 

numbers raised new questions about whether passage through estuaries and the ocean might be 

critical to determining numbers of returning adults. Salmon researchers in the 1950s and 1960s 

began to recognize that nonfreshwater factors had a role in determining numbers of returning 

adults (e.g., Manzer and Shepard 1962, Gilhousen 1962). The development and analysis of longterm data sets on salmon production suggested freshwater conditions could not by themselves 

adequately explain variability in numbers of returning adults (e.g., Salo and Bayliff 1958, Hunter 

1959, Gilhousen 1962, Parker 1968, Peterman 1978). Beginning in the late 1960s, research on 

the estuarine and early marine life of juvenile salmon rapidly expanded throughout the Pacific 

Northwest. 

Initially, scientists adopted the production-oriented view that estuaries were a bottleneck 

to salmon production. This bottleneck concept was based on research suggesting that juvenile 

salmon mortality during this period could be especially high (e.g., Parker 1968, Bax 1983). The 

estuarine and early marine period came to be regarded by many researchers as the critical period 

of salmon life that significantly affected overall survival rates and adult returns (Kaczynski et al. 

1973, Peterman 1978, Healey 1980, Nickelson 1986, Pearcy 1992). 

In the 1970s, proposed expansions in hatchery production generated concerns that there 

could be a limit or carrying capacity to estuarine and coastal environments. Simenstad et al. 

(1980) expressed concern that the carrying capacity of the Hood Canal, Washington estuarine 

environment for pink salmon (O. gorbuscha) and chum salmon would be exceeded if enough 

hatchery fish were released. Bailey et al. (1975) suggested that releases of hatchery pink and 

chum salmon in Alaska coastal areas could exceed carrying capacities of estuaries for hatchery 

fish and result in fewer than expected adult returns. Studies were initiated to estimate the 

quantities or carrying capacity of hatchery fish that could be supported by estuaries (e.g., 

Reimers et al. 1979) and to find the optimum conditions in the estuary that would maximize 

production. Because some managers questioned whether salmon were really estuarine 

dependent, further studies were conducted to ascertain whether the estuary could be bypassed 

altogether and so render moot the issue of carrying capacity in this environment (MacDonald et 

al. 1988, Solazzi et al. 1991). 

Current Views of the Role of the Estuary: Population Perspective 

In more recent years, we have shifted from the more production-oriented views of the 

estuary to the developing perspective that the estuary is part of the continuum of ecosystems that 

salmon utilize to complete their life cycle, rather than a place that should be avoided. Estuaries, 

as well as other places used by salmon throughout their lives, are therefore necessary and 

important parts of the salmon life cycle. Fundamental to this view of estuaries is the concept that 

salmon species are comprised of populations. Populations are geographically discrete, self 

perpetuating, and semiisolated (in terms of genetic exchange) groups of reproducing salmon. 

They are the unit that much of modern research and management of salmon is organized around. 

The population perspective of salmon is in part an outgrowth of studies by Willis Rich on 

Columbia River salmon (e.g., Rich 1920, 1939). Rich evaluated scale patterns of juveniles 

13
passing through the Columbia River estuary and found a variety of patterns of estuarine use. 

Fish exhibited a wide diversity in the time at which they arrived in the estuary, the amount of 

time they were spending there, and the size at which they arrived (Rich 1920, 1939); some 

salmon were present nearly year round in the estuary. 

To explain these observations, Rich (1939) suggested that the Columbia River estuary 

was a mixing ground of fish from many different sources or populations, each of which exhibited 

a range of behaviors that were defined by the particular set of conditions found in the full range 

of spawning and nursery areas available to the population. He concluded that there was not a 

unique or singular way for a salmon species or population to use the estuary or any other habitat. 

Instead populations employed a diversity of approaches that were determined by variability in 

climate, instream flow conditions, origin of the fish, harvest practices, hatchery operations, and 

accessibility of habitats by adults and juveniles. Groups of salmon became locally adapted to the 

conditions they experienced. 

The concept that habitat use by salmon can depend on the population of origin is 

supported by a wide body of literature (e.g., Wilmot and Burger 1985, Burger et al. 1985, 

Beachum and Murray 1987, Burgner 1991, Healey 1991, Wood 1995, Woody et al. 2000, 

Hodgson and Quinn 2002, Miller and Sadro 2003, Ramstad et al. 2003). Our understanding of 

the specifics concerning between- and within-population variability in estuarine habitat use is 

still increasing. However, what we know is consistent with the population perspective of habitat 

use. For example, Beamer1 has found that early migrating Chinook salmon fry in the Skagit 

River, Washington, use a different suite of Puget Sound habitats than later migrating fish. 

Reimers (1973) was able to define different patterns of estuarine habitat use and seaward 

movement in Chinook salmon in the Sixes River, Oregon, and link those to their ultimate success 

(i.e., survival). Carl and Healey (1984) concluded that variations in migration behavior and 

estuarine use within the Nanaimo River, British Columbia basin were linked to different 

subpopulations associated with geographically distinct spawning areas. 

The Estuary and Viability of Anadromous Salmonid 

Populations and ESUs 

NOAA Fisheries Service’s Northwest Fisheries Science Center (NWFSC) developed a 

conceptual approach to evaluating the status of anadromous populations and ESUs that defines 

status based on a population’s viability over long time scales (McElhany et al. 2000). The 

authors defined a viable population or ESU as one that has a negligible risk of extinction over a 

100-year time period. For populations or ESUs to recover, the ability of a population or ESU to 

persist must increase over time, or conversely, the risk that they will go extinct needs to decline 

(McElhany et al. 2000). Four viable salmonid population (VSP) performance criteria are used to 

define viability (McElhany et al. 2000): abundance, productivity, spatial structure, and diversity. 

All four VSP criteria are critical to the viability of salmon populations, all are interrelated, and 

levels of all four attributes in aggregate define extinction risk or the likely persistence of the 

population or ESU. This approach to evaluating population status differs from traditional salmon 

management, which typically assessed the status of anadromous salmonids from a production 

 

1

 E. Beamer, Skagit River System Cooperative, La Connor, WA. Pers. commun., February 2004. 

14
perspective using numbers of harvested fish or reproducing adults. Using the NOAA Fisheries 

Service VSP criteria incorporates a much broader view of how to define population status. This 

perspective recognizes that factors affecting salmon populations vary widely, so using a variety 

of metrics can provide insight into what types of actions are needed to help populations and 

ESUs recover. 

Abundance is a measure of the number of members in the population (e.g., numbers of 

spawners or returning adults), while productivity is the rate of growth of the population over a 

given time interval. Productivity can also be expressed as life-stage specific survivals, since the 

cumulative effects of those survivals results in a population’s growth rate over time. Populations 

that have a lot of members and a positive population growth rate are more likely to persist than 

populations that do not have these characteristics. Changes in abundance and productivity of a 

population can be measured over multiple time scales. Evidence clearly suggests that estuarine 

habitats contribute to the abundance and productivity of salmon populations (e.g., MacDonald et 

al. 1988). For example, Reimers (1973) demonstrated that for the one broodyear of Chinook 

salmon that he studied in the Sixes River, Oregon, most adult returns originated from fish that 

made extensive use of the estuary. Magnusson and Hilborn (2003) similarly concluded that 

survival to adult return of hatchery Chinook salmon populations in coastal environments was 

directly and positively correlated with the condition of the estuary. The Kareiva et al. (2001) 

matrix population model suggested that improving survival during the estuarine and early ocean 

stages could significantly increase salmon population growth rates. Changes in conditions in the 

nearshore zone of Puget Sound, which serves as an extension of the estuary, account for 

significant variability in adult returns of Skagit Bay Chinook salmon.2

Although conservation of diversity and spatial structure are emerging paradigms in 

recovery and management of Pacific Salmon (e.g., McElhany et al. 2000, Waples et al. 2001, 

Hilborn et al. 2003, Issak et al. 2003) and other fish species (e.g., Gresswell et al. 1994), their 

application to salmon recovery remains a considerable challenge. For example, within Puget 

Sound, quantitative abundance and productivity goals have been developed for many threatened 

Chinook salmon populations, but population specific goals for spatial structure and diversity do 

not yet exist. Moreover, guidance on improving spatial structure and diversity in salmon 

recovery has thus far focused primarily on the effects of spawning characteristics (i.e., amount, 

quantity, location, and diversity of spawning habitats available to a population) rather than on 

characteristics occurring during other life stages. Because understanding the role of the estuary 

in affecting spatial structure and diversity is as important as understanding its effect on 

abundance and productivity, we consider these concepts and their application to salmon recovery 

efforts in greater detail below. 

Spatial structure refers to the geographic distribution of individuals in the population and 

the processes that generate that distribution. The conceptual basis of spatial structure originates 

from principles of metapopulation dynamics (Hanski and Gilpin 1996), which describe how 

groups of populations interact with their habitat and with one another. Metapopulation principles 

suggest that persistence of a species in a variable environment will depend in part on the spatial 

distribution of suitable habitat, including the numbers, quality, and quantities of habitat patches 

occupied; patterns in the use of patches; when patches are occupied; when patches are available; 

 

2

 C. Greene, NWFSC, Seattle, WA. Pers. commun., February 2004. 

15
and the ability of members to colonize and use habitat patches. At any one time, there may be a 

wide variety of habitats that can be occupied by members of a population, although not all 

suitable habitats that are available will necessarily be occupied. The application of 

metapopulation principles to the conservation of salmonids has attracted considerable interest in 

recent years (e.g., McElhany et al. 2000, Rieman and Dunham 2000, Issak et al. 2003, 

Ruckelshaus et al. 2004). 

Salmon populations clearly exhibit complex geographic structure that can be defined at 

multiple spatial scales. For example, at any moment, a population can be distributed across 

many thousands of square miles, ranging from the headwater spawning areas to Pacific Ocean 

feeding grounds (e.g., Healey 1991). Within one area, such as the estuary, multiple habitat types 

such as deep channels, mudflats, and emergent marshes can be simultaneously occupied by 

members of one population. Distributing members of a population through an array of habitats 

helps reduce the vulnerability of the population to shifts in environmental conditions (McElhany 

et al. 2000, Hilborn et al. 2003). There are, however, few studies directly linking geographic 

structure to observed patterns of estuarine use. Carl and Healey (1984) concluded that variations 

in migration behavior and estuarine use by Chinook salmon within the Nanaimo River basin 

were linked to different subpopulations associated with geographically distinct spawning areas. 

Diversity consists of the variability in life history and discrete genetic traits exhibited by 

salmon. Diversity in salmon life histories exists along a continuum and includes individuals, 

subpopulations, populations, ESUs, and species. Along with spatial structure, phenotypic 

diversity helps buffer populations from environmental variability (e.g., Taylor 1990, Healey and 

Prince 1995, Hilborn et al. 2003). Life history diversity can be measured as variability in a wide 

variety of traits, including body size, fecundity and egg size, timing of life history events such as 

spawning, where spawning and rearing occurs, residence time in various habitats, habitat use, 

size at age, age at maturity, ocean distribution patterns, and physiological characteristics (Koski 

1971, Healey and Heard 1984, Burger et al. 1985, Beachum and Murray 1987, Tallman and 

Healey 1991, Taylor 1990, 1991, Quinn and Unwin 1993, Roni and Quinn 1995, NRC 1996, 

Quinn et al. 2000, Waples et al. 2001, Hodgson and Quinn 2002, Beckman et al. 2003, Miller 

and Sadro 2003, Ramstad et al. 2003, Brannon et al. 2004). Variability in life histories can arise 

as a result of genetic variation, variation in environments the fish experience, or both; 

differentiating these is a considerable challenge. Thus some of the variability we see in life 

history patterns may be adaptive (i.e. genetically based) and reflect local adaptations that 

different salmon populations have evolved to cope with the specific conditions that they 

experience, including variability in estuarine habitats (Taylor 1991, Hansen and Jonsson 1991, 

Gharrett and Smoker 1993, Quinn et al. 2000). Other genetically based variations may not be 

adaptive, but instead may be due to random genetic drift (Stearns 1992). 

One way to conceptualize life history diversity is as a set of alternate life history 

strategies or trajectories (we use these terms to refer to the same thing) that individual members 

of a salmon population can follow (Wissmar and Simenstad 1998). Each trajectory represents an 

approach to using the spawning, rearing, and migration habitats that are available to the fish in 

space and time. A variety of phenotypic differences (age at return, size at return, fecundity, and 

time spent in particular habitats) can exist between trajectories based on how habitats are used. 

From the perspective of the estuary, studies have demonstrated a broad range in the use of 

estuarine habitats between and within populations in such attributes as residence time, timing of 

16
arrival in the estuary, habitat usage, and size of arrival in the estuary (e.g., Reimers 1973, Carl 

and Healey 1984, Levings et al. 1986, Quinn and Unwin 1993, Miller and Sadro 2003, Bottom et 

al. 2005, Bottom3

). 

A major factor affecting the number and quality of life history strategies (quality is 

defined as how successful the trajectory is at producing recruits) present within a population will 

be the distribution and quality of habitats that can potentially be used (NRC 1996). If the 

habitats do not exist because of either natural or anthropogenic factors, then population members 

cannot use them and distinct life history strategies can potentially be eliminated from the 

population. This can reduce viability of the population by diminishing productivity, spatial 

structure, and diversity. For a population to use diverse habitats, the habitats must be available 

and the right fish must be available to use these habitats (e.g., the appropriate genotype). 

Although each member of a population is unique and has its own trajectory, these 

individual trajectories can be bundled or aggregated into a more limited number of general 

trajectories based on spatial and temporal patterns in use of habitats (e.g., Reimers 1973, Carl 

and Healey 1984, Beamer4

). A variety of metrics associated with these general trajectories can 

then be used as measures of life history diversity including number of trajectories, condition of 

the trajectories (e.g., quality of habitats being used), distribution of members across trajectories, 

and success or survival of members using different strategies. In general, the abundance of 

members using some strategies will be greater than the abundance of members using other 

strategies within a population because those strategies are more successful under the prevailing 

environmental conditions. As conditions change, the distribution or proportion of members 

associated with each life history strategy can then shift. Over short time scales (e.g., annually), 

the distribution of strategies can vary in response to annual variability in such factors as flow, 

water temperature, and the occurrence of El Niño events. A sustained shift in conditions (e.g., 

climate shift, anthropogenic influences) potentially can produce more significant shifts in the 

distribution of life history traits (Hilborn et al. 2003). 

The complex geographic distribution of members within populations and the alternate 

approaches to completing life cycles are not unique to salmon or anadromous species 

(Roughgarden et al. 1988, Sinclair 1988, Secor 1999, Able et al. 2003, King and MacFarlane 

2003). As with salmon it is not clear in most cases, whether diversity is more facultative or 

genetically determined. The relative roles of genetics and the environment in inducing diversity 

will have a significant effect on any population’s persistence in the face of changing 

environmental conditions. Within the Alagnak River, Alaska, Meka et al. (2003) found that 

rainbow trout (Oncorhynchus mykiss) exhibited three life history patterns based on their 

migratory movements within this river system. A similar diversity in movements within 

Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri) was described by Gresswell et al. 

(1994). Although little genetic differentiation existed, they concluded that the range in variation 

in life history strategies within the cutthroat trout was an adequate basis for providing protection 

to each life history type. Curry et al. (2002) found a range of tactics related to the use of 

freshwater and estuarine habitats within one riverine brook trout population. Recent research has 

also revealed that striped bass (Morone saxatilis) exhibit a variety of life history approaches that 

 

3

 D. Bottom, NWFSC, Newport Research Station, Newport , OR. Pers. commun., February 2004. 

4

 E. Beamer, Skagit River System Cooperative, La Conner, WA. Pers. commun., January 2004. 

17
can vary within and between populations in use of freshwater and estuarine landscapes (Secor 

and Piccoli 1996). Limburg (2001) found that there was differential mortality of American shad 

(Alosa sapidissima) based on fish size and age the fish emigrated from freshwater. Many 

populations of marine fish also exhibit complex approaches to how they distribute themselves in 

space and time that are similar to the tactics exhibited by anadromous species (e.g., Roughgarden 

et al. 1988, Able et al. 2003, King and McFarlane 2003). 

In summary, estuaries are part of the continuum of habitats salmon use. Rather than 

serving as a bottleneck to production, estuarine habitats clearly contribute to the viability and 

persistence of salmon populations. They accomplish this in a number of ways. The amount of 

estuarine habitat that is accessible affects the abundance and productivity of a population. The 

distribution, connectivity, number, sizes, and shapes of estuarine habitat affects both the diversity 

and the spatial structure of a population. Attributes of estuarine habitats (e.g., temperature and 

salinity regimes, food web relationships) affect diversity and productivity of populations as lifestage specific survivals vary with habitat characteristics. 

18
Analyzing Effects of Factors on 

Population Viability 

In this section, we describe our approach to analyzing effects of estuarine factors on 

salmonid population viability. We first describe how we linked estuarine factors to their 

potential to affect the viability of each listed population. Because we had limited empirical 

information describing estuarine and plume habitat use by specific anadromous populations or 

ESUs in the Columbia River estuary and plume, we used an alternate approach. Specifically, 

effects of candidate factors were linked to viability of an ESU based on the life history type of 

each ESU and how a factor affected the distribution and quality of life history strategies 

associated with each life history type. As each ESU consists of an aggregate of populations, we 

can then infer responses of populations based on what we predict will occur for the ESU. 

Second, we describe which factors were included in our analyses and how they were selected. 

Finally, we describe the system we used to rate effects of each factor on viability of ESUs. 

Defining Life History Type and Life History Strategy 

We first defined the life history type of each ESU as either stream-type or ocean-type. 

The terms stream-type and ocean-type originated from Gilbert (1912) to discriminate Chinook 

salmon based on their length of stream residence. Based on banding patterns he observed on 

scales, Gilbert referred to stream-type fish as those fish having scales with a banding pattern 

consistent with a period of poor growth in winter in cold freshwater habitats. Ocean-type scales 

(he used the term sea-type) did not show this poor winter growth, indicating the fish moved into 

warmer, more productive marine waters before winter. Subsequently, Healey (1991) extended 

use of the terms to include both juvenile residence patterns and ocean distribution patterns. 

Healey (1991) proposed that ocean-types and stream-types were separate races that were 

independent and geographically isolated from one another except in the southern part of their 

range where they separated temporally in areas of sympatry. Recently, Healey’s racial model 

explaining variability in Chinook salmon life history patterns at broad spatial scales has been 

challenged (Brannon et al. 2004, Waples et al. 2004). 

We use the terms stream-type and ocean-type to separate ESUs into two groups based 

strictly on certain characteristics exhibited by juveniles during their first year of life, including 

how long they rear in freshwater, when they outmigrate, and how long they spend in estuarine 

habitats (Table 2). Populations are referred to as ocean-type if most of the members of the 

population migrate to sea early in their first year of life after spending only a short period (or no 

time) rearing in freshwater. A shorter period of freshwater rearing is usually correlated with 

more extensive use of estuarine and oceanic habitats. In contrast, most members of a streamtype population migrate to sea after rearing for at least a year in freshwater (Table 2). Thus 

ocean-type fish have a greater reliance on estuarine and ocean habitats during their first year of 

life, while stream-type salmon tend to depend on freshwater habitats during this same period. 

Differences in other life history characteristics can also occur as a function of juvenile life 

19
Table 2. A summary of the juvenile characteristics of stream and ocean life history types as used in 

this report. 

 Stream-type fish Ocean-type fish 

Species 

Coho salmon Coho salmon 

Some Chinook populations Some Chinook populations 

Steelhead Chum 

Sockeye Pink 

Attributes 

Long period of freshwater rearing (>1 yr) Short period of freshwater rearing 

Shorter ocean residence Longer ocean residence 

Short period of estuarine residence Longer period of estuarine residence 

Larger size at time of estuarine entry Smaller size at time of estuarine entry 

Mostly use deeper, main channel estuarine habitats Mostly use shallow water estuarine habitats, 

especially vegetated ones 

history characteristics including differences in age and size at return and timing of return 

migrations (Healey 1991). However, there is not a simple relationship between these other life 

history characteristics and life history type. For example, while stream-type fish are often spring 

spawners and ocean-type fish are generally fall spawners, there are numerous exceptions 

(Brannon et al. 2004, Waples et al. 2004). 

An ESU was classified as stream type if the majority of populations within that ESU fit 

the stream-type life history model; an ESU was classified as ocean type if the majority of 

populations fit that life history type. Information documented in the following species status 

reviews was used to classify the populations and ESUs: Myers et al. (1998) for Chinook salmon, 

Johnson et al. (1997) for chum salmon, and Busby et al. (1996) for sockeye and steelhead. 

Individual members within a population exhibit a variety of alternative spatial and 

temporal trajectories, or life history strategies, for using available habitat. We defined alternative 

life history strategies based solely on the size at estuarine entry and arrival time in the estuary. 

Size at entrance into the estuary can be used to classify life history strategy because there is a 

linkage between fish size, habitat use, and residence time (Healey 1980, 1982, Levy and 

Northcote 1981, 1982, Simenstad et al. 1982, Levings et al. 1986, Tschplanski 1987, Miller and 

Sadro 2003). In general, residence time in the estuary decreases as the size of the fish entering 

the estuary increases (with the exception of pink salmon). In addition, juvenile salmon are 

generally distributed based on water depth, with the depth of the water occupied by the fish 

increasing as the size of the fish increases (McCabe et al. 1986). Larger fish can result from 

growth either in estuarine or freshwater habitats. There is not necessarily a continuous 

relationship between habitat occupied and fish size but rather there may be transitional or 

20
threshold sizes where most fish shift from use of one habitat type to another. For example, 

Simenstad et al. (1980) suggested that juvenile chum shifted from shallow littoral habitats to 

more offshore habitats in Puget Sound at a size of about 50 mm. 

The time the fish arrive in the estuary also varies within a general size class of individuals 

(Carl and Healey 1984, Bottom et al. 2005). Because available resources and habitats can be 

different depending on when a fish arrives in the estuary, arrival timing represents a reasonable 

way to define how the fish use habitats. The wide range in variability in size at estuarine entry 

and time of entry that can occur is illustrated by Figure 2 from Bottom et al. (2005). In this 

analysis, Bottom et al. (2005) classified historical early life history strategies for juvenile salmon 

recovered in the Columbia River estuary based on size at entry, time of entry, freshwater life 

history (where and how long the fish reared in freshwater), and estuarine growth data generated 

from scale pattern analyses performed by Rich (1920). For example, under historical conditions, 

fry (fish < 60 mm at estuarine entry) were found in the estuary nearly year round, while yearlings 

were present from February to June. The source populations were not identified in these 

analyses, but it is reasonable to assume that many ESUs contributed to the patterns historically 

observed in the Columbia River estuary. 

Based primarily on size at arrival in the estuary and time of estuarine entry data derived 

from Burke’s (2005) reanalysis of Rich’s scale information, we defined six general life history 

strategies that used the estuary historically (Table 3): 1) early fry, 2) late fry, 3) early fingerling, 

4) late fingerling, 5) subyearling, and 6) yearling. Fry were defined as fish that enter the estuary 

at a size less than 60 mm, with early fry entering in approximately March and April and late fry 

from May to June. Fingerlings were identified as fish that enter the estuary at a larger size than 

fry, which implies there was some period of freshwater rearing; fingerlings have yet to begin the 

physiological transition associated with smolting. Fingerlings rear in the estuary for some 

period, with early fingerlings entering between January and July and late fingerlings from 

August to December. Subyearlings are fish that rear for less than a year in freshwater, rear little 

in the estuary, and smolt as they outmigrate during their first year of life. They reside in the 

estuary for less time than fry or fingerling salmon. Yearlings rear for at least one year in 

freshwater and then emigrate; these fish generally spend less time in the estuary than fry or 

fingerlings. 

Although any one population can potentially produce all strategies, some strategies will 

be more abundant or dominant than others within a population. In general, yearlings will tend to 

be the dominant life history strategy in stream-type populations, while nonyearlings will be most 

abundant in ocean-type populations. The distribution or proportion of members within a 

population associated with each life history strategy will depend on the environmental conditions 

the fish are experiencing (e.g., ocean conditions, freshwater spawning habitat, and predator 

populations). The distribution of members within different strategies can vary in response to 

climate changes, flow, water temperature, and ocean conditions. 

Considering the dramatic changes that have occurred over the last 100 plus years in 

climate, estuarine habitats, ocean conditions, and the freshwater spawning and rearing habitats 

that produce the source populations, it seems reasonable to assume that these changes have 

altered the distribution of life history strategies within populations and therefore within ESUs. 

This change is suggested by comparing current and historical use of the estuary by different 

21
Table 3. Some general attributes of life history strategies associated with Columbia River anadromous 

salmon populations based upon historical use of the system. Information from D. Bottom, 

NWFSC, and J. Burke, University of Washington School of Aquatic and Fishery Sciences, was 

used to develop this table. All values should be considered general estimates. 

Life history strategy Attributes 

Early fry Time of estuarine entry: March–April 

Size at estuarine entry: <50 mm 

Estuarine residence time: 0–40 days 

Freshwater rearing: 0–60 days 

Late fry Time of estuarine entry: May–June, present through September 

Size at estuarine entry: <60 mm 

Estuarine residence time: < 50 days 

Freshwater rearing: 20–60 days 

Early fingerling Time of estuarine entry: April–May 

Size at estuarine entry: 60–100 mm 

Estuarine residence time: <50 days 

Freshwater rearing: 60–120 days 

Late fingerling Time of estuarine entry: June–October, present through winter 

Size at estuarine entry: 60–130 mm 

Estuarine residence time: 0–80 days 

Freshwater rearing: 50–180 days 

Subyearling (smolt) Time of estuarine entry: April–October 

Size at estuarine entry: 70–130 mm 

Estuarine residence time: <20 days 

Freshwater rearing: 20–180 days 

Yearling Time of estuarine entry: February–May 

Size at estuarine entry: >100 mm 

Estuarine residence time: <20 days 

Freshwater rearing: >1 year 

strategies of Chinook salmon (Figure 2). For the estuary as a whole, all life history strategies 

were evident for longer periods of time throughout the year (Rich 1920); clearly, the current use 

of the estuary is more limited now than in the past. We examined possible changes in expression 

of different life history strategies for each ESU between historical and current conditions. Such a 

change analysis is restricted by the limited information on the distribution of life history 

strategies under either current or historical conditions for specific ESUs or populations. We 

defined the mix of life history strategies that we believe is likely being expressed by each ESU, 

under current conditions based on a variety of information sources including the life history type 

of that ESU, origin, unpublished data from the ongoing studies of Columbia River estuary 

(Bottom unpubl. data), and status reviews. We then extrapolated the likely mix of life history 

strategies historically employed by each ESU, using such information as Figure 2, and predicted 

22
23

how different types of changes affecting each ESU would have impacted each life history 

strategy (Table 4). The changes in distribution of life history strategies described in Table 4 

should be considered hypotheses. 

Selection of Estuarine Factors for Analysis 

To facilitate recovery of endangered salmon stocks in the Columbia River basin, factors 

that currently act to suppress an increase in their viability need to be identified. If the factors are 

appropriately and correctly pinpointed and can be manipulated, it is logical to conclude that 

reducing their affect should improve the recovery potential of targeted populations. Further, 

incorporating the influence of a factor’s impact on recovery of salmon populations should 

improve policy and management decisions. 

We recognize that identifying single habitat factor solutions to salmon survival problems 

in isolation has not been historically effective. A growing body of evidence suggests that a 

broader scale view of ecosystem restoration that focuses on how alteration to landscape 

processes and ecosystem attributes affects salmon via habitat changes is more likely to succeed 

(NRC 1996, Beechie and Bolton 1999, Stouder et al. 1999, Roni et al. 2002, Beechie et al. 

2003a, 2003b). Identification of limiting factors in the estuary represents a logical first step that 

needs to be incorporated into a broad, landscape-scale assessment of strategies to improve the 

recovery potential for endangered salmon populations. Our goal here is to consider the effects of 

several estuarine factors on recovery of listed anadromous salmonids. 

The major estuarine related factors that we identified that can potentially affect salmonid 

population viability in the Columbia River estuary are climate and climate change (which can 

control other factors): water flow; access to and quality of habitats; sediment; salinity; 

temperature; toxics/contaminants; predators such as Caspian terns (Sterna caspia), cormorants 

(Phalacrocorax auritus), marine mammals, and northern pikeminnow (Ptychocheilus 

oregonensis); hatchery practices; and harvest practices. Although it would be useful to evaluate 

the role of each of these factors, we selected water flow, habitat, Caspian tern predation, and 

contaminants for detailed analysis. These four were selected based on four criteria: 

1. Was there a significant change in the factor from historical condition? 

2. Could the factor potentially affect population viability? 

3. Was quantitative data available that could be used to analyze effects of the factor? 

4. Could the factor be linked to hydropower operations in the Columbia River basin? 

We relied primarily on the first three criteria and did not use the fourth to exclude any factor. 

We wish to emphasize that factors were not selected based on whether or not we believed 

they had a significant affect on salmonid population viability. Some factors that were not 

selected for consideration in this report may have a significant affect on viability. For example, 

we expect that water temperatures have warmed from historical levels, which could exclude 

some habitat from use by juveniles during part of the year and affect metabolic processes of both 

salmon and their predators. These changes in water temperature could alter growth and survival. 

A major purpose in our evaluation was to lay out a framework for future consideration of other 
Table 4. Linkage between anadromous salmonid ESU, life history type (ocean-type or stream-type), and dominant life hist

juvenile salmon in the Columbia River. We estimated general contribution to the outmigrant population of each lif

Abundant (>50%), Medium (10–50%), Rare (1–9%), or Absent (<1%) listed for each ESU under historical (early 1

conditions.(C) We made these estimates using a variety of data sources and our judgment about how the various ch

system would have affected each strategy within each ESU. 

Life history strategy 

ESU Life history type Early fry Late fry Early fingerling Late fingerling SubyearliColumbia River chum salmon 

Ocean Abundant (H)

Abundant (C)

Abundant (H)Abundant (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Absent (HAbsent (C

Snake River sockeye salmon 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Rare (H)Rare (C)

Lower Columbia River coho salmon 

Stream Rare (H)

Absent (C)

Rare (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Rare (C)

Upper Columbia River steelhead 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C

Snake River steelhead 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C

Lower Columbia River steelhead 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Absent (C)

Medium Rare (C)

Middle Columbia River steelhead 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Absent (C)

Medium Rare (C)

Upper Willamette River steelhead 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C

24
25

Table 4 continued. Linkage between anadromous salmonid ESU, life history type (ocean-type or stream-type), and domin

strategies of juvenile salmon in the Columbia River. We estimated general contribution to the outmigrant populatistrategy as Abundant (>50%), Medium (10–50%), Rare (1–9%), or Absent (<1%) listed for each ESU under histor

and current conditions.(C) We made these estimates using a variety of data sources and our judgment about how th

occurring in the system would have affected each strategy within each ESU. 

Life history strategy 

ESU Life history type Early fry Late fry Early fingerling Late fingerling SubyearliSnake River fall Chinook salmon 

Ocean Absent (H)

Absent (C)

Absent (H)Absent (C)

Medium (H)Rare (C)

Medium (H)Rare (C)

AbundanAbundan

Upper Willamette River Chinook salmon 

Ocean Rare (H)

Absent (C)

Rare (H)Absent (C)

Medium (H)Rare (C)

Medium (H)Rare (C)

Rare (H)Medium 

Lower Columbia River fall Chinook salmon 

Ocean Medium (H)

Rare (C)

Medium (H)Rare (C)

Medium (H)Rare (C)

Medium (H)Rare (C)

Medium Abundan

Upper Columbia River spring Chinook salmon 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Rare (C)

Snake River spring/summer Chinook salmon 

Stream Absent (H)

Absent (C)

Absent (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Absent (C)

Rare (H)Rare (C)
factors that may affect juvenile salmon use and that could be used as more comprehensive 

information becomes available. 

For each factor, we considered how it could affect population viability based on available 

data and analyses. We then developed a series of hypotheses or principles about each factor that 

helped guide how we rated their relative importance for each ESU. In addition, we assessed 

changes in each factor from historical conditions. Such a comparison between historical and 

current conditions is a useful way to help identify causes and mechanisms of ecosystem change 

(e.g., Borde et al. 2003, Beechie et al. 2003b, Collins et al. 2003). 

Analyzing and Rating the Relative Importance of Estuarine Factors 

To rate the importance of each factor, we developed a simple rating system that ranked 

each factor as having a high, medium, or low ability to improve the status of anadromous salmon 

populations. We defined improvement in population status to mean improvement in population 

viability (McElhany et al. 2000). We drew inferences about how a factor affects an ESU based 

on the life history type of that ESU, how we believed the factor would affect the life history 

strategies that characterized that life history type, and the hypotheses and principles developed 

from the overviews of each factor. The limiting factors for all stream-type ESUs were ranked 

similarly while those for ocean-type ESUs were ranked similarly. Ratings were developed by 

considering each factor relative to other estuarine factors within an ESU; ratings were not 

considered relative to other nonestuarine factors such as tributary habitat. 

The rating system consisted of two levels. The level 1 screen evaluated if the factor was 

likely a concern for an ESU based on its affects on VSP and changes in that factor from 

historical conditions. The level 2 screens asked how the factor affected an ESU based on where 

the affects occurred and the life history strategies affected. 

Level 1: Is the Factor Likely a Concern for the ESU? 

What is the affect on each VSP parameter? 

Each factor will have some affect on each VSP parameter. We assumed, however, that if 

the factor affected large numbers of individuals in the ESU and individuals associated with 

multiple life history strategies (again, relative to other factors) that there was a significant affect 

on abundance and productivity. If a factor primarily affected only one or two particular life 

history strategies or specific habitat types more than others, we assumed the primary affect of the 

factor was on spatial structure and diversity. Because most populations in threatened or 

endangered status are at low levels of abundance, we reasoned that the abundance levels of these 

depressed populations needed to be increased as soon as possible. Therefore, we doubled the 

score if the factor affected abundance and productivity. 

Has the factor changed from historic conditions and what it is the likelihood that it could 

be improved relative to the other factors? 

We considered whether each factor had changed significantly from historical conditions. 

Because we intentionally selected factors that we believed had changed significantly from 

26
historical conditions, this screen did not differentiate much between factors. We also considered 

from a practical perspective how much change in each factor was possible. A factor could be 

significantly changed from historical levels but relatively difficult to change relative to other 

estuarine factors. 

Level 2: How Does the Factor Affect the ESU? 

Does the factor have a significant affect on the abundance of the dominant life history 

strategy? 

For the dominant life history strategy, we asked how the factor affected the abundance of 

juveniles of that life history type in shallow water habitats (upstream of the river’s mouth), 

deepwater habitats (upstream of the river’s mouth), and plume habitats. We only considered 

these three areas because available information indicates that use of habitats in the plume and 

confined portion of the estuary (river mouth to Bonneville Dam) is quite different. Thus 

separation of the estuary into these two large zones was warranted. Within the zone from 

Bonneville Dam to the river’s mouth, we also differentiated use of shallow, low velocity habitats 

from medium and deep, higher velocity channel habitats because this was also consistent with 

available information. Studies indicate that smaller juveniles more extensively use shallow, low 

velocity habitats (e.g., swamps, emergent marshes, and shallow flats) than medium and deep, 

higher velocity channel habitats; the opposite pattern exists for larger size classes such as 

yearlings (Healey 1980, 1982, Levy and Northcote 1981, 1982, Simenstad et al. 1982, Levings et 

al. 1986, Miller and Sadro 2003). 

For the dominant life history strategy, does the factor affect habitat quality, quantity, and 

opportunity? 

For the dominant life history strategy, we asked what type of affect the factor had in 

shallow water (upstream of the river’s mouth), deepwater (upstream of the river’s mouth), and 

plume habitats. We considered effects of the factor on habitat quantity, quality, and opportunity. 

The concepts of opportunity and quality (or capacity) were proposed by Simenstad and Cordell 

(2000) and adopted by Bottom et al. (2005) for the Columbia River estuary. 

Opportunity attributes relate to the accessibility of habitat to juvenile salmon. In general, 

opportunity metrics are largely physical and chemical in nature such as tidal elevation, 

temperature, and location of habitat. For example, extreme high temperatures and diminished 

flows can constrain accessibility of shallow water habitat. Capacity measures primarily relate to 

the biotic and ecological functions (i.e., acquiring food and avoiding being eaten) of habitat. 

Capacity metrics must be considered within the context of the species and life stage using the 

habitat, and the location of that habitat within the landscape. In addition to capacity and 

opportunity, we also included quantity of habitat as a separate metric. For toxics, we rated 

effects separately in shallow water and deepwater estuarine habitat for waterborne and sedimentborne contaminants. For example, if there were risks to the main life history type from both 

types of contaminants in shallow water, then the score would double. 

Each of the four questions listed above was evaluated for each factor and each ESU based 

on whether the ESU was classified as an ocean or stream life history type. Each cell in a matrix 

27
was either scored as a yes (+1) or no (0) with two exceptions: 1) abundance and productivity 

which were given a +2 score, and 2) toxics in deep and shallow water which each could be 

scored a +2 if there was effects from both waterborne and sediment-associated toxics. This 

affected the maximum possible score that could be assigned to a factor. For flow, habitat, and 

predation, the maximum possible score was 20, whereas the maximum possible toxics score was 

28. The final rating was computed as the ratio between the assigned score and maximum 

possible score; a ratio of >0.66 was assigned a high ranking, 0.34–0.66 a medium ranking, and 

<0.34 a low ranking. 

28
Analyses of the Effects of Estuarine Factors on 

Columbia River Basin Salmonids 

Water Flow 

Water, interacting with the land, creates and maintains the mosaic of estuarine habitats 

that juvenile salmon occupy. The estuarine habitat features to which salmon have adapted are 

largely the result of riverine and tidal processes and the physical characteristics of the watershed. 

The major geologic feature affecting flows through the basin is the Cascade mountain range, 

which divides the Columbia River drainage basin into interior and western subbasins. The moist 

and relatively warm western subbasin contains only about 8% of the total surface area of the 

660,480-km2

 basin, but contributes almost one quarter of the total river flow (Orem 1968). Most 

of the western subbasin is at too low an elevation to accumulate a large seasonal snow pack. 

Thus the highest flows are observed during and after winter storms, between December and 

March. In contrast, most of the flow in the interior subbasin occurs as the result of the seasonal 

snow pack melt between April and July. Much of the interior subbasin is relatively arid, but its 

Canadian component experiences heavy winter snowfall and plays a major role in spring freshet 

flows. 

Effects of Climate on Flow 

Natural variations in Columbia River flows associated with both short and long term 

fluctuations in climate have a significant affect on amount and timing of water delivered to the 

estuary. These variations directly affect habitat conditions in the estuary, and help determine 

what areas are wetted and potentially accessible to juvenile salmon and how estuarine salinity 

gradients vary. Climate-induced variations in Columbia River flow occur on time scales from 

months to centuries (Chatters and Hoover 1986, 1992). One example of a longer term climate 

effect is the Pacific Decadel Oscillation, commonly known as the PDO (Francis and Hare 1994, 

Mantua et al. 1997), which alternates between cold and warm phases at approximately 30-year 

time scales. During the cold phase, more rainfall is typical in the Pacific Northwest, whereas in 

the warm phase, less rainfall occurs. The cold phase of the PDO (e.g., the 1945–1976 period) 

was regarded as benefiting salmonid production in the Pacific Northwest, while being less 

favorable for salmon originating in northern British Columbia and Alaska (Hare et al. 1999). 

The opposite circumstance prevails during the warm phase, characteristic of the recent period 

between 1977 to about 1998, when listing of salmon in the basin occurred. Another cold, wet 

phase seems to have commenced about 1998 (Peterson and Schwing 2003). PDO-related 

fluctuations in salmonid survival have been linked to the degree of density stratification of the 

coastal ocean (Gargett 1997), but they are also likely influenced by conditions within the river 

and estuary (e.g., salinity, turbidity, and river flow). 

Another climate related feature is the El Niño-Southern Oscillation (ENSO; typically 3–7 

years in duration) cycles (Redmond and Koch 1991, Kahya and Dracup 1993, Dracup and Kahya 

29
1994, Gershunov et al. 1999, Jay 2001). ENSO cycles are shorter in duration compared to the 

PDO cycle, typically amplifying conditions associated with the cold or warm phase of the PDO. 

El Niño winters in the Pacific Northwest often bring high sea level, warm air temperature, low 

precipitation, low snowpack, and weak subsequent spring freshet flows (Kahya and Dracup 

1993, Dracup and Kathya 1994). La Niña winters (the contrast to El Niño) typically exhibit an 

opposing climate and hydrological response. As a consequence, the annual average flows of the 

Columbia and the Willamette rivers during years with a strong El Niño winter are 91% and 92% 

of the long-term annual average, while in case of strong La Niña winters, they are 110% and 

111%, respectively. El Niño effects are intensified during a warm-PDO phase, while those of La 

Niña are enhanced during a cold-PDO phase (Gershunov et al. 1999). Conversely, El Niño 

effects are suppressed during the cold-PDO phase, as are those of La Niña during the warm-PDO 

phase (Jay 2001). 

The Columbia River basin’s climate response is conditioned by its position between 

41o

30' and 54o40'N lat., within a latitudinal band of strong response to the ENSO cycle and to the 

PDO (Mantua et al. 1997). However, the affects of climate on flow vary considerably depending 

on location within the basin. While the river flow per unit area is much larger in the western 

than in the interior subbasin, there are only modest variations across the basin in response to 

ENSO or PDO forcing. Still, the relatively large north-south extent of the basin brings about 

important differences in flow seasonality—the incidence of winter floods and timing of spring 

snowmelt—even within the interior subbasin. 

What Changes Have Occurred in Flow Attributes 

Changes in flow attributes, such as when and how much water arrives in the estuary, are 

an integral measure of alterations in a river system. In a recent analysis and review, Jay (2005) 

provided a detailed estimate of changes in flows in the Columbia River for the past 100 years, 

thereby providing an accounting of flow conditions during the historical and current period. One 

measure of hydrological change is the overall quantity of water delivered to the estuary. Jay 

concluded that there has been approximately a 16.4% reduction in river flow during the last 100 

years. He evaluated the contribution of climate and human perturbation on the observed flow 

and concluded that approximately half of this change was due to climate (less rainfall) and half 

to human activities (e.g., water withdrawal for irrigation). In addition, a small percentage of the 

decrease was assigned to a combination of uncertainty (error) and evaporation from the 

impoundment of water in reservoirs due to increased surface area in the basin. Jay’s conclusions 

were based on the record of observed flows for the past 100 years and an estimated adjusted flow 

provided by the U.S. Geological Survey (USGS) to account for reservoir manipulations; this was 

used to estimate the virgin river flow (flow unadulterated due to hydropower operations and 

irrigation removal) from approximately 100 years ago (Figure 6). 

Reductions in the total amount of water (i.e., annual average flow) are only a small part 

of the total hydrological changes that have occurred in the Columbia River basin. Seasonal 

changes, particularly those involving the timing and magnitude of the spring freshet, have been 

much larger than changes in annual average flow. Spring freshets are extremely important for 

juvenile salmonids in that high flows (especially overbank flows) provide habitat, transport fish 

downstream, limit predation by increasing turbidity, and maintain favorable water temperatures 

during the spring and early summer. Organic matter supplied by the river during the freshet 

30
Figure 6. Comparison of the monthly averaged Columbia River eastern subbasin virgin, adjusted, and 

observed river-flow (cubic meters per second) estimates from 1970 to 1999. Flow regulation and 

irrigation depletion decreased spring and summer flows (May to August), while fall and winter 

flows (September to March) increased. (Reprinted from Bottom et al. 2005.) 

season is also a major factor maintaining a detritus-based food web, centered in the estuarine 

turbidity maximum (ETM). 

Very large freshets before modern flow regulation (i.e., before ≈1970) lasted 30–60 days, 

with the sharpness of the peak largely governed by the relative timing of snowmelt throughout 

the basin. Flows in the Columbia River interior subbasin (the flow measured at the The Dalles) 

are primarily driven by spring snowmelt, although there are rain-on-snow freshets in some 

winters. Before 1900, the highest flows typically occurred during May–July (Figure 7). 

The timing of the maximum spring freshet flow has also changed (Figure 8). Maximum 

daily spring freshet flow now typically occurs at about water-year Day 242 (29 May), whereas 

maximum flow occurred in the 19th century at about water-year Day 256 (12 June), a change of 

about two weeks. In terms of the phase of the annual flow fluctuation, the freshet is about a 

month earlier. Part of this change is due to climate warming, but a component is also due to prerelease of water for flood control before the spring freshet. Irrigation withdrawal usually peaks 

in June, which tends to further curtail the freshet. 

Another change in water flow, significant to salmon, is the occurrence of overbank flows. 

The historical bankfull flow level was an estimated 18,000 m3

s

-1 for the main stem below 

Vancouver (Jay 2005). Modern bankfull level is set by the standard project flood level of 

approximately 24,000 m3

s

-1 for the lower river. According to Jay (2005), some overbank flow 

occurred in many years before 1900, both in winter and spring (Figure 9), whereas substantial 

overbank flow (above 24,000 m3

s

-1) is now rare, with significant events occurring only five times 

during the last half century. Historical bankfull levels of 18,000 m3

s

-1 are now rarely exceeded 

due to the combined effects of flood control measures and irrigation depletion. The season when 

0

2,000

4,000 

6,000

8,000

10,000 

12,000 

14,000 

16,000 

October December February April June August 

Stream flow (m3

s-1) 

Virgin

Adjusted

Observed

31
0

2,000

4,000

6,000

8,000

10,000

12,000

14,000

16,000

18,000

20,000

December April August 

Stream flow (m3

s-1) 

1878–1903

1970–1999

October February June 

Figure 7. Changes in the annual Columbia River flow cycle at Beaver Army Terminal, near Quincy, 

Oregon, 1878–1903 versus 1970–1999. (Reprinted from Bottom et al. 2005.) 

13-Apr

23-Apr

3-May

13-May

23-May

2-Jun

12-Jun

22-Jun

2-Jul

12-Jul

22-Jul

18751885189519051915192519351945195519651975198519952005

Figure 8. Peak freshet day versus year suggests that the freshet is now about two weeks earlier than in the 

19th century in the Columbia River basin. (Reprinted from Bottom et al. 2005.) 

32
0

20

40

60

1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000

Number of days

>18000

>24000

Figure 9. The incidence of flows above 18,000 m3s

-1 (the pre-1900 estimated bankfull flow level) 

and above 24,000 m3

s

-1 (the present bankfull flow level). The present bankfull flow level 

has been exceeded only five times (twice in 1956) in four years since 1948. (Reprinted from 

Bottom et al. 2005.) 

overbank flow typically occurs has also shifted from spring to winter, because western subbasin 

winter floods (not interior subbasin spring freshets) are now the major source of such flows (Jay 

2005). 

Factors Causing Changes in Flow Attributes 

Potentially, flow changes (e.g., decreased spring freshets) can be a result of climate 

change, flow regulation, and water withdrawal. Jay (2005) apportioned the timing and 

magnitude of the freshet change to these three factors and found that flow regulation is clearly 

the source of the largest reduction in spring flow. The total reduction in freshet season (May 

through July) mean flow due to climate change, irrigation depletion, and flow regulation is 5,870 

m3

s

-1 or 43% of the virgin flow for this period. Overall the present freshet season flow decrease 

due to flow regulation was an estimated 33.1% (a reduction of 31.6% for May, 32.4% for June, 

and 19.8% for July, respectively). Jay found that the flow decrease in the freshet period resulting 

from climate was 5.6%. Similarly, the present decrease in freshet season flow due to water 

withdrawal was an estimated 10.5% (a reduction of 5.7% for May, 12.5% for June, and 20.8% 

for July, respectively). The January through July virgin flow average for 1879–1899 was 8,050 

m3

s

-1, while for 1945–1989 it was 7,850 m3

s

-1, a decrease of only 2.5%. Thus most of the loss of 

freshet flow represents flow that now occurs during other time periods. 

Climate was found to be a secondary factor in the incidence of overbank flow (Jay 2005). 

Overbank flow events were more common during the cold-PDO phase (1945–1977) than during 

the preceding warm-PDO phase (1921–1944), even though the degree of flow regulation and 

irrigation depletion grew over time (Figure 10). Jay concluded flood protection, diking, flow 

regulation, and water withdrawal largely eliminated climate’s influence on overbank flow. 

33
0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

1875 1885 1895 1905 1915 1925 1935 1945 1955 1965 1975 1985 1995

Cold Warm Cold Warm

Stream flow (m3

s-1) Figure 10. Monthly average flows at Beaver Army Terminal present and historical bankfull flow levels, 

and warm and cold PDO cycles, 1878–1999. Present bankfull flow levels are 24,000 m3

s

-1 and 

historical bankfull flows are 18,000 m3

s

-1. Historically there was a major difference between 

the warm and cold phases of the PDO cycle in disturbance frequency. This has been largely 

eliminated by flow regulation and diking; overbank flow is now a rare event. (Reprinted from 

Bottom et al. 2005.) 

Flow Effects on Sediment Transport 

A significant consequence of altering flow regimes is change in movements of sediment 

through the Columbia River system. Understanding changes in sediment are important because 

sediment is a direct part of habitat—it helps form habitat (via sediment deposition and erosion), 

has associated nutrients from upriver sources (supporting food production in the lower river, 

estuary, and plume), and contributes to a turbid environment (further enabling the habitat to 

serve as a refugia from predation). Our ability to evaluate the role of change in flow on supply 

of sediment through the lower river and estuary is limited, primarily because all the particles 

comprising sediment are not equally characterized. For example, sand and gravel movement is 

transport-capacity limited. Material is always available on the bed and will move whenever flow 

conditions are suitable. Therefore, sand-transport estimates are nearly as accurate as the flow 

estimates, at least within the limited flow range of the data set used to calibrate sand transport 

(Jay 2005). In contrast, transport of fine sediments is supply-limited, thus the capacity to move 

the material is greater than the supply. Since direct measurements are absent from the historical 

record, characterization of change in fine sediment is not possible. 

The effects of climate change on interior subbasin total sediment supply can be assessed 

by considering historical changes in sediment transport associated with virgin flow at The Dalles 

(Figure 11). The hindcast total load (sand plus finer fractions) associated with The Dalles virgin 

flow was 20.5 × 106

 t for 1879–1899, whereas hindcast annual average total virgin flow sediment 

34
Figure 11. Hindcast total sediment load for the Columbia River eastern subbasin associated with 

observed flow and estimated virgin flow. The two are very similar before 1900, but the sediment 

transport hindcast from observed flow after about 1970 is much smaller than virgin flow sediment 

transport, because of flow regulation and water withdrawal. (Reprinted from Bottom et al. 2005.) 

0

10

20

30

40

50

60

1875 1885 1895 1905 1915 1925 1935 1945 1955 1965 1975 1985 1995

Suspended particle matter 

in metric tons

 Observed flow

 Virgin flow

transport was 17.2 × 106 t for 1945–1999. The estimated decrease in total sediment transport due 

to climate change was approximately 17% (Jay 2005). This is considerably larger than the 

climate-driven change in flow for two reasons: 1) sediment transport varies with a power n of 

the flow, n ≈ 2.5, and 2) decreased mean flow also reflects decreased flow variability and a 

decreased incidence of the very high-flow days that transport most of the total load. 

Because there is a nonlinear relationship between sediment transport and flow, it is not 

possible to precisely apportion the reduction in sediment transport between climate change, 

water withdrawal, and flow regulation. The largest single factor is, however, reduction in spring 

freshet flow. This is demonstrated when evaluating the impact of flow on sediment volumes 

under recent conditions, compared to a more historical period when the spring freshet was less 

impacted. Jay (2005) reported the average sediment transport associated with the observed 

1945–1999 flow was approximately 10.0 × 106

 t, whereas sediment transport associated with the 

1970–1999 observed flow was approximately 8.0 × 106

 t. Therefore, the difference between 

annual average sediment transport at Vancouver for the 1858–1899 virgin flow and 1945–1999 

observed flow was 10.8 million × 106

 metric or 52% of the 19th century sediment transport. The 

difference between annual average sediment transports for the 1879–1899 virgin flow and 1970–

1999 observed flow is approximately 12.5 × 106 t or 61.5% of the 19th century sediment 

transport. The sand transport associated with the 1945–1999 observed flow was approximately 

3.2 × 106

 t. Therefore, the difference between annual average sand transport for the 1879–1899 

virgin flow and 1945–1999 observed flow was approximately 7.7 × 106

 t or approximately 71% 

of the 19th century sand transport. The consequence of the reduced transport of sediment through 

the lower Columbia River estuary and plume are unknown at this time, but the magnitude of the 

decrease likely impacts the support of habitat-forming processes as well as increasing predation 

35
pressure on juvenile salmon utilizing and migrating through the lower river, estuary, and plume 

because of increased visibility. 

Impacts of Water Flow Changes on Salmonid Habitat in the Estuary 

Alterations in the amount and timing of water delivery to the estuary has significantly 

affected availability of the habitat needed in the estuary to sustain the diverse life history 

strategies for the various source populations of salmon and steelhead. Several recent analyses 

provide some empirical evidence on the effects of the altered flow regime described above on 

habitat in the Columbia River estuary. Baptista (2005) used a hydrologic model developed 

specifically for the Columbia River and found the estuary during the historical period (late 

1800s) was able to sustain habitat features important to salmon (characterized as water velocities 

less than 30 cm/sec—important to smaller juvenile salmon) to a greater degree than is evident 

now (Figure 12). 

0 0.5 1 1.5 2 2.5

340

360

380

400

420

440

460

480

500

520

540

+ 1997

X 1998 

Y 1999 

Z 1880 

 1880* 

 1880**

Stream flow 104 (m3s-1) 

Habitat opportunit

y (hours)

Figure 12. Habitat opportunity in Cathlamet Bay as a function of stream flow. Habitat opportunity, 

shown in hours normalized to a 30-day month, is defined as a site with water velocity less than 30 

cm/sec. There are marked differences between habitat opportunity in the modern (1970 to 

present) and predevelopment (pre-1900) systems. In the figure, 1880 represents conditions 

associated with pre-1900 discharge and pre-1900 bathymetry, 1880* represents conditions 

associated with pre-1900 discharge and modified pre-1900 bathymetry to assess effect of change 

in bathymetry, and 1880** represents conditions associated with modern discharge and pre-1900 

bathymetry to assess change in discharge. (Adapted from Bottom et al. 2005.) 

36
Kukulka and Jay (2003) demonstrated that there was approximately a 62% loss of 

shallow water habitat (defined by depth between 10 cm and 2 m) that was attributable to diking 

(physically removing access of water to the tidal floodplains) and the reduction of peak flows by 

40% (consistent with the freshet flow reduction discussed earlier) for the region between RM 50 

and RM 90 on the Columbia River (Figure 13). The analysis incorporated the spring freshet 

period, when maximal use of estuarine habitat by different life history types employing a variety 

of strategies appears to occur (Bottom unpubl. data). Within the freshwater tidally influenced 

region of the Columbia River estuary, flow reductions and diking have reduced the amount of 

shallow water habitat by 52% and 29%, respectively (Bottom et al. 2005). 

The hydrological changes—particularly those associated with flow regulation and water 

withdrawals, along with floodplain diking (discussed in the next section)—represent a 

fundamental shift in the physical state of the Columbia River ecosystem. Such changes can have 

significant consequences for viable salmonid populations. Major departures from the historical 

template of an ecosystem can potentially result in the loss of habitat capacity needed to rear fish, 

resulting in a reduction in abundance of the population. In addition, diversity of salmonid 

Figure 13. The change in availability of shallow water habitat (SWH) in the tidally influenced region 

between RM 50 and RM 90 on the Columbia River under unmodified and modified flow 

conditions only. The top panel represents conditions under virgin flow with no dikes, where 

extensive inundation of the floodplain occurs for long durations. The bottom panel represents 

conditions under modern flow conditions with no dikes, where river stage has been lowered and 

the floodplain for shorter duration innundated. (From Kukulka and Jay 2003.) 

37
rearing and migration behaviors are linked to various habitats and environmental conditions that 

can support each developmental stage (e.g., egg, fry, smolt). Alteration of the physical 

environment of the estuary can create mismatches between established salmon behaviors and the 

physical environment or, similarly, prevent the expression of potential behaviors by eliminating 

habitat opportunity. The loss of these behaviors can reduce the life history diversity of 

populations. 

The effort to stabilize flows in the Columbia River basin may create less stable conditions 

for salmonids whose migration and rearing behaviors have adapted to historical patterns of 

hydrologic variability. Of particular importance is the reduction of the spring freshet, to which 

the timing of downstream migrations and patterns of habitat use of some subyearling and 

yearling life history types may have been linked. One potential result of dampening 

flowvariations in the Columbia River could be a greater uniformity of migration patterns with 

potential consequences in the timing and sizes of salmon arriving in the estuary or ocean. 

The nearly complete elimination of overbank flooding may pose some of the most 

significant consequences for Columbia River salmonids. One consequence of the loss of 

overbank flooding is that access to off-channel floodplain habitats and refugia during high flow 

events is eliminated. If, as we suspect, patterns of extended estuary use by small subyearling 

migrants are directly linked to the availability of shallow water habitat, the loss of these habitats 

has significant implications for these estuarine-dependent strategies. 

In addition to the lost opportunity to use shallow water habitats on salmon diversity, flow 

regulation, in conjunction with floodplain diking, may influence the productive capacity of the 

estuary by regulating “ecological processes” such as food production, competition, and 

predation. Elimination of overbank flooding can prevent the pulsed delivery of structural and 

energetic components to the rest of the estuary, including large wood, sediments, detritus, and 

prey organisms produced in adjacent riparian and floodplain habitats. Floodplain inundation can 

also greatly increase the surface area of tidal estuarine and riverine habitats available to 

salmonids, allowing fish to expand their distribution into potentially more productive offchannel. For example, recent studies in a nontidal portion of the lower Sacramento River found 

that tagged juvenile Chinook salmon released in the seasonally inundated floodplain had better 

growth, higher consumption rates, and improved survival compared with others released into the 

main river channel (Sommer et al. 2001). 

The effect of flow changes is not restricted to the area traditionally considered the estuary 

in the Columbia River system (i.e., upstream of the river mouth). Flow from the Columbia 

River, as well as other physical changes in the estuary (e.g., dredging), can modify the features 

that define habitat in the plume (Barnes et al. 1972). Attributes of the plume affected by flow 

changes that define habitat important to salmon include surface area of the plume, the volume of 

the plume waters, the extent and intensity of frontal features, and the extent and distance offshore 

of plume waters. Both natural and anthropogenic factors that modify flow can logically be 

considered to modify habitat used by salmon as they make the transition to marine life. 

Clearly any such changes are only relevant if the plume has a role that influences how 

juveniles make the transition from a freshwater to marine environment. As noted previously, 

evidence to date suggests the plume serves salmon in multiple ways, such as facilitating primary 

38
production during the spring freshet period (Thomas et al. 2003), distributing juvenile salmon in 

the coastal environment, concentrating food resources such as zooplankton, and providing a 

refuge from predators in the more turbid low salinity plume waters. Effects of changing plume 

attributes on juvenile salmon performance are largely speculative. It seems reasonable to 

hypothesize that a change in plume size would reduce the amount of foraging habitat potentially 

available to the juvenile salmon. A significant enough reduction in plume size could result in 

density-dependent interactions that diminish growth. Another affect of reducing the size of the 

plume would be to increase predation on yearlings occupying this habitat since the fish are 

occupying a smaller space. If one function of the plume is to transport fish offshore, then having 

the plume closer to shore could affect the ability of fish to migrate toward oceanic feeding 

grounds. 

Summary of Flow Effects 

In summary, flow is a fundamental factor affecting characteristics of salmon and their 

habitat in the estuary and plume. Large scale effects on flow occur as a result of spatially 

explicit interactions of short- and long-term climate cycles (ENSO and PDO, respectively) with 

the watershed. The generation of electricity, flood control, and irrigation have had significant 

affects on attributes of flow. These include a reduction in the mean annual flow, reductions in 

the size of the spring freshets, an almost complete loss of overbank flows, changes in timing of 

ecologically important flow events, and altered sediment processes. The hydrological changes, 

along with floodplain diking, represent a fundamental shift in the physical characteristics of the 

Columbia River ecosystem. Such changes potentially have significant consequences for both 

expression of salmonid diversity and productivity of the populations by affecting accessibility, 

quantity, and quality of estuarine habitat. In particular, because the changes in habitat are most 

pronounced in shallow water areas, we conclude that effects on the ESUs and life history 

strategies (the fry and fingerling strategies) that use these shallow water areas will be most 

significant. Further, we conclude that flow alterations are an important limiting factor in the 

plume. Primarily as a result of flow, but also no doubt as a result of physical changes to the 

estuary (e.g., dredging and diking), the shape, behavior, size, and composition of the plume has 

been changed. 

Habitat 

Estuarine Habitat and its Use by Juvenile Salmon 

Habitat is the physical, biological, and chemical characteristics of a specific unit of the 

environment occupied by a specific plant or animal. Thus habitat is unique to specific organisms 

and basically encompasses all the physiochemical and biological requirements of that organism 

within a spatial unit. Characterizing habitat and its role in salmon life history and ecology has 

been a consistent objective in many studies focusing on salmon biology, particularly in 

freshwater spawning and rearing habitats. Comparatively less is known about estuarine habitat 

use by juvenile salmonids, including in the Columbia River estuary. The need for more 

quantitative descriptions of habitat attributes important to salmon in the Columbia River estuary 

has intensified recently as the calls for habitat restoration actions have increased in response to 

mandates to reduce risks to endangered salmon populations. Asking what to recover represents 

the most common response to this call. In lieu of specific knowledge, restoring the entire estuary 

39
for all plants and animals becomes the primary option embraced (LCREP 1999). This type of 

broadscale approach is limiting, however, because estuaries are typically extensively urbanized 

environments, so any changes that restore historical attributes are costly, particularly those 

associated with land acquisition. Questions quickly erupt as to what specifically needs to be 

restored, once real costs for the broad-brush approach become evident. 

Although specific studies in the Columbia River estuary are limited, the summary of 

information from a variety of other sources can be used to provide perspective on what habitat 

attributes are important to juvenile salmon, how they use this habitat, and benefits of this habitat 

use. Research in estuarine systems throughout the Pacific Northwest has demonstrated that 

estuaries are composed of a variety of habitats that are used differently by salmon depending on 

their life history strategy and population of origin (Healey 1980, 1982, Levy and Northcote 1981, 

1982, Simenstad et al. 1982, Levings et al. 1986, Miller and Sadro 2003). For example, the 

timing of catches of juvenile Chinook salmon in different zones of the Columbia River estuary 

varies (Figure 14). One of the most important features of life history strategies employed by 

salmon that affects habitat specific use is juvenile size (Figure 15). Smaller fish tend to be most 

abundant in shallow water areas. Larger juveniles typically use deeper water habitats within the 

estuary, located more centrally to mainstem channels; the larger juveniles are associated with 

yearling and subyearling life history strategies and are often of hatchery origin (Figure 16). The 

smaller juvenile salmon use the more peripheral side channel areas associated with the more 

shallow water habitats including tidal emergent marsh and forested marsh habitats (McCabe et 

al. 1986). These smaller fish are associated with the fry and fingerling strategies (Figure 16) and 

are naturally produced. 

The size structure of Chinook salmon in the estuary demonstrates several attributes of 

estuarine habitat use (Figure 15). During the early winter months, the sizes of juveniles entering 

and leaving the estuary are nearly identical, consistent with salmon exhibiting the fry life history 

strategy. However, as the size of Chinook salmon entering the estuary increases in length as the 

year proceeds, the corresponding length of juvenile Chinook salmon exiting the estuary during 

the same period are significantly larger, suggesting growth and thus rearing is occurring in the 

estuary. 

Information currently being collected by NOAA Fisheries Service demonstrates that 

populations exhibit a variety of approaches in how they use estuarine habitats.5

 For example, 

although it has been argued by Bottom et al. (2005) that salmon occupying shallow marsh 

habitats express the range of strategies characteristic of ocean-type salmon, it is now evident that 

salmon representing many of the endangered ESUs are using these habitats of the Columbia 

River estuary. Using genetic analysis employing recently developed microsatellite DNA 

techniques, both ocean and stream-type Chinook salmon from upper and lower basin sources 

were found in these marsh and forested wetland habitats (Figure 17). 

Although the predominant source of fish in marsh habitats was from the lower Columbia 

River Chinook salmon ESU (Bottom et al. 2005), juvenile Chinook salmon from a variety of 

other source populations were evident. Confirmation that ESUs express a variety of strategies in 

their use of estuarine habitats is gained from ongoing studies evaluating the role of the Columbia 

 

5

 See footnote 3. 

40
Figure 14. Catch per unit effort (CPUE) for juvenile Chinook salmon for 2002 and 2003 at several sites 

in the mouth of the Columbia River estuary (circle), in the mixing zone (square), or in the tidal 

freshwater zone (triangle). (From Curtis Roegner, NWFSC.) 

 

Figure 15. Mean fork length (FL) of juvenile Chinook salmon for 2002 and 2003 at several sites in the 

mouth of the Columbia River estuary (circle), in the mixing zone (square), or in the tidal 

freshwater zone (triangle). (From Curtis Roegner, NWFSC.) 

Jan Mar May July Sept Nov Jan Mar May July Sept Nov

CPUE

0

50

100

150

200

250

300

350 2002 2003

Mouth Mixing Tidal fresh 

Jan Mar May July Sept Nov Jan Mar May July Sept Nov

Mean FL (±SE)

0

20

40

60

80

100

120

140

160

Mouth Mixing Tidal fresh 

41
Fork length (mm)

0 50 100 150 200 250

Trapnet marked n=10

Trapnet unmarked

Beach seine unmarked

Beach seine marked

n=581

n=1196

n=60

Figure 16. Box plots of size of juvenile salmon captured in peripheral habitats (trapnets) and near the 

main channels (beach seine) of the Columbia River estuary. Marked salmon (adipose clipped) 

represent hatchery fish, whereas unmarked fish (adipose fin present) represent an unknown 

mixture of naturally produced and hatchery released juvenile salmon. (From D. Bottom, 

NWFSC.) 

River plume as habitat for juvenile salmon. Spring Chinook salmon that express both yearling 

and subyearling strategies have been identified in the plume environment (Figure 18). Clearly, 

salmon expressing a variety of strategies from source populations originating throughout the 

basin can use estuarine habitats throughout the year. 

Another distinguishing feature of salmon that influences their use of estuarine habitat is 

physiological condition relative to their conversion from parr to smolt. Those animals having 

made the physiological transformation associated with the endocrine-driven smolting process 

exhibit negative rheotactic behavior and typically use deeper water main channel habitats 

(associated with the stronger flow signals). Juvenile salmon that have not entered smoltification, 

but still are moving from natal rearing areas into the mainstem, estuary, and ocean habitats more 

frequently use side channel, shallow water habitats within the estuary. However, even for 

juvenile salmon that have smolted and have been shown to migrate through the estuarine habitat 

for short periods of time (days), a majority of them are found with prey items in their stomachs, 

suggesting they are feeding in estuarine habitats. 

Although abundance of juveniles in the estuary fluctuates considerably throughout the 

year, juvenile salmon use the estuary during the entire year (Figures 2 and 14). Obviously 

existence of sufficient amounts of the appropriate subtypes of habitats allows all salmon species 

and steelhead in the Columbia River basin to express the appropriate spatial structure and 

42
2.2% Upper Willamette 

Figure 17. Proportion of Chinook salmon ESUs originating from various parts of the basin identified in 

samples taken from marsh, forested, and shrub habitat of the lower Columbia River estuary 

during 2002 from April to August. Lower Columbia, upper Willamette, Deschutes River/Snake 

River, and upper Columbia River refer to fall type Chinook salmon ESUs whereas interior refer 

to mid-Columbia River, upper Columbia River and Snake River spring type Chinook salmon 

ESUs. (From Paul Moran, NWFSC.) 

diversity of life history strategies demanded by the environmental and biological conditions the 

juveniles encounter. This characteristic year long presence is consistent with the historical 

record reconstructed by Burke (2005) from research conducted by Willis Rich in the early 1900s 

(Figure 2). It is apparent that over the entire year, juvenile salmon expressing varying life 

history strategies were using the Columbia River estuary. 

The characterization of how salmon employing varying strategies use the Columbia River 

estuary is comparable to recent evidence developed regarding the role of the Skagit River estuary 

in Puget Sound, Washington. These studies have suggested that smaller, naturally produced wild 

salmon are abundant in the estuary for longer periods of time (Figures 19 and 20) and associated 

with the more peripheral marsh habitats than larger juvenile salmon.6

 These larger fish either are 

hatchery fish (earlier in the season) or wild fish that have grown larger (mostly later in the 

season) (Figures 19 and 20). 

 

6

 C. Rice, NWFSC, Mukilteo Field Station, Mukilteo, WA, and E. Beamer, Skagit River System Cooperative, La 

Conner, WA. Pers. commun., January 2004. 

Lower Columbia River

Upper Willamette River

Deschutes River/Snake River

Upper Columbia River

Interior basin

3.3% Interior spring run 

Lower Columbia River

Upper Willamette River

Deschutes River/Snake River

Upper Columbia River

Interior basin

2.2% Upper Willamette 3.3% Interior spring run 

43
0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

Columbia Basin spring Columbia Basin

fall/summer

All non-Columbia

Percent contribution

Lower Columbia River

Upper Willamette River

Above Bonneville Dam

California and Oregon

Washington

Figure 18. Stock composition of subyearling Chinook salmon in Columbia River plume study area June 

1998–2001. 

An important question to consider about estuarine habitat is whether habitat availability 

in the estuary can be a limiting factor to production and expression of a diversity of life history 

strategies. Although this information is forthcoming for the Columbia River estuary explicitly, 

studies in the Skagit River system have identified a density-dependent limit to the number of 

juveniles in the estuary relative to the overall abundance of young salmon in the system (Figure 

21). In the face of altered (i.e., reduced) habitat availability, reducing the opportunity to access 

habitats can be a limiting factor in recovery of salmon and steelhead populations. 

How Have Estuarine Habitats Changed 

Considering the importance of estuarine habitat to juvenile salmon, what evidence from 

the historical and more current record can be used to identify changes in the habitat in the 

system? Thomas (1983) and Sherwood et al. (1990) have calculated losses of emergent marsh 

and forested wetland habitats in the Columbia River estuary (to approximately RM 42). They 

characterize the change as substantial and likely a significant factor reducing the estuary’s ability 

to support juvenile salmon. Approximately 121.6 km2 of tidal marshes (43% decline) and 

swamps (77% decline) that existed prior to 1870 have been lost (Figure 22). Together with a 

12% loss of deep-water habitat, these changes reduced the estuary’s tidal prism from 12% to 

20%. In addition, the historical surface area of the estuary has decreased by approximately 20% 

as a result of diking or filling of tidal marshes and swamps. 

44
 

Mean catch per tow 

0

2

4

6

8

10

12

Wild

Hatchery

Apr Jun Aug Oct

Month

Figure 19. Catch of naturally and hatchery produced juvenile Chinook salmon over time in Skagit Bay, 

Washington, an enclosed olgohaline region associated with the Skagit River watershed. Fish 

were caught with a two-boat surface trawl. (From C. Rice, NWFSC.) 

0.0

0.1

1

10

100

1,000

10,000

Jan Mar May July Sept

Juvenile Chinook / hectare

Pocket estuary

Nearshore

Subtidal 

Figure 20. Shifts in distribution of juvenile Chinook salmon in the Skagit River estuary system. 

Juveniles are initially more prevalent in pocket estuary habitats, then shift to deeper, nearshore 

habitats later in the year, and more subtidal habitats toward the end of the year. The proportion of 

wild (unmarked) salmon ranged from 98%, 82%, and 73%. (From E. Beamer, Skagit River 

System Cooperative, and C. Rice, NWFSC. See also Beamer et al. 2005.) 

45
Youngs Bay—characterized by a broad flood plain and historically abundant in tidal marsh and 

swamp habitat; diking and flood control structures used to convert land to pasture resulted in 

86.4% loss of tidal marsh and 95.7% loss of tidal swamp habitat. Much of the tidal marsh habitat 

lost throughout the estuary has occurred in this region. 

Youngs Bay—characterized by a broad flood plain and historically abundant in tidal marsh and 

swamp habitat; diking and flood control structures used to convert land to pasture resulted in 

86.4% loss of tidal marsh and 95.7% loss of tidal swamp habitat. Much of the tidal marsh habitat 

lost throughout the estuary has occurred in this region. 

Mixing zone—characterized by a network of mid-channel shoals and flats; highest variation in 

salinity based on tide cycle and river flow; relatively little change in amount of the five major 

habitat types. 

Mixing zone—characterized by a network of mid-channel shoals and flats; highest variation in 

salinity based on tide cycle and river flow; relatively little change in amount of the five major 

habitat types. 

Entrance—dominated by subtidal habitat; highest salinity in estuary; historically a high-energy 

area of natural fluvial land forms, a complex of channels, shallow water, and sand bars; supports 

the Columbia Plume; abrupt changes have resulted from dredging and jetty construction that 

limit the ocean-fed supply of sediment; deep water habitat (18.9%) and a loss of medium-depth 

(41.1%) and tidal flat (43.6%) habitat types. 

Entrance—dominated by subtidal habitat; highest salinity in estuary; historically a high-energy 

area of natural fluvial land forms, a complex of channels, shallow water, and sand bars; supports 

the Columbia Plume; abrupt changes have resulted from dredging and jetty construction that 

limit the ocean-fed supply of sediment; deep water habitat (18.9%) and a loss of medium-depth 

(41.1%) and tidal flat (43.6%) habitat types. 

46

 

Figure 21. The relationship between freshwater wild Chinook smolt population size and density of 

juvenile wild Skagit Chinook in Skagit River delta habitat, 1992–2002. The number of Chinook 

per unit area within the delta levels off as the total number of outmigrants increases, indicating 

density-dependent use of the delta. (From E. Beamer, Skagit River System Cooperative. See 

also Beamer et al. 2005.) 

Figure 21. The relationship between freshwater wild Chinook smolt population size and density of 

juvenile wild Skagit Chinook in Skagit River delta habitat, 1992–2002. The number of Chinook 

per unit area within the delta levels off as the total number of outmigrants increases, indicating 

density-dependent use of the delta. (From E. Beamer, Skagit River System Cooperative. See 

also Beamer et al. 2005.) 

As part of developing a restoration plan for the Columbia River estuary, Johnson et al. 

(2003) refined the losses of different habitat types within particular zones of the estuary using 

information from Thomas (1983), Graves et al. (1995), USACE (1996), and Garono et al. (2002). 

To facilitate this comparison, the Columbia River estuary was delineated into eight distinct areas 

based on physical characteristics. A brief description of each estuary area, a summary of habitat 

changes, and a qualitative description of changes in select habitat characteristics were extracted 

from Johnson et al. (2003) and the subbasin review developed by the Lower Columbia Fish 

Recovery Board as follows: 

As part of developing a restoration plan for the Columbia River estuary, Johnson et al. 

(2003) refined the losses of different habitat types within particular zones of the estuary using 

information from Thomas (1983), Graves et al. (1995), USACE (1996), and Garono et al. (2002). 

To facilitate this comparison, the Columbia River estuary was delineated into eight distinct areas 

based on physical characteristics. A brief description of each estuary area, a summary of habitat 

changes, and a qualitative description of changes in select habitat characteristics were extracted 

from Johnson et al. (2003) and the subbasin review developed by the Lower Columbia Fish 

Recovery Board as follows: 

0

1,000

2,000

3,000

4,000

0 2,000,000 4,000,000 6,000,000 8,000,000

Freshwater outmigrants

Fish/hectare of blind 

tidal channel
47

Total area loss = 24%

0

10,00020,00030,00040,00050,000

Medium

depth

Shallow/flats Tidal marsh Tidal swamp Developed

floodplain

Uplandsnatural

and filled

Acres

1870 1980

- 24.8 %

+ 10 %

- 43.1 %

- 76.8 %

+ 75 %

Figure 22. Change in acreage of various habitat types used by juvenile salmon in the Columbia River estuary (to approxim

from 1870 to 1980 (data source: Thomas 1983). 
Baker Bay—historically a high energy area from ocean currents and wave action; migration of 

mid-channel islands toward the interior of Baker Bay has sheltered the area; some tidal marsh 

habitat recently started to develop because of decreased wave action (−75.0% deep water, 

−71.3% medium depth, +74.9% tidal flats, −55.5% tidal marsh, and −100% tidal swamp habitat). 

Grays Bay—pile dikes adjacent to the main Columbia River navigation channel have decreased 

circulation in the bay and caused flooding problems in the valley bottoms; accretion in the bay 

has led to development of tidal marsh habitat, increasing 145.2% compared to historical 

conditions; dike construction for pasture conversion has isolated the main channel from its 

historical floodplain and decreased tidal swamp habitat 88.4% compared to historical levels. 

Cathlamet Bay—large portion of area protected by the Lewis and Clark Refuge; other portions 

are heavily impacted by diking (Brownsmead area and Swenson Island) causing a 48.9% decline 

in tidal swamp; medium and deep water habitats have decreased (30.4% and 12.5%, 

respectively) as a result of dredge material disposal; fringe of dredge disposal areas has 

developed into tidal marsh habitat, resulting in 6.8% increase over historical conditions. 

Upper estuary—characterized by deep channels and steep shorelines on both sides of river; 

typically dominated by freshwater, except during low river flow or large flood tides; extensive 

diking and clearing has resulted in substantial loss of tidal marsh (64.3%) and tidal swamp 

(79.9%) habitat compared to historical levels. 

Tidal freshwater—although comprising nearly one third of the estuary (based on River Miles), 

little quantitative information on changes occurring in this region is available. This area is 

distinct in geology, vegetation, and climate; influenced by major tributaries; contains elongate 

islands that divide the river and form oxbow lakes, sloughs, and side channels; was historically 

dominated by a combination of tidal plant communities, ash riparian forests, and marshy 

lowlands. Changes in this reach of the estuary from RM 46 to 102 include increased upland 

habitat in the middle reach and substantial loss of nontidal water/wetland, tidal flats, and tidal 

marsh habitat types; from RM 105 to 146, there has been an increase in nontidal water/wetland 

and upland habitat and substantial loss of tidal flats and tidal marsh habitat types. 

As reported in the Lower Columbia Mainstem and Estuary Subbasin Plan (LCMESP 

2004), Thomas (1983) also investigated five categories of nonestuarine habitat (i.e. developed 

floodplain, natural and filled uplands, nontidal swamps, nontidal marshes, and nontidal water) to 

identify the fate of floodplain areas that were removed from the estuarine system. Developed 

floodplain habitat was defined as all diked floodplain converted to agriculture, residential, or 

other land use. Natural and filled uplands included areas where measurable acreages have been 

filled, primarily through disposal of dredge material. Nontidal swamps were areas of the diked 

floodplain that were never cleared or were cleared and converted back to swamp. Nontidal 

marshes included areas of the diked floodplain that support emergent wetland vegetation; these 

were typically abandoned pastures dominated by rush and sedge. Nontidal water consisted of 

former tidal sloughs that were separated from the river by dikes and tidegates. The largest 

increase, by far, of nonestuarine habitat from 1870 to 1983 was that of developed floodplain 

habitat. Of the 36,970 total acres of lost estuarine habitat, 64.8% was converted to developed 

floodplain (Thomas 1983). 

48
As discussed earlier, absolute changes in habitat opportunity alone should not be used to 

directly infer changes in the ability of the estuary to support salmon. For instance, despite 

considerable loss of emergent and forested wetlands in the estuary and associated declines in 

macrodetrital production, the total area of estuarine shallows and flats actually increased 7% 

between 1870 and 1980. This was independently substantiated by Sherwood et al. (1990), who 

estimated 68.4 × 106 m3 net sediment gain within the estuary between 1868 and 1958. Areas of 

sediment increase include peripheral bays such as Cathlamet Bay and Grays Bay, which had 

shoaling rates of 0.61 cm yr−1

 and 0.63 cm yr−1and net volumetric increases of 76.2 × 106 m3 and 

19.1 × 106

 m3, respectively. 

Loss of estuarine wetlands has not only reduced the total amount of shallow rearing 

habitat available to young salmon but also altered the magnitude and character of habitat 

capacity (Sherwood et al. 1990). The resulting decline in wetland primary production eliminated 

approximately 15,800 mt carbon year−1

 (84%) of macrodetritus that historically supported 

estuarine food webs. This macrodetritus originated from the vascular plants and microscopic 

algae produced within the estuary’s wetlands. However, these losses were accompanied by an 

increase of approximately 31,000 t carbon year−1 of microdetritus from upriver sources, 

originating principally from increased phytoplankton production in the reservoirs behind the 

mainstem dams (Sherwood et al. 1990). The shifts in the sources and types of detritus available 

may have altered estuarine food webs, including those leading to salmon. For example, the 

epibenthic-pelagic food web supported by microdetrital sources favors production of calanoid 

copepods and other pelagic organisms that typically are not consumed by juvenile salmon 

(Bottom and Jones 1990, Sherwood, et al. 1990, Simenstad et al. 1990). 

As a result of the loss of habitat, altering the spatial distribution of the food web may also 

be an important determinant of habitat capacity in the estuary. Whereas the macrodetrital food 

web was historically distributed throughout the lower river and estuary, the contemporary 

microdetrital food web is most concentrated within the localized mid-estuary region of the ETM. 

We have no objective means of quantifying these types of ecological effects of the habitat 

shift from emergent and forested wetlands to shallows and flats. For example, no historical data 

are available for salmonid diet composition or stomach fullness within tidal wetlands to compare 

with other estuarine habitats. Although juvenile salmon may not directly benefit from the 

microdetrital food web, there is some evidence that they have higher stomach fullness in the mid 

estuary compared with other estuarine regions (Bottom and Jones 1990). One possible 

mechanism that has yet to be verified for any increase in feeding rates is that enhanced detrital 

concentrations within the ETM may also stimulate secondary production in adjacent mid-estuary 

shallows and flats. However, we do know that prey production and salmon stomach fullness 

values are relatively high in protected flats compared with many other estuarine habitats. Jones 

et al. (1990) found that the standing crop of infauna in protected flats of the estuarine mixing 

region (≈RM 7 to RM 21) was more than an order of magnitude higher (2.058 g m−2

 AFDW [ash 

free dry weight]) than benthic fauna standing crop in any of the other channel or unprotected flat 

habitats (0.098–0.136 g m−2 AFDW) within the same estuarine region. 

Another recent analysis shows the loss of habitat in the tidal freshwater region of the 

estuary. This is where we most lack the empirical evidence of change and contribution to 

expression of spatial structure and salmon life history diversity. Kukulka and Jay (2003) 

49
indicated that diking removed nearly 52% of the shallow water flood plain habitat in the tidally 

influenced freshwater zone of the estuary (Figure 23). 

Removing dikes alone would restore accessibility of considerable amounts of shallow 

water estuary habitats such as tidal floodplains since diking entirely removes habitat from the 

estuarine system. Other anthropogenic factors change estuary habitats from one type to another 

(Thomas 1983). Other benefits of removing dikes would include increasing the amount of prey 

resources available to the juvenile salmon and increasing organic matter inputs. The degree to 

which estuary habitat types have been affected by diking is directly proportional to elevation; 

thus the highest elevation habitat types (i.e., tidal swamp) have been most impacted by diking 

(Thomas 1983). 

Mainstem estuarine habitats in the Columbia River have for the most part been reduced to 

a single channel where floodplains have been reduced in size and off-channel habitat has been 

lost or disconnected from the main channel. Dikes prevent overbank flow and affect the 

connectivity of the river and floodplain (Tetra Tech Inc. 1996); thus the diked floodplain is 

higher than the historical floodplain and inundation of floodplain habitats only occurs during 

times of extremely high river discharge (Kukulka and Jay 2003). There is a critical level (i.e., 

the elevation of the diked floodplain) that water level must reach before substantial floodplain 

habitats are inundated (Kukulka and Jay 2003). Above this critical water level, large amounts of 

shallow water floodplain habitats become available with small increases in water level up to an 

optimum threshold (Kukulka and Jay 2003). 

Under a modern bathymetry and flow regime scenario, the critical river discharge level in 

which significant shallow water habitats become available through floodplain inundation is 

relatively high, and the frequency of occurrence of this river discharge is rare; thus floodplain 

inundation is uncommon and availability of shallow water habitats is limited under current 

conditions (Kukulka and Jay 2003). As is the case in the estuary (Bottom et al. 2005), loss of 

these vital mainstem floodplain habitats has likely reduced the availability and diversity of 

habitats in the Columbia River estuary for juvenile salmonids, particularly those juveniles 

employing life history strategies associated with these peripheral, shallow water habitats. 

Many of the changes in the biological production processes of the estuary described 

above can be attributed directly to physical causes. For example, the apparent shift from 

macrodetrital to microdetrital food chains in the estuary stems from the diking and filling of 

intertidal wetlands and the creation of deep reservoirs behind mainstem dams. While changes in 

the quality and quantity of prey resources could well be a proximal factor affecting the use of the 

estuary, the ultimate cause is the physical removal of those habitats that supported both 

macrodetrital production and the diversity of estuarine life histories among salmon. 

This is not to say that all biological effects are physically driven. Nonetheless, we find 

that many of the significant biological changes now observed in the Columbia River estuary are 

best explained by physical modifications that have altered the habitat landscape to the benefit 

and detriment of different species and assemblages. These findings have important implications 

for developing restoration strategies that address the ultimate causes rather than the symptoms of 

salmon decline. 

50
A 

B 

C 

D 

Figure 23. Daily shallow water habitat (SWH) area from 1974 to 1998 for virgin (A) and observed (B) 

river flows without dikes, and for virgin (C) and observed (D) flows with dikes. (From Kukulka 

and Jay 2003.) 

51
Habitat Summary 

In summary, the location and types of habitats present in the Columbia River estuary 

have been substantially changed from historical conditions. Although the entire estuary has not 

yet been surveyed, the main changes that have been quantified in the estuary are a loss of 

emergent marsh, tidal swamp, and forested wetlands. Shallow water dependent life history 

strategies (fry and fingerlings) have been most affected by the loss of these vegetated habitat 

types. Alterations in attributes of flow and diking have caused these changes. Diking is a 

significant change primarily because it completely isolates habitat from the river and eliminates 

it from use by juvenile salmon. Further, it has potentially altered estuarine food webs from 

macrodetrital to microdetrital based. Clearly, restoration of shallow water vegetated habitat by 

removing dikes is a tactic that can benefit those life history strategies that depend on these 

shallow water habitats. In the case of populations that have large numbers of shallow water 

dependent members, restoring these habitats can significantly affect abundance and productivity. 

Toxics 

In addition to eliminating and physically altering salmon habitat in the estuary, the 

quality of habitats has been degraded through the release of toxic contaminants. With the 

exception of some metals and natural products, concentrations of toxic contaminants in the 

Columbia River estuary were historically low. However, beginning in the early 1800s, activities 

such as agriculture, logging, mining, industrial discharges, and storm water runoff began to 

degrade water quality in the estuary. Currently, the Columbia River below Bonneville Dam is 

the most urbanized section of the river, encompassing the major urban centers of Portland, 

Oregon, and Vancouver, Washington, and numerous minor cities such as Longview, 

Washington, and Astoria, Oregon. The estuary receives contaminants from over 100 point 

sources (Fuhrer et al. 1996), as well as numerous nonpoint sources such as surface and storm 

water runoff from urban and agricultural areas. 

The largest sources of effluent are the Portland and Vancouver sewage treatment plants 

and associated combined sewer overflows in the Willamette River and the Columbia Slough 

(LCREP 1999). Contaminants may also be transported downstream to the estuary from areas 

above the Bonneville Dam such as the Yakima River (Rinella et al. 2000, Fuhrer et al. 1996), 

Lake Roosevelt (Bortleson et al. 1994), and other tributaries (Fuhrer 1989, Roy F. Weston Inc. 

1998). Spills or other accidental releases of toxic substances at Bonneville Dam itself may also 

contribute to contamination in the estuary (WDOE 2004), although inputs are probably relatively 

small compared to those from the large urban centers. 

A number of potentially toxic water-soluble contaminants have been detected in the 

estuary. The USGS NASQAN (National Stream Quality Accounting Network) program has 

reported a wide range of current-use pesticides in the water column at sampling sites at 

Warrendale at RM 141 near the Bonneville Dam; the confluence of the Willamette and Columbia 

rivers near Portland at RM 101.5; and the Beaver Army Terminal at RM 53.8 (Fuhrer et al. 1996, 

Hooper et al. 1997). These water-soluble contaminants include simazine, atrazine, chlorpyrifos, 

metolachlor, diazinon, and carbaryl. Water concentrations and frequency of detection were 

highest at the Willamette/Columbia confluence, with detections in 80–100% of samples at 

52
concentrations up to 300 ng/L; these compounds were also frequently reported at the Beaver 

Army Terminal. 

Various trace metals have also been monitored as part of this program, revealing high 

concentrations of iron and manganese, especially near the Willamette/Columbia confluence, and 

high levels of arsenic in the Columbia River estuary (Fuhrer et al. 1996). These compounds 

come partly from natural sources, as well as anthropogenic activities, such as the use of lead 

arsenate as an insecticide for apples. Concentrations of other trace metals were similar to 

background concentrations in other North American streams (Fuhrer et al. 1996). 

Contaminants that have been documented in estuary sediments include trace metals 

(cadmium, copper, and zinc), dioxins, furans, chlorinated pesticides and other chlorinated 

compounds (e.g., dieldrin, lindane, chlordane, PCBs, and DDT and its metabolites), polycylic 

aromatic hydrocarbons (PAHs), and other semivolatile compounds (Fuhrer and Rinella 1983, 

Fuhrer 1986, Harrison et al. 1995, Tetra Tech Inc. 1996, USACE 1998, Roy F. Weston Inc. 

1998). Many of these compounds, particularly lipophilic compounds such as PAHs and 

organochlorine compounds (OCs), are rarely detected as dissolved material in the water, but 

rather tend to bind to organic carbon or particulate materials; thus they commonly occur in 

association with fine-grained materials in the streambed or in suspension (Horowitz 1991, Tetra 

Tech Inc. 1993). 

The fine-grained sediments to which these toxicants adsorb will most likely be deposited 

in areas with slower water velocities, including backwater areas in side channels and along the 

river’s margins. Elevated concentrations of toxic contaminants are more likely to occur in these 

areas (Tetra Tech Inc. 1994). In the main navigation channel of the Columbia River, current 

velocities are generally high, so there is little deposition of fine-grained sediments. Coarse, 

sandy sediment with relatively low contaminant concentrations typically make up 99% of the 

bulk bed material in the navigation channel (USACE 1998, 1999, McCabe et al. 1997). 

Some contaminants, including PAHs, have been detected at levels that exceed state or 

federal sediment quality guidelines, or are considered harmful to humans and aquatic life (Tetra 

Tech Inc. 1996). These contaminants have been detected in sediments from the lower 

Willamette River in the Portland area (concentrations up to 900 mg/kg wet wt (ODEQ 1994, 

Harrison et al. 1995, Roy F. Weston Inc. 1998) and in some sediments from other urban and 

industrial areas in the estuary (Tetra Tech Inc. 1996). Recent sediment data, collected in 2000 by 

EPA as part of EMAP (the Environmental Monitoring and Assessment Program), identified a 

few hot spots for the PCBs and DDTs within the estuary, including sites near Longview (total 

PCBs 860 ng/g dry wt), West Sand Island (total PCBs 965 ng/g dry wt), the Astoria Bridge 

(DDTs 597 ng/g dry wt), and Vancouver (DDTs 128 ng/g wet wt). 

It is noteworthy that PCB and DDT concentrations in the majority of sediments tested in 

these studies were much lower (below 50 and 5 ng/g dry wt, respectively). To put these values 

in perspective, the sediment screening guidelines for the protection of marine life are typically in 

the 20–200 ng/g dry wt range for PCBs (MacDonald 1994, USACE 1998, WAC 1995, Meador et 

al. 2002, CCME 2002), and in the 3–7 ng/g dry wt range for DDTs (MacDonald 1994, USACE 

1998, WAC 1995, Meador et al. 2002, CCME 2002), depending on the organic carbon content of 

the sediment. 

53
Suspended material may also be an important source of contaminants in the Columbia 

River estuary (LCREP 1999). This material is predominantly fine-grained, and contains many of 

the toxic compounds that have been detected in streambed sediments. McCarthy and Gale (2001) 

analyzed water samples collected with semipermeable membrane devices from nine mainstem 

and six tributary sites throughout the Columbia River basin (Washington and Oregon) and found 

dioxins, dibenzofurans, PCBs, organochlorine pesticides, and PAHs throughout the basin, with 

the highest concentrations of many compounds in the Portland-Vancouver area. Metals 

including arsenic, lead, chromium, copper, iron, manganese, mercury, and zinc have also been 

detected in suspended sediments in the estuary (Fuhrer et al. 1996). 

Mobilization and transport of suspended sediments during extreme stream flow events 

can make their adsorbed contaminants available to salmon and other aquatic organisms. For 

example, during the flood of February 1996, several legacy organic pesticides that are typically 

associated with the sediment phase, including dieldrin and DDE, were mobilized in the lower 

Columbia and Willamette rivers and detected in the water column at some sites for the first time 

(Kelly 1997). During this event, the estimated whole water concentration of p,p’-DDE exceeded 

the chronic ambient water-quality criterion for the protection of aquatic organisms by at least 

fivefold. Suspended particulates and associated contaminants may also occur in areas of high 

turbidity, such as the estuarine turbidity maximum, which may be an important feeding area for 

salmon (Bottom and Jones 1990). However, currently, the relative contributions of contaminants 

in water column versus those in bed sediment or body burdens in resident biota are poorly 

understood (LCREP 1999, SEI 2001). 

Exposure to contaminants, and hence the potential effects of these compounds in the 

estuary, likely varies with life history type or ESU. Stream-type ESUs (e.g., Snake River 

sockeye, upper Willamette River steelhead, and Snake River spring Chinook) are less likely to 

accumulate high body burdens of bioaccumulative, sediment-associated contaminants such as 

PCBs and DDTs because most members of these populations migrate rapidly through the estuary 

as yearlings or older. However, they may be affected by short-term exposure to waterborne 

contaminants such as organophospate pesticides (OPs) and dissolved metals. 

Ocean-type fish (e.g., lower Columbia River chum salmon and upper Willamette River 

Chinook salmon), which enter the estuary as fry, fingerlings, or subyearlings, and may rear for 

an extended period in the estuary, are also at risk for exposure to current-use pesticides and 

dissolved metals. At the same time, they are more likely than stream-type fish to be affected by 

bioaccumulative toxicants (DDTs, PCBs) that they may absorb through their diet during 

estuarine residence. Ocean-type populations may also be more at risk because of their greater 

use of shallow-water habitats with slower water velocities, including backwater areas in side 

channels and along the river’s margin, where fine-grained sediments to which toxics adsorb are 

most likely to accumulate. This may be particularly true for naturally produced wild salmon 

that, as noted earlier in this document, are more commonly found in side-channel, peripheral 

tidal marsh, and forested marsh habitats than the larger, hatchery size salmon that mostly use 

deeper mainstem habitat. 

Many of the contaminants found in streambed and suspended sediments in the estuary are 

accumulated by resident biota. A number of studies have identified trace metals, dioxins and 

furans, chlorinated compounds such as PCBs and DDTs, and PAH metabolites in nonsalmonid 

54
fish from the estuary (Tetra Tech Inc. 1993, 1996, Brown et al. 1998, Foster et al. 2001a, 2001b), 

in some cases at concentrations exceeding health guidelines (LCREP 1999). Although data on 

contaminant concentrations in listed salmon are more limited, they indicate that chemical 

contaminants are present in prey and tissues of juvenile salmon from the Columbia River estuary 

(Figures 24–27). 

In studies conducted by the NWFSC in collaboration with the U.S. Army Corps of 

Engineers (Johnson et al. 2004), contaminant concentrations were measured in juvenile fall 

Chinook salmon from several sites in the estuary (near the confluence of the Columbia and 

Willamette rivers, near Longview, White Island, West Sand Island, between East and West Sand 

islands, Chinook Point, east Trestle Bay, west Trestle Bay, lower Desdemona Sands, and middle 

Desdemona Sands, Figures 24–27). Fish from the Willamette/Columbia River confluence, 

Longview, and West Sand Island were collected in shallow water habitats by beach seine, while 

fish from the other sites within the lower estuary were collected in deeper water by purse seine. 

The primary contaminants found in whole body samples of both purse seine and beach 

seine fish from all sites were PCBs and DDTs. Chlordanes, lindane, hexachlorobenzene, 

dieldrin, and mirex were also detected in fish from the confluence and Longview/Kalama. 

Average concentrations of PCBs at estuarine sampling sites ranged from 23 to 90 ng/g wet wt, 

while average DDT concentrations ranged from 32 to 115 ng/g wet wt. In individual fish, DDT 

levels as high as 270 ng/g wet wt and PCB levels as high as 340 ng/g wet wt were measured. 

These concentrations were among the highest levels measured by the NWFSC at estuarine sites 

in Washington and Oregon (Stein et al. 1995, Collier et al. 1998a, Stehr et al. 2000, Arkoosh 

unpubl. data). 

Measurable concentrations of DDTs and PCBs, were also detected in stomach contents of 

juvenile fall Chinook salmon from West Sand Island, White Island, Longview, and the 

Willamette/Columbia confluence (at other sites, contaminants in stomach contents were not 

measured), indicating that fish were absorbing some of these compounds from prey during 

estuarine residence. Contaminant concentrations in fish from the Willamette/Columbia 

confluence are shown in Figure 23. Concentrations of PCBs in stomach contents of fish from 

this area were comparable to those in fish from the heavily industrialized Hylebos Waterway in 

Puget Sound (Stehr et al. 2000), while DDT concentrations were higher than at any other 

sampled sites in the Pacific Northwest. Several additional chlorinated pesticides, including 

lindane, hexachlorobenzene, dieldrin, and certain DDT isomers (o,p-DDD, o,p-DDT, p,p-DDT) 

were detected only in stomach contents of salmon from the confluence or Longview. 

Although the fish used for these analyses were almost entirely unmarked, genetic 

analyses showed that a high proportion of beach seine collected fish from West Sand Island, 

Longview, and the confluence were most likely of hatchery origin (40–70%) (Johnson et al. 

2004). Consequently, DDTs and PCBs in hatchery feed may have contributed to contaminant 

body burdens in these fish, since these substances, especially PCBs, have been detected in 

hatchery feed and in juvenile Chinook salmon collected from Pacific Northwest hatcheries 

(Johnson et al. 2004, Ylitalo unpubl. data; Figures 24–26). However, no data are available on 

contaminant concentrations in feed from the specific hatcheries where these fish originated 

(predominantly hatcheries on the Elokoman, Cowlitz, and Sandy rivers), so this cannot be 

confirmed. In spite of the potential for hatchery contribution, it is clear from the elevated levels 

55
0 20 40 60 80 100 120 140 160

Tillamook Bay (1)

Elk River Upstream (1)

Salmon River Estuary (5)

Alsea Bay Estuary (4)

East Trestle Bay (5)

Elk River Estuary (4)

Coquille River (1)

Lower Desdemona Sands (3)

Coos Bay Estuary (4)

Longview (2)

Middle Desdemona Sands (4)

Grays Harbor (1)

Willipa Bay Estuary (1)

Upper Desdeoma Sands (2)

Skokomish (1)

Chinook Point (5)

Confluence (2)

West Sand Island (23)

Nisqually River Estuary (1)

West Trestle Bay (5)

Yaquina Bay (3)

East/West Sand Island (5)

Duwamish (4)

Hatchery (7)

Total whole body PCBs (ng/g wet wt)

Columbia River Estuary

Other Pacific Northwest estuaries

Pacific Northwest hatcheries

Figure 24. Mean concentrations (±SE) of total PCBs (ng/g wet wt) in whole bodies of juvenile fall 

Chinook salmon sampled from Pacific Northwest estuaries. 

0 20 40 60 80 100 120 140 160 180

Elk River Upstream (1)

Tillamook Bay (1)

Alsea Bay Estuary (1)

Salmon River Estuary (5)

Alsea Bay Estuary (4)

Elk River Estuary (4)

Coquille River (1)

Grays Harbor (1)

Yaquina Bay (3)

Coos Bay Estuary (4)

Willapa Bay Estuary (1)

East Trestle Bay (5)

Upper Desdemona Sands (2)

Skokomish (1)

Duwamish (3)

Longview (2)

Chinook Point (5)

Nisqually River Estuary (1)

Confluence (2)

Lower Desdemona Sands (3)

West Sand Island (20)

East-West Sand Island (5)

Middle Desdemona Sands (4)

West Trestle Bay (5)

Hatchery (7)

Total whole body DDTs (ng/g wet wt)

Hatchery

Lower Columbia Estuary 

Other Pacific Northwest Estuary

Figure 25. Mean concentrations (±SE) of DDTs (ng/g wet wt) in whole bodies of juvenile fall Chinook 

salmon sampled from Pacific Northwest estuaries. 

56
0 20 40 60 80 100 120 140 160 180

Salmon River (1)

Elk River (2)

Alsea Bay (1)

Yaquina Bay (1)

Coos Bay (1)

Nisqually (2)

W Sand Is (8)

White Island (1)

Grays Harbor (1)

Longview (3)

Hylebos (2)

Confluence (2)

Hatchery (7)

PCBs in stomach contents (ng/g wet wt)

Columbia River Estuary

Other Pacific Northwest estuaries

Pacific Northwest hatcheries

0 20 40 60 80 100 120 140

Elk River (2)

Alsea Bay (1)

Nisqually (2)

Salmon River (1)

Coos Bay (1)

Yaquina Bay (1)

Hylebos (2)

W Sand Is (8)

Longview (3)

White Island (1)

Grays Harbor (1)

Confluence (2)

Hatchery (2)

DDTs in stomach contents (ng/g wet wt)

Figure 26. Mean concentrations (±SE) of PCBs and DDTs (ng/g wet wt) in stomach contents of juvenile 

fall Chinook salmon sampled from Pacific Northwest estuaries. 

1 10 100 1000 10000

Elk River (5)

Salmon River (7)

Nisqually (2)

Alsea Bay (7)

W Sand Island (9)

Coos Bay (3)

White Island (2)

Grays Harbor (2)

Yaquina Bay (4)

Longview (3)

Confluence (2)

Duwamish River (1)

Willipa Bay (2)

Hatchery (2)

PAHs in stomach contents (ng/g wet wt)

Columbia River Estuary

Other Pacific Northwest estuaries

Pacific Northwest hatcheries

1 10 100 1000 10000

Alsea Bay (7)

Elk River (5)

Yaquina Bay (4)

Nisqually (2)

Coos Bay (3)

Salmon River (7)

W Sand Island (8)

Willipa Bay (2)

Grays Harbor (2)

Skokomish (3)

Duwamish River

(1)

BaP metabolites (ng/g bile)

Figure 27. Mean concentrations (±SE) of high molecular weight polycyclic hydrocarbons (PAHs) in 

stomach contents, and metabolites of PAHs in bile, of juvenile fall Chinook salmon sampled from 

Pacific Northwest estuaries. 

57
of DDTs and PCBs in stomach contents of fish from sites within the estuary that fish are also 

being exposed to these contaminants through their natural prey. Additionally, DDT/PCB ratios 

were several times higher in salmon from Columbia River sites (average 1–4) than in hatchery 

fish (average 0.7), suggesting uptake of DDTs from the environment. 

Less information is available on exposure to PAHs in juvenile salmon from the Columbia 

River estuary. Data collected by NOAA Fisheries Service between 1998 and 2002 showed that 

concentrations of PAHs in stomach contents and PAH metabolites in bile were low to moderate 

in juvenile fall Chinook salmon from West Sand Island in comparison to levels found in fish 

from other estuaries along the Washington and Oregon Coast (Figure 26). No data were 

available on metabolites of PAHs in bile of fish from other sites in the estuary. PAHs were 

measured in stomach contents of juvenile Chinook salmon from several lower Columbia sites 

(the Willamette/Columbia confluence, West Sand Island, White Island, and Longview). While 

levels in fish from West Sand Island and White Island were moderate, concentrations in fish 

from Longview and the confluence were higher than or comparable to concentrations in juvenile 

salmon from the Hylebos Waterway in Puget Sound (Figure 27). 

Data on contaminant concentrations in salmon prey and other benthic invertebrates are 

limited. Little has been published for contaminants in aquatic macroinvertebrates, although 

some work has been done on clams, crayfish, and Corophium, a benthic amphipod that is 

important in the diets of several fish species, including salmonids (McCabe et al. 1983, 1986, 

1997, Muir and Emmett 1988, LCREP 1999). A small-scale reconnaissance study conducted by 

NWFSC’s Newport Research Station in the mid-1990s measured PAH concentrations in 

Corophium salmonis7

 from several sites in the lower Columbia River, including Longview 

Bridge and the Multnomah Channel in the Columbia River, and sites at the Willamette River 

mouth, North Portland Harbor, and Hayden Island in the Willamette River. 

At the three sites where sediment PAH concentrations were highest (Hayden Island, 

Longview Bridge, and Multnomah Channel), no amphipods were present in sediments, 

suggesting C. salmonis has specific habitat requirements, including sediment particle size 

preferences and possibly concentrations of contaminants, that may prevent it from occupying 

these sites. PAH concentrations in tissues of Corophium were up to 50 ng/g wet wt 

benzo[a]pyrene (BaP) equivalents or about 150 ng/g wet wt high molecular weight PAs. 

Average concentrations of high molecular weight PAs in stomach contents from juvenile salmon 

for the Columbia River estuary ranged from approximately 3,000 ng/g wet wt and approximately 

600 ng/g wet wt the Confluence and Longview, respectively, to 20–30 ng/g wet wt at West Sand 

Island and White Island (Johnson et al. 2004). 

In general, these studies show that PCB and PAH concentrations in salmon or their prey 

from the Columbia River estuary are comparable to those reported in juvenile salmon from other 

moderately to heavily urbanized sites, while DDT levels are high relative to levels in other 

Pacific Northwest estuaries. Although concentrations of contaminants were higher in stomach 

contents of salmon juveniles collected from near the Willamette/Columbia confluence, body 

 

7

 Data are from preliminary studies conducted by Bruce McCain, NWFSC, Newport, Oregon. Concentrations of 

PAHs in amphipods were measured using a semiquantitative method that employs high performance liquid 

chromatography (HPLC) and a photodiode array (PDA) detector (Krahn et al. 1993). 

58
burdens of bioaccumulative OCs were similar throughout the estuary. Sources and pathways of 

exposure are unclear, and could include contaminated bed sediments, contaminated prey, 

contaminants in suspended material, and contaminants in hatchery feed for those fish that are of 

hatchery origin. 

Studies suggest that, at least for some contaminants, exposure levels in juvenile salmon 

from the Columbia River estuary are approaching concentrations that could affect their health 

and survival. For PCBs, Meador et al. (2002) estimated a critical body residue of 2,400 ng/g 

lipid for protection against 95% of effects ranging from enzyme induction to mortality. They 

based this on a range of sublethal effects observed in salmonids in peer-reviewed studies 

conducted by NMFS and other researchers. On a wet weight basis, the threshold would be 24–

48 ng/g for fish with lipid content of 1–2%, typical of juvenile salmon from the Columbia River. 

Mean PCB body burdens in juvenile salmon analyzed by the NWFSC (Johnson et al. 2004) were 

at or above the 2,400 ng/g threshold at 7 of 10 sites sampled in the lower Columbia (Figure 28). 

Of individual fish analyzed from sites within the estuary, approximately 60% had PCB body 

burdens at or above this threshold. 

The likely impact of DDTs, another major contaminant of concern in the lower 

Columbia, on salmon is less clear. Most reported effects of DDTs on salmonids are associated 

with whole body tissue concentrations above those typically found in salmon obtained from the 

Columbia River estuary (≥500 ng/g wet wt) (Allison et al. 1963, Burdick et al. 1964, Johnson 

0

2000

4000

6000

8000

10000

12000

14000

16000

18000

East/West Sand Island (5)

Chinook Point (5)

Confluence (3)

East Trestle Bay (5)

Longview (3)

Lower Desdemona Sands (3)

Middle Desdemona Sands (4)

Upper Desdemona Sands (2)

West Sand Island (23)

West Trestle Bay (5)

PCBs (ng/g lipid)

beach seine fish

purse seine fish

PCB effects threshold

Figure 28. Mean concentrations (±SE) of PCBs (ng/g lipid) in juvenile fall Chinook salmon sampled 

from the Columbia River estuary as compared to the 2,400 ng/g lipid biological effects threshold 

of Meador et al. (2002). 

59
and Pecor 1969, Buhler et al. 1969, Peterson 1973, Poels et al. 1980, Hose et al. 1989). More 

recent studies suggest that certain DDT isomers (e.g., o,p-DDT) may have endocrine-disrupting 

or immunotoxic effects (Donohoe and Curtis 1996, Celius and Walther 1998, Khan and Thomas 

1998, Arukwe et al. 1998, 2000, Christiansen et al. 2000, Zaroogian et al. 2001, Milston et al. 

2003, Papoulis et al. 2003). 

These effects were typically observed at body burdens or dietary exposure concentrations 

in the 10–20 ng/g wet range or above, while concentrations of o,p-DDTs in the bodies and 

stomach contents of juvenile Chinook salmon from the lower Columbia were near or below 

detection limits (<2 ng/g wet wt) (Johnson et al. 2004). This suggests that o,p-DDT, DDE, and 

DDD levels are below concentrations likely to be associated with estrogenic activity and related 

effects. However, these effect thresholds were obtained with laboratory fish, whose lipid content 

is typically higher than in wild fish (8–10% vs. 1–3%; Meador et al. 2002). This is important, 

because for a given wet or dry weight tissue concentration, the higher the lipid content, the 

higher the resistance to the toxicant because a higher proportion of the hydrophobic compound is 

associated with the lipid and is not available to cause toxicity (Meador et al. 2002). If we assume 

that test fish had a lipid content of 10%, then the DDT body burden on a lipid weight basis for 

toxic effects would be 5,000 ng/g lipid. Lipid-adjusted DDT concentrations in or above this 

range were observed in juvenile Chinook salmon from some sites in the lower Columbia River 

estuary (e.g., between East and West Sand islands, middle Desdemona Sands, west Trestle Bay). 

Moreover, some of the DDT isomers could work additively in conjunction with other estrogenic 

contaminants (e.g., plasticizers, pharmaceuticals, and surfactants) to alter reproductive processes 

or other physiological functions, if these are also present in the estuary. 

DDTs also have the potential to affect salmonid prey, as invertebrate species are 

generally quite susceptible to impacts of these compounds. Results of laboratory and field 

investigations, as well as equilibrium partitioning calculations, suggest that thresholds for 

chronic effects occur at total DDT concentrations in sediments of approximately 10 ng/g dry wt 

(Pavlou et al. 1987, Long et al. 1995). These DDT concentrations are not uncommon in estuary 

sediments (Tetra Tech Inc. 1994, Johnson et al. 2004). Moreover, studies in the Columbia River 

estuary have shown that DDTs represent a hazard to fish-eating predators through 

bioaccumulation and bioconcentration (Anthony et al. 1993, USFWS 1999, Thomas and 

Anthony 1999, 2003, Henny et al. 2003). 

Recently, Nendza et al. (1997) estimated a no-observable-effect concentration of 22–50 

ng/g wet wt for food-chain related impacts for DDTs, based on studies with a number of fish 

from marine estuaries. Many juvenile salmon sampled from the Columbia River estuary have 

DDT body burdens at or above this level. 

The potential for contaminant-related injury to juvenile salmonids in the estuary is also 

supported by field studies at Puget Sound sites contaminated with PAHs, PCBs, and other OCs 

similar to those present in the lower Columbia. In these studies, juvenile salmon from two 

urbanized waterways, the Hylebos and the Duwamish, showed demonstrable effects, including 

immunosuppression, reduced disease resistance, and reduced growth rates, due to contaminant 

exposure during their estuarine residence (Arkoosh et al. 1991, 1994, 1998, Varanasi et al. 1993, 

Casillas et al. 1995, 1998a). For example, juvenile Chinook salmon from the Duwamish 

Waterway were not able to produce the normally enhanced secondary immune response 

60
0

10

20

30

40

50

60

70

80

90

Hatchery Estuary Hatchery Estuary

PFC/culture

Primary response

Secondary response

Green/Duwamish System Nisqually System

*

*

*

Figure 29. The leucocyte primary and secondary in vitro plaque forming cell response per culture 

(PFC/culture) against an antigen. The mean (+SD) PFC response was analyzed in Chinook 

salmon from the Green/Duwamish system (urban) and the Nisqually system (nonurban). The 

asterisk (*) indicates the secondary PFC/culture is significantly higher (p < 0.05) than that 

observed in the primary response. (Adapted from Arkoosh et al. 1991.) 

observed in nonexposed control fish from the Nisqually River estuary and fish from the natal 

hatcheries (Figure 29) (Arkoosh et al. 1991). 

Salmon exposed in the laboratory to PCBs and PAHs were also immunosuppressed 

(Arkoosh et al. 1994). Additionally, in disease challenge studies with Vibrio anguillarum, a 

marine bacterial pathogen that infects juvenile Chinook salmon from estuaries along the 

Washington and Oregon coast (Arkoosh et al. 2004), juvenile Chinook salmon from the 

Duwamish Waterway were more susceptible to disease and exhibited higher cumulative 

mortality than fish from natal hatcheries on a noncontaminated estuary (Arkoosh et. al. 1998, 

Figure 30). Similar effects were found in juvenile Chinook salmon injected in the laboratory 

with extracts of sediments from the Hylebos Waterway in Commencement Bay (Arkoosh et al. 

2001). 

In related studies designed to assess the effects of contaminants on growth (Casillas et al. 

1995), juvenile fall Chinook salmon collected from the Duwamish Waterway and held in the 

laboratory for up to 90 days did not grow as well as similarly treated fish from the natal hatchery 

on the Green River. In contrast, juvenile salmon from the nonurban estuaries showed no 

difference in growth compared to fish from the natal hatcheries. Concentrations of insulin-like 

growth factor, a plasma hormone involved in the regulation of growth, were also lower in fish 

61
0

10

20

30

40

50

60

70

Non-urban Urban

% Cumulative mortality

Hatchery

Estuary

Figure 30. Cumulative mortality of juvenile Chinook salmon collected from the Duwamish Waterway 

(urban) and the associated hatchery-estuary system, and the Nisqually hatchery estuary system 

(nonurban) following disease challenge with the marine bacterium Vibrio anguillarum. (Adapted 

from Arkoosh et al. 1991.) 

from the urban estuary than in fish from the corresponding hatchery or the nonurban estuaries 

and hatcheries. In a separate laboratory study (Casillas et al. 1998a), growth was reduced in 

juvenile Chinook salmon exposed to PCBs and to extracts of sediments from the Hylebos 

Waterway, another urban estuary. Because growth of salmon during the first year of life appears 

to be critical to recruitment success (Holtby et al. 1990, Pearcy 1992, Unwin 1997), contaminantrelated reductions in juvenile growth rates could increase the risk of salmon mortality. 

In other studies in Puget Sound, juvenile salmon from urban estuaries (e.g., the 

Duwamish and Hylebos Waterways) had significantly higher levels of DNA damage (i.e., PAHDNA adducts in liver) than salmon from relatively uncontaminated sites. In addition, salmon 

from the urban estuaries had significantly higher induction of cytochrome P4501A (CYP1A), the 

enzyme that metabolizes selected contaminants including PAHs, dioxins and furans, and dioxinlike PCBs (Stein et al. 1995, McCain et al. 1990, Varanasi et al. 1993, Collier et al. 1998a, 

1998b, Stehr et al. 2000). These biochemical alterations are not necessarily indicative of adverse 

health effects in themselves, but are associated with reproductive and developmental 

abnormalities and liver disease (Williams et al. 1998, Whyte et al. 2000, Myers et al. 2003). 

At the two contaminated sites where most of the work described above was done, the 

Duwamish and Hylebos Waterways, average sediment PCB concentrations ranged from 400–500 

ng/g dry wt and average PAH concentrations were about 10,000 ng/g dry wt (Collier et al. 

62
1998a, Krahn et al. 1998). These sediment concentrations are within the range of those reported 

in the estuary (e.g., Tetra Tech Inc. 1996, Johnson et al. 2004), although higher than those 

typically found in estuary sediments. Total body PCB concentrations in fish collected from the 

Duwamish and Hylebos sites were in the 250–350 ng/g wet wt range, comparable to some fish 

sampled from sites within the estuary. 

Various health effects have also been documented in nonsalmonid fish and other aquatic 

biota from the lower Columbia River, including fish with external abnormalities or skeletal 

deformities (Markle 1995, Tetra Tech Inc. 1995), alteration in endocrine response function 

(Goodbred et al. 1997, Foster et al. 2001a, 2001b), and pollution-associated liver lesions (Myers 

et al. 1994). Although the exposure patterns and life histories of listed salmon may differ from 

those of these fish species, these data raise additional concern about the potential for exposure 

and health impacts on salmon. 

In addition to bioaccumulative contaminants, waterborne contaminants such as dissolved 

metals and current use pesticides may pose a threat to listed salmon. Various OPs such as 

diazinon, carbofuran, and chlorpyriphos at concentrations of 1–10 ug/L can disrupt olfactory 

function in salmon after exposures of as little as a few hours or days (Moore and Waring 1996, 

Waring and Moore 1997, Scholz et al. 2000, Sandahl et al. 2004). Scholz et al. (2000) reported 

that diazinon disrupted olfactory function in Chinook salmon at concentrations of 1–10 ug/L; as 

a result, fish failed to show normal antipredator responses or homing behavior (Figure 31). 

Similar responses were observed by Sandahl et al. (2004) with chlorpyrifos at 

concentrations as low as 0.72 μg/L. Moore and Waring (1996) and Waring and Moore (1997) 

found that exposure to diazanon and carbofuran in a similar range could desynchronize the 

reproductive physiology of prespawning Atlantic salmon (Salmo salar) by inhibiting the male’s 

ability to detect sex pheromones. Concentrations of diazanon in the 1–10 ug/L range have been 

reported in USGS NASQAN sampling in the estuary, and other pesticides with related modes of 

action that would be likely to have the same effects (e.g., chlorpyriphos, malathion, aldicarb, 

carbaryl, carbofuran) are detected even more frequently and at higher concentrations. 

Similarly, Baldwin et al. (2003) and Sandahl et al. (2004) found that exposure to copper 

at concentrations in the 3–6 μg/L range for as little as 30 minutes affected olfactory function in 

coho salmon so they could no longer respond normally to test odorants (Figure 32). This could 

impair the ability of juveniles to find prey and avoid predators, or interfere with homing and 

reproductive behavior in adults. Dissolved copper concentrations at the estuary sites sampled in 

the NASQAN survey were within this range (Fuhrer et al. 1996), and copper in suspended 

sediments was substantially higher (45–120 μg/L). Other contaminants in the water column, 

including endocrine-disrupting substances such as synthetic hormones, are only beginning to be 

characterized in this part of the basin, but potentially could also have substantial impacts on 

salmon. 

More research is clearly needed to document exposure and associated effects of chemical 

contaminants on endangered Columbia River estuary salmon, but the available data show that 

environmental concentrations and tissue burdens of several classes of contaminants are within 

the range where they could primarily affect abundance and population growth rate in listed 

stocks. The true magnitude of the effect is uncertain, but a recent modeling study suggests it 

63
Figure 31. Foraging activity in the presence of olfactory signals of a potential predator in juvenile 

Chinook salmon exposed to diazinon. Control fish (solid bar) responded to the conspecific skin 

extracts by reducing their foraging activity and freezing. The magnitude of the antipredator 

response was reduced in diazinon-exposed fish (2 h at 0.1, 1.0, and 10.0 ug·L–1), and they were 

more active and fed more often than controls. The effect of diazinon was significant at the 1.0 

and 10.0 ug·L–1 exposures (P = 0.05, Fisher’s test). (From Scholz et al. 2000.) 

could be significant for at least some ESUs. Spromberg and Meador (in press) used life cycle 

models to examine the impacts of low-level toxic effects (10–25% response level for mortality, 

immune suppression, and growth) on the population dynamics of fall run Chinook salmon. 

Responses in this general range might be expected in estuary fish exceeding, for example, 

the tissue benchmark for PCBs developed by Meador et al. (2002). These results indicate that 

after 20 years of continued reductions at the 10% level, population abundance was severely 

depressed (up to 2–3 times lower than nonimpacted populations) for several of the endpoints. 

When the 25% toxicity response was modeled for 20 years, population abundance was between 3 

and 20 times lower, depending on the endpoint. 

In summary, exposure to chemical contaminants has the potential to affect survival and 

productivity of both ocean-type and stream-type stocks in the estuary. Stream-type ESUs are 

most likely to be affected by short-term exposure to waterborne contaminants such as current use 

pesticides and dissolved metals that may disrupt olfactory function and interfere with associated 

behaviors, such as capturing prey, avoiding predators, imprinting, and homing. Ocean-type 

ESUs will also be exposed to these types of contaminants, but will also be affected by persistent, 

bioaccumulative toxicants such as PCBs and DDTs, which they may absorb during their more 

extended estuarine residence. Consequently, it is likely that the impact on ESUs exhibiting the 

ocean life history type is greatest. 

64
Figure 32. Dose-response curves and threshold determinations for sublethal copper neurotoxicity. Data 

were obtained from six treatment groups (control and five copper exposures; n = 6 fish per 

group). The evoked electro-olfactogram (EOG) amplitudes for all copper exposures were 

normalized to the mean response of the controls and expressed as a group (mean ± 1 standard 

error). The dashed line indicates a benchmark criterion of 0.75, or a 25% reduction in evoked 

response (relative to controls). Three vertical lines in the upper right show the lower limits of the 

95% confidence interval for the control response to the three different odorants. Filled circles 

indicate the benchmark concentrations for the different olfactory pathways (Lserine, taurocholic 

acid [TCA], and the amino acid mixture). Note that the benchmark values are nominal 

concentrations, or a change (increase) from the copper present at approximately 3 mg/L in the 

source water for the NWFSC hatchery, Seattle. (From Baldwin et al. 2003.) 

65
Caspian Tern Predation of Juvenile Salmon 

In the preceding analyses, we suggested that changes in estuarine habitats affect 

population viability but that quantifying these changes is problematic. One factor that can be 

quantitatively linked to VSP criteria is predation. Estimates of life-stage specific predation 

mortality can be directly linked to changes in population growth rate or productivity. In general, 

predation by many predators in the Columbia River estuary has potentially increased from 

historical levels including predation by marine mammals, such as California sea lions (Zalophus 

californianus), smallmouth bass (Micropterus salmoides), northern pikeminnow (Ptychocheilus 

oregonensis), and double-crested cormorants (Phalacrocorax auritus) (e.g., Beamesderfer et al. 

1996, Collis et al. 2001b, Ryan et al. 2003). For most of these predators, we have little 

quantitative data on historical or current levels of predation and how predation affects population 

viability. 

In this subsection, we consider mortality of juvenile salmon as a result of predation by 

Caspian terns (Sterna caspia). Caspian terns met the criteria we described previously for 

selection of limiting factors for analysis. For example, levels of predation are greater at present 

than historically, and increasing numbers of terns nesting on islands in the Columbia River 

estuary annually consume large numbers of migrating juvenile salmonids (Roby et al. 1998). 

They are considered one of the factors that may currently limit salmonid stock recovery (Roby et 

al. 1998, IMST 1998). In the last section of this report, we examine predation by northern 

pikeminnow. Although much is known about northern pikeminnow predation, we do not 

consider it as a limiting factor comparable to terns, because of some key information gaps that 

we were unable to address (e.g., historical levels of predation are unknown). 

Caspian terns are highly migratory and are cosmopolitan in distribution (Harrison 1983, 

Harrison 1984). Nesting has been reported throughout North America and in Australia, New 

Zealand, South Africa, Asia, and Europe. The numbers of Caspian terns in western North 

America more than doubled between 1980 and 1999 (Cuthbert and Wires 1999). One reason for 

the increase is that human-created habitat provides high quality nest sites and is associated with 

population increases in many parts of North America (Cuthbert and Wires 1999). 

In the early 1990s, a substantial increase in the size of newly established Caspian tern 

nesting colonies on man-made islands in the Columbia River estuary was noted by NOAA 

Fisheries Service staff. Three estuary islands on which piscivorous birds nest were created from 

or augmented by materials dredged to maintain the Columbia River Federal Navigation Channel. 

Before 1984 there were no recorded observations of terns nesting in the Columbia River estuary, 

when approximately 1,000 pairs apparently moved from Willapa Bay to nest on newly deposited 

dredge material on East Sand Island. In 1986 those birds moved to Rice Island, a man-made 

island. The Caspian tern colonies in the estuary have since expanded to 9,000–10,000 pairs. In 

1999 the colony was encouraged to relocate to East Sand Island. By 2001 the entire Columbia 

River estuary population of terns, representing the majority of this species on the West Coast, 

nested on just four acres on East Sand Island; in 2002 the terns nested on six acres. 

Caspian terns arrive in the Columbia River estuary in March through April and begin 

nesting soon thereafter (Roby et al. 1998). To avoid mammal and avian predators, terns 

construct their nests on islands (Harrison 1984) and show a preference for barren sand. They are 

66
piscivorous in nature (Harrison 1984), requiring about 220 grams (roughly one-third of their 

body weight) of fish per day during the nesting season. The timing of courtship, nesting, and 

chick rearing corresponds with the outmigration of many of the salmonid stocks in the basin 

(Collis et al. 2002). 

Salmon and steelhead constitute a major portion of tern diets, particularly when the birds 

nested on Rice Island. Based on diet analyses conducted in 1997–1998, juvenile salmonids 

constituted 77.1% of prey items and 76.7% of prey diet mass of Caspian terns nesting on Rice 

Island (Collis et al. 2002). During the May peak in the smolt outmigration of steelhead, yearling 

Chinook salmon, and coho salmon through the estuary, the diet of Caspian terns on Rice Island 

was over 80% juvenile salmonids (Collis et al. 2002). In early May, steelhead were the primary 

salmon eaten while coho salmon were the primary salmonid prey eaten in late May. 

Efforts to relocate the terns to East Sand Island from Rice Island that began in 1999 have 

succeeded in reducing consumption of smolts without decreasing tern productivity. East Sand 

Island is a site lower in the estuary with abundant alternate prey sources. Over the last few years, 

studies suggest that consumption of salmonids in the estuary has been lower than previous levels 

while consumption of alternative prey species has increased. Relocating the colony to East Sand 

Island, which is lower in the estuary and closer to periodically abundant Pacific herring (Clupea 

harengus pallasi) and anchovies (Engraulis mordax), has contributed to the reduction. Observed 

diets, which consisted almost exclusively of salmonids at Rice Island (77% in 1999 and 90% in 

2000), shifted to 46%, 47%, and 33% salmonids at East Sand Island in 1999, 2000, and 2001, 

respectively (Collis et al. 2001a, Roby et al. 2003). 

These data suggest that substantial declines in juvenile salmonid mortalities from Caspian 

tern predation occurred from relocating the colony. This is supported by studies estimating tern 

consumption of salmonids. In 2000 salmonid consumption by terns was estimated at 7.3 million 

smolts, which is 4.4 million less than in 1999—the last time a substantial number of terns nested 

on Rice Island (Collis et al. 2001a, USFWS 2001). In 2001 salmonid consumption was 

estimated at 5.9 million smolts, which is 5.8 million less than in 1999 (Collis et al. 2001a). 

These data were substantiated by PIT (passive integrated transponder) tag detections on the two 

islands in 1999 and 2002. Approximately two to four times fewer tags per pair of terns were 

detected per nest on East Sand Island in 1999 and 2000 than were detected on Rice Island in 

1999 and 2000. 

In a recent evaluation of the impact of Caspian tern predation on juvenile salmon (Good 

et al. 2003), two approaches were recognized as providing the types of predation rate estimates 

that are needed for salmon life cycle models that are used to assess the effects of various factors 

on risk of extinction in the Columbia River basin (Kareiva et al. 2000). One approach uses 

bioenergetics modeling. Since 1997 biologists with the Bonneville Power Administrationfunded research project, Avian Predation on Juvenile Salmonids in the lower Columbia River, (a 

joint project of Oregon State University, the U.S. Geological Survey, the Columbia River InterTribal Fish Commission, and Real Time Research Consultants) have used observed salmonid 

consumption at tern colonies in a bioenergetics model (Roby et al. 1998) to estimate the 

consumption of salmonids in the Columbia River estuary. Smolt consumption estimates from 

1999–2002 using this approach ranged from a low of 5.9 to a high of 11.7 million smolts eaten. 

67
Another approach uses detections of PIT tags on Caspian tern colonies to estimate 

salmonid predation rates overall, as well as by ESU (Collis et al. 2001b, Ryan et al. 2001). Since 

1987, researchers in the Columbia River basin have placed over five million PIT tags in juvenile 

salmonids for a variety of studies (Ryan et al. 2001). Identifying PIT tags on bird colonies can 

provide a minimum estimate of proportion of the stocks that were consumed by terns in these 

colonies. In recent years, approximately one million juvenile salmonids have been PIT-tagged 

annually (Collis et al. 2001b), the vast majority of which are steelhead and Chinook salmon from 

the Snake River basin. Over 115,000 PIT tags were detected on Rice Island in 1998 and 1999 

(Ryan et al. 2001). 

Of the PIT tags placed in steelhead smolts in 1997 that were detected at Bonneville Dam, 

2.8% of wild smolts and 5.4% of hatchery-raised smolts were subsequently detected on the Rice 

Island tern colony (Collis et al. 2001b). For steelhead that were PIT tagged in 1998 and detected 

at Bonneville Dam, 11.7% of wild smolts and 13.4% of hatchery-raised smolts were 

subsequently detected on the Rice Island tern colony (Collis et al. 2001b). For yearling Chinook 

salmon that were PIT tagged in 1998 and detected at Bonneville Dam, 0.5% of wild smolts and 

1.6% of hatchery-raised smolts were subsequently detected on the Rice Island tern colony (Collis 

et al. 2001b). 

Ryan et al. (2003) analyzed PIT-tag data from 1998 to 2000 on Rice Island and East Sand 

Island and determined that steelhead experienced higher predation rates (0.6% to 8.1% on East 

Sand Island, and 1.3% to 9.4% on Rice Island) than Chinook salmon (0.2% to 2.0% on East Sand 

Island, and 0.6% to 1.6% on Rice Island). Overall, Caspian terns consumed approximately 6% 

to 14% of the estimated outmigrating population of juvenile salmonids originating from the 

Columbia River basin. 

In a recent analysis of the impact of Caspian tern predation on salmon recovery, efforts 

focused on determining whether a unique predation rate could be identified. The effort focused 

on the Caspian tern colonies on East Sand Island in the lower estuary of the Columbia River 

because the colony currently represents the majority of the West Coast Caspian tern population. 

The focus period was 1999–2002 because this represents the time period after relocation from 

Rice Island during which this colony has dominated Caspian tern predation activity in the 

Columbia River estuary. Bioenergetics modeling was used to calculate predation rates 

(estimated number of salmon consumed/estimated number of salmon available in the estuary) 

using updated and refined estimates of the number of outmigrating salmon that migrate through 

the river or are transported and released below Bonneville Dam. PIT-tag detections were also 

used to generate estimates of predation rates on salmon. 

The relationship between tern abundance and mortality rate due to tern predation is not 

known with certainty. The estimated predation rate based on either bioenergetics modeling or 

PIT-tag data was linearly related to the number of Caspian terns nesting on East Sand Island 

during the breeding seasons of 1999–2002 (Figure 33). Moreover, PIT-tag detection also 

allowed ESU-specific predation rate estimates to be derived. Per capita consumption rates 

(number of smolts consumed per adult tern) have been relatively constant throughout the range 

of colony sizes on East Sand Island from 1999 to 2003. The per capita consumption rate in 1999 

(mean = 437.5) was nearly equivalent to that of 2000 (mean = 431.1), even though there was an 

almost fivefold difference in colony size (Figure 34). 

68
12.0

10.0

8.0

6.0

4.0

2.0

0

12.0

10.0

8.0

6.0

4.0

2.0

0

Predation rate 

PIT tag or bioenergetics

0 5,000 10,000 15,000 20,000 25,000

Number of Caspian terns breeding on East Sand Island

Figure 33. Estimated predation rates on all steelhead in the Columbia River estuary by Caspian terns, 

1999–2002, using bioenergetics modeling (black symbols) and recovery of PIT tags (grey 

symbols). Error bars on bioenergetics estimates represent 95% confidence limits. 

NWFSC has developed a matrix model to assess salmonid population trends and the 

impact of anthropogenic activity on those trends. This model has application when mortality 

rates can be constructed and attributed to a particular source. The value of life cycle models 

derive from providing an objective outcome for comparing the influence of various factors 

influencing population growth rates, rather than attempting to estimate real gains from any 

management action. Assessing the impact of predation by Caspian terns on juvenile salmonids 

during a particular life history phase was amenable to such evaluation. 

Using the Cumulative Risk Initiative (CRI) model, Good et al. (2003) estimated the 

impact of Caspian tern predation on the population growth rate (λ) of all steelhead and spring 

Chinook salmon in the basin using predation rate estimates derived from bioenergetics modeling 

and PIT-tag detections. Because of the similarity in the results between the two approaches, we 

present information only from estimates derived from PIT-tag detections, as ESU-specific 

impacts can also be derived with this information. 

The predation rate for 20,000 Caspian terns feeding on all steelhead and spring Chinook 

salmon was estimated using the regression equations generated from PIT-tag detections. This 

number of terns represents the maximum number observed to date on East Sand Island. 

Reductions in predation rate corresponding to reduced tern population sizes were used to model 

the potential increase in λ, assuming all steelhead or spring Chinook salmon mortality 

69
East Sand Island

Rice Island

1,200

1,000

800

600

400

200

0

Smolts consumed / individual 

adult tern

0 5,000 10,000 15,000 20,000 25,000

Number of individual adult terns

Figure 34. Per capita smolt consumption by Columbia River estuary Caspian terns on all salmonids, 

1997–2003 (with 95% CI). (Courtesy of D. Lyons and D. Roby, Oregon Fish Cooperative Unit, 

Oregon State University.) 

attributable to terns is not compensated for by mortality due to other sources. The maximum 

proportional increase in λ corresponding to complete elimination of mortality due to tern 

predation (i.e. removal of all terns from the estuary) was 1.9% and 0.8% for steelhead and spring 

Chinook salmon, respectively, using the PIT-tag estimate of predation rate. 

The PIT-tag detection approach enables the calculation of ESU-specific estimates of 

predation rate (and hence proportion increase in λ). Good et al. (2003) used the CRI model to 

estimate impact of Caspian tern predation on the population growth rate (λ) of steelhead and 

spring Chinook salmon ESUs. They used predation rates estimated from PIT tag detections for 

which reasonable estimates of the number of smolts available to be consumed could be 

generated. Predation rates for 20,000 Caspian terns on four of the five ESA-listed steelhead and 

spring Chinook salmon ESUs were estimated using linear regression. The maximum proportional 

increase in λ corresponding to complete elimination of mortality due to tern predation ranged 

from 1.9% to 4.9% for steelhead ESUs. 

Several factors must be considered when interpreting the results of these calculations. 

Perhaps the most important is that this type of calculation assumes that there is no compensatory 

mortality later in the life cycle, and that any reduction in tern predation is fully realized. In their 

assessment of predation impact by Rice Island terns on salmonids in 1997–1998, Roby et al. 

(2003) hypothesized that tern predation was 50% additive. Given these limitations and 

uncertainties, the estimates of percent change in population growth rates should be viewed as 

maximum potential improvements. Realized improvements in population growth would likely 

70
be lower from any management action that reduces Caspian tern predation impacts on salmonid 

ESUs. 

These results may not be as easy to achieve as they are to calculate. It is important to 

recognize that other factors, such as ocean conditions, may also influence population growth rate 

to a greater degree than the potential gains that may be realized from reducing predation by one 

species of avian predator on one island located in the lower estuary of the Columbia River basin. 

Overall, it is evident that Caspian tern predation primarily affects salmon and steelhead 

that exhibit a stream-type life history rather than an ocean-type life history. This is primarily a 

result of the dominant migratory periods employed by salmonids with a stream-type life history. 

Salmon from this life history type move in great numbers at the time Caspian terns begin nesting 

(May through June) and have the greatest energetic needs for chick production. 

Although there are some impacts to juvenile salmon exhibiting an ocean-type life history, 

characteristic of fall Chinook in the Columbia River basin, the impact is less than for the streamtype salmonids (Roby et al. 2003). Good et al. (2003) concluded that gains in λ for steelhead 

ESUs were comparable to gains that could be derived from additional improvements to the 

FCRPS to increase survival, but much less than can be achieved by harvest modifications. 

Because steelhead ESUs were most strongly affected by Caspian tern predation, improvements 

to λ by managing terns were considered to benefit other salmon ESUs in the basin, albeit to a 

much lesser degree. 

In summary, predation is a major source of mortality of all salmonid populations. 

Although many predator-prey interactions in the Columbia River estuary have probably changed 

from historical conditions (e.g., northern pikeminnow), we have little quantitative data on most 

predator-prey interactions. One exception is the Caspian tern predation which has significantly 

increased recently due to a change in nesting habits of the birds in the Columbia River estuary. 

The main impact of tern predation is on ESUs with stream-type life history types, especially 

steelhead. This is primarily because the dominant migratory periods employed by salmonids 

with a stream-type life history most overlap with the nesting period of the terns. Improvements 

to productivity of populations by managing terns would be expected to benefit stream-type ESUs 

especially, although lesser benefits to other salmonid ESUs in the basin should also occur. 

71
72

Effects of Estuarine Factors on Recovery 

Potential of ESUs 

In this section, ESUs, life history type, life history strategy, limiting factor impacts, 

habitat attributes, and population viability are integrated in order to compare and contrast the 

importance of each limiting factor on population viability. We consider each factor separately 

from the others and do not consider cumulative impacts. All listed ESUs in the Columbia River 

basin are included in addition to lower Columbia River coho salmon because of the possibility 

that this ESU will get listed in the future. The focus of this analysis is on effects of estuarine 

factors on population viability, not on the importance of the estuary relative to other factors 

operating at other life stages. That broader analysis is outside the scope of this review. 

We evaluated effects of factors within two zones of the estuary. Bonneville Dam to the 

river’s mouth was defined as one zone and the plume was considered a second major zone. 

Within the first zone, we also differentiated shallow, low velocity, vegetated habitats from 

medium and deep, higher velocity habitats generally associated with the main channels. We 

were limited to this broadscale analysis because a finer scale evaluation of how juvenile life 

history strategies use habitats and zones is not possible with existing information. 

For example, we know fry and fingerling strategies are more closely associated with 

shallow, low velocity habitats (e.g., swamps, emergent marshes, and shallow flats), while the 

opposite pattern exists for larger size classes such as yearlings, which are more abundant in 

deeper, higher velocity channel habitats (Healey 1980, 1982, Levy and Northcote 1981, 1982, 

Simenstad et al. 1982, Levings et al. 1986, Miller and Sadro 2003). But we do not know how 

different types of shallow water habitats are used (e.g., emergent marsh vs. swamp vs. mudflat) 

within a zone. While differences are likely in use of different habitats between zones, we lacked 

the ability to make this type of discrimination other than between the confined portion of the 

estuary and the plume. 

To guide our evaluation, we used the following hypotheses about use of estuarine habitats 

by juvenile salmon and the effects of specific limiting factors that were developed in previous 

sections: 

1. Tern predation differentially affects the larger yearling strategies, especially steelhead, 

more than smaller life history strategies, such as fingerling Chinook (Ryan et al. 2003). 

Tern predation is assumed to occur in the estuary zone but primarily in medium and deep 

water channel habitat, rather than shallow water areas (Tables 5 and 6). Tern predation is 

assumed to be minimal in the plume. 

2. Mortality of juvenile salmon in the estuary is occurring due to predation by species other 

than terns. We did not consider these other predators in this analysis. 
73

Table 5. Linkages between limiting factors associated with the estuary upstream of the river’s mouth, life history strategie

(ocean-type and stream-type), and ESU (for a complete list see Table 3). Only two general habitat types in the estushallow, low velocity, and medium/deep channel higher velocity. Factors were ranked as having a high, medium, o

the relative abundance of particular life history strategies. 

Shallow, low velocity Deep c

ESU*

Life history type

Life history strategy Flow Habitat Terns Toxics Flow Habitat 

Early fry High High Low Medium Low Low Late fry High High Low Medium Low Low Early fingerling High High Low Medium Low Low Late fingerling High High Low Medium Low Low Subyearling Low Low Medium Low Medium Low 

SR Fall, LCRC, 

Ocean-type 

Yearling Low Low Medium Low Medium Low Early fry Medium Medium Low Low Low Low Late fry Medium Medium Low Low Low Low Early fingerling Medium Medium Low Low Low Low Late fingerling Medium Medium Low Low Low Low Subyearling Low Low Medium Medium Medium Low 

LCRS, UCRSC 

Stream-type 

Yearling Low Low Medium Medium Medium Low 

* Examples: SR Fall = Snake River fall Chinook salmon, LCRC = Columbia River chum salmon, LCRS = lower Columbia River steeColumbia River spring Chinook. 
Table 6. Linkages between limiting factors associated with the plume, life history strategies, life history 

type (ocean-type and stream-type), and ESU (for a complete list, see Table 3). The plume was 

considered as one habitat zone. Factors were ranked as having a high, medium, or low ability to 

affect the relative abundance of particular life history strategies using the plume. 

Plume 

ESU*

Life history 

type

Life history 

strategy Flow Habitat Terns Toxics 

Early fry Low Low Low Low 

Late fry Low Low Low Low 

Early fingerling Medium Low Low Low 

Late fingerling Medium Low Low Low 

Subyearling Medium Low Medium Low 

SR Fall, 

LCRC, 

Ocean-type 

Yearling Medium Low Medium Low 

Early fry Low Low Low Low 

Late fry Low Low Low Low 

Early fingerling Medium Low Medium Low 

Late fingerling Medium Low Medium Low 

Subyearling Medium Low Medium Low 

LCRS, 

UCRSC 

Stream-type 

Yearling Medium Low Medium Low 

* Examples: SR Fall = Snake River fall Chinook salmon, LCRC = lower Columbia River chum salmon, 

LCRS = lower Columbia River steelhead, UCRSC = upper Columbia River spring Chinook. 

3. The main effects of flow reductions are on the amount of shallow water habitat available 

to fish and the opportunity for the fish to use the habitat. The main effect of habitat 

changes is on distribution, quantity, and quality of habitat. The main effect of toxics is 

on habitat quality (capacity). 

4. Any reduction in quality or quantity of shallow water habitat affects smaller juvenile 

salmonids employing strategies such as fry and fingerlings significantly more than 

yearlings (Tables 5 and 6). Changes in the quantity and quality of shallow water habitats 

most impacts viability of ocean-type populations. 

5. Subyearlings use shallow, medium, and deep water habitats, whereas yearlings primarily 

use medium and deep channel habitat. 

6. Fry and early fingerling life history strategies do not make extensive use of the plume, 

but more likely utilize the surf zone when they exit the estuary proper. 

7. Reductions in flow above Bonneville Dam affect the size and shape of the plume. 

Primarily as a result of flow, but also no doubt as a result of physical changes to the 

estuary (eg., dredging and diking), the shape, behavior, size, and composition of the 

plume has been changed. 

8. Toxics impact the quality of habitat, but consequences of toxics can occur downstream of 

where the burden was acquired. The impact, though, is assumed to be associated with the 

habitat where the exposure occurs. 

74
9. Flow and habitat changes in the estuary are interrelated. 

For stream-type ESUs (e.g., Snake River spring/summer Chinook salmon and midColumbia River steelhead), the primary estuarine factors affecting population viability are tern 

predation and flow (Tables 7, 8, and 9). Tern predation was ranked in the medium category for 

several reasons. First, tern predation is primarily directed at subyearling and yearling size fish, 

which are the dominant strategies in stream-type ESUs such as Snake River steelhead. Second, 

these larger fish occur in habitats (deeper water channel habitats) where they are most vulnerable 

to the terns. Third, these larger fish migrate at a time when they are most susceptible to tern 

predation. Fourth, tern predation significantly affects abundance and productivity; scores for 

these parameters were doubled if we concluded there was an affect. Based on anecdotal 

observations of NOAA Fisheries Service working in the Columbia River plume, we assumed that 

most tern predation occurred upstream of the river mouth. If significant predation did occur in 

the plume, then the score for this factor would increase. 

Flow changes were also ranked medium for stream-type ESUs because both abundance 

and productivity were affected. Further, the main life history strategies for these ESUs are 

abundant in the plume, where they are most vulnerable to flow-related changes in plume habitat. 

Table 7. Summary rating table for listed Columbia River basin ESUs for estuary factors. Ranks were 

assigned based on the following ranges: low (<0.34), medium (0.34–0.66), and high (0.67–1.00). 

Life history type Stream-type Ocean-type 

ESUs Snake River spring/summer Chinook Columbia River chum salmon 

Upper Columbia River Chinook Snake River fall Chinook 

Snake River steelhead Upper Willamette River Chinook 

Upper Columbia River steelhead Lower Columbia River fall Chinook 

Middle Columbia River steelhead 

Lower Columbia River steelhead 

Upper Willamette River steelhead 

Upper Snake River sockeye 

Lower Columbia River coho salmon 

Factor for stream-type Factor for ocean-type 

Tern 

predation Toxics Habitat Flow 

Tern 

Rating level predation Toxics Habitat Flow 

Level 1 6 5 4 7 3 5 8 7 

Level 2 6 2 0 3 2 6 6 7 

Total score 12 7 4 10 5 11 14 14 

Total possible 20 28 20 20 20 28 20 20 

Ratio 0.60 0.25 0.20 0.50 0.25 0.39 0.70 0.70 

Rank Medium Low Low Medium Low Medium High High 

75
76

Table 8. Level 1 ratings of estuary factors for stream-type ESUs (Snake River spring/summer Chinook, 

upper Columbia River Chinook, Snake River steelhead, upper Columbia River steelhead, middle 

Columbia River steelhead, lower Columbia River steelhead, upper Willamette River steelhead, 

upper Snake River sockeye, and lower Columbia River coho salmon). An answer to a question of 

yes equals a 1 other than for the VSP criteria of productivity and abundance, which are scored a 2 

for yes. An answer of no equals a zero. 

 Factor 

Screening criteria

Tern 

predation Toxics Habitat Flow 

Level 1—Is the factor of concern for the ESU? 

 What is the relevance of the factor to the ESU? 

 Are there large numbers of fish affected? (2x) 2 2 0 2 

 Is there a significant affect on productivity? (2x) 2 2 0 2 

 Is there a significant affect on LH diversity? 0 0 1 1 

 Is there a significant affect on spatial structure? 0 0 1 1 

 What is the level of change possible in factor? 

 Is there a significant change from historical levels? 1 1 1 1 

 Is the amount of improvement possible substantial? 1 0 1 0 

Score 6 5 4 7 

Maximum Possible Score 8 8 8 8 

Toxics and habitat were ranked low for stream-type ESUs because the main life history strategies 

associated with them do not occupy the habitat where the main effects occurs, although there 

may be some risk associated with short-term exposure to waterborne contaminants for these fish. 

For ocean-type ESUs (lower Columbia River fall Chinook salmon and Columbia River 

chum), flow and habitat were rated as having a high ability to affect population viability (Tables 

7, 10, and 11). Flow and habitat affects are most significant in shallow water areas; both the 

quantity of habitat and the opportunity to use this habitat are affected. Finally, both the flow and 

habitat limiting factors affect all VSP parameters for ocean-type populations. The loss of 

shallow water habitat and changes in its distribution and quality caused by flow and habitat 

changes will reduce the capacity of estuarine habitats to support ocean-type populations; this will 

reduce abundance and productivity of these populations. Further, loss and degradation of 

shallow water habitat will also diminish the spatial structure and number of life history pathways 

available to the fish. This has the potential to make these populations more vulnerable to effects 

of extreme events such as severe droughts or strong El Niño events. As we have noted, the 

losses of shallow water habitats due to the combined effects of flow and habitat changes are 

dramatic while losses of deeper water habitats appear to be minimal. 

Flow and habitat also have a significant affect on ocean-type populations because these 

populations are dominated by small size classes (fry and fingerlings) that make extensive use of 

shallow water habitats and have the longest residence time in the estuary (i.e., they are most 

dependent on shallow water habitats) (e.g., Bottom et al. 2005). A major function of these 

shallow water habitats for these small size classes is to support their feeding and growth; high 
77

Table 9. Level 2 ratings of estuary factors for stream-type ESUs (Snake River spring/summer Chinook, upper Columbia R

River steelhead, upper Columbia River steelhead, middle Columbia River steelhead, lower Columbia River steelhe

River steelhead, upper Snake River sockeye, and lower Columbia River coho salmon). With the exception of toxicanswer to a question with a yes equals a 1. An answer of no equals a zero. 

Terns Toxicsa Habitat 

Screening criteria SWb DW Pl SW DW Pl SW DW Pl 

Level 2—Significance of factor  For the dominate LHS, is the relative impact on numbers  by habitat type significant? 1 1 1 1  For the dominate LHS, does the factor significantly affect habitat? 

1 

 1. Quantity  2. Quality  3. Opportunity 1 1 1 

Score 2 2 2 0 2 0 0 0 0 Total factor score 6 2 0 Maximum possible score 12 20 12 a Scores for toxics include a value for sediment and water in estuary (i.e., the SW quality score can be a 2 and water in the plume. b SW = Shallow water from the river’s mouth to Bonneville Dam; DW = Deep water from the river’s mouth to Bonneville Dam; Pl = P
78

Table 10. Level 1 ratings of estuary factors for ocean-type ESUs (lower Columbia River chum salmon, 

upper Willamette River Chinook, lower Columbia River fall Chinook, and Snake River fall 

Chinook). An answer to a question of yes equals a 1 other than productivity and abundance, 

which are scored a 2 for a yes. An answer of no equals a zero. 

 Factor 

Screening criteria

Tern 

predation Toxics Habitat Flow 

Level 1—Is the factor of concern for the ESU? 

 What is the relevance of the factor to the ESU? 

 Are there large numbers of fish affected? (2x) 0 2 2 2 

 Is there a significant affect on productivity? (2x) 0 2 2 2 

 Is there a significant affect on LH diversity? 1 0 1 1 

 Is there a significant affect on spatial structure? 0 0 1 1 

 What is the level of change possible in factor? 

 Is there a significant change from historical levels? 1 1 1 1 

 Is the amount of improvement possible substantial? 1 0 1 0 

Score 3 5 8 7 

Maximum Possible Score 8 8 8 8 

growth rates experienced here can help population members avoid (i.e., outgrow) some of the 

predation that these small fish experience (Simenstad et al. 1982). Yearling and subyearling fish 

are generally not abundant in the habitats where they are most vulnerable to the effects of these 

two factors. Because relatively few stream-type fish use shallow water habitats, we predict that 

flow and habitat will have less of an effect on capacity of these habitats to rear and support 

stream-type populations, but a more significant affect on diversity and spatial structure of these 

populations (Table 7). Because of the loss of shallow water, estuarine dependent strategies (i.e., 

fry and fingerlings), the number and quality of the life history trajectories expressed by these 

populations will decline. 

Effects of toxic contamination on ocean-type ESUs was rated medium. Both waterborne 

and sediment contaminants can affect these life history strategies in shallow water areas where 

the dominant life history strategies are most abundant. We assumed that toxics impact the 

quality of habitat upstream of the river mouth and that there was not significant affects in the 

plume. The consequences of the uptake of toxics can occur downstream of where the burden 

was acquired. We assumed the impact was associated with the habitat where the exposure 

occurred. Tern predation has a low effect on these ESUs because terns do not target fry and 

fingerling strategies (the dominant ones associated with these ESUs). 
Terns Toxicsa Habita

79

Table 11. Level 2 ratings of estuary factors for ocean-type ESUs (lower Columbia River chum salmon, upper Willamette R

Columbia River fall Chinook, and Snake River fall Chinook). With the exception of toxics (see footnote), an answ

yes equals a 1. An answer of no equals a zero. 

Screening criteria SWb DW Pl SW DW Pl SW DW 

Level 2—Significance of factor  For the dominate LHS, is the relative impact on numbers  significant by habitat type? 1 2 1 1  For the dominate LHS, does the factor significantly  affect habitat?  1. Quantity 1  2. Quality 1 2 1 1  3. Opportunity 1 Score 2 0 0 4 2 0 4 0 Total factor score 2 6 6 

12 20 12 

a Scores for toxics include a value for both sediment and water in estuary (i.e., the SW quality score can be a 2 and water only in the plub SW = Shallow water from the river’s mouth to Bonneville Dam; DW = Deep water from the river’s mouth to BonnevilleDam; Pl = Pl

Maximum possible score 
Other Considerations in Evaluating 

the Role of the Estuary in Recovery 

of Anadromous Salmonids 

Data Gaps 

While our intent in this report was not to define all major information needs (this is done 

more comprehensively by Bottom et al. 2005), there were several data gaps that notably 

constrained our ability to analyze effects of factors on population viability, that are important to 

highlight. One of these is the lack of information on juvenile salmon use of the estuary by 

different populations, especially how salmon use different geographic zones and different 

habitats within each zone. This is particularly true of the upper estuary above Jones Beach 

where sampling has been very limited. Because of this lack of habitat and zone-specific data, we 

had to assume that all shallow water areas are similarly used between the river’s mouth and 

Bonneville Dam. We expect that the results of ongoing research conducted by NOAA Fisheries 

Service will significantly increase our understanding of the use of different estuarine habitats and 

zones. 

A second major data gap was the lack of knowledge regarding adult salmon use of the 

estuary. Our entire analysis was based on juvenile salmon use of the estuary. Although it seems 

reasonable to hypothesize that some of the factors we considered could impact adult salmon in 

the estuary, we had no information on adult salmon and their use of estuarine habitats. For 

example, adult salmon are probably exposed to toxics in the estuary with unknown effects, while 

changes in flow attributes may alter the timing of adult salmon migrations and expose them to 

predators such as marine mammals for longer periods. 

A third major data gap was that we were only able to consider the effects of four factors 

on population viability. The selection of these four factors was based on the relative effects of 

each limiting factor within the estuary and plume and the availability of empirical information to 

include in the evaluation. These four factors were not selected because we felt that they would 

have the most significant impact; some of the factors not included may have a considerable 

affect on population viability of some ESUs. For example, we expect that estuarine water 

temperatures have warmed from historical levels, which could affect metabolic processes of both 

salmon and their predators. These changes could increase mortality rates of salmon while in the 

estuary. Further, warmer water temperatures may exclude some habitats from use by juveniles 

during part of the year. 

A fourth important data gap is our lack of knowledge of habitat changes in the upper 

estuary (above RM 46). Quantitative analyses by Thomas (1983) and others have been limited to 

the lower estuary and have not quantified the nature and extent of habitat changes in this large 

80
portion of the estuary. Finally, with the exception of tern predation, we were unable to quantify 

the effects of other predators. 

Hatchery Fish Effects 

We did not consider any potential effects of the large numbers of anadromous salmonids 

released from hatcheries throughout the Columbia River basin that pass through the estuary. 

There are several possible implications of these releases. First, because our ability to distinguish 

wild and hatchery fish captured in the estuary has been limited, and remains so even at present, 

many of the spatial and temporal patterns of habitat use suggested by historical data sets may 

apply to hatchery fish rather than wild fish (Dawley et al. 1985, 1986). For example, the large 

peak in abundance of juveniles in the estuary reported by Burke (2005) in July is probably 

comprised largely of hatchery fish. 

Second, hatchery salmonids can potentially affect the growth and survival of wild 

salmonids in a variety of ways (Fresh 1997). Large numbers of hatchery fish co-occurring with 

wild fish might actually increase survival of wild fish by buffering them from predators such as 

Caspian terns. In addition, hatchery fish can reduce growth and survival of wild fish by 

competing for food resources. Some of the larger hatchery salmonids could prey on wild fish. 

Northern Pikeminnow Predation on Juvenile Salmonids 

As we noted previously, many predator-prey interactions in the Columbia River estuary 

involving juvenile salmon have potentially changed from historical conditions. We treated 

predation by Caspian terns on juvenile salmonids as a “full” limiting factor because it met our 

criteria for inclusion. While other predators were not included because they did not meet our 

criterion, one predator that nearly had enough information to include as a limiting factor was 

northern pikeminnow. We include a discussion here of predation by northern pikeminnow as 

another example of the effects of a predator. 

Northern pikeminnow are relatively large, long-lived, slow-growing, predaceous 

minnows native to the Columbia River basin and other parts of the Pacific Northwest. Maximum 

fork length, weight, and age are approximately 600 mm, 2.5 kg, and at least 16 years in the 

Columbia River (Parker et al. 1995). Large, old individuals typically dominate unexploited 

populations of northern pikeminnow. Juvenile salmonids are generally an important diet 

component only for these large, old northern pikeminnow (Vigg et al. 1991, Zimmerman 1999), 

and consumption rates of juvenile salmonids by northern pikeminnow increase as size increases. 

Zimmerman (1999) found that fish consumed by northern pikeminnow in all reaches of the 

Columbia River were overwhelmingly juvenile salmonids, and that numerical frequency of 

Chinook salmon greatly exceeded that of steelhead. Daily consumption of juvenile salmonids 

was greater in summer than in spring. 

Development of the hydropower system in the Columbia River basin has resulted in 

increased losses of juvenile salmonids to northern pikeminnow. At dams, migrating juvenile 

salmonids are concentrated in forebays and tailraces, causing increased predation and salmonid 

loss (Poe et al. 1991, Vigg et al. 1991, Ward et al. 1995). Migration past dams also causes injury 

and physiological stress, which may increase the vulnerability of salmonids to predators (Mesa 

81
1994). Impoundments increase travel time for migrating juvenile salmonids, prolonging their 

exposure to predators (Raymond 1988, Poe et al. 1991). 

Significant losses of juvenile salmonids occur downstream of Bonneville Dam. 

Beamesderfer et al. (1996) estimated that about 10 million juvenile salmonids were consumed 

annually by northern pikeminnow in the Columbia River downstream from Bonneville Dam 

prior to implementation of a Northern Pikeminnow Management Program (NPMP). This was 

about 5% of the approximately 200 million juvenile salmonid migrants in the Columbia River 

basin, but a much higher percentage of salmonids that reached the river downstream from 

Bonneville Dam. This estimated loss exceeded the total estimate for the remainder of the lower 

Columbia and Snake rivers. Estimates of predation losses were relatively unbiased by 

consumption of juvenile salmonids killed by dam passage (Gadomski and Hall-Griswold 1992, 

Petersen et al. 1994). Abundance of northern pikeminnow downstream from Bonneville Dam 

greater than 250 mm fork length likely ranged from 600,000 to 800,000 individuals 

(Beamesderfer et al. 1996). 

Unlike other resident fish predators, population dynamics and behavior of northern 

pikeminnow indicate that reductions in predation through a removal program are feasible. The 

NPMP began in 1990, based on findings from the earlier work conducted in John Day Reservoir 

(Rieman and Beamesderfer 1990, Poe et al. 1991, Vigg et al. 1991, Beamesderfer and Rieman 

1991, Rieman et al. 1991). Since 1990 over 750,000 northern pikeminnow have been removed 

from the Columbia River downstream from Bonneville Dam. Abundance of large northern 

pikeminnow downstream from Bonneville Dam has been reduced to about 500,000 individuals. 

Based on changes in the population structure of northern pikeminnow resulting from this harvest, 

Friesen and Ward (1999) estimated that predation on juvenile salmonids by northern 

pikeminnow was reduced by approximately 25% annually. 

Empirically derived estimates of predation indicate that reductions since implementation 

of the NPMP may be more substantial. Zimmerman and Ward (1999) estimated that predation 

from 1994 to 1996 was about 50% of predation in 1992. Zimmerman et al. (2000) reported 

similar results for 1999. 

The major uncertainties that precluded our including northern pikeminnow predation as a 

limiting factor were: 

1. Uncertainty about historical levels of predation in this reach of the river. While the high 

levels of predation in the tailrace of Bonneville Dam is a change from historical levels, 

we could not determine whether predation downstream of this point had increased from 

historical levels. 

2. Uncertainty about where predation occurs. While predation is generally regarded as most 

significant in littoral areas this is defined as depth less than 13m. We could not 

determine more specifically where predation in the littoral areas was occurring. 

3. Uncertainty about what size classes were affected in the portion of the river. While 

Zimmerman (1999) provides data on size of salmonids eaten by northern pikeminnow 

throughout the basin, we could not determine what sizes of salmonids were being eaten in 

the river below Bonneville Dam. 

82
Direct Affects of the Hydropower System on the Estuary 

One of the outcomes of this analysis is that we identified a clear linkage between 

hydropower operations and two of the factors we considered: flow and habitat. We did not 

consider the operation of the hydropower system to have a direct affect on either toxics or tern 

predation other than by perhaps increasing travel time and hence exposure of the fish to both 

predators and toxics. We concluded that most of the flow changes and some of the changes in 

habitat in the estuary could be directly attributed to affects (e.g., reduction in magnitude of the 

spring freshets) of the FCRPS. 

For example, reductions in flow can permanently eliminate some habitats from use by 

estuarine dependent life history strategies. Even though the habitat may not be diked, it becomes 

functionally “too high” in elevation for the fish to use because of reductions in flow. In addition, 

because there is a relationship between flow and habitat, the value of some habitats can be 

diminished by a reduction in flow because it becomes accessible for less time than under 

historical conditions. Many attributes of the plume environment are also directly affected by the 

hydropower system including the size, shape, and seasonal movements. 

While some of the affects of the hydropower system in the estuary could potentially be 

mitigated by altering flow regimes (e.g., increasing flows in spring and summer), there are 

clearly a variety of other consequences that would need to be considered with such changes (e.g., 

an increase in gas bubble disease). Some habitat changes not directly linked to affects of the 

hydropower system are possible, however. This involves restoring some of the shallow water 

habitat used by ocean-type ESUs and the fry and fingerling portions of stream-type ESUs that 

have been isolated from the system by levees and dikes. Dikes permanently isolate this habitat 

and make either direct use by the juvenile salmonids (access) or indirect use (organic matter 

transport) impossible. Breaching or leveling dikes is clearly a strategy that can be used to restore 

some of the shallow water habitat important to these shallow water dependent strategies. 

How Much Change Is Necessary to Affect Population Status 

From the perspective of the estuary, population viability of stream-type ESUs is most 

affected by tern predation and flow, while ocean-type ESUs are most affected by flow and 

habitat. At this time, we do not know how much of a change in each factor is required to affect 

viability of relevant ESUs. Probably the greatest opportunity to affect ESUs by manipulating 

one of these factors is by restoring lost, shallow water, low velocity, vegetated habitat (e.g., 

emergent marsh). This is because there is a strong linkage between dominant life history 

strategies of ocean-type ESUs and shallow water habitat. A large amount of that habitat type has 

been lost due to diking. Clearly, restoration of some shallow water habitat can be done without 

changing hydropower operations. 

While more shallow water habitat could be made available with flow changes, this would 

have to be very carefully considered because it could have other, unintended consequences such 

as an increase in gas bubble disease. We must also recognize that any questions about how much 

restoration is needed must address the question of how much change is possible. There are now 

constraints on the system such as climate change and “permanent” changes in the landscape such 

as from urbanization that clearly constrain how much change is possible; a return to 

83
presettlement conditions is unreasonable to expect. We expect that studies now underway will 

provide more insight into how much change in shallow water habitat is both possible and needed. 

Our analyses did not attempt to compare the ability of estuary factors and nonestuary 

factors to affect viability. The analysis by Kareiva et al. (2000) and more recent analyses suggest 

that the estuary and plume environment are generally important to the productivity of 

anadromous populations. In general, recovery is a life cycle process that requires strategies that 

focus on crafting and evaluating alternative scenarios involving all life stages of the animals. 

Thus addressing estuarine factors can potentially improve population status and help 

recovery and should be included in any comprehensive plans for recovering populations in the 

basin. A variety of factors (such as landscape connectivity within and between habitat zones) 

will need to be considered in deciding how to distribute recovery efforts directed at any suite of 

limiting factors. Any recovery actions directed at shallow water habitats will also need to 

consider the cumulative effects of all factors affecting ocean-type populations in these habitats. 

For example, some recovery actions directed at habitat restoration in shallow water areas may 

need to simultaneously reduce toxic contamination if sites targeted for restoration are found to be 

contaminated. 

84
References 

Able, K. W., P. Rowe, M. Burias, and D. Byrne. 2003. Use of ocean and estuarine habitats by young-ofthe-year bluefish (Pomatomus saltatrix) in the New York Bight. Fish. Bull. 101:201–214. 

Allison, D., B. J. Kallman, O. B. Cope, and C. V. Valin. 1963. Insecticides: Effects on cutthroat trout of 

repeated exposure to DDT. Science 142:958–961. 

Anthony, R. G., M. G. Garrett, and C. Schuler. 1993. Environmental contaminants in bald eagles in the 

Columbia River estuary. J. Wildl. Manag. 57:10–19. 

Arkoosh, M. Unpubl. data. Data from study on pathogen prevalence and contaminant body burdens in 

juvenile outmigrant salmon, May 2002. (Available from M. Arkoosh, NWFSC, Newport 

Research Station, 2032 SE OSU Drive, Newport, OR 97365.) 

Arkoosh, M. R., E. Casillas, E. Clemons, P. Huffman, A. N. Kagley, T. Collier, and J. E. Stein. 2001. 

Increased susceptibility of juvenile Chinook salmon to vibriosis after exposure to chlorinated and 

aromatic compounds found in contaminated urban estuaries. J. Aquat. Anim. Health 13:257–268. 

Arkoosh, M. R., E. Casillas, E. Clemons, B. McCain, and U. Varanasi. 1991. Suppression of 

immunological memory in juvenile Chinook salmon (Oncorhynchus tshawytscha) from an urban 

estuary. Fish Shellfish Immunol. 1:261–277. 

Arkoosh, M. R, E. Casillas, P. Huffman, E. Clemons, J. Evered, J. E. Stein, and U. Varanasi. 1998. 

Increased susceptibility of juvenile Chinook salmon from a contaminated estuary to Vibrio 

anguillarum. Trans. Am. Fish. Soc. 127:360–374. 

Arkoosh, M. R., E. Clemons, A. N. Kagley, C. Stafford, A. C. Glass, K. Jacobson, P. Reno, M. S. Myers, 

E. Casillas, L. L. Johnson, and T. K. Collier. 2004. Ecological epizootiology of pathogens in 

juvenile Pacific salmon: I. Parasites of salmonid (Oncorhynchus spp.) populations from Pacific 

Northwest estuaries. J. Aquat. Anim. Health 16:186–196. 

Arkoosh, M. R., E. Clemons, M. Myers, and E. Casillas. 1994. Suppression of B-cell mediated 

immunity in juvenile Chinook salmon (Oncorhynchus tshawytscha) after exposure to either a 

polycyclic aromatic hydrocarbon or to polychlorinated biphenyls. Immunopharmacol. 

Immunotoxicol. 16:293–314. 

Arukwe, A., T. Celius, B. T. Walther, and A. Goksoeyr. 1998. Plasma levels of vitellogenin and eggshell 

zona radiata proteins in 4-nonphenyl and o,p’-DDT treated juvenile Atlantic salmon (Salmo 

salar). Mar. Environ. Res. 46:133–136. 

Arukwe, A., T. Celius, B. T. Walther, and A. Goksoeyr. 2000. Effects of xenoestrogen treatment on 

zona radiata protein and vitellogenin expression in Atlantic salmon (Salmo salar). Aquat. 

Toxicol. 49:159–170. 

Bailey, J. E., B. L. Wing, and C. R. Mattson. 1975. Zooplankton abundance and feeding habits of fry of 

pink salmon Oncorhynchus gorbuscha and chum salmon O. keta in Traitors Cove, Alaska, with 

speculations on the carrying capacity of the area. Fish. Bull. 73:846–861. 

85
Baldwin, D. H., J. F. Sandahl, J. S. Labenia, and N. L. Scholz. 2003. Sublethal effects of copper on coho 

salmon: Impacts on nonoverlapping receptor pathways in the peripheral olfactory nervous system. 

Environ. Toxicol. Chem. 22:2266–2274. 

Baptista, A. M. 2005. Estuarine habitat opportunity. In D. L. Bottom, C. A. Simenstad, J. Burke, A. M. 

Baptista, D. A. Jay, K. K. Jones, E. Casillas, and M. H. Schiewe. Salmon at river’s end: The role 

of the estuary in the decline and recovery of Columbia River salmon. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-68. 

Barnes, C., A. C. Duxbury, and B. A. Morse. 1972. Circulation and selected properties of the Columbia 

River plume at sea. In A. T. Pruter and D. L. Alverson (eds.), The Columbia River estuary and 

adjacent ocean waters, p. 41–80. University of Washington Press, Seattle. 

Bax, N. 1983. Early marine mortality of marked juvenile chum salmon (Oncorhynchus keta) released 

into Hood Canal, Puget Sound, Washington, in 1980. Can. J. Fish. Aquat. Sci. 40:426–435. 

Beachum, T. D., and C. B. Murray. 1987. Adaptive variation in body size and developmental biology of 

chum salmon (Oncorhynchus keta) in British Columbia. Can. J. Fish. Aquat. Sci. 44:244–262. 

Beamer, E., A. McBride, C. Greene, R. Henderson, G. Hood, K. Wolf, K. Larsen, C. Rice, and K. L. 

Fresh. 2005. Delta and nearshore restoration for the recovery of wild Skagit River Chinook 

salmon: Linking estuary restoration to wild Chinook salmon populations. Supplement to Skagit 

Chinook Recovery Plan. June 17, 2005. Skagit River System Cooperative, La Conner, WA. 

Beamesderfer, R. C., and B. E. Rieman. 1991. Abundance and distribution of northern squawfish, 

walleyes, and smallmouth bass in John Day Reservoir, Columbia River. Trans. Am. Fish. Soc. 

120:439–447. 

Beamesderfer, R. C., D. L. Ward, and A. A. Nigro. 1996. Evaluation of the biological basis for a 

predator control program on northern squawfish (Ptychocheilus oregonensis) in the Columbia and 

Snake rivers. Can. J. Fish. Aquat. Sci. 53:2898–2908. 

Beamish, R. J., and D. R. Bouillon. 1993. Pacific salmon production trends in relation to climate. Can. 

J. Fish. Aquat. Sci. 50:1002–1016. 

Beamish, R. J., D. J. Noakes, G. A. McFarlane, L. Klyashtorin, V. V. Ivanov, and V. Kurashov. 1999. 

The regime concept and natural trends in the production of Pacific salmon. Can. J. Fish. Aquat. 

Sci. 56:516–526. 

Beckman, B. R., D. A. Larsen, and W. W. Dickhoff. 2003. Life history plasticity in Chinook salmon: 

Relation of size and growth rate to autumnal smolting. Aquaculture 222:149–165. 

Beechie, T. J., and S. Bolton. 1999. An approach to restoring salmonid habitat-forming processes in 

Pacific Northwest watersheds. Fisheries 24(4):6–15. 

Beechie, T. J., G. Pess, E. Beamer, G. Lucchetti, and R. E. Bilby. 2003a. Role of watershed assessments 

in recovery planning for salmon. In D. R. Montgomery, S. B. Bolton, D. B. Booth, and L. Wall 

(eds.), Restoration of Puget Sound rivers, p. 194–225. University of Washington Press, Seattle. 

Beechie, T. J., E. A. Steel, P. R. Roni, and E. Quimby (eds.). 2003b. Ecosystem recovery planning for 

listed salmon: An integrated assessment approach for salmon habitat. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-58. 

86
Bisbal, G. A., and W. E. McConnaha. 1998. Consideration of ocean conditions in the management of 

salmon. Can. J. Fish. Aquat. Sci. 55:2178–2186. 

Bonn, B. A. 1998. Dioxins and furans in bed sediment and fish tissue of the Willamette Basin, Oregon, 

1992–1995. U.S. Geological Survey Water Resources Investigations Report 97-4082. U.S. 

Geological Survey, Portland, OR. 

Borde, A. B., R. M. Thom, S. Rumrill, and L. M. Miller. 2003. Geospatial habitat change analysis in 

Pacific Northwest coastal estuaries. Estuaries 26(4B):1104–1116. 

Bortleson, G. C., S. E. Cox, M. D. Munn, R. J. Schumaker, E. K. Block, L. R. Bucy, and S. B. Cornelius. 

1994. Sediment-quality assessment of Franklin D. Roosevelt Lake and the upstream reach of the 

Columbia River, Washington, 1992. U.S. Geological Survey Open-File Rep. 94–315. U.S. 

Geological Survey, Tacoma, WA. 

Bottom, D. L. 1997. To till the water: A history of ideas in fisheries conservation. In D. J. Stouder, P. A. 

Bisson, and R. J. Naiman (eds.), Pacific salmon and their ecosystems, p. 569–597. Chapman and 

Hall, New York. 

Bottom, D. Unpubl. data. Columbia River estuary juvenile salmon studies. (Available from D. Bottom, 

NWFSC, Newport Research Station, 2032 SE OSU Drive, Newport, OR 97365.) 

Bottom, D. L., and K. K. Jones. 1990. Species composition, distribution, and invertebrate prey of fish 

assemblages in the Columbia River estuary. Prog. Oceanogr. 25:243–270. 

Bottom, D. L., K. K. Jones, and M. J. Herring. 1984. Fishes of the Columbia River estuary. Internal 

report. Columbia River Data Development Program. (Available from Columbia River Estuary 

Study Task Force, 750 Commercial St., Astoria, OR 97103.) 

Bottom, D. L., C. A. Simenstad, J. Burke, A. M. Baptista, D. A. Jay, K. K. Jones, E. Casillas, and M. H. 

Schiewe. 2005. Salmon at river’s end: The role of the estuary in the decline and recovery of 

Columbia River salmon. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-68. 

Brannon, E. L., M. S. Powell, T. P. Quinn, and A. Talbot. 2004. Population structure of Columbia River 

basin Chinook salmon and steelhead trout. Rev. Fish. Sci. 12:99–232. 

Brown, D. H., B. B. McCain, B. H. Horness, C. A. Sloan, K. L. Tilbury, S. M. Pierce, D. Burrows, S-L 

Chan, J. T. Landahl, and M. M. Krahn. 1998. Status, correlations and temporal trends of 

chemical contaminants in fish and sediment from selected sites on the Pacific Coast of the USA. 

Mar. Pollut. Bull. 37(1–2):67–85. 

Buhler, D. R., M. E. Rasmusson, and W. E. Shanks. 1969. Chronic oral DDT toxicity in juvenile coho 

and Chinook salmon. Toxicol. Appl. Pharmacol. 14:535–555. 

Burdick, G. E., E. J. Harris, H. J. Dean, T. M. Walker, J. Skea, and D. Colby. 1964. The accumulation of 

DDT in lake trout and the effect on reproduction. Trans. Am. Fish. Soc. 93:127–136. 

Burger, C. V., R. L. Wilmot, and D. B. Wangaard. 1985. Comparison of spawning areas and times for 

two runs of Chinook salmon (Oncorhynchus tshawytscha) in the Kenai River, Alaska. Can. J. 

Fish. Aquat. Sci. 42:693–700. 

87
Burgner, R. L. 1991. Life history of sockeye salmon (Oncorhynchus nerka). In C. Groot and L. 

Margolis (eds.), Pacific salmon life histories, p. 1–117. University of British Columbia Press, 

Vancouver. 

Burke, J. 2005. Life histories of juvenile Chinook salmon in the Columbia River estuary, 1916 to the 

present. Masters thesis. Oregon State University, Corvallis. 

Busby, P. J., T. C. Wainwright, G. J. Bryant, L. J. Lierheimer, R. S. Waples, F. W. Waknitz, and I. V. 

Lagomarsino. 1996. Status review of West Coast steelhead from Washington, Idaho, and 

California. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-27. 

Carl, C. M., and M. C. Healey. 1984. Differences in enzyme frequency and body morphology among 

three juvenile life history types of Chinook salmon (Oncorhynchus tshawytscha) in the Nanaimo 

River, British Columbia. Can. J. Fish. Aquat. Sci. 41:1070–1077. 

Carter, V., F. C. Golet, and E. T. LaRoe. 1979. Classification of wetlands and deepwater habitats of the 

United States. FWS/OBS-79-31. U.S. Fish and Wildlife Service, Biological Services Program, 

Washington, DC. 

Casillas E., M. R. Arkoosh, E. Clemons, T. Hom, D. Misitano, T. K. Collier, J. E. Stein, and U. Varanasi. 

1995. Chemical contaminant exposure and physiological effects in out-migrant juvenile Chinook 

salmon from selected urban estuaries of Puget Sound, Washington. In M. Keefe (ed.), Salmon 

ecosystem restoration: Myth and reality: Proceedings of the 1994 Northeast Pacific Chinook and 

Coho Salmon Workshop, p. 85–102. American Fisheries Society, Oregon Chapter, Corvallis, 

OR. 

Casillas, E., B-T. L. Eberhart, T. K. Collier, M. M. Krahn, and J. E. Stein. 1998a. Exposure of juvenile 

Chinook salmon to chemical contaminants specific to the Hylebos Waterway: Tissue 

concentrations and biochemical responses. Interpretive report prepared for NOAA Damage 

Assessment Center. Online at http://www.darp.noaa.gov/northwest/cbay/admin.html [accessed 

18 March 2005]. 

Casillas, E., B-T. L. Eberhart, F. C. Sommers, T. K. Collier, M. M. Krahn, and J. E. Stein. 1998b. 

Effects of chemical contaminants from the Hylebos Waterway on growth of juvenile Chinook 

salmon. Interpretive report prepared for NOAA Damage Assessment Center. Online at 

http://www.darp.noaa.gov/northwest/cbay/admin.html [accessed 18 March 2005]. 

CCME (Canadian Council of Ministers of the Environment). 2002. The Canadian sediment quality 

guidelines for the protection of aquatic life. National Guidelines and Standards Office, 

Environment Canada, Ottawa. 

Celius, T., and B. T. Walther. 1998. Differential sensitivity of zonagenesis and vitellogenesis in Atlantic 

salmon (Salmo salar L) to DDT pesticides. J. Exp. Zool. 281:346–353. 

Chatters, J. C., and K. A. Hoover. 1986. Changing late Holocene flooding frequencies on the Columbia 

River, Washington. Quat. Res. 26:309–320. 

Chatters, J. C., and K. A. Hoover. 1992. Response of the Columbia River fluvial system to Holocene 

climate change. Quat. Res. 37:42–59. 

88
Christiansen, L. B., K. L. Pedersen, S. N. Pedersen, B. Korsgaard, and P. Bjerregaard. 2000. In vivo 

comparison of xenoestrogens using rainbow trout vitellogenin induction as a screening system. 

Environ. Toxicol. Chem. 19:1867–1874. 

Church, M., and D. G. McLean. 1992. Sedimentation in the lower Fraser River, British Columbia: 

Implications for management in large alluvial rivers. In S. A. Schumm and B.R. Winkley (eds.), 

The variability of large alluvial rivers, p. 221–241. American Society of Civil Engineers Press, 

New York. 

Collier, T. K., L. L. Johnson, C. M. Stehr, M. S. Myers, M. M. Krahn, and J. E. Stein. 1998a. Fish injury 

in the Hylebos Waterway of Commencement Bay, Washington. U.S. Dept. Commer., NOAA 

Tech. Memo. NMFS-NWFSC-36. 

Collier, T. K., L. L. Johnson, C. M. Stehr, M. S. Myers, and J. E. Stein. 1998b. A comprehensive 

assessment of the impacts of contaminants on fish from an urban waterway. Mar. Environ. Res. 

46:243–247. 

Collins, B. D., D. R. Montgomery, and A. J. Sheikh. 2003. Reconstructing the historical riverine 

landscape of the Puget lowland. In D. R. Montgomery, S. B. Bolton, D. B. Booth, and L. Wall 

(eds.), Restoration of Puget Sound rivers, p. 79–128. University of Washington Press, Seattle. 

Collis, K., D. D. Roby, D. P. Craig, S. L. Adamany, J. Y. Adkins, and D. E. Lyons. 2002. Colony size 

and diet composition of piscivorous waterbirds on the lower Columbia River: Implications for 

losses of juvenile salmonids to avian predation. Trans. Am. Fish. Soc. 131:537–550. 

Collis, K., D. D. Roby, D. P. Craig, B. A. Ryan, and R. D. Ledgerwood. 2001b. Colonial waterbird 

predation on juvenile salmonids tagged with passive integrated transponders in the Columbia 

River estuary: Vulnerability of different salmonid species, stocks, and rearing types. Trans. Am. 

Fish. Soc. 130:385–396. 

Collis, K., D. D. Roby, D. E. Lyons, R. M. Suryan, M. Antolos, S. K. Anderson, A. M. Meyers, and M. 

Hawbecker. 2001a. Caspian tern research on the lower Columbia River: Final 2001 summary. 

Columbia Bird Research. Online at www.columbiabirdresearch.org [accessed 30 August 2004]. 

Curry, R. A., D. Sparks, and J. van de Sande. 2002. Spatial and temporal movements of a riverine brook 

trout population. Trans. Am. Fish. Soc. 131:551–560. 

Cuthbert, F. J., and L. R. Wires. 1999. Caspian tern (Sterna caspia). In A. Poole and F. Gill (eds.), The 

birds of North America. No. 403. The Birds of North America, Inc., Philadelphia, PA. 

Dawley, E. M., R. D. Ledgerwood, T. H. Blahm, C. W. Sims, J. T. Durkin, R. A. Kirn, A. E. Rankis, G. 

E. Monan, and F. J. Ossiander. 1986. Migrational characteristics, biological observations, and 

relative survival of juvenile salmonids entering the Columbia River estuary. Rep. to Bonneville 

Power Administration, Contract DE-A179-84BP-39652. Online at http://www.efw.bpa.gov/ 

Publications/D39652-1.pdf [accessed 18 March 2005]. 

Dawley, E. M., C. W. Sims, and R. D. Ledgerwood. 1978. A study to define the migrational 

characteristics of Chinook and coho salmon and steelhead trout in the Columbia River estuary. 

Processed Report. U.S. National Marine Fisheries Service. 

89
Donohoe, R. M., and L. R. Curtis. 1996. Estrogenic activity of chlordecone, o,p'-DDT and o,p'-DDE in 

juvenile rainbow trout: Induction of vitellogenesis and interaction with hepatic estrogen binding 

sites. Aquat. Toxicol. 36:31–52. 

Dracup, J. A., and E. Kahya. 1994. The relationships between U.S. streamflow and La Niña events. 

Water Resour. Res. 30:2133–2141. 

Emmett, R. L., R. D. Brodeur, and P. M. Orton. 2004. The vertical distribution of juvenile salmon 

(Oncorhynchus spp.) and associated fishes in the Columbia River plume. Fish. Oceanogr. 

13:392–402. 

Fisher, J., and W. G. Pearcy. 1995. Distribution, migration, and growth of juvenile Chinook salmon, 

Oncorhynchus tshawystcha, off Oregon and Washington. Fish. Bull. 93:274–289. 

Foster, E. P., M. S. Fitzpatrick, G. W. Feist, C. B. Schreck, and J. Yates. 2001a. Gonad organochlorine 

concentrations and plasma steroid levels in white sturgeon (Acipenser transmontanus) from the 

Columbia River, USA. Bull. Environ. Contam. Toxicol. 67:239–245. 

Foster, E. P, M. S. Fitzpatrick, G. W. Feist, C. B. Schreck, J. Yates, J. M. Spitsbergen, and J. R. Heidel. 

2001b. Plasma androgen correlation, EROD induction, reduced condition factor, and the 

occurrence of organochlorine pollutants in reproductively immature white sturgeon (Acipenser 

transmontanus) from the Columbia River, USA. Arch. Environ. Contam. Toxicol. 41:182–191. 

Fox, D. S., S. Bell, W. Nehlsen, and J. Damron. 1984. The Columbia River estuary: Atlas of physical 

and biological characteristics. Columbia River Estuary Data Development Program, Columbia 

River Estuary Study Taskforce, Astoria, OR. 

Francis, R. C., and S. Hare. 1994. Decadal-scale shifts in the large marine ecosystems of the northeast 

Pacific: A case of historical science. Fish. Oceanogr. 3:279–291. 

Fresh, K. L. 1997. The role of competition and predation in the decline of Pacific salmon and steelhead. 

In D. J. Stouder, P. Bisson, and R. Naiman (eds.), Pacific salmon and their ecosystems: Status and 

future options, p. 245–276. Chapman and Hall, New York. 

Fresh, K. L., D. Rabin, C. A. Simenstad, E. O. Salo, K. Garrison, and L. Matheson. 1979. Fish ecology 

studies in the Nisqually Reach area of southern Puget Sound, Washington. FRI-UW-7904. Univ. 

Washington, Fisheries Research Institute, Seattle. 

Friesen, T. A., and D. L. Ward. 1999. Management of northern pikeminnow and implications for 

juvenile salmonid survival in the lower Columbia and Snake rivers. N. Am. J. Fish. Manag. 

19:406–420. 

Fuhrer, G. J. 1986. Extractable cadmium, mercury, copper, lead, and zinc in the lower Columbia River 

estuary, Oregon and Washington. U.S. Geological Survey Water Resource Investigations Rep. 

98–4052. U.S. Geological Survey, Portland, OR. 

Fuhrer, G. J. 1989. Quality of bottom material and elutriates in the lower Willamette River, Portland 

Harbor, Oregon. U.S. Geological Survey Water Resources Investigations Rep. 89-4005. U.S. 

Geological Survey, Portland, OR. 

90
Fuhrer, G. J., and F. A. Rinella. 1983. Analysis of elutriates, native water, and bottom material in 

selected rivers and estuaries in western Oregon and Washington. U.S. Geological Survey OpenFile Rep. 82-922. U.S. Geological Survey, Portland, OR. 

Fuhrer, G. J., D. Q. Tanner, J. L. Morace, S. W. McKenzie, and K. A. Skach. 1996. Water quality of the 

lower Columbia River basin: Analysis of current and historical water-quality data through 1994. 

U.S. Geological Survey Water Resources Investigations Rep. 95-4294. U.S. Geological Survey, 

Portland, OR. 

Gadomski, D. M., and J. A. Hall-Griswold. 1992. Predation by northern squawfish on live and dead 

juvenile Chinook salmon. Trans. Am. Fish. Soc. 121:680–685. 

Gargett, A. E. 1997. The optimum stability ‘window’: A mechanism underlying decadal fluctuations in 

North Pacific salmon stocks? Fish. Oceanogr. 6:109–117. 

Garono, R. J., R. Robinson, and C. A. Simenstad. 2002. Estuarine land cover along the Columbia River 

estuary determined from Landstat 7 ETM+ imagery. Report to the Lower Columbia River 

Estuary Partnership, Portland, OR. (Available from D. Bottom, NWFSC, Newport Research 

Station, 2032 SE OSU Drive, Newport, OR 97365.) 

Gershunov A., T. P. Barret, and D. R. Cayan. 1999. North Pacific interdecadal oscillation seen as factor 

in ENSO-related North American climate anomalies. EOS, Trans. Am. Geophys. Union 80:25–

30. 

Gharrett, A. J., and W. W. Smoker. 1993. Genetic components in life-history traits contribute to 

population structure. In J. G. Cloud and G. Thorgaard (eds.), Conservation of salmonid fishes, p. 

197–201. Plenum Press, London. 

Gilbert, C. H. 1912. Age at maturity of the Pacific coast salmon of the genus Oncorhynchus. Fish. Bull. 

32:57–70. 

Gilhousen, P. 1962. Marine factors affecting survival of Fraser River pink salmon. In N. J. Wilimovsky 

(ed.), Symposium on pink salmon, p. 105–111. H. R. MacMillan Lectures in Fisheries, Univ. 

British Columbia, Vancouver. 

Good, T. P., K. Barnas, D. M. Marsh, M. M. McClure, B. A. Ryan, B. P. Sandford and E. Casillas. 2005. 

Caspian tern predation on juvenile salmonid outmigrants in the Columbia River estuary. In

Caspian tern management to reduce predation of juvenile salmonids in the Columbia River 

estuary, Final environmental impact statement, January 2005, Appendix C. U.S. National Marine 

Fisheries Service. 

Goodbred, S. L., R. L. Gillion, T. S. Gross, N. P. Denslow, W. L. Bryant, and T. R. Shoeb. 1997. 

Reconnaissance of 17beta estradiol, 11-ketotestosterone, vitellogenin, and gonad histopathology 

in common carp of United States streams: Potential for contaminant-induced endocrine 

disruption. U.S. Geological Survey Open File Rep. 96–627. U.S. Geological Survey, Denver, 

CO. 

Graves, J. K., J. A. Christy, P. J. Clinton, and P. L. Britz. 1995. Historic habitats of the lower Columbia 

River. Internal report. (Available from Columbia River Estuary Study Task Force, 750 

Commercial St., Astoria, OR 97103.) 

91
Gray, A., C. A. Simenstad, D. L. Bottom, and T. J. Cornwell. 2002. Contrasting functional performance 

of juvenile salmon habitat in recovering wetlands of the Salmon River estuary, Oregon, USA 

Restor. Ecol. 10:514–526. 

Gresswell, R. E., W. J. Liss, and G. L. Larsen. 1994. Life-history organization of Yellowstone cutthroat 

trout (Oncorhynchus clarki bouvieri) in Yellowstone Lake. Can. J. Fish. Aquat. Sci. 51:298–309. 

Hansen, L. P., and B. Jonsson. 1991. Evidence of a genetic component in the seasonal return pattern of 

Atlantic salmon, Salmo salar L. J. Fish Biol. 38:21–258. 

Hanski, I., and M. Gilpin. 1996. Metapopulation biology: Ecology, genetics, and evolution. Academic 

Press, San Diego. 

Hare, S. R., N. H. Mantua, and R. C. Francis. 1999. Inverse production regimes: Alaska and west coast 

Pacific salmon. Fisheries 24(1):6–14. 

Harrison, P. 1983. Seabirds: An identification guide. Houghton Mifflin, Boston, MA. 

Harrison, C. S. 1984. Terns: Family Laridae. In D. Haley (ed.), Seabirds of eastern North Pacific and 

Arctic waters, p. 146–160. Pacific Search Press, Seattle. 

Harrison, H. E., C. W. Anderson, F. A. Rinella, T. M. Gasser, and T. R. Pogue, Jr. 1995. Analytical data 

from phases I and II of the Willamette River basin water quality study 1992–1994. U.S. 

Geological Survey Open-File Rep. 95-373. U.S. Geological Survey, Portland, OR. 

Healey, M. C. 1979. Detritus and juvenile salmon production in the Nanaimo Estuary. Production and 

feeding rates of juvenile chum salmon (Oncorhynchus keta). J. Fish. Res. Board Can. 36:488–

496. 

Healey, M. C. 1980. Utilization of the Nanaimo River estuary by juvenile Chinook salmon, 

Oncorhynchus tshawytscha. Fish. Bull. 77:653–668. 

Healey, M. C. 1982. Juvenile Pacific salmon in estuaries: The life support system. In V. S. Kennedy 

(ed.), Estuarine comparisons, p. 315–341. Academic Press, New York. 

Healey, M. C. 1991. Life-history of Chinook salmon (Oncorhynchus tshawytscha). In C. Groot and L. 

Margolis (eds.), Pacific salmon life histories, p. 311–393. University of British Columbia Press, 

Vancouver. 

Healey, M. C., and W. R. Heard. 1984. Inter- and intra-population variation in the fecundity of Chinook 

salmon (Oncorhynchus tshawytscha) and its relevance to life history theory. Can. J. Fish. Aquat. 

Sci. 41:476–483. 

Healey, M. C., and A. Prince. 1995. Scales of variation in life history tactics of Pacific salmon and the 

conservation of phenotype and genotype. Am. Fish. Soc. Symp. 17:176–184. 

Henny, C. J., J. L. Kaiser, R. A. Grove, V. R. Bentley, and J. E. Elliott. 2003. Biomagnification factors 

(fish to osprey eggs from Willamette River, Oregon, USA) for PCDDs, PCDFs, PCBs and OC 

pesticides. Environ. Monit. Assess. 84:275–315. 

Hilborn, R., T. P. Quinn, D. E. Schindler, and D. E. Rogers. 2003. Biocomplexity and fisheries 

sustainability. Proc. Natl. Acad. Sci. 100:6564–6568. 

92
Hodgson, S., and T. P. Quinn. 2002. The timing of adult sockeye salmon migration into freshwater: 

Adaptations by populations to prevailing thermal regimes. Can. J. Zool. 80:542–555. 

Holtby, L. D., B .C. Andersen, and R. K. Kadowski. 1990. Importance of smolt size and early ocean 

growth to interannual variability in marine survival of coho salmon (Oncorhynchus kisutch). 

Can. J. Fish. Aquat. Sci. 47:2181–2194. 

Hooper P. R., D. A. Goolsby, D. A. Rickert, and S. W. McKenzie. 1997. NASQUAN—A program to 

monitor water quality of the nation’s large rivers. U.S. Geological Survey Fact Sheet FS-055-97. 

U.S. Geological Survey, Reston, VA. 

Horowitz, A. J. 1991. A primer on sediment-trace element chemistry (Second Edition). Lewis 

Publishers Inc., Chelsea, MI. 

Hose, J. C., J. N. Cross, S. G. Smith, and D. Diehl. 1989. Reproductive impairment in a fish inhabiting a 

contaminated coastal environment of southern California. Environ. Pollut. 57:139–148. 

Hunter, J. G. 1959. Survival and production of pink and chum salmon in a coastal stream. J. Fish. Res. 

Board Can. 16:835–886. 

IMST (Independent Multidisciplinary Science Team). 1998. Pinniped and seabird predation: 

Implications for recovery of threatened stocks of salmonids in Oregon under the Oregon Plan for 

Salmon and Watersheds. Technical report 1998-2 to the Oregon Plan for Salmon and 

Watersheds. Governor’s Natural Resources Office. Salem, OR. 

ISG (Independent Scientific Group). 2000. Return to the river: Restoration of salmonid fishes in the 

Columbia River ecosystem. Northwest Power Planning Council Document 2000-12. Northwest 

Power Planning Council, Portland, OR. 

Issak, D. J., R. F. Thurow, B. E. Rieman, and J. B. Dunham. 2003. Temporal variation in synchrony 

among Chinook salmon (Oncorhynhus tshawytscha) redd counts from a wilderness area in central 

Idaho. Can. J. Fish. Aquat. Sci. 60:840–848. 

Jay, D. A. 2005. Change in hydrological conditions. In D. L. Bottom, C. A. Simenstad, J. Burke, A. M. 

Baptista, D. A. Jay, K. K. Jones, E. Casillas, and M. H. Schiewe. Salmon at river’s end: The role 

of the estuary in the decline and recovery of Columbia River salmon. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-68. 

Jay, D. A., and P. Naik. 2002. Separating human and climate impacts on Columbia River hydrology and 

sediment transport. In G. Gelfenbaum and G. M. Kaminsky (eds.), Southwest Washington 

Coastal Erosion Workshop Rep. 2000, U.S. Geological Survey Open File Rep. 02-229. U.S. 

Geological Survey, Portland, OR. 

Johnson, G., H. Diefenderfer, T. Berguam, B. Ebberts, C. Tortorici, and J. Wilcox. 2004. Plan for 

research, monitoring, and evaluation of salmon in the Columbia River estuary. Final draft 

submitted to the Bonneville Power Administration. Document No. PNNL-14632. Battelle 

Pacific Northwest National Laboratory, Richland, WA. 

Johnson, H. E., and C. Pecor. 1969. Coho salmon mortality and DDT in Lake Michigan. In Transactions 

of the 34th North American Wildlife Conference 34:159. Wildlife Management Institute, 

Washington, DC. 

93
Johnson, L. L., G. M. Ylitalo, D. Brown, P. Moran, B. F. Anulacion, D. Boylen, M. Arkoosh, A. Kagley, 

and T. Collier. 2004. Chemical contaminant exposure in outmigrant juvenile Chinook salmon in 

the lower Columbia Estuary. Tech. Rep. to Army Corps of Engineers, Portland District. 

(Available from L. Johnson, NWFSC, 2725 Montlake Blvd. E., Seattle, WA 98112.) 

Johnson, O. W., W. S. Grant, R. G. Kope, K. Neely, F. W. Waknitz, and R. S. Waples. 1997. Status 

review of chum salmon from Washington, Oregon, and California. U.S. Dept. Commer., NOAA 

Tech. Memo. NMFS-NWFSC-32. 

Jones, K. K., C. A. Simenstad, D. L. Higley, and D. L. Bottom. 1990. Structure, distribution, and 

standing crop of benthos, epibenthos, and plankton in the Columbia River estuary. Prog. 

Oceanogr. 25:211–242. 

Kaczynski, V. W., R. J. Feller, and J. Clayton. 1973. Trophic analysis of juvenile pink and chum salmon 

(Oncorhynchus gorbuscha and O. keta) in Puget Sound. J. Fish. Res. Board Can. 30:1003–1008. 

Kareiva, P., M. Marvier, and M. McClure. 2000. Recovery and management options for spring/summer 

Chinook salmon in the Columbia River basin. Science 290:977–979. 

Kahya, E., and J. A. Dracup. 1993. U.S. streamflow patterns in relation to the El Niño/southern 

oscillation. Water Resour. Res. 29:2491–2503. 

Kelly, V. J. 1997. Water quality in the lower Columbia River basin during the flood of February, 1996. 

In The Pacific Northwest floods of February 6–11, 1996. Proceedings of the Pacific Northwest 

Water Issues Conference, Portland, Oregon, 7–8 Oct. 1997. 

Khan, I. A, and P. Thomas. 1998. Estradiol-17 beta and o,p'-DDT stimulate gonadotropin release in 

Atlantic croaker. Mar. Environ. Res. 46:149–152. 

King, J. R., and G. A. McFarlane. 2003. Marine life history strategies: Application to fishery 

management. Fish. Manag. Ecol. 10:249–264. 

Koski, K. 1971. The survival and fitness of two stocks of chum salmon (Oncorhynchus keta) from egg 

deposition to emergence in a controlled-stream environment at Big Beef Creek. Doctoral thesis 

Univ. Washington, Seattle. 

Krahn, M. M., G. M. Ylitalio, J. Buzitis, S-L. Chan, and U. Varanasi. 1993. Comparison of highperformance chromotography/fluorescence screening and gas chromotography/mass spectrometry 

analysis for aromatic compounds in sediments samples after the Exxon Valdex oil spoll. Environ. 

Sc. Technol. 27(4):699–708. 

Krahn, M. M., J. Buzitis, G. Ylitalo, C. A. Sloan, D. W. Brown, D. G. Burrows, J. Bolton, T. K. Collier, 

and J. E. Stein. 1998. Analyses for PCBs and PCTs in Duwamish River sediments. Interpretive 

report prepared for NOAA Northwest Damage Assessment Center, May, 1998. (Available from 

M. Krahn, NWFSC, 2725 Montlake Blvd. E., Seattle, WA 98112.) 

Kukulka, T., and D. A. Jay. 2003. Impacts of Columbia River discharge on salmonid habitat; changes in 

shallow-water habitat. J. Geophys. Res. 108:3294. 

LCMESP (Lower Columbia Mainstem and Estuary Subbasin Plan). 2004. Lower Columbia Salmon 

Recovery and Fish and Wildlife Subbasin Plan. Volume II, Subbasin Plan, Chapter A, Lower 

94
Columbia Mainstem and Estuary. Prepared for Lower Columbia Fish Recovery Board. Online at 

http://www.nwcouncil.org/fw/subbasinplanning/lowerColumbia/plan [accessed 20 May 2005]. 

LCREP (Lower Columbia River Estuary Partnership). 1999. Lower Columbia River Estuary Program 

comprehensive conservation and management plan. (Available from Lower Columbia River 

Estuary Partnership, 811 SW Naito Parkway, Suite 120, Portland, OR 97204.) 

Levings, C. D., C. D. McAllister, and B. D. Chang. 1986. Differential use of the Campbell River 

estuary, British Columbia, by wild and hatchery-reared juvenile Chinook salmon (Oncorhynchus 

tshawytscha). Can. J. Fish. Aquat. Sci. 43:1386–1397. 

Levy, D. A., and T. G. Northcote. 1981. The distribution and abundance of juvenile salmon in marsh 

habitats of the Fraser River estuary. Tech. Rep. 25. Westwater Research Center, Univ. British 

Columbia, BC, Canada. 

Levy, D. A., and T. G. Northcote. 1982. Juvenile salmon residency in a marsh area of the Fraser River 

estuary. Can. J. Fish. Aquat. Sci. 39:270–276. 

Lichatowitch, J. 1999. Salmon without rivers: A history of the Pacific salmon crisis. Island Press, 

Washington, DC. 

Lichatowitch, J. A., and J. D. McIntyre. 1987. Use of hatcheries in management of Pacific salmon. Am. 

Fish. Soc. Symp. 1:131–136. 

Limburg, K. E. 2001. Through the gauntlet again: Demographic restructuring of American shad by 

migration. Ecology 82:1584–1596. 

Long, E. R., D. D. MacDonald, S. L. Smith, and F. D. Calder. 1995. Incidence of adverse biological 

effects within ranges of chemical concentrations in marine and estuarine sediments. Environ. 

Manag. 19:81–97. 

MacDonald, D. D. 1994. Development and evaluation of sediment quality assessment guidelines. 

Prepared for Florida Dept. Environmental Policy, Office of Water Policy, Tallahassee, FL. 

MacDonald, J. S., I. K. Birtwell, and G. M. Kruzynski. 1987. Food and habitat utilization by juvenile 

salmonids in the Campbell River estuary. Can. J. Fish. Aquat. Sci. 44:1233–1246. 

MacDonald, J. S., C. D. Levings, C. D. McAllister, U. H. M. Fagerlund, and J. R. McBride. 1988. A 

field experiment to test the importance of estuaries for Chinook salmon (Oncorhynchus 

tshawytscha) survival: Short-term results. Can. J. Fish. Aquat. Sci. 45:1366–1377. 

Magnusson, A., and R. Hilborn. 2003. Estuarine survival rates of coho (Oncorhynchus kisutch) and 

Chinook salmon (Oncorhynchus tshawytscha) released from hatcheries on the U.S. Pacific Coast. 

Estuaries 26 (4B):1094–1103. 

Mantua, N. J., S. R. Hare, Y. Zhang, J. M. Wallace, and R. C. Francis. 1997. A Pacific interdecadal 

climate oscillation with impacts on salmon production. Bull. Am. Meteorol. Soc. 78:1069–1079. 

Manzer, J., and M. P. Shepard. 1962. Marine survival, distribution, and migration of pink salmon off the 

British Columbia coast. In N. J. Wilimovsky (ed.), Symposium on pink salmon, p. 113–121. H. 

R. MacMillan Lectures in Fisheries. Univ. British Columbia, Vancouver. 

95
Markle, D. F. 1995. Evaluation of fish identifications for the Willamette River Basin Water Quality 

Study Phase II. Skeletal deformities in northern squawfish. Final report to Oregon Department 

of Environmental Quality from Oregon State University, Corvallis, Oregon. (Available from 

Oregon Dept. Environmental Quality, 811 SW Sixth Ave., Portland, OR 97204.) 

Mason, J. C. 1974. Behavioral ecology of chum salmon fry (Oncorhynchus keta) in a small estuary. J. 

Fish. Res. Board Can. 31:83–92. 

Mason, J. C. 1975. Seaward movement of juvenile fishes, including lunar periodicity in movement of 

coho salmon (Oncorhychus kisutch) fry. J. Fish. Res. Board Can. 32:2542–2547. 

McCabe Jr., G. T., R. L. Emmett, W. D. Muir, and T. H. Blahm. 1986. Utilization of the Columbia River 

estuary by subyearling Chinook salmon. Northwest Sci. 60:113–124. 

McCabe Jr., G. T., W. D. Muir, R. L. Emmett, and J. T. Durkin. 1983. Interrelationships between 

juvenile salmonids and nonsalmonid fish in the Columbia River estuary. Fish. Bull. 81:815–826. 

McCabe, Jr., G. T., S. A. Hinton, R. L. Emmett, and B. P. Sanford. 1997. Benthic invertebrates and 

sediment characteristics in main channel habitats in the lower Columbia River. Northwest Sci. 

71:45–55. 

McCain, B. M., D. C. Malins, M. M. Krahn, D. W. Brown, W. D. Gronlund, L. K. Moore, and S-L. Chan. 

1990. Uptake of aromatic and chlorinated hydrocarbons by juvenile Chinook salmon 

(Oncorynchus tshawytscha) in an urban estuary. Arch. Environ. Contam. Toxicol. 19:10–16. 

McCarthy, K. A., and R. W. Gale. 2001. Evaluation of persistent hydrophobic organic compounds in the 

Columbia River basin using semi permeable-membrane devices. Hydrol. Process. 15:1271–1283. 

McClure, M. M., E. E. Holmes, B. L. Sanderson, and C. E. Jordan. 2003. A large-scale, multispecies 

status assessment: Anadromous salmonids in the Columbia River basin. Ecol. Appl. 13:964–989. 

McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, and E. P. Bjorkstedt. 2000. Viable 

salmon populations and the recovery of evolutionary significant units. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-42. 

Meador, J. P., T. K. Collier, and J. E. Stein. 2002. Use of tissue and sediment-based threshold 

concentrations of polychlorinated biphenyls (PCBs) to protect juvenile salmonids listed under the 

U.S. Endangered Species Act. Aquat. Conserv.: Mar. Freshw. Ecosys. 12:493–516. 

Meka, J. M., E. E. Knudsen, D. C. Douglas, and R. B. Benter. 2003. Variable migratory patterns of 

different adult rainbow trout life history types in a southwest Alaska watershed. Trans. Am. Fish. 

Soc. 132:717–732. 

Mesa, M. G. 1994. Effects of multiple acute stressors on the predator avoidance ability and physiology 

of juvenile Chinook salmon. Trans. Am. Fish. Soc. 123:786–793. 

Miller, B. A., and S. Sadro. 2003. Residence time and seasonal movements of juvenile coho salmon in 

the ecotone and lower estuary of Winchester Creek, South Slough, Oregon. Trans. Am. Fish. 

Soc. 132:546–559. 

Miller, J. A., and C. A. Simenstad. 1997. A comparative assessment of a natural and created estuarine 

slough as rearing habitat for juvenile Chinook and coho salmon. Estuaries 20:792–806. 

96
Milston, R. H., M. S. Fitzpatrick, A. T. Vella, S. Clements, D. Gundersen, G. Feist, T. L. Crippen, J. 

Leong, and C. B. Schreck. 2003. Short-term exposure of Chinook salmon (Oncoryhnchus 

tshawytscha) to o,p ́-DDE or DMSO during early life-history stages causes long-term humoral 

immunosuppression. Environ. Health Perspect. 111:1601–1607. 

Moore, A., and C. P. Waring. 1996. Sublethal effects of the pesticide diazinon on olfactory function in 

mature male Atlantic salmon parr. J. Fish Biol. 48:758–775. 

Morgan, C. A., A. D. Robertis, and R. W. Zabel. In press. Columbia River plume fronts: Hydrography, 

zooplankton distribution, and community composition. Mar. Ecol. Prog. Ser. 

Muir, W. D., and R. L. Emmett. 1988. Food habits of migrating salmonid smolts passing Bonneville in 

the Columbia River, 1984. Regul. Rivers Res. Manag. 2:1–10. 

Myers, J. M., R. G. Kope, G. J. Bryant, D. Teel, L. J. Lierheimer, T. C. Wainwright, W. S. Grand, F. W. 

Waknitz, K. Neely, S. T. Lindley, and R. S. Waples. 1998. Status review of Chinook salmon 

from Washington, Idaho, Oregon, and California. U.S. Dept. Commer., NOAA Tech. Memo. 

NMFS-NWFSC-35. 

Myers, M. M., L. L. Johnson, and T. K. Collier. 2003. Establishing the causal relationship between 

polycyclic aromatic hydrocarbon (PAH) exposure and hepatic neoplasms and neoplasia-related 

liver lesions in English sole (Pleuronectes vetulus). Hum. Ecol. Risk Assess. 9:67–94. 

Myers, M. M, C. M. Stehr, O. P. Olson, L. L. Johnson, B. B. McCain, S-L. Chan, and U. Varanasi. 1994. 

Relationships between toxicopathic hepatic lesions and exposure to chemical contaminants in 

English sole (Pleuronectes vetulus), starry flounder (Platichthys stellatus), and white croaker 

(Genyonemus lineatus) from selected marine sites on the Pacific Coast, USA. Environ. Health 

Perspect. 102:200–215. 

Nendza, M., T. Herbst, C. Kussatz, and A. Gies. 1997. Potential for secondary poisoning and 

biomagnification in marine organisms. Chemosphere 35:1875–1885. 

Nickelson, T. E. 1986. Influences of upwelling, ocean temperature, and smolt abundance on marine 

survival of coho salmon (Oncorhynchus kistuch) in the Oregon production area. Can. J. Fish. 

Aquat. Sci. 43:527–535. 

NRC (National Research Council). 1996. Upstream: Salmon and Society in the Pacific Northwest. 

National Research Council. National Academy Press, Washington, DC. 

Odum, H. T. 1988. Self-organization, transformity, and information. Science 242:1132–1139. 

Oregon Dept. Environment Quality. 1994. Willamette River toxics study 1998/1991. (Available from 

Oregon Dept. Environmental Quality, 811 SW Sixth Ave., Portland, OR 97204.) 

Oregon Health Division. 1997. Elevated levels of mercury in sport-caught bass and squawfish from the 

Willamette River, Portland, Oregon. Human Resources News, February 13. 

Orem, H. M. 1968. Discharge in the lower Columbia River basin, 1928–1965. U.S. Geological Survey 

Circular 550. U.S. Geological Survey, Washington, DC. 

Papoulias, D. M., S. A. Villalobos, J. Meadows, D. B. Noltie, J. P. Giesy, and D. E. Tillitt. 2003. In ovo 

exposure to o,p ́-DDE affects sexual development but not sexual differentiation in Japanese 

medaka (Oryzias latipes). Environ. Health Perspect. 111:29–32 (2003). 

97
Parker, R. R. 1968. Marine mortality schedules of pink salmon of the Bella Coola River, central British 

Columbia. J. Fish. Res. Board Can. 25:757–794. 

Parker, R. R. 1971. Size selective predation among juvenile salmonid fishes in a British Columbia inlet. 

J. Fish. Res. Board Can. 28:1503–1510. 

Parker, R. M., M. P. Zimmerman, and D. L. Ward. 1995. Variability in biological characteristics of 

northern squawfish in the lower Columbia and Snake rivers. Trans. Am. Fish. Soc. 124:335–346. 

Pavlou, S., R. Kadeg, A. Turner, and M. Marchlik. 1987. Sediment quality criteria methodology 

validation: Uncertainty analysis of sediment normalization theory for nonpolar organic 

contaminants. Work Assignment 45, Task 3. Battelle, Washington, DC. EPA No. 822R87101. 

(Available from National Technical Information Service, 5285 Port Royal Road, Springfield, VA 

22161.) 

Pearcy, W. G. 1992. Ocean ecology of North Pacific salmon. Washington Sea Grant Program, 

University of Washington Press, Seattle. 

Peterman, R. M. 1978. Testing for density-dependent marine survival in Pacific salmonids. J. Fish. Res. 

Board Can. 35:1434–1450. 

Petersen, J. H. 1994. Importance of spatial pattern in estimating predation on juvenile salmonids in the 

Columbia River. Trans. Am. Fish. Soc. 123:924–930. 

Petersen, J. H., D. M. Gadomski, and T. P. Poe. 1994. Differential predation by northern squawfish 

(Ptychocheilus oregonensis) on live and dead juvenile salmonids in the Bonneville Dam tailrace 

(Columbia River). Can. J. Fish. Aquat. Sci. 51:1197–1204. 

Peterson, R. H. 1973. Temperature selection of Atlantic salmon (Salmo salar) and brook trout 

(Salvelinus fontinalis) as influenced by various chlorinated hydrocarbons. J. Fish. Res. Board 

Can. 30:1091–1100. 

Peterson, W. T., and F. B. Schwing. 2003. A new climate regime in northeast Pacific ecosystems. 

Geophys. Res. Lett. 30:OCE 6–4. 

Poe, T. P., H. C. Hansel, S. Vigg, D. E. Palmer, and L. A. Prendergast. 1991. Feeding of predaceous 

fishes on out-migrating juvenile salmonids in John Day Reservoir, Columbia River. Trans. Am. 

Fish. Soc. 120:405–420. 

Poels, C. L. M., M. A. van der Gaag, and J. F. J. van de Kerkhoff. 1980. An investigation into the longterm effect of Rhine water on rainbow trout. Water Res. 14:1029–1033. 

Pritchard, D. W. 1967. What is an estuary: Physical viewpoint. In H. Lauff (ed.), Estuaries, p. 3–5. 

Publ. No. 83. American Association for the Advancement of Science, Washington, DC. 

PSWQAT (Puget Sound Water Quality Action Team). 2002. Puget Sound update: Eighth report of the 

Puget Sound ambient monitoring program. Puget Sound Water Quality Action Team, Olympia, 

WA. 

Quinn, T. P., and M. J. Unwin. 1993. Variation in life-history patterns among New Zealand Chinook 

salmon (Oncorhynchus tshawytscha) populations. Can. J. Fish. Aquat. Sci. 50:1414–1421. 

98
Quinn, T. P., M. J. Unwin, and M. T. Kinnison. 2000. Evolution of temporal isolation in the wild: 

Genetic divergence in timing of migration and breeding by introduced Chinook salmon 

populations. Evolution 54:1372–1385. 

Ramstad, K. M., C. J. Foote, J. Olsen, and D. Rogers. 2003. Genetic and phenotypic evidence of 

reproductive isolation between seasonal runs of sockeye salmon in Bear Lake, Alaska. Trans. 

Am. Fish. Soc. 132:697–1013. 

Raymond, H. L. 1988. Effects of hydroelectric development and fisheries enhancement on spring and 

summer Chinook salmon and steelhead in the Columbia River basin. N. Am. J. Fish. Manag. 

8:1–24. 

Redmond, K. T., and R. W. Koch. 1991. Surface climate and streamflow variability in the western 

United States and their relationship to large-scale circulation indices. Water Resour. Res. 

27:2381–2399. 

Reimers, P. E. 1973. The length of residence of juvenile fall Chinook salmon in Sixes River. Oreg. Fish. 

Comm. Res. Rep. 4(2):1–43. 

Reimers, P. E., J. W. Nicholas, D. L. Bottom, T. W. Downey, K. M. Maciolek, J. D. Rodgers, and B. A. 

Miller. 1979. Coastal salmon ecology project. Fish Research Project 9-M02-ORIC, Annual 

Progress Report. Oregon Dept. Fish and Wildlife, Portland, OR. 

Rich, W. H. 1920. Early history and seaward migration of Chinook salmon in the Columbia and 

Sacramento rivers. Fish. Bull. 37:1–74. 

Rich, W. H. 1939. Local populations and migration in relation to the conservation of Pacific salmon in 

the western states and Alaska. Am. Assoc. Adv. Sci. Publ. 8:45–50. 

Rieman, B. E., and R. C. Beamesderfer. 1990. Dynamics of a northern squawfish population and the 

potential to reduce predation on juvenile salmonids in a Columbia River reservoir. N. Am. J. 

Fish. Manag. 10:228–241. 

Rieman, B. E., R. C. Beamesderfer, S. Vigg, and T. P. Poe. 1991. Estimated loss of juvenile salmonids 

to predation by northern squawfish, walleyes, and smallmouth bass in John Day Reservoir, 

Columbia River. Trans. Am. Fish. Soc. 120:448–458. 

Rieman, B. E., and J. B. Dunham. 2000. Metapopulations and salmonids: A synthesis of life history 

patterns and empirical observations. Ecol. Freshw. Fish 9:51–64. 

Rinella, J. F., S. W. McKenzie, K. J. Crawford, W. T. Foreman, G. J. Fuhrer, and J. L. Morace. 2000. 

Surface-water quality assessment of the Yakima River basin, Washington: Distribution of 

pesticides and other organic compounds in water, sediments, and aquatic biota, 1987–91. U.S. 

Geological Survey Water Supply Paper 2354-B. U.S. Geological Survey, Denver, CO. 

Roby, D. D., D. P. Craig, K. Collis, and S. L. Adamany. 1998. Avian predation of juvenile salmonids in 

the lower Columbia River. 1997 Annual Report. Oregon State Univ. and Columbia River 

Intertribal Fish Commission, Corvallis and Portland, OR 

Roby, D. D., D. E. Lyons, D. P. Craig, K. Collis, and G. H. Visser. 2003. Quantifying the effects of 

predators on endangered species using a bioenergetics approach: Caspian terns and juvenile 

salmonids in the Columbia River estuary. Can. J. Zool. 81: 250–265 

99
Roni, P., T. J. Beechie, R. E. Bilby, F. E. Leonetti, M. M. Pollock, and G. R. Pess. 2002. A review of 

stream restoration techniques and a hierarchical strategy for prioritizing restoration in Pacific 

Northwest watersheds. N. Am. J. Fish. Manag. 22:1–20. 

Roni, P., and T. P. Quinn. 1995. Geographic variation in size and age of North American Chinook 

salmon. N. Am. J. Fish. Manag. 15:325–345. 

Roughgarden, J., S. Gaines, and H. Possingham. 1988. Recruitment dynamics in complex life cycles. 

Science 241:1460–1466. 

Roy F. Weston Inc. 1998. Portland Harbor sediment investigation report: Portland, Oregon. Prepared 

for U.S. EPA, Region 10, Contract No. 68-W9-0046. (Available from U.S. EPA, Region 10. 

1200 Sixth Ave., Seattle, WA 98101.) 

Ruckelshaus, M., P. McElhany, M. McClure, and S. Heppell. 2004. Chinook salmon in Puget Sound: 

Effects of spatially correlated catastrophes on persistence. In R. Ackakaya, M. Burgman, O. 

Kindvall, C.C. Wood, P. Sjogren-Gulve, J. S. Hatfield and M. A. McCarthy (eds.), Species 

conservation and management: Case studies, p. 208–218. Oxford University Press, New York. 

Ryan, B. A., J. W. Ferguson, R. D. Ledgerwood, and E. P. Nunnallee. 2001. Detection of passive 

integrated transponder tags from juvenile salmonids on piscivorous bird colonies in the Columbia 

River basin. N. Am. J. Fish. Manag. 21:417–421. 

Ryan, B. A., S. G. Smith, J. M. Butzerin, and J. W. Ferguson. 2003. Relative vulnerability to avian 

predation of juvenile salmonids tagged with passive integrated transponders in the Columbia 

River estuary, 1998–2000. Trans. Am. Fish. Soc. 132:275–288. 

Salo, E. O., and W. H. Bayliff. 1958. Artificial and natural production of silver salmon (Oncorhynchus 

kisutch) at Minter Creek, Washington. Research bulletin. (Available from Washington Dept. 

Fish and Wildlife, 600 Capitol Way N., Olympia, WA 98501.) 

Salo, E. O., N. J. Bax, T. E. Prinslow, C. J. Whitmus, B. P. Snyder, and C. A. Simenstad. 1980. Studies 

of the outmigration of juvenile chum salmon in Hood Canal, Washington with emphasis on the 

effects of construction of naval installations. Final Report, FRI-UW-8006. Univ. Washington, 

Fisheries Research Institute, Seattle. 

Sandahl, J. F., D. H. Baldwin, J. J. Jenkins, and N. L. Scholz. 2004. Odor-evoked field potentials as 

indicators of sublethal neurotoxicity in juvenile coho salmon (Oncorhynchus kisutch) exposed to 

copper, chlorpyrifos, or esfenvalerate. Can. J. Fish. Aquat. Sci. 61: 404–413. 

Schabetsberger, R., C. A. Morgan, R. D. Brodeur, C. L. Potts, W. T. Peterson, and R. L. Emmett. 2003. 

Prey selectivity and diel feeding chronology of juvenile Chinook (Oncorhynchus tshawystcha) 

and coho (O. kisutch) salmon in the Columbia River plume. Fish. Oceanogr. 12:523–540. 

Scholz, N. L., N. K. Truelove, B. L. French, B. A. Berejikian, T. P. Quinn, E. Casillas, and T. K. Collier. 

2000. Diazinon disrupts antipredator and homing behaviors in Chinook salmon (Oncorhynchus 

tshawytscha). Can. J. Fish. Aquat. Sci. 57: 1911–1918. 

Secor, D. H. 1999. Specifying divergent migration patterns in the concept of stock: The contingent 

hypothesis. Fish. Res. 43:13–34. 

100
Secor, D. H., and P. M. Piccoli. 1996. Age- and sex-dependent migrations of striped bass in the Hudson 

River as determined by chemical microanalysis of otoliths. Estuaries 19:778–793. 

SEI (Sustainable Ecosystems Institute) 2001. Report of Channel River Channel Improvement 

Reconsultation Project. Online at http://www.sei/org/Columbia/home.html. [accessed 30 August 

2004]. 

Sherwood, C. R., D. A. Jay, R. B. Harvey, P. Hamilton, and C. A. Simenstad. 1990. Historical changes 

in the Columbia River estuary. Prog. Oceanog. 25:299–357. 

Shreffler, D. K., C. A. Simenstad, and R. M. Thom. 1990. Temporary residence by juvenile salmon in a 

restored estuarine wetland. Can. J. Fish. Aquat. Sci. 47:2079–2084. 

Shreffler, D. K., C. A. Simenstad, and R. M. Thom. 1992. Juvenile salmon foraging in a restored 

estuarine wetland. Estuaries 15:204–213. 

Sibert, J., T. J. Brown, M. C. Healey, B. A. Kask, and R. J. Naiman. 1977. Detritus-based food webs: 

Exploitation by juvenile chum salmon (Oncorhynchus keta). Science 196:649–650. 

Simenstad, C. A. 2000. Commencement Bay aquatic ecosystem assessment. Ecosystem-scale 

restoration for juvenile salmon recovery. Univ. Washington, School of Fisheries, Seattle. 

Simenstad, C. A., and J. R. Cordell. 2000. Ecological assessment criteria for restoring anadromous 

salmon habitat in Pacific Northwest estuaries. Ecol. Eng. 15:283–302. 

Simenstad, C. A., K. L. Fresh, and E. O. Salo. 1982. The role of Puget Sound and Washington coastal 

estuaries in the life history of Pacific salmon: An unappreciated function. In V.S. Kennedy (ed.), 

Estuarine comparisons, p. 343–364. Academic Press, New York. 

Simenstad, C. A., D. Jay, and C. R. Sherwood. 1992. Impacts of watershed management on land-margin 

ecosystems: The Columbia River estuary. In R. J. Naiman (ed.), Watershed management: 

Balancing sustainability and environmental change, p. 266–306. Springer-Verlag, New York. 

Simenstad, C. A., W. J. Kinney, S. S. Parker, E. O. Salo, J. R. Cordell, and H. Buecher. 1980. Prey 

community structures and trophic ecology of outmigrating juvenile chum and pink salmon in 

Hood Canal, Washington: A synthesis of three years’ studies, 1977–1979. Final Report to 

Washington Dept. Fisheries. Univ. Washington, Fisheries Research Institute, Seattle, WA. 

Simenstad, C. A., C. D. McIntire, and L. F. Small. 1990. Consumption processes and food web structure 

in the Columbia River estuary. Prog. Oceanogr. 25:271–298. 

Sinclair, M. 1988. Marine populations: An essay on population regulation and speciation. Washington 

Sea Grant Program and University of Washington Press, Seattle. 

Solazzi, M. F., T. E. Nickelson, and S. L. Johnson. 1991. Survival, contribution, and return of hatchery 

coho salmon (Oncorhynchus kisutch) released in freshwater, estuarine, and marine environments. 

Can. J. Fish. Aquat. Sci. 48:248–253. 

Sommer, T. R., M. L. Nobriga, W. C. Harrell, W. Batham, and W. J. Kimmerer. 2001. Floodplain 

rearing of juvenile Chinook salmon: Evidence of enhanced growth and survival. Can. J. Fish. 

Aquat. Sci. 58:325–333. 

101
Spromberg, J. A., and J. P. Meador. 2005. Relating results of chronic toxicity responses to populationlevel effects: Modeling effects on wild Chinook salmon. Integrated Environ. Monit. Assess. 1:9–

21. 

Stearns, S. C. 1992. The evolution of life histories. Oxford University Press, New York 

Stehr, C. M., D. W. Brown, T. Hom, B. F. Anulacion, W. L. Reichert, and T. K. Collier. 2000. Exposure 

of juvenile Chinook and chum salmon to chemical contaminants in the Hylebos Waterway of 

Commencement Bay, Tacoma, Washington. J. Aquat. Ecosyst. Stress Recovery 7:215–227. 

Stein J. E., T. H. Hom, T. K. Collier, D. W. Brown, and U. Varanasi. 1995. Contaminant exposure and 

biochemical effects in outmigrant juvenile Chinook salmon from urban and non-urban estuaries 

of Puget Sound, Washington. Environ. Toxicol. Chem. 14:1019–1029. 

Stober, Q. J., and E. O. Salo. 1973. Ecological studies of the proposed Kiket Island nuclear power site. 

FRI-UW-7304. Univ. Washington, Fisheries Research Institute, Seattle. 

Stouder, D. J., P. Bisson, and R. Naiman (eds.). 1999. Pacific Salmon and their ecosystems: Status and 

future options. Chapman and Hall, New York. 

Tallman, R. F., and M. C. Healey. 1991. Phenotypic differentiation in seasonal ecotypes of chum 

salmon, Oncorhynchus keta. Can. J. Fish. Aquat. Sci. 48:661–671. 

Taylor, E. B. 1990. Environmental correlates of life-history variation in juvenile Chinook salmon, 

Oncorhynchus tshawytscha (Walbaum). J. Fish Biol. 37:1–17. 

Taylor, E. B. 1991. A review of local adaptation in Salmonidae, with particular reference to Pacific and 

Atlantic salmon. Aquaculture 98:185–207. 

Tetra Tech Inc. 1993. Reconnaissance survey of the lower Columbia River. Final reconnaissance report 

TC-8526-06. Prepared for Lower Columbia River Bi-State Water Quality Program. Online at 

http://www.lcrep.org/bistate.htm [accessed 18 March 2005]. 

Tetra Tech Inc. 1994. Lower Columbia River backwater reconnaissance survey, reconnaissance report 

TC 9405-01, Redmond, WA. Prepared for Lower Columbia River Bi-State Water Quality 

Program. Online at http://www.lcrep.org/bistate.htm [accessed 18 March 2005]. 

Tetra Tech Inc. 1995. Willamette River basin water quality study phase II—ecological monitoring 

component, assessment of communities and biological indices. Tetra Tech report TC 9925-03. 

Online at http://www.lcrep.org/bistate.htm [accessed 18 March 2005]. 

Tetra Tech Inc. 1996. Lower Columbia River Bi-State Program—the health of the river, 1990–1996. 

Integrated Tech. Rep. 0253-01. Prepared for Oregon Dept. Environmental Quality and 

Washington Dept. Ecology. Online at http://www.lcrep.org/bistate.htm [accessed 18 March 

2005]. 

Thomas, D. W. 1983. Changes in the Columbia River estuary habitat types over the past century. 

Columbia River Estuary Data Development Program, Astoria, OR. (Available from Columbia 

River Estuary Study Task Force, 750 Commercial St., Astoria, OR 97103.) 

Thomas, A. C., P. T. Strub, and P. Brickley. 2003. Anomalous satellite-measured chlorophyll 

concentrations in the Northern California current in 2001–2002. Geophys. Res. Lett. 10:1029–

2003. 

102
Thomas, C. M., and R. G. Anthony. 1999. Environmental contaminants in great blue herons (Ardea 

herodias) from the lower Columbia and Willamette rivers, Oregon and Washington, USA. 

Environ. Toxicol. Chem. 18: 2804–2816. 

Thomas, C. M., and R. G. Anthony. 2003. Environmental contaminants and nesting behavior of great 

blue herons from the Columbia and Willamette rivers, Oregon and Washington. Northwest Sci. 

77:320–330. 

Tschaplinski, P. J. 1987. The use of estuaries as rearing habitats by juvenile coho salmon. In T. W. 

Chamberlin (ed.), Proceedings of workshop applying 15 years of Carnation Creek results, p. 123–

142. Dept. Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, BC.

Turner, M. G. 1989. Landscape ecosystem: The effect of pattern on process. Annu. Rev. Ecol. Syst. 

20:171–197. 

Unwin, M. J. 1997. Fry-to-adult survival of natural and hatchery-produced salmon (Oncorhynchus 

tshawytscha) from a common origin. Can. J. Fish. and Aquat. Sci. 54:1246–1254. 

USACE (United States Army Corps of Engineers). 1996. Lower Columbia River Bi-State Water Quality 

Program fish, wildlife and wetlands GIS mapping. USACE Portland District, Geotechnical 

Engineering Branch, GIS, Survey, and Mapping Section. Report submitted to the Bi-State Water 

Quality Program. Portland, OR. 

USACE (United States Army Corps of Engineers). 1998. Dredged material evaluation framework. 

Lower Columbia River management area. Prepared by the US Army Corps of Engineers, 

Northwest Division, EPA Region 10, the Oregon Dept. Natural Resources, and the Oregon Dept. 

Environmental Quality, Portland, OR. 

USACE (United States Army Corps of Engineers). 1999. Integrated feasibility report for channel 

improvements and environmental impact statement. Columbia and lower Willamette River 

Federal Navigation Channel. Prepared by the US Army Corps of Engineers, Portland District, 

Portland, OR. 

USEPA (United States Environmental Protection Agency). 1980. Ambient water quality criteria for 

DDT. EPA440/5-80-083. U.S. Environmental Protection Agency, Office of Water Regulations 

and Standards, Criteria and Standards Division, Washington, DC. 

USEPA (United States Environmental Protection Agency). 1994. Drinking water regulations and health 

advisories, Washington, DC Office of Water, November 1994. (Available from National 

Technical Information Service, 5285 Port Royal Road, Springfield, VA 22161.) 

USEPA (United States Environmental Protection Agency). 1995. 304(a) criteria chart (toxic substance 

spreadsheet): Region IV Water Management Division, January 1995. (Available from U.S. 

Environmental Protection Agency, Region 4, Sam Nunn Atlanta Federal Center, 61 Forsyth St. 

SW, Atlanta, GA 30303.) 

USFWS (U.S. Fish and Wildlife Service). 1999. Organochlorine contaminants in double-crested 

cormorants from Lewis and Clark National Wildlife Refuge in the Columbia River estuary. 

Unpubl. report. (Available from U.S. Fish and Wildlife Service, 2600 S.E. 98th Ave., Portland, 

OR 97266.) 

103
USFWS (U.S. Fish and Wildlife Service). 2001. Seabird predation and salmon recovery in the Columbia 

River estuary. U.S. Fish and Wildlife Service, Portland, OR. 

Varanasi, U., E. Casillas, M. R. Arkoosh, T. Hom, D. A. Misitano, D. W. Brown, S-L Chan, T. L. Collier, 

B. B. McCain, and J. E. Stein. 1993. Contaminant exposure and associated biological effects in 

juvenile Chinook salmon (Oncorhynchus tshawytscha) from urban and non-urban estuaries of 

Puget Sound. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-8.

Vigg, S., T. P. Poe, L. A. Prendergast, and H. C. Hansel. 1991. Rates of consumption of juvenile 

salmonids and alternative prey fish by northern squawfish, walleyes, smallmouth bass, and 

channel catfish in John Day Reservoir, Columbia River. Trans. Am. Fish. Soc. 120:421–438. 

Walters, C. J., R. Hilborn, R. M. Peterman, and M. J. Staley. 1978. Model for examining early ocean 

limitation of Pacific salmon production. J. Fish. Res. Board Can. 35:1303–1315. 

Waples, R. S., R. G. Gustafson, L. A. Weitkamp, J. M. Meyers, O. W. Johnson, P. J. Busby, J. J. Hard, G. 

J. Bryant, F. W. Waknitz, K. Neely, D. J. Teel, W. S. Grant, G. A. Winans, S. Phelps, A. R. 

Marshall, and B. M. Baker. 2001. Characterizing diversity in salmon from the Pacific 

Northwest. J. Fish Biol. 59(Supplement A):1–31. 

Waples, R. S., D. J. Teel, J. M. Myers, and A. R. Marshall. 2004. Life-history divergence in Chinook 

salmon: Historic contingency and parallel evolution. Evolution 58:386–403. 

Ward, D. L., J. H. Petersen, and J. Loch. 1995. Index of predation on juvenile salmonids by northern 

squawfish in the lower and middle Columbia River and in the lower Snake River. Trans. Am. 

Fish. Soc. 124:321–334. 

Waring, C. P., and A. P. Moore. 1997. Sublethal effects of a carbamate pesticide on pheromonal 

mediated endocrine function in mature male Atlantic salmon (Salmo salar) parr. Fish Physiol. 

Biochem. 17: 203–211. 

Warner, K., B. Lafore, and R. Anderson. 1992. Portland/Vancouver toxic water: Portland. 

Columbia/Willamette RiverWatch, Portland. (Available from Northwest Environmental 

Advocates, P.O. Box 12187, Portland, OR 97212.) 

Washington State Dept. Health, and Oregon Health Division. 1996. Health analysis of chemical 

contaminants in lower Columbia River fish. Washington State Dept. Health, Olympia. 

WAC (Washington State Administrative Code). 1995. Sediment Management Standards. Chapter 173–

204. State of Washington, Olympia. 

WDOE (Washington Dept. Ecology). 2004. Corps of Engineers cited for spills on the Columbia and 

Snake rivers. News Release # 04-086, 17 May 2004. Washington Dept. Ecology, Olympia. 

Weitkamp, L. A. 1994. A review of the effects of dams on the Columbia River estuarine environment 

with special reference to salmonids. Rep. to Bonneville Power Administration, Contract 

DE_A179-93BP99021. (Available from Northwest Fisheries Science Center, 2725 Montlake 

Blvd. E., Seattle, WA 98112.) 

Whyte J. J., R. E. Jung, C. J. Schmitt, and D. E. Tillitt. 2000. Ethoxyresorufin-O-deethylase (EROD) 

activity in fish as a biomarker of chemical exposure. Crit. Rev. Toxicol. 30(4):347–570.

104
Williams D. E., J. J. Lech, and D. R. Buhler. 1998. Xenobiotics and xenoestrogens in fish: Modulation 

of cytochrome P450 and carcinogenesis. Mutat. Res. 399(2):179–92 

Williams, J. G., S. G. Smith, R. W. Zabel, W. D. Muir, M. D. Scheuerell, B. P. Sandford, D. M. Marsh, 

R. A. McNatt, and S. Achrod. 2005. Effects of the federal Columbia River power system on 

salmonid populations. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-63. 

Wilmot, R. L., and C. V. Burger. 1985. Genetic differences among populations of Alaska sockeye 

salmon. Trans. Am. Fish. Soc. 114:236–243. 

Wissmar, R., and C. A. Simenstad. 1998. Variability of riverine and estuarine ecosystem productivity for 

supporting Pacific salmon. In G. R. McMurray and R. J. Bailey (eds.), Change in Pacific 

Northwest coastal ecosystems, p. 253–301. Decision Analysis Series No. 11. NOAA Coastal 

Ocean Program, Silver Springs, MD. 

Wood, C. C. 1995. Life history variation and population structure in sockeye salmon. In J. L. Nielsen 

(ed.), Evolution and aquatic ecosystem: Defining unique units in population conservation, p. 195–

216. Am. Fish. Soc. Symp. 17. American Fisheries Society, Bethesda, MD. 

Woody, C. A., J. Olsen, J. Reynolds, and P. Bentzen. 2000. Temporal variation of phenotypic and 

genotypic traits in two sockeye salmon populations, Tustumena Lake, Alaska. Trans. Am. Fish. 

Soc. 129:1031–1043. 

Ylitalo, G. Unpubl. data. Data on contaminant concentration in hatchery feed, May 2003. (Available 

from G. Ylitalo, NWFSC, 2725 Montlake Blvd. E., Seattle, WA 98112.) 

Zaroogian, G. Gardner, D. Borsay Horowitz, R. Gutjahr-Gobell, R. Haebler, and L. Mills. 2001. Effect 

of 17 beta-estradiol, o,p’-DDT, octylphenol, and p,p’-DDE on gonadal development and liver and 

kidney pathology in juvenile male summer flounder (Paralichthys dentatus). Aquat. Toxicol. 54 

(2001):101–112 

Zimmerman, M. P. 1999. Food habits of smallmouth bass, walleyes, and northern pikeminnow in the 

lower Columbia River basin during outmigration of juvenile anadromous salmonids. Trans. Am. 

Fish. Soc. 128:1036–1054. 

Zimmerman, M. P., and D. L. Ward. 1999. Index of predation on juvenile salmonids by northern 

pikeminnow in the lower Columbia River basin from 1994–96. Trans. Am. Fish. Soc. 128:995–

1007. 

Zimmerman, M. P., T. A. Friesen, D. L. Ward, and H. K. Takata. 2000. Development of a system wide 

predator control program: Indexing and fisheries evaluation. Annual report to Bonneville Power 

Administration. Oregon Dept. Fish and Wildlife, Salem. 

105

Most NOAA Technical Memorandums NMFS-NWFSC are available online at the

Northwest Fisheries Science Center web site (http://www.nwfsc.noaa.gov).

Recent NOAA Technical Memorandums NMFS

published by the

Northwest Fisheries Science Center

NOAA Tech. Memo.

NMFS-NWFSC68 Bottom, D.L., C.A. Simenstad, J. Burke, A.M. Baptista, D.A. Jay, K.K. Jones, E. Casillas, and M.H.

Schiewe. 2005. Salmon at river's end: the role of the estuary in the decline and recovery of Columbia

River salmon. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-68, 246 p. NTIS number

pending.

67 Holmes, E.E., W.F. Fagan, J.J. Rango, A. Folarin, J.A. Sorensen, J.E. Lippe, and N.E. McIntyre.

2005. Cross validation of quasi-extinction risks from real time series: an examination of diffusion

approximation methods. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-67, 37 p. NTIS

number pending.

66 Good, T.P., R.S. Waples, and P. Adams (editors). 2005. Updated status of federally listed ESUs of West

Coast salmon and steelhead. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-66, 598 p. NTIS

number pending.

65 Fleischer, G.W., K.D. Cooke, P.H. Ressler, R.E. Thomas, S.K. de Blois, L.C. Hufnagle, A.R. Kronlund,

J.A. Holmes, and C.D. Wilson. 2005. The 2003 integrated acoustic and trawl survey of Pacific hake,

Merluccius productus, in U.S. and Canadian waters off the Pacific coast. U.S. Dept. Commer., NOAA

Tech. Memo. NMFS-NWFSC-65, 45 p. NTIS number pending.

64 Ferguson, J.W., G.M. Matthews, R.L. McComas, R.F. Absolon, D.A. Brege, M.H. Gessel, and L.G.

Gilbreath. 2005. Passage of adult and juvenile salmonids through federal Columbia River power system

dams. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-64, 160 p. NTIS PB2005-104828.

63 Williams, J.G., S.G. Smith, R.W. Zabel, W.D. Muir, M.D. Scheuerell, B.P. Sandford, D.M. Marsh,

R.A. McNatt, and S. Achord. 2005. Effects of the federal Columbia River power system on salmonid

populations. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-63, 150 p. NTIS PB2005-107352.

62 Krahn, M.M., M.J. Ford, W.F. Perrin, P.R. Wade, R.P. Angliss, M.B. Hanson, B.L. Taylor,

G.M. Ylitalo, M.E. Dahlheim, J.E. Stein, and R.S. Waples. 2004. 2004 Status review of Southern

Resident killer whales (Orcinus orca) under the Endangered Species Act. U.S. Dept. Commer., NOAA

Tech. Memo. NMFS-NWFSC-62, 73 p. NTIS PB2005-106089.

61 Berejikian, B.A., and M.J. Ford. 2004. Review of relative fitness of hatchery and natural salmon. U.S.

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-61, 28 p. NTIS PB2005-106090.

60 Ford, M.J., T.A. Lundrigan, and P.C. Moran. 2004. Population genetics of Entiat River spring Chinook

salmon. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-60, 45 p. NTIS PB2004-107039.