U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

NOAA Technical Memorandum NMFS-NWFSC-68

Salmon at River's End:

The Role of the Estuary in the Decline

and Recovery of Columbia River Salmon

August 2005
NOAA Technical Memorandum

NMFS Series

The Northwest Fisheries Science Center of the National

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

appropriate or feasible due to time constraints. Documents published in this series may be referenced in the

scientific and technical literature.

The NMFS-NWFSC Technical Memorandum series of

the Northwest Fisheries Science Center continues the

NMFS-F/NWC series established in 1970 by the

Northwest & Alaska Fisheries Science Center, which

has since been split into the Northwest Fisheries

Science Center and the Alaska Fisheries Science

Center. The NMFS-AFSC Technical Memorandum

series is now being used by the Alaska Fisheries

Science Center.

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:

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.
NOAA Technical Memorandum NMFS-NWFSC-68

Salmon at River's End:

The Role of the Estuary in the Decline

and Recovery of Columbia River Salmon

Daniel L. Bottom, Charles A. Simenstad1, Jennifer Burke1,

Antonio M. Baptista2, David A. Jay2, Kim K. Jones3,

Edmundo Casillas, and Michael H. Schiewe

Northwest Fisheries Science Center

Fish Ecology Division

2725 Montlake Boulevard East

Seattle, Washington 98112

University of Washington

School of Aquatic and Fishery Sciences

Seattle, Washington 98195

Oregon Health and Science University

OGI School of Science and Engineering

Department of Environmental and Biomolecular Systems

Beaverton, Oregon 97006

Oregon Department of Fish and Wildlife

Aquatics Inventories

Corvallis, Oregon 97333

August 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

1

2

3
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:

National Technical Information Service

5285 Port Royal Road

Springfield, VA 22161

phone orders (1-800-553-6847)

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

ii
Table of Contents 

List of Figures.............................................................................................................................................vii

List of Tables ...............................................................................................................................................xi

Executive Summary ...................................................................................................................................xiii

Acknowledgments...................................................................................................................................xxvii

Abbreviations and Acronyms ..................................................................................................................xxix

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

Estuarine Development History and Salmon Decline...................................................................................5

Estuary Description ..................................................................................................................................5

Estuarine Requirements of Juvenile Salmon ............................................................................................6

Historical Change in Salmon Populations and Estuarine Habitats...........................................................9

Population Decline .............................................................................................................................10

Factors of Decline ..............................................................................................................................12

History of Research in the Columbia River Estuary ..............................................................................19

A Conceptual Framework for Evaluating Estuarine Habitat Conditions....................................................21

Introduction ............................................................................................................................................21

Historical Perspectives on Salmon in Estuaries .....................................................................................22

Production Thinking in Estuarine Research.......................................................................................22

Population Thinking in Estuarine Research .......................................................................................25

A Theory of Populations with Complex Life Cycles.............................................................................27

Population Pattern and Richness........................................................................................................28

Abundance and Variability.................................................................................................................30

Applications of the Theory to Salmon and Estuaries .............................................................................30

Geographic Structure of Populations and Life Histories....................................................................31

Salmon Resilience and Production.....................................................................................................33

Salmon Imprinting and Homing.........................................................................................................34

Geographic Mechanisms of Population Control ................................................................................36

A Framework for Evaluating Estuarine Requirements of Columbia River Salmon..............................40

Evaluation Principles..........................................................................................................................40

Evaluation Criteria .............................................................................................................................41

Subyearling Chinook Salmon as an Indicator of Estuarine Conditions .............................................44

Changes in Hydrological Conditions..........................................................................................................47

Introduction ............................................................................................................................................47

iii
General Hydrological Characteristics.....................................................................................................48

Data Sources Used for Hydrological Analyses ......................................................................................50

Hydrological Effects of Climate Cycles.................................................................................................50

El Niño Southern Oscillation and Pacific Decadal Oscillation Effects 

on the Annual Flow Cycle..................................................................................................................51

Sediment Transport: Amplification of Climate Effects......................................................................52

Subbasin Sources of Flow and Major Freshets.......................................................................................54

Subbasin Sources of Flow..................................................................................................................54

Inferences from Selected Flow Histories ...........................................................................................54

Human- and Climate-induced Changes to the River-flow Magnitude and Timing................................55

Total Annual Average River Flow from the Eastern Subbasin..........................................................55

Eastern Basin, Spring-freshet Magnitude and Timing .......................................................................61

Changes in Western Subbasin Flows .................................................................................................64

River Flows at the Head of the Estuary..............................................................................................65

Flows from Estuary Tributaries..........................................................................................................66

Total Columbia River Flow at the Mouth ..........................................................................................67

Human- and Climate-induced Changes in Sediment Transport .............................................................67

Human and Climate Effects on Disturbance Frequency.........................................................................72

Historical Changes in Overbank Flow ...............................................................................................72

Changes in the River-flow Frequency Distribution............................................................................73

Climate and Human Influences on Freshet Styles..............................................................................75

Downstream Effects of Hydrological Alterations..................................................................................77

Salinity Intrusion and Salinity Stratification ......................................................................................77

Tidal Regime and River Stage............................................................................................................78

Shallow-water Habitat Availability....................................................................................................79

Estuarine Sediment Dynamics............................................................................................................80

Effects of Future Climate Change ..........................................................................................................80

Implications of Hydrological Change for the Member/Vagrant Hypothesis..........................................81

Conclusions ............................................................................................................................................83

Human and Climate Influences on Flow and Sediment Transport.....................................................83

Large-scale Geography.......................................................................................................................83

Climate Change ..................................................................................................................................84

Climate Cycles ...................................................................................................................................84

Pacific Decadal/El Niño Southern Oscillation Interaction.................................................................84

Latitudinal Position ............................................................................................................................84

Climate Effects on Sediment..............................................................................................................84

Annual Average Flow at The Dalles..................................................................................................85

Spring-freshet Properties....................................................................................................................85

Maximum Daily Flow at The Dalles..................................................................................................85

Spring-freshet Timing at The Dalles..................................................................................................85

Willamette River Hydrology..............................................................................................................85

Columbia River Flow at the Mouth....................................................................................................85

Changes in Sediment Transport .........................................................................................................86

iv
Disturbance Frequency.......................................................................................................................86

Changes in Shallow-water Habitat Area ............................................................................................86

Changes in the River-flow Frequency Distribution............................................................................86

Spring-freshet Styles..........................................................................................................................86

Winter-freshet Styles..........................................................................................................................87

Downstream Effects of Hydrological Alterations..............................................................................87

Effects of Future Climate Change ......................................................................................................87

Implications for Salmon Diversity and Productivity..........................................................................87

Estuarine Habitat Opportunity ....................................................................................................................89

Introduction ............................................................................................................................................89

Dynamics of Habitat Opportunity ......................................................................................................89

Modeling Approach............................................................................................................................90

Establishing Criteria for Habitat Opportunity ....................................................................................93

Simulation Scenarios, Methods, and Uncertainty...................................................................................94

Choice of the Computational Domain................................................................................................94

Creation of the Bathymetric Database................................................................................................94

Creation of a Computational Grid ......................................................................................................97

Specification of Boundary Conditions...............................................................................................97

Simulation Model...............................................................................................................................98

Results....................................................................................................................................................98

Habitat Opportunity............................................................................................................................98

Combined Criteria ............................................................................................................................111

Residence Times ..............................................................................................................................112

Residual Velocities...........................................................................................................................113

Implications for the Member/Vagrant Hypothesis...............................................................................118

Conclusions ..........................................................................................................................................121

Representation of Modern Bathymetry, Particularly in the Shallowest Areas.................................124

Characterizing Habitat Opportunity .................................................................................................124

Implications for Salmonid Rearing Habitat......................................................................................125

Estuarine Habitat Capacity .......................................................................................................................127

Introduction ..........................................................................................................................................127

Foraging Habitat and Food-web Changes............................................................................................129

Salmonid Use of Shallow Estuarine Habitats...................................................................................129

Effects of Wetland Loss...................................................................................................................130

Prey Availability ..............................................................................................................................132

Nonindigenous Species ........................................................................................................................132

Asian Clam.......................................................................................................................................132

Zooplankton .....................................................................................................................................134

American Shad .................................................................................................................................135

Predation...............................................................................................................................................137

Changes in Habitat Capacity and Implications for the Member/Vagrant Hypothesis..........................137

Conclusions ..........................................................................................................................................140

v
Change in Juvenile Salmon Life History, Growth, and Estuarine Residence..........................................142

Introduction ..........................................................................................................................................142

Approach and Objectives .................................................................................................................144

Data Sources and Methods for Life History Analysis......................................................................144

Life History Reconstruction .................................................................................................................149

Stream-type Juveniles.......................................................................................................................149

Ocean-type Juveniles........................................................................................................................149

Historical Estuarine Residence Times and Performance......................................................................156

Length Characteristics......................................................................................................................156

Estuarine Growth and Residence Times...........................................................................................156

Contemporary Estuarine Residence Times and Performance...............................................................159

Patterns of Abundance......................................................................................................................159

Habitat Use.......................................................................................................................................161

Length Characteristics......................................................................................................................163

Estuarine Residence .........................................................................................................................164

Discussion ............................................................................................................................................166

Change in Estuarine Life Histories ..................................................................................................166

Historical and Contemporary Factors Affecting Salmonid Life Histories.......................................171

Conclusions ..........................................................................................................................................180

Synthesis: Review of the Conceptual Framework ...................................................................................185

Introduction ..........................................................................................................................................185

Evidence ...............................................................................................................................................185

Geographic Structure........................................................................................................................185

Habitat Linkages ..............................................................................................................................186

Spatial and Energetic Process...........................................................................................................187

Implications..........................................................................................................................................189

Conservation Programs Must Account for Diverse Estuarine Life Histories...................................189

Recovery Actions Should Expand Habitat Opportunity, Life History Variation.............................190

Reference Conditions Must Be Defined To Establish Recovery Goals...........................................190

Conserving Habitat Linkages Requires Ecosystem-scale Planning .................................................191

New Research Approaches Needed .................................................................................................192

Summary and Conclusions...................................................................................................................194

Conclusions and Recommendations .........................................................................................................196

Conclusions ..........................................................................................................................................196

Recommendations ................................................................................................................................197

References.................................................................................................................................................205

Appendix A: Timeline for the Columbia River Basin, 1775–2000 .........................................................229

vi
List of Figures 

Figure 1. The tidal influence of the Columbia River extends upstream from its mouth 

at the Pacific Ocean to the Bonneville Dam. ................................................................................................6

Figure 2. Current and historical distribution of anadromous salmonids in the 

Columbia River basin. ................................................................................................................................11

Figure 3. Present distribution of pink, coho, chum, and sockeye salmon in the 

Columbia River basin.. ...............................................................................................................................13

Figure 4. Present distribution of summer and winter steelhead in the Columbia River basin.. .................14

Figure 5. Present distribution of spring-, summer-, and fall-run Chinook salmon 

in the Columbia River basin........................................................................................................................15

Figure 6. Present distribution of salmon hatcheries and mainstem and secondary dams 

along rivers and streams of the Columbia River basin. ..............................................................................17

Figure 7. The continuum in population richness of selected anadromous and marine species 

in the northern Atlantic. ..............................................................................................................................29

Figure 8. Salmon production as influenced by life history diversity. ........................................................35

Figure 9. Generalized view of a salmon life cycle and three scenarios of spatial losses 

that can affect life cycle closure..................................................................................................................37

Figure 10. Criteria for evaluating estuarine-rearing conditions for subyearling salmon 

as implied by the member/vagrant hypothesis............................................................................................42

Figure 11. Proposed model of relative migration rates and residence times for salmonid species in 

freshwater and estuarine rearing environments of the Columbia River basin. ...........................................45

Figure 12. External factors at regional and basin scales that affect the physical template 

of the estuary and the performance of subyearling salmon.........................................................................48

Figure 13. The ENSO/PDO response of eastern subbasin flow at The Dalles. .........................................53

Figure 14. The ENSO/PDO response of eastern subbasin total sediment load calculated 

at Vancouver using flow data at The Dalles. ..............................................................................................53

Figure 15. Daily observed Columbia River eastern subbasin flow at The Dalles, 1879–1999..................56

Figure 16. Daily adjusted Columbia River eastern subbasin flow at The Dalles, 1879–1999...................57

Figure 17. Estimated daily virgin Columbia River eastern subbasin flow at The Dalles, 1879–1999. .....58

Figure 18. Comparison of the monthly averaged Columbia River eastern subbasin virgin, 

adjusted, and observed river-flow estimates at The Dalles, 1970–1999.....................................................59

Figure 19. Comparison of the monthly averaged Columbia River eastern subbasin 

virgin river flow at The Dalles between 1878–1899 and 1945–1999.........................................................59

Figure 20. Seasonal magnitude and timing of Columbia River eastern subbasin freshets 

at The Dalles, 1878–1999. ..........................................................................................................................62

vii
Figure 21. A linear fit to of peak freshet day versus year; the spring freshet now occurs 

about two weeks earlier than in the 19th century........................................................................................63

Figure 22. Reduction of the monthly mean June flow...............................................................................64

Figure 23. Observed daily Willamette River flow at Albany, 1893–1998. ...............................................66

Figure 24. Historical changes in the annual flow cycle of the Willamette River at Albany, 

1878–1903 versus 1970–1999. ...................................................................................................................67

Figure 25. The combined eastern and western subbasin flows: estimated observed daily 

Columbia River flow at Beaver, 1892–1999.. ............................................................................................68

Figure 26. Changes in the annual flow cycle of the Columbia River at the Beaver Army Terminal, 

1878–1903 versus 1970–1999. ...................................................................................................................69

Figure 27. Hindcast total sediment load for the Columbia River eastern basin calculated 

at Vancouver from the observed flow and estimated virgin flow...............................................................70

Figure 28. The incidence of flows above 18,000 m3s

-1 and above 24,000 m3

s

-1........................................72

Figure 29. Monthly average flows at the Beaver Army Terminal, 1878–1999, 

present and historical bankfull flow levels, and warm and cold PDO cycles. ............................................73

Figure 30. Power spectra of the observed daily flow at The Dalles, 1878–1910 and 1970–1999.............74

Figure 31. Scaleogram of observed flow at The Dalles.............................................................................75

Figure 32. Maximum and minimum salinity intrusion distance in the Columbia River estuary, 

based on 1980 bathymetric conditions........................................................................................................78

Figure 33. External factors affecting disturbance processes and the physical template of the estuary......82

Figure 34. Changes in flow and bathymetry alter the dynamics of habitat opportunity for salmon 

within the estuary........................................................................................................................................90

Figure 35. Different domains of simulation within CORIE.......................................................................91

Figure 36. A model of bathymetry for the Columbia River estuary.. ........................................................95

Figure 37. A model of predevelopment 1880 bathymetry of the Columbia River estuary........................96

Figure 38. A model of corrected bathymetry for the Columbia River estuary 

predevelopment system...............................................................................................................................96

Figure 39. A model of Columbia River estuary predevelopment 1880 bathymetry.. ................................97

Figure 40. Isolines of Columbia River estuarine habitat opportunity for May 1997, 

in hours normalized to a 30-day month, using depth , velocity , and combined criteria. ........................100

Figure 41. Different environments in the Columbia River estuary offer distinct 

habitat opportunity. ..................................................................................................................................101

Figure 42. Isolines of habitat opportunity in Region 4 for May 1997, in hours normalized 

to a 30-day month, using depth, velocity, and combined criteria. ............................................................102

Figure 43. Isolines made by comparing the differences in Columbia River habitat opportunity 

available in Region 4, using depth, velocity, and combined criteria. .......................................................103

Figure 44. Seasonal variation of Columbia River estuarine habitat opportunity in Region 4 

for velocity and depth criterion.................................................................................................................104

viii
Figure 45. River flow and seasonal variation of Columbia estuarine habitat opportunity 

in Region 4 for modern versus predevelopment systems..........................................................................105

Figure 46. River flow and seasonal variation of Columbia River estuarine habitat opportunity 

in Region 4 for modern bathymetry and flows and predevelopment bathymetry with 1997 flows..........106

Figure 47. River flow and seasonal variation of Columbia River estuarine habitat opportunity 

in Region 4 for predevelopment bathymetry and flows and predevelopment bathymetry 

with 1997 flows.........................................................................................................................................107

Figure 48. Columbia River estuarine habitat opportunity as a function of river flow, 

for the modern and predevelopment systems............................................................................................108

Figure 49. Region-by-region comparison of predevelopment and modern estuarine 

habitat opportunity as a function of river flow, for the velocity criterion.................................................109

Figure 50. Region-by-region comparison of predevelopment and modern estuarine 

habitat opportunity as a function of river flow, for the depth criterion.....................................................110

Figure 51. Columbia River estuary habitat opportunity in Region 4 as a function of river flow 

for velocity, depth, and combined criteria.. ..............................................................................................111

Figure 52. Sensitivity of habitat opportunity in modern Region 4 to the cut-off value 

of the velocity criterion.............................................................................................................................112

Figure 53. Residence times for high flow conditions in June 1997 and for low flow conditions 

in July 1997 in hours normalized to a 30-day month................................................................................114

Figure 54. Influence of river flow on residence times, at four fixed locations in the estuary..................115

Figure 55. Residence times for June 1997 at eight release times over the tidal cycle. ............................116

Figure 56. Time-series of residence times for a 5-plus-day period in June 1997 

at selected locations in the estuary............................................................................................................117

Figure 57. Residual velocities for high flow months in the predevelopment and modern systems.........119

Figure 58. Residual velocities show marked seasonality, with highest values 

corresponding to freshet months...............................................................................................................120

Figure 59. Residual velocities increase sharply with increasing river flow, with what appears 

to be a quasilinear correlation. ..................................................................................................................121

Figure 60. Reference bathymetry and modified bathymetry for Region 4 in the 

Columbia River estuary for May 1880 .....................................................................................................122

Figure 61. Variations of daily averaged residual velocities for May 1880 in isoline form, 

and estuary-wide correlation of standard deviations with flow for selected modern 

and predevelopment years.........................................................................................................................123

Figure 62. Conceptual model of physical linkages to estuarine habitat opportunity 

for subyearling salmon..............................................................................................................................124

Figure 63. Habitat capacity refers to various habitat qualities that mediate biological interactions 

and, thereby, influence salmon performance within the estuary...............................................................128

Figure 64. Counts of adult American shad and adult spring and fall Chinook salmon at 

Bonneville Dam, 1975–1999. ...................................................................................................................136

Figure 65. Network of physical and biological linkages influencing estuarine habitat capacity 

for subyearling salmon..............................................................................................................................139

ix
Figure 66. Together with habitat opportunity and habitat capacity, salmon performance 

within the estuary is directly linked to population structure upriver.........................................................143

Figure 67. The Columbia River estuary and tributaries, with sites sampled by Rich, 1914–1916..........145

Figure 68. Example of subyearling Chinook salmon scale patterns analyzed by Rich............................147

Figure 69. Range of subyearling Chinook salmon fork lengths collected by Rich at Point Ellice, 

March–August 1916..................................................................................................................................147

Figure 70. Proportion of subyearling and yearling Chinook salmon collected concurrently in 1916. ....150

Figure 71. Subyearling Chinook salmon fork length at time of collection and percent 

of total length attributed to estuarine growth............................................................................................158

Figure 72. Subyearling Chinook salmon size at arrival in the estuary and percent 

of total length attributed to estuarine growth............................................................................................160

Figure 73. Timing correlation between peak abundance at Jones Beach and the arrival 

of hatchery-reared subyearling Chinook salmon. .....................................................................................162

Figure 74. Recovery timing of wild and hatchery subyearling Chinook salmon 

from the Lewis River at Jones Beach........................................................................................................163

Figure 75. Fork length characteristics of subyearling Chinook salmon collections 

from three studies in 1916, 1966, and 1980 in the lower Columbia River estuary...................................164

Figure 76. Fork length characteristics of subyearling Chinook salmon of wild and 

hatchery origin recovered in the Columbia River estuary at Megler, Washington, in 1966. ....................165

Figure 77. Fork length characteristics of subyearling Chinook salmon of hatchery origin 

recovered in the Columbia River estuary between RKm 16 and RKm 20 in 1980. .................................166

Figure 78. Fork length characteristics of subyearling Chinook salmon of unknown origin 

recovered in the Columbia River estuary at McGowan in 1980...............................................................167

Figure 79. Historical and contemporary early life history types for one broodyear 

of Chinook salmon in the Columbia River estuary...................................................................................172

Figure 80. Harvest timeline for Chinook salmon, 1800–1916 based on significant events 

presented by Oregon State Board of Fish Commissioners........................................................................174

Figure 81. The effect of seasonal protection of salmon runs in the Columbia River...............................176

Figure 82. Interpretation of early life history behavior based on scale patterns from returning 

salmon adults collected in the Columbia River estuary, 10 May–12 September 1919.............................177

Figure 83. River flows for 1916, 1966, and 1980. ...................................................................................180

Figure 84. Time and relative duration of subyearling Chinook outmigration from six tributaries 

into the Columbia River estuary during 1963...........................................................................................181

Figure 85. Linkages to life history and geographic structure of salmon populations 

upriver affect salmon performance within the estuary..............................................................................183

Figure 86. Linkages among salmon environments implied by the member/vagrant hypothesis. ............188

x
List of Tables 

Table 1. Listings and proposed listing of Columbia River salmonids under the ESA...............................12

Table 2. Contrasting views of salmon conservation in estuaries based on production 

and population thinking. .............................................................................................................................27

Table 3. Juvenile life history types for Chinook salmon in the Sixes River..............................................32

Table 4. Possible mechanisms of increased straying of fish through hatchery 

and transportation manipulations................................................................................................................39

Table 5. Factors affecting estuarine-habitat opportunity for juvenile salmon. ..........................................42

Table 6. Effects of PDO variations the annual average flows of the Columbia 

and Willamette rivers..................................................................................................................................52

Table 7. Estimated effects of climate change on total sediment transport and 

on sand transport based on virgin-flow estimates at The Dalles.................................................................70

Table 8. Long-term changes in total sediment and sand transport based 

on hindcast virgin flows and observed flows at The Dalles........................................................................71

Table 9. Summary of two-dimensional simulation database for bathymetric and velocity analyses. .......94

Table 10. Interpretation of subyearling Chinook life history from scale analyses. .................................150

Table 11. Attributes of fry collected in the Columbia River estuary by Rich..........................................151

Table 12 Sampling effort and juvenile Chinook salmon attributes interpreted from scale patterns, 

1914–1916. ...............................................................................................................................................154

Table 13. Summary table of Chinook subyearlings collected at Point Ellice, May–August 1916. .........157

Table 14. Estuarine and freshwater growth rates from Pacific Northwest river systems. .......................159

Table A-1. Time line of historical, scientific, legal, and natural events affecting salmonids in the 

Columbia River basin. ..............................................................................................................................229

xi
xii
Executive Summary 

The continued decline of Columbia River salmon (Oncorhynchus spp.) populations has 

long focused concerns on habitat changes upriver, particularly the effects of large hydroelectric 

dams. Increasing evidence that ocean conditions strongly influence salmon production, however, 

has raised questions about the importance of the estuarine environment to salmon and whether 

the hydropower system has affected estuarine-rearing habitats. In response to Northwest Power 

Planning Council recommendations, we initiated a review of what is known about the effects of 

the hydroelectric system on the hydrology, habitats, and ecology of the Columbia River estuary. 

Our goal was to develop recommendations for improving estuarine conditions or to identify 

research that may be needed before appropriate salmon-management changes can be defined. 

Our review and analyses addressed four major questions: 

1) What habitats and processes support native salmon populations during the estuarine 

phase of their life cycle? 

2) Have changes to the estuary had a significant role in salmon decline? 

3) What have been the impacts of flow regulation on the hydrology, habitat, and biological 

interactions in the estuarine ecosystem? 

4) What estuarine conditions are necessary to maintain salmonid diversity in the Columbia 

River basin? 

Conclusions and Recommendations 

The results indicate that habitat and food-web changes within the estuary and other 

factors affecting salmon population structure and life histories have altered the estuary’s capacity 

to support juvenile salmon. Diking and filling activities that decrease the tidal prism and 

eliminate emergent and forested wetlands and floodplain habitats have likely reduced the 

estuary’s salmon-rearing capacity. 

However, simplification of the population structure and life-history diversity of salmon 

possibly is the most important factor affecting juvenile salmon performance. In the absence of 

data on present-day estuarine use by wild, subyearling (“ocean-type”) salmon, we concluded that 

basin-wide upriver habitat losses, overharvest, and production-oriented hatchery management 

practices clearly influence patterns of salmon abundance, diversity, and residency in the estuary. 

Restoration of estuarine habitats, particularly diked emergent and forested wetlands, and 

flow manipulations to restore historical flow patterns might significantly enhance the estuary’s 

productive capacity for salmon. It is possible that historical changes in population structure and 

salmon life histories, however, prevent salmon from fully utilizing the productive capacity of 

estuarine habitats even in their presently altered state. Therefore, efforts to improve or restore 

xiii
the estuary for salmon must be developed in concert with hatchery, harvest, and upriver habitat 

improvements to recover those life history types that can benefit from estuary restoration. 

A sound historical and evolutionary context for interpreting modern estuarine habitat 

conditions and for developing salmon recovery strategies is needed. Without proper context, 

recovery actions may inappropriately target those few salmon life history types and habitats that 

are abundant today, further reinforcing salmon decline symptoms rather than expanding the 

basin’s productive capacity. A strategy that continues emphasis on improving survival of a few 

Chinook salmon (O. tshawytscha) dominant types, particularly large hatchery yearlings and 

subyearlings with short estuarine residence times, may further narrow the distributions of size, 

migration timing, and rates of migration. This would result in concentrated use of the estuary 

and thus would prevent salmon from utilizing its full productive potential. 

While the extinction risk of many Columbia River populations implies the need for 

immediate recovery action, lack of data on estuarine habitat use by salmon requires that further 

study may be necessary before we can define appropriate restorative measures. Both of these 

concerns can be addressed by simultaneously initiating targeted restoration activities, where 

there is reasonable confidence in their ecological benefits, and collecting new data to better 

understand salmon habitat requirements and restoration needs. To achieve these ends, the 

following specific recommendations are offered: 

Adopt an Explicit Ecologically Based Conceptual Framework 

for Estuary Management and Restoration 

The lack of an explicit ecological framework for salmon conservation is a fundamental 

impediment to recovery efforts in the Columbia River basin. Such a framework is particularly 

important to direct recovery efforts in the estuary, where physical and biological interactions are 

complex and continually changing in response to tidal forces, river flows, and seasonal 

fluctuations in the composition of species assemblages. 

The lack of information about the estuarine-rearing requirements of juvenile salmon is 

the result of a long-standing “production” approach to salmon management and research. This 

approach assumes the estuary is a simple migration corridor in which mortality factors must be 

controlled, rather than a productive nursery ground where the varied habitat needs of diverse 

populations and life history types must be protected. 

In the estuary, the ecological requirements of salmon also must be placed in the broader 

context of factors at other life stages that shape population structure and life history. These 

factors determine whether juvenile salmon can realize the full productive potential of the estuary. 

We adapted a conceptual framework for this assessment (i.e., the “member/vagrant” hypothesis) 

that accounts for life cycle linkages to salmon performance in the estuary and for the diverse life 

histories and resilience of Columbia River populations. 

Protect and Restore Opportunity for Salmon to Access Emergent and Forested Wetlands 

in the Estuary and Riparian Wetlands in the Tidal Floodplain 

Historical losses of peripheral floodplain, wetland, and riparian habitats from diking and 

filling activities in the Columbia River estuary have reduced available rearing habitat for salmon 

xiv
with subyearling life histories. Such effects may not be limiting to yearling, stream-type 

juveniles at present because hatcheries, harvest, and upriver habitat losses tend to favor these life 

histories. Any effort to increase life history diversity, however, will require reestablishment of 

important rearing habitats that have been substantially modified or removed from the estuary. 

Studies in other Northwest estuaries indicate that wetland restoration could offer a 

cost-effective method to improve salmonid rearing conditions. Reestablishment of more natural 

flow regimes in the basin might also diversify estuarine habitat opportunity and its associated 

variety of salmon rearing and migration behaviors. 

Reacquire Phenotypic Diversity of Salmon, Including a Broader Range of Sizes, 

Times of Entry, and Periods of Residency in the Estuary 

Although increased genetic and life history diversity of salmon may ultimately require 

long-term expansion of habitat opportunity upriver and in the estuary, rapid progress in the use 

of existing or restored habitats could be made by expanding phenotypic diversity of salmon now 

heavily influenced by hatchery programs. Such improvements could require reductions in 

hatchery releases or changes in hatchery rearing practices. 

Any management changes to benefit salmonid use of the estuary, however, will require 

an improved accounting system and a greater degree of coordination of basin-wide hatchery 

programs than presently exists. For example, incomplete records of hatchery release groups, 

variations in rearing and release practices that confound interpretation of management effects, 

and difficulties in distinguishing the hatchery or wild origin of unmarked salmon preclude a full 

accounting of the influence of hatchery practices on salmon behavior and performance in the 

estuary. 

Monitor Variations in Life History Diversity, Habitat Use, 

and Performance of Juvenile Salmon in the Estuary 

Because the abundance and life histories of salmon in the estuary are linked to source 

populations and habitats upstream, changes in life history diversity and the relative proportions 

of wild juveniles in the estuary may indicate whether recovery efforts are working basin wide. 

Unfortunately there is no established monitoring program to describe long-term trends in salmon 

rearing behaviors in the estuary. Since 1914–1916, neither salmon scales nor otoliths have been 

collected or archived to evaluate changes in estuarine life history patterns. 

Most contemporary estuarine studies are of short duration, including numerous 

local-impact studies, and only rarely have they sampled many of the shallow habitats typically 

preferred by smaller subyearling salmon. Furthermore, the most consistent monitoring in the 

estuary has emphasized the migration rates and survival of large, hatchery-tagged fish, and 

poorly represents wild, ocean-type species and life histories that are likely most dependent upon 

estuarine conditions. A more representative sampling program is needed to monitor variability 

in the estuarine life histories and performance of salmon. 

xv
Review the Scientific Basis for Proposed Habitat and Bathymetric Changes in the Estuary 

Relative to the Restoration Goals of the Columbia Basin Fish and Wildlife Program 

Habitat changes and economic activities within the estuary have been evaluated 

independently of management or restoration efforts that affect salmon and their habitats 

elsewhere in the Columbia River basin. For example, the potential effects of ongoing or 

proposed estuarine dredging, spoil disposal, or habitat-restoration activities on the Columbia 

Basin Fish and Wildlife Program have not been explicitly evaluated. 

Because all anadromous salmonids in the Columbia River pass through or rear in the 

estuary before migrating to the ocean, changes in estuarine conditions could determine the 

effectiveness of salmonid recovery efforts throughout the basin. Modeling results show that 

estuarine habitat opportunity for salmonids is sensitive to bathymetric change. In addition, the 

response of predacious birds to artificially created dredge-spoil islands in the lower estuary 

illustrates that at least some estuarine habitat changes may have unexpected ecological 

consequences. 

Impact assessments associated with dredging and disposal activities usually have focused 

on localized impacts and have not considered salmonid responses to changes in habitat 

opportunity or capacity at a landscape scale. Nor have the assessments considered the history of 

incremental change upon which each new project is superimposed or the broader responses of 

the ecosystem to physical habitat modifications. 

Use Physical Observations and Hydrodynamic Modeling to Assess the Effects 

of Bathymetric Change, Flow Regulation, and Alternative Restoration Designs 

on Habitat Opportunity for Juvenile Salmon 

The hydrodynamic model applied in this assessment has proven to be a useful approach 

for evaluating the relative effects of flow modification and bathymetric change on habitat 

opportunity for salmon. However, its present application is limited by several critical data gaps, 

including the lack of present-day, high resolution bathymetric data and physical observations for 

shallow regions of the estuary. For example, the ability of the model to characterize physical 

habitat opportunity relative to the depth criterion (much more so than opportunity determined 

with respect to the velocity criterion) was very sensitive to assumed bathymetric configurations 

in the shallow areas of the estuary. This emphasizes the need to obtain accurate bank-to-bank 

bathymetric data for the lower river and estuary for improved understanding of the river flow 

impacts on physical habitat opportunity. 

Review Results of Estuarine Predation Studies in the Context 

of Salmon Population and Habitat Change 

It is unclear whether the high rates of salmon predation by Caspian terns (Sterna caspia) 

and other marine birds in the estuary is a significant factor affecting salmon recovery or an 

ecological symptom of other changes. Those changes might include alteration of estuarine 

habitats, simplification of the geographic structure of salmon populations, and reduced variation 

in salmon rearing and migration behaviors. 

xvi
High juvenile salmonid predation rates, however, could result from replacing a broad 

continuum of salmon life history types with punctuated releases of large hatchery fish that are 

concentrated in relatively few estuarine habitats over reduced time periods. Hatchery-induced 

changes in surface-feeding behavior also could be a factor increasing the vulnerability of salmon 

smolts to predators. Emphasis on estimating predation rates alone thus may lead to inappropriate 

salmon recovery proposals unless these results are evaluated in a broader historical and 

ecological framework. 

Assess the Effects of Altered Habitats and Food Webs on the Capacity 

of the Estuary to Support Juvenile Salmon 

The results indicate that a variety of ecological changes may have affected the estuary’s 

capacity to support wild subyearling Chinook salmon. These changes include loss of floodplain 

and other wetland habitats, the effects of climatic changes on physical processes and estuarine 

food webs, interactions with an increasing number of nonindigenous species, and shifts in the 

timing of established patterns of river flow and salmon migrations. The direction or magnitude 

of these ecological changes, unfortunately, cannot be assessed from the limited empirical data 

available. 

The effects of altering food-web sources through habitat modifications, for example, have 

not been directly evaluated. We also have little data to assess the effects of a two-week advance 

in the spring freshet because of flow regulation and a substantial delay in peak salmon 

migrations because of hatchery and other influences. If estuarine prey-production cycles and 

salmon-migration behaviors are adaptive and linked to flow variations, then such changes could 

create a mismatch between salmon and their prey resources, reducing the productive capacity of 

the estuary. 

Changes in the coarse and fine sediment budgets, particularly the quality of organic 

matter input to the system, also are poorly understood. 

Research Approach and Results 

The first two sections establish the context for this evaluation, including a review of 

historical changes throughout the basin that have affected salmon and estuarine habitats, and the 

conceptual framework upon which our analyses and interpretations are based. The subsequent 

four sections describe results of the following analyses: 

• A review of climatic variations and human-induced changes in river flow during the past 

140 years that have influenced estuarine-rearing opportunities and capacities for 

Columbia River salmon. 

• An evaluation of simulation modeling to understand the dynamics of salmon habitat 

opportunity within the estuary. 

• An assessment of ecological changes in the estuary that could affect the capacity of 

estuarine habitats to support salmon. 

• An analysis of historic changes in the estuarine performance of salmon using indicators 

of growth and life history variation. 

xvii
From the results of these analyses, we reexamine the validity of our conceptual framework and 

its implications for salmon and estuarine-habitat conservation. 

The principal findings of each of these chapters are briefly summarized below: 

Estuarine Development History and Salmon Decline 

Industrial development of the Columbia River and its estuary and declines in salmon 

populations are well documented. The effects of intensive harvest were apparent throughout the 

Columbia River basin by 1911, just as dam construction and irrigation diversion were beginning, 

and alterations to the estuary for navigation were unfolding. Increased salmon-conservation 

measures and management initiatives, however, coincided with the decline in freshwater habitat, 

regulation and diversion of river flow, and estuarine habitat loss and degradation. 

Installation of hydroelectric and irrigation diversion dams without providing for fish 

passage reduced salmon spawning and rearing habitat by 55%. Today, 23 mainstem and more 

than 300 tributary dams regulate the flow of the Columbia to the Pacific Ocean. Through this 

development history, the Columbia River became progressively channelized and detached from 

its floodplain. 

Approximately 65% of the tidal marsh and swamp habitat below Jones Beach (RKm 75) 

in Oregon had been diked or filled by the middle of the 20th century. The loss of these habitats 

between Jones Beach and Bonneville Dam (RKm 235) was likely greater but has not been 

quantified. Many other activities have degraded habitat throughout the estuary including upland 

logging and agriculture, shoreline armoring, construction of over-water structures, removal of 

large wood, and channel deepening and widening. 

In order to compensate for habitat losses and salmon decline, resource managers 

developed intensive hatchery programs that substituted concentrated releases of a few artificially 

produced stocks for the more diverse populations and life-history types that were formerly 

distributed throughout the watershed. As a consequence of these and other factors addressed in 

this analysis, historical Columbia River salmon returns between 11 million and 16 million fish 

annually have now declined to fewer than 12% of predevelopment levels. 

A Conceptual Framework for Evaluating Estuarine Habitat Conditions 

An agricultural approach to fisheries management that sought to eliminate apparent 

production “bottlenecks” has long ignored the estuary’s role in supporting salmon populations. 

A fundamental impediment to salmon and estuary recovery, therefore, is the lack of a conceptual 

framework that adequately explains the evolutionary and ecological requirements of diverse 

salmon populations. 

For this assessment, we adapted a conceptual framework (the “member/vagrant” 

hypothesis) that was developed to explain the dynamics and population richness of marine 

species with complex life cycles. The member/vagrant hypothesis suggests that life history 

diversity in salmon is based on the geography of local, self-perpetuating populations and the 

variety of habitats that can support salmon life cycles. A crucial assumption of this framework is 

that the resilience of Columbia River salmon to natural environmental variability is embodied in 

xviii
population and life history diversity, which maximizes the ability of populations to exploit 

available estuarine rearing habitats. This framework recognizes variation in rearing behavior 

(phenotypic diversity) as the result of diverse salmon genotypes interacting with unique habitat 

features, including those within estuaries. 

These interactions result in a variety of alternative behavioral “solutions” for salmon to 

successfully complete their life cycles, such as variations in the timing and age of migration, 

duration of residency in the river and estuary, and size at ocean entry. The total productive 

capacity of the Columbia River basin for salmon, therefore, is a function of all combinations of 

genotype and habitat that allow for the full expression of salmon rearing and migration 

behaviors, including diverse life histories in the estuary. 

Any changes that sever the link between salmon behavior and habitat may affect the 

productive potential of the Columbia River estuary, for example: 

• removing or degrading estuarine habitats that salmon require to express the full diversity 

of potential rearing behaviors, 

• altering the geographic structure or genetic characteristics of component populations 

throughout the basin that converge in the estuary en route to the ocean, or 

• directly altering the phenotypic behavior of salmon through hatchery rearing and release 

practices, transportation of fish around dams, etc., regardless if the underlying genetic 

structure of populations is affected. 

In this evaluation, an effort was made to distinguish the role of the Columbia River 

hydropower system from other factors that influence the salmon rearing capacity of the estuary, 

including phenotypic or genetic effects that can determine whether salmon fully utilize this 

capacity. Our analyses emphasized subyearling “ocean-type” Chinook salmon, because this life 

history type makes maximum use of estuarine habitats and likely would be most sensitive to 

changes affecting the estuary. However, results of these analyses also should apply to other 

salmon species with “ocean-type” life histories, particularly chum salmon. 

Changes in Hydrological Conditions 

The magnitude and timing of river flow, which significantly influence estuarine habitat of 

juvenile salmon, have been highly modified at the watershed level. The predevelopment flow 

cycle of the Columbia River has been totally reshaped by hydropower regulation and irrigation 

withdrawal. While there is a prominent climate signal in river-flow variability over the period of 

the analysis (1859–present), the magnitude of maximum spring-freshet flow has decreased more 

than 40% from the predevelopment period (1859–1899) to the present. Flow regulation is 

responsible for approximately 75% of this loss, irrigation withdrawal for approximately 20%, 

and climate change for approximately 5%. 

The timing of maximum spring-freshet flow also has changed, primarily because of 

hydropower and irrigation development upriver, resulting in an approximate two-week shift 

earlier in the year (mean predevelopment date of 12 June compared to modern mean date of 29 

May). Flow regulation now exacerbates early maximum spring-freshet peak flows, such as the 

23 April freshet peak in the year 2000. Gradual climate warming also has contributed to the 

xix
change in freshet timing. Also, the annual average flow at the mouth has been reduced from 

about 8,500 m3

s

-1 to less than 7,000 m3

s

-1, with climate change and water withdrawal each 

responsible for approximately 50% of the reduction. 

Changes in hydrology have had a significant impact on salmon habitat. Suppression of 

winter- and spring-freshet flows, compounded by flood-control diking and wetland reclamation 

below Bonneville Dam, has greatly reduced the frequency of overbank flows. Thus salmon 

rearing habitat in riparian areas and backwater channels has been blocked during flood events, 

and the input of large woody debris has been eliminated in the upper tidal floodplain. 

Riverine sediment transport to the estuary, an important process affecting the quantity 

and quality of estuarine habitat for salmon, is correlated with peak river flows. It is impossible 

to separate the effects of flow regulation and irrigation withdrawal precisely from climatic 

variability. However, it is estimated that the corresponding change in annual average sediment 

transport (at Vancouver, Washington) for 1945–1999 flows has been about 50–60% of the 19th 

century (1858–1899) virgin sediment transport. The reduction in sands and gravels is higher 

(>70% of predevelopment) than for silts and clays. 

In addition to peak spring-freshet flow and sediment-transport changes, the frequency in 

river-flow cycles is highly altered by the hydroelectric system’s peaking cycle. Low frequency 

variations with periods between approximately two years and six months have been suppressed, 

and high frequency variations with periods of a week or less have been accentuated. 

We conclude that the hydrological changes in the basin have caused a fundamental shift 

in the physical state of the Columbia River ecosystem. The member/vagrant hypothesis implies 

that such changes, including stabilization of river flows and elimination of overbank flooding, 

may have significant consequences for salmon populations, whose migration and rearing 

behaviors have adapted to historical patterns of hydrologic variability. 

Estuarine Habitat Opportunity 

We evaluated a two-dimensional numerical circulation model as a tool for understanding 

the dynamics of habitat opportunity for juvenile salmon and the potential effects of 

anthropogenic changes in the estuary that affect these dynamics. The model simulated changes 

in the occurrence and distribution of shallow-water, low-velocity habitat during predevelopment 

(1880) and modern (1997–1999) periods. Predevelopment and modern river flows and estuarine 

bathymetry were used to simulate and compare the habitat opportunity (total hours that “suitable 

habitat” occur in a one-month simulation period) for salmon in the historical and present estuary. 

“Suitable habitat” for juvenile salmon was operationally defined using two physical criteria: 

areas with water depths ranging from 0.1 to 2 m and areas with water velocities less than 

0.3 m3

s

-1. 

Results showed that availability of suitable habitat varies significantly within the estuary 

in response primarily to bathymetry but also to tides and river flows. 

Seasonal and interannual variability also is very significant, particularly in the upriver, 

tidal-freshwater mainstem region and upper-estuary peripheral bays, where habitat opportunity is 

reduced during freshet months. Based on meeting the velocity criterion in model simulations, 

xx
habitat opportunity under modern river flows and estuarine bathymetry has generally declined in 

the upriver, tidal-freshwater mainstem region and the upper-estuary peripheral bays (Cathlamet 

and Grays), while it has not changed dramatically in the lower regions of the estuary. 

Model simulations of habitat opportunity based on the depth criterion, however, provide 

different results. Simulated depth regimes across the estuary suggest that habitat opportunity 

under modern flows and bathymetry has increased relative to historical conditions, except in the 

upper tidal-freshwater region. Yet limitations in the representation of modern bathymetry in the 

hydrodynamic model reduce confidence in the model simulation results based on the depth 

criterion. 

Moreover, estimates based on the velocity criterion appear much less sensitive to model 

uncertainties than those based on the depth criterion. Since our level of confidence in the 

simulation results varies for each criterion, the modern and historical habitat opportunity based 

on the depth and velocity criteria combined cannot be interpreted now. Furthermore, because 

peripheral wetlands that were historically diked and filled are not well represented in the 

predevelopment bathymetry, the simulations may underestimate predevelopment habitat 

opportunity to an unknown degree. 

Overall, model simulations have revealed several important features relating river flow 

and bathymetry to habitat opportunity: 

• First, the results suggest that habitat opportunity in some regions of the predevelopment 

estuary was more resilient to increasing river flows than it is in the modern estuary. 

Resilience in this context refers to a reduced rate of change (slope) when correlating 

hours of habitat opportunity with river flow. This result was evident only in the upriver, 

tidal-freshwater mainstem region (above the main body of the lower estuary) and the 

upper-estuary peripheral bays (Cathlamet and Grays). 

• Second, in the model simulations, estuarine bathymetry largely determined habitat 

availability as defined by the velocity and depth criteria described above. In addition, 

simulations of habitat opportunity under predevelopment bathymetry but with modern 

flows again suggested that bathymetric changes and habitat loss may be more influential 

in changing habitat opportunity than flow regulation. 

• Third, seasonal changes in habitat opportunity have shifted between historical and 

modern conditions. Minimum habitat opportunity in the estuary is associated with 

freshets that now occur earlier in the year than they did in the late 1800s. The impact of 

advancing the period of minimum habitat opportunity for juvenile salmon is unknown. 

These characterizations of change in shallow-water habitat are preliminary and must be 

viewed cautiously. Model predictions have not been empirically validated in regions without 

instrumentation, including the important shallow-water environments of Cathlamet Bay. 

Moreover, inadequacies in the modern bathymetric data affect habitat opportunity estimates, and 

substantial shoreline wetland and floodplain habitat lost to diking and filling are not fully 

incorporated in the simulations. 

Although preliminary, these results demonstrate that simulation modeling can provide 

useful insights into the physical dynamics of the estuary and may help to identify the relevant 

xxi
constituents of salmon “habitat.” The model also predicts temporal and spatial changes in 

habitat opportunity that the member/vagrant hypothesis suggests could be significant to salmon 

diversity and resilience. 

Estuarine Habitat Capacity 

The productive capacity of the estuary has likely declined over the past century through 

the combined effects of diking and filling of shallow-water habitats, shifts from a 

macrodetritus-based to a microdetritus-based food web, and effects of introduced species. Loss 

of approximately 65% of the tidal marshes and swamps that existed in the estuary prior to 1870, 

combined with the loss of 12% of deepwater area, has contributed to a 12–20% reduction in the 

estuary’s tidal prism. 

The absolute change in habitat area does not necessarily capture changes in habitat 

quality. For instance, while the dramatic loss of emergent and forested wetlands in the estuary 

has likely impacted foraging resources, the area of shallows and flats actually increased 7% 

between 1870 and 1980, which would have provided some additional foraging habitat. We have 

no means to objectively quantify the ecological effects of this habitat tradeoff because of the lack 

of historical data on the flora and fauna of these habitats. 

Although a substantial decline in wetland primary production and associated 

macrodetritus for the estuarine food web is implied by direct loss of emergent, forested, and 

other wetland rearing areas, reduced macrodetrital input to the food web may have been 

supplanted to some degree by an increase in microdetritus from upriver sources. The increase is 

principally in the form of phytoplankton production from the hydropower and flood-control 

reservoirs. 

The modern food web, however, does not support the same diversity of salmon life 

history types that occurred historically. The present microdetritus-based food web, which is 

centralized in the highly productive estuarine turbidity maximum region of the estuary, largely 

supports a pelagic food web that may contribute only indirectly to larger, yearling salmon. 

Significant changes in the modern estuarine community through species introductions 

have not been assessed. However, the Asian bivalve, Corbicula fluminea, has expanded far into 

the lower mainstem reservoirs and tributary basins since its introduction into the estuary in 1938. 

Pseudodiaptomus inopinus, a calanoid copepod also introduced from Asia, has appeared 

prominently in the estuary since 1980, and American shad (Alosa sapidissima) has grown to a 

substantial population in the Columbia River since its introduction in 1885–1886. 

Fifteen other nonindigenous fishes are now common in the estuary. The specific impacts 

on the estuarine ecosystem or on juvenile salmon in particular from any of these populations are 

speculative. However, given the tremendous abundance of C. fluminea and American shad (peak 

Bonneville Dam passage counts of 3 × 106

), it is not unreasonable to expect that their 

consumption rates may have significantly modified the estuarine food web. 

Predation on juvenile salmon in the estuary by piscivorous fishes, marine mammals, and 

birds has always been a mortality factor. Yet there are no data to compare historical and modern 

predation rates or predator populations. Several unique predator populations, including Caspian 

xxii
terns, have increased significantly in recent decades and could constitute potential limiting 

factors on juvenile salmon survival. A major limitation of contemporary predation studies is that 

predator consumption may be substantially affected by changes in salmon migration behavior 

associated with hatchery rearing and release programs. 

Many of the changes in biological production processes that have occurred in the 

Columbia River estuary may be explained substantially by physical modifications that have 

altered the habitat landscape. These results lend further support to the member/vagrant 

hypothesis, which emphasizes the important role of physical and geographic factors (e.g., habitat 

opportunity) in shaping the dynamics and diversity of marine populations. These underlying 

physical linkages to estuarine production processes must be understood if salmon recovery 

programs are to treat the ultimate causes rather than the proximal symptoms of population 

decline. 

Change in Juvenile Salmon Life History, Growth, and Estuarine Residence 

The member/vagrant hypothesis predicts that the many biological and physical changes 

observed in the estuary could diminish salmon performance (e.g., growth, foraging success, and 

life history diversity) relative to historic conditions. We compared results of historical and 

contemporary fish surveys to assess change in the potential use of estuarine habitats by salmon 

based on these factors: 

1) life history diversity of subyearling, ocean-type Chinook salmon, 

2) periods of estuarine residence, and 

3) growth and size characteristics. 

Our analyses indicate that the population structure and life history diversity of 

subyearling Chinook salmon have been simplified significantly since the early 1900s. Reflecting 

the variability in emergence timing, migration distances, and growth rates among populations 

throughout the watershed, juvenile Chinook historically migrated to the estuary during much of 

the year and resided there for various time periods before migrating to the ocean. 

In the predevelopment period, subyearling Chinook entered the estuary as fry in May and 

again as fry and fingerlings between July and August. Based on scale analyses, fish that resided 

in the estuary between June and July demonstrated rapid and substantial increases in mean 

length. To account for this average growth, many subyearling salmon would have resided in the 

estuary for as long as several months. 

In contrast, contemporary patterns of estuarine use suggest that life history diversity of 

Chinook salmon has declined. Most data from modern fish collection are from marked, 

hatchery-reared fish, sampled predominantly along mainstem channels. 

Relative to historical descriptions of Chinook salmon fry and fingerlings, modern fish 

enter the estuary considerably later (by at least two weeks), in pulses that coincide with hatchery 

releases, in a smaller range of fish sizes, and with a more homogeneous size distribution. 

Smaller subyearlings historically present during early fall are lacking in modern fish collections. 

xxiii
Unlike the historical continuum of rearing behaviors for juvenile Chinook salmon, three 

principal life history types are now dominant in the basin: subyearling migrants that rear in natal 

streams, subyearling migrants that rear in natal streams or main rivers or both, and a group of 

yearling migrants. Thus, the analyses suggest that ocean-type Chinook salmon with estuarinerearing life histories are now substantially reduced in importance relative to their historical 

levels. 

Our interpretations of historical and contemporary estuarine life histories and habitat use 

by juvenile salmon are limited by lack of systematic surveys in the estuary. Yet despite the 

many data deficiencies, the uniform sizes and rapid migrations of present-day salmon compared 

with those found at a nearby site in 1916 are consistent with the patterns expected from our 

conceptual framework based on the changes that have occurred throughout the Columbia River 

basin during the past 80 years, including: 

• extinction of some salmon runs, 

• loss of river reaches and shallow, estuarine habitats, 

• flow modifications that have dampened established disturbance regimes and altered 

estuarine habitat, 

• intensive harvest and other selection pressures, and 

• hatchery programs that release large batches of similarly sized juveniles over a short 

period. 

Synthesis: Review of the Conceptual Framework 

We conclude that the member/vagrant hypothesis provides a valid framework for 

understanding the Columbia River estuary’s contribution to the dynamics and diversity of 

salmon populations. Key assumptions of the hypothesis are supported by evidence that: 

• salmon populations and life histories in the Columbia River basin are geographically 

structured, 

• salmon performance in the estuary is directly linked to processes and conditions upriver, 

and 

• “spatial losses”—factors that sever the linkages between salmon behavior and estuarine 

habitat—have played a significant role in population decline. 

The member/vagrant hypothesis underscores the estuary’s contribution to life history 

diversity and the geographic structure of salmon populations throughout the Columbia River 

basin. It argues that salmon recovery programs should be designed to expand habitat 

opportunities and the breadth of salmon life histories in the basin rather than simply targeting the 

few populations and life history types that have come to dominate salmon production under 

currently degraded habitat conditions and intensive hatchery programs. 

The member/vagrant hypothesis provides the foundation for a new research agenda, 

including studies needed to reconstruct historic estuarine habitats and salmon life histories as a 

benchmark for setting restoration goals. It also emphasizes the need for broad, ecosystem-scale 

xxiv
planning to reestablish estuarine-riverine habitat linkages that allow for the full expression of life 

history traits characteristic of each salmon population. 

The member/vagrant hypothesis does not define a minimum quantity of habitat necessary 

to achieve population viability and, contrary to traditional production-based management 

approaches, argues that a single optimum condition for salmon production does not exist. 

Instead it emphasizes restoring flexibility to the ecosystem and its salmon populations by 

expanding habitat opportunities and life history diversity. We conclude that the member/vagrant 

hypothesis, while largely conceptual rather than prescriptive, promotes understanding of 

processes and linkages that will move the Columbia River ecosystem in a more favorable 

direction toward population persistence. 

xxv
xxvi
Acknowledgments 

The authors are deeply indebted to Willis Horton Rich (1885–1972), whose 1920 study 

“Early history and seaward migration of Chinook salmon in the Columbia and Sacramento 

rivers” provided important historical data in this technical memorandum. Rich was a pioneer in 

the study of Pacific salmon migrations and life cycles, setting the foundation for generations of 

future biologists. His research demonstrated that juvenile Chinook salmon migrated through 

the mainstem Columbia River throughout the year, which he attributed to the movements of 

many independent populations distributed throughout the basin. From tagging studies with 

colleagues at the Bureau of Fisheries, Rich further demonstrated that spring and fall migrations 

of Chinook salmon were not random events but were inherited traits. Rich was among the first 

to recognize that the return of salmon to their natal streams creates a complex structure of 

isolated, self-sustaining populations within species. He proposed a revolutionary approach to 

salmon management based on the conservation of local populations within their native habitats. 

Rich resigned as director of the Bureau of Fisheries Pacific Fishery Investigations in 1930 to 

become a full professor at Stanford University and was named the first chief of research for the 

Oregon Fish Commission in 1937. In the 1940s, Rich and several other biologists with the U.S. 

Fish and Wildlife Service faced the daunting task of designing a fisheries conservation program 

to mitigate for proposed Columbia Basin hydroelectric development, including 40 dams, many 

on the mainstem Columbia and Snake rivers. 

The authors thank the following individuals and organizations for contributing data: Jo 

Miller, David Newsom, Romeo Wisco, Nancy Stephan, the U.S. Geological Survey, the Water 

Resources Division of the USGS regional office in Portland, Oregon, Environment Canada, BC 

Hydro, the Bonneville Power Administration, the U.S. Bureau of Reclamation, the Western 

Regional Climate Center, and state climatologists in Oregon, Washington, and Idaho. In 

addition, Pradeep Naik carried out many of the hydrologic calculations, and Nate Mantua 

provided useful discussion. Edward P. Myers III, Phil Pearson, Charles Seaton and Wendy 

Sommerfield contributed greatly to the circulation simulations and to the habitat-opportunity and 

residence-time analyses. 

We are indebted to Susan Hinton, Earl Dawley, and George McCabe of the NWFSC’s 

Point Adams Research Station for their persistence and willingness to retrieve and decipher the 

Columbia River Data Development Program data, and Jim Meyers of the NWFSC for his 

research through NOAA archives for the juvenile salmon scales collected and preserved by 

Willis Rich. 

The authors thank Bill Pearcy and Jim Lichatowich for their helpful reviews and 

suggestions and Cathy Tortorici for her ideas and support of this research. We also are grateful 

for the editorial assistance provided by Joann Butzerin for the prepublication draft and Gordon 

Sholtys for the NOAA technical memorandum. 

xxvii
xxviii
Abbreviations and Acronyms 

ADCIRC – Advanced Circulation model 

BPA – Bonneville Power Administration 

CORIE – Columbia River Estuary Evaluating System 

CREDDP – Columbia River Data Development Program 

ENSO – El Niño Southern Oscillation 

ESA – Endangered Species Act 

ETM – estuarine turbidity maximum 

ESU – evolutionary significant units 

FL – fork length 

GIS – Geographic Information System 

Ls – salinity intrusion length

mt – metric ton or metric tons 

NMFS – National Marine Fisheries Service 

NRC – National Research Council 

NPPC – Northwest Power Planning Council 

PDO – Pacific Decadal Oscillation 

PIT – passive integrated transponder 

QR – river flow

RKm – river kilometers 

SWHA – shallow-water habitat area 

USACE – U.S. Army Corps of Engineers 

USGS – U.S. Geological Survey 

xxix
xxx
Introduction 

In the late 18th century, the entrance to the “Great River of the West” was expected to 

provide a Northwest Passage across the American continent and an inland highway for 

transpacific trade. The long-awaited Northwest Passage, however, repeatedly eluded European 

maritime explorers. Based on the currents and discolored water encountered near shore, Spanish 

explorer Bruno de Heceta believed he had found the continental passageway in 1775, but de 

Heceta did not attempt to enter the river he called the Rio San Roque. He was soon followed by 

an armada of unsuccessful Britons. James Cook tried three times to find the river, including a 

final attempt in 1778, when he sailed past the Columbia River mouth during the night. 

A decade later, John Meares could not see beyond the long wall of surf and concluded 

that no river existed. He proclaimed his displeasure by dubbing the inlet Deception Bay and the 

rocky cape at its northern end Cape Disappointment (its present name). On 27 April 1792, 

George Vancouver discounted signs of discolored water as “some streams falling into the bay,” 

and continued sailing northward past the river entrance. Finally, a few weeks later, American 

Robert Gray sailed the Columbia Rediva across the bar at Cape Disappointment and into the 

mouth of the Great River (Egan 1990, Dietrich 1995). 

Difficult as the river was to find, its strategic importance was never in doubt. Gray 

verified the Columbia River’s commercial potential; his first official acts included trade with the 

Chinook natives—a nail for two salmon (Salmonidae), two nails for a beaver (Castor 

canadensis) skin, and a sheet of copper for four otter (Enhydra lutris) pelts. Gray not only 

redrew the regional map, but in symbolic exchanges of two of the river’s principal assets—furs 

and salmon—he ushered in new and far-reaching economies that would forever reshape the 

Columbia River ecosystem. Along the 15 miles he ventured upstream, Gray collected more than 

3,000 otter pelts that he sold in China (Egan 1990, Detrich 1995). 

Although the commercial importance of the Columbia River estuary was immediately 

obvious, the natural economy of its murky waters remains as elusive today as its entry was to 

early explorers. The vast river network of the Columbia Basin drains an area about the size of 

Texas and funnels through a narrow tidal reach at the mouth in a roiling slurry of freshwater and 

saltwater, sediments, and organisms. From this narrow constriction of a few miles across its 

mouth, the Columbia River shoots a powerful jet of river water into the North Pacific, a plume 

that can be traced 1,040 km southward to San Francisco, California. 

If the entrance to the mighty river was difficult to discover, how much more so will be 

the intricate physical and biotic interactions at its ocean juncture? It is not surprising that interest 

in the estuary the past 200 years has centered on practical uses and resources rather than on the 

obscure ecological interrelationships that support them. Yet crises have a way of exposing 

hidden obstructions and redirecting the focus. The rapid decline of Pacific salmon 
(Oncorhynchus spp.) has expanded the need to explore the ecological depths of the Great River’s 

estuary. This technical memorandum is part of that exploration.

In the past several decades, the Columbia Basin’s bountiful populations of Pacific salmon 

have diminished to a small fraction of their former diversity and abundance. Numerous 

populations have declined or become extinct as a consequence of industrialized fisheries, habitat 

loss, hydropower development, and salmon hatchery programs. Since 1991, 13 Columbia River 

salmon stocks have been added to the list of threatened or endangered species under the U.S. 

Endangered Species Act (ESA). While traditional environmental assessments often have 

focused on habitat changes upriver, including the loss of spawning and rearing area following 

construction of large hydroelectric dams, questions are being raised about the estuary’s role in 

the salmon’s decline and potential recovery. 

One analysis proposes that small survival improvements when spring and summer 

Chinook salmon (O. tshawytscha) enter the estuary and ocean could yield some of the most 

significant population increases (Kareiva et al. 2000). The need to better understand the effects 

of the Columbia River estuary and plume on salmon populations was recognized in recent policy 

changes governing salmon recovery programs throughout the basin. 

On 12 September 1996, Congress amended the Pacific Northwest Electric Power 

Planning and Conservation Act of 1980 to include a section that requires the Northwest Power 

Planning Council (NPPC) to “consider the impact of ocean conditions on fish and wildlife 

populations” when recommending hydropower mitigation projects for the Columbia River basin. 

This new amendment to the Power Act applies directly to anadromous fish populations, 

particularly Pacific salmon and steelhead (O. mykiss), which have continued their precipitous 

decline despite decades of effort to mitigate effects of harvest and hydroelectric development in 

the basin. This legislation also focused attention on the estuary, which provides important 

rearing habitat for juvenile salmon during their seaward migration and is impacted by ocean 

conditions at the mouth and hydropower development upstream. 

Concerns about the estuary and ocean represent a departure from previous management 

policy in the Columbia River basin. Earlier restoration had focused almost exclusively on the 

freshwater phase of the salmon life cycle, even though salmon spend most of their lives at sea. 

Recent research has shown that decades-long shifts in climatic and oceanic conditions can 

produce fluctuations in salmon production across the entire North Pacific Ocean (Francis and 

Sibley 1991, Beamish and Bouillon 1993, Mantua et al. 1997). Such natural variability must be 

taken into account to develop appropriate recovery goals, actions, and expectations for Columbia 

River salmon. 

Legislation that requires a resource manager to look beyond freshwater recognizes that 

marine, estuarine, and riverine environments are components of an extended salmonid ecosystem 

and cannot be treated independently (ISG 2000, Williams in press, Bisbal and McConnaha 

1998). While it is impossible to control fluctuations in the North Pacific, hydroelectric 

development and other upriver alterations affect the estuarine and nearshore coastal habitats of 

salmon, and the health and diversity of salmonids that enter the ocean. Ultimately these factors 

may decide whether salmon from the Columbia Basin can realize the full productive potential of 

2
the ocean under any particular set of environmental conditions. In response to the legislative 

mandate to consider the ocean, the NPPC recommended two management strategies: 

1) improve estuarine and nearshore habitat conditions, which have been adversely affected 

by local habitat changes and upriver management activities, and 

2) preserve the diversity of life history characteristics in salmon, which allows populations 

to withstand environmental fluctuations (NPPC 1997). 

The NPPC also recommended several research initiatives to improve the understanding 

of ocean effects on fish and wildlife management activities, including “a synthesis of what is 

known about the impacts of the construction and operation of the Columbia River hydroelectric 

system on the hydrology, habitats, and ecology of the Columbia River estuary and river plume 

and opportunities for management actions related to this understanding” (NPPC 1998). 

In 1999 the National Marine Fisheries Service (NMFS) formed an estuarine research 

team to evaluate whether existing information is adequate to: 

• interpret effects of the hydroelectric system on the Columbia River estuary as outlined in 

the NPPC research initiative, and 

• support NPPC strategies concerning ocean viability such as improvement of estuarine 

and nearshore habitats and preservation of life history diversity in salmon. 

This technical memorandum summarizes the assessment of conditions in the Columbia 

River estuary. The purpose is to offer management recommendations for improving estuarine 

conditions for salmon or to identify research that will be needed before management changes can 

be defined or both. This report focuses on four key questions about salmon in the Columbia 

River estuary: 

1. What habitats and processes support native salmon populations during the estuarine 

phase of their life cycle? 

2. Have changes to the estuary had a significant role in salmon decline? 

3. What have been the impacts of flow regulation on the hydrology, habitat, and biological 

interactions in the estuarine ecosystem? 

4. What estuarine conditions are necessary to maintain salmonid diversity in the Columbia 

River basin? 

To address these questions this technical memorandum summarizes existing knowledge 

about the estuarine requirements of juvenile salmon, reconstructs historical changes in estuarine 

conditions, and uses simulation modeling to predict changes in rearing opportunities for juvenile 

salmon. The historical analysis considers changes in the estuarine environment and changes in 

the salmon populations that may determine whether these fish can fully use the habitats that are 

available. The emphasis is on subyearling fish, primarily juvenile fall Chinook salmon, because 

these are considered the most estuarine dependent and because less information is available for 

other species or Columbia River age classes. The analyses are designed to distinguish effects of 

flow regulation from bathymetric and other changes and to put these anthropogenic effects in the 

context of long-term climatic fluctuations. 

3
This technical memorandum summarizes the available information regarding salmon 

habitats and life histories in the Columbia River estuary. In lieu of empirical data depicting 

long-term trends or changes in estuarine habitat use by salmon, we evaluate whether simulation 

modeling can provide a means to characterize historic and present rearing opportunities for 

subyearling salmon. This approach relies on literature values for estuarine water depths and 

velocities generally preferred by subyearling salmon. The simulations characterize 

salmon-habitat opportunity as the total number of hours that the proposed shallow-water or low 

velocity criteria are met under selected tidal, river-flow, and bathymetric conditions. 

The first two sections of this technical memorandum establish the context for the 

evaluation, including a review of historical changes in the basin that have affected salmon 

populations and estuarine conditions, and the conceptual approach upon which the specific 

analyses and interpretations are based. 

The subsequent sections describe the results of our analyses, including: 

• hydrologic and climatic fluctuations in the Columbia River basin for the past 140 years 

and the effects of hydroelectric operations and other management activities on 

established flow patterns, 

• preliminary model simulations to compare availability of estuarine habitat for salmon 

under historic and present bathymetric and flow conditions, 

• the status of knowledge about ecological changes within the estuary that have affected 

habitat quality and rearing capacity for salmon, and 

• the performance of salmon in the estuary using indicators of growth and life history. 

We review the results in the context of our conceptual approach and conclude with 

recommendations for future estuarine management and research. 

The depth of this estuarine exploration is limited, because little data have been collected 

on juvenile salmon and their habitat use in the estuary. Although the habitat modeling 

demonstrated the sensitivity of the ecosystem to changes in flow and bathymetry, the results are 

preliminary, because existing bathymetric data are inadequate to resolve habitat response to these 

changes. 

This technical memorandum is more than a compilation of facts and conclusions about 

the estuary; it also proposes an alternative framework for interpreting the effects of estuarine 

habitat change on Columbia River salmon populations. Traditional assumptions about the 

factors regulating salmon populations have undermined understanding of the estuary and have 

played a prominent role in salmon decline (Lichatowich 1999). We believe an alternative way of 

thinking about salmon, therefore, is a prerequisite for their recovery. This review is as much an 

illustration of how such a framework of ideas can be applied to the Columbia River estuary as it 

is a presentation of results based on that framework. 

4
Estuarine Development History 

and Salmon Decline 

Estuary Description 

With a watershed of roughly 660,500 square kilometers (km2) encompassing seven states, 

two Canadian provinces, and two major continental mountain ranges (Cascades and Rockies), 

the Columbia River is the second largest river in the United States. The river and estuary are 

dominant features in the circulation of the northeast Pacific Ocean with a mean annual discharge 

at the mouth of approximately 5,500 cubic meters per second (m3s

-1). We define the Columbia 

River estuary (Figure 1) to include the free-flowing waters that are influenced by oceanic tides: a 

reach spanning 235 river kilometers (RKm) from the mouth to the base of Bonneville Dam. 

Relative to juvenile salmon migration along the estuarine gradient, this system includes three 

physiographic subsystems: 

• the tidal freshwater portion or fluvial region (Simenstad et al. 1990a) from Bonneville 

Dam to the maximum upstream extent of salinity intrusion (≈55 RKm from the entrance), 

• the brackish-mesohaline region above the open expanse of the main estuary (≈30–55 

RKm from the entrance), and 

• the broad, euryhaline region in the lower 30 RKm of the estuary. 

Ecological studies in the estuary during the early 1980s further partitioned the euryhaline 

region into seven subareas (Simenstad et al. 1990a): 

1) entrance, 

2) Trestle and Baker bays in Oregon, 

3) Youngs Bay in Oregon, 

4) estuarine channels, 

5) mid-estuary shoals of the estuarine mixing zone, 

6) Grays Bay in Washington, and 

7) Cathlamet Bay in Oregon. 

This lower estuarine area encompasses a complex network of main, distributary, and 

dendritic tidal channels; non-vegetated shoals; emergent and forested wetlands; and extensive 

mudflats in peripheral bays. Approximately 26,550 (≈ 71.2%) of the 37,289 hectares in the 

estuarine region are composed of shallow-water habitats (6 m or less relative to mean lower low 

water). Except in peripheral bays, where silt and clay sediments dominate, most of the estuary’s 

sediments are composed of sand. More detailed descriptions of the river flow and sediment 

5
Figure 1. The tidal influence of the Columbia River extends upstream from its mouth at the Pacific 

Ocean to the Bonneville Dam (RKm 235). 

transported through the estuary can be found in the “Changes in Hydrological Conditions” 

section (page 47). 

The low salinity surface water of the Columbia River plume forms an offshore extension 

and fourth physiographic province of the estuary. The plume affects surface density gradients 

and the physical properties of coastal waters, and it may be an important feature influencing 

biological production processes and potential rearing opportunities for seaward migrating 

salmonids. For the purposes of this technical memorandum, however, we limit our assessment to 

the eastern portion of the estuary encompassing the three physiographic provinces described 

above. 

Estuarine Requirements of Juvenile Salmon 

All anadromous salmonids that survive to reproduce pass through estuaries at least twice 

during their life cycle: first as juveniles en route to the Pacific Ocean and then as adults when 

they return to spawn in their natal streams. In the estuary, all seaward migrating juveniles must 

make the transition from shallow, freshwater, lotic environments to a deep, salty, open ocean 

within a period of days to months. 

6
Estuaries are often presumed to offer three advantages to juvenile salmon for making this 

transition: 

1) a productive feeding area capable of sustaining increased growth rates, 

2) a temporary refuge from marine predators, and 

3) a physiological transition zone where juvenile fish can gradually acclimate to saltwater 

(Simenstad et al. 1982, Thorpe 1994). 

Pacific salmon species and populations have evolved diverse strategies for using all 

available freshwater and estuarine nursery habitats within a river basin (Healey 1982, Groot and 

Margolis 1991). The duration of estuarine residence varies considerably among species and 

sizes of juvenile salmon. Salmonids that rear in freshwater for a year or more before migrating 

downstream (some Chinook, sockeye [O. nerka], and coho [O. kisutch]) are believed to move 

rapidly through the estuary and may not spend substantial periods adapting to saltwater before 

ocean entry. These are frequently referred to as “stream-type” fish. 

However, subyearling migrants that enter the estuary as fry or fingerlings, so-called 

“ocean-type” salmon, exhibit a wide range of residence periods depending on the species. Pink 

salmon (O. gorbuscha) exhibit little estuarine rearing; chum salmon (O. keta) stay in estuaries 

for days to weeks; and subyearling Chinook salmon may remain for several months (Thorpe 

1994). 

Chinook salmon, which have the greatest diversity of juvenile life histories among all 

Pacific salmon (Healey 1991, Wissmar and Simenstad 1998), have the most varied patterns of 

estuarine use. Healey (1982) proposed that Chinook salmon are the most estuarine-dependent of 

salmonid species since virtually all life history types spend time feeding and growing in 

estuaries, a physiological transition zone where juvenile fish can gradually acclimate to saltwater 

(Simenstad et al. 1982, Thorpe 1994). 

Regardless of the residence times of individual fish, juvenile salmon may occur in the 

estuary all year, as different species, size classes, and life history types continually move 

downstream and enter tidal waters from multiple upstream sources. Peak estuarine migration 

periods vary among and within species, suggesting that different life history strategies may 

provide a mechanism for partitioning limited estuarine habitats (Myers and Horton 1982). The 

varied juvenile life histories in Chinook salmon are manifest in the wide range of sizes and times 

of estuarine entry (Rich 1920, Healey 1982). In the Columbia River estuary, subyearling 

Chinook salmon are most abundant from May through September but are present all year (Rich 

1920, McCabe et al. 1986). Rich (1920) first reported that for each Chinook brood in the 

Columbia River, juvenile migrations span an 18-month period, including fry that migrate soon 

after emerging in December and yearlings that do not leave until late in their second spring. 

The size of Chinook salmon at the time of ocean entry may reflect the various alternative 

rearing options available to juveniles before they make the complete transition to an ocean 

environment. Large numbers of Chinook enter estuaries in southern British Columbia, Canada, 

as fry and leave at relatively small sizes (60–70 millimeters fork length [mm FL]) at about the 

time subyearling Chinook smolts migrate downstream (Healey 1982). In the Nanaimo River 

system on the east coast of Vancouver Island, subyearling smolts reside in the outer estuary in 

7
June and July and some remain year-round. The earlier disappearance of most Chinook from 

southern British Columbia estuaries may reflect the availability of protected habitat along the 

complex archipelago of the Strait of Georgia (Healey 1982). Although fewer fry migrants have 

been reported in coastal Oregon estuaries (e.g., Reimers 1973, Myers 1980), many subyearling 

Chinook often use estuaries through the summer and into early autumn before they migrate at 

relatively large sizes. Estuaries along the open Oregon coastline thus may be particularly 

important as shelter for juvenile salmon that must migrate directly into an open ocean 

environment. 

Many studies indicate that the movements of juvenile salmon and their habitat use within 

estuaries are size related. Small Chinook and chum salmon (subyearling) fry usually occupy 

shallow, nearshore habitats, including salt marshes, tidal creeks, and intertidal flats (Levy and 

Northcote 1982 , Myers and Horton 1982, Simenstad et al. 1982, Levings et al. 1986). As 

subyearling salmon grow to fingerling and smolt stages, their distribution typically shifts toward 

deeper habitats farther away from the shoreline (Healey 1982, 1991, Myers and Horton 1982). 

Although the specific size transitions may vary, numerous estuarine studies have found juvenile 

salmon distributed along a habitat continuum: juvenile Chinook and chum less than 50–60 mm 

FL occur primarily in shallow water (e.g., <1 m); fish 60–100 mm FL are found in slightly 

deeper habitats (shoals, distributary channels); and fish greater than 100 mm FL may be found in 

deep- and shallow-water habitats. This direct relationship between size and habitat depth tends 

to break down during hours of darkness, when schooling fry or fingerlings often disperse from 

shore (Schreiner 1977, Kjelson et al. 1982, Bax 1983, Healey 1991, Salo 1991). 

The distribution of juvenile salmon in the Columbia River estuary is consistent with this 

notion of differential habitat use based on fish size. McCabe et al. (1986) reported that 

subyearling Chinook in shallow intertidal habitats of the Columbia River estuary were smaller 

than subyearlings captured in deeper pelagic areas. Large yearling migrants may spend 

relatively little time in shallow estuarine habitats. A 1980–1981 survey of the estuary found 

most yearling Chinook salmon at deeper channel sites rather than at nearshore intertidal sites 

(Bottom et al. 1984). 

Rapid changes in salinity gradients, water depths, and the accessibility of habitats impose 

important ecological and energetic constraints that salmon do not experience in freshwater: 

salmon must continually adjust their habitat distribution, particularly in shallow-water areas, 

with twice-daily tidal fluctuations and seasonal variations in river flow. The landscape 

distribution of habitats throughout an estuary may be important in juvenile salmon adaptation to 

tidal and seasonal changes. In most estuaries, salmon fry move twice daily from low tide refuge 

areas at the junction of major and minor channels to salt marsh habitats at high tide and back 

again (Healey 1982, Levy and Northcote 1982). Chum and Chinook salmon fry remain in 

marshes of the Fraser River estuary in British Columbia for an average of 11 and 30 days, 

respectively (Levy and Northcote 1982). Thus access to suitable low tide refugia located 

immediately adjacent to marsh habitats may be an important factor in salmon production and 

survival as juveniles traverse the estuarine landscape. 

Appropriate sequences of habitat distributed across the entire estuarine salinity gradient 

also may be necessary to support the seasonal migrations of juvenile salmon (Simenstad et al. 

2000b). Throughout their migration and rearing period in estuaries, subyearling migrants 

8
traverse a continuum of salinities, depths, and water velocities as they gradually grow and 

migrate from upper tidewater to lower estuary and from shallow nearshore to deeper offshore 

areas. For species (e.g. chum and Chinook salmon) that remain in the estuary for extended 

periods, a broad spectrum of habitat types may be needed to satisfy feeding and refuge 

requirements within each salinity zone. But even large coho smolts may require a sequence of 

habitat types to allow for extended holding periods during their relatively brief stay in the 

estuary. Radio-tagged coho salmon in the Gray’s Harbor estuary in Washington interspersed 

periods of passive downstream movement in strong currents with periods of holding in low 

velocity habitats (Moser et al. 1991). Because the parr-smolt transformation is a key period 

when salmon gather the olfactory information they need for successful homing, and because the 

cues for imprinting may depend upon environmental gradients experienced during migrations 

and physiological changes, habitat sequences at a landscape scale may be important even for 

those salmonids that move through the estuary relatively quickly (Dittman et al. 1996). 

Marsh habitats, tidal creeks, and associated dendritic channel networks may be 

particularly important to small subyearling salmonids as areas of high secondary production of 

insect and other invertebrate prey; sources and sinks for detritus; and potential refuge from 

predators afforded by complex habitat structure, including sinuous channels, overhanging 

vegetation, and undercut banks (Levy and Northcote 1982, McIvor and Odum 1988, Gray et al. 

2002). Salmonid production in Northwest estuaries is supported largely by detrital food chains 

through a variety of animals that live in or near the estuary bottom (Healey 1979, 1982). 

Habitats that produce or retain detritus are particularly important. Detrital sources vary along the 

estuarine tidal gradient but include emergent vegetation in tidal wetlands, low intertidal and 

subtidal eelgrass, macro-algal beds, and epibenthic algae (Naiman and Sibert 1979, Sherwood et 

al. 1990). Historically, before the Columbia River was isolated from its floodplain, considerable 

organic matter was probably imported into the estuary during seasonal freshets and winter 

flooding events. 

In the Columbia River estuary, low velocity, peripheral bay habitats (e.g., Baker, Youngs, 

and Grays bays) and the estuarine turbidity maximum (ETM) in the mid-estuary are regions 

where organic matter is concentrated. It is also where invertebrate prey production and fish and 

macro-invertebrate feeding are elevated relative to other estuarine locations (Bottom and Jones 

1990, Jones et al. 1990, Simenstad et al. 1990a). Loss of historic wetlands and macro-algal 

habitats (e.g., mud and sand flats) within the estuary and enhanced phytoplankton production in 

impoundments upriver may have shifted estuarine food chains from macrodetrital to 

microdetrital sources (Sherwood et al. 1990). Such changes would likely benefit food chains 

supporting pelagic-feeding fishes such as northern anchovy (Engraulis mordax), longfin smelt 

(Spirinchus thaleichthys), surf smelt (Hypomesus pretiosus), Pacific herring (Clupea harengus 

pallasi), and American shad (Alosa sapidissima) with commensurate loss of food webs 

supporting epibenthic-feeding fishes such as juvenile salmon. 

Historical Change in Salmon Populations and Estuarine Habitats 

To understand patterns of habitat use within the estuary, we must account for changes at 

all life stages that shape the structure and life histories of salmon populations. Salmon species 

composition, abundances, sizes, and migration periods in the estuary are linked to changes 

upriver or in the ocean that determine which populations and juvenile life history types survive 

9
to enter tidewater. The biological characteristics and density of salmon in the estuary may be 

influenced by these multiple factors: 

• selective harvest in ocean and river fisheries, 

• adult access to upriver spawning and rearing habitats, 

• rearing and release practices in hatcheries, and 

• climate and river flow. 

Historic changes to the Columbia River populations and habitats (see Appendix A, page 

229), which may affect salmon rearing conditions in the estuary, are detailed elsewhere (NRC 

1996, Lichatowich 1999, ISG 2000, Williams in press) and briefly summarized in the following 

subsections. 

Population Decline 

Prior to European settlement, the Columbia River system sustained annual adult returns 

from 11–16 × 106

 salmon1 of which Native North Americans likely harvested between 

4.6–6.3 × 106 fish (Craig and Hacker 1940, NPPC 1986). All five species of Pacific salmon 

were historically present in the Columbia River, although pink salmon abundance was always 

quite low (Heard 1991, NRC 1996). Less than 190,000 km2 (<45%) of the more than 422,000 

km2 of habitat originally available for salmon spawning and rearing is now accessible (NRC 

1996, [Figure 2]). In the Snake River, ocean-type Chinook salmon now occupy approximately 

17% of the historic habitat (Hassemer et al. 1997). Virtually none of the historic salmon habitat 

in the portion of the Columbia River in Canada is accessible. Through habitat loss and other 

changes, present natural production of salmon in the Columbia River basin has been reduced to 

approximately 12% of historic levels. Since 1991 sustained population declines have resulted in 

listings of 13 salmonid stocks as threatened or endangered under the ESA (Table 1). 

Different species and life history types of salmon occur in somewhat different spawning 

and rearing areas of the Columbia River basin (Figure 3 and Figure 4). Thus the geographic 

patterns of habitat and population loss on the landscape may determine the particular species and 

life history types represented in the estuary. Scientific observations of salmon, however, 

occurred after habitat losses and harvest effects had altered biological patterns in the Columbia 

River basin. Therefore the understanding of salmon life history, including the generalizations in 

this report, may be substantially oversimplified. 

Chum salmon are confined principally to the lower Columbia River tributaries, excluding 

the Willamette River drainage in Oregon; coho salmon once occupied all tributaries west of the 

Cascade Mountains and larger tributary systems (e.g., the Yakima, Wenatchee, Entiat, Methow 

and Spokane rivers in Washington; and the Grand Ronde River in Oregon) on the eastern side; 

sockeye salmon primarily use lake systems high in the watershed; steelhead are found 

throughout the major headwater systems; and three to four types of Chinook salmon occupy the 

mainstem channel and primary tributaries (Fulton 1970). 

 

1

 Other estimates of total run-sizes are often significantly lower, such as 7.5 × 106 (Chapman 1986) and 6.2 × 106

(PFMC 1979). 

10
Figure 2. Current and historical distribution of anadromous salmonids in the Columbia River basin. 

11
Table 1. Listings and proposed listings of Columbia River salmonids under the ESA. Listings include 

various evolutionary significant units (ESU) within each species as designated by the NMFS. 

Species ESA status ESU Date 

Coho salmon Listed Lower Columbia River/ 

Southwest Washington 

Threatened: June 28, 2005 

Chinook salmon Listed Snake River fall run Threatened: April 1992 

Snake River spring/summer run Threatened: April 1992 

Lower Columbia River Threatened: March 1999 

Upper Willamette River Threatened: March 1999 

Upper Columbia River 

spring run 

Endangered: March 1999 

Chum salmon Listed Columbia River Threatened: March 1999 

Sockeye salmon Listed Snake River Endangered: November 1991

Steelhead Listed Upper Columbia River ESU Endangered: August 1997 

Snake River basin Threatened: August 1997 

Lower Columbia River Threatened: March 1998 

Upper Willamette Threatened: March 1999 

Middle Columbia River Threatened: March 1999 

Chinook salmon were once distributed throughout the basin, but distinct stocks or run 

types2

 occupied somewhat discrete regions (Figure 5). Ocean-type, fall-run Chinook were 

concentrated in the lower watersheds west of the Cascades and in the mainstem Columbia east of 

the Cascades. Stream-type, spring-run Chinook extended throughout the Columbia River basin 

but were most commonly found in the Snake River watershed. Summer-run Chinook spawned 

and reared primarily in mainstem reaches of the Columbia east of the Cascades, particularly in 

the Snake River drainages. 

Factors of Decline 

Rapid growth of European civilization in the Pacific Northwest brought dramatic changes 

to Columbia River salmon and their riverine and estuarine habitats. For the past century, the 

overall trend in salmon abundance has been one of decline, reflecting a myriad of factors that 

undermined the natural productive capacity of the Columbia River basin (see Appendix A, page 

229). The principal causes of salmon decline are discussed in the following subsections (NRC 

1996). 

 

2

 It is important when considering Columbia River salmon population and life history structure to understand that 

our present-day characterization of fall-run, spring-run, and summer-run stocks was the product of a terminology 

derived from the commercial fishery rather than a scientific differentiation of independent breeding populations. 

Recent genetic typing may improve our understanding of this complex stock structure. 

12
Figure 3. Present distribution of pink, coho, chum, and sockeye salmon in the Columbia River basin. 

Salmon presence from StreamNet (2003). 

 

13
Figure 4. Present distribution of summer and winter steelhead in the Columbia River basin. Steelhead 

presence from StreamNet (2003). 

Salmon harvest 

Fisheries for Columbia River salmon became well established within four decades after 

de Heceta’s 1775 discovery of the river’s outlet to the Pacific Ocean. During a similar period of 

fishing activity, targeted salmon stocks (i.e., spring Chinook) were already showing signs of 

depression. Commercial harvest of adult salmon began in about 1818 with packing of salmon as 

a salted or pickled product, but it increased dramatically with the advent of commercial canning 

in 1866. 

Harvest intensity increased rapidly in response to cannery demand starting in 1866 for an 

eight-year period (Lichatowich et al. 1996). Commercial fishermen initially targeted spring-run 

Chinook, considered the superior canning variety. By 1890 the concentrated harvest of these fish 

in the estuary and the lower river was blamed for the dramatic reduction in the number of adults 

returning to spawn in the Snake River basin (Evermann 1895). Salmon populations had declined 

throughout the Columbia River system by 1911. 

14
Figure 5. Present distribution of spring-, summer-, and fall-run Chinook salmon in the Columbia River 

basin. Salmon presence from StreamNet (2003). 

Changes in freshwater habitat 

Although irrigation in the basin began about the same time as the development of 

industrial salmon fisheries, it did not increase substantially until after implementation of the 

Reclamation Act of 1902, which stimulated expansion of irrigated lands from 2,000 km2

 to 

nearly 40 × 106

 km2 today (NPPC 1986, NRC 1996). Yet surface water withdrawal did not 

accelerate until after World War II, principally in the mid-1960s, with technological advances 

and the availability of inexpensive electrical power. Irrigation not only decreased stream flow, 

but it also became a sink for migrating juvenile salmon that were diverted into irrigation canals 

15
and stranded in farmers’ fields. As early as 1890, state fish commissioners reported substantial 

losses of juvenile salmon in irrigation networks in Eastern Oregon (OSBFC 1890). 

Extensive streambed and water modifications began to eliminate upriver spawning, 

rearing, and migratory habitats for salmon by the late 1800s. As early as 1894 mining in the 

Snake River watershed destroyed Chinook spawning beds and was credited with the collapse of a 

popular American Indian fishing site (Taylor 1999). Habitat loss increased after the turn of the 

century, because of logging and other intensive land uses such as cattle grazing. Even prior to 

1900 some practices damaging to salmon spawning and rearing habitat were prevalent, including 

removal of large woody debris from streams and the operation of splash dams (Sedell and 

Luchessa 1982, NRC 1996). 

Dam construction throughout the Columbia River basin also has depleted salmon 

populations, and it accounts for much of the present-day reduction in historic salmon distribution 

(Figure 2). Chinook salmon populations from the upper Columbia River basin in Canada, 

middle Snake River basin and above in Idaho, and the greater part of the Deschutes River basin 

in Oregon have been extinct for at least 40 years because of dams built without fish passage 

capabilities. There are 23 major hydropower and flood control dams on the mainstem Columbia 

and Snake rivers today, and more than 300 smaller dams distributed on tributaries throughout the 

U.S. portion of the watershed (Figure 6). 

Salmon hatcheries 

Resource managers responded to declining Columbia River harvests in the mid-1890s by 

building salmon hatcheries, promoted as a means to boost salmon production to avoid the need 

for harvest regulations, and to improve on nature by using efficient technology to increase 

freshwater survival (Baird 1875, NRC 1996, Taylor 1999). 

Despite poor accounting for their performance and a general decline in support for 

hatcheries in the 1930s and 1940s, hatchery production expanded substantially in later years, 

stimulated by a new promise that artificial production could mitigate for the deleterious effects of 

dams and irrigation development (NRC 1996). Ultimately more than 80 hatcheries were 

constructed in the basin (Figure 6). 

Hatchery adults now comprise more than 95% of the coho, 70% of the spring Chinook, 

about 80% of the summer Chinook, more than 50% of the fall Chinook, and about 70% of the 

steelhead returning to the Columbia River (CBFWA 1990, Genovese and Emmett 1997). 

Hatchery influence on Chinook populations is now greatest for fall Chinook in the middle 

and lower Columbia River subbasins (>85% of total juvenile salmon production [Genovese and 

Emmett 1997]), and for spring and summer Chinook in the Snake and Salmon rivers subbasins 

(90–100% of the total production). More than 75% of the Chinook salmon in the Deschutes, 

John Day and upper Columbia rivers subbasins still results from natural production. On average, 

most hatchery fall Chinook are released as fed fry, and 70% of the chum salmon now produced 

in the lower Columbia River subbasin are released from hatcheries as fed fry or fingerlings. 

16
Figure 6. Present distribution of salmon hatcheries and mainstem and secondary dams (StreamNet 2003) 

along rivers and streams of the Columbia River basin. 

Intensive hatchery programs have had multiple effects on natural salmon production in 

the Columbia River basin and on the recovery potential of at-risk populations (NRC 1996). 

Among these effects are reduced genetic diversity, competition between hatchery and naturally 

produced salmon, and depletion of wild populations in mixed stock fisheries. Loss of genetic 

and life history diversity through large-scale hatchery production (Reisenbichler 1997) could be 

an important factor determining patterns of estuarine habitat use and the overall performance of 

juvenile salmon in the estuary. 

17
Changes in the estuary 

Most loss and degradation of habitat within the Columbia River estuary occurred after the 

1880s. Following a century of diking and filling activity, only 35% of the former area of marsh 

and swamp habitat remained in the estuary in 1980 (Thomas 1983). However, this is a gross 

estimate of the total habitat loss based on historical surveys. Other qualitative changes in 

physical conditions also may have had important effects on the salmon rearing capacity of the 

estuary. 

Shoreline armoring and construction of structures over water, channel dredging and 

removal of large woody debris, channelization by pile dikes and other structures, and discharge 

of pollutants have significantly modified estuarine habitats. The effects of such alterations on 

either juvenile or adult salmon rarely have been assessed. 

Early channel dredging and hatchery production began to alter estuarine conditions in the 

second half of the 19th century; it was not until the 20th century that channelization and filling 

removed considerable amounts of estuarine habitat, and hydropower and irrigation developments 

significantly altered river flows. The salmon harvest was already in a state of decline (Taylor 

1999). Although there were at least 174 dams in the basin by 1936 (see Appendix A, page 229), 

many of the mainstem dams that would comprise the Columbia River hydropower system were 

not completed until the 1950s. Significant coordinated flow modifications did not occur until the 

late 1960s (Sherwood et al. 1984). 

Climate variability 

Development activities in the Columbia River watershed and estuary were superimposed 

on a background of natural environmental changes, including substantial variations in climate, 

precipitation, and river flow (see the “Changes in Hydrological Conditions section, page 47). 

Climatic fluctuations often accounted for a greater degree of variation than those resulting from 

human interventions. Prior to 1910, spring freshets recorded at The Dalles, Oregon, often 

exceeded 20 × 103 m3s

-1, and winter flood flows in the Willamette River exceeded 5 × 103

 m3s

-1

(18 of 60 years). Spring and winter peaks decreased dramatically thereafter, especially during 

the drought years of the 1930s (Sherwood et al. 1984). 

Although the magnitudes of these changes are impressive and suggest major shifts in 

riverine and estuarine disturbance regimes, Columbia River salmon stocks have withstood such 

disturbances for millennia (Chatters et al. 1995). Long-term productivity and the resilience of 

salmon species are the result of diverse life history strategies that have evolved in a highly 

variable environment (Healey 1991, Healey and Prince 1995). A primary concern of recent 

salmon declines is whether habitat changes and reduced salmon diversity in the Columbia River 

basin have severely undermined the capacity of populations to withstand large fluctuations, 

particularly major changes in long-established patterns of precipitation, temperature, and stream 

flow that some predictions suggest could accompany future global warming (Mantua et al. 

1997). 

18
Institutional fragmentation 

A vast number of governmental agencies, management jurisdictions, and laws have been 

created that directly affect salmon populations and their habitats. The net result is a fragmented 

and often-conflicting array of resource-management programs with jurisdictional boundaries and 

land ownerships that do not coincide with the spatial distributions of salmonid species with 

anadromous life cycles. One analysis of the Columbia River basin estimated that a Chinook 

salmon hatched in the Lochsa River in Idaho crosses at least 17 separate international, federal, 

state, and tribal jurisdictions during the later stages of its life cycle (Wilkenson 1992). The 

National Research Council (NRC 1996) concluded that fragmentation of institutional 

responsibilities and a mismatch between the spatial scales of salmon habitats and management 

jurisdictions severely undermine salmon conservation throughout the Pacific Northwest. 

In conclusion 

The cumulative effects of upstream developments on salmon-rearing conditions in the 

estuary are poorly understood. Yet the combined influences of river-flow regulation and 

industrial hatchery production are noteworthy because of their direct impact on salmon life 

histories or on the disturbance processes to which those life histories have adapted. 

Hydroelectric development now largely regulates the timing and magnitude of river flows, with 

potential effects on salmon migrations and on circulation processes and habitat conditions in the 

estuary. Hatchery programs now regulate the size, time of arrival, distribution, and rearing 

periods of most salmonids in the estuary. Thus upriver controls placed on water and on fish have 

fundamental linkages to salmon production in the estuary. 

History of Research in the Columbia River Estuary 

Scientific and engineering research on the Columbia River estuary has been modest given 

the river’s social, cultural, economic, and strategic importance to the region (see Appendix A, 

page 229). As described in Simenstad et al. (1990a), studies prior to 1980 tended to be 

fragmented, focusing on applied issues and target resources rather than on a broader ecological 

understanding of the interactions among the estuary’s physical environment, chemical structure, 

and biota. Early estuarine research projects were either engineering studies required to construct 

the jetty or navigation channels, or to compensate for depleted salmon runs. Infrequent 

biological studies of the timing and distribution of juvenile salmon began as early as 1914–1916, 

when Rich conducted his first studies in the estuary (Rich 1920). With few exceptions, including 

McIssac’s (1990) research on the Lewis River in Washington, fall Chinook studies have not 

attempted to link population structure and performance of upriver salmon stocks to their 

utilization of the estuary. 

The richest source of information on juvenile salmon and their habitats in the estuary 

originates from studies conducted since the early 1970s by NMFS biologists stationed at the 

Point Adams Research Station at Hammond, Oregon. These efforts evaluated migration 

behavior of juvenile salmon and steelhead transported around hydropower dams (Dawley et al. 

1978, 1981, 1985, and 1986), dredging and dredged-material disposal impacts, particularly on 

the benthic biota (Durkin et al. 1979 and 1981, Emmett et al. 1986, Hinton et al. 1990, 1992a, 

and 1992b), or stranding of juvenile salmon on beaches from ship traffic (Durkin et al.1977). 

19
Results for salmon, crab, and estuarine habitat characteristics in the Columbia River estuary were 

ultimately reported in scientific literature (Durkin 1982, McCabe et al. 1983). 

Scientific investigations of the spatial and temporal distributions of nutrients and biota 

and the supporting ecology of the Columbia River estuary are described by Haertel and 

Osterberg (1967) and Haertel et al. (1969). These complemented the results of comprehensive 

studies sponsored by the U.S. Atomic Energy Commission to determine the fate of radionuclides 

from the Hanford Nuclear Reservation in Washington (Pruter and Alverson 1972), providing a 

description of the estuary’s physical and biological conditions. 

The Columbia River Data Development Program (CREDDP) studies during 1979–1980 

(Simenstad et al. 1990a) represent the most noteworthy interdisciplinary examination of the 

estuary to date. The CREDDP investigations provided the first description of fundamental 

estuarine processes, including sediment accretion (shoaling) and productivity and trophic 

structure (Bottom and Jones 1990, Jay et al.1990, Jay and Smith 1990, Jones et al. 1990, 

Sherwood and Creager 1990, Small et al. 1990). The CREDDP studies also modeled 

estuary-scale circulation patterns (Hamilton 1990), quantified organic matter transfer through the 

estuarine food web (Simenstad et al. 1990b), and assessed effects of historical change on the 

estuarine ecosystem (Sherwood et al. 1990). Results of the CREDDP studies are summarized in 

a synthesis report by Simenstad et al. (1984) and in a series of articles in Progress in 

Oceanography (1990, Vol. 25). 

The CREDDP studies supported the first comprehensive recovery of marked juvenile 

salmon below the tidal-freshwater reaches of the lower river. Not since the early scale analyses 

of Rich (1920) had studies linked estuarine residence times to early freshwater life histories 

(McIssac 1990). The CREDDP studies also documented changes in the estuary from the May 

1980 eruption of Mount St. Helens, including declines in juvenile salmon foraging efficiency 

(Emmett 1982, Emmett et al. 1991). The CREDDP studies inspired more than a decade of 

ecological research on the estuarine turbidity maxima by the National Science Foundation’s 

Land-Margin Ecosystem Research Program (Simenstad et al. 1994). 

Despite these efforts, fundamental studies evaluating the links between juvenile salmon 

and estuarine conditions in the Columbia River generally are lacking. Notably missing is 

information delineating: 

1) specific (especially shallow-water) habitats used by salmon during rearing and 

outmigration through the estuary, 

2) effects of physicochemical and biological conditions on estuarine residence times, 

growth, or survival of juvenile salmon, 

3) food-chain relationships (feeding and predation) among juvenile salmon, invertebrate 

prey, and vertebrate predators, and 

4) differences in these estuarine habitat needs and ecological relationships among salmon 

species, life history types, and source populations. 

Until the basic biological data have been assembled, biologists can only speculate about the 

dependence of juvenile salmon on estuarine habitats or the relative impacts of historic changes in 

river flow, estuarine bathymetry, or ecological interactions in the estuary. 

20
A Conceptual Framework for Evaluating 

Estuarine Habitat Conditions 

Introduction 

The lack of information about the esturary’s role in salmon life history is surprising 

considering the importance of the Columbia River basin to the salmon. The estuary is a huge 

system; however, with some exceptions (Levy and Northcote 1982), present understanding of 

salmonid ecology comes from studies of small estuaries undertaken within recent decades 

(Reimers 1973, Healey 1980, Tallman and Healey 1994). While this research provides 

information about wild fry and subyearlings, much of what is known about salmon in the 

Columbia River estuary is based on larger yearling or fed subyearling fish released from 

hatcheries. As a result we lack information about the specific life-support functions of the 

Columbia River estuary for salmon for two reasons: 

1) ecological processes in much smaller estuaries may not apply directly to this large, 

river-dominated system, and 

2) the behaviors of hatchery fish in the Columbia may not represent the estuarine needs of 

naturally produced salmonids. 

Despite a few ecological surveys of fish assemblages and food chains (Haertel and Osterberg 

1967, Bottom and Jones 1990), the estuarine life histories of diverse populations of salmon and 

the physical and biological processes that influence their estuarine habitats have rarely been 

investigated and are poorly understood. 

What is or is not known about the estuarine requirements of Columbia River salmon 

reflect certain underlying principles and assumptions in traditional fishery management. These 

concepts set limits on the kinds of information that were collected and also determined how that 

information was interpreted (Sinclair and Solemdal 1988, Lichatowich et al. 1996, ISG 2000, 

Williams in press). Traditional lack of interest in the estuary resulted in part from assumptions 

about the factors that regulate salmon production. 

Recent concerns about the estuary, including recommendations that led to this evaluation 

(NPPC 1997), suggest a fundamental change in the conceptual approach to salmon ecology. 

These concerns are reinforced by numerous listings of Columbia River salmon stocks under the 

ESA (Table 1), which emphasizes the importance of conserving biological diversity and the 

native ecosystems upon which it depends. It is important the scientific basis for these changing 

ideas be understood in order to develop a satisfactory framework for this evaluation. 

Fisheries science developed from an agricultural perspective of resource management 

(Bottom 1997). This perspective supported a progressive conservation philosophy that 

emphasized efficient production of natural resources for the benefit of all people. Science 

provided the methods and technologies to increase production of natural resources, compensate 

21
for losses to development, and provide for an equitable distribution of resources among all users 

(Bottom 1997, ISG 2000, Williams in press). To meet these utilitarian goals, resource 

management programs relied on a framework of scientific ideas we might call “production 

thinking.” This perspective measured success by the output of natural resources (e.g., pounds or 

numbers of salmon, angler days of use, etc.) and favored predictive methods and technologies to 

achieve production goals. Production thinking emphasized short-term changes in the abundance 

of salmon populations, which were defined arbitrarily as any geographic unit of management 

interest (e.g., river basin, state or nation). From a production viewpoint, the term “population” 

was an abstraction defined by a particular management need or question. 

Recent mandates to improve estuarine conditions and to protect life history diversity in 

salmon (NPPC 1997) are derived from a different conceptual framework that was proposed 

explicitly to support salmon recovery programs in the Columbia River basin (ISG 2000, 

Williams in press). This framework emphasizes continuity of the chain of freshwater, estuarine, 

and marine habitats that support salmon life cycles; it requires information about the life histories 

and evolutionary adaptations of salmon to their natural environments; and it places salmon 

survival at any one life stage in the context of the animals’ prospective success in navigating the 

entire habitat chain. 

This long-term perspective is based on “population thinking,” which defines populations 

as reproductively isolated and self-sustaining groups of animals within particular geographic 

areas (Mayr 1982, Sinclair 1988, Sinclair and Solemdal 1988). In contrast to the arbitrarily 

defined units of the production approach, this perspective views populations as functional 

reproductive units with distinct genetic and geographic characteristics (Kingsland 1995). 

Population thinking raises new questions, for example, about the geographic structure of 

populations on the landscape and the specific habitats that support them. 

A primary challenge for this analysis was how to answer questions about estuarine 

habitats and salmon recovery that require a geographic and an evolutionary perspective (ISG 

2000, Williams in press), when most of the available information has been collected and 

interpreted from a production view. To establish a conceptual framework appropriate for the 

objectives of this evaluation, the first step is to review the underlying assumptions applied to past 

salmon research and management in Northwest estuaries. We contrast ideas from estuarine 

studies that were based on production thinking to those based on population thinking. We then 

examine a theory of populations derived from marine fish ecology as a starting point for the 

conceptual approach and the specific analyses selected for this assessment.

Historical Perspectives on Salmon in Estuaries 

Production Thinking in Estuarine Research 

Although the traditional assumptions of fisheries management have received increased 

scrutiny in recent years (McEvoy 1986, Finlayson 1994, Lichatowich 1999, ISG 2000, 

Williams in press), the impact of these ideas on salmon research and management in estuaries 

has not been examined specifically. The lack of research interest in Northwest estuaries stems 

in part from long-held assumptions that populations are regulated by density-dependent 

interactions—biological factors such as predation, disease, or food competition—during the 

22
earliest and presumably most vulnerable stages of salmon life. These ideas focused attention on 

the freshwater habitats where salmon are most easily observed and where the sources of 

mortality can be controlled. 

Salmon hatcheries, for example, developed from the assumption that adult abundance is 

limited by freshwater mortality, and that abundance increases in direct proportion to the number 

of additional eggs that survive when they are reared in a controlled environment (Lichatowich 

1999). Theoretical models in population ecology and the concept of “maximum sustained yield” 

similarly assumed density-dependent control of salmon and developed equations to describe the 

apparent relationship between population size and the resulting number of recruits (e.g., Ricker 

1948, Larkin 1977). 

Salmon hatcheries and harvest models have had widespread appeal for two reasons. 

1. They reinforced the fundamental economic view of fishery management (Bottom 1995, 

1997). 

2. They also met new standards of scientific legitimacy, as modern ecology actively 

shunned historical and descriptive explanations for the reductionist and predictive 

methods of the physical sciences (Kingsland 1995). 

Both achieved this predictability by simply eliminating natural variation: hatcheries through 

technological control of the only variations assumed to be important (i.e., those in freshwater), 

and harvest models by averaging the apparent relationship between population size and 

recruitment over the period of observation (Cushing 1995). In both cases, the assumption that 

populations are regulated by a predictable, freshwater struggle for existence allowed fishery 

management to avoid the messier stages of the salmon life cycle that were more difficult to 

understand or control. 

This is not to say that the estuarine life of salmon has been ignored altogether. But even 

when the estuary has been considered, management and research activities often extended to tide 

water the same agricultural ideas used to remove production constraints upriver. After the turn 

of the century, for example, state fish commissioners sought legislative support and later 

successfully established bounties for marine birds and mammals under the assumption that large 

numbers of estuarine predators constituted a significant “waste” of an economic resource and 

should be destroyed (Reed 1901). When hatchery technology had developed the means to rear 

salmon for extended periods and control most of their freshwater mortality, fishery managers 

looked for additional ways to protect their investment by eliminating other perceived threats 

immediately below the hatcheries. 

In the late 1940s, Gharrett (1955) transferred groups of hatchery Chinook and coho 

fingerlings directly into the Nehalem River estuary in Oregon to test whether the procedure could 

be used to avoid instream competition with wild fish, predation during downstream migration, 

and the expense of holding subyearling fish in hatchery ponds until their second spring. A few 

decades later similar ideas were implemented on a larger scale when the Oregon State Game 

Commission constructed an estuarine impoundment for holding salmon fry in Lint Slough in the 

Alsea River estuary (Raynor and Garrison 1965, Garrison 1966, Holm 1969). By regulating tidal 

and river flows and trapping nutrient-rich ocean water in the shallow slough, fishery managers 

hoped that salmon would thrive on a rich estuarine prey base, eliminating hatchery food costs, 

23
increasing growth rates, and protecting fish from riverine and estuarine predators (Holm 1969, 

Bottom and Simenstad 2001). 

Declining salmon runs in the late 1970s highlighted the failure of traditional hatchery 

operations to maintain or increase salmon returns and raised new questions about whether 

estuaries might be “bottlenecks” to production. Based on the apparent success of Japan’s 

massive chum salmon production program, several large U.S. corporations developed 

ocean-ranching facilities with salmon release and recapture sites located near the mouths of 

several Oregon estuaries. Researchers began monitoring potential interactions between private 

hatchery and wild juveniles, concerned that hatchery-released fish might not migrate directly to 

sea and could compete with wild, estuarine-rearing salmonids (Nicholas et al. 1979, Myers and 

Horton 1982, Nicholas and Herring 1983, Nicholas and Lorz 1984). Some initiated “carrying 

capacity” studies to estimate the quantities of hatchery Chinook salmon that estuaries could 

support (Reimers et al. 1979, Nicholas and Downey 1983, Nicholas et al. 1984). 

To test the estuary bottleneck theory, researchers conducted experiments to compare 

smolt survival of hatchery coho and Chinook salmon released in river and barged various 

distances offshore of the Columbia (Solazzi et al. 1991) and Fraser rivers estuaries (Macdonald 

et al. 1988, Levings et al. 1989). Reminiscent of the early experiments that moved fish to the 

estuary to eliminate potential in-river mortalities (Gharrett 1955, Raynor and Garrison 1965, 

Garrison 1966), these experiments tested whether salmon are “estuarine dependent” or whether 

survival could be increased if salmon simply avoided the estuary altogether. 

Present research in the Columbia River estuary remains a downstream extension of 

upriver ideas to control salmon production and mitigate for hydropower-system effects. Some 

estuarine studies are designed around fish tagging technologies and the incidental availability of 

experimental groups of marked fish used to evaluate hatchery rearing practices, barging 

operations for transporting fish around dams, and the relationships between river flow and fish 

passage through the dams. The NMFS has maintained a monitoring site at Jones Beach (RKm 

75) in Oregon to provide a tidewater recovery point below Bonneville Dam (RKm 235) where 

migration timing, travel times, and survival for various groups of marked salmon can be 

estimated to the upper estuary (Dawley et al. 1986). Ongoing research on salmon predation by 

Caspian terns (Sterna caspia, [Roby et al. 1998, Collis et al. 1999, USACE 1999, Ryan et al. 

2001 and 2003]) similarly relies on estuarine recoveries of Passive Integrated Transponder (PIT) 

tags from fish marked upriver, extending to the estuary earlier concerns about fish predation 

below mainstem dams and in the reservoirs (Beamesderfer and Rieman 1988, Beamesderfer at 

al. 1990, Rieman and Beamesderfer 1990). 

It is unclear, however, how the migrations, rearing requirements, or survival of estuarine 

salmonids should be interpreted from various upriver tagging studies. The probabilities of 

recapturing marked fish at Jones Beach or recovering tags at a Caspian tern colony in the lower 

estuary depend on the numbers and characteristics of individuals chosen for numerous upriver 

experimental groups. Marked fish do not represent the full diversity of sizes, geographic origins, 

or life histories of juvenile salmonids throughout the basin. Estimates of travel times or 

predation rates for marked fish may not apply to those of smaller subyearlings that are most 

likely to rear in the estuary for extended periods but are least likely to be tagged upriver. 

24
Because the design of these studies is dictated by the sampling opportunities that are 

created by hatchery, tagging, and recapture technologies—opportunities that emphasize 

relatively large hatchery fish with yearling life histories—it is unlikely the results apply similarly 

to all juvenile life history types in the estuary. Results for tagged hatchery fish, even if the 

results did represent behaviors of the majority of individuals that are now produced in the 

Columbia River ecosystem, provide little information about the historical habitats or life history 

types that have been lost and that a successful recovery program ultimately may need to 

reestablish. 

In summary, a common theme of production thinking in salmon management is the 

notion that estuaries, like rivers (Lichatowich 1999), are hazardous places. A primary goal of 

production-oriented research is to identify, eliminate, or avoid apparent ecological constraints, 

particularly any obvious predators or competitors in the estuary. This approach emphasizes the 

need to reduce estuarine mortality of juvenile salmon regardless of their geographic origins or 

life histories or whether any of the additional survivors would be destined to return as adults. 

Because it focuses on presumed threats to salmon, production thinking provides little or no 

information about the estuarine habitats and conditions that salmon need. Instead, the estuary is 

seen as a corridor through which a single, large, and undifferentiated mass of fish must confront 

predators before they can escape to the ocean. Among the many assumptions inherent to this 

view are the following: 

• The factors that limit salmon production in estuaries are separable from conditions 

experienced during other life stages and can be treated independently. 

• Estuaries have significant excess carrying capacity to accommodate large releases of 

hatchery fish (ISG 2000, Williams in press). 

• Estuarine abundance of juvenile salmon is regulated top down by predators (or 

sometimes bottom up by competitors) through density-dependent processes. 

• The number of adult salmon produced each year is a function of the rate of predation (or 

competition) that occurs in the estuary. 

• To avoid predators or competitors and improve survival rates, salmon must move rapidly 

through the estuarine corridor. 

• Adult returns will increase in proportion to the number of estuarine predators or 

competitors that are removed or otherwise prevented from interacting with salmon. 

Population Thinking in Estuarine Research 

Not all research in the Columbia River estuary has taken a strictly production-oriented 

view of salmon. The first significant study in the estuary (Rich 1920) was a descriptive survey to 

understand Chinook salmon biology and life history in the Columbia River basin. This survey 

began as an outgrowth of Gilbert’s (1913) early studies of sockeye salmon in British Columbia 

rivers, where he devised methods for interpreting salmon life histories from the patterns of 

circuli recorded on their scales. 

Rich’s (1920) research was not an estuary study, per se; it was a survey of the periods of 

migration, sizes, and ages of juvenile salmon migrants as they moved through the main river and 

25
estuary toward the ocean. To interpret the migration behaviors he found in the estuary, Rich 

looked upstream. Despite a comparatively short period of spawning for Chinook salmon 

throughout the basin, Rich found young salmon of a wide variety of age-and size-classes moving 

downstream and through the estuary throughout the year. From the distinct rearing histories 

recorded on the salmon scales, he inferred that this continuous estuarine migration was the sum 

of many independent populations whose separate movements and rearing patterns reflected 

different climatic and environmental conditions across the basin. For fish that remained in 

brackish water, Rich also documented, from scale patterns, a significant increase in growth rate 

relative to growth in freshwater, suggesting improved rearing conditions in the estuary. 

Rich’s (1925 and 1927) continued research on adult salmon in the Columbia River basin 

provided much of the information he used to demonstrate that salmon indeed return to their 

home streams to spawn. He concluded that each salmon species is composed of a large number 

of local, self-perpetuating populations, whose behaviors are molded by the particular sets of 

conditions found in their spawning and nursery areas (Lichatowich 1999). These results 

contributed to Rich’s (1939) ideas for an entirely new management approach that defined each 

population and its associated watershed as the fundamental unit of salmon conservation. 

The population ideas that Rich (1939) developed from empirical observation defined a 

different kind of estuary from the one envisioned based on production thinking (Table 2). Rather 

than a simple corridor through which a single, homogeneous group of outmigrants move as 

rapidly as possible to avoid voracious predators, Rich’s estuary was a complex nursery ground 

where a continuous stream of individuals from geographically discrete populations converged 

and remained for varying periods of time. From this perspective, diverse salmon rearing 

behaviors in the estuary became linked to habitats upriver where self-sustaining populations 

spawned and reared. Thus a fundamental implication of population thinking is that estuarine 

habitat use and salmon migration patterns may depend as much on the status of upriver habitats 

and source populations as on the environmental conditions within the estuary itself. 

In the past few decades, population thinking has played a significant role in 

understanding the estuarine ecology of salmon, particularly in some smaller Northwest estuaries 

(Reimers 1973, Carl and Healey 1984, Healey 1982, Simenstad et al. 1982). Ironically these 

ideas have had little influence on research in the Columbia River estuary since the 1930s, despite 

the fact this system provided much of the early data from which population thinking and the 

entire stock concept of salmon conservation originally developed (Rich 1939 and Ricker 1972). 

By then hydroelectric and irrigation development in the Columbia Basin had shifted attention 

back to the more familiar production approach that emphasized the development of hatchery, fish 

bypass, and transportation systems to compensate for upriver habitat and population losses 

(Lichatowich 1999). Despite the implications of Rich’s early population studies, and except for 

occasional concerns about estuarine predators and competitors, the expanding business of fish 

production had little interest in the estuary. 

26
Table 2. Contrasting views of salmon conservation in estuaries based on production and population 

thinking.

Production thinking Population thinking

Goals Efficiency, production Resilience, reproduction 

Population units Arbitrarily defined Biologically defined 

Time frame Short Evolutionary 

Objectives Control survival and abundance Conserve local populations 

and life history diversity 

Estuary function Corridor for a single, 

homogeneous group of salmon 

Nursery area for many 

self-sustaining populations 

Estuary 

management 

Control predators, promote 

rapid salmon seaward migration 

Protect habitats of diverse 

life history types 

A Theory of Populations with Complex Life Cycles 

Marine ecologists have become increasingly aware that species with complex life 

cycles—distinct developmental stages located in spatially discrete habitats—may be regulated by 

ecological processes coupled among different environments. Roughgarden et al. (1988) noted 

that marine rocky intertidal communities at some sites are regulated by adult interactions and 

competition for space, while at other sites distant ocean currents and upwelling processes control 

populations by limiting the larval supply. Thus traditional stock-recruitment approaches may not 

adequately describe the dynamics of marine populations with complex life cycles, whose 

transport or migrations link processes in distant habitats, and whose survival can be regulated by 

physical processes unrelated to population density. 

The migrations of anadromous salmonids similarly integrate processes across vastly 

different aquatic environments. Research indicating that salmon production is regulated by 

large-scale shifts in the North Pacific Ocean and atmosphere (Francis and Sibley 1991, Beamish 

and Bouillon 1993, Mantua et al. 1997) contradicts traditional ideas that density-dependent 

interactions during the earliest life stages are sufficient to explain salmon variability. The role of 

density-independent processes in salmon production may be particularly important in the 

California Current region, which is considered a physically controlled ecosystem, wherein 

plankton assemblages and carrying capacities are regulated by ocean currents and upwelling 

events rather than biological interactions (McGowan and Walker 1993). 

Climatic shifts in the North Pacific not only influence marine survival of salmon but also 

control processes at all other stages of the salmon life cycle by modifying flow and temperature 

conditions upriver and salinity gradients and sediment transport in estuaries (Greenland 1994, 

Melack et al. 1997). A framework for understanding salmon variability must account for 

freshwater, marine, and estuarine processes that are linked through salmon migrations.

27
One approach that may be useful for understanding the role of estuarine habitats for 

salmon is Sinclair’s (1988) member/vagrant hypothesis, which proposes a set of general 

principles for understanding the dynamics of marine species with complex life cycles. Unlike 

the production focus of traditional fishery management, Sinclair’s hypothesis uses population 

thinking to account for four characteristics of marine populations simultaneously: 

1) differences between species in population richness, 

2) the geographic patterns of populations within species, 

3) control of absolute (e.g., mean) abundance, and 

4) control of population variance. 

The member/vagrant hypothesis provides a useful perspective for evaluating the specific needs 

of salmon within estuaries while placing the needs in context of the entire continuum of habitats 

needed to sustain salmon life cycles. 

Population Pattern and Richness 

The member/vagrant hypothesis states that the pattern and richness (diversity) of 

populations are determined by the number and location of geographic features where a species’ 

life cycle can be brought to closure (Sinclair 1988). According to this idea, complex life cycles 

of marine populations have evolved in response to certain persistent features in the environment 

that allow sexually reproducing individuals to find a mate with a similar genome. Because 

membership in a population (e.g., successful reproduction) requires that individuals be in the 

right place at the right time, certain geographic features provide a predictable setting in which 

organisms of reproductive age can converge at an appropriate time in otherwise diffuse and 

dispersive aquatic environments. 

Thus life histories of marine and anadromous species involve transport and migration 

behaviors that are linked to particular geographic features including streams, estuaries, offshore 

banks, currents, ocean gyres, and upwelling systems. Sinclair’s hypothesis suggests that the 

number of geographic settings allowing a species to complete its life cycle successfully 

determines the number of its component populations. 

According to this idea, marked differences in population richness among marine species 

are associated with the number of various egg and larval retention areas around which the life 

histories of populations have become adapted. The European eel (Anguilla anguilla, [Figure 7]), 

which consists of one panmictic population whose egg and larval retention area is the entire 

North Atlantic gyre (Sinclair 1988), are at the low end of the spectrum. The Atlantic herring 

(Clupea harengus), which consists of multiple populations that result from a series of discrete 

larval retention areas maintained within coastal embayments, estuaries, and certain tidal 

circulation features of open-ocean spawning grounds, are at the high end. 

The most population-rich of Sinclair’s examples is Atlantic salmon (Salmo salar), which, 

like Pacific salmon, have a diverse population structure defined by the number of streams and 

rivers flowing into the ocean and to which adults home for spawning. Precise homing allows 

even populations in adjacent streams to become isolated and adapted to local conditions 

28
Figure 7. The continuum in population richness of selected anadromous and marine species in the 

northern Atlantic (adapted from Sinclair 1988). 

(Miller and Brannon 1981, Carl and Healey 1984). Common to these examples is the 

segregation of early life stages among population groups and the interpopulation mixing during 

later stages. Differences among species in population richness are explained by this separation 

of populations during the early life stages based on the same specific geographic features to 

which adults home to reproduce. 

A critical underpinning of the member/vagrant hypothesis is the interaction between 

physical geography and the behavior (e.g., life histories) of individuals that use various persistent 

features of aquatic systems to maintain membership in a population. The vertical migration 

behaviors of many zooplankton and pelagic stages of benthic invertebrates, for example, are 

adapted to the two-layered, estuarine tidal circulation that aids their retention in estuaries and 

minimizes individual losses from populations (Sinclair 1988). 

Such interactions between physical geography and behavior similarly characterize the 

anadromous life cycles of Pacific salmon. Diverse salmon life histories that include broad 

variations in timing and size of seaward-migrating fish and periods of estuary residence represent 

alternative time/space solutions for completing anadromous life cycles within the overall 

distributional range and physiological constraints of each species. Distinctions in migration 

timing, size, and rearing periods are linked to fine-scale features within each aquatic 

environment (stream, river, estuary, and ocean) where salmon seek refuge, feed, and delay their 

passive transport for varying periods as needed to complete each developmental stage (egg, fry, Many 

 Atlantic salmon 

 American shad 

 Atlantic herring 

 Atlantic cod 

 Rainbow smelt 

 Haddock 

 Atlantic mackerel

Many 

One 

One 

Atlantic menhaden 

European eel

Number of larval retention areas

Number of populations 

29
smolt, adult). Strung together the physical features in each environment and at each ontogenetic 

stage constitute a chain of habitats in time and space that salmon navigate to complete their life 

cycles and maintain membership in a population. 

Abundance and Variability 

A second important component of the member/vagrant hypothesis is the assumption that 

temporal variability in abundance is determined by the loss of individuals from the area that 

ensures membership within a given population (Sinclair 1988). This idea suggests that loss of 

members from a population (vagrancy) occurs throughout a life cycle and may be the result of 

biological interactions or purely physical (geographic) factors. Sinclair distinguishes what he 

calls spatial processes, which involve geographic displacement from the area and time necessary 

to ensure population membership, from energetics processes, which include mortality from 

predation, competition, or disease. Spatial losses may result from advection of individuals away 

from the area/time necessary to complete their life cycle. Such losses do not necessarily require 

mortality of individuals but simply the failure to find a mate or reproduce successfully within the 

appropriate area and time. 

Adult salmon vagrants (strays) include individuals that return to spawning grounds 

outside their natal stream. Some level of straying may be evolutionarily advantageous, allowing 

species to test new environments, increase genetic heterogeneity, and expand their range or 

recolonize habitats destroyed by disturbance. However, many strays may simply not contribute 

to the next generation, because they fail to find a mate at the precise time or place of return or 

because their genetic patterns of emergence, rearing, and migration are mismatched for the 

conditions represented in a new environment. Using electrophoretic analysis, for example, 

Tallman and Healey (1994) estimated that gene flow among chum salmon populations in 

Vancouver Island streams was less than 5%, although straying rates estimated from tagging 

studies were considerably higher (as much as 46% in one instance). These results suggested that 

most strays to nonnatal streams did not reproduce successfully. 

Spatial and energetics losses may involve either density dependent or independent 

processes. However, the member/vagrant hypothesis suggests in principle that spatial processes 

alone can be sufficient to account for density-dependent losses from a population. The size of 

the geographic area capable of maintaining members of a population, for example, determines its 

carrying capacity and controls fish density (Sinclair 1988). This mechanism has been suggested 

to explain strong year-classes of sardines (Sardinops melanostictus) off Japan, when 

oceanographic changes expand the total area available for successful spawning and prey 

production, and increase the survival of post-larvae (Lluch-Belda et al. 1992). Climatically 

driven expansion or contraction of the ocean habitat area suitable for survival also might be 

important for salmon in the Pacific Northwest, which is located near the subarctic boundary of 

the North Pacific and encompasses the southern edge of the range of several salmon species 

(Fulton and LeBrasseur 1985, Bottom et al. 1998). 

Applications of the Theory to Salmon and Estuaries 

The member/vagrant hypothesis has a number of important implications for 

understanding the structure and dynamics of salmon populations: 

30
• First, if the hypothesis is correct, then salmon populations and life history types should 

exhibit a geographic structure associated with the varied features and characteristic 

patterns of variability encountered across their broad distributional range. 

• Second, such a complex life history structure should maximize productivity and 

resilience of salmon by diversifying habitat use and spreading risks unevenly in time and 

space. 

• Third, unlike traditional population theories, the hypothesis suggests that a variety of 

geographic and density-independent processes throughout all stages of the salmon life 

cycle might explain fluctuations in population abundance. 

The following evidence offers support for these conclusions and suggests that Sinclair’s (1988) 

hypothesis can provide a general framework for evaluating the role of estuarine habitats in 

salmon life cycles. 

Geographic Structure of Populations and Life Histories 

Biologists have documented examples of the complex geographic structure of salmon 

populations and described considerable life history diversity within and among populations (e.g., 

Taylor 1990, Healey and Prince 1995) consistent with the patterns expected from Rich’s (1939) 

observations and Sinclair’s (1988) hypothesis. Yet the importance of this geographic structure to 

observed patterns of estuarine residency and habitat use has rarely been considered in salmon 

research and management. Nonetheless results from several population studies in the past few 

decades support the member/vagrant hypothesis and its application to salmon in estuarine 

environments. 

Perhaps the best example is a detailed study of Chinook salmon life histories in the Sixes 

River in Oregon. Within this small watershed, Reimers (1973) documented five different life 

history types of Chinook salmon based on the patterns of seaward movement by juveniles (Table 

3). By comparing migration and rearing patterns of outmigrants with those recorded on the 

scales of returning adult salmon, Reimers concluded that approximately 90% of the fish 

returning to spawn were Type 3: those that had spent an extended period of time in the late 

summer rearing in the estuary where they grew to a large size before migrating to the ocean. Yet 

this was not the most abundant pattern among the juveniles Reimers sampled. 

Although Reimers’ (1973) results are often cited to demonstrate that extended estuarine 

rearing and growth are critical for Chinook salmon, it is possible that if he had studied several 

broods of Chinook, he might have found other life history types that survived equally well during 

other years and environmental conditions. This possibility is supported by an experiment that 

compared the survival of Campbell River juvenile Chinook released in British Columbia over 

three broodyears into four different environments (Macdonald et al. 1988, Levings et al. 1989): 

1) the river, 

2) the estuary, 

3) an offshore transition area, and 

4) the ocean. 

31
Table 3. Juvenile life history types for Chinook salmon in the Sixes River (Reimers 1973). 

Life history type Pattern of seaward movement 

1 Fry move directly to sea within a few weeks 

2 Juveniles stay in the river or tributaries until early summer, move to the 

estuary for a short period, and go to sea before late summer 

3 Same as above except fish stay in the estuary through late summer and go to 

sea in the autumn 

4 Juveniles stay in tributaries until autumn rains and then migrate to sea 

5 Juveniles stay in tributaries through the summer, rear in the main river the 

following spring, and enter the ocean as yearlings 

Although fish with access to the estuary (groups released upriver or directly in the estuary) had a 

higher survival to return during the first two years of the experiment, in the third year, survival 

was about equal for all four release groups. Thus changing environmental conditions from year 

to year may favor different rearing and migration behaviors within a river system. 

In the Nanaimo River in British Columbia, Carl and Healey (1984) identified three 

juvenile life history types for Chinook salmon associated with differences in their age of seaward 

migration, including subyearling estuarine smolts (fry move directly to the estuary and enter the 

ocean in June or July), subyearling riverine smolts (fry rear in the river two months and briefly in 

the estuary before entering the ocean), and yearling riverine smolts (juveniles stay in the river a 

full year and move seaward in the spring). Genetic isolation of the three life history types was 

suggested by variations in allozyme frequencies and differences in body morphology of each 

type. Carl and Healey (1984) concluded that variations in migration behavior within the 

Nanaimo River basin are linked to different subpopulations associated with geographically 

distinct spawning areas. Thus, as suggested by the member/vagrant hypothesis, subpopulations 

have developed around specific geographic settings where different groups of salmon complete 

their life cycles through different times and ages of migration. 

The present-day distribution of Chinook salmon in the Columbia Basin also reveals a 

geographic structure of spawning populations and juvenile life histories, although it is a 

fragmented remnant of the mosaic of spawning races and life history types that once existed 

(ISG 2000, Williams in press). Stream-type (yearling migrant) life histories today are most 

common in the Columbia River headwater streams and in the Snake and Salmon rivers 

subbasins, while ocean-type (subyearling migrant) life histories predominate in lower reaches of 

the Columbia (Taylor 1990). 

These present-day patterns generally coincide with different adult spawning runs: 

ocean-type life histories today are most often associated with fall spawning runs in the lower 

reaches, and stream-type are common among spring and summer-run adults in the upper basin. 

The Independent Scientific Group (ISG 2000) found that this presumed dichotomy of juvenile 

migrant types based on adult run timing is an oversimplification that ignores upriver habitat 

32
losses and associated ocean-type life histories that were likely prevalent among some spring and 

summer spawning populations. Nonetheless the general principle of a geographic structure of 

life histories associated with particular habitat features applies to salmon populations in the 

Columbia River basin. 

Salmon Resilience and Production 

The geographic structure of salmon populations and the diversity of life histories within 

and among populations have been described as a strategy that spreads risks and avoids brood 

failure (Healey 1991). Because not all individuals behave in the same manner or use the same 

habitats at the same time, life history diversity affords resilience to salmon in uncertain 

environments. The use of different spawning and rearing areas maximizes the possibility that 

any year-class will contribute to future generations and maximizes the total production of 

juveniles from a river system (Carl and Healey 1984). 

The importance of life history diversity is illustrated by the effects of various ocean 

disturbances on populations that leave estuaries at different times or rear in different areas. 

Although the population-specific patterns of ocean migration are poorly understood, gross 

differences among geographically distinct groups of populations (stocks) may affect the capacity 

of salmon to withstand strong El Niño events or interdecadal shifts in ocean regimes (e.g., 

Mantua et al. 1997). Tule fall Chinook stocks, which spawn in the lower Columbia-Bonneville 

pool area, migrate primarily off Washington and southern British Columbia, whereas upriver 

brights3

 from the area between the McNary and Priest Rapids dams rear far north off northern 

British Columbia and southeastern Alaska (Van Hyning 1973, Beaty 1992). Coastal Chinook 

stocks south of Cape Blanco in Oregon rear off southern Oregon and northern California, while 

stocks to the north of Cape Blanco migrate northward (Nicholas and Hankin 1988). 

Differences in ocean rearing areas may explain different responses to the strong 

1982–1983 El Niño event: Chinook stocks off southern Oregon and locally distributed stocks 

from the lower Columbia River suffered high mortality and low returns, whereas northward 

migrating populations from the Columbia River showed little or no decline in abundance 

(Johnson 1988). 

Differences in the timing of migration of salmon from the estuary to the ocean also may 

affect the capacity of salmon to adapt to variable ocean conditions. While coho salmon 

production, for example, has been positively associated with periods of strong coastal upwelling 

in the spring (Nickelson 1986), the timing, strength, and duration of upwelling events is episodic 

and variable along the coast. The seasonal shift from winter conditions to a spring/summer 

upwelling regime, characterized by changes in winds, coastal currents, temperatures, and density 

gradients, occurs suddenly at different times each year (Huyer 1983, Strub et al. 1987). 

A single upwelling event lasting a few days in the spring may be sufficient to cause the 

shift to a spring/summer regime (Huyer 1983). Thus different times of ocean migration may be 

advantageous in different years depending, for example, on the onset of the spring/summer 

transition, the timing and location of upwelling events, the distribution of the Columbia River 

 

3

 Bright is the common name for a particular run of Chinook salmon in the Columbia River basin. 

33
plume, or the northward extent of warming caused by occasional strong El Niño Southern 

Oscillation (ENSO) events in the tropics (ISG 2000, Williams in press). 

Spence (1995) concluded that variability in ocean entrance by coho salmon has evolved 

in response to characteristic degrees of ocean variability in different regions of the North Pacific. 

Comparing 50 smolt populations from California to Kodiak Island, Alaska, Spence described 

latitudinal patterns in the timing, duration, and variability of migration. Although migration 

times varied locally, results suggested that this variability exists within certain temporal windows 

of opportunity among different regions of the North Pacific. Spence further concluded that a 

more protracted period of migration among coho salmon populations south of the Queen 

Charlotte Islands in British Columbia is possibly an adaptive response to increased ocean 

variability and uncertainty relative to more northern areas. 

Diversity of salmon life histories not only minimizes risk in uncertain environments, it is 

fundamental to salmon productivity. As conditions in freshwater, estuarine, and marine 

environments vary between years, so may the number of alternative behaviors that will permit 

life cycle closure. In relatively favorable conditions a greater number of life history types and 

populations may be captured, producing a stronger year-class for the species as a whole (Figure 

8, [Bottom et al. 1998]). Thus as proposed by the member/vagrant hypothesis (Sinclair 1988), 

the absolute abundance of a species may be a function of physically driven expansion and 

contraction of the spatial (and temporal) extent of areas where life cycle closure is possible. 

Life history diversity thus may affect the overall carrying capacity of an estuary for 

salmon. Some studies present evidence of density-dependent estuarine growth of salmon, which 

could affect size at ocean entrance and, through size-specific mortality, ocean survival of smolts 

(Reimers 1973, Reimers et al. 1979, Healey 1982, Nicholas and Downey 1983, Nicholas and 

Hankin 1988). As illustrated by the varied life history types in the Sixes (Reimers 1973) and 

Nanaimo rivers (Carl and Healey 1984), density-dependent effects may be minimized if the 

contributing populations of each species in a basin have somewhat different times and sizes at 

entrance, duration of residence, and migratory paths through the estuary. By spreading their 

rearing patterns through time and space, not all salmon use the same areas and resources at the 

same time. Variation in life history thus maximizes basin productivity by allowing a continued 

turnover of available estuarine habitat by different groups of fish staged to move through the 

system at different times (Myers and Horton 1982). 

Salmon Imprinting and Homing 

Added support for the member/vagrant hypothesis comes from studies of salmon 

imprinting and homing. These results suggest that the idea of salmon navigating a chain of 

habitats to complete their life cycles may be literally (and not just metaphorically) correct. One 

hypothesis of the mechanism of homing suggests that juvenile salmon imprint on a series of 

olfactory signatures as they migrate through a gradient of habitats to the ocean and retrace this 

sequence upon returning to their home streams (Harden Jones 1968, Dittman et al. 1996). In 

experiments to test imprinting of coho salmon at various life stages, Dittman et al. (1996) 

concluded that simple exposure to odors may not be sufficient but that olfactory stimuli 

experienced by migrating through a gradient of environmental cues—varying water chemistry, 

temperatures, lunar cycles, and water velocities, etc.—may be necessary for optimal imprinting. 

34
Least favorable Most favorable 

Environmental conditions 

Low High 

Salmon production 

= Salmon life history type 

E3 

E2 

E1 

Figure 8. Salmon production as influenced by life history diversity. Each life history type experiences a 

different environment based on the temporal and spatial sequence of habitats (freshwater, estuary, 

and ocean) used throughout its life cycle. As conditions (e.g., E1, E2, and E3) become more 

favorable, the ecosystem captures (i.e., expresses) a greater variety of life histories, producing a 

stronger year-class for the species. 

A proposed mechanism for this response to migration is the apparent stimulation of thyroxine 

production by varying environmental cues, which may facilitate olfactory imprinting (Dittman 

et al. 1996). 

A highly sensitive period for imprinting is the end of the parr-smolt transformation. 

Dittmann et al. (1996) found little evidence that hatchery salmon imprinted to homing cues 

before the smolt stage. Fish held for lengthy periods and not allowed to migrate during the 

parr-smolt transformation were impaired in their homing ability. This suggests that conditions 

experienced during migration through the tidal-freshwater and estuarine gradient, where salmon 

gradually adapt to saltwater conditions and reach the end of the smolt stage, may be particularly 

important to successful imprinting. Interestingly, although wild fish show a capacity to imprint 

at early ages before the smolt stage, hatchery presmolts in these experiments did not. A stable 

environment and lack of migration associated with hatchery rearing may have been the cause of 

this (Dittman et al. 1996). 

35
Geographic Mechanisms of Population Control 

In addition to mortalities associated with competition, predation, and disease, the 

member/vagrant hypothesis underscores the importance of geographic processes of population 

control for species that migrate among spatially distant habitats. Even biological interactions at a 

local scale may be controlled by physical processes that determine, for example, the temporal 

and spatial availability of salmon habitat or the particular suite of species that salmon encounter 

when they enter the ocean. Patterns of salmon abundance and use in an estuary also are linked 

directly to various processes upriver that determine the size, migration timing, and physiological 

state of downstream migrants. Mechanisms of population control implied by the 

member/vagrant hypothesis (Sinclair 1998) that may be particularly relevant for understanding 

salmon in estuaries are described in the following subsections and depicted in Figure 9. 

Habitat availability and connectivity 

If salmon migration and rearing behaviors are tied to specific geographic features, then 

population members may be lost if these features are changed or eliminated by natural or 

human causes (Figure 9, Scenario 1). Scale analyses comparing past and contemporary life 

histories among Rogue River Chinook salmon in Oregon, for example, suggest that a former 

estuarine-rearing life history may have been eliminated, possibly through modifications of the 

tiny estuary during construction of the jetties and boat basin (Schlucter and Lichatowich 1976). 

A review of the five life history types described in Sixes River (Reimers 1973) raised similar 

questions about whether warming of the mainstem river possibly eliminated an early large 

migrant pattern, which is found in other coastal estuaries (Bottom et al. 1998). Extensive loss of 

historic estuarine wetlands through widespread diking and filling in Northwest estuaries could 

reduce or eliminate some subyearling migrant life histories that have been linked to the 

availability of shallow marsh habitats (e.g., Levy and Northcote 1981 and 1982). 

If salmon life cycles require specific sequences of habitat in time and space, then areas 

otherwise capable of supporting salmon may remain unoccupied when their connection to other 

habitats is lost (Bottom et al. 1998). Thus habitat conditions and associated subpopulations 

upriver may ultimately limit the array of life histories expressed in the estuary. Certain estuarine 

habitats might not be fully occupied, for example, if upstream habitats lost to dam construction, 

pollution, or other factors supported populations with distinct estuarine rearing behaviors. 

One example noted above is the loss of some ocean-type life histories among Chinook 

salmon populations in the Columbia River (ISG 2000, Williams in press). Temperature 

variations affecting growth opportunity and time of smolting in different areas of the basin may 

be an important factor determining the geography of Chinook life histories (Taylor 1990). Dam 

construction combined with temperature increases in the main stem and lower subbasins have 

diminished habitat opportunity upriver and substantially reduced the proportion of subyearling 

(ocean-type) migrants that are now produced in the Columbia (ISG 2000, Williams in press). 

Loss of subyearling migrant types from summer and spring spawners probably has occurred in 

many areas that historically offered optimal growth opportunity, particularly the warmer middle 

portions of the Columbia River subbasins (Lichatowich and Mobrand 1995, ISG 2000, Williams 

in press). Because subyearling migrants typically reside in the estuary for longer periods and use 

different habitats than those with yearling life histories, such losses could have an important 

36
Stream 

rearing 

(S) 

Estuary 

rearing

(E) Ocean 

rearing 

(O) 

Spawning & 

incubation 

(S & I)

Emergence 

River 

rearing 

(R) 

Salmon 

life cycle 

R 

E 

O 

S S & I 

Hatchery

E 

O 

R 

E 

O 

S S & I 

Scenario 1:

Habitat loss 

Scenario 2: 

Displacement in 

time and space

Scenario 3: 

Genetic selection, 

loss of a 

life history type

R 

E 

O 

S S & I 

Figure 9. Generalized view of a salmon life cycle (top) and three scenarios of spatial losses that can 

affect life cycle closure (bottom). In Scenario 1, habitat losses in the estuary prevent extended 

periods of estuarine rearing and growth prior to ocean entry (dotted arrow and estuary-rearing box 

indicate loss after the river-rearing stage). In Scenario 2, hatchery rearing modifies the migration 

sequence—timing, distribution, and developmental stage—which may prevent optimal imprinting 

and homing back to a river basin (external hatchery pathway without a connection to the 

spawning stage). In Scenario 3, intensive selection pressures (e.g., harvest, interbreeding with 

hatchery fish, etc.) modify the genetic composition of a population, eliminating particular life 

history pathways that are genetically programmed (dotted lines and absence of arrows). 

influence on contemporary patterns of estuarine rearing by Chinook salmon and could leave 

vacant various shallow-water habitats favored by smaller ocean-type juveniles. 

Disturbance processes 

Changes in disturbance processes that displace salmon from the appropriate time and 

location needed to complete their life cycles or that reduce availability of critical habitats may 

37
contribute to population losses. It is probable that Columbia River salmon diversified their 

migration and rearing behaviors to fully use the wide array of tributary habitats and flow 

conditions historically represented in the Columbia River basin. Because populations varied 

widely in their migration timing and behaviors, Columbia River salmon were not equally 

vulnerable to environmental disturbance. Disturbance conditions most favorable for one life 

history type may have been detrimental to another. However, if the relative benefits of various 

behaviors changed from year to year, the diversity of life histories would be maintained (ISG 

2000, Williams in press). 

Regulation of flows in the Columbia River by mainstem dams has dampened natural 

fluctuations in the system and may have created a mismatch between certain migration behaviors 

and the flow/habitat conditions that now exist. Stabilization of river flows and establishment of a 

system of slack-water reservoirs, for example, possibly shifted the fitness landscape toward 

less-favorable conditions for salmon with subyearling life histories, whose migration and feeding 

behaviors depend on flooded shorelines and complex backwater areas maintained by the 

interaction of the river with riparian and floodplain habitats (ISG 2000, Williams in press). Flow 

regulation may similarly influence access to habitats in the estuary because of changes in salinity 

structure, water velocity, and depths. 

Displacement of fish in time and space 

Artificial manipulations of salmon development (e.g., smolting), release locations, and 

migration timing may contribute to population losses by altering the time and space use of 

estuarine and marine habitats and increasing rates of straying by adults (Figure 9, Scenario 2). 

The large proportion of hatchery Chinook salmon now released in the Columbia Basin (see the 

“Estuarine Development History and Salmon Decline” section, page 5), many of which are 

held for extended periods and raised to relatively large sizes, could substantially affect size and 

time-dependent rearing and migration patterns in the estuary. 

In studies on the effects of release date and transportation on hatchery Chinook salmon 

from two Columbia River hatcheries, Pascual and Quinn (1995) documented varying effects on 

homing ability, which they attributed to disruptions in the sequence and timing of imprinting 

events through artificial manipulations. From these and other studies, they suggest that the 

sequence of imprinting events is characterized by the time fish experience a particular location 

and the physiological state of the fish at that time. Thus manipulations of release date and 

transportation of fish may disrupt the migration sequence and increase straying through effects of 

release date on spawning time, effects of holding fish on the sequence of juvenile imprinting, and 

interference of imprinting through off-station transport of smolts (Table 4). 

Population losses due to disruption of the migration sequence are illustrated by the 

experiments of Solazzi et al. (1991) who compared the survival of hatchery coho salmon 

released directly into the estuary and various distances offshore. The results showed 

progressively greater rates of straying to river basins outside the Columbia River with transport 

distance from the hatchery rearing site. The level of homing reported for some Columbia River 

hatcheries is much lower than has usually been reported for salmonids, indicating significant 

spatial losses and raising concerns about genetic interchange among populations (Quinn et al. 

1991). 

38
Table 4. Possible mechanisms of increased straying of fish through hatchery and transportation 

manipulations (from Pascual and Quinn 1995). 

 I. Effects of release date 

 A. Affects time of return 

 1. Month at return 

 2. Age at return 

 B. Affects sequence of imprinting by seaward migrating fish 

 1. Mismatch between the location and developmental state of fish 

 2. Mismatch between the location and the time (e.g., environmental conditions) 

II. Effects of transportation 

A. Reduced opportunity to imprint 

B. Genetic adaptation to local conditions 

Population structure and life history 

Many life history variations in salmon populations have been demonstrated 

experimentally to be under some degree of genetic control, including age at maturity (Hankin et 

al. 1993), time of spawning and rate of egg and larval development (Beacham and Murray 1987), 

growth rate of juveniles, and age of seaward migration (Carl and Healey 1984, Taylor 1990). 

Strong selection pressures through harvest, hatchery practices, or other factors that alter the 

genetic structure of Columbia River populations may thus affect the patterns of migration and 

rearing through the estuary even if the habitats needed to support each life history type are 

available (Figure 9, Scenario 3). 

Changes in the time salmon spawn (and therefore emerge) may be critical to match 

subsequent developmental stages and life histories to various time windows in the environment 

(e.g., Beaty 1992, Spence 1995). Einum and Fleming (2000), for example, demonstrated a 

causal link between time of breeding (and thus time of hatching and emergence) and the success 

of offspring in Atlantic salmon. In this case, later emerging juveniles were smaller than early 

emerging ones so that reproductive success also could be affected through differential size 

selection at subsequent life stages. 

In the Salmon River in Oregon, the spawning time of coho salmon has advanced 1–2 

months, and the duration of spawning activity has decreased since the hatchery began operating 

in the mid-1970s (Mullen 1978, 1979, Jacobs unpubl. data). Although the specific effects on 

juvenile rearing patterns in the estuary are uncertain, such changes undoubtedly influence the 

times of emergence and downstream migration. In recent years, early adult returns has meant 

that few if any coho salmon spawned after late November flood events, which likely reduced 

survival of eggs already in the gravel. The possibility of a mismatch between present spawning 

times and the Salmon River environment is suggested by the lack of successful recruitment from 

most naturally spawning hatchery fish: each year about 95% of the fish spawning naturally in 

Salmon River are adults produced from a new hatchery brood (Jacobs et al. 2000). 

39
A Framework for Evaluating Estuarine Requirements 

 of Columbia River Salmon 

Evaluation Principles 

To summarize, the member/vagrant hypothesis (Sinclair 1988) and the supporting 

evidence from studies of salmon populations and life histories offer the following principles as 

an alternative to production thinking (Table 1) for interpreting the role of estuaries in salmon life 

cycles: 

• Salmon have evolved complex life cycles that require a chain of habitats in spatially 

discrete environments (freshwater, estuary, and ocean). 

• The resilience and productivity of salmon species depend on their diversity of life 

histories, including variations in the use of estuarine habitats by juveniles. 

• The geographic pattern and diversity of salmon life histories reflect the variety of habitat 

combinations in time and space by which each species can complete its life cycle. 

• Estuaries offer one of many alternative rearing opportunities for salmon to achieve life 

cycle closure. Salmon with subyearling life histories are among the most dependent on 

estuaries for juvenile rearing. 

• Variability in salmon abundance is a result of losses from the time/area necessary to 

ensure membership in a population. Such losses may occur throughout all stages of the 

salmon life cycle and may involve geographic (spatial) and biological (energetics) 

processes that may be density-dependent or independent. 

These principles emphasize the interaction between behavior (life histories) and various habitat 

features that salmon use to complete each stage of their life cycle and maintain membership in a 

population. Thus conservation of population richness requires protection of the diverse 

geographic features that salmon use to achieve life cycle closure (Sinclair 1988). 

From an evolutionary perspective, Healey and Prince (1995) similarly describe the 

diversity of salmon rearing behaviors as the consequence of unique salmon genotypes interacting 

with available habitat features. Thus different combinations of habitat and genotype result in a 

variety of phenotypic behaviors by which salmon can successfully complete their development 

and reproduce. Among these behaviors are varied times and ages of salmon migration, periods 

of residency in the estuary, and times and sizes of ocean entry, all behaviors that require a 

particular temporal and spatial sequence of habitats to support them. 

The total productive capacity of the Columbia River basin and the resilience of salmon 

species are a function of all combinations of genotype and habitat that allow for the full 

expression of salmon rearing and migration behaviors, including diverse life histories in the 

estuary. To maintain the diversity and productivity of salmon requires the conservation of 

populations within their habitats, protecting the full variety of genotype-phenotype combinations 

(Healey and Prince 1995). 

40
Evaluation Criteria 

It follows logically from the “Evaluation Principles” subsection that the productive 

capacity of the Columbia River estuary can be affected by any changes that sever the link 

between salmon behavior and habitat, including the various categories of spatial losses depicted 

in the examples in Figure 9: 

1) removing habitats, altering habitat functions, or changing disturbance processes that 

salmon require to express the full diversity of potential rearing behaviors, 

2) altering the geographic structure and genetic characteristics of the component populations 

of each species that converge in the estuary en route to the ocean, and 

3) changing the phenotypic behavior of salmon, including displacement of fish from the 

time/space sequence of habitats they need to complete their life cycles in their home 

streams, regardless if the underlying genetic structure of populations is affected. 

In consideration of these and other categories of change implied by the member/vagrant 

hypothesis (Sinclair 1998), including the role of energetics losses from populations, we patterned 

our evaluation of estuarine-rearing conditions on the following criteria (Figure 10): 

• Habitat opportunity—the availability of estuarine habitat for salmon, often determined by 

physical (spatial) processes. 

• Habitat capacity—the quality of estuarine habitat for salmon, determined by biological 

interactions and bioenergetic conditions (energetics processes). 

• Population structure/life history—phenotypic and genotypic effects at other life stages 

that are linked to salmon behaviors in the estuary. 

• Performance—the ultimate outcome for salmon within the estuary, as measured by 

growth, life history diversity, and foraging success. 

We discuss our definition of each criterion and its application in the following subsections. 

Habitat opportunity 

Opportunity involves the capability of juvenile salmon to access and benefit from 

occupying a habitat. We define this capability broadly based on physical factors, physiological 

constraints, and ecological interactions (Sanfriel and Ben-Eliahu 1991, Simenstad et al. 2000b). 

These factors involve spatial processes that are largely unaffected by fish density (Table 5). 

We distinguish opportunity to occupy habitat from the probability of doing so. 

Probability involves many other external factors that affect whether juvenile salmon access 

habitat (i.e., variability in salmon populations and life histories that dictate run timing and fish 

size, density-dependent interactions, the presence and practices of salmon hatcheries, etc.) Thus 

whether a habitat is occupied at a particular time does not affect opportunity. 

41
Habitat 

opportunity 

(access) 

Habitat 

capacity

(quality) Population 

structure/ 

life history 

(upriver genetic, 

life history, and 

geographic 

structure) 

Performance

(estuarine foraging 

success, growth, diversity)

Figure 10. Criteria for evaluating estuarine-rearing conditions for subyearling (“ocean-type”) salmon as 

implied by the member/vagrant hypothesis (Sinclair 1988). 

Table 5. Factors affecting estuarine-habitat opportunity for juvenile salmon. 

Physical 

Physiological/ 

behavioral 

Water characteristics 

and quality Ecological 

Tidal flooding 

 Depth 

 Duration 

Fluvial flooding 

 Frequency 

 Depth 

 Duration 

 Timing 

Distributary and 

tidal channel 

structure 

Water velocity 

Turbidity 

Temperature 

Salinity 

Dissolved oxygen 

Turbidity 

Toxicants 

Proximity to 

disturbance (e.g., 

noise, movement, 

etc.) 

Refugia from 

predation 

(e.g., extent of 

overhanging 

vegetation, marsh 

vegetation height, 

proximity to 

deepwater habitats) 

42
We first describe historical patterns of environmental disturbance, specifically climate 

and river flow, which regulate the physical state of the basin-wide ecosystem within which the 

estuary is embedded. Climatic and hydrologic processes set broad limits in estuarine habitat 

opportunity while exerting direct selection pressures on salmon populations. In the “Changes in 

Hydrological Conditions” section (page 47), we examine natural climatic variations and 

human-induced changes in river flow and sediment transport that could have an overriding 

influence on estuarine-habitat opportunities and capacities for Columbia River salmon. 

Following this basin-wide assessment, we apply a hydrodynamic modeling approach 

to evaluate the sensitivity of salmon-habitat opportunity to historic changes in river flow as well 

as bathymetric conditions within the estuary in the “Estuarine Habitat Opportunity” section 

(page 89). The purpose is to determine whether modeling is a useful tool for predicting 

habitat-opportunity change and the potential salmonid response to past and future management 

scenarios. For these analyses, we use depth and velocity as indicators of habitat opportunity for 

subyearling Chinook salmon in the “Subyearling Chinook Salmon as an Indicator of Estuarine 

Conditions” subsection (page 44). We chose these criteria because: 

1) they are important physical features to which juvenile salmon respond, 

2) they can be simulated with some accuracy by modeling (as compared to water 

characteristics or quality), and 

3) they are useful descriptors of the major physical changes that have affected conditions in 

the estuary. 

Habitat capacity 

We define capacity to support juvenile salmon as those habitat qualities that promote 

juvenile-salmon production, including conditions necessary for feeding, growth, growth 

efficiency, and eluding predators (see the “Estuarine Habitat Capacity” section, page 127). 

Capacity thus encompasses what Sinclair (1988) terms energetics processes, including biological 

interactions and bioenergetic relationships: 

• productivity of selected invertebrate prey, including quantity and availability, 

• physicochemical and ecological conditions that maintain prey production, 

• salinities and temperatures that promote high assimilation efficiencies, and 

• predation levels as affected by habitat structure and relative vulnerability of salmon (e.g., 

refugia in vegetation or shallow water) as well as the habitat attributes of predators. 

Capacity is time dependent, because prey production can be punctuated, and predation 

intensity may vary with alternative prey availability, food demands, etc. Many variables interact 

to affect capacity. Turbidity may reduce the feeding efficiency and growth potential of salmon 

in a particular habitat and, at the same time, reduce their vulnerability to predators. In contrast to 

the physical factors that regulate habitat opportunity, the variables affecting habitat capacity are 

often density dependent. Salmon abundance may affect food-consumption rates and predation 

levels. 

43
Life history/population structure 

Whether salmon fully realize the opportunity and capacity of the estuarine habitats 

available to them may depend heavily on factors at other life stages that affect fish behaviors and 

their patterns of estuarine use. Such effects may be entirely phenotypic (e.g., changes in fish size 

and times of migration associated with hatchery release schedules, transportation of fish around 

dams, or changing temperatures or flow regimes); however, selection pressures from hatcheries, 

harvest, or elimination of upriver habitat also may alter the underlying genetic and geographic 

structure of upriver populations and thereby eliminate certain rearing behaviors. Changing 

release dates from hatcheries, for example, may alter time and age of return, with subsequent 

effects on emergence times and downstream patterns of estuarine use. Loss or substantial 

decline of upriver populations through overharvest of wild stocks or loss of spawning habitats 

may eliminate various combinations of genotype-habitat interaction that are responsible for 

unique life history patterns downstream. Although the focus of this study is the estuary, our 

conceptual approach dictates that we also must be aware of genetic or behavioral factors at other 

life stages that can influence the juvenile-salmon estuarine performance. Similarly, performance 

within the estuary may affect salmon population structure and associated marine and freshwater 

life histories (Figure 10). 

Performance 

The ultimate measure of performance for Columbia Basin salmonids is the diversity of 

self-sustaining populations within their natal habitats, which is reflected in the overall resilience 

and productivity of each species from the basin as a whole. For the purpose of this evaluation, 

performance is defined more narrowly based on the diversity of physiological and behavioral 

patterns of subyearling Chinook within the estuary. We assume that the diversity of 

habitat-specific residence times, range in migration timing, growth, and foraging success in the 

estuary are all indicators of the relative capacity of the estuary to accommodate Chinook salmon 

and all the component populations and life history types. In the “Change in Juvenile Salmon 

Life History, Growth, and Estuarine Residence” section (page 142), we compare historic and 

present life history diversity of juvenile Chinook salmon in the Columbia River estuary. 

Our conceptual approach suggests that optimal performance in the estuary as defined by 

these indicators also will favor salmon diversity and productivity in the basin as a whole. We 

interpret salmonid performance and the effects of flow regulation in light of our results for all 

three factors: 

1) opportunity, 

2) capacity, and 

3) life history/population structure. 

Subyearling Chinook Salmon as an Indicator of Estuarine Conditions 

The patterns of habitat use within the Columbia River estuary vary among salmon species 

and life history types within species (Figure 11). Juvenile pink salmon, sockeye salmon, or 

steelhead likely spend the least amount of time in the estuary. Various life history types of 

44
Age at ocean 

entry

 Ocean type

 Chum Fingerlings

 Coho - late run (type N) Variable

 Coho - early run (type S) Variable

 Sockeye Unknown

 Chinook Variable

 Intermediate type

 Chinook (fall migrants) Variable

 Stream type

 Sockeye Variable

 Steelhead Variable

 Chinook Variable

 Coho Age 0+ Age 1+ Variable

 Legend

 Life history and species

Unknown

Unknown

Unknown Unknown

Uncertain

Unknown

Unknown

Unknown

Rearing environment

Euryhaline Freshwater 

rearing Tidal freshwater

Minimal Moderate Extensive

Residency

Rapid Unknown

Re-entry

Migration

Figure 11. Proposed model of relative migration rates and residence times for salmonid species in 

freshwater and estuarine rearing environments of the Columbia River basin. 

Chinook and most chum salmon may remain for longer periods, while they actively feed and 

grow before ocean entrance (Healey 1982, Thorpe 1994). Although coho salmon may use 

estuarine habitats for significant periods, particularly in the tidal-freshwater zone (and there is 

increasing evidence that subyearling migrants in some estuaries may grow rapidly enough to 

migrate to sea in their first year of life), we have insufficient data to verify estuarine life histories 

of coho in the Columbia River. 

Two major types of life history are commonly distinguished among Chinook salmon: 

1) stream-type juveniles that rear in freshwater for at least a year before migrating directly 

to sea, and 

2) ocean-type juveniles that spend variable amounts of time in the river and estuary before 

migrating seaward as subyearlings. 

For this evaluation, we emphasize subyearling Chinook salmon, because they have the longest 

period of estuarine residency among salmonids, and past surveys provide at least some 

information to interpret variations in their rearing behavior. Results for Chinook also may apply 

to other species with subyearling migrants, particularly chum salmon. 

The continuous influx of individuals to the estuary from diverse tributaries noted by Rich 

(1920) raises the possibility that subyearling Chinook salmon may exhibit a broader continuum 

of estuarine rearing and migratory tactics in the Columbia Basin than has been presumed from 

relatively few estuarine studies. Evaluating 11 tributaries within the lower Columbia River, 

Reimers and Loeffel (1967) found that juveniles from various streams either migrated 

45
immediately after emergence or remained in freshwater for as long as five months. Ric

found that some individuals enter the estuary soon after emergence where they may remain for 

up to several months before migrating to the ocean, a pattern that has been observed in some 

small estuaries (Reimers 1973, Carl and Healey 1984). Duration of freshwater residence amo

populations scattered widely throughout the Columbia River basin may be affected by the 

migration distance downstream. As part of our analysis in the “Change in Juvenile Salmon

History, Growth and Estuarine Residence” section (page 142), we reassess diversity of 

subyearling rearing behaviors from the results of previous salmon inventories in the Colum

River estuary. 

h (1920) 

ng 

 Life 

bia 

46
Changes in Hydrological Conditions 

Introduction 

The member/vagrant hypothesis (Sinclair 1998) emphasizes the importance of certain 

persistent (i.e., predictable) physical features of aquatic environments around which salmonid 

life histories possibly developed. In the “Estuarine Development History and Salmon Decline” 

section (page 5), for example, we reviewed evidence that the estuarine rearing behaviors of small 

subyearling salmon may be adapted to productive, shallow-water habitats that are intermittently 

accessible during particular tide and river stages (Kukulka and Jay 2003a and 2000b). Some 

downstream-migrating salmon move into and out of intertidal and floodplain habitats on daily 

and seasonal ebb and flood cycles (Levy and Northcote 1982; Levings et al. 1986), effectively 

delaying their seaward transport for extended periods of estuarine rearing and growth. 

The estuarine features to which salmon life histories have adapted are largely the result of 

riverine and tidal processes that transport sediments, other materials, and biota; establish salinity 

and temperature gradients; and regulate water levels and velocities. The highly productive nature 

of pulsed estuarine systems is a direct result of this dynamic interplay between river and tide. 

These interactions are not controlled entirely within the estuary, but they are determined by 

regional and basin-wide variations in climate, hydrology, and ocean conditions. Because these 

external factors establish the physical template for the entire estuary, they also directly or 

indirectly affect each of the major attributes of salmonid performance implied by the 

member/vagrant hypothesis (see the “Conceptual Framework for Evaluating Estuarine Habitat 

Conditions” section, page 21): 

• availability of estuarine habitat (habitat opportunity), 

• the quality of estuarine habitat (habitat capacity), and 

• salmon population structure and life history (Figure 12). 

In the “Changes in Hydrological Conditions” section, we analyze the history of 

basin-wide hydrologic changes and disturbances—natural and anthropogenic—that have 

established the physical template of the Columbia River estuary during the past 140 years. We 

describe the general hydrological characteristics of the Columbia River system, the data sources 

used in our analysis, and the regional climatic cycles and properties of subbasin flows that 

influence Columbia River hydrology. We analyze human and climatic effects on specific 

hydrological processes that are potentially important to salmonids. These processes include: 

• magnitude and timing of river flow, 

• fine and coarse sediment input, 

• frequency of extreme events and overbank flow, 

• occurrence of freshet styles, and 

47
Figure 12. External factors at regional and basin scales that affect the physical template of the estuary 

and the performance of subyearling (“ocean-type”) salmon. 

• changes in subbasin flow characteristics. 

We also review the implications of these results for juvenile salmon and the member/vagrant 

hypothesis. 

General Hydrological Characteristics 

The Columbia River has the largest average flow (≈7,300 m3s

-1) of any river on the 

Pacific coast of North America; however, its sediment flow (≈107

 metric tons per year 

[mt year-1]) is less than that of the Eel River in California and that of the Fraser River in British 

Columbia (Church and McLean 1992, Jay and Naik 2002). The Columbia River contributes 

some 60% (winter) to 90% (summer) of the total freshwater input between San Francisco and the 

Strait of Juan de Fuca, and it strongly affects regional seawater properties of the northeast Pacific 

Ocean (Barnes et al. 1972). 

Habitat 

opportunity 

(access) 

Habitat 

capacity

(quality) Population 

structure/ 

life history 

(upriver genetic, 

life history, and 

geographic 

structure) 

Anthropogenic 

modifications

(diking, dredging, 

filling, etc.) 

Regional 

climate 

Flow

regulation 

Performance

(estuarine foraging 

success, growth, diversity)

48
The Cascade Mountain range divides the Columbia River drainage basin into eastern and 

western subbasins in Oregon and Washington. The moist and relatively warm western subbasin 

contains only about 8% of the total surface area of the 660,500 km2

 basin, but it contributes 

almost 25% of the total river flow (Orem 1968). Most of the western subbasin elevation is too 

low to accumulate a large seasonal snowpack. Thus the highest flows are observed during and 

following winter storms between December and March. Most of the eastern subbasin flow is 

from the seasonal snowpack melting between April and June. Much of the eastern subbasin is 

relatively arid, but its Canadian component experiences heavy winter snowfall and plays a major 

role in spring-freshet flows. 

Irrigation-water withdrawal and the construction of 28 large and numerous small dams 

have altered Columbia River flows and sediment loads (Simenstad et al. 1992). Water 

withdrawal was minimal before 1890, but it increased rapidly between 1890 and 1920, and again 

after 1960. Dams were constructed to generate power, control floods, and facilitate irrigation. 

The first two dams with more than 106

 m3 of active storage were built on the Snake River 

(Jackson Lake in Wyoming, 1916, and American Falls in Idaho, 1926). The first major 

mainstem dams completed were Bonneville (1937, with only a modest storage capacity) on the 

Washington-Oregon border and Grand Coulee in Washington (1938). Seven large dams high in 

the basin completed between 1967 and 1973 more than doubled the storage capacity of the total 

dam system to 70 × 106

 m3 and provided an increase in water retention time. 

These factors, plus an integrated system-management approach, suggest the 1969–1970 

period as the boundary dividing the developmental (1901–1969) and modern (1970–present) 

periods of hydrological system management, a division we employed in data analyses. Our 

analyses suggested that the 19th century also had distinctive climate patterns; moreover, flow 

regulation was insignificant and diversions were small until the 1890s (Simons 1953). Thus the 

pre-1900 period (predevelopment) also is distinct (Naik and Jay 2004). 

The hydrological characteristics of the Columbia River reflect regional climatic patterns. 

At a continental scale, base river flow decreases north to south because of glacial melt and 

annual snow cover. Because more northerly rivers have a stable base flow, seasonal flow 

fluctuations and interannual variability increase southward from the Fraser River to the 

Columbia eastern subbasin, to the Willamette River in Oregon, and to California rivers such as 

the Sacramento and San Joaquin (Milliman 1980, Berg et al. 1991, Cayan et al. 1993). 

Flow regulation and water withdrawals also increase from north to south. Approximately 

only 3% of the Fraser River flow has been diverted compared to about 50% of the flow from 

tributaries to San Francisco Bay (McLean and Church 1986, Rozengurt et al. 1987). The 

Columbia River occupies an intermediate position with a 15–17% total reduction in flow from 

human and climatic factors. Furthermore, sediment transport in the Columbia River is more 

strongly dependent on flow than is the case in other major West Coast rivers (Jay and Naik 

2002). Consequently the sediment transport regime of the Columbia River is sensitive to 

changes in the annual flow cycle. 

49
Data Sources Used for Hydrological Analyses 

The Columbia River daily flow record compiled by the U.S. Geological Survey (USGS 

1999a) at The Dalles, Oregon, (1878–present) is the longest for any Pacific coast river. Annual 

maximum flow is available from 1858 (Henshaw and Dean 1915), but the dates of the maximum 

flows were not noted until the daily record was initiated in 1878. USGS (1999a) daily river-flow 

records for the Willamette River at Albany, Oregon, also were initiated in 1878 but are 

fragmentary until 1892; the Albany gauge includes about 63% of the total flow of the Willamette 

River. A USGS (1999b) record for the Spokane River at Spokane, Washington, since 1891 is 

available. Daily flow records for the oldest Canadian gauging station (Nicholson, British 

Columbia, compiled by Environment Canada) began in 1903, while USGS daily records for the 

Snake River began in 1912 at Ice Harbor Dam in Washington. 

It also is important to have an estimate of total flow from the eastern and western 

subbasins combined, determined as close to the mouth of the Columbia River as possible. The 

USGS (1999a) has measured flows at the Beaver Army Terminal (RKm 85) near Quincy, 

Oregon, only from 1968 to 1970 and from 1991 to the present. We have used regression analysis 

of daily records for Beaver, Albany, and The Dalles to hindcast a Beaver daily flow for the 

common period of record for Albany and The Dalles. This record is complete for 1895 to the 

present, and partial for 1878–1894. USGS sediment transport records for the main stem are 

available for 1963–1970 (Vancouver, Washington, or Beaver; Haushild et al. 1966, Hubbell et al. 

1971, USGS 1999a, 1999b). USGS (1999a) sediment transport data for the Willamette River are 

available for 1910–1913 (some daily data are missing; Van Winkle 1914a, 1914b) and 

1962–1963 (Haushild et al. 1966). 

All hydrological data discussed in the remainder of this section are compiled by water 

year; the water year begins 1 October and ends 30 September. Flows typically have been 

rounded to 10 m3

s

-1 and sediment transports to two or three significant digits. Confidence limits 

have not been calculated in most cases, because systematic biases may outweigh random errors. 

Hydrological Effects of Climate Cycles 

Climate-induced variations in Columbia River flow occur on time scales from a few 

years to centuries (Chatters and Hoover 1986 and 1992), and these fluctuations are important to 

salmonid survival. For example, indices of the Pacific Decadal Oscillation (PDO, typically 

40–50 years in duration) are correlated with salmon catches since 1900 in the Pacific Northwest 

and the Bering Sea (Mantua et al. 1997). A cold phase of the PDO that occurred from 1945 to 

1976 was generally favorable for salmonid production in the Pacific Northwest and unfavorable 

in the Bering Sea. The opposite circumstance prevailed during a warm phase from 1977 to about 

1995. Another cold, wet phase may have commenced in the late 1990s, and salmon runs have 

rebounded somewhat. For purposes of this section, we define the climatic present in terms of 

PDO cycles as the 1945–1999 period. These PDO-related fluctuations in salmonid survival have 

been linked to the degree of density stratification of the coastal ocean (Gargett 1997), but 

survival also is influenced by conditions within the river and estuary (e.g., salinity, turbidity, and 

flow). 

50
ENSO (typically 3–7 years in duration) indices are correlated with Columbia River flow 

(Redmond and Koch 1991) and sediment transport (Jay and Naik 2002). In addition to 

modifying fluvial processes, ENSO cycles may affect upwelling and primary production and 

therefore survival of salmonids in coastal waters. 

The Columbia Basin climate response is conditioned by its position between lat. 41o30' 

and lat. 54o40'N, within a latitudinal band of strong response to the ENSO cycle and to the PDO 

cycle (Mantua et al. 1997). While the flow-per-unit area is larger in the western subbasin than in 

the eastern subbasin, the response to ENSO or PDO forcing varies little across the basin. Still 

the relatively large north-south extent of the basin brings about important differences in flow 

seasonality (e.g., the incidence of winter floods and timing of spring snowmelt) even within the 

eastern subbasin. In the next two subsections, we explore important estuarine and fluvial 

impacts of these climate cycles that may affect salmonids. 

The lack of standard hydrological time series creates significant uncertainties about 19th 

century climatic conditions. The status of the PDO before 1890 remains uncertain although the 

fluctuations described by the PDO index have been occurring for at least 300 years and possibly 

for thousands of years (Finney et al. 2000). Moreover, it is difficult to find any evidence in the 

Columbia River flow data that a lengthy, warm PDO phase occurred between about 1849 and 

1920. If the entire 1849–1920 period is considered to be a cold PDO phase, then it was much 

more persistent relative to cold PDO phases during the 20th century. 

The results of Finney et al. (2000) may also suggest that conditions in the latter part of 

the 19th century were simultaneously favorable for salmonids in the Columbia River and in 

Alaska, a situation that has not occurred since 1900. Alternatively, estimates of Columbia River 

salmon abundance before 1900 are confounded by a decline in native fisheries followed by the 

rapid growth of commercial fisheries, and the data may not be sufficiently accurate to correlate 

with climate. We therefore explore correlations between climate and Columbia River 

hydrological processes with the caveat that climate cycles before 1900 are not well understood. 

El Niño Southern Oscillation and Pacific Decadal Oscillation 

 Effects on the Annual Flow Cycle 

Variations in Columbia River flows associated with El Niño and the PDO affect habitat 

conditions by: 

• determining what areas are wetted and potentially accessible to juvenile salmon, 

• changing estuarine salinity gradients, 

• influencing sediment transport processes, and 

• altering the distributions of marine and freshwater species with which salmon interact. 

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 Kahya 1994). La Niña winters typically exhibit an opposing 

climate and hydrological response. The annual average flows of the Columbia and the 

51
Willamette rivers during years with a strong El Niño winter are 91% and 92% of the long-term 

annual average. 

During years with a strong La Niña winter the annual average flows are 110% and 111% 

respectively. PDO cycles also affect Columbia and Willamette flows. Cold PDO winters tend to 

be associated with above average flow years, while warm PDO winters are associated with 

below average flows (Table 6). 

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). The net effect is that during an El 

Niño/warm PDO combination, respective average annual Columbia River flows at The Dalles 

and Willamette River flows are 85% and 81% of the long-term annual average; while during a 

La Niña/cold PDO combination, they are 111% and 119%, respectively (Figure 13). (These 

differences are significant at the 95% confidence limit.) El Niño effects are suppressed during 

the cold PDO phase as are those of La Niña during the warm PDO phase. The number of years 

in these extreme categories is limited. 

Sediment Transport: Amplification of Climate Effects 

Because sediment flow increases more than linearly with flow, the effects of climate 

cycles are amplified in the sediment flow. During El Niño years, annual average total sediment 

transports in the Columbia and the Willamette rivers are 12.7 × 106 and 1.4 × 106 mt, 

respectively, while in La Niña years, they are 21 × 106 and 2.3 × 106 mt, or about 65% larger. El 

Niño years in the warm PDO phase typically exhibit a low sediment transport (10 × 106 mt in the 

Columbia and 1.1 × 106

 mt in the Willamette) while in the La Niña/cold PDO combination, the 

transport of suspended particulate matter is more than twice that during the El Niño/warm PDO 

years (23 × 106 mt for the Columbia and 2.2 × 106 mt for the Willamette, [Figure 14]). 

Further amplification of climate effects may take place through estuarine circulation and 

by the detritally based estuarine food web (i.e., by the organic matter supplied during the spring 

freshet that supports estuarine secondary production throughout the summer and fall seasons). 

However, for this organic matter to be utilized by the estuarine food web, it must first be retained 

or trapped by estuarine circulation processes active in the estuarine turbidity maximum (ETM). 

Analyses of data from fixed moorings in the estuary (Fain et al. 2001, Jay et al. 2003) 

suggest that particle trapping is relatively weak during extremely high river flows, because 

Table 6. Effects of PDO variations the annual average flows of the Columbia and Willamette rivers. 

Years Winter type 

Columbia River 

 at The Dalles 

Willamette River 

 at Albany 

1890–1921 Cold PDO 109% 102% 

1922–1944 Warm PDO 86% 87% 

1945–1976 Cold PDO 102% 110% 

1977–1995 Warm PDO 88% 88% 

52
0 

2,000 

4,000 

6,000

8,000 

10,000 

12,000 

14,000 

October December February April June August

Stream flow (m3

s-1) 

1878–1999 

El Niño/warm PDO years 

La Niña/cold PDO years

Figure 13. The ENSO/PDO response of eastern subbasin flow at The Dalles. (Data adapted from USGS 

records.) 

0 

2 

4 

6 

8 

10 

12 

October December February April June August 

Suspended particulate matter (SPM) 

 in metric tons 

1878–1999 

El Niño/warm PDO years

La Niña/cold PDO years

Figure 14. The ENSO/PDO response of eastern subbasin total sediment load calculated at Vancouver 

using flow data at The Dalles. (Data adapted from USGS records.)

extreme flows decrease the upriver extent of salinity intrusion where particles can be trapped. 

Decreasing river-flow levels enhance the strength of upstream flow near the bottom, enhancing 

particle trapping despite reduced sediment supply. Suspended particulate matter also is stored in 

peripheral bays during high flow periods and subsequently released to the ETM. Thus the most 

efficient trapping of particulates occurs during years when there is a strong spring freshet and 

53
low-to-moderate summer flows to provide a continuous supply of suspended matter, initially 

from the river, then from peripheral areas. 

Subbasin Sources of Flow and Major Freshets 

Subbasin Sources of Flow 

Understanding the response of the Columbia Basin to perturbations requires attention to 

the diverse properties of its subbasins. There is, for example, wide variability in the percentage 

of flow from various parts of the basin during the spring freshet and over the rest of the water 

year. The Canadian part of the eastern subbasin also has a high runoff per unit area. Canada 

accounts for about 50% of the flow at The Dalles (37% of the flow at the mouth), but it has only 

25% of the total surface area of the eastern subbasin (19% of the total surface area). The Snake 

River is relatively dry, with approximately 40% of the eastern subbasin surface area but only 

30% of the flow at The Dalles. 

In high flow years, half or more of the spring flow at The Dalles comes from Canada. 

During the largest known freshet (1894), the peak flow at the Grand Coulee Dam in Washington 

was approximately 20,500 m3

s

-1 compared to a maximum flow of 34,800 m3

s

-1 at The Dalles and 

approximately 39,400 m3

s

-1 at Beaver (estimated). The Canadian contribution to the spring 

freshet has been declining since 1970 because of the long water-retention time of the dams in 

Canada. These dams are effective in delaying spring snowmelt flow and changing the 

seasonality of the flow in the upper Columbia, which in turn affects flows in the entire main 

stem. 

An important feature of the hydrological regime is that the snowmelt occurs earlier in the 

Snake River area (the most southerly part of the eastern subbasin) than in the upper Columbia. 

The difference in the time of maximum flow among the subbasins determines freshet duration 

and affects the maximum flow level. In years when snowmelt occurs almost simultaneously 

throughout the Columbia River basin, maximum flows increase because the duration of the 

freshet is shorter. These conditions occur when delayed snowmelt in the Snake River subbasin 

coincides more closely with that of the upper Columbia River or when heavy rain accelerates 

snowmelt throughout the basin, as occurred in 1894 and 1948. When spring is cold, the late 

snowmelt in the Canadian part of the basin delays the freshet into July. Because of higher 

temperatures this pattern is now rarely seen in the Columbia River, but it is still sometimes 

observed in the Fraser River (e.g., in 1999). 

Inferences from Selected Flow Histories 

Spring freshets are important to the downstream migrations of juvenile salmon. Large 

freshets also modify habitat structure and distribution, and they thereby affect future salmon 

year-classes. In contrast, water quality and habitat opportunity may decline during very dry 

years, effects that are further exacerbated by human alterations. Thus the flow histories of 

extreme years convey important lessons, because salmon are most severely tested under extreme 

climatic conditions. 

54
Very large freshets before modern flow regulation (i.e., before 1970) lasted 30–60 days, 

with the sharpness of the peak largely governed by precipitation and the relative timing of 

snowmelt throughout the basin. Significant winter snowmelt events occur in many winters 

before a major spring freshet (e.g., 1862, 1894, 1948, 1956, 1974, and 1997). These winter 

freshets reduce the intensity of the following spring freshet. The occurrence of major freshets, 

even after winter melt events, emphasizes the magnitude of the snowpack in such years. 

Flow regulation and irrigation decrease spring-freshet magnitude and increase flows 

during the rest of year through winter draw-down of reservoirs, filling of the reservoirs during 

the freshet, irrigation return flow, and desynchronization of flow peaks throughout the basin. 

The result is a spring freshet in high flow years such as 1996 and 1997 that lasts from January to 

June. The effects of human manipulation (especially a weekly power-peaking cycle) are 

prominent during very low flow years (e.g., 1977 and 1992), when the spring freshet becomes 

largely an artificial event. The closest preregulation analog to such years (1926) still showed a 

marked annual cycle, although its intensity was reduced. 

The years 1880 and 1916 play a prominent role in the present study. The model 

simulations described in the “Estuarine Habitat Opportunity” section (page 89) use 1880 to 

represent a high flow year before significant water withdrawal and navigational developments 

had altered the system. We chose 1880 for modeling purposes because: 

• it was the earliest year for which complete flow records were available at The Dalles and 

for the Willamette River, and 

• navigational development and irrigation withdrawal began soon afterward. 

The first scientific survey of juvenile salmon in the Columbia River estuary was 

completed in 1916 (Rich 1920). Both 1880 and 1916 are notable for their late freshets—the 

latest in the 1878–2000 period—when peak flows in both years occurred in early July. Elevated 

flows in 1880 continued until early September leading to the highest August flows ever observed 

in the system. At the other extreme is the year 2000. Although the total annual flow volume was 

not particularly low, 2000 is unique for having the earliest recorded spring-freshet peak 

(23 April) because of flow regulation and a very mild winter. 

Human- and Climate-induced Changes 

to the River-flow Magnitude and Timing 

Total Annual Average River Flow from the Eastern Subbasin 

Changes in annual average flow are an important integral measure of changes in a river 

system. In the Columbia River, about 97% of the flow from the eastern subbasin (>70% of the 

flow at the mouth) passes the gauge at The Dalles, making the 1878–present record useful for 

understanding changes in this part of the system. To separate human and climatic influences on 

river flow requires three distinct measures at The Dalles: 

1. Observed flow—the flow observed at a gauge, available on a daily basis for 1878–present 

(Figure 15). 

2. Estimated adjusted flow—the observed flow corrected for reservoir manipulations 

55
Years 

km3s-1

Figure 15. Daily observed Columbia River eastern subbasin flow (cubic kilometers per second) at The 

Dalles, 1879–1999. The daily observed flow is flow recorded off measurements by a water 

gauge. Peak flows are typically observed in the April to May period (black and white peaks 

around day 270). Peak flows appear to occur earlier in the year in the modern period (the light 

gray areas at the top of the figure) compared to the predevelopment era. A floor has been set at 

1,500 m3

s

-1 to emphasize high flow periods. (Data adapted from USGS records.) 

Water days from 1 October 

calculated by the USGS on a monthly basis for 1878–present as per Orem (1968). 

We have calculated a daily adjusted flow index for the 1878–1999 period (Figure 16). 

3. Estimated virgin flow—an estimate of the river flow as it would be without human 

alteration (i.e., the observed flow corrected for reservoir manipulation and irrigation 

depletion and return flows for the 1929–1989 period). These values were determined 

from the information tabulated by the Bonneville Power Administration (BPA 1993). 

We have completed the monthly virgin flow time series for the 1878–1999 period and 

calculated a daily virgin flow index (Naik and Jay 2004, [Figure 17]). 

56
Years 

km3s-1

Water days from 1 October 

Figure 16. Daily adjusted Columbia River eastern subbasin flow (cubic kilometer per second) at The 

Dalles, 1879–1999. The adjusted flow is the observed flow corrected for reservoir manipulations. 

The daily adjusted flow diminishes after 1900 (the lack of dark areas on the peak) and ends 

earlier as the years progress toward 1975. A floor has been set at 1,500 m3

s

-1 to emphasize high 

flow periods. (Data adapted from USGS data per Naik and Jay 2005.) 

The effects of flow regulation and hydropower generation can be determined by 

comparing the observed and adjusted flows at The Dalles. The effects of water withdrawal can 

be determined by comparing the adjusted and virgin flows (Figure 18). The effects of climate 

change and land use can be estimated by examining changes in the magnitude and timing of the 

virgin flow over a time period (Figure 19). The total of all climatic and anthropogenic effects 

can be seen by comparing the virgin flow before 1900 at The Dalles to the observed flow since 

1945. There is one significant caution in interpreting the calculations in this section: they are 

based on flow at The Dalles; however, flows at The Dalles represent the eastern subbasin only. 

57
 Years 

km3

s-1

Figure 17. Estimated daily virgin Columbia River eastern subbasin flow (cubic kilometers per second) at 

The Dalles, 1879–1999. The virgin flow would have occurred in the absence of human 

manipulation. The heaviest flow (dark areas in peak) occurred before 1900. The flow diminishes 

and begins earlier in the spring as the years progress toward 2000. A floor has been set at 1,500 

m3

s

-1 to emphasize high flow periods. (Flow estimated from USGS data per BPA 1993 and Jay 

and Naik 2002.) 

Water days from 1 October 

Virgin and adjusted flow estimates are not available for the western subbasin and anthropogenic 

and climatic effects on western subbasin rivers are not well understood. 

It also is difficult to partition the total reduction in flow between human and climate 

factors, because of the need to average over climate cycles (especially the PDO) and to account 

for changes in flow regulation and irrigation that take place over shorter time periods. As noted 

previously, the present averaged over PDO cycles can be defined using the 1945–1999 period. 

In terms of flow regulation and irrigation, it is useful to define the post-1970 period as the 

present. 

58
Figure 18. Comparison of the monthly averaged Columbia River eastern subbasin virgin, adjusted, and 

observed river-flow estimates at The Dalles, 1970–1999. (Data adapted from USGS records.) 

Figure 19. Comparison of the monthly averaged Columbia River eastern subbasin virgin river flow at 

The Dalles between 1878–1899 and 1945–1999. (Data adapted from USGS records.)

0 

2,000 

4,000 

6,000 

8,000

10,000 

12,000 

14,000 

16,000 

18,000 

October December February April June August

Stream flow (m3

s-1) 

Virgin (1879–1899)

Virgin (1945–1999)

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

59
The mean annual average Columbia River virgin flow at The Dalles has decreased 

approximately 7.4% or 470 m3

s

-1 from 6,320 m3

s

-1 for 1879–1899 to 5,850 m3

s

-1 for 1945–1999. 

This represents the flow decrease because of climate change (Figure 19). If annual average flow 

is estimated from the maximum freshet flow each year for 1858–1978, then annual average flow 

for 1858–1899 was 6,280 m3

s

-1, only slightly different from 1879–1899. Glacial retreat during 

the last half of the 19th century (following the end of the Little Ice Age) may have played a role 

in the observed high 19th century virgin flow in the Columbia River, but it is unlikely to account 

for most of the difference between the present and the late 19th century. Thus the last half of the 

19th century had a rather different (wetter and cooler) climate regime, and very high spring flows 

occurred in many years between 1858 and 1900. 

The 1945–1999 annual average loss because of water withdrawal for irrigation 

(difference between virgin flow and flow adjusted for reservoir manipulation) is 440 m3

s

-1

 or 

approximately 7% of the 19th century virgin flow. The 1970–1999 annual average loss because 

of water withdrawal for irrigation is 470 m3

s

-1 or approximately 7.4% of the 19th century virgin 

flow. 

The total reduction of annual average flow (difference between 19th century virgin flow 

and 1945–1999 observed flow of 5,360 m3

s

-1) is 960 m3

s

-1 or 15.2% (Figure 19). This is larger 

than the climate change (7.4%) plus irrigation withdrawal (7.0%). The discrepancy (about 0.8% 

of the original virgin flow) represents an uncertainty level related to the different averaging 

periods used in the estimates. If we consider the 1970–1999 period as the present, then the total 

reduction is somewhat larger, 1,070 m3

s

-1 or 16.9%. We apportion this net change as follows: 

climate change (8.9%), irrigation depletion (7.4%), and uncertainty (0.5%). The longer 

averaging period (1945–1999) more realistically represents climate effects; the shorter period 

(1970–1999) more realistically represents the impacts of the present management regime. 

The annual average flow is not only reduced by human manipulations, but the year when 

flow occurs may be changed by the storage time of water in reservoirs. The total average flow of 

the Columbia River at The Dalles is 171.2 cubic kilometers per year (km3year-1) whereas the 

storage capacity is 77.7 km3

, yielding a ratio of storage capacity to annual flow of 0.45. 

Regulation of river flow does not normally result in large interannual transfers of flow, as it 

would in a basin with a larger storage capacity relative to the total annual water production (e.g., 

the Colorado River). Nonetheless interannual transfers of plus or minus 370–790 m3

s

-1 occurred 

in 1974, 1976–1978, and 1992. These interannual transfers decrease the interannual variability 

of the flow. 

The above discussion has not considered the consequences of land use, especially 

deforestation, on river flow. Deforestation may alter the hydrologic cycle by decreasing 

transpiration and accelerating snowmelt, thereby increasing total flow and altering its timing. 

Matheussen et al. (2000) suggested that these factors have modified eastern subbasin flow 

seasonality, changing individual average monthly flows by as much as 5–10%. Still, the change 

in annual average flow suggested by Matheussen et al. is small relative to the current irrigation 

depletion; the net change in flow over a time period is only plus 1–2%. Nonetheless 

deforestation may have contributed to changes in the flow cycle in certain months by requiring 

larger alterations to meet specific flow targets or the needs of power generation, even though the 

effect on annual average flow is small. Our virgin flow estimates are largely unaffected by 

60
changes in land use and deforestation, because these changes would have been compensated by 

reservoir flow adjustments. If changes because of deforestation are taken into account, the actual 

reduction in virgin flow because of climate change is more than 7.4%; however, a decrease of 

8–9% may be more accurate. These considerations might modestly increase the total estimated 

flow decrease of approximately 15% (1945–1999) or 17% (1970–1999) by 1-2%. 

Eastern Basin, Spring-freshet Magnitude and Timing 

The changes in annual average flow are only a small part of the total hydrological 

changes in the Columbia River. Seasonal changes, particularly those in spring-freshet timing 

and magnitude, have been much larger than those in annual average flow. Spring freshets are 

extremely important for juvenile salmonids, because high flows (especially overbank flows) 

provide habitat, 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 season is also a major factor maintaining a detritally based food web, centered in the 

ETM. 

Flows from the Columbia River eastern subbasin (the flow measured at The Dalles) are 

primarily driven by spring snowmelt, although rain-on-snow freshets occur in some winters. 

Before 1900, the highest flows typically occurred during May–July. Monthly Columbia River 

virgin flows at The Dalles for 1879–1899 were 11,480 m3

s

-1 for May, 16,760 m3

s

-1 for June, and 

12,600 m3s

-1 for July. The corresponding figures for 1945–1999 were 13,300 m3

s

-1 for May 

(+15.9%), 15,840 m3s

-1 for June (–9.5%), and 9,420 m3

s

-1 for July (–25.2%). 

The decrease in July flows and the increase in May flows have been caused by the earlier 

onset of spring freshets (Figure 20 and Figure 21). Also the May–July average virgin flow for 

1879–1899 was 13,610 m3s

-1, while for 1945–1989 it was 12,850 m3

s

-1 (–5.6%). This represents 

the freshet-season flow decrease because of climate change. Note that the January–July 

virgin-flow average for 1879–1899 was 8,050 m3

s

-1 compared to 7,850 m3

s

-1 for 1945–1989, a 

decrease of only 2.5%. Thus most of the loss of freshet flow represents flow that now occurs 

during winter, early spring, or late summer and fall. 

The modern freshet-season flow decrease caused by water withdrawal can be determined 

from the 1970–1999 differences between the monthly Columbia River virgin and adjusted flows 

at The Dalles. The virgin-flow reductions were 750 m3

s

-1 for May (5.7%), 1,900 m3

s

-1 for June 

(12.5%), and 1,890 m3s

-1 for July (20.8%). The total May–July seasonal water-withdrawal 

decrease was about 10.5%. 

The present freshet-season flow decrease because of flow regulation can be determined 

from the 1970–1999 differences between the monthly Columbia River adjusted and observed 

flows at The Dalles. These virgin-flow reductions were 4,100 m3

s

-1 for May (31.6%), 4,920 

m3s

-1 for June (32.4%), and 1,790 m3

s

-1 for July (19.8%) for the period. The total freshet-season 

flow decrease because of flow regulation was 3,600 m3

s

-1, 29.1% of the present spring virgin 

flow and 33.1% of the present spring-adjusted flow. Flow regulation is clearly the source of the 

largest reduction in spring flow. 

61
0

5

10

15

20

25

30

35

40

1-May6-May11-May16-May21-May26-May31-May5-Jun10-Jun15-Jun20-Jun25-Jun30-Jun5-Jul

Date

 m

3 -1 Streamflow, 1000

s

1926

1934

1989

198 5

1947

1988

1994

1890

19 71

19 10

19 76

196 9 1936

19 75

1993

1987

1949

1995

1939

1992

19 57

19 54

1897

1932

1904

19 79

1991

19 2 419 70

19 14

1952

1998

1946

19 51

19 28

1895

19 58

1938

19 48

19 15

19 06

1983

19 19

19 12

19 02

190 1

1891

19 56

19 86

19 99

18 89

19 40

1962

19 07

1894

1960

194 5

1961

19 22

1967

19 65

1990

19 78

1941

1981

1935

1921

199 6

19 66

19 13

1882

188 41893

1968

1930

1883

1923

1905

1997

1942

1881

19 11

19 53

1980

1963

188 8

1903

1933

192 7

1964

190 8

18 79

192 9

1900

1909

1887

1944

1982

19 17

1898

19 72

19 74

1943

1899

189 2

19 86

19 59

1885

1937

19 50

1918

19 55

1920

1984

18 80

19 16

1931

18 78

1925

Stream flow 1,000 (m3

s-1)

Date

Figure 20. Seasonal magnitude and timing of Columbia River eastern subbasin freshets at The Dalles, 

1878–1999. (Data adapted from USGS records.) 

62
13-Apr

23-Apr

3-May

13-May

23-May

2-Jun

12-Jun

22-Jun

2-Jul

12-Jul

22-Jul

18751885189519051915192519351945195519651975198519952005

Figure 21. A linear fit to of peak freshet day versus year; the spring freshet now occurs about two weeks 

earlier than in the 19th century. (Data adapted from USGS records.) 

The total reduction in freshet-season (May–July) mean flow because of climate change, 

irrigation depletion, and flow regulation was 5,870 m3s

-1, 43% of the virgin flow for this period. 

The present freshet season flow of 7,740 m3

s

-1 was about 148% of the current annual average 

flow. In contrast, 19th century freshet flows were approximately 215% of the contemporary 

mean. 

The reduction in peak flows of freshets has been slightly larger than that of the freshet 

season as a whole. The observed maximum annual daily spring-freshet flow for 1858–1899 was 

19,300 m3s

-1, which is close to virgin spring-freshet magnitude because water withdrawals 

during the 19th century were small. Present (1970–1999) observed annual maximum daily 

spring-freshet flow was 10,870 m3

s

-1, 44% less than before 1900. Peak freshet flow for 

1945–1999 was 13,530 m3s

-1, 30% less than before 1900. Freshet reduction was less effective 

before 1970. 

Because of the disparate time scales involved, it is difficult to separate reductions in 

daily maximum flow caused by climate, deforestation, irrigation, and flood control. The 

climate-change component is not the largest factor, given the small climate-induced change in 

the May–July average flows. Present irrigation withdrawal during the spring-freshet season is 

normally less than 1,800 m3

s

-1, also small relative to the freshet reduction. Most of the loss in 

maximum spring-freshet flow, therefore, is because of flow regulation. Flood-control reductions 

of more than 10,000 m3

s

-1 occur in high flow years such as 1974 and 1997 (Figure 22). The 

original maximum daily flow 305% of the mean, whereas this figure has been reduced to 205% 

at present. 

Still the role of climate change in reducing freshet magnitude over the past 140 years 

should not be totally neglected. Even though climate-induced changes in annual average flow 

63
-15,000 

-10,000 

-5,000 

0 

5,000 

10,000 

15,000 

20,000 

25,000 

30,000 

35,000 

1875 1885 1895 1905 1915 1925 1935 1945 1955 1965 1975 1985 1995

Stream flow (m3

s-1) 

Observed Adjusted 

Figure 22. Reduction of the monthly mean June flow. (Data adapted from USGS records.) 

have been modest, the annual flow cycle has changed also, probably because of a combination of 

higher average air temperatures and deforestation. The Columbia River has shifted from a 

climate regime (before 1900) when winter freshets in the eastern basin were unusual to a climate 

regime when substantial flow events now occur in many winters. 

One result of climate change is that the incidence of very large spring freshets was 

greater during the last half of the 19th century. Peak-flow information is available for only 43 

years in the 19th century (1849, 1858–1999), yet 10 of the 14 largest known freshets occurred 

before 1900. This compilation is based upon estimated virgin daily flow, so that direct human 

manipulation is not the reason for the difference. Similarly, four of the five largest known 

freshets in the Willamette River occurred in the 19th century. 

The timing of the maximum spring-freshet flow also has changed (Figure 21). Maximum 

daily spring-freshet flow now typically occurs at about water-year Day 242 (29 May), whereas 

maximum flow occurred at about water-year Day 256 (12 June) in the 19th century, a change of 

about two weeks. In terms of the phase of the annual flow fluctuation (as determined by wavelet 

transformation of the flow data), the freshet is about a month earlier. Part of this change is 

because of climate warming, but prerelease of water for flood control before the spring freshet is 

also a component. Irrigation withdrawal usually peaks in June, which tends to further curtail the 

freshet. 

The relative size of these three effects on freshet timing cannot be determined. However, 

the very early 2000 spring-freshet peak on 23 April (the only April freshet ever recorded) 

occurred largely as the result of flow regulation. 

Changes in Western Subbasin Flows 

The eastern subbasin flow at The Dalles described previously accounts for about 75% of 

the total flow to the estuary. Flows in the Willamette River are typical of the remaining 25% 

from the western subbasin. The Willamette is the largest river in the western subbasin, with 

Virgin

Obs-Adj Obs-Vir

64
approximately 60% of the western subbasin flow, or 15% of the total flow for the basin. Climate 

influences on the Willamette are similar to those on other western subbasin tributaries (e.g., the 

Cowlitz, Kalama, and Lewis rivers in Washington) draining the west side of the Cascade 

Mountains, although the Cowlitz has a larger contribution from seasonal snowpack, and 

anthropogenic effects are system-specific. 

The Willamette River responds primarily to winter rainfall and melting of recently 

deposited snow, with only modest storage of water in seasonal snowpack and glaciers. The 

largest freshets in the system are caused by winter, rain-on-snow events. The Willamette River 

basin is much smaller than the eastern subbasin; its flows are not as heavily regulated and there 

are no mainstem storage dams. 

For these reasons, and because the Willamette Basin area is small relative to that of 

synoptic weather events, Willamette River flows are much more variable on short time scales 

than those at The Dalles (Figure 23). 

The observed annual average Willamette River flow at Albany has decreased from 460 

m3s

-1 for 1893–1900 to 418 m3

s

-1 for 1945–1999 (9.5%) and to 390 m3

s

-1 for 1970–1999 

(14.8%). It is not currently possible to separate the components into losses associated with 

climate and water withdrawal, but irrigation withdrawal was small before 1900 (Sedell and 

Frogatt 1984). Still it appears that historical changes in annual average flow have been smaller 

in the Willamette than in the eastern subbasin. 

The seasonality of Willamette River flow at Albany has been altered by climate change, 

the irrigation cycle, and flow regulation for flood control (Figure 24). Late summer to early 

winter flows (August–December) have been augmented (comparing the historic and modern 

flows), likely by irrigation-return flow and by prerelease of any surplus water before winter. 

Average monthly flows during the January–July periods have decreased, especially those in 

January and February, when the reduction has exceeded 120 m3s

-1, out of the original 

approximately 920 m3

s

-1. The decrease in mid-winter average (and extreme) flows is probably 

because of a combination of climate effects and flood control. The difference between the 

historic and modern flows peaks again in May at greater than 120 m3s

-1. Irrigation and storage of 

water for summer power generation are likely reasons for the spring-flow decrease. However, 

the seasonal snowpack also may be smaller. The effects of land-use changes on Willamette 

River flow are unknown. 

River Flows at the Head of the Estuary 

The best measure of total mainstem freshwater input at the head of the estuary is the 

Columbia River flow at Beaver. Flow properties at Beaver are the sum of those for the eastern 

and western subbasins (Figure 25). The average estimated observed annual flow (1892–1999) at 

Beaver is 6,960 m3

s

-1. It is not possible to separate climate, flow regulation, and 

water-withdrawal effects on the flow at Beaver, but the average flow is now substantially lower. 

The average annual flow for 1892–1902 was roughly 8,300 m3

s

-1. Reflecting the alteration of 

eastern basin flows, the spring freshet at Beaver has become longer, weaker, and earlier, while 

winter flows are less sharply peaked than before flow regulation. Monthly average winter flows 

65
Years 

km3s-1

Figure 23. Observed daily Willamette River flow (cubic kilometers per second) at Albany, 1893–1998. 

This flow is representative of the western subbasin. Almost all of western subbasin flow is from 

rain events (peak flows in the winter), while eastern subbasin flow is mainly from the melting 

snowpack (peak flows in the spring). A floor has been set at 200 m3 s

-1 to emphasize high flow 

periods. (Data adapted from USGS records.) 

Water days from 1 October 

are slightly larger than before 1900 (Figure 26). There are no long-term sediment transport 

estimates available for Beaver. 

Flows from Estuary Tributaries 

The flow at Beaver is not the total flow of the Columbia River. Several smaller rivers 

enter the estuary seaward of Beaver (e.g., the Elochoman and Grays rivers in Washington and the 

Youngs and Lewis and Clark rivers in Oregon). These river basins have very high runoff 

intensities, but they contribute an estimated annual average of only 3% of the total flow at the 

river mouth, or approximately 230 m3s

-1 (Orem 1968). Their contribution during winter storms 

is probably much higher, but it has not been systematically assessed. 

66
0 

100 

200 

300 

400 

500 

600 

700 

800 

900 

1,000 

December April August 

Stream flow (m3

s-1) 

1878–1903

1970–1999

October February June 

Figure 24. Historical changes in the annual flow cycle of the Willamette River at Albany, 1878–1903 

(from 1878 to 1894 not all daily values are present) versus 1970–1999. (Data adapted from 

USGS records.) 

Little is known regarding historical changes to the hydrological properties of the estuary 

tributaries, and no systematic sediment-transport records are available. Downstream transport of 

logs to tidewater during early logging operations severely disrupted several of these streams. 

Total Columbia River Flow at the Mouth 

The total annual average flow at the mouth of the Columbia River can be estimated by 

adding the estuary tributary flow to the long-term average for Beaver. The result is 

approximately 7,300 m3s

-1 for 1892–1999. This is somewhat smaller than the figure 

(7,720 m3

s

-1) given by Orem (1968) for two reasons: 

1) Orem used primarily data from a cold PDO phase of elevated flows (1943–1957), and 

2) the average observed flow has decreased slightly since Orem’s work was published. 

Finally, the value of the Columbia River flow at the mouth prior to 1900 was probably about 

8,500 m3

s

-1; it decreased to about 7,080 m3

s

-1 (1970–1999). 

Human- and Climate-induced Changes in Sediment Transport 

Sediment transport processes are a vital determinant of habitat conditions for salmon and 

other species in the estuary. The organic component of the fine sediment supply (silts and clays) 

supports a detritus-based food web that now provides the bulk of estuarine secondary 

productivity in the system (Simenstad et al. 1990a, 1994). The turbidity caused by fine sediment 

67
Years 

km3s

-1

Figure 25. The combined eastern and western subbasin flows: estimated observed daily Columbia River 

flow at Beaver, 1892–1999. Note the combination of characteristics derived from the eastern and 

western subbasins (light gray areas). Peak flows are typically observed in the April–May period 

(black and white peaks around day 270). Peak flows appear to occur earlier in the year in the 

present period (the wide gray area at the top of the figure) compared to the predevelopment 

period (before 1900). A floor has been set at 1,500 m3

s

-1 to emphasize high flow periods. (Data 

adapted from USGS records.) 

Water days from 1 October

may hinder predation on juvenile salmonids, but excessive levels may be injurious to juveniles 

and damage spawning habitat. The coarser fractions (sands and gravels) are critical to natural 

habitat construction in the estuary and to maintenance of spawning habitat higher in the basin. 

During the past century, dredging and disposal of sands and gravels have been major causes of 

estuarine habitat loss. For scientific reasons, it is important to distinguish between the fine and 

coarse-sediment fractions. For methodological reasons, sediment transport is reported in terms 

of total load (all fractions) and sand, which includes gravel. 

68
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 26. Changes in the annual flow cycle of the Columbia River at the Beaver Army Terminal, 

1878–1903 (from 1878 to 1894 not all daily values are present from Albany) versus 1970–1999. 

(Data adapted from USGS records.) 

Daily sediment-transport data (at Vancouver) for the eastern subbasin are available only 

for 1963–1970. Therefore, we have hindcast total load and sand transport at Vancouver for the 

entire period (1878–1999) of the daily flow record at The Dalles, estimating the sand fraction 

based on measurements described in Haushild et al. (1966). This calculation has been carried 

out for the observed and virgin flow (Figure 27). Willamette River total load has been hindcast 

for 1892–1999 on the basis of 1910–1913 and 1962–1963 sediment-transport data. 

Estimated sediment supply for the two systems assumes that land use and channel 

development have not materially altered sediment transport. Sand movement is transport 

limited; material is available on the bed and will move whenever flow conditions are suitable. 

We expect that the sand-transport estimates, therefore, are relatively accurate, at least within the 

limited flow range of the data set used to calibrate sand transport. Transport of fines, however, is 

supply limited; normally, the capacity to move the material is greater than the supply. 

Fine sediment transport can only be hindcast under the assumption that the supply of 

these materials has not changed. In fact, timber harvest, agriculture, and urban development 

have likely affected the supply of fine material. The available evidence suggests that the supply 

of fines depends on the source and timing of the flow. Still a consistent estimate of sediment 

transport unaffected by land use has some advantages. It is useful to compare the contributions 

of climate and human manipulations to the flow cycle. 

The effects of climate change on total sediment supply can be determined from historical 

changes in sediment transport at Vancouver associated with virgin flow at The Dalles (Table 7). 

Combining the hindcast total load (sand + finer fractions) for 1879–1899 with the annual average 

69
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 

Figure 27. Hindcast total sediment load (metric tons) for the Columbia River eastern basin calculated at 

Vancouver from the observed flow (cubic meters per second) and estimated virgin flow. 

(Observed-flow data adapted from USGS records; virgin-flow data adapted from Jay and Naik 

2003 and BPA 1993.) 

Table 7. Estimated effects of climate change on total sediment transport and on sand transport (at 

Vancouver) based on virgin-flow estimates at The Dalles. 

Flow 

condition 

Period 

of record 

Total sediment 

transport 

(×106

 mt)*

Sand transport 

(×106

 mt)*

19th century 1879–1899 20.5 10.9 

 1858–1878 21.2 9.8 

1858–1899 (mean) 20.8 10.4 

20th century 1945–1999 17.2 8.3 

Change (because 

of climate) 

(1858–1899)– 

(1945–1999) 

–3.6 (–17%) –2.1 (–20%) 

*

 Average annual sediment transport (×106 mt) estimated from maximum daily flows. 

sediment transport (estimated from annual maximum daily flow) for 1858–1878, we estimate 

annual average sediment transport for 1858–1899 was approximately 20.8 × 106

 mt. Compared 

to similar estimates for 1945–99 virgin flows, total sediment transport decreased approximately 

3.6 × 106

 mt (≈17%) because of climate change. This is a considerably larger decrease than the 

climate-driven change in flow for two reasons: 

1) sediment transport varies with a power n of the flow (n is approximately 2.5), and 

70
2) decreased mean flow also reflects reduced flow variability and frequency of high flow 

days that transport most of the total load. 

Climate change similarly accounted for an estimated decrease of 2.1 × 106 mt (≈20%) in 

annual average sand transport from 1858–1899 to 1945–1999 (Table 7). The percentage 

decrease in sand transport is larger than that in total sediment transport, because the percentage 

of sand in the total sediment load increases as flow increases. 

The total change in sediment transport (including the effects of human manipulation of 

flow such as dams and irrigation) on sediment supply can be estimated by subtracting average 

annual sediment transport under virgin flows with similar estimates for observed flows (Table 8). 

The difference between annual average sediment transport at Vancouver for 1858–1899 virgin 

flow and for 1945–1999 observed flow was 10.8 million × 106

 mt (52%) of the 19th century 

sediment transport. The changes are larger if we consider sediment transport for observed flows 

after 1970, when the Columbia River became fully regulated. The difference between annual 

average sediment transports for the 1879–1899 virgin flow and 1970–1999 observed flow is 

approximately 12.5 × 106 mt (≈61.5%) of the 19th century sediment transport. 

Decreases in sand transport because of flow manipulations are similarly high (Table 8). 

The sand transport associated with the 1945–1999 observed flow was approximately 3.2 × 106

mt, approximately 7.7 × 106

 mt less than the 1879–1899 virgin flow (≈71% of the 19th century 

sand transport). Because sediment transport is related to flow in a nonlinear way, it is not 

possible to apportion the reduction in sediment transport precisely between climate change, 

water withdrawal, and flow regulation. The largest single factor is reduction in spring-freshet 

flow for power generation, flood control, and irrigation. 

The reduction of western subbasin winter freshets by climate change and flow regulation 

also has decreased sediment transport. The Willamette River total sediment transport hindcast 

for 1893–1903 was 2.4 × 106

 mt; whereas it was only 1.5 × 106 mt for 1970–1999, a reduction of 

Table 8. Long-term changes in total sediment and sand transport (at Vancouver) based on hindcast virgin 

flows and observed flows at The Dalles. 

Flow 

conditions 

Period of record

(total sediment

transport 

Total sediment

transport 

(×106

 mt)*

Period of 

record (sand 

transport 

Sand transport

(×106

 mt)*

Virgin flow 1858–1899 20.8 

Observed flow 1945–1999 10.0 

Long-term 

change 

(1858–1899)– 

(1945–1999) 

–10.8 (–52%) 

Virgin flow 1879–1899 20.5 1879–1899 10.9 

Observed flow 1970–1999 8.0 1945–1999 3.2 

Long-term 

change 

(1879–1899)– 

(1970–1999) 

–12.5 (–61.5%) (1879–1899)– 

1945–1999) 

–7.7 (–71%) 

*

 Average annual sediment transport (×106 mt) estimated from maximum daily flows. 

71
approximately 35%. It is not possible to separate human and climate effects in this estimate. 

The Willamette River channel has been more heavily altered (by straightening and elimination of 

backwater areas, possibly increasing transport capacity) than even the Columbia River channel. 

The effects of agriculture and urban development also have been pervasive in the Willamette 

Valley. This may indicate that hindcast estimates are less useful in the Willamette than the 

Columbia. Still no systematic difference was found between the 1910–1913 and 1962–1963 

sediment transport rating curves for the Willamette. 

Human and Climate Effects on Disturbance Frequency 

The frequency and magnitude of hydrologic disturbances to the river system are 

important to the development, availability, and quality of salmonid habitat upstream and in the 

estuary. Overbank flow contributes large woody debris that helps to structure fluvial and 

estuarine environments. The bulk of the sediment input to the system also occurs during high 

flow events. This is particularly true for the input of sand that helps to build shallow-water 

estuarine habitat. In the following subsections we examine historic changes in the frequency and 

patterns of extreme flows. 

Historical Changes in Overbank Flow 

The historic bankfull flow level is estimated at about 18,000 m3s

-1 for the mainstem 

Columbia River below Vancouver. This is the two-year flow recurrence level for The Dalles 

augmented by the typical spring-flow level for the western tributaries. Modern bankfull level is 

set by the standard project flood level of approximately 24,000 m3s

-1 for the lower river. Some 

overbank flow occurred in many years before 1900, in winter and in spring (Figure 28). 

0

20

40

60

1890 1900 1910 1920 1930 1940 1950 1960 1970 1980 1990 2000

Number of days

>18000

>24000

Figure 28. 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. (Data adapted from USGS 

records.) 

72
Substantial overbank flow (>24,000 m3

s

-1) is rare now, with significant events occurring 

only five times during the past half century—in 1948 (spring), 1956 (winter and spring), 

1964–1965 (winter), and 1996 (winter). Today even historical bankfull levels of 18,000 m3

s

-1

are rarely exceeded because of flood-control measures and irrigation depletion. The season 

when overbank flow is most likely also has shifted from spring to winter, because western 

subbasin winter floods (not eastern subbasin spring freshets) are now the major source of such 

flows. 

Climate is a secondary factor in the incidence of overbank flow. 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 29). Overbank flow is rare now even during cold PDO phases, 

and it was totally absent during the last PDO warm phase (1977–1995). 

Changes in the River-flow Frequency Distribution 

Another important symptom of human intervention in the flow cycle is the change in the 

frequency spectrum of the flow. There are two convenient ways to examine this spectrum: 

1) the power spectrum gives a high resolution picture of the average frequency content of a 

process over a time period, and 

2) the wavelet transformation gives a less detailed view of the time dependence of the 

frequency content. 

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)

24,000 

18,000 

Figure 29. Monthly average flows at the Beaver Army Terminal, 1878–1999, present and historical 

bankfull flow levels, and warm and cold PDO cycles. Major differences between warm and cold 

phases of the PDO cycle in the disturbance frequency have been largely eliminated by flow 

regulation and diking; overbank flow is now a rare event. (Data adapted from USGS records.) 

73
Comparison of the power spectra for the 1878–1910 and 1970–1999 periods defines the 

nature of the changes that have occurred (Figure 30). Low frequency flow variations with 

periods between about 6 and 24 months have been suppressed relative to 1878–1910 conditions; 

however, high frequency variations associated with power peaking have been augmented. These 

changes are not related to climate; the virgin-flow spectra for the two periods are similar. 

The daily power-peaking cycle also perturbs the diurnal (daily) tidal signal in the river, 

and this effect can be seen at least as far seaward as Beaver (RKm 85). The wavelet presentation 

of the flow spectrum (Figure 31) shows: 

1) the truncation of the annual flow cycle by flow regulation after about 1970 (despite very 

high virgin flows in 1972 and 1974), 

2) a sharp increase in high frequency energy associated with the hydroelectric operations 

after about 1965, and 

3) a climate (PDO cycle) influence on freshet strength (e.g., spring freshets were unusually 

low during 1922–1944 and higher during 1945–1976 despite flow regulation). 

Figure 30. Power spectra of the observed daily flow at The Dalles, 1878–1910 and 1970–1999. The 

peaks at 1 year and 6, 4, and 3 months, which are clearly visible in the 1878–1910 record, have 

been greatly reduced by flow regulation and irrigation depletion. The power-peaking cycle has 

added energy to the system at frequencies above approximately 20 days, but especially at 7 and 

3.5 days. Also shown are 95% confidence limits. (Data adapted from USGS records.) 

74
1880 1900 1920 1940 1960 1980 2000 

Time in years 

Lo

g2 fre

quenc

y, c

ycles 

year-1

-3 

-2 

-1 

0 

1 

2 

3 

4 

5 

6,000 

0 

Figure 31. Scaleogram of observed flow at The Dalles. Time in years is on the x-axis, and log (base 2) of 

frequency in cycles per year is on the y-axis, showing periods of eight years (bottom) to 3.5 days 

(top). The annual cycle is denoted by log2 (frequency) = 0 (1 cycle year-1 or 20

 = 1), and a period 

of six months by log2 (frequency) = 1 (2 cycles year-1 or 21

 = 2) (modified from USGS). The 

annual cycle becomes markedly weaker after approximately 1970 (as indicated by the loss of 

black and dark gray areas after 1970), primarily due to flow regulation. Climate variations such 

as the PDO cycle also affect the annual cycle. Also after 1970, high frequency (weekly) flow 

variations are much more prominent (note gray lines at top right), due to power peaking. (Flow 

data adapted from USGS records.) 

Climate and Human Influences on Freshet Styles 

Although the flow cycle is different each year, certain frequently occurring types of flow 

events or freshet styles are apparent. These patterns strongly affect flow and sediment transport 

processes in tributaries and the mainstem Columbia River, and they are sensitive to human and 

climatic change. Three principal kinds of spring freshets are evident, distinguished by the source 

of flow: 

1. Large winter snowpack without exceptional spring rain (e.g., 1880, 1916, 1972, 1974, 

and 1997). Very late spring freshets are likely to be in this category. 

2. A normal winter snowpack followed by a very wet spring. The result is heavy snow in 

April and early May and then very heavy spring rains that rapidly melt an unconsolidated 

snowpack (e.g., 1948). 

75
3. A large winter snowpack and heavy rains. The only certain example of this is 1895 

(USGS 1949), although some of the other very high spring freshets of the 19th century 

were likely of this sort (e.g., 1849, the second-highest known freshet, intermediate 

between 1948 and 1894). 

Heavy spring rains in 1894 and 1948 accelerated the spring freshet so that the maximum 

flow was not unusually late, even though a cold spring had allowed the low elevation snowpack 

to grow until the onset of the freshet. Winter freshets caused by rapid snowmelt and thawing of 

poorly vegetated eastern subbasin soils are known to cause unusually large sediment transport, 

especially for fines (Haushild et al. 1966, Waananen et al. 1971). Sediment-transport data 

collected during 1963–1964 by the USGS suggest that the Snake River basin also contributes 

considerable fine sediment during spring in some years. The U.S. Army Corps of Engineers 

(USACE) indicates that 75–110 × 106

 m3 (roughly 150–220 106 mt) of sediment have 

accumulated behind the four Snake River dams built since these measurements were conducted, 

considerably reducing the supply of sediment to the mainstem Columbia. 

Most major winter freshets in the Columbia Basin are the result of rain-on-snow events 

that cause rapid melting of a low elevation snowpack. Four types of winter freshets can be 

defined based on the importance and location of the low elevation snowpack that is melted: 

1) primarily western subbasin, with snowmelt (e.g., 1894 and 1997), 

2) eastern and western subbasin, with snowmelt (e.g., 1861, 1881, and 1996), 

3) primarily eastern subbasin, with snowmelt (e.g., December 1933, although the Cowlitz 

and some coastal rivers also flooded), and 

4) primarily western subbasin, with little snowmelt (e.g., January 1923, although 1909 and 

1927 had similar storms). 

The first three of these freshet types require that a low elevation snowpack be melted by a 

“Pineapple Express” storm, a weather pattern from the south carrying warm temperatures. If no 

low elevation snowpack exists, a major winter freshet rarely occurs. Exceptional rainfall for 

several weeks, however, did lead to a flood in January 1923 although the low elevation 

snowpack had melted before the main flood peak (Brands 1947). 

Winter freshets are spatially more diverse than spring freshets, because winter freshets 

are primarily a response to a specific storm or series of storms, with attendant large spatial 

variability. The 1933–1934 winter storms affected the Wenatchee River in Washington and 

tributaries very strongly. Flows in 1881 were very high in the Willamette and Umatilla rivers in 

Oregon. The Canadian part of the basin usually plays only a minimal role in winter freshets, 

because high temperatures do not penetrate to this part of the basin during most storms. 

While total winter snowpack differs among subbasins, spring freshets are more similar 

from year to year, because they represent an average over the entire winter of storm intensity. 

Winter freshets are, as noted previously, a very potent source of sediment. Flow regulation is 

most effective in controlling freshets related solely to the spring melting of a large winter 

snowpack, because a planned prerelease of water can begin in December or January, 5–6 months 

before the onset of the freshet. It is more difficult to anticipate or predict the occurrence of 

heavy spring rains, and little preparation can be expected for such events. Winter freshets also 

76
are difficult to control, especially when they originate largely in the western subbasin, where 

precipitation rates are higher and storage capacity relatively low. Flow from rain-on-snow 

events, whether in the winter or the spring, is more difficult to control than the normal spring 

snowmelt, because the melt rate is higher. 

Warming of the climate over the past century and flood control appears to have reduced 

the intensity of flow resulting from winter rain-on-snow events in the western subbasin. There 

were four large 19th century Willamette River floods (1813, 1861, 1881, and 1890) but only two 

major events during the 20th century (1964 and 1996); flows in 1813 and 1861 appear to have 

been larger than in any 20th century winter event, and maximum flow during the freshet of 1996 

was only approximately 53% of that estimated for 1861, the largest known event. Newspaper 

accounts from the 19th century indicate that more than 1 m of snow sometimes accumulated on 

the ground in the Willamette Valley, a rare event since 1900. The incidence of winter freshets 

that affected the western and eastern subbasins, however, may have increased during the past 

century. 

Spring freshets related to heavy spring rains are uncommon, and it is not known whether 

their incidence has changed. 

Downstream Effects of Hydrological Alterations 

Salinity Intrusion and Salinity Stratification 

Salinity intrusion length and density stratification because of vertical salinity gradients 

have likely increased over the past century. Salinity intrusion is governed by three primary 

factors: 

1) channel controlling depth, 

2) the strength of the tides, and 

3) river flow. 

The dependence of salinity intrusion on the channel controlling depth (H) is very strong. The 

landward, near-bed mean flow that drives salinity intrusion varies with the H or H , and the 

dependence of salinity stratification is even stronger, H or H . The tides have a complex effect 

on salinity. Tide-induced vertical turbulent mixing inhibits salinity intrusion, while horizontal 

transport by the

2 3

4 5

 tides is the primary salt transport mechanism during periods of strong tides and 

low-to-moderate river flows. 

Salinity stratification increases with river flow, whereas the relationship between salinity 

intrusion length (LS) and river flow (QR) is inverse LS ≈ QR

-n. Values of n vary from system to 

system from about 0.5 to greater than 1; the value for the Columbia River is not known. While 

this might suggest that the river-flow influence is smaller than other factors, river flow may vary 

seasonally by an order of magnitude. 

Before flows were regulated, the possible range of observed flow variation was even 

larger than at present, ranging from 1,000 to 35,000 m3s

-1 at The Dalles. In contrast the tidal 

range varies by only a factor of about two over the neap-spring cycle. The tidal prism has been 

77
reduced by about 15% by diking and filling, and the controlling channel depth has doubled over 

the past 120 years. Changes in bathymetry probably have caused the largest changes in salinity 

intrusion and density stratification (Figure 32), but reduction of the spring freshet also has 

increased salinity intrusion and salinity stratification. 

Figure 32. Maximum (end of flood) and minimum (end of ebb) salinity intrusion distance in the 

Columbia River estuary, based on 1980 bathymetric conditions. Present salinity intrusion may be 

somewhat different because of deepening of the navigation channel at the entrance. (Reprinted 

with permission from Jay 1984.) 

78
Tidal Regime and River Stage 

River flow and tidal propagation interact strongly (Jay and Flinchem 1999, Kukulka and 

Jay 2003a). The major daily and twice-daily tidal components (the major tidal species) are 

damped by river flow QR; tidal amplitudes and tidal range vary according to QR

n

, n is between 

negative 0.1 to negative 0.5. The distortion of the tide that determines the timing of high and 

low waters is more strongly affected. Daily and weekly power peaking by the hydropower 

system further complicates river tides by adding pseudotides that propagate seaward from 

Bonneville Dam (rather than landward from the ocean). Pseudotides can be larger than the 

natural tide landward of Portland. Changes in the seasonal flow cycle have increased tides and 

tidal currents in the spring and early summer and damped them in the fall and winter. Dredging 

also may have influenced tidal propagation in the tidal-fluvial reach, contributing to 

approximately an 8% increase in tidal amplitudes over the past century. 

While little is known about the direct impacts on juvenile salmonids because of increased 

tidal fluctuations and currents during the spring season, substantial changes in the availability of 

shallow-water habitat area (SWHA) have occurred.

Shallow-water Habitat Availability 

River stage (the water level averaged to remove tidal variations) increases rapidly with 

river flow. Reduction of maximum flow levels, dredged material disposal, and diking/flood 

protection measures have essentially eliminated overbank flow (Figure 28 and Figure 29) in the 

estuary and the tidal-fluvial part of the system below Bonneville Dam. The greatest reductions 

in river stage have occurred during the spring-freshet season, when juvenile salmonid densities 

are high. Kukulka and Jay (2003b) investigated the changes in SWHA (including SWHA in the 

former floodplain) for a sample reach extending from Skamokawa, Washington, to Beaver (RKm 

50–RKm 85) during the 1974–1998 period. They defined SWHA as areas with water depths 

between 0.1 and 2 m for any given river stage. 

Four scenarios were considered: 

1) the natural state (virgin flow, no dikes), 

2) present conditions (observed flow with dikes), 

3) virgin flow with dikes, and 

4) observed flow without dikes. 

Analysis of these scenarios allows evaluation of the impacts of diking and flow regulation, 

separately and together. 

During the spring-freshet season (May–July), dikes and flow alteration combined reduced 

average SWHA in the study reach by 62%, from 4.5 to 1.7 × 107

 m2. Taken individually, diking 

would have reduced average freshet-season SWHA by 52%, from 4.5 to 2.2 × 107

 m2; flow-cycle 

alteration would have reduced SWHA by 29%, from 4.5 to 3.2 × 107

 m2. Not only has habitat 

been lost, but the remaining SWHA is at a lower elevation than was historically the case because 

of the reduction of river stage during the spring season. The remaining SWHA also experiences 

stronger tides than occurred historically. That the total reduction (62%) is less than the sum of 

79
individual reductions from flow regulation (29%) and diking (52%) indicates that the 

flood-protection engineering for the system is redundant, a common engineering strategy. This 

redundancy implies that any habitat restoration in this reach will probably require some balance 

between flow restoration and dike removal. 

Kukulka and Jay (2003b) found that higher river stages greatly increase SWHA over a 40 

RKm stretch, but numerical modeling results (see the “Estuarine Habitat Opportunity” section, 

page 89) do not show such a clear pattern. This difference is explained by the inclusion of the 

entire floodplain (including the dike portion) in the Kukulka and Jay model; model results (see 

the “Estuarine Habitat Opportunity” section, page 89) do not include diked areas. This contrast 

emphasizes the historical importance of the prediked floodplain in providing shallow habitat. 

Estuarine Sediment Dynamics 

The estuary and its food web can be affected by sediment inputs in a variety of ways: 

1. Continual sediment supply is needed to counter erosion of marshes and sea-level rise (≈1 

mm per year in the estuary). The effects of changes in quantities and types of sediment 

input on estuarine wetlands have not been investigated. 

2. The organic component of the sediment supply is a vital source of nutrition to the food 

web of the ETM (Sherwood et al. 1990, Simenstad et al. 1990a and 1992), which is based 

on microbial processing of fluvial organic detritus. Much of this organic matter now 

stems from phytoplankton production in the reservoirs, whereas it previously contained a 

much higher percentage of material from floodplain inundation and estuarine marshes. 

These changes may have affected the food supply for juvenile salmonids, but the changes 

have not been quantified. 

3. Decreased turbidity during the freshet season may increase vulnerability of salmon to 

avian predators. This could be an important factor in light of the increased numbers of 

predators that have become established on artificial sand islands in the estuary (see the 

“Estuarine Habitat Capacity” section, page 127). 

4. The reduction in sediment transport to the estuary has affected navigation by reducing the 

amount of sand that must be dredged from estuarine channels. 

The ecological responses to changes in sedimentary regime have been poorly 

investigated. Understanding the effects on juvenile salmonids will require physical/chemical, 

geological, and biological observations, and perhaps numerical sediment-transport modeling. 

Effects of Future Climate Change 

Human intervention in the flow cycle has had a bigger effect on Columbia River 

hydrology than climate variations during the past 140 years. The projected near-term effects of 

climate are not large enough to rival the impacts of human alterations to the flow cycle. Future 

climate change, however, may exacerbate conflicts over water supply by increasing demand and 

decreasing natural flows during the critical spring-freshet period (Hamlet and Lettenmaier 1999). 

To the extent that future climatic changes alter the spatial and temporal patterns of flow across 

the basin, influences on local salmon populations and life histories could be significant. 

80
Changes in the PDO could have an important impact on future patterns of flow and 

sediment flow in the Columbia River basin. While it was widely believed that the PDO cycle 

changed back to a cold phase in the late 1990s, these conditions did not persist and have given 

way to warm coastal temperatures off Oregon since 2002. It remains unclear whether global 

warming will affect the characteristic interdecadal cycling of warm and cold phases observed in 

the past. 

An important factor in the PDO cycle is its synergy with ENSO cycles. La Niña winters 

during the cold PDO phase tend to be unusually severe (e.g., 1997 and 1999), while the effects of 

El Niño are muted. It is possible, however, that global warming could alter the duration of cold 

and warm phases or the relationship between the PDO and ENSO cycles. 

Climate projections predict gradual regional warming, possibly accompanied by higher 

precipitation, especially in winter (Hamlet and Lettenmaier 1999). Just as the ratio of winter to 

spring flows is naturally higher than in the Fraser River because of the Columbia River’s more 

southerly position, a warmer climate will likely increase Columbia River flows in winter and 

decrease peak and average spring-freshet flows. Of the three spring-freshet styles, flow 

regulation and diversion already have decreased flow volumes associated with the two that 

depend on an exceptional winter snowpack. Climate change probably will decrease (and already 

may have decreased) the probability of a 1948-style freshet caused by heavy spring precipitation 

on a late-arriving snowpack, because increased temperatures may not allow significant snow 

accumulation in April and early May. 

Effects of global warming also may vary among Columbia River subbasins. The 

frequency of major winter freshets (rain-on-snow events) in the eastern subbasin probably will 

increase unless the warming is sufficient to eliminate the low elevation snowpack. This probably 

will increase the supply of fine sediment to the river and estuary. Winter freshets in the western 

subbasin that do not involve snowmelt might increase in frequency or severity. However, low 

elevation snow accumulation west of the Cascades probably will decrease, reducing the 

frequency of major western subbasin freshets from rapid snowmelt even if rainfall increases. 

The net effects of such change on sediment supply in the western subbasin are unclear. 

Implications of Hydrological Change 

for the Member/Vagrant Hypothesis 

The member/vagrant hypothesis (Sinclair 1988, see the “Conceptual Framework for 

Evaluating Estuarine Habitat Conditions” section, page 21) predicts that diverse salmon life 

histories have developed in response to certain persistent features of the physical environment. 

Thus alternative salmon rearing and migration behaviors become linked to various habitats and 

environmental conditions capable of supporting each developmental stage (e.g., egg, fry, smolt, 

etc.) within a suitable range of times and locations for individuals to complete their life cycles. 

If this is an accurate depiction of salmon life histories, then major departures from the historical 

template of an ecosystem may create mismatches between established salmon behaviors and the 

physical environment or prevent the expression of potential behaviors by eliminating habitat 

opportunities (Figure 9). The hydrological changes, particularly those associated with flow 

regulation, water withdrawals, floodplain diking, and habitat loss, represent a fundamental shift 

81
in the physical state of the entire Columbia River ecosystem. Such changes have significant 

consequences for salmonids whose migration and rearing behaviors have adapted to historical 

conditions for the estuary and, therefore, for each of the components of salmon performance 

defined by our conceptual framework (Figure 33). 

For example, the effort to stabilize flows in the Columbia River basin ironically may 

create less stable patterns for salmonids whose migration and rearing behaviors have adapted to 

historical patterns of hydrologic variability. 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 is particularly important. By creating selective 

advantage for those behaviors that match the operations of bypass, spill, and transportation 

systems, life history variation among salmonids may be simplified to conform to narrow 

Bathymetry

Habitat 

opportunity

(access) 

Habitat 

capacity

(quality) 

Population 

structure/ 

life history 

(upriver 

genetic, 

life history, 

and 

geographic 

structure) Performance

(estuarine foraging 

success, growth, 

diversity) 

Regional 

climate

(ENSO, 

PDO, etc.)

Figure 33. External factors affecting disturbance processes and the physical template of the estuary. 

Flow 

regulation

Anthropogenic 

modifications

(diking, 

 dredging, 

filling, etc.) Water 

withdrawal

Transport 

 of sediments 

and organic 

debris 

Tidal regime 

River 

 flow 

(volume, 

 hydro period)

82
windows of opportunity now prescribed by the management system (ISG 2000, Williams in 

press). One potential result of dampening flow variations in the Columbia River could be a 

greater uniformity of migration patterns with potential consequences for the variety of times and 

sizes at which salmon arrive in the estuary or ocean or both. 

The nearly complete elimination of overbank flooding throughout the expansive tidal 

freshwater portion of the estuary may pose some of the most significant consequences for 

Columbia River salmonids. Flow regulation and diking effects have largely eliminated access to 

off-channel floodplain habitats and refugia during high flow events. If, as we suspect, patterns of 

extended estuary use by small subyearling migrants are directly linked to the availability of 

shallow-water habitat, then loss of the tidal floodplain may simplify salmon diversity. In the 

“Estuarine Habitat Opportunity” section (page 89), we evaluate use of a hydrodynamic model to 

better understand the habitat-opportunity dynamics and the implications for estuarine-rearing 

salmonids. 

In addition to the physical effects of reduced habitat opportunity on salmon diversity, 

flow regulation and diking may influence the productive capacity of the estuary by regulating 

energetics processes (e.g., habitat capacity), including food production, competition, and 

predation. Floodplain inundation greatly increases the surface area of tidal estuarine and riverine 

habitats available to salmonids. This allows fish to expand their distribution into productive offchannel areas and may relax competitive interactions by reducing fish densities. Studies on a 

nontidal portion of the lower Sacramento River in California found that tagged juvenile Chinook 

salmon released in the seasonally inundated floodplain had better growth, higher consumption 

rates, and improved survival compared to others released into the main river channel (Sommer et 

al. 2001). Elimination of overbank flooding also prevents the pulsed delivery of structural and 

energetic components to the rest of the estuary (e.g., large wood pieces, sediments, detritus, and 

prey organisms produced in adjacent riparian and floodplain habitats). In the “Estuarine Habitat 

Capacity” section (page 127), we will examine what is known about changes in habitat capacity 

of the Columbia River estuary. 

Conclusions 

Human and Climate Influences on Flow and Sediment Transport 

Columbia River mainstem flow and sediment transport affect salmonids directly and 

indirectly. Major changes during the past 120 years in Columbia River hydrological processes 

have resulted primarily from human alteration to the system and secondarily from climate 

processes. 

Large-scale Geography 

The Columbia River has the largest flow (≈7,300 m3

s

-1) of any river on the Pacific coast 

of North America. Its annual average sediment transport (≈107

 mt year-1) is not unusually large, 

and is exceeded by several other western rivers. For hydrological purposes, the Columbia River 

basin can be divided into western and eastern subbasins by the Cascade Mountains. Except for 

the Canadian portion, the eastern subbasin (with 92% of the surface area and 75% of the flow) is 

relatively arid. Almost all flows from the eastern subbasin pass the gauge at The Dalles, which 

83
has the longest daily flow record on the West Coast (1878–present). The western subbasin 

contains only 8% of the area of the entire Columbia River basin, but it contributes about 25% of 

the flow. The Willamette River is typical of the western subbasin; the flow record at Albany 

extends from 1892 to the present. 

Climate Change 

Climate and flow conditions during the last half of the 19th century reflected the end of 

the Little Ice Age from about 1400 to 1850. This period was significantly cooler and wetter than 

present conditions. For example, 10 of the 14 strongest known spring freshets in the system 

occurred between 1849 and 1900, even after accounting for human manipulation of the flow. 

Climate Cycles 

Cyclical climate phenomena exert a strong influence on Columbia River hydrology. 

Although the history of regional climate fluctuations during the 19th century is unclear, effects 

of two cyclical processes were prominent throughout the 20th century: 

1. The PDO has a cycle that lasts 40–60 years and probably has been active for at least 300 

years. Cold PDO phases (e.g., 1945–1976) are generally associated with high river flows 

and are favorable for salmonid production in the Pacific Northwest; warm phases (e.g., 

1977–1995) are characterized by low river flows and are less favorable for salmonid 

production. 

2. Indices of the ENSO (typically 3–7 years in duration) also are correlated with Columbia 

River flow. ENSO cycles affect survival of salmonids in the fluvial, estuarine, and ocean 

environments. 

Pacific Decadal/El Niño Southern Oscillation Interaction 

The PDO and ENSO cycles interact such that El Niño years are most intense during the 

warm PDO phase and La Niña years during the cold PDO phase. The average annual Columbia 

River flow at The Dalles is 111% of normal during cold PDO/La Niña years, whereas it is only 

85% during warm PDO/El Niño years. The corresponding figures for the Willamette River are 

119% and 81%. 

Latitudinal Position 

The Columbia Basin’s climate response is conditioned by its position within a latitudinal 

band of strong response to the ENSO and PDO cycles. The flow-per-unit area is greater in the 

western than in the eastern subbasin, and latitudinal differences in the timing of snowmelt 

influence spring-freshet properties. Still variations across the basin in response to ENSO or PDO 

forcing are modest. 

Climate Effects on Sediment 

Flow fluctuations are amplified by fluvial sediment transport, because sediment transport 

varies more than linearly with flow. Total sediment load during cold PDO/La Niña years is more 

84
than 200% of that during warm PDO/El Niño years in the Columbia (at Vancouver) and the 

Willamette rivers. Climate effects on sand transport are even stronger than those on total load. 

Annual Average Flow at The Dalles 

Changes in annual average flow are an important integral measure of system alteration. 

The mean annual average flow of the Columbia River at The Dalles has decreased about 16.9% 

from 6,320 m3s

-1 (1879–1899 estimated natural or virgin flow) to 5,250 m3

s

-1 (1970–1999 

observed flow). We estimate that climate change accounts for an 8–9% decrease, deforestation a 

1–2% increase, and irrigation depletion approximately a 7.4% decrease in average annual flow. 

Spring-freshet Properties 

Spring-freshet timing, strength, and duration are important to downstream migrant 

juvenile salmon. Spring-freshet properties have been much more highly altered than the mean 

flow. The average natural or virgin flow for the spring-freshet season (May–July) was 

approximately 13,600 m3

s

-1 before 1900. This has decreased by approximately 5,870 m3

s

-1

(43%) to 7,740 m3s

-1, with 26.5% because of flow regulation, 11% because of irrigation 

depletion, and 5.6% because of climate change. Thus freshet-season flow at The Dalles is now 

only 148% of the present (reduced) mean flow, while it was 215% of the higher 19th century 

flow. Flow regulation and the annual irrigation cycle also have increased fall and winter flows, 

the latter because of water released before the freshet. 

Maximum Daily Flow at The Dalles 

The observed maximum daily spring-freshet flow has been reduced slightly more than 

freshet-season flow, from 19,300 m3

s

-1 (1858–1999) to 10,870 m3

s

-1 (1970–1999), a decrease of 

44%. This is a drop from 305% to 207% of the mean flow. 

Spring-freshet Timing at The Dalles 

The timing of the maximum spring-freshet flow also changed. Maximum daily springfreshet flow now typically occurs at about water-year Day 242 (May 29), whereas maximum 

flow occurred in the 19th century at about water-year Day 256 (June 12), a shift of two weeks. 

Willamette River Hydrology 

Changes in the western subbasin have been similar to those in the eastern subbasin, but 

the changes are not as well documented. The observed annual average Willamette River flow at 

Albany has decreased from 462 m3

s

-1 for 1893–1900 to 394 m3

s

-1 for 1970–1999, or 14.8%. 

Late summer and fall (August–December) flows have been augmented; whereas, average 

monthly flows during the January to July period have decreased. 

Columbia River Flow at the Mouth 

The long-term average flow at the mouth of the Columbia River was 7,300 m3s

-1 for 

1892–1999. The Columbia River flow at the mouth prior to 1900 was approximately 8,530 m3

s

-1 

and has decreased to approximately 7,080 m3s

-1 for 1970–1999 (≈17%). 

85
Changes in Sediment Transport 

Sediment transport is a vital system characteristic for salmonids. Hindcasts from limited 

data collected during the 1960s suggest that the annual average sediment transport from the 

eastern subbasin decreased from about 21 × 106

 mt for 1858–1878 to approximately 8 × 106 mt 

for 1970–1999, (≈60%). We estimate that historical sand transport of more than 10 × 106

 mt for 

1858–1899 decreased to 3.2 × 106 mt (≈70%). Most of the reduction in eastern subbasin 

sediment transport is related to the dam system, especially its reduction of spring-freshet flow. 

In the Willamette River, historical sediment transport for 1893–1903 was approximately 2.4 × 

106

 mt, compared to only 1.5 × 106 mt for 1970–1999, a reduction of approximately 35%. 

Disturbance Frequency 

The frequency and magnitude of disturbance to the river system is important to 

salmonids. The historical bankfull flow level was approximately 18,000 m3

s

-1 for the main stem 

below Vancouver. Modern bankfull level is set by the standard project flood level of 

approximately 24,000 m3

s

-1 for the lower river. Some overbank flow occurred in many years 

before 1900. Flow regulation and water withdrawal have made overbank flow (above 24,000 

m3s

-1) rare, with significant events occurring only five times since 1948. Climate is a secondary 

factor with regard to the incidence of overbank flow. Overbank flow is now rare even during 

cold PDO phases, and it was totally absent during the last PDO warm phase (1977–1995). 

Changes in Shallow-water Habitat Area 

Hindcasts based on topography and simple tidal models suggest that, during the springfreshet season (May–July), dikes and flow alteration combined have reduced average SWHA in 

the Skamokawa to Beaver reach by 62%, from 4.5 to 1.7 × 107 m

2

. Individually, diking would 

have reduced average freshet-season SWHA by 52% (from 4.5 to 2.2 × 107

 m

2

); flow-cycle 

alteration alone would have reduced SWHA by 29% (from 4.5 to 3.2 × 107 m

2

). Not only has 

habitat been lost, but the remaining SWHA is at a lower elevation than it was historically 

because of the reduction of river stage during the spring season. The remaining SWHA also 

experiences stronger tides relative to those of the historic period. 

Changes in the River-flow Frequency Distribution 

Low frequency flow variations with periods between about 2 years and 6 months have 

been suppressed by the dam system, whereas high frequency variations associated with power 

peaking have been augmented. The daily power-peaking cycle also perturbs the diurnal (daily) 

tidal signal in the river. 

Spring-freshet Styles 

The flow cycle is different each year, but three patterns of spring freshets commonly 

occur: 

1) large winter snowpack without exceptional spring rain, 

2) normal winter snowpack with very high spring rainfall, and 

86
3) large winter snowpack combined with very high spring rainfall. 

The largest known freshet (1894) was Type 3, and the second largest (1948) was Type 2. 

Winter-freshet Styles 

Four types of winter freshets are evident, based on the source of the flow: 

1) western subbasin only, with extensive snowmelt, 

2) eastern plus western subbasin, 

3) eastern subbasin only, and 

4) western subbasin only, without extensive snowmelt. 

The first three types of winter freshets are generated by rain-on-snow events, and the largest 

known freshets (e.g., 1861, 1881, and 1892) involved both subbasins. The Canadian portion of 

the eastern subbasin is not usually affected by these floods. 

Downstream Effects of Hydrological Alterations 

Changes in Columbia River flow and sediment transport have exerted an important 

influence on the estuary, but these changes are not well understood. Effects of these 

hydrological changes on the Columbia River buoyant plume in the coastal ocean are almost 

unknown. The following downstream effects of hydrological change should be considered by 

future studies: 

• estuarine salinity intrusion and salinity stratification, 

• habitat availability, 

• the fluvial tidal regime, 

• sediment dynamics, and 

• Columbia River plume area, volume, turbidity, and seasonality. 

Effects of Future Climate Change 

Although climate effects on hydrology have been and probably will remain smaller than 

those of human manipulation, it is still vital to consider how climate will constrain future 

management options in the Columbia Basin, including efforts to restore depleted salmon 

populations. Climate projections suggest gradual regional warming, possibly accompanied by 

higher precipitation, especially in winter. This would likely lead to increased incidence of winter 

freshets and lower natural spring-freshet flows. 

These changes would likely exacerbate conflicts over water supply during the critical 

spring-freshet period, by increasing demand and decreasing natural flows. 

Implications for Salmon Diversity and Productivity 

Dampening of established flow variations in the Columbia River estuary through flow 

regulation may have important impacts on salmon diversity and productivity. Simplification of 

87
flow patterns may reduce the diversity of salmon migration patterns with potential effects on 

arrival times and sizes of fish entering the estuary and ocean. Reduced floodplain inundation has 

eliminated shallow-water habitats, which probably were seasonally important rearing areas and 

refugia for juvenile salmon, particularly for small subyearling migrants. Disconnecting the tidal 

river from its floodplain also prevents delivery of wood debris, organic matter, and prey 

resources to the estuary, with potential consequences for estuarine food chains. 

88
Estuarine Habitat Opportunity 

Introduction 

Dynamics of Habitat Opportunity 

In the previous section, we reviewed changes in regional climate and basin-wide 

hydrology that define the past and present range of physical conditions for salmon upstream and 

within the Columbia River estuary (see the “Changes in Hydrological Conditions” section, page 

47). In this section,4 we shift our perspective to the internal dynamics of physical change within 

the estuary. We examine the effects of changing river flows and estuarine bathymetry on one of 

the principal attributes of salmon performance as defined by the member/vagrant hypothesis (see 

the “Conceptual Framework for Evaluating Estuarine Conditions,” section, page 21)—habitat 

opportunity (Figure 34). 

Estuarine habitat opportunity for salmon is naturally dynamic, because physical 

characteristics of the estuary (e.g., water depths, current velocities and directions, salinities, and 

temperatures) continually change with tides and river flow. Young salmon in the estuary may 

constantly need to adjust their distributions and behaviors to a shifting habitat landscape. 

Accessibility of some estuarine habitats depends on two factors: 

1) the frequency of tidal or seasonal inundation, or 

2) whether changes in physical or chemical conditions at a particular site remain within a 

suitable range of physiological or ecological tolerance among individuals. 

For example, many productive shallow-water habitats that subyearling salmon use for extended 

periods of estuarine rearing drain at low tide and are only accessible for a limited number of 

hours during each tidal cycle (Levy and Northcote 1982, Healey 1982). 

In this section, we evaluate a simulation model as a tool for understanding the 

habitat-opportunity dynamics for salmon and the potential effects of anthropogenic changes in 

the estuary that affect these dynamics. We begin by describing our modeling approach and the 

physical indicators we have chosen to define habitat opportunity for subyearling salmon. We 

then use the model to assess the behavior of these criteria under present and historic river-flow 

and bathymetric conditions. We also review these model results and their implications for the 

member/vagrant hypothesis. 

 

4

 Since the time of research described in this section (1998–2000), the methodology has been substantially extended 

through the development of three-dimensional baroclinic circulation models and simulation databases for the 

Columbia River (Zang et al. 2004, Baptista et al. 2005) and by the modification of criteria for habitat opportunity to 

account for three-dimentional information on velocities and for information on salinity (USACE 2001) and 

temperature. While the results herein no longer reflect state-of-the-art modeling capabilities, the section correctly 

depicts the concepts underlying the methodology and their application to the dynamics of salmon habitat 

opportunity. 

89
Figure 34. Physical modifications to the estuary affect habitat opportunity for salmon. This chapter uses 

simulation modeling to examine effects of flow regulation and bathymetric change. 

Modeling Approach 

The Center for Coastal and Land-Margin Research (CCALMR) has been developing an 

observation and forecasting system for the Columbia River estuary since 1996 (OGI 1997, 

Baptista et al. 1999). The Columbia River Estuary Forecasting System (CORIE), a multipurpose 

infrastructure system for science and management, includes integrated modeling and observation 

components that regularly generate a variety of products describing the physical environment of 

the Columbia River below Bonneville Dam (RKm 235). 

Daily forecasts of depth-averaged circulation made since 1997 are among the regular 

CORIE products (OGI 1997). At the core of the forecasts is a numerical model, which solves for 

mass and momentum conservation equations inside a predefined computational domain, given 

bathymetric and boundary forcings. Circulation is described in the form of water levels and 

velocities, in a computational grid that extends from Longview, Washington (RKm 105), to the 

Pacific Ocean (Figure 35). Circulation forecasts are generated daily, with predictions compared 

against real-time observations from the CORIE network (Baptisa et al. 1998 and 1999). This 

Habitat 

opportunity 

(access) 

Habitat 

capacity

(quality) Population 

structure/ 

life history 

(upriver genetic, 

life history, and 

geographic 

structure) 

Anthropogenic 

modifications

(estuarine bathymetry) Regional 

climate 

Flow 

regulation 

Performance 

(estuarine foraging 

success, growth, diversity)

90
(a)

(b)

(c)

Figure 35. Different domains of simulation within CORIE. The domain for depth-averaged hindcasts 

(bottom left) conducted 1997–2001 is the basis for the simulations in this technical memorandum. 

It extends from the Bonneville Dam, the Willamette Falls in the Willamette River, and the 

upstream Cowlitz River into the continental shelf. Tides are applied at the ocean boundary (bold 

line). Wind forcing is applied at the ocean (big arrow). The small arrows represent river 

discharges applied as boundary conditions. The Beaver Army Terminal (dot) is no longer a 

boundary condition. The domain for depth-averaged forecasts (top left) conducted 1997–2001 

extends from Beaver into a limited portion of the continental shelf. Three-dimensional baroclinic 

forecasts and hindcasts (right) conducted since fall 2000 often extend north to British Columbia 

and south to California to account for the effect of upwelling and downwelling regimes due to 

winds alongshore (Baptista et al. 2005). 

comparison allows a continued understanding of the capabilities and limitations of the model, 

which has led to better predictions over a time period. 

A complementary product, generated more sporadically, consists of monthlong hindcasts 

of depth-averaged circulation. We complete these simulations retrospectively using a larger 

computational grid, extending from the Bonneville Dam to the Pacific Ocean (Figure 35). 

Boundary conditions are imposed based on observations rather than predictions of the external 

forcings. Prior to the beginning of this review, monthlong hindcasts were available for 1997 and 

part of 1998. 

91
The ability to represent water levels and velocities with good spatial resolution, for long 

periods of time and within reasonably controlled quality, allows us to explore patterns and trends 

of physical behavior and estuarine habitat opportunity for juvenile salmon in the modern 

Columbia River system. We can process the model-generated data to evaluate indices of 

physical performance of the estuary and apply these results to interpret fisheries data. 

The computation of these indices is flexible in time and space, because model results are 

available at small intervals (15 minutes) and as a pseudocontinuum within the computational 

grid. Indices for spatial patterns and seasonal and interannual trends can be conveniently 

analyzed relative to external forcings such as river flow. We also can perform model simulations 

and calculate associated indices for predevelopment (historical) conditions and future 

management scenarios. Thus the model offers an analytical tool for evaluating past and future 

effects of various management actions on estuarine habitat. 

One goal of this report was to explore the feasibility of using CORIE modeling products 

to characterize modern variability and historical trends in the physical habitat of the Columbia 

River. We focused on concepts and methods for utilizing simulation databases to analyze the 

influence of estuarine physical habitat on salmon life history and performance in the estuary. 

These preliminary outcomes will need to be revised and extended in the future. The robustness 

and extent of the circulation simulation database can and should be increased over a time period. 

The findings of this investigation, therefore, should be considered as guiding hypotheses rather 

than established protocols. 

One of the challenges faced in this investigation was the definition of indices of physical 

habitat most relevant to salmon and to the member/vagrant hypothesis (see the “Conceptual 

Framework for Evaluating Estuarine Habitat Conditions,” section, page 21). After several 

iterations, we selected indices of habitat opportunity, including: 

• threshold depths and velocities for subyearling salmon, 

• residual velocities, and 

• hydrodynamic residence times. 

The concept of modeling indices of physical habitat opportunity is novel, but it provides 

a natural link between estuarine physics and interpretation of ecological and fisheries data. The 

concept involves a simple binary decision about whether the physical habitat is favorable to 

juvenile salmon, as defined in this technical memorandum by water velocities, depths, or both. 

Specifying the criteria for favorable conditions is more challenging. The rationale for this 

specification is discussed in the “Establishing Criteria for Habitat Opportunity” subsection. 

Residence times and residual velocities are conventional indices of physical estuarine 

behavior that reflect net transport. As defined in this investigation, they relate strictly to net 

hydrodynamic transport (i.e., they are not tied to any particular biological or ecological tracer, 

and thus do not reflect self-propelling motion or deposition/erosion processes). Each index 

integrated water motion over space or time. In the case of residence times, integration is over 

space and time, along the path of a parcel of water as it leaves the estuary. In the case of residual 

velocities, integration is over a multiple of a tidal period, at a fixed position in space. 

92
Establishing Criteria for Habitat Opportunity 

Juvenile salmon respond to a variety of habitat characteristics that collectively affect their 

migration behavior through estuaries, including abiotic (i.e., temperature, salinity, and turbidity) 

and biotic conditions (i.e., prey availability). The emphasis on species with subyearling life 

histories, particularly Chinook and chum salmon, defines specific limits for model simulations 

distinct from those that would apply to larger stream-type migrants. 

Depth 

Subyearling salmon, migrating through estuaries as fry or fingerlings, tend to restrict their 

movements to shallow water until they reach larger sizes required to exploit deeper channels, 

open-water habitats, and associated prey resources (Groot and Margolis 1991). Chum and 

Chinook fry prefer shallow-water areas; at sizes ranging from 30–60 mm FL (millimeters fork 

length), both species occupy tidal wetland sloughs and channels, mud and sand flats, or beaches 

(Healey 1982 and 1991, Simenstad et al. 1982, Salo 1991). At 55–60 mm FL, chum fry often 

move into deeper offshore waters (Bax et al. 1980, Simenstad and Salo 1982). Subyearling 

Chinook may occupy estuarine marsh and other shallow-water habitats until they exceed 100 

mm FL (Healey 1982, Levy and Northcote 1982). Various investigations suggest that salmon fry 

and fingerlings often remain within water depths between approximately 10 cm and 2 m. While 

admittedly there is considerable variation in fish movements, and salmon can and do migrate 

outside this range, we chose this depth window as a reasonable criterion for simulating estuarine 

habitat opportunity for subyearling, ocean-type Chinook. 

Velocity 

The opportunity for salmon fry and fingerlings to access estuarine habitats also may be 

determined by their swimming performance and the energetic constraints of maintaining position 

against tidal or river currents. We defined velocity, therefore, as a second criterion for 

simulating habitat opportunity for salmon fry and subyearlings. 

Juvenile salmonids swimming performance is a function of fish size (body length); 

duration of swimming activity, including sustained versus burst speeds; and various 

environmental variables, including temperature and dissolved oxygen (Hoar and Randall 1978). 

Beamish (1978) reviewed swimming performance of fish from various laboratory studies, 

including sustained swimming speeds, defined as speeds that fish could maintain for long periods 

(>200 minutes) without muscle fatigue. Davis et al. (1963) reported sustained swimming speeds 

of 23–67 centimeters per second (cm s-1) for 81–126 mm Chinook salmon at an acclimation 

temperature of 11.5°C. For somewhat smaller subyearling Chinook (51–73 mm FL) acclimated 

at 15°

C, maximum sustained swimming speeds ranged from 29 to 53 cm s-1. Based on these 

results, 30 cm s-1 was chosen as a threshold velocity for modeling the availability of low velocity 

rearing habitat for subyearling Chinook within the Columbia River estuary. To assess model 

sensitivity to different assumptions of habitat suitability, we also evaluated habitat opportunity 

using a 50 cm s-1 threshold velocity. 

93
Simulation Scenarios, Methods, and Uncertainty 

The two-dimensional circulation database used in the present investigation is summarized 

in Table 9. The database includes simulations for modern and predevelopment bathymetry and 

for modern and predevelopment river flows. Simulations for the modern system cover 1997 and 

1998, the first five months of 1999, and selected months in the spring of 1980. Simulations for 

the predevelopment system include selected months in 1880 typically associated with high (May, 

July) or low (December) river flows. The 1880 simulations were often conducted for two 

alternative bathymetries, as discussed in the “Creation of the Bathymetric Database” subsection. 

In some cases, 1880 bathymetry and 1997 river flows were combined in an attempt to separate 

the effects of change in river flow from effects of bathymetric change. 

The 1997 and 1998 simulations already were available for our analysis, but other 

simulations were necessary. The process used in all simulations was similar, and involved the 

steps described in the following subsections. 

Choice of the Computational Domain 

The modern and predevelopment systems were represented from Bonneville Dam to the 

Pacific Ocean (Figure 35). Our incorporation of shallow peripheral areas in the computational 

domain for the modern and the predevelopment systems is not fully consistent. 

Creation of the Bathymetric Database 

Generating the bathymetric database for the computational domain is a resource- and 

time-consuming task. We realized early in the project that resources were insufficient to 

Table 9. Summary of two-dimensional simulation database for bathymetric and velocity analyses. 

Simulation months are online at http://www.ccalmr.ogi.edu/bpa/simulations.html. 

1880 1880* 1880** 1980 1997 1998 1999 

January January January 

February February February 

March March March 

April April April April 

May May May May May May May 

June June 

July July July July 

August August 

September September 

October October 

November November 

December December December December 

*

 Simulations with predevelopment bathymetry (sensitivity to vertical datum interpretation, as described in 

the appendix of Sanders et al. 2000). 

** Simulations with predevelopment bathymetry but with 1997 river flows. 

94
generate two bathymetric databases. Therefore we used the existing CORIE representation of 

modern bathymetry and concentrated our efforts on a careful reconstruction of predevelopment 

bathymetry. While this decision was critically important to make this investigation feasible, 

comparisons between modern and predevelopment bathymetrics require several assumptions. 

The modern CORIE bathymetry (Figure 36) was generated in 1996, when modeling 

emphasized the circulation dynamics of the deeper regions of the estuary (e.g., navigation and 

north channels). The bathymetric base for the entire estuary utilizes National Oceanic and 

Atmospheric Administration (NOAA) survey results from the period in 1958, but it is overridden 

in the channel and vicinity by the 1996 USACE surveys (Sanders et al. 2000). While shallow 

areas are represented in this base map, assumptions for regions without survey data (in particular, 

island formations, such as in Cathlamet Bay) tend to overestimate depth. 

The Geographic Information System (GIS)-based process followed the generation of the 

predevelopment bathymetry (Figure 37). Careful analysis of historical bathymetry relied on 

informed assumptions when survey data were unavailable. Areas of uncertainty typically 

focused around island formations (Figure 38). To test the sensitivity of the characterization of 

physical estuarine habitat to our bathymetric assumptions, we created a second 

predevelopment bathymetric coverage (Figure 39) that probably overestimated water depth 

around island formations. This overestimation roughly approximates that of the modern CORIE 

Figure 36. A model of bathymetry for the Columbia River estuary. Modern and predevelopment model 

bathymetry were derived at different times, with different modeling purposes and support 

technologies. The darker shades are areas with greater depths. Modern model bathymetry 

predates this study, without focus on detailed representation of very shallow areas (e.g., in 

Cathlamet Bay), which may be deeper than in reality. Outside the navigation channel area of 

influence (where there are modern USACE surveys), this bathymetry is based on surveys from 

the late 1950s. 

95
Figure 37. A model of predevelopment bathymetry of the Columbia River estuary. It is based on surveys 

from the 1870s and 1880s. The darker shades are areas with greater depths. While the density of 

the survey points is smaller than for the modern bathymetry, more sophisticated GIS techniques 

were used to render the bathymetry, and more care was used in representing shallow areas as 

accurately as allowed by survey data (Sanders et al. 2000). 

Figure 38. A model of corrected bathymetry for the Columbia River estuary predevelopment system. 

The darker shades are areas with greater depths. Corrected bathymetry involves introducing 

controlled changes to enable an analysis of the sensitivity of habitat opportunity to the 

uncertainties in bathymetry (Sanders et al. 2000). 

96
Figure 39. A model of Columbia River estuary predevelopment bathymetry. The polygon bounds the 

area affected by the changes introduced to create the corrected bathymetry. The changes tend to 

deepen the Cathlamet Bay area and are described in detail in Sanders et al. 2000. 

bathymetry and allows us to test the sensitivity of the model to alternative assumptions about 

historical depths. 

Creation of a Computational Grid 

The hydrodynamic model used in this study (see the “Simulation Model” subsection, 

page 98) solves the conventional shallow-water equations (partial differential equations 

reflecting conservation of mass and momentum) in an unstructured computational grid formed 

by triangular elements (Figure 35). Generation of this grid requires positioning the 

computational nodes (the vertices of the triangles) over the domain in ways that reflect the 

desired level of resolution (which typically varies from region to region of the domain). Higher 

resolution is sought in areas representing high gradients in bathymetry or water circulation. 

Specification of Boundary Conditions 

Prior to any simulation, external forcings must be specified at the boundaries of the 

computational domain. The barotropic circulation in the Columbia River estuary is primarily 

controlled by two external forcings: ocean tides and river flows. 

For the period of simulation, we specified tides by harmonic synthesis of tidal 

constituents derived from the eastern North Pacific Ocean tidal model of Myers and Baptista 

(2000). David Jay and co-workers provided representative flows at the Bonneville Dam, in the 

Willamette River, and in the Cowlitz River (see the “Changes in Hydrological Conditions” 

section, page 47). 

97
Simulation Model 

We conducted simulations with ADCIRC, an advanced circulation model developed at 

the U.S. Army Corps of Engineers Waterways Experimental Station in Vicksburg, Mississippi 

(Luettich et al. 1991, Luettich and Westerink 1995). The two-dimensional version of the model 

is used in this analysis with options enabled for treatment of wetting and drying. We calibrated 

and validated the model for the modern system (part of the CORIE modeling procedures). A 

verified model that properly reflects current conditions presumably will depict accurately the 

historical estuary within the limits of uncertainty for bathymetry and external forcing. 

Analysis of the data was consistent across simulations, and typically involved: 

• calculation of indices (residence times, residual velocities, and habitat opportunity) at the 

nodes or elements of the computational grid, and typically as a function of time, 

• spatial mapping of indices, either for the entire domain or subregions, 

• integration of indices, across time or space or both, in the latter case over the entire 

domain or subregions, and 

• correlation of integrated indices with river flows at Bonneville Dam. 

Modeling, whether for modern or predevelopment conditions, has inherent errors and 

uncertainties that are challenging to overcome, especially for a complex system such as the 

Columbia River. The CORIE infrastructure approaches this challenge with a long-term 

perspective. Each new application or research project contributes incrementally to extend 

modeling capabilities, database coverage, reliability, and awareness of modeling limitations. 

This investigation focused on extending modeling capabilities (through the creation of a 

predevelopment bathymetry and through the systematic creation of indices of physical habitat 

opportunity and net hydrodynamic transport) and database coverage (through simulation of 

selected months in 1880, 1980, and 1999). Some modeling limitations also were identified, and 

will be discussed. It was beyond the scope of this investigation, however, to identify modeling 

uncertainty systematically or to improve the inherent quality of the hydrodynamic simulations. 

Important goals of the simulations reported in this section are: 

1) to evaluate this new method for assessing estuarine habitat opportunity, and 

2) to understand the relative sensitivities of the model to changes in physical variables, 

principally depth and river flow. 

Results 

Habitat Opportunity 

For each of the three criteria identified, we computed hours of habitat opportunity 

(defined as hours within a month in which the criterion is met locally) for each node of the 

computational grid, for all available months in the simulation database, and we normalized the 

results to 720-hour months. Isolines of the resulting normalized habitat opportunity for the entire 

98
estuary were plotted for each (predevelopment and modern) month of the simulation database. 

Isolines for May 1997 are shown in Figure 40. 

To facilitate the analysis, we divided the estuary into six regions of distinct characteristics 

relative to topology, bathymetry, and distance to the ocean (Figure 41): 

• Region 1, Baker Bay 

• Region 2, the lower estuary 

• Region 3, Youngs Bay 

• Region 4, Cathlamet Bay 

• Region 5, Grays Bay 

• Region 6, the upper main stem of the estuary 

Within each region we computed integral indicators of habitat opportunity as weighted 

averages over the appropriate portion of the computational domain. Habitat-opportunity isolines 

were drawn for each region and month (e.g., Figure 42 shows Cathlamet Bay in May 1997). We 

also computed differences of habitat opportunity relative to selected reference months (May 

1997, July 1880, May 1880, and May 1880* with adjusted predevelopment bathymetry, [Table 

9]) and drew the resulting isolines (e.g., Figure 43). We plotted the seasonal variation of integral 

indicators of habitat opportunity (Figures 44, 45, 46, and 47), as well as the relationship of these 

indicators to river flow (Figures 48, 49, 50, and 51) to compare the responses of different regions 

and of modern and predevelopment systems. 

The results constitute a massive amount of information from simulations of habitat 

opportunity (for depth and velocity criteria), retention times, and residual velocities for various 

combinations of historical and modern bathymetry and river flow. In the following subsections 

we synthesize the results for each criterion and discuss the implications. 

Velocity criterion 

Several distinct patterns and trends emerge in the characterization of habitat opportunity 

based on the velocity criterion. Habitat opportunity correlates strongly with river flow, but the 

results are distinct for the various regions under consideration (Figure 41) and for the modern 

and predevelopment systems (Figure 48). Habitat opportunity is highest in Region 3 (Youngs 

Bay) and Region 1 (Baker Bay), the two lateral bays closest to the ocean, and tends to decrease 

in an upstream direction. Habitat opportunity is high to moderate, clearly decreasing with 

increasing river flow, in Region 4 (Cathlamet Bay) and Region 5 (Grays Bay), two lateral bays 

located upstream in the estuary. Habitat opportunity is moderate to essentially nil in Region 6 

(the upper estuary) and decreases sharply with river flow. Habitat opportunity is low in Region 2 

(the main stem of the lower estuary) and insensitive to river flow. 

99
Figure 40. Isolines of Columbia River estuarine habitat opportunity for May 1997, in hours normalized 

to a 30-day month, using depth (top), velocity (middle), and combined criteria (bottom). When 

combined, depth criterion is a stronger factor than velocity criterion, which leads to similarities in 

the patterns of the darker gray areas between depth and combined criteria in the bottom panel. 

May 1997 is online at http://www.ccalmr.ogi.edu/~ppearson/BPA5/1997-May.html. Other 

months are online at http://www.ccalmr.ogi.edu/~ppearson/BPA5/habitat.html. 

100
Figure 41. Different environments in the Columbia River estuary offer distinct habitat opportunity. In an 

attempt to capture differences in trends and patterns, the estuary was divided into the subregions 

shown for rough consistency with a prior CREDDP study. Online at http://www.ccalmr.ogi.edu/ 

bpa/habopp_synthesis.html. 

Habitat opportunity in the modern and predevelopment estuaries is not fundamentally 

different in Regions 1, 2, and 3 (Figure 49). However, in Regions 4 and 6 the predevelopment 

opportunity is significantly higher and much more resilient to increases in river flow. The 

change in Region 4 is noteworthy, given the amount of potential wetland rearing habitat 

available in that region for subyearling Chinook salmon. Changes between predevelopment and 

modern habitat opportunity with river flow were less apparent in Region 5. This difference is 

worth further investigation and may be related to a disproportionate effect of the channel 

contained within Region 5. 

Seasonal variability of habitat opportunity also is distinct from region to region. In 

Regions 4, 5, and 6, where opportunity decreases with river flow in the predevelopment and 

modern systems, freshet periods consistently provide the lowest habitat opportunity (Figure 44). 

In Regions 1, 2, and 3, freshets also offer minimum opportunity in the predevelopment system, 

but this is not the case for the modern system, where seasonal patterns are ambiguous. 

Interannual variability appears largely associated with river flow, with one notable 

exception: in Regions 1 and 3, habitat opportunity in 1997 is largely uncorrelated with that for 

1998 and 1999. For this reason modern habitat opportunity in Regions 1 and 3 shows anomalous 

scatter (Figure 49 and Figure 50). We find no explanation for this behavior, and we recommend 

101
Figure 42. Isolines of habitat opportunity in Region 4 for May 1997, in hours normalized to a 30-day 

month, using depth (top), velocity (middle), and combined criteria (bottom). The lighter shades 

in the combined criteria constitute optimum habitat relative to primary and secondary channels. 

May 1997 is online at http://www.ccalmr.ogi.edu/~ppearson/BPA5/REG4-HST1997-May.html. 

Other months are online at http://www.ccalmr.ogi.edu/~ppearson/BPA5/habitathist.html. 

102
Figure 43. Isolines made by comparing the differences in Columbia River habitat opportunity available in 

Region 4 (July minus May 1997), in hours normalized to a 30-day month, using depth (top), 

velocity (middle), and combined criteria (bottom). Darker areas are positive values (clearly 

dominant under any criteria) and represent higher opportunity in July, which has lower river 

flows. This month is online at http://www.ccalmr.ogi.edu/~ppearson/BPA5/REG4-HST 

1997-July.html. Simulations for all months listed in Table 9 and for all subregions are online at 

http://www.ccalmr.ogi.edu/~ppearson/BPA5/habitathist.html. 

103
300 

350 

400 

450 

500 

550 

600 

February April June August October December

1997 1998 1999 1880

Opportunity (hours) 

50 

100 

150 

200 

250 

February April June August October December

Opportunity (hours) 

1997 1998 1999 1880 

Figure 44. Seasonal variation of Columbia River estuarine habitat opportunity in Region 4 for velocity 

(top) and depth (bottom) criterion. Habitat opportunity is shown in hours normalized to a 30-day 

month. Habitat opportunity based on the velocity criterion shows marked minima during freshet 

season. Velocity criterion is online at http://www.ccalmr.ogi.edu/bpa/newfigures/R4velsea.gif. 

Depth criterion is online at: http://www.ccalmr.ogi.edu/bpa/newfigures/R4velsea.gif. Simulations 

for all subregions and criteria are available at http://www.ccalmr.ogi.edu/bpa/habopp_synthesis 

.html. 

104
Stream flow 

104 (m3

s-1) Opportunity (hours) Opportunity (hours) Opportunity (hours) 

Figure 45. River flow and seasonal variation of Columbia estuarine habitat opportunity in Region 4 for 

modern versus predevelopment systems (criterion from top to bottom: river flow, combined, 

velocity, and depth). Habitat opportunity is shown in hours normalized to a 30-day month. 

Habitat opportunity based on the velocity criterion but not on the depth criterion shows marked 

minima during freshet season. 

that this aspect be further investigated, because it might help explain the contrast between El 

Niño (as in 1997) and non-El Niño years. While the possibility that a numerical or processing 

artifact is biasing the results cannot be excluded, there was no evidence of such. 

Temporal shifts in freshets from June to July in the predevelopment system to May/June 

in the modern system (see the “Changes in Hydrological Conditions” section, page 47) correlate 

with shifts in the periods of minimal habitat opportunity in the middle and upper estuary, that is, 

in the subregions where the correlation of opportunity with river flow is strongest (Figure 44). 

105
Opportunity 

(hours) 

Opportunity 

(hours) 

Stream flow 

104 (m3

s-1) Opportunity (hours) 

Figure 46. River flow and seasonal variation of Columbia River estuarine habitat opportunity in Region 4 

(criterion from top to bottom: river flow, combined, depth, and velocity) for modern bathymetry 

and flows (1997–1999) and predevelopment bathymetry with 1997 flows (1880** refers to 

simulations listed in Table 9). 

Excluding local detail, habitat opportunity based on the velocity criterion appears only 

modestly sensitive to the controlled bathymetric modification introduced in Region 4 (Figure 

51). Although only indirectly, this suggests that the criterion is robust regarding one of the 

known weaknesses of the circulation model: representation of modern bathymetry in very 

shallow areas. 

Habitat opportunity is sensitive to the value chosen for the velocity criterion (Figure 52). 

The 30 and 50 cm s-1 criteria applied were within the range of literature values that Beamish 

106
Stream flow 

104 (m3 s-1)

Stream flow 

104 (m3

s-1)

Opportunity 

(hours) 

Opportunity 

(hours) 

Opportunity 

(hours) 

Figure 47. River flow and seasonal variation of Columbia River estuarine habitat opportunity in Region 4 

(criterion from top to bottom: river flow, combined, depth, and velocity) for predevelopment 

bathymetry and flows (1997–1999) and predevelopment bathymetry with 1997 flows (1880** 

refers to simulations listed in Table 9). 

107
Stream flow (m3

s-1) 

Opportunit

y (hours)

Figure 48. Columbia River estuarine habitat opportunity as a function of river flow, for the modern (top) 

and predevelopment (bottom) systems. Habitat opportunity shown in hours normalized to a 

30-day month is based on the velocity criterion. Different subregions provide distinct habitat 

opportunity and have distinctive correlations with river flow. The modern system is online at 

http://www.ccalmr.ogi.edu/bpa/newfigures/velsynthesis.gif and the predevelopment system is at 

http://www.ccalmr.ogi.edu/bpa/newfigures/velsynthold.gif. The online database contains plots 

for the depth and combined criteria at http://www.ccalmr.ogi.edu/bpa/habopp_synthesis.html. 

Stream flow (m3s-1) 

Opportunit

y (hours)

108
Opportunity 

(hours) 

Opportunity 

(hours) 

Stream flow 104 (m3s

-1) 

Figure 49. Region-by-region comparison of predevelopment and modern estuarine habitat opportunity as 

a function of river flow, for the velocity criterion. In Regions 1, 2, 3, and 5, the habitat 

opportunity is similar. In Regions 4 and 6, the differences are recognizable. The x-axis in all 

regions represents stream flow 104

(m3s

-1). 

(1978) reported for sustained swimming speeds of subyearling Chinook salmon. A limited 

analysis suggests that the alternative threshold velocities yield different absolute estimates of 

habitat opportunity under varying flow conditions. Yet the general decreasing trend in habitat 

opportunity with increasing river flows did not change with threshold velocity (Figure 52). 

Depth criterion 

Distinct patterns and trends also emerge in the characterization of habitat opportunity 

based on the depth criterion. We explored these patterns and trends in less detail than was shown 

for the velocity criterion, because the weak representation of shallow-water bathymetry in the 

modern estuary may have limited the robustness of this criterion. 

Results indicate a high degree of sensitivity of habitat opportunity to the controlled 

modification of predevelopment bathymetry in the shallowest Region 4 areas. Artificially 

deepening that bathymetry greatly increases habitat opportunity (Figure 51). The important, 

albeit indirect, implication is that modern habitat opportunity based on the depth criterion is 

substantially overestimated by our results: the model’s modern bathymetry is least accurate (and 

109
Stream flow 104 (m3

s-1)

Opportunity 

(hours)

Opportunity 

(hours) 

Figure 50. Region-by-region comparison of predevelopment and modern estuarine habitat opportunity as 

a function of river flow, for the depth criterion. Limitations in the representation of modern 

bathymetry may artificially limit opportunity in the modern system. The x axis in all regions 

represents stream flow 104

(m3s

-1). 

artificially too deep) in the shallowest areas of the estuary. While Figure 50 shows the 

comparison between habitat opportunity in the modern and predevelopment systems based on 

this criterion, overestimation of modern opportunity strongly reduces the meaning of this 

comparison. The problem is solvable by correcting the modern bathymetry and redeveloping the 

simulation database, but that is not within the scope of this study. 

Habitat opportunity in general is smaller when based on the depth criterion than on the 

velocity criterion. While the magnitude will vary, the sign of this difference appears unlikely to 

change when the modern bathymetry is corrected. 

Plots of habitat opportunity versus river flow still enable separation of the different 

regions in which the estuary was divided in clusters of similar behavior. The composition and 

behavior of each cluster, however, differ from those of the velocity criterion. In particular, all 

lateral bays show modest sensitivity to river flow when habitat opportunity is defined by the 

depth criterion. Within the lateral bays cluster, habitat opportunity decreases progressively from 

Region 3 to Region 4/Region5 and Region 1. Thus proximity to the ocean is not driving the 

differences in regional habitat opportunity based on the depth criterion. 

110
Opportunity (hours) 

 0.0 1.0 2.0 3.0 

50 

100 

150 

200 

250 

Stream flow 104 (m3s-1) 

Figure 51. Columbia River estuary habitat opportunity in Region 4 as a function of river flow for velocity 

(top left), depth (bottom), and combined criteria (top right). Habitat opportunity shown in hours 

normalized to a 30-day month is based on the velocity criterion. There are marked differences 

between habitat opportunity in the modern and predevelopment systems. Sensitivity to controlled 

changes in bathymetry is much larger for the depth criterion than for the velocity criterion. 

Habitat opportunity for the depth criterion in the modern system is overestimated by weaknesses 

in the model bathymetry. For 1880* and 1880** see simulations listed in Table 9. The plot for 

velocity is online at http://www.ccalmr.ogi.edu/bpa/newfigures/R4vel.gif; depth is at 

http://www.ccalmr.ogi.edu/bpa/newfigures/R4elv.gif; and plot for combined criteria is at 

http://www.ccalmr.ogi.edu/bpa/newfigures/R4com.gif. Similar plots for other subregions are at 

http://www.ccalmr.ogi.edu/bpa/habopp_synthesis.html. 

Combined Criteria 

As illustrated for Region 4 (Figure 51), habitat opportunity defined by conditions when 

the velocity and depth criteria are met, is more restrictive relative to estimates for each individual 

criterion. Adding more criteria would probably increase this effect. 

111 Opportunity (hours) 

0.0 1.0 2.0 3.0

Stream flow 104 (m3s-1) S 4 3 -1 tream flow 10 (m s ) 0.0 1.0 2.0 3.0 

Stream flow 104 (m3s-1) 

200

150

100

50

600 

500 

400 

300 

Opportunity (hours) 
Opportunit

y (hours)

Stream flow (m3s-1)

Figure 52. Sensitivity of habitat opportunity in modern Region 4 to the cut-off value of the velocity 

criterion (50 cm s-1 vs. the 30 cm s-1 used elsewhere in this work). Differences are significant, 

illustrating the need for integration of physically based criteria with biological data. 

Meaningful combination of criteria requires that individual error/uncertainty is 

comparable for all individual criteria. This is not the case in this investigation, where 

bathymetric error/uncertainty affects the robustness of the depth criterion results much more than 

the velocity criterion results. Thus, while Figure 51 illustrates a potential approach for 

synthesizing information by applying multiple habitat criteria, the results may not provide an 

appropriate contrast between modern and predevelopment opportunity. 

Figure 51 suggests the interesting hypothesis that the modern system may offer better 

habitat opportunity up to some critical flow range, beyond which the predevelopment system is 

superior. Before this hypothesis can be evaluated, however, a critical understanding of the true 

bathymetry in the shallow regions around the estuary’s islands must be undertaken. This is not 

within the scope of the present exercise, but it represents a future analytical need. 

Residence Times 

Residence times are important descriptors of estuarine behavior (Pilson 1985, 

Zimmerman 1988). No real consensus, however, exists on the definition of residence time, 

mostly because the definitions are operational. The operational definition of residence times for 

this study is purely hydraulic, excluding consideration of settling/erosion or self-motion of the 

particles. 

112
Sommerfield (1999) used the method proposed by Oliveira and Baptista (1997) to 

investigate residence times in the Columbia River. This method is based on time-consuming 

numerical simulations. Using preexisting numerical simulations of circulation, a large number of 

virtual particles are released inside the estuary and followed to determine the time that they take 

to leave the estuary. Information from individual particles, mapped at their starting locations, is 

then aggregated into estuary-wide isolines of residence times. Because of the previous work of 

Sommerfield (1999), and of the computation expense involved in the method, limited 

simulations of residence times were conducted (OGI 1999) for the modern estuarine bathymetry 

only. 

The results supported Sommerfield’s (1999) analysis and findings. Residence times in 

the estuary typically were short, often in the range of one to a few tidal cycles (Figures 53, 54, 

and 55). Even short residence times varied significantly in space, with the longest retention 

times for particles in shallow, constrained environments. Lateral bays are a prime example of a 

constrained environment in an estuary (Figure 53). Local freshwater inputs, which can 

significantly affect residence times in such constrained environments, are difficult to quantify 

and were not included in the simulations. 

Residence times decreased with increasing river flow, but time of release and tidal 

coefficients introduced significant variation around this trend (Figure 54). Residence times were 

dependent on the time of release of the particles within a tidal cycle. This dependency is 

complex, and the notion that residence times are smallest for particle releases during ebb can be 

misleading depending on the location in the estuary (Figure 55). Aside from lateral bays, 

residence times tended to increase with distance from the mouth of the estuary (Figure 53 and 

Figure 56). Also, a time series of residence times in the upper estuary, particularly upstream 

from Tongue Point, exhibits much stronger evidence of tidal stirring and less organized flushing 

patterns (Figure 56). 

The results just presented and in Sommerfield (1999) provide insights into patterns of 

variability of residence times in space and time that are important complements to our 

understanding of the net hydraulic transport in the Columbia River estuary. An indicator that is 

easier to calculate, however, was chosen to investigate net hydraulic transport (see the “Residual 

Velocities” subsection below), because it facilitated portrayal of the dependencies of natural 

system variability on postdevelopment changes. 

Residual Velocities 

Residual velocities are defined as the net velocity at a fixed point over a predefined time 

period that is typically a multiple of the tidal cycle. This Eulerian measurement is a complement 

and counterpart to residence times, which are inherently Lagrangian. Residual velocities 

characterize net hydraulic transport from the perspective of an observer fixed at a specific 

location, whereas residence times provide the perspective of an observer being passively 

transported by the water. Residual velocities are much faster to compute than residence times, 

given a preexisting simulation of the flow field, and results are easier to synthesize and interpret. 

We computed residual velocities as month average for modern and predevelopment 

conditions across the entire simulation database (Figure 57). Within each month, we also 

113
Figure 53. Residence times for high flow conditions (top) in June 1997 and for low flow conditions 

(bottom) in July 1997 in hours normalized to a 30-day month. Large percentages of the estuary 

have residence times of the order of one or a few tidal cycles. Lateral bays have substantially 

higher residence times than the main stem. The darker gray areas are noticeably bigger in the top 

panel, indicating residence times were lower in June 1997 than in July 1997. (Adapted from 

Sommerfield 1999.) 

computed daily averages and estimated standard deviations. Isolines of monthly residual 

velocities and standard deviations are available as are plots that depict variations in residence 

times (integrated over the entire estuary) with season and river discharge (OGI 1999). 

From estuary-wide integrated values, it becomes clear that residual velocities have 

significant seasonality, reflecting the seasonality of river flow (Figure 58). The residual 

velocities confirm analyses presented in the “Changes in Hydrological Conditions” section 

114
Residence time (hours)

Stream flow (m3s-1)

|

U 



Figure 54. Influence of river flow on residence times, at four fixed locations in the estuary. The stations 

marked with a triangle and circle are in the navigation channel (near CORIE stations red26 and 

am169, respectively), the station marked with a diamond is in the north channel (near CORIE 

station am012), and the station marked by a square is in the shallow divide between channels. 

Results show that although residence times tend to decrease with increasing river flow, the 

correlation is complex, possibly because of tides and their nonlinear interactions with local 

topography and river flow. (Adapted from Sommerfield 1999.) 

115
1 

2 

5

3 

4 

7

6

8

1 

2 5

3 4 7

6

8

Figure 55. Residence times for June 1997 at eight release times over the tidal cycle. The lighter shades 

of gray represent areas with longer residence times. (Adapted from Sommerfield 1999.) 

116
Hours 

Figure 56. Time-series of residence times (in hours) for a 5-plus-day period in June 1997 at selected 

locations in the estuary. All locations (black dot, white circle, and square) are either in the 

navigation or the north channel (bottom). With increasing distance from the mouth, there is a 

progressive evolution from a tidal-controlled, quasiperiodic pattern of short (<12.4 hour) 

residence times to a more irregular pattern of residence times of the order of multiple tidal cycles 

(top, graph is cropped at 37.2 hours). This pattern of increasing disorganization toward the upper 

estuary reflects a higher opportunity of upper estuary, longer-residence-time particles to steer 

away from the main channels, in particular during tidal reversals. Black dot, white circle, and 

square (top) correlate to the nearby lines. 

117
(page 47) that showed freshets occurred later in the predevelopment Columbia River estuary than 

in the modern system. 

Seasonal trends indicate that residual velocities tend to increase with increasing river 

flow in an approximately linear manner (Figure 59). For the same river flow, the modern system 

exhibits higher residual velocities than the predevelopment system, likely reflecting a higher 

degree of canalization (i.e., fewer buffer regions) in the modern system. This suggests that net 

hydraulic transport is less sensitive to flow changes in the predevelopment estuary than it is in 

the modern estuary. The highest residual velocities, however, corresponded to July 1880, the 

highest flow month on the simulation database. Predevelopment freshets were more effective 

flushing events than modern freshets, even if the modern system is more canalized and more 

responsive to increases in river flow. 

Estuary-wide residual velocities show little sensitivity to the controlled bathymetric 

changes introduced in the model for Region 4 (Figure 60). Local effects in the areas of 

bathymetric change are more significant, but uncertainties derived from not knowing the exact 

bathymetric configuration of the estuary in the predevelopment period appear to be a relatively 

minor concern. This finding is consistent with simulations of habitat opportunity based on the 

velocity criterion, which were similarly insensitive to bathymetric uncertainty. 

Daily variations of residual velocities (as measured by standard deviations) are 

significant: for instance, local maxima in the standard deviation of the daily residual velocities 

exceed 15 cm s-1 in May 1880 (Figure 61). These daily variations follow correlations with river 

flow (Figure 61) that are similar to the pattern described for the monthly averages: trends in the 

variability of residual velocities increase linearly with river flow, and variations tend to be 

greater in the modern than the predevelopment estuary for a particular flow condition. 

Implications for the Member/Vagrant Hypothesis 

Our results illustrate that simulation modeling can be a useful tool to evaluate effects of 

spatial processes on salmon populations that are a central tenet of the member/vagrant hypothesis 

described in the “Conceptual Framework for Evaluating Estuarine Habitat Conditions” section, 

page 21. This tool is particularly suited to the Columbia River estuary, because the established 

CORIE observation network provides a means to refine and validate the hydrodynamic model 

continually. 

Responses of the model to changing tides, river flows, and bathymetric conditions can be 

used to depict the range of alternative rearing and migration possibilities for salmon during their 

estuarine residency. Interactions among physical processes, including the basin-wide processes 

described in the “Changes in Hydrological Conditions” section, page 47, regulate estuarine 

circulation and, therefore, the distribution of physical conditions such as velocity, depth, 

temperature, etc. (Figure 62). The dynamics of these conditions, in turn, define the temporal and 

spatial sequence of habitat potentially available for salmon to express alternative rearing and 

migration behaviors. 

The simple velocity and depth criteria we used to characterize habitat opportunities for 

salmon are limited by a lack of empirical data for salmon-habitat associations within the 

118
Figure 57. Residual velocities for high flow months in the predevelopment (top) and modern (bottom) 

systems. Differences follow closely the modifications in topology of the two systems, and in 

particular in the channel layout. Predevelopment is for July 1880 and modern is for May 1997. 

Columbia River estuary. Nonetheless the model provides some useful insights into the physical 

dynamics of the estuary that may improve our ability to define the relevant constituents of 

salmon habitat. 

Our results, for example, show that the velocity response to river flow varies among 

estuarine subregions. The suitability of particular geographic features (intertidal flats, marshes, 

and shore lands, etc.) for young salmon may depend on the hydrodynamics of the larger 

subregions within which each type of habitat is embedded. Subregional characteristics thus 

define distinct changes in the habitat-opportunity landscape as salmon pass from the narrowly 

constrained tidal river through the expansive intertidal wetlands of Region 4 and into the more 

119
0 

5 

10 

15 

20 

25 

30 

35 

40 

45 

February April June August October 

Residual velocity (m3

s-1) 

1997 1998 1880

December

Figure 58. Residual velocities show marked seasonality, with highest values corresponding to freshet 

months. Freshets occurred later in the predevelopment system, a shift that is reflected in the 

residual velocities. There is a significant interannual variability (e.g., 1997 vs. 1998), with high 

flow years having larger residual velocities. All values of residual velocity shown in this figure 

are estuary wide, having been obtained by spatial integration of local values. 

saline and highly energetic estuary mouth. Other physical parameters affected by estuarine 

circulation (e.g., salinity and temperature) could be evaluated similarly through model 

simulations if appropriate habitat-opportunity criteria for subyearling salmon can be defined. 

Substantial changes in habitat dynamics could affect the expression of certain salmon 

rearing or migration behaviors associated with historic estuarine conditions. For example, 

significant changes in the timing of the spring freshet—a period of maximum velocities and 

minimum habitat opportunity—(see the “Changes in Hydrological Conditions” section, page 47) 

were reinforced by model predictions, particularly among upriver subregions that are most 

sensitive to flow variations. Thus in Region 4, minimum estuarine habitat opportunity based on 

our velocity threshold now occurs approximately one month later than during the 

predevelopment period (Figure 44). The effects of such change on salmonid life histories, 

including time and size at ocean entry, are uncertain. 

A decrease in the resilience of upper-estuarine subregions to peak flows since the 

predevelopment period (Figure 51) is consistent with the apparent canalization of the estuary, 

including loss of peripheral wetland and floodplain habitats that may have afforded important 

off-channel refugia for salmon. While flood control from mainstem dams now minimizes spring 

peak flows, increased flow sensitivity as predicted by the model could limit rearing opportunities 

for small subyearling salmon in the upper estuary. Because historic floodplain and riparian 

habitats in these regions are poorly represented in the bathymetric data available for our 

simulations, the predicted decrease in habitat opportunity may be underestimated by our model 

results. In the “Change in Juvenile Salmon Life History, Growth and Estuarine Residence” 

120
Residual velocity (m3

s-1) 

Stream flow 104 m3s-1 ( )

Figure 59. Residual velocities increase sharply with increasing river flow, with what appears to be a 

quasilinear correlation. Predevelopment and modern systems have distinguishable correlation 

fingerprints. For an equal river flow, the modern system has higher residual velocities than the 

predevelopment system, possibly because of a higher degree of canalization. Values of residual 

velocity shown in this figure are estuary wide, having been obtained by spatial integration of local 

values. Estuary-wide residual velocities show little sensitivity to controlled changes in Region 4 

bathymetry (1880 vs. 1880*; see Table 9). 

cal 

section (page 142), we will present evidence for life history change among juvenile Chinook 

salmon and assess whether changes in estuarine habitat opportunity may have contributed to 

these effects. 

section (page 142), we will present evidence for life history change among juvenile Chinook 

salmon and assess whether changes in estuarine habitat opportunity may have contributed to 

these effects. 

Conclusions 

Numerical circulation models appear to be effective tools for identifying and 

characterizing physical patterns and trends in the Columbia River, and their responses to external 

change such as river flow. Results presented in this technical memorandum are based on a 

first-generation circulation model. Based on these preliminary results, we recommend the 

following improvements to our bathymetric database, our habitat-opportunity indicators, and the 

hydrodynamic model. 

Numerical circulation models appear to be effective tools for identifying and 

characterizing physical patterns and trends in the Columbia River, and their responses to external 

change such as river flow. Results presented in this technical memorandum are based on a 

first-generation circulation model. Based on these preliminary results, we recommend the 

following improvements to our bathymetric database, our habitat-opportunity indicators, and the 

hydrodynamic model. 

121
Figure 60. Reference bathymetry (top) and corrected bathymetry (bottom) for Region 4 in the Columbia 

River estuary for May 1880. Outside the area directly affected, residual velocities show very 

little sensitivity to controlled changes in the predevelopment Region 4 bathymetry. Residual 

velocities in Region 4 show a finer structure for the modified bathymetry, consistent with its 

higher degree of resolution. Results for May 1880 are online at http://www.ccalmr.ogi.edu/ 

~ppearson/BPA/RSD1880-May.html and http://www.ccalmr.ogi.edu/~ppearson/BPA/RSD 

1880-Mayb.html, respectively. 

122
Standard deviation 

(centimeters per second)

Figure 61. Variations of daily averaged residual velocities for May 1880 in isoline form (top), and 

estuary-wide correlation of standard deviations with flow for selected modern and 

predevelopment years (bottom). Patterns and trends are similar, scale aside, to those of monthly 

averaged residual velocities. Isoline form is online at http://www.ccalmr.ogi.edu/~ppearson/ 

BPA/RSD1880-May.html, and standard deviations are at http://www.ccalmr.ogi.edu/bpa/figures/ 

Resstd.gif. 

Stream flow 104 (m3s-1)

123
Figure 62. Conceptual model of physical linkages to estuarine habitat opportunity for subyearling 

salmon. 

Representation of Modern Bathymetry, Particularly in the Shallowest Areas 

An improved base map depicting modern bathymetry is essential to establish confidence 

in the model results for shallow areas. Significant improvements could be made from existing 

survey data and aerial photography. We recommend new bank-to-bank surveys be completed, 

because important shallow areas of the estuary have not been inventoried since the late 1950s. 

We expect that a more accurate depiction of modern bathymetry, particularly in shallow areas, 

would decrease our estimates of physical habitat opportunity based on depth and the combined 

depth and velocity criteria. 

Characterizing Habitat Opportunity 

Although our criteria for physical habitat opportunity have a biological basis, they have 

not been explicitly tested in the Columbia River estuary. Our model results indicate that the 

chosen threshold values for velocity and depth affect the absolute estimates of habitat 

opportunity more than they affect the overall trends under varying flow conditions. Salinity and 

124
temperature are key physical variables that should be incorporated in future simulations to 

provide a more complete characterization of salmon habitat opportunity. 

Vertical structure and density effects also should be included in the model to improve 

representation of estuarine velocities and transport processes. A three-dimensional baroclinic 

circulation model for the Columbia River (Myers and Baptista 2000) is a major step toward 

addressing this need. The new model not only offers a more complete representation of the 

physics of estuarine circulation, but it is also significantly faster than the model used in this 

analysis. The new model will require systematic validation. 

Implications for Salmonid Rearing Habitat 

Despite the limitations, the model provides a new and powerful means to conceptualize 

habitat opportunity in the estuary and its response to physical change. In particular our results 

support the following interpretations: 

• Habitat opportunity is strongly controlled by bathymetry and, at least in the upper 

estuary, river flow (Figure 48, Regions 4, 5, and 6). We did not systematically analyze 

tidal effects, but tides are probably another important factor controlling habitat 

opportunity. 

• Physical relationships to habitat opportunity are distinct in different regions of the 

estuary. Differences appear correlated with proximity to the ocean and with the type of 

environment in each subregion (Figure 48). The estuarine subregions selected in this 

study were chosen to coincide roughly with those used in the CREDDP surveys 

(Simenstad et al. 1990b). In the future it may be useful to apply a finer definition of 

subregions based on objective criteria for bathymetry and habitat connectivity. 

• Habitat opportunity varies seasonally and is often smallest during freshets. The timing of 

minimum habitat opportunity often reflects known shifts in the timing of freshets from 

predevelopment to modern times. 

• The modern and predevelopment systems are distinctive in their morphology, residual 

circulation, and habitat opportunity. 

• While it may be useful to combine two or more criteria to depict habitat opportunity, 

meaningful interpretation of combined results requires knowledge of relative errors and 

uncertainty. This is beyond the scope of this work, but it is arguably within reach of 

available technology. 

• The velocity criterion is much less sensitive than the depth criterion to known 

weaknesses of the model in representing modern bathymetry (Figure 51). Differences in 

error and uncertainty suggest that the two criteria should not yet be combined into a 

single indicator of habitat opportunity. 

• The most biologically relevant threshold values for the depth and velocity criteria remain 

uncertain (Figure 52). In future studies, an interdisciplinary analysis of 

physical/biological relationships is needed to develop strong indicators of estuarine 

habitat opportunity. 

125
• The increased canalization of the Columbia River estuary, from predevelopment to 

modern times, is visible across all indices of net hydrodynamic transport. Particularly 

revealing are maps of spatial distribution of residual velocities (Figure 52). Moreover 

these effects may be significantly underestimated in this analysis, because historical and 

present-day floodplain, riparian, and wetland habitats are not fully represented in the 

bathymetric base maps used for our simulations. Effects of canalization may be greater if 

we also could account for widespread diking and filling of peripheral shallow-water 

habitats. 

• There is a general level of consistency across observed trends in residual velocities and in 

habitat opportunity. Correlation between indices of net hydrodynamic transport and 

indices of physical habitat opportunity were beyond the scope of the present investigation 

but should be pursued in the future. 

• The model predicts temporal and spatial changes in habitat opportunity that the 

member/vagrant hypothesis suggests could be significant to salmon diversity and 

resilience. Among these are changes in the timing and magnitude of river flows, 

increased sensitivity of upper-estuarine subregions to peak flows, and effects of increased 

canalization on estuarine velocities. Improved representation of historic and modern 

floodplain habitat in the model bathymetry is needed to better assess diking and filling 

effects on subyearling salmon with estuarine life histories. 

126
Estuarine Habitat Capacity 

Introduction 

In the previous two sections (“Changes in Hydrological Conditions,” page 47, and 

“Estuarine Habitat Opportunity,” page 89), we emphasized the potential role of spatial processes 

(Sinclair 1988) in shaping salmon population diversity and dynamics in the Columbia River 

estuary. We examined the effects of river flow, bathymetry, and other physical influences on the 

total quantity and distribution of habitats potentially available to estuarine-rearing salmonids 

(i.e., habitat opportunity). The member/vagrant hypothesis suggests that these or other 

geographic factors ultimately may determine the variety of life histories that juvenile salmon can 

express in the estuary (see the “Conceptual Framework for Evaluating Estuarine Habitat 

Conditions” section, page 21). Individuals, for example, with different sizes and times of 

estuarine entry, residency, and ocean migration may require particular suites of habitat 

appropriately arrayed in time and space to support particular rearing and migration behaviors. 

In addition to the physical and geographic processes that affect habitat opportunity, the 

member/vagrant hypothesis acknowledges that biological interactions (i.e., energetics 

processes)—competition, predation, or disease, for example—also may influence the 

performance of salmon within accessible habitats. Habitat capacity refers to various habitat 

qualities that can mediate biological interactions by regulating, for example, the composition and 

availability of prey species, the assimilation efficiency of salmon, or the ability of individuals to 

successfully elude predators. In this way salmon performance, as indicated by feeding success, 

growth, or survival, is a product of habitat opportunity and habitat capacity (Figure 63, 

[Simenstad and Cordell 2000]). 

The factors that determine habitat capacity are not always independent or mutually 

exclusive. While improved water clarity, for example, increases prey detection and the reactive 

distance for visually feeding fish such as juvenile salmon, reduced turbidity also increases the 

visibility of juvenile salmon to aquatic and aerial predators. Complex ecological changes in the 

capacity of the estuary to support salmonids thus are difficult to quantify and cannot be 

simulated as readily as the physical variables that regulate habitat opportunity, such as changes 

in water elevation or current velocity. The assumption that food or predation in the estuary 

limits juvenile salmon productivity and estuarine carrying capacity has never been rigorously 

tested. 

Furthermore, the notion of habitat capacity does not imply a single optimal condition by 

which salmon production is continually maximized. Just as salmon migrations and habitat 

opportunity vary in time and space, habitat capacity also must be understood in a broader 

landscape perspective. The structure of the habitat-capacity landscape, which establishes the 

growth and survival potential for diverse life history types and therefore the resilience of 

127
Regional 

climate 

Flow 

regulation 

Performance 

(estuarine foraging 

success, growth, 

diversity)

Population 

structure/ 

life history 

(upriver genetic, 

life history, and 

geographic 

structure) 

Habitat capacity 

(quality)

Food web

Anthropogenic 

modifications 

(diking, dredging, 

filling, etc.)

Nonindigenous 

species 

Habitat 

opportunity 

(access) 

Figure 63. Habitat capacity refers to various habitat qualities that mediate biological interactions 

(competition, predation, etc.) and, thereby, influence salmon performance within the estuary. In 

this section we include altered estuarine food webs and introductions of nonindigenous species 

among the relevant biological factors affecting habitat capacity. 

Columbia River populations, may be equally or more important than the magnitude of 

production. 

In this section, we review what is presently known about changes in the Columbia River 

estuary that could influence habitat capacity for juvenile salmon, including changes in estuarine 

food webs, introductions of nonindigenous species, and predation effects. We then examine the 

implications of these changes for the member/vagrant hypothesis (see the “Conceptual 

Framework for Evaluating Estuarine Habitat Conditions” section, page 21). 

128
Foraging Habitat and Food-web Changes 

Substantial evidence indicates that the productive capacity of the Columbia River estuary 

possibly declined during the past century. Together, habitat removal by diking and filling, 

simplification of distributary channels, changes in detrital sources, and introductions of 

nonidigenious species may have disrupted food webs and other estuarine functions that 

historically supported juvenile salmon. However, the specific effects of such changes on salmon 

performance in the estuary or on adult returns to the Columbia River basin are poorly 

understood. 

The importance of estuarine rearing to salmon recruitment has not been tested fully. In a 

study of one brood of native fall Chinook from the Sixes River in Oregon, Reimers (1973) 

demonstrated that juveniles with an extended period of estuarine rearing contributed 

disproportionately to the number of returning adults. Based on a series of experimental releases, 

however, Levings et al. (1989) found that subyearling Chinook salmon with access to the 

Campbell River estuary (i.e., released upstream or directly above the estuary) in British 

Columbia did not always (i.e., only three of four years) survive significantly better than salmon 

that were released directly offshore. The estuarine processes that may affect salmon survival are 

not well defined. Most studies have inferred that duration of estuarine residency, total growth in 

the estuary, and size at ocean entry are key determinants of salmon survival. 

Salmonid Use of Shallow Estuarine Habitats 

Ocean-type Chinook and other species and life history types (e.g., chum salmon) 

considered most estuarine dependent (see the “Conceptual Framework for Evaluating Estuarine 

Habitat Conditions,” section, page 47) rear in estuaries for up to several months. Studies in 

British Columbia and Washington estuaries have shown that subyearling salmon use 

shallow-water habitat and prey resources at least during their early stages of estuarine residency 

(Groot and Margolis 1991, Levy et al. 1979, Levy and Northcote 1981 and 1982, Healey 1982, 

and Simenstad et al. 1982). Studies in several Oregon estuaries further confirm that small, 

subyearling juvenile salmon typically occupy shallow habitats, including emergent marshes, 

forested wetlands, and peripheral floodplain channels and beaver ponds (Gray et al. 2002; Miller 

and Sadro 2003). 

Throughout their estuarine residency, juvenile salmon consume a wide variety of prey 

taxa and often are described as opportunistic feeders (Healey 1991). Yet within particular 

estuarine regions and habitats, salmon appear to feed more selectively. In oligohaline and 

brackish habitats, for example, juvenile salmon feed extensively on emergent insects 

(particularly larvae, pupae, emergent chironomid (Chironomidea), and other dipteran flies, and 

aphids (Apidae) and epibenthic crustaceans (e.g., mysids [Mysidacea], gammarid amphipods 

[Grammaridea], [Levy and Northcote 1982, Miller and Simenstad 1997, Simenstad and Cordell 

2000]). In more saline portions of the estuary, salmon often consume epibenthic crustaceans, 

including gammarid amphipods and harpacticoid copepods. 

The diet composition of juvenile salmon that move far into shallow tidal channels and 

sloughs suggests that small fry and fingerlings associate with the vegetated edges of estuarine 

wetlands (Levy and Northcote 1982, Simenstad et al. 2000b). During low tide and reduced river 

129
flows, these fish often use shallow subtidal areas, including mud and sand flats. Principal food 

items of juvenile salmon in wetlands and unvegetated shallow-water habitats are the 

tube-dwelling benthic amphipods Corophium spp. 

Information about habitat use and feeding ecology of juvenile salmon in the Columbia 

River estuary is extremely limited. Most studies on this estuary have emphasized salmon with 

stream-type (i.e., yearling smolt) life histories sampled in or near deep channels. Such large 

juveniles are less likely to rear in estuarine habitats for extended periods compared to smaller 

subyearling migrants. One analysis, for example, showed that the seaward migration rate of 

subyearling Chinook salmon decreased as individuals entered the estuary, whereas no such 

slowing of migration was shown for larger yearling Chinook (Bottom et al. 1984). 

Existing documentation of salmonid diets in the Columbia River estuary is similarly 

biased toward large, stream-type fish. However, results of the Columbia River Estuary Data 

Development Program (CREDDP) in 1980–1981 showed that subyearling and yearling Chinook 

salmon in the tidal fluvial and estuarine mixing regions of the estuary preyed extensively on 

invertebrates from shallow-water habitats (Bottom et al. 1984, McCabe et al. 1986, Bottom and 

Jones 1990). Corophium salmonis tended to be the most prominent prey item. Other important 

prey species included C. spinicorne, unidentified insects, and opossum shrimp (Neomysis 

mercedis). Planktonic organisms were not important food items except during the summer 

(August) when freshwater cladocerans (Daphnia spp.) dominated the diet of subyearling 

Chinook. 

Thus juvenile Chinook, coho, and steelhead showed no evidence of consuming 

planktonic copepods (e.g., calanoids) that are produced within the estuary. Juvenile salmon 

apparently select5 Corophium spp. and insects from shallow-water and vegetated habitats, 

respectively, during the period of peak salmonid abundance in the estuary. Salmon also are 

supported primarily by pelagic zooplankton produced upriver, particularly in the reservoirs 

behind the Columbia River dams (Sherwood et al. 1990). 

Effects of Wetland Loss 

Losses of emergent marsh and forested wetland habitats in the Columbia River estuary 

have been substantial and are likely a significant factor reducing the estuary’s opportunity and 

capacity to support juvenile salmon. Approximately 121.6 km2

 of tidal marshes (77%) and 

swamps (62%) that existed prior to 1870 have been lost. Together with a 12% loss of deepwater 

habitat, these changes reduced the estuary’s tidal prism from 12% to 20% (Thomas 1983, 

Sherwood et al. 1990). In addition, the historic surface area of the estuary has decreased by 

approximately 20% as a result of diking or filling of tidal marshes and swamps. 

The loss of estuarine wetlands not only reduced the total amount of shallow rearing 

habitat available to young salmon, but it also altered the magnitude and character of habitat 

capacity. The resulting decline in wetland primary production eliminated approximately 15,800 

metric tons of carbon per year (mt carbon year-1) or 84% of macrodetritus that historically 

 

5

 All inferences about habitat and prey utilization of juvenile salmon based on the 1980–1981 CREDDP sampling 

must be considered provisional, because that sampling design significantly underrepresented shallow-water habitats 

such as bays, emergent marshes, and forested wetlands that may be the location of considerable subyearling salmon. 

130
supported estuarine food webs. This macrodetritus originated from the vascular and macrophytic 

plants and microscopic algae historically produced within the estuary’s wetlands. However, 

these losses were accompanied by an increase of approximately 31,000 mt 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). 

Absolute changes in habitat opportunity alone should not be used to directly infer 

changes in the capacity of the estuary to support salmon. Despite considerable loss of emergent 

and forested wetlands in the estuary and associated declines in macrodetrital production, for 

example, 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 a 

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 centimeters per year (cm year-1) and 0.63 cm year-1and net volumetric increases of 

76.2 × 106

 m3 and 19.1 × 106 m3, respectively. These increases have contributed to the estuary’s 

capacity by providing some additional foraging habitat. 

Shifts in the sources and types of detritus available may have altered estuarine food webs, 

including those leading to salmon. The epibenthic-pelagic food web, for example, 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). 

Calanoid and cyclopoid copepods, however, are used by abundant forage fishes in the 

estuary, such as northern anchovy (Engraulis mordax), Pacific herring (Clupea harengus 

pallasi), and longfin smelt (Spirinchus thaleichthys). These species, in turn, often appear in the 

diets of salmon in the nearshore ocean. The survival tradeoffs between historic food webs that 

lead directly to subyearling salmon versus contemporary food webs that might enhance prey 

availability for larger outmigrants in the nearshore ocean are unknown. 

The spatial distribution of the food web also may 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 concentrated 

within the localized mid-estuary region of the ETM. 

We have no objective means to quantify the ecological effects of the habitat shift from 

emergent and forested wetlands to shallows and flats. No historic data, for example, 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 evidence that they have higher stomach fullness in the mid 

estuary compared to other estuarine regions (Bottom and Jones 1990). One possible mechanism 

for the increased feeding rates is that enhanced detrital concentrations within the ETM also may 

stimulate secondary production in adjacent midestuary shallows and flats. Yet this remains an 

untested hypothesis. However, we do know that prey production and salmon stomach fullness 

values are relatively high in protected flats compared to many estuarine habitats. Jones et al. 

(1990) found that the standing crop of benthic infauna in protected flats of the estuarine mixing 

region (≈RKm 4–RKm 11) was more than an order of magnitude higher (2.058 grams per square 

meter ash free dry weight [g m-2 AFDW]) than benthic fauna standing crop in any of the other 

131
channel or unprotected flat habitats (0.098–0.136 g m-2 AFDW) sampled within the same 

estuarine region. 

Prey Availability 

Another issue in assessing the estuary’s capacity to support juvenile salmon is variability 

in the relative production and availability of prey. Fish foraging efficiency is limited by prey 

availability and their capacity to perceive prey. Other behavioral constraints, such as innate 

responses to predation cues, can also influence prey selection (Gerking 1994). In some estuaries 

prey resource density or distribution has been shown to limit juvenile salmonid growth (Reimers 

1973). Little information is available, however, to assess the potential effects of prey resource 

variability on salmon in the Columbia River estuary. 

High turbidities in the upper and middle reaches of the Columbia River estuary may be 

an important factor in fish feeding success, although historic turbidity levels likely have 

decreased following the construction of mainstem dams and regulation of river flows (see the 

“Changes in Hydrological Conditions” subsection, page 21). Contemporary evidence of 

turbidity effects is suggested by dietary changes among juvenile salmonids sampled at Jones 

Beach before and after the 18 May 1980 eruption of Mount St. Helens. Following the eruption, 

benthic amphipods in salmonid stomachs were supplanted by insects and cladocerans (McCabe 

et al. 1981, Emmett 1982, Kirn et al. 1986) suggesting that either benthic amphipods became less 

available or were not visible during very high turbidities. The specific impacts of these 

turbidity-induced changes on salmonid growth or survival are impossible to discern after the fact. 

Given the fundamental lack of information on absolute growth and variability of juvenile 

salmon in the estuary (see the “Estuarine Growth and Residence Times” subsection, page 156), it 

is impossible to conclude whether the capacity of the Columbia River estuary to support salmon 

is limited or has significantly changed relative to historic levels. This is an important gap in our 

analysis because our conceptual approach (i.e., the member/vagrant hypothesis) implies in 

principle that spatial processes affecting habitat opportunity alone might be sufficient to explain 

variations in salmon production and diversity. 

Nonindigenous Species 

Introductions of nonindigenous species also have changed the Columbia River estuary. 

Weitkamp (1994) catalogued 16 exotic fish and four invertebrate species that have become 

established in the estuary. The unassembled list of introduced plants is undoubtedly much 

longer. While the number of nonindigenous plants, invertebrates, and fishes is expanding, the 

competitive, predatory, or other effects on juvenile salmon have not been assessed. A few 

prominent examples of introduced species with potentially important effects on estuarine and 

salmonid ecology are discussed in the following subsections. 

Asian Clam 

Evidence of introduction of the Asian clam (Corbicula fluminea) was discovered in North 

America in 1924, when empty shells were found in the Nanaimo River estuary in British 

Columbia (Britton 1979, Counts 1981, Britton and Prezant 1986). The Asian clam was first 

132
found on the banks of the Columbia River in 1938 (Burch 1944). It spread eastward into the 

lower midwestern and southeastern United States by the 1950s and appeared in Florida in the 

1960s (McMahon 1983, Counts 1986). Tourists, fishermen, bilgewater from pleasure boats, 

aquarium hobbyists, migrating waterfowl, and sand and gravel mining operations are cited as 

vectors for spreading the clam over these long distances (Heinsohn 1958, Sinclair and Isom 

1963, Abbott 1960). The economic costs of the Asian clam have been estimated at 

approximately $1 billion per year as a result of significant fouling of canals, culverts, and water 

intakes (Isom 1986, OTA 1993). 

Since its appearance in the estuary in 1938, the Asian clam has expanded its distribution, 

including documented occurrences in the lower mainstem reservoirs and in the Willamette and 

tributary basins (Wentz et al. 1998). Asian clam distribution is restricted primarily to tidal 

freshwater regions of the Columbia River estuary, but it also extends into brackish habitats. 

Relatively high biomass concentrations—from 10 to 100 metric grams of carbon per square 

meter (mg carbon m-2)—have been found in protected and unprotected tidal flats, demersal 

slopes, and marsh and main-channel habitats. Biomass estimates as high as 10,000 mg carbon 

m-2 have been measured in subsidiary channels (Holton et al. 1984, Simenstad et al. 1984). 

Despite the long history of colonization and expansion in North America, effects of the 

Asian clam on indigenous communities are poorly known (Strayer 1999). At high densities, Eng 

(1979) reported concentrations of approximately 131,000 m-2 in California canals), potential 

community-level impacts may be significant, including increased competition for space and food 

with indigenous species (Boozer and Mirkes 1979, Clarke 1986). In channel habitats of the 

Columbia River estuary, the Asian clam commonly occurs in association with important juvenile 

salmonid prey, including Corophium spp., other amphipods, and dipteran (Ceratopogonidae) 

larvae (McCabe et al. 1997, 1998). But ecological interactions among the Asian clam and 

salmonid prey species have not been investigated. 

Under extreme conditions, high densities of the Asian clam could alter estuarine trophic 

structure by filtering large volumes of water (Stites et al. 1995, Thompson et al. 2003), an effect 

that has been hypothesized for another nonindigenous clam, Potamocorbula amurensis, in San 

Francisco Bay (Carlton et al. 1990, Kimmerer et al. 1994). Cahoon and Owen (1996), however, 

suggested that their experimentally measured filtering rates of 1.12–1.78 liters per day for 

individual Asian clams were too low to control phytoplankton biomass in a North Carolina lake. 

Others (Lauritsen 1986) found that the Asian clam can have a significant effect on riverine 

phytoplankton biomass and nutrient cycling. The influences of the Asian clam in the Columbia 

River estuary are not easily predicted given differences in suspended particulate matter relative 

to other systems where filtering effects have been evaluated. 

By some measures the effects of the Asian clam may be deemed neutral or positive. For 

example, in some systems where it has been introduced, the Asian clam has become a common 

food item of fish and wildlife (Keup et al. 1963). In the Columbia River estuary, the Asian clam 

is recorded as prey for steelhead (Bottom and Jones 1990) and is a prominent food item for 

raccoon (Procyon lotor) and surf scoter (Melanitta perspicillata, [Simenstad et al. 1984]). In 

other systems, the Asian clam has been shown to have little or no effect on native species (Isom 

1974, Fuller and Imlay 1976, Klippel and Parmalee 1979, Kraemer 1979, Taylor 1980a and 

133
1980b) and may play a significant role in reducing turbidity and restoring submerged aquatic 

vegetation (Phelps 1994). 

Given the ambiguity of results, the impacts of the Asian clam population in the lower 

Columbia River and estuary on juvenile salmon cannot be predicted from studies in other 

ecosystems. Research is needed for several reasons: 

• to understand community interactions in the Columbia River among the Asian clam and 

salmonid prey species, 

• to assess whether the Asian clam filters significant proportions of the sediment particulate 

or organic matter supplied to the estuary, and 

• to assess whether the Asian clam modifies the estuary’s capacity to support native 

species, including juvenile salmon. 

Zooplankton 

An introduced calanoid copepod, Pseudodiaptomus inopinus, also an Asian species, first 

appeared in the Columbia River estuary after 1980 and has since become abundant (Cordell et al. 

1992, Cordell and Morrison 1996). These changes raise concerns about potential impacts on 

native calanoid copepods and associated estuarine food chains. Pseudodiaptomus inopinus

overlaps spatially, although not entirely temporally, with one of the most dominant ETM 

zooplankters, Eurytemora affinis. Ironically, the status of Eurytemora affinis as an indigenous 

zooplankter in the Columbia River estuary also may be in doubt (Lee 1999). 

In the Sacramento-San Joaquin Delta and San Francisco Bay, researchers hypothesize 

that Pseudodiaptomus inopinus has displaced Eurytemora affinis (Orsi 1995), but no such effects 

have been observed in the Columbia River estuary (Cordell et al. 1992, Bollens et al. 2002). 

During the 1980–1981 CREDDP surveys, calanoid copepods never were prominent in the diets 

of juvenile salmon but seasonally were the principal prey taxa among many pelagic fishes, 

including American shad, longfin smelt, surf smelt (Hypomesus pretiosus), whitebait smelt 

(Allosmerus elongatus), Pacific herring, Pacific tomcod (Microgadus proximus), threespine 

stickleback (Gasterosteus aculeatus), shiner perch (Cymatogaster aggregata), and English sole 

(Pleuronectes [Parophrys] vetulus) (Bottom and Jones 1990). 

The abundance and availability of Pseudodiaptomus inopinus and Eurytemora affinis to 

visually feeding pelagic fishes probably are tied to advective processes that transport 

concentrations of zooplankton from the ETM into surface waters. Moreover, estuarine dynamics 

supporting particle and zooplankton trapping in the ETM have likely increased with river-flow 

regulation (Jay et al. 1990), suggesting that production of this zooplankton assemblage has been 

enhanced since at least the mid-1960s, when flow regulation became coordinated throughout the 

hydropower system. However, as described in the “Effects of Wetland Loss” subsection (page 

130), salmon may derive few direct benefits from the increased pelagic production now 

concentrated in the ETM compared to the historic macrodetrital food chains that were once 

distributed throughout the lower estuary, including the extensive tidal-freshwater and brackish 

regions above the ETM. 

134
American Shad 

Among the 16 nonindigenous fishes now common in the Columbia River estuary, 

including common carp (Cyprinus carpio), banded killifish (Fundulus diaphanus), and yellow 

perch (Perca flavescens), only American shad, a clupeid from the Atlantic coast, have reached 

extraordinary abundance. Shad appeared in the Columbia as early as 1876 or 1877 after first 

being introduced into the Sacramento River, where they were planted in 1871 (Green 1874, 

Lampman 1949). In 1885 and 1886, the U.S. Fish Commission also shipped consignments of 

shad fry from the East Coast for release directly into the upper Columbia and Willamette rivers 

(Lampman 1949). 

American shad are now a dominant species in the Columbia River (Wydoski and 

Whitney 1979). Their rapid rate of population increase generally encompasses the period since 

the Columbia River dams began regulating mainstem flows, with counts of fish past Bonneville 

Dam recorded by the U.S. Army Corps of Engineers beginning in 1949 (Figure 64). Misitano 

(1977) reported only one American shad larvae among monthly ichthyoplankton samples 

collected in 1973, but adult shad passing Bonneville Dam exceeded 1 million by the mid-1980s. 

Passage of adult American shad at Bonneville reached a peak of almost 3 million in the early 

1990s, but it has declined progressively until a recent surge in 2001 (Figure 64). 

Although American shad are now a prominent member of the lower river and estuarine 

ecosystem, we do not know whether they have impacted production of indigenous species. In 

the estuary they feed primarily on cladocerans (Daphnia) and secondarily on calanoid and 

harpacticoid copepods (Corophium salmonis) and the mysid Neomysis mercedis (Bottom and 

Jones 1990), indicating some overlap with juvenile salmonid diets. Shad are prey of white 

sturgeon (Acipencer transmontanus), harbor seals (Phoca vitulina) and marine birds, such as 

Caspian terns. Whether they have contributed to population increases in piscivorous predators in 

the estuary, and thus indirectly contributed to increased predation rates on juvenile salmon, also 

is unknown. 

Few data exist to interpret the effects of any of these nonnative introductions on 

Columbia River salmon. Presumed deleterious effects on salmon are entirely speculative, 

because no documentation or experimental evidence exists to establish a potential interference 

mechanism. Despite the tremendous increases in American shad abundance, for example, we 

have no evidence for competitive interactions or other adverse effects on juvenile salmonids. 

Given the abundance of the Asian clam and American shad and the consequences of 

comparable infestations in other estuaries such as the San Francisco Bay and the Sacramento and 

San Joaquin rivers delta, it is not unreasonable to hypothesize that their feeding activities could 

significantly modify, rather than enhance, the estuarine food web. The likely introduction rate of 

nonindigenous species through vectors such as ballast water flow can only increase under the 

existing practices; the recent appearance of additional nonindigenous species, such as the shrimp 

Exopalaemon modestus (Emmett 1997), can only magnify the challenges of predicting their 

expansion and ecological influences. However, in the absence of scientific evidence of direct 

competition or resource limitation, we cannot assume a deleterious effect on juvenile salmonids. 

135
0

500,000

1,000,0001,500,0002,000,0002,500,0003,000,0003,500,000

1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005

American shad

050101520253035404550

American shad adult spring Chinook adult fall Chinook

Figure 64. Counts of adult American shad and adult spring and fall Chinook salmon at Bonneville Dam, 1975–1999 (CRD

Chronology: 1885–1886, first transplants of Atlantic shad into Columbia, Willamette, and Snake rivers; 1889, comreported in Columbia; 1956, American shad pass McNary Dam; 1995, American shad spawning up to Priest RapidColumbia River and to Lower Granite Dam on the Snake River. 

136
Predation 

Predation on juvenile salmonids in the estuary by other fishes, marine mammals, and 

birds has always been a mortality factor. In many cases predation pressures may have 

diminished with the declines of some predator populations. Studies suggest that juvenile salmon 

occur infrequently in the diets of some likely predators, such as harbor seals (WDG 1984). 

However, several predator populations have increased significantly in recent decades, including 

Caspian terns and double-crested cormorants (Phalacrocorax auritus), which have been shown 

to consume significant numbers of seaward migrating juvenile salmon. 

By 1999 more than 94,000 PIT tags had been retrieved from piscivorous bird colonies on 

artificial dredge material islands in the Columbia River estuary, representing 1.8% of the total 

number of PIT-tagged fish released since 1987 (USACE 1999, Good 2005). In 1998, PIT-tag 

codes from 15.8% of Snake River hatchery steelhead and 13.9% of Snake River wild steelhead 

that were either marked at Lower Granite Dam or detected at Bonneville Dam were recovered on 

Rice Island in the upper estuary. In the same year, tags from 2.3% and 1.3% of the hatchery and 

wild Snake River spring/summer Chinook salmon, respectively, were detected on Rice Island. In 

1999, respective detections were 10.9% and 9.4% for hatchery and wild Snake River steelhead, 

and 2.3% and 1.3% for hatchery and wild Snake River spring/summer Chinook salmon (Ryan et 

al. 2001). Because the ratio of PIT tags deposited over water and nonnesting land sites to those 

deposited on nesting sites is unknown, the actual mortality rate estimates from PIT-tag recoveries 

is uncertain. However, estimates based on consumption rates and bioenergetic needs to maintain 

Caspian tern chick growth and health leads to estimates greater than 10 million seaward 

migrating juvenile salmon consumed in the estuary (Roby et al. 1998). 

The mortality rates associated with this predation constitute a potential limiting factor on 

juvenile salmon survival in the lower river and estuary. Of interest are preliminary PIT-tag 

recoveries at Rice Island indicating that steelhead smolts were consumed in greater proportion to 

availability than other salmonid species, and that juvenile salmonids of hatchery origin were 

consumed in greater proportion to availability than wild smolts (Roby et al. 1998). 

Changes in Habitat Capacity and Implications 

 for the Member/Vagrant Hypothesis 

Our results illustrate that the habitat opportunity and capacity of the Columbia River 

estuary may have declined through reductions in the estuarine tidal prism, surface area, and the 

amount of peripheral wetland habitat. Moreover, changes in the detrital sources that support 

estuarine food webs and increased prominence of nonindigenous species have affected 

competitive and predatory interactions in the estuary with uncertain, but potentially significant, 

consequences for salmon survival. 

Yet many changes in the biological production processes of the estuary can be linked 

directly to physical causes (e.g., habitat opportunity). These results lend support to the 

member/vagrant hypothesis (see the “Conceptual Framework for Evaluating Estuarine Habitat 

Conditions” section, page 21), which emphasizes the role of spatial processes in shaping the 

dynamics and diversity of marine populations (Sinclair 1988). 

137
The apparent shift from macrodetrital to microdetrital food chains in the estuary, for 

example, 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 be a proximal factor affecting the productive capacity of the estuary, the ultimate cause is 

the physical removal of those vegetated habitats that supported macrodetrital production and 

associated epibenthic food webs. 

Other biological changes in the estuary could result from nonindigenous species filling 

open estuarine niches or from underlying shifts in the physical conditions that have allowed these 

species to thrive. The population explosion by American shad (see “American Shad” subsection, 

page 135), for example, could reflect new habitat opportunities created for pelagic-feeding fishes 

with the establishment of mainstem reservoirs, the microdetrital food web, and increased 

trapping efficiency of the ETM. Rather than a major new competitor affecting salmonid growth 

or survival, American shad abundance may be a symptom of physical habitat change. 

Intensive predation by Caspian terns, however, is a biological factor that may now 

significantly affect estuarine survival of some Columbia River salmonids. Yet one underlying 

cause for this apparent biological affect is the new physical habitat opportunity afforded to 

nesting terns when dredge-spoil islands were artificially created along the route of ocean-bound 

salmon smolts. Concentrated hatchery releases of stream-type salmonids, particularly steelhead, 

that migrate past these islands en route to the ocean possibly are another contributing factor. It 

becomes difficult if not impossible to separate physical from biological effects on juvenile 

salmon within the estuary. 

We are not arguing that all biological effects are physically driven or somehow 

unimportant to salmon survival and abundance. We find, however, that many of the significant 

biological changes we now observe in the Columbia River estuary may be explained 

substantially by physical modifications that have altered the habitat landscape to the benefit and 

detriment of different species and assemblages. Habitat capacity involves a network of natural 

and human-induced physical changes that structure the estuarine habitat landscape, and thereby 

mediate many of the biological production processes leading to salmon (Figure 65). These 

linkages have important implications for developing restoration strategies that can address the 

ultimate causes rather than the proximal symptoms of salmon decline. 

138
Bathymetry 

Transport of 

sediments and 

organic debris

Tidal regime 

River flow 

volume, 

hydro period, 

phytoplankton, 

detritus, 

zooplankton, 

fish

Structure of estuarine habitat mosaic 

Velocity 

distribution 

Salinity and 

temperature

distribution 

Water level 

fluctuation 

Turbidity 

distribution 

Sediment 

distribution 

Geomorphic 

structure & 

attributes

(e.g., LWD)

Anthropogenic 

modifications 

(diking, dredging, 

filling, etc.) 

 an

Detrital retention 

 and decomposition 

Invertebrate community structure and production 

Habitat capacity 

Introduction/ 

expansion of 

nonidigenious 

species 

Production 

 and availability

 of preferred 

prey organisms

Vegetation 

community 

structure 

and production 

Figure 65. Network of physical and biological linkages influencing estuarine habitat capacity for subyearling salmon. 

139
Conclusions 

The most significant changes to the capacity of the Columbia River estuary to support 

juvenile salmon are likely the results of habitat loss. Support of the natural, macrodetritus-based 

estuarine food web has been significantly diminished by historical diking and filling of 121.6 

km2 of emergent marsh and tidal wetland habitat. Expansion of shallows and flats throughout the 

estuary, plus a reduction in the spring-freshet energy, may have compensated to an unknown 

degree by promoting productive shallow-water habitat. Concurrent changes to the estuary, 

especially increases in the abundance of nonindigenous species and predators, also may have 

affected the estuary’s capacity to sustain juvenile salmon of diverse life history types. Yet no 

scientific evidence substantiates or refutes these speculations, and, regardless, many of these 

biological effects are also a direct expression of habitat change in the estuary. 

Given the present scientific information, we draw the following conclusions: 

• Habitat loss is well documented in the lower portion of estuary, but it is unknown for the 

tidal-fluvial region. The effects on the carrying capacity of the estuary to support salmon 

are unknown. 

• Foraging and refuge habitat for salmon has been lost, and peripheral wetlands that are 

among the most critical off-channel rearing areas may have been most impacted; 

however, because subyearling, ocean-type salmon that utilize these habitats also appear 

to have declined, the estuary’s rearing capacity presently may not be limiting. 

Nonetheless, recovery of those salmon life histories that depend on shallow-water rearing 

habitat will require restoration of peripheral estuarine wetlands. 

• Habitat loss implies qualitative change in food-web pathways since we have no evidence 

to suggest that the ETM-based food-web supplants the former macrodetritus-based food 

web. The cumulative effects of such change on juvenile salmon remain uncertain. 

• Nonindigenous species have assumed an increasingly prominent role in the estuarine 

biotic community and food web. Yet the impacts on juvenile salmon are speculative. 

Indirect effects, such as those imposed by increased filtering capacity of the Asian clam, 

may be the most identifiable impacts. 

• We have no data to evaluate potential impacts on juvenile salmon of the well-established 

Asian clam population in the lower Columbia River and estuary. Understanding the 

significance and scale of the Asian clam effects on the estuarine ecosystem will require 

scientific studies of benthic community interactions among co-occurring salmonid prey 

species (e.g., Corophium spp.) and Asian clam utilization of suspended or benthic organic 

matter, which may be a limiting resource. 

• Predation of salmon may have increased artificially, principally because of indirect 

enhancements of predator populations resulting from dredged material disposal practices 

and hatchery operations. Given that salmonids probably evolved in the presence of even 

higher predator populations than at present, it is unlikely that natural predation rates and 

temporal and spatial distributions of predators are primary limiting factors. 

140 
• A fundamental lack of information on absolute growth and variability of juvenile salmon 

in the estuary (see the “Change in Juvenile Salmon Life History, Growth, and Estuarine 

Residence” section, page 142) prevents any reliable interpretation of carrying capacity 

limitations at present or restored population levels. Precise estimates of growth are 

needed from juvenile salmon of different life history types corresponding to a range of 

residence times in the estuary. Approaches that utilize existing or new mark and 

recapture designs, as well as new techniques such as RNA/DNA analysis and the 

microstructure and microchemistry of otoliths to estimate estuarine residency, will be 

required to effectively obtain individual growth measurements. 

• The most obvious biological changes in the estuary during the past century can be linked 

to severe modifications of physical habitat, including the diking and filling of peripheral 

wetlands, channelization and loss of connection with tidal floodplains, the creation of 

slack-water reservoirs behind mainstem dams, control of river flows and estuarine 

circulation, and the creation of dredge-spoil islands in the lower river. Restoration 

strategies intended to improve the productive capacity of the estuary for salmon or other 

native species must address the underlying physical causes rather than the biological 

symptoms of such change. 

141 
Change in Juvenile Salmon Life History, 

Growth, and Estuarine Residence 

Introduction 

The conceptual framework for this evaluation assumes that salmonid diversity, resilience, 

and productivity in a river basin depend on established linkages between salmon behavior and 

habitat. Applying Sinclair’s (1988) member/vagrant hypothesis, we proposed three general 

mechanisms of change (spatial processes) in a river basin that can sever these linkages (Figure 

9): 

1) loss or degradation of physical habitat, 

2) change in the geographic structure and genetic characteristics of salmon populations, or 

3) changes in phenotypic behavior (e.g., artificial rearing or release strategies or flow 

modifications) that displace individuals from the appropriate habitat sequence in time or 

space necessary to retain membership in a population. 

In addition to these spatial processes, our conceptual framework proposed that biological 

interactions (energetic processes), such as competition or predation, also may influence salmon 

performance within the estuary. 

The previous sections provide examples of all the geographic changes that, for more than 

a century, have modified connections between salmon behavior and physical habitat in the 

estuary. Moreover significant biological changes, including altered food webs, increased 

abundance of introduced species, and expanded predator populations, have affected the quality of 

estuarine habitat for salmon (see the “Estuarine Habitat Capacity” section, page 89). Based on 

our conceptual framework, we predict that such changes should have diminished salmon 

performance (e.g., growth, foraging success, and life history diversity) in the estuary relative to 

historic conditions. 

In this section we examine historic and contemporary data for evidence of change in the 

life history and performance of juvenile salmon in the Columbia River estuary (Figure 66). We 

use historic information to reconstruct former life histories and estuarine growth of juvenile 

salmon and compare these results with contemporary data. We evaluate the adequacy of 

available evidence to infer life history change and its potential causes, including various factors 

affecting population structure upriver. We also review the implications of these findings for our 

conceptual framework. 

142 
Figure 66. Together with habitat opportunity and habitat capacity, salmon performance within the estuary is directly linked 

upriver. To the extent that hatchery releases, salmon harvest, and watershed modifications alter population structurpatterns of salmon rearing and migration in the estuary. 

Habitat 

opportunity 

(access) 

Habitat 

capacity 

(quality)

Population 

structure/ 

life history 

(upriver genetic, 

life history, and 

geographic 

structure)

Anthropogenic 

modifications 

(diking, dredging, 

filling, etc.) Regional climate Flow regulation 

Performance 

(estuarine foraging 

success, growth, 

diversity) 

Food 

web 

Nonindigenous 

species 

Salmon 

hatcheries 

Salmon 

harvest 

143 
Approach and Objectives 

All anadromous salmonids must pass through the Columbia River estuary en route to the 

ocean, and many rear there for extended periods during that transition. The patterns of estuarine 

use by Chinook salmon are an aggregate measure of the biological characteristics of all 

populations throughout the river basin and of the rearing opportunities within the estuary itself. 

Diversity of rearing behaviors may be apparent, for example, by the variation in sizes of 

individuals collected in the estuary, the times of estuarine entry, and duration of estuarine 

residency. 

We focus our analysis of life history change on Chinook salmon for biological and 

practical reasons. From a biological perspective, Chinook salmon exhibit the greatest variety of 

rearing behaviors, and they may be the most sensitive indicators of life history change in the 

Columbia River basin. Because they are the most estuarine dependent of salmonid species 

(Healey 1982), Chinook salmon offer the best example to evaluate changes in rearing conditions 

of the estuary. From a practical view, there are few data available to assess effects of estuarine 

habitat change on other salmonid species. While information about Chinook salmon in the 

estuary is sparse, for most other species, it does not exist. If the data are not sufficient to 

evaluate effects of anthropogenic changes on estuarine rearing Chinook, we will be unable to do 

so for the remaining salmonid species. 

Our analysis of Chinook salmon in this section is organized in three parts. We begin by 

reconstructing and classifying historical juvenile life histories from Rich’s (1920) survey, the 

first detailed evaluation of Chinook salmon life histories in the Columbia River basin. These 

results provide a snapshot of the diversity of juvenile life histories that existed before 

hydropower development and other activities had substantially modified the river system. We 

then reanalyze Rich’s data to describe historical residence times and size variations of Chinook 

salmon migrants upriver and in the estuary. In the third part of this section, we contrast Rich’s 

results with modern surveys of estuarine residence times and size characteristics to evaluate 

potential changes in Chinook salmon life histories. 

Data Sources and Methods for Life History Analysis 

We reviewed published and unpublished data for wild Chinook salmon in the Columbia 

River basin. The principal sources we used to evaluate past and present estuarine rearing 

patterns are described in the following subsection. 

Historical life histories and growth 

Rich (1920) investigated life histories of juvenile Chinook from 1914 to 1916. During 

this period Rich sampled juvenile Chinook salmon throughout the estuary with a 100-foot beach 

seine (1.27 cm mesh in the wings and .64 cm mesh in the pocket) and to a lesser degree, by 

“hook and line” (Figure 67). Rich did not report catch per effort, thereby limiting our ability to 

estimate abundance or determine seasonal trends. He did describe, however, fork lengths (FL) of 

juvenile fish and analyzed scale samples to determine migration patterns and growth. We further 

144 
Figure 67. The Columbia River estuary and tributaries, with sites sampled by Rich (1920), 1914–1916. 

analyzed his data to assess early life history attributes of subyearling Chinook salmon in the 

estuary, including the duration of their estuarine residency. 

Gilbert (1913) was the first to recognize the relationship between scale patterns and 

anadromous salmon rearing behavior. Gilbert (1913) noted variations in the thickness and 

bandwidth of scale circuli, which indicated changes in environmental conditions. An increase in 

growth rate was noted by a widening of the circuli bandwidth, whereas a narrowing of the bands 

formed a pronounced “check” on the scales denoting slower growth rates. Gilbert (1913) and 

Rich (1920) identified incremental increases in circuli width that coincided with successive 

periods of rearing in freshwater, estuarine, and marine environments. Similar scale methodology 

has been used more recently to interpret juvenile rearing behaviors and their contribution to adult 

Chinook salmon returns in the Rogue (Schluchter and Lichatowich 1976, 1977) and Sixes 

(Reimers 1973) rivers in Oregon. 

Rich (1920) identified and interpreted four patterns associated with check marks 

(narrowing of the circuli rings) on juvenile Chinook salmon scales based on the methods of 

Gilbert (1913): 

1) no check, 

2) a primary check, 

3) an intermediate check, or 

4) a first-year annulus. 

145 
If no check mark was observed then the juvenile had presumably reared only in its natal stream. 

A primary check formed when a juvenile migrated and reared in a river system downstream from 

its natal stream. The preceding growth was similar to the growth succeeding the check. An 

intermediate check indicated migration into the estuary and was associated with a notably higher 

growth rate compared to freshwater growth, but it was significantly less than that observed in the 

ocean (Gilbert 1913, Rich 1920; [Figure 68]). The beginning of a first-year annulus was first 

observed on scale margins of fish sampled in October and was not discernable from an 

intermediate or primary check because of the similar growth rates with the onset of winter 

(Figure 68). 

Rich (1920) mathematically correlated the sizes of juveniles at the time of sampling with 

patterns on their scales to interpret rearing behavior, which we used to classify life history 

attributes. Rich analyzed the scale patterns using direct proportionality, a method developed by 

Dahl (1911), to back-calculate the fork length for each individual fish at various life history 

events denoted by checks on the scale. In the direct proportionality method, the ratio of the 

distance between the outermost edge of the scale and a check on the scale is proportional to the 

fork length at capture and the fork length at the time of formation of the mark. Rich (1920) 

back-calculated the size at estuary entrance for juvenile Chinook based on the fork length at 

capture and the distance on the scale from the outer margin to the intermediate check. 

Rich’s (1920) back-calculations of fish size may be subject to certain limitations 

associated with the direct-proportionality method. The direct-proportionality method assumes a 

constant relationship between growth (i.e., fork length) and scale radius. This assumption, 

however, may be valid since the collection occurred within one growing season (Ricker 1992). 

The direct-proportionality method also is subject to Lee’s Phenomenon (Ricker 1992), 

whereby back-calculations from larger fish tend to overestimate the growth or provide a smaller 

than appropriate back-calculated length when the check formed. This occurs because the method 

assumes the origin of the regression line for scale radius and fish fork length is zero (Ricker 

1992), when in fact scales develop when juvenile Chinook salmon are about 30–40 mm (Rich 

1920). Thus the slope of the relationship between scale radius and fork length is less than direct 

proportionality estimates. Rich (1920) unfortunately reported his results as averages for each 

size class (5 mm), which leaves no record of variability in scale circuli counts, scale radii, or 

back-calculated fork lengths within each size class and no possibility of adjusting the 

back-calculated values. The analyses and results we present, therefore, may be mathematically 

biased, particularly for the larger juveniles. Our life history classifications and relative fish 

comparisons, however, should not be affected by the bias. 

Because Rich (1920) rarely sampled each site more than once during the three years of 

his survey, we cannot compare trends in population abundance, size, or life history 

characteristics throughout the estuary. However, he collected a consistent series of samples from 

31 March to 26 August 1916 at Point Ellice, a Washington site 19 RKm upstream (Figure 67 and 

Figure 69). These data provide a comparative time series of Chinook life history attributes 

during the summer and early fall. Rich (1920) combined two beach seine sets in May, one from 

Tenasillihee Island in Oregon, approximately 38 RKm upstream, with those from Point Ellice, 

since he observed no significant differences in scale patterns between the sites. We used Rich’s 

(1920) back-calculations of fish size to estimate the total growth from estuary entrance until their 

146 
A

B 

Figure 68. Example of subyearling Chinook salmon scale patterns analyzed by Rich (1920). Both scales 

were collected at Point Ellice on 16 October 1915. Scale on the left depicts natal stream growth 

rings, an intermediate check mark, and estuarine growth (starting at A) on the outer margin. 

Scale on the right depicts a fall migrant with riverine rearing (starting at B) and the start of winter 

band on the outer margin (reprinted from Rich 1920). 

20 40 60 80 100 120 140 160

Fork length (mm)

12 and 26 August

19 July

12-13 June

11 May

31 March-2 April

(64)

(166)

(96)

(103)

(102)

Figure 69. Range of subyearling Chinook salmon fork lengths collected by Rich (1920) at Point Ellice, 

March–August 1916 (31 March collection in Oregon included samples from Mayger, Sand 

Island, and Grims Island). Data are presented in quartiles with boxes representing 25th and 75th 

percentiles, whiskers extend to1.5 multiplied by the interquartile range, median is solid circle, all 

outliers are hollow circles, and number in collection is in parentheses. 

147 
capture at Point Ellice. We also applied a conservative estimate for estuarine growth rates of 

Chinook salmon based on literature values to estimate residence times for juveniles collected at 

Point Ellice. We also examined the size structure of the subyearling Chinook population in the 

collection. Although clearly not representative of all habitats or salmon life histories in the 

estuary, the Point Ellice results provide the only consistent data series for interpreting sizes at 

estuary entrance or growth rates of juvenile Chinook before substantial alterations occurred 

throughout the Columbia River basin and the estuary. 

Contemporary life histories and size characteristics 

We know of no contemporary estuarine surveys or scale analyses of wild Chinook 

salmon directly comparable to Rich (1920). Consequently we cannot quantitatively assess 

changes in estuarine life histories and residency of Chinook salmon since 1916. No 

contemporary growth rates for salmon exist for the Columbia River estuary. Several surveys in 

the estuary and in tributary streams allow us to qualitatively compare historical and 

contemporary life history attributes and size structure. Reimers and Loeffel (1967) reported the 

timing and duration of migration into the estuary from 11 tributaries of the lower Columbia 

River, from which we extracted examples of the diverse migration patterns of wild juveniles 

within a subbasin. McIsaac (1990) compared migration timing and adult contribution between 

wild and hatchery-reared subyearling Chinook salmon in the Lewis River in Washington. We 

further analyzed the Lewis River data to describe recent abundance patterns and timing of 

salmon migrations to the estuary. 

To compare recent size characteristics of juvenile salmon to the results of Rich (1920), 

we analyzed a variety of published and unpublished records from miscellaneous surveys 

conducted near Point Ellice. The most comparable data were from Dawley et al. (1986) and 

Dawley6, who used similar gear and sampled habitat similar to Rich during a 1966 beach-seine 

survey at Megler, approximately 1.5 RKm downstream from Point Ellice. Dawley et al. (1986) 

used a 95 m beach seine with variable mesh in the wings (1.27–1.9 cm mesh) and 0.64 cm mesh 

in the pocket. Because hatchery fish were not marked in the 1960s, we were unable to separate 

wild from hatchery subyearlings in these records. 

More recent surveys comparable to Rich (1920) were conducted as part of the CREDDP, 

a comprehensive ecological survey of the estuary below Puget Island, 75 RKm upstream. NMFS 

biologists inventoried fish assemblages monthly using a variety of gear types at 63 stations from 

January 1980 to July 1981. Analyses of salmonid catches during the NMFS surveys were 

presented in Durkin (1982), Bottom et al. (1984), and McCabe et al. (1986). We analyzed size 

characteristics of juvenile Chinook from unpublished purse seine and trawl data collected in the 

north channel (18.9–19.4 RKm) during CREDDP and additional 1980 purse-seine data collected 

at McGowan, Washington (16 RKm) and reported in Dawley et al. (1985). In contrast to the 

1966 survey data, a proportion of the fish released from Columbia River hatcheries during the 

more recent surveys were marked so that some of the hatchery fish are identifiable in the data. 

Unmarked Chinook salmon, however, represent a mixture of hatchery and wild juveniles. 

 

6

 Earl Dawley, NMFS Point Adams Field Station, Hammond, Oregon. Pers. commun., March 2000. 

148 
Most of the present-day information about the estuarine life history and movements of 

Chinook salmon is derived from migration rate and survival studies of marked hatchery fish. 

NMFS biologists have been monitoring Chinook salmon at Jones Beach from 1966 to 1972, 

1977 to 1983, and 1995 to the present (Dawley et al. 1986, Ledgerwood et al. 1997). We 

selected tag groups of hatchery fish collected during the Jones Beach surveys prior to 1983 to 

analyze population size structure, timing, and abundance of migrant hatchery Chinook salmon. 

Salmon were collected at Jones Beach primarily by beach and purse seine, with subyearling 

salmon concentrated in the beach seine collections (Dawley et al. 1986). Approximately 

2.3–6.5% of all fish recovered at Jones Beach were tagged or fin clipped. The vast majority of 

the marked fish had coded-wire tags bearing numbers unique to a particular hatchery or study. 

This marking method is used to track groups of fish but not individuals. More than 90% of these 

marked fish were hatchery-reared juveniles. The remaining unmarked fish (93.5–97.7%) were of 

either wild or hatchery origin (Dawley et al. 1986). 

Life History Reconstruction 

Our interpretation and classification of Rich’s (1920) historical survey of juvenile 

Chinook salmon and their scale patterns revealed evidence of at least five forms of ocean-type 

juveniles (Table 10) in addition to stream-type juveniles. The characteristics of each stream- and 

ocean-type life history interpreted from Rich (1920) are described in the following subsections. 

Stream-type Juveniles 

Stream-type juvenile Chinook salmon migrate to the ocean as yearlings (age 1) and were 

present in late March to early May estuary samples. Fork lengths of yearling fish ranged from 

81–125 mm. Rich (1920), however, was confident that most yearlings left the estuary for the 

ocean by June since they were absent in all subsequent samples. 

Ocean-type Juveniles 

Ocean-type juvenile Chinook salmon, which migrate to sea during their first year, vary 

considerably in their early life histories. During Rich’s (1920) surveys, ocean-type juveniles 

were substantially more abundant than stream-type juveniles in all samples where both were 

present (Figure 70). Rich grouped the juveniles according to the presence and absence of scale 

marks and discussed the mechanisms responsible for the observed differences. We further 

classified ocean-type juveniles into a series of subgroups based on their size, rearing behavior, 

and seasonal time of capture in the estuary (Table 10). Since the data from Rich are inadequate 

to conclude the time at which the juveniles entered the ocean, the following interpretations of 

ocean-type life histories are presented as hypotheses. 

Fry 

Chinook salmon fry (defined in this analysis as fish < 60 mm FL) arrived in the estuary 

over an extended period and were distributed throughout tidewater. Fry were consistently 

collected in the marine, brackish, tidal-riverine regions of the estuary from late March through 

September 1916, and in December 1915 (Figure 67, Table 11). Fry less than 50 mm FL 

comprised 25% of all the juveniles Rich (1920) sampled in the Columbia River estuary. 

149 
Table 10. Interpretation of subyearling Chinook life history from scale analyses (Rich 1920). 

Scale structure 

Life history 

type collected Rearing behavior 

Percent of

total 

No check marks Fry Short rearing period in natal stream 33 

No check marks Fingerling smolts 

and recent arrivals 

Reared in natal system. Migrated 

immediately as a fry to riverine 

system following emergence. 

28 

Primary check 

only 

Fingerling 

adfluvial rearing 

Natal-rearing as fry. 

Riverine rearing as fingerling. 

6 

Intermediate 

check only 

Fingerling 

estuarine rearing 

Began rearing in estuary as fry. 

Natal-rearing followed 

by estuarine rearing. 

25 

Primary and 

intermediate 

checks present 

Fingerling 

riverine and 

estuarine rearing 

Riverine rearing succeeded by 

estuarine rearing. Indistinguishable 

from primary and annulus 

combination if intermediate check 

formed in early winter. 

8 

0

20

40

60

80

100

120

31 March-2 April 13 April 10 May 11 May 12 and 13 June

Proportion (%)

Subyearlings

YYearling earling

Subyearling 

Figure 70. Proportion of subyearling and yearling Chinook salmon collected concurrently in 1916 (Rich 

1920). Yearling Chinook salmon did not appear in samples after May. 

150 
Table 11. Attributes of fry collected in the Columbia River estuary by Rich (1920). 

Attributes 

3 Dec 

1915 

31 Mar–

Apr 1916 

13 Apr 

1916 

10 May 

1916 

11 May 

1916 

25 May 

1916 

12–13 Jun

1916 

19 Jul 

1916 

1

Site* 5, 8, 10, 

12, 13, 14

1, 2, 9, 10 11, 12 7, 9 1, 2 4 2 2 

Brackish or tidal-riverine (TR) 

TR TR and 

brackish 

TR TR TR and 

brackish

Freshwater Brackish Brackish 

FL range (mm) 35.5 31–50 31–60 31–60 32–60 36–60 51–60 56–60 Fry less than 50 mm (%) 100 100 88 69 73 75 – – Number of fry smaller than 60 mm 

1 102 24 166 100 23 7 1 

Percentage of collection less than 60 mm 

6 100 92 76 97 96 9 2 

Number of circuli formed (fry < 60 mm) 

– 2–3 2–5 1–6 2–6 2–7 4–7 9 

Number of migrants smaller than 70 mm 

1 102 26 191 102 25 26 6 

* The site numbers correspond to the site numbers in Figure 67. 

151
Fry collected in the estuary were as small as 31 mm FL. All subyearling fish collected from 31 

March to 2 April 1916 were less than 50 mm FL range (n = 102). Most of these fish were 

collected at Sand Island (≈7 RKm) and Point Ellice (≈19 RKm). Almost half (45%) of the fry in 

this sample showed evidence of riverine or estuarine growth on their scales. Successive fry 

collections are described in Table 11. August and September samples confirmed a late fry 

migration into the estuary. Several smaller subyearlings in the 40–70 mm FL range were found 

in brackish waters at Point Ellice in mid-August and in the tidal-riverine region as late as 

September (Table 11). 

Rich (1920) contended that the recent arrivals less than 60 mm might have originated 

from stream systems with conditions that produced relatively low growth rates. Alternatively, 

the fry may have originated from upper Columbia River tributary streams that coincided with a 

later emergence time. The possibility of later emergence times was supported by more recent 

studies in the Lewis River, which provided evidence that salmon fry continued to emerge from 

the gravel for at least a 3.5-month period (April–August; [Reimers and Loeffel 1967, McIsaac 

1990]). While the number of fry arriving in the fall is extremely small, the data indicated a large 

range in the emergence times and that at least some fry arrived in the estuary late in the season. 

Fry that did not rear in the lower estuary for an extended period may have headed directly 

seaward. The presence and survival of individuals of this life history type were supported by 

typical ocean-type scales with the juveniles arriving in the ocean as small fry, which Rich and 

Holmes (1928) found among returning adults sampled in 1923–1924. 

Fingerlings 

Subyearling Chinook salmon greater than 60 mm FL (fingerlings) were present at lower 

and middle estuary sampling sites from April to December 1916. Fingerlings first appeared in 

samples collected on 13 April and 11 May in the upper estuary, although they were less abundant 

than fry. The collection of 12–13 June showed an increase in fingerling abundance in the middle 

estuary. 

There are four distinct types of fingerling life histories identified from the scale patterns 

documented by Rich (1920). 

Recent arrivals—Rich (1920) interpreted scales without checks as subyearlings that had 

recently migrated to the estuary and had not yet had an opportunity to feed after leaving their 

natal stream. Approximately 63% of the fingerlings collected had scales that did not possess 

check marks. Without specific data from Rich (1920), we must assume that the recent arrivals 

could have included smolts headed seaward and fingerlings bound for estuarine rearing habitats. 

Estuarine rearing—Fingerlings with only an intermediate scale check (14% of total 

collection) had reared for a short period in their natal stream and migrated to the estuary to rear. 

Fingerlings of this type, which were present in the estuary from June through September, arrived 

as either fry or fingerlings. For instance, subyearlings collected from June to August 1916 at 

Point Ellice ranged from 61 to 130 mm FL and, based on back-calculations from scale 

measurements, had arrived in the estuary at 38–80.5 mm FL. All subyearlings with evidence of 

estuarine growth were greater than 60 mm FL at capture and were on average larger than those 

152
lacking estuarine growth in the same collection (Table 12). The proportion of subyearlings with 

evidence of estuarine growth varied by month, but peaked at 70% in the mid-July sample. The 

fork length at arrival in the estuary was highly variable between sample sites and months. An 

unusual collection in September 1914 at Ilwaco, Washington, under a cannery yielded 

subyearlings that had entered the estuary at 70–118 mm FL. Rich (1920) found that these large 

fish fed exclusively on the discarded offal and may have delayed ocean entry due to optimum 

feeding opportunities. 

Riverine rearing—Rich (1920) defined fingerlings with only a primary scale check as 

individuals that had migrated to a lower, larger stream system (riverine system) early in their life 

history, forming the primary check. Fingerlings with only a primary check were first collected in 

the estuary in October 1914. They constituted 26% of the total 332 fingerlings collected from 

October to November 1914 and from October to December 1915. 

All subyearlings of this life history type were 95–150 mm FL. The primary check 

formed when individuals were 40.5–88 mm FL, indicating that some of the juveniles had 

migrated to a lower stream system as fry, while the others had remained to rear in the natal 

stream for an extended period prior to seaward outmigration. The amount of riverine growth was 

equal to or greater than their natal-stream growth, based on the length of the anterior scale radius. 

The lack of widening of the bands, however, precluded classification as estuarine growth. The 

primary check, therefore, indicated that the subyearlings had migrated from their natal stream to 

rear in a larger stream system before arriving in the estuary. 

Riverine rearing with an additional check mark—Fall samples (October–December 

1914 and 1915) were composed of larger subyearlings (90–205 mm FL) with two check marks 

signifying that they had reared for a short period in the riverine, and potentially, the estuarine 

environment (second mark) or formed a first-year annulus. Primary or intermediate checks that 

formed in the late fall and winter were not distinguishable from annuli. Rich (1920) classified 

the outermost check regardless of what point in the fish’s life history that the mark formed as 

intermediate, but he recognized that it may have been an annulus. These fingerlings had 

migrated to a larger stream system (forming the primary check) and had either reared in the 

estuary (forming an intermediate check) or laid down an annulus in the river or the estuary. The 

primary checks were formed at 38–88 mm FL, the majority of which were fry indicating 

formation early in their life history. The subyearlings with both scale checks averaged about the 

same fork length or were larger than the subyearlings without the second check in the same 

collection. The estimated fork length at which the intermediate check formed on all the fish was 

within the last 30 mm of total growth, which means the placement of the intermediate check was 

relatively recent and does not eliminate the possibility that it was an annulus. All intermediate 

checks formed in late fall were likely annuli so that subsequent growth on the scales represented 

second-year growth rather than estuarine growth. 

153
Table 12. Sampling effort and juvenile Chinook salmon attributes interpreted from scale patterns, 1914–1916. (The secon

page 155 is a horizontal, right-hand continuation of the first page.) 

No circ

Number Number of fish 

Type and Date Site

*

Gear type of fish ≤60 mm >60 mm 

Percent of 

sample with 

estuarine 

growth

Number 

of fish 

Perce

 of sam

Subyearling17 September 1914 1 Hook and line 35 – 35 80 7 20 24–27 October 1914 1 Beach seine 100 – 100 94 3 3 

7 November 1914 3 Hook and line 6 – 6 100 – 16 October 1915 2 Beach seine 119 – 119 24 30 25 

17 October 1915 3 Hook and line 61 – 61 70 7 11 19 November 1915 15 Beach seine 7 – 7 6 86 3–8 December 1915 5,8,10, 

12,13,14 

Beach seine 39 1 38 54 18 44 

31 March–2 April 1916 1, 2, 9, 10 Beach seine 102 102 – 102 100 13 April 1916 11,12 Beach seine 26 24 2 26 100 10 May 1916 7, 9 Beach seine 218 166 52 218 100 

11 May 1916 1, 2 Beach seine 103 100 3 103 100 

13 June 1916 4 Beach seine 36 33 3 36 100 

12–13 June 1916 2 Beach seine 96 7 89 17 80 83 

19 July 1916 2 Beach seine 166 1 165 70 50 30 

12 & 26 August 1916 2 Beach seine 64 1 63 58 27 42 

15 September 1916 Totals

9 Beach seine 69 

1,247

1 

436

68 

811

4 66 

779

96 

Yearling 31 March–2 April 1916 1, 2, 9, 10 Beach Seine 47 72 – 

13 April 1916 11, 12 Beach Seine 22 77 – 10 May 1916 9 Beach Seine 39 100 – 11 May 1916 2, 6 Beach Seine 10 100 – Subtotals 118 – Totals 1,365 779 

*

The site numbers correspond to the site numbers in Figure 67.

154
Table 12 continued. Sampling effort and juvenile Chinook salmon attributes interpreted from scale patterns, 1914–1916. (

right-hand, horizontal continuation of page 154.) 

Primary check only Estuarine growth (second year growth by October

(without estuarine growth) Primary check 

Riverine Fork length 

growth

(%) 

Number

of fish 

Number

of fish 

FL range

Range Mean Range at Range 

Riverine 

growth 

(%) 

Number 

of fish 

Percent 

of 

sample 

FL range 

at onset 

(mm) 

at onset 

Type and date (mm) (mm) (mm) onset (mm) (mm) 

Subyearling 17 September 1914 – – – – 28 – – – 101–155 123.5 70–118 15–55 24–27 October 1914 3 100 49.7 60 94 36 38–88 – 106–205 148.3 88–123 20–83 7 November 1914 – – – – 6 5 48.8 – 131–135 133 111.6 21.4 16 October 1915 60 67 47.1–88.0 40.5–60.5 29 17 43–5 – 96–135 112.1 86–118 10–30 17 October 1915 11 30 40.5–65.5 42.0–67.1 43 33 43–63 – 96–180 130.9 78–123 5–60 19 November 1915 1 14 No data No data – – – – – – 

–

– 

3–8 December 1915 – – – – 21 – – – 76–130 91.5 63–98 10–35 31 Mar–2 Apr 1916 – – – – – – – – – – 

–

– 

13 April 1916 – – – – – – – – – – 

–

– 

10 May 1916 – – – – – – – – – – 

–

– 

11 May 1916 – – – – – – – – – – 

–

– 

13 June 1916 – – – – – – – – – – 

–

– 

12–13 June 1916 – – – – 16 – – – 66–95 83 49–63 20–38 19 July 1916 – – – – 116 – – – 61–130 93.3 38–77 13–85 12 & 26 Aug 1916 – – – – 37 – – – 76–125 98.4 48–81 30–50 

15 September 1916 Totals

– 

75

– – – 3 

393

– 

91

– – 86–90 88 39–39 49–49 

Yearling 31 Mar–2 Apr 1916 – – – – 34 4 – – 86–115 96.4 70–86 19–28 13 April 1916 – – – – 17 – – – 106–110 108 87.2 20.8 10 May 1916 – – – – 39 – – – 81–125 103 53–101 22–43 

11 May 1916 – – 106–110 108 73.7 34.3 Subtotals

– 0

– 10 

100

3 7

– – 

Totals 75 493 98 

155
Historical Estuarine Residence Times and Performance 

Length Characteristics 

Rich’s (1920) series of fish collections at Point Ellice provide the best data to interpret 

historical sizes and growth of juvenile Chinook salmon within the Columbia River estuary. 

Although these results are clearly inadequate to characterize estuary-wide rearing patterns or to 

quantify absolute abundances, the results demonstrate considerable variation in juvenile size 

classes as might be expected from the diverse life histories that Rich (1920) identified based on 

scale analysis. 

Rich’s (1920) results indicated that small subyearling Chinook salmon continued to 

arrive at Point Ellice from March until August 1916, while the upper size ranges of subyearlings 

steadily increased (Figure 69). The earliest collection at Point Ellice in March and April was 

primarily fry (n = 102) that had recently emerged and migrated to the estuary. Subyearlings in 

the June and July collections were progressively larger, and the average fork length was 

significantly greater (P < 0.05) than the previous month (Table 13). The mean and median fork 

lengths, however, were essentially identical between the July and August collections (P > 0.05, 

[Table 13]), which may reflect the later influx of smaller fry and fingerlings as well as the 

continued outmigration of larger smolts to the ocean. The continuous influx of fry and 

fingerlings of relatively similar size reflects the variability in emergence timing, migration 

distances, and growth rates among individuals entering the estuary from tributaries throughout 

the basin. 

Estuarine Growth and Residence Times 

Rich’s (1920) time series of scale samples collected at Point Ellice can be used to 

estimate the growth of those subyearling Chinook that resided in the estuary for an extended 

period (e.g., showed evidence of an intermediate scale check [Table 13]). The estimates of 

estuarine growth of large juveniles collected may be overestimated because of Lee’s 

Phenomenon (Ricker 1992). The minimum and maximum ranges of values, however, represent 

a mix of size classes. 

Of the entire collection, 17% of the subyearlings had evidence of estuarine growth, which 

accounted for 29–44% of their total length at the time of capture (Figure 71). By July, 70% of 

the subyearlings exhibited estuarine growth, which contributed 20–66% of their total length 

(Figure 71). Mean estuarine growth nearly doubled from June to July but remained steady from 

July to August (Table 14). The proportion of subyearlings with estuarine growth decreased to 

58% in August and accounted for one-third to half of the total body length of these fish. 

We have no direct measurements of how long individual fish remained in the estuary. To 

approximate residence times for all subyearlings with an intermediate scale check, we applied 

literature values for growth rates to total growth in the estuary as estimated from scale analyses 

(Table 14). Healey (1980, 1991), for example, reported estuarine growth rates from 0.4 to 1.32 

mm per day. If we assume an optimistic rate of 1.5 mm per day, then the fish collected at Point 

Ellice in June that exhibited estuarine growth had remained in the estuary for an average of 18.5 

156
Table 13. Summary table of Chinook subyearlings collected at Point Ellice, May–August 1916. Fork 

length data from Rich (1920). 

Attributes 11 May 12–13 June 19 July 12 and 26 August

Mean (mm) 46.8 76.9 92.3 93.9 

Median (mm) 48 78.0 93.0 93.0 

Range (mm) 31–85 51–105 56–130 46–125 

Subyearling with intermediate check 

Average estuarine growth (mm) – 27.7 40.0 40.6 

Range of estuarine growth (mm) – 28.7–43.6 19.8–66.4 31.8–52.6 

Estimated estuarine residency 

(days) based on 

1.5 mm/day rate 

– 18.5 26.7 27.1 

Mean FL difference 

to previous sample 

(t-test, two-sided P-value) 

– P < 0.05 P < 0.05 P = 0.384 

Median FL difference 

to previous sample 

(Mann-Whitney W test, 

two-sided P-value) 

– P < 0.05 P < 0.05 P = 0.152 

days with a range of 13.0–25.6 days. The time range increased to 8–57 days by July with an 

average of 27 days. Residence time values were less variable in August (20–33 days) but still 

averaged about four weeks. 

Assuming a more conservative growth rate of 1 mm per day, estuarine residence times in 

July and August to the time of capture at Point Ellice averaged approximately 40 days (Table 

13). The largest fish at the time of collection typically had the most estuarine growth (Figure 

71). These same fish had arrived in the estuary at the smaller size classes (Figure 72). The 

estimates of growth for the larger fish may be overestimated because of limitations with the 

scale-interpretation method. Variability within each size class could not be accounted for 

because Rich (1920) presented the scale analysis as averages by 5 mm size class. 

According to the back-calculation results, spring and summer fry migrants (in contrast to 

fingerling migrants) contributed largely to the estuarine-rearing groups netted in June and July. 

While fry dominated the early spring collections, it is apparent that at least a portion remained 

and survived to rear in the estuary. 

 

157
12 and 13 June 1916 (n =16)

0

20

40

60

80

33 43 53 63 73 83 93 103 113 123 133 143

Estuarine growth (%)

Estuarine growth (%) 

Average length at collection (mm)

 19 July 1916 (n = 116)

0

20

40

60

80

33 43 53 63 73 83 93 103 113 123 133 143

verage length at collection (mm)

Average length at collection (mm)

Estuarine growth (%)

Estuarine growth (%) 

Average length at collection (mm) A

12 and 26 August 1916 (n = 37)

0

20

40

60

80

33 43 53 63 73 83 93 103 113 123 133 143

verage length at collection (mm)

Estuarine growth (%) Estuarine growth (%) 

A

Figure 71. Subyearling Chinook salmon fork length at time of collection and percent of total length 

attributed to estuarine growth. All fish collected at Point Ellice in 1916 by Rich (1920). 

Estuarine growth may be overestimated for larger juveniles in the collection.

Average length at collection (mm)

158
Table 14. Estuarine and freshwater growth rates from Pacific Northwest river systems. Rates are based 

on changes in average fork length and monitoring of marked individuals. 

Location 

Average 

growth rate Details Source 

Sacramento River delta 

(freshwater) 

0.86 mm day-1 0.57–1.23 mm day-1 

in 1980 

Kjelson et al. 1982 

0.53 mm day-1 0.40–0.69 mm day-1

in 1981 

Sacramento River bay 1.01 mm day-1 1980 Kjelson et al. 1982 

Nanaimo River estuary 1.32 mm day-1 (average) Healey 1980 

Fraser River estuary 0.56 mm day-1 1978 Levy and Northcote 

1981 

0.39 mm day-1 1979 

Coos Bay 0.29 and 0.54 

 mm day-1

1987 Fisher and Pearcy 1988

Sixes River 0.9 mm day-1 April–June Reimers 1973 

0.07 mm day-1 June–August 

0.5 mm day-1 September–November 

Nitinat estuary 

(British Columbia) 

0.62 mm day-1 Fedorenko et al. 1986 

Contemporary Estuarine Residence Times and Performance 

Patterns of Abundance 

Subyearling Chinook salmon populations in contemporary surveys exhibited a seasonal 

pattern in abundance but were present in the estuary throughout the year (Bottom et al. 1983, 

Dawley et al. 1986, McCabe et al. 1986). Peak abundance occurred from May to September, 

when the majority of the subyearlings migrated into the estuary (McCabe et al. 1986). McCabe 

et al. partitioned subyearling abundance in the estuary by regions above and below Tongue Point 

and by pelagic and intertidal habitat within each region. In the pelagic habitat of the upper 

estuary in 1980, subyearling Chinook showed a bimodal peak in abundance (May and July); 

while in the pelagic habitat in the lower estuary, subyearling abundance peaked in June. 

Abundance in the intertidal habitat peaked in June in the upper and lower estuary. In 1981, 

abundances throughout the estuary peaked in the pelagic habitat in July and in the intertidal 

habitat in June. The biomodal abundance pattern in the upper pelagic habitat may have been 

influenced by the eruption of Mount St. Helens in 1980 since that pattern did not occur in 1981. 

In the analysis of Jones Beach seine surveys from 1966 to 1972, Dawley et al. (1986) 

reported bimodal peak abundance timing from May or June and late July or early August. This 

159
12 and 13 June 1916 (n =16)

0

20

40

60

80

30 40 50 60 70 80

Estuarine growth (%) Estuarine 

growth (%)

Average length at arrival in estuary (mm) Average length at arrival in estuary (mm)

19 July 1916 (n = 116)

0

20

40

60

80

30 40 50 60 70 80

verage length at arrival in estuary (mm)

Estuarine growth (%) Estuarine 

growth (%)

AAverage length at arrival in estuary (mm) 

12 and 26 Aug 1916 (n = 37)

0

20

40

60

80

30 40 50 60 70 80

verage length at arrival in estuary (mm)

Estuarine growth (%) Estuarine 

growth (%)

Average length at arrival in estuary (mm) A

Figure 72. Subyearling Chinook salmon size at arrival in the estuary and percent of total length attributed 

to estuarine growth. All fish collected at Point Ellice in 1916 by Rich (1920). Average length at 

arrival to estuary and percent of FL attributed to estuarine growth may be overestimated for larger 

juveniles in collection. 

160
same pattern, however, was not apparent during the same surveys from 1977 to 1982, when the 

primary peak in abundance occurred in early May or early June with smaller but significant 

peaks later in the summer and fall (Dawley et al. 1986). Independent peaks in abundance at 

Jones Beach for particular populations deviated from the main peaks in the estuary. Abundance 

of wild subyearling Chinook from the Lewis River, for example, consistently peaked in August 

at Jones Beach during a study from 1977 to 1979 (McIsaac 1990). Peak catches at Jones Beach 

were primarily composed of hatchery-reared fish and were highly correlated with the timing of 

hatchery releases (Figure 73). 

McIsaac (1990) determined that peak abundance in the estuary of wild Lewis River 

juveniles reared in the hatchery were highly influenced by the date of hatchery release and did 

not necessarily track the timing of naturally reared fish (Figure 74). Hatchery-reared Chinook 

fingerlings were released between May and September during the three-year study. The arrival 

times for the first subyearlings at Jones Beach were 3–5 days following the date of release from 

the hatchery, regardless of the time of year of the release. Conversely, Lewis River wild fish 

arrived at Jones Beach in early or mid-July during the study except for 1980 migrants, which 

arrived June 1, probably because of the eruption of Mount St. Helens. The Lewis River study 

determined that the wild Lewis River juveniles contributed to a higher rate of adult returns than 

the hatchery-reared stock (McIsaac 1990). Wild subyearlings from the Lewis River have a 

unique late migratory period to the estuary compared to other lower Columbia River stocks, 

which may contribute to higher rates of return to the Lewis River (McIsaac 1990). 

Habitat Use 

The present knowledge of estuarine habitat use in the Columbia River by juvenile 

Chinook salmon is limited. The only study designed to differentiate habitat use was by 

CREDDP. However, NMFS biologists primarily surveyed sloping beaches off main channels 

(demersal slopes), peripheral bays, and open, pelagic habitats (e.g., McCabe et al. 1986). 

Because NMFS biologists infrequently surveyed small tidal channels, sloughs, or other shallow, 

off-channel habitats, fish abundance was associated with a limited number of habitat types. 

Durkin (1982) reported high concentrations of subyearlings in peripheral bays and 

shallow intertidal areas, particularly in Cathlamet Bay in 1980. The majority of these 

subyearlings originated from Washington State hatcheries and may have sought refuge in these 

shallow areas following their translocation and premature release into the lower estuary after the 

eruption of Mount St. Helens in 1980 (Durkin 1982). Fish originating from Oregon streams 

were generally collected in the nearshore habitats on the Oregon side of the river (Durkin 1982). 

McCabe et al. (1986) extended the analysis of Durkin (1982) and determined that subyearlings 

were more abundant in intertidal than in pelagic habitats, although such comparisons were 

difficult, because different gear types were used to sample each habitat type. Stomach analyses 

showed that the subyearlings were actively feeding in the estuary (Durkin 1982, McCabe et al. 

1986). Dawley et al. (1986) and McCabe et al. (1986) found that the mean sizes of subyearlings 

increased in the deeper habitats and hypothesized that as subyearlings grew, they migrated from 

neritic to deeper habitats. 

Migration routes and habitat preferences of yearling Chinook salmon have been well 

documented, particularly for hatchery fish. Rich (1920) and Dawley et al. (1986) observed that 

161
Figure 73. Timing correlation between peak abundance at Jones Beach and the arrival of hatchery-reared 

subyearling Chinook salmon. The solid black line represents fish of unknown origin (reprinted 

from Dawley et al. 1986). 

yearling migrants (wild and hatchery) found in the estuary before June were concentrated along 

the shoreline. These migrants comprised the highest catches of yearlings for Dawley et al. 

(1986). In a three-year study, hatchery-reared yearlings were radio-tagged and tracked through 

the estuary (Schreck et al. 1995, 1996, and 1997, Schreck and Stahl 1998). These fish primarily 

used deepwater channels, side channels, and, in two seasons of observation, shallow-water areas 

(<1.5m deep at high tide) of the estuary. 

 

162
15 March

14 April

14 May

13 June

13 July

12 August

11 September

11 October

10 November

Hatchery 1978

Wild 1978

Hatchery 1979

Wild 1979

Hatchery 1980

Wild 1980

Released: 

17-22 May 1978

Released: 19 July and 

5 September 1979

Released:

15 July 1980

Figure 74. Recovery timing of wild and hatchery subyearling Chinook salmon from the Lewis River at 

Jones Beach (McIsaac 1990). 

Length Characteristics 

Recent observations in the fork lengths of juvenile Chinook salmon differed from those 

described by Rich (1920). Relative to Rich’s results, contemporary surveys revealed a narrower 

range of Chinook salmon sizes and a more homogeneous distribution of size classes (Figure 75). 

The modern collections lacked smaller subyearlings during early fall (Figure 76). In addition, 

modern subyearling Chinook salmon collections had a less dramatic increase in length and an 

earlier stabilization in mean size during the juvenile rearing period compared to the 1916 

collections (Figure 69 and Figure 77). 

Contemporary size distributions of Chinook salmon during the spring and summer 

rearing periods differ from those recorded during Rich’s (1920) survey. The mean fork length of 

subyearling Chinook salmon collected by beach seine in May 1916 was 46.8 mm and steadily 

increased through July (Figure 69). Mean fork length remained the same from July to August 

(Figure 69). In contrast, subyearling fish of unknown or hatchery origin collected at Megler in 

1966 (Figure 76) and McGowan in 1980 (Figure 77), and between RKm 16 and RKm 20 in 1980 

(Figure 78) were substantially larger during the initial sampling period (mean FL > 70 mm). 

Mean fork length did not steadily increase during the spring and summer (Figures 69, 76, and 

77), although mean fork length increased by mid-August (Figures 69, 76, 77, and 78). 

163
Figure 75. Fork length characteristics of subyearling Chinook salmon collections from three studies in 

1916, 1966, and 1980 in the lower Columbia River estuary (Rich 1920, Dawley et al. 1985, 

Dawley7

). Data are presented in quartiles with boxes representing 25th and 75th percentiles, 

whiskers extend to 1.5 multiplied by interquartile range, median is solid circle, all outliers are 

hollow circles, and number in collection is in parentheses. 

Estuarine Residence 

Present-day estimates of estuarine residence times are based primarily on mark-recapture 

studies, because there no contemporary scale data are available to reconstruct life history 

characteristics and estuarine growth of Chinook salmon. Most of these studies were designed to 

estimate travel times down to the estuary and survival rates of selected groups of hatchery-reared 

fish rather than to assess estuarine residency. 

The only estimate of estuarine residency was determined from estimated travel rates of 

marked subyearling Chinook salmon released from hatcheries throughout the basin and 

recovered at Jones Beach and in the estuary plume. Dawley et al. (1986) established a migration 

rate of six days or less from Jones Beach to the river mouth as determined by the recovery of fish 

 

7

 See Footnote 6. 

20 40 60 80 100 120 140 160

Fork length (mm)

5

4

3

2

1

(164)

(334)

(69)

(609)

(429) 1916 Wild origin 

Beach seine 

1966 Wild and hatchery 

origin 

Beach seine 

1980 Hatchery origin 

Purse seine—CREDDP 

1980 Hatchery origin 

Purse seine—NMFS 

1980 Wild and hatchery 

origin 

Purse seine—NMFS 

Fork length (mm) 

164
20 40 60 80 100 120 140 160

Fork length (mm)

15 August

1 August

18 July

11 July

4 July

27 June

23 May

16 May

9 May

(53)

(199)

(25)

(33)

(75)

(27)

(54)

(75)

(59)

Figure 76. Fork length characteristics of subyearling Chinook salmon of wild and hatchery origin8

recovered in the Columbia River estuary at Megler, Washington, in 1966. Data are presented in 

quartiles with boxes representing 25th and 75th percentiles, whiskers extend to 1.5 multiplied by 

interquartile range, median is solid circle, all outliers are hollow circles, and number in collection 

is in parentheses. 

from 16 uniquely marked groups of hatchery fish. The estimate was based on the date of the first 

arrival to pass Jones Beach and the date of the first arrival recovered at Clatsop Spit. This rapid 

movement through the estuary suggests only minimal periods of estuarine rearing below Jones 

Beach for hatchery-reared subyearling Chinook salmon. This method, however, may not 

accurately represent estuarine residency, because the timing describes group movement, 

comprised of hundreds of thousands of similarly marked fish. 

There are no representative samples of an estuarine-rearing Chinook population. Dawley 

et al. (1986), however, recovered six groups of hatchery-reared fry at Jones Beach that had been 

released in six different locations in the lower Washougal River in Washington on 16–18 June 

1969. They determined that these small fry utilized the estuary for an extended period 

(approximately three months) and moved above and below Jones Beach based on repeat captures 

of individuals. The average size of these fish was larger than the remaining hatchery-reared fish 

passing Jones Beach that apparently did not use the estuary (Dawley et al. 1986). 

 

8

 See Footnote 6. 

165
20 40 60 80 100 120 140 160

Fork length (mm)

25 August

19 August

28 July

21 July

14 July

7 July

2 July

23 July

16 June

9 June

19 May

12 May

(2)

(2)

(11)

(19)

(89)

(53)

(10)

(50)

(81)

(9)

(63)

(6)

Figure 77. Fork length characteristics of subyearling Chinook salmon of hatchery origin recovered in the 

Columbia River estuary between RKm 16 and RKm 20 in 1980 by Dawley et al. (1985) and 

Dawley.9

 Data are presented in quartiles with boxes representing 25th and 75th percentiles, 

whiskers extend to 1.5 multiplied by interquartile range, median is solid circle, all outliers are 

hollow circles, and number in collection is in parentheses. 

Discussion 

Change in Estuarine Life Histories 

Chinook salmon in the Columbia River historically exhibited a diversity of life history 

strategies, using a continuum of streams, rivers, the estuary, and potentially the plume as nursery 

areas at different times of their life cycle. Anthropogenic changes to the Columbia River 

ecosystem and the salmon populations have constrained and homogenized the present-day life 

histories. This interpretation is consistent with recent reconstructions of Chinook salmon life 

histories upriver (Lichatowich and Mobrand 1995, ISG 2000, Williams in press) and by our 

comparison of past and present life histories in the estuary. Our assessment further supports the 

 

9

 See Footnote 6. 

166
20 40 60 80 100 120 140 160

Fork length (mm)

25 August

18 August

11 August

4 August

28 July

21 July

14 July

7 July

30 June

23 June

16 June

19 May

(11)

(16)

(11)

(10)

(29)

(17)

(38)

(13)

(9)

(3)

(4)

(2)

Figure 78. Fork length characteristics of subyearling Chinook salmon of unknown origin recovered in the 

Columbia River estuary at McGowan (RKm 16) in 1980 by Dawley et al. (1985). Data are 

presented in quartiles with boxes representing 25th and 75th percentiles, whiskers extend to 1.5 

multiplied by interquartile range, median is solid circle, all outliers are hollow circles, and 

number in collection is in parentheses. 

hypothesis that the simple ocean-type and stream-type dichotomy traditionally used to 

characterize Chinook salmon life histories is an oversimplification of juvenile rearing behaviors. 

The diversity of life history strategies of Chinook salmon is evident from the historical 

collections of Rich (1920). Several forms of ocean-type life histories were described based on 

fork length, time of collection, and the results of Rich’s (1920) scale analyses. Variations in 

juvenile life histories were apparent by differences in the timing and duration of rearing in natal 

stream, river, estuary, and ocean environments. Rich (1920) suggested that subyearlings that 

originated from the same tributary migrated as a group based on similarities in fork length and 

scale characteristics in each collection. Ocean-type juvenile salmon migrated to the estuary as 

fry or fingerlings. Fry continuously migrated to the estuary from early spring to August. 

Fingerlings arrived in the estuary throughout the year. Some remained for extended periods 

while others probably migrated rapidly seaward. 

Our interpretation of Rich’s (1920) collections and scale analyses suggest as many as five 

variants of ocean-type life histories, including fry migrants and four types of fingerling migrants. 

Subyearlings devoid of scale checks reared in their natal stream and migrated directly to the 

167
estuary. Fish with this scale pattern were collected throughout the sampling period. Estuarine 

rearing subyearlings possessed an intermediate check and, depending on its position, arrived in 

the estuary as fry or fingerlings. Subyearlings with only a primary check, indicating a riverine 

life history, did not appear in estuary collections until late fall. Subyearlings with primary and an 

additional outer check constituted 59% of all fish collected in the fall of 1914 and 1915. 

Depending on when in the life history the additional outermost checkmark formed, it could be 

classified as an intermediate check or an annulus (Rich 1920). 

Rich (1920) discussed in detail the ambiguity surrounding the interpretation of the annual 

and intermediate checks. Based on the fork-length ranges and approximate timing at which the 

outermost check mark may have occurred, we cannot rule out that a component of subyearling 

Chinook with a riverine and an additional check mark had reared for a time in the estuary. 

The uniform sizes of subyearling Chinook salmon in modern collections may reflect the 

influence of hatchery production on size characteristics or a reduced abundance in diversity of 

wild fish entering the estuary from upriver or both. This homogeneity of size characteristics is 

clear when comparing estuary collections from 1916 to 1966 and 1980 (Figure 75). Differences 

in gear type (purse or beach seine) or year of sampling (1966 and 1980) do not explain apparent 

changes in juvenile size distribution in the estuary. 

While deepwater gear (purse seine and trawl nets) may have been biased for larger fish, 

we think the size structure of the subyearlings has been truncated and that these changes cannot 

be explained solely by gear selectivity. Dawley et al. (1986) determined that the purse seine 

satisfactorily sampled subyearlings as small as 60 mm FL. McCabe et al. (1986) stated that 

small subyearlings were collected in purse seines and large subyearlings were captured in beach 

seines early in the summer. 

McCabe et al. (1986) found the opposite was true later in the summer when small 

subyearlings dominated the beach seine collections and large subyearlings were predominately 

collected in purse seines. These patterns suggest a shift in habitat use among juvenile salmon of 

various sizes, which may explain some of the differences in salmon size characteristics among 

gear types and habitats. Such differences do not exclude the possibility that small subyearlings 

(<60 mm) may be collected by either gear type. 

Hatchery-released fish probably had little influence on the size distribution of Chinook in 

Rich’s (1920) samples. Although it is possible that Rich (1920) collected some hatchery fish, he 

was confident that all of the subyearlings sampled in the estuary were of wild origin. Hatchery 

practices in Oregon shifted in 1910 from releasing unfed fry to feeding fry in runway ponds and 

releasing juveniles as larger fingerlings. In 1916, hatcheries released approximately 95 million 

fry and fingerlings (Lichatowich et al. 1996). Bonneville Hatchery, the largest production 

facility at that time, released fingerling Chinook salmon from April to September (Wallis 1964). 

The fry that Rich (1920) recovered in March, therefore, were probably wild fish. Rich 

(1920) contrasted scales of fry collected in the estuary in 31 March and 1–2 April with those 

from fry sampled at the Clackamas Hatchery in Oregon on 11 April. While all hatchery fry had 

well-developed scales, many of the wild juveniles did not. Hatchery fry were somewhat larger 

than wild fry, 36–65 mm FL (n = 62) versus 31–50 mm FL (n = 102), respectively. 

168
The Columbia River estuary may provide critical rearing opportunities and refuge for 

juveniles prior to ocean migration. Subyearlings in Canadian and the Puget Sound river systems 

enter the ocean at relatively small sizes (maximum 70 mm FL) and may use the sheltered marine 

transition areas in the Strait of Georgia and Puget Sound, respectively, as refugia before 

migrating to the open ocean (Healey 1980, Levy and Northcote 1982, Simenstad et al. 1982, 

Levings et al. 1986). Because the Columbia River lacks a protected marine embayment, there 

may be advantages for subyearling Chinook salmon to rear for an extended period and grow to 

relatively large sizes before leaving the estuary. 

Studies in other Oregon rivers suggest that subyearling Chinook salmon may need to 

migrate at relatively large sizes (100 mm or greater) to have a high probability of surviving in the 

ocean. Limited data reported for a variety of subyearling Chinook salmon in estuaries reveal 

maximum lengths in the estuary ranging from 80 mm to about 148 mm (Reimers 1973, 

Schluchter and Lichatowich 1977, Kjelson et al. 1982, Myers and Horton 1982, Levings et al. 

1986, Fisher and Pearcy 1988, Wallace and Collins 1997, MacFarlane and Norton 2002). These 

results further support the concept that estuaries are important rearing grounds for subyearling 

migrants, particularly along the open Oregon and California coasts, where no alternative marine 

transition areas are available to salmon during their seaward migration. 

Although larger sizes at migration may often favor ocean survival, the persistence of 

smaller fry and subyearling life history types among Oregon populations suggests that there is no 

single threshold size or time that Chinook salmon must migrate to return successfully as adults 

(Nicholas and Hankin 1988). The wide diversity of historical times and sizes of migration 

through the Columbia River estuary may have evolved to accommodate a considerable range of 

oceanographic, estuarine, and riverine conditions. Rich’s (1920) scale analyses indicate that 

juvenile Chinook that reared in the estuary spent at least one week to a few months in the 

estuary. 

Rich and Holmes (1928) examined adult scales and determined that Columbia River 

juvenile salmon migrated to the ocean as a continuum between ocean-type and stream-type life 

histories with the whole range of life histories contributing to returning adults. Ocean-type fry 

and stream-type juveniles were present but minor relative to other (subyearling) life histories. 

Diversity in residence times, migration times, and size at ocean entry suggests a strategy for 

maintaining flexibility within and among salmon populations in an unpredictable ocean (Spence 

1995) even though larger sizes or later migration periods or both may be advantageous under 

some environmental conditions (Reimers 1973). 

Estuarine residence times inferred from Rich (1920) concur with estimates for the Fraser, 

Nanaimo, Sixes, and Rogue rivers but differ markedly from more recent estimates in the 

Columbia River. Many estuarine studies in the region report Chinook rearing in estuaries for 

several weeks to two months (Healey 1980, Levings et al. 1986, Nicholas and Hankin 1988, 

Reimers 1973). In contrast, contemporary estimates of residency for subyearlings in the 

Columbia River estuary were about a week for 16 groups of marked hatchery fish migrating past 

Jones Beach and recovered in the lower estuary (below 18 RKm [Dawley et al. 1986]), except 

for Washougal River hatchery juveniles that reared for approximately three months in the estuary 

after being released early at a very small size. 

169
Because individual fish were not monitored and only a small number of fish from each 

marked group were recaptured in the lower estuary, we cannot be certain whether the estimated 

residence times are characteristic of most contemporary populations. Residence times were 

derived from the first fish from each tagged group captured at Jones Beach and at the estuary 

mouth and, therefore, do not characterize the range of estuarine residence times. Dawley et al. 

(1986) concluded that the majority of fall Chinook salmon fingerlings remain in the estuary for a 

relatively short period. If this is correct, then the residency of most ocean-type Chinook salmon 

has declined relative to the historical estimates reported by Rich (1920). 

Our interpretations of past and present juvenile life histories for Chinook salmon are 

clearly limited by the lack of basic biological surveys in the Columbia River estuary. The range 

of life history types, estuarine-residence times, and growth estimates are based upon a 

comparison of three years of data (1916, 1966, and 1980) at a single site in the lower estuary. 

These data are not sufficiently comprehensive to depict the former or present diversity of salmon 

found among the full variety of habitats throughout the estuary or to describe variability in 

rearing behaviors over a time period. Without independent surveys or methods to validate 

Rich’s (1920) results, scale analyses from 1914 to 1916 could be subject to unknown errors or 

misinterpretations. The inability to distinguish an annulus from an intermediate check prevents 

precise classification of some life history types. But the effect of most past or present data 

limitations would seem to underestimate rather than overestimate the diversity of rearing 

behaviors in the basin. 

The lack of research on subyearlings in shallow estuarine habitats, particularly tidal 

channels, sloughs, and marshes, also may limit understanding of life history diversity as well as 

the rearing requirements of Columbia River Chinook salmon. These shallow habitats, which are 

heavily used by subyearling salmon in other Northwest estuaries, may be particularly important 

off-channel refugia in a high energy, river-dominated system such as the Columbia (Healey 

1982, Levy and Northcote 1982). While limited sampling has occurred in the lower Columbia 

River estuary (below 75 RKm), the upper estuary (above 75 RKm) has not been studied. A 

variety of sloughs and side channels in the upper estuary offers potential refugia and rearing 

habitat for downstream migrants. 

Modern methodologies used to monitor groups of salmon as they pass through the 

Columbia River estuary do not differentiate among various life history types. Because of the 

difficulty of estuarine recovery of marked salmon, residency estimates have been based on a very 

small proportion (<6%) of the marked population (Dawley et al. 1986). Such estimates are 

derived primarily from hatchery-reared fish, which constitute more than 95% of the marked 

population and are biased toward larger fish that can retain tags (Dawley et al. 1986). 

Contemporary estuarine peaks in salmon abundance have been associated with the timing of 

hatchery releases (Dawley et al. 1986). Hatchery influence on patterns of salmon abundance 

may help to explain the relative uniformity of juvenile size classes because of the release of large 

groups of similarly sized subyearling or yearling Chinook. Reported size distributions, however, 

may underestimate present-day diversity in the estuary because of the limited sampling and 

recovery design, which targets groups of marked hatchery fish and ignores smaller subyearlings 

and the shallow-water habitats they may prefer. 

170
While basic data on the life history of wild Chinook salmon was available in the early 

1900s, the lack of scale collections and pertinent data in recent years prevents us from similarly 

classifying the juvenile life histories of contemporary salmon populations. We have found a 

limited scale archive for estuary samples of coho and yearling Chinook salmon only, and these 

have yet to be interpreted. Interpretation of the coho salmon scales may be particularly useful 

given the multiple life histories of juvenile coho salmon described in the South Slough National 

Estuarine Research Reserve in Oregon and in several other coastal estuaries (McMahon and 

Holtby 1992, Miller and Simenstad 1997, Miller and Sadro 2003). 

The diversity of Chinook salmon life histories we described from historical Columbia 

River data is consistent with the variety of life histories reported in other Northwest estuaries. 

The Rogue and Sixes rivers estuaries, two small systems on the southern Oregon coast, had a 

similar or greater number of early life history types than those documented in the Columbia 

River (Schlucter and Lichatowich 1976, Reimers 1973). Healey (1980) and Carl and Healey 

(1984) described at least three genetically distinct life history types in addition to various times 

of migration for Chinook salmon in the Nanaimo River basin on Vancouver Island, British 

Columbia. 

In the “Conceptual Framework for Evaluating Habitat Conditions” section (page 21), 

three generalized life history strategies (Figure 11) were proposed for Chinook salmon in the 

Columbia River basin. These strategies were distinguished by length of time spent in each 

freshwater environment, time spent in the estuary, and time and size at ocean entrance. From the 

analysis of Rich’s (1920) data, this simple model was expanded to recognize six life history 

types in the Columbia River, including five variants of subyearling life history (Figure 79). 

Based on Rich’s results and the extent of freshwater habitat available before most 

Columbia River dams were constructed, we hypothesize that one or more Chinook life history 

types historically used natal streams, mainstem rivers, or estuarine environments as alternative 

nursery habitats, with each brood of Columbia River salmon represented by a continuum of 

rearing and migrant behaviors spanning an 18-month period (Figure 79). By contrast, we infer 

that ocean-type Chinook salmon with estuarine rearing life histories are now substantially 

reduced in importance, leaving three principal life history types in the basin: 

1) fry migrants, 

2) subyearling migrants that rear in natal streams (including hatchery-reared juveniles), or 

main rivers or both, and 

3) yearling migrants (Figure 79). 

Historical and Contemporary Factors Affecting Salmonid Life Histories 

The watershed, estuary, and salmon populations have undergone significant changes in 

the 85 years since Rich’s (1920) study. Many changes, however, already had occurred prior to 

1916: 

• commercial harvest of salmon reduced spring and summer Chinook runs to remnant 

levels, 

171
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

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

b

Relative abundance Relative abundance 

Figure 79. Historical and contemporary early life history types for one broodyear of Chinook salmon in 

the Columbia River estuary. Historical timing and relative abundance (top) based on historical 

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

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

smoothed for appearance. 

172
• migrant juveniles suffered massive losses to irrigation diversions, timber harvest, and 

related activities such as roads and splash dams that impacted watersheds and stream 

channels, 

• large-scale mining was active in many watersheds, and 

• sheep and cattle grazing were extensive (Lichatowich and Mobrand 1995, Lichatowich 

et al. 1996). 

The results interpreted from Rich’s (1920) study, therefore, may not accurately reflect the full 

diversity of life histories that existed prior to European settlement in the region. 

The apparent increased proportions of larger subyearlings with short estuarine residence 

times is consistent with the life history response we might expect from the changes that have 

affected the Columbia Basin and salmon populations since Rich’s survey. As suggested by our 

conceptual model (Figure 9) and supported by our assessment of estuarine changes in the 

previous four sections, factors reducing diversity of estuarine rearing behaviors may include: 

• the quantity and quality of salmon habitat, both in the estuary and upriver, 

• reduced genetic diversity through harvest pressures, population extinctions, and other 

causes, and 

• the effects of hatchery rearing, release, and fish transportation practices on salmon size 

distributions and phenotypic behaviors. 

Although we cannot distinguish their individual contributions to life history change or salmon 

decline, the historical factors discussed in the following subsections together may largely 

determine the present-day performance of Chinook salmon in the estuary. 

Salmon harvest 

Effects of commercial harvest on particular components of the total Columbia River 

production of Chinook salmon were realized well before the start of the 20th century. 

Commercial harvest of adult salmon runs began in the early 1800s (Figure 80), when salmon 

were so abundant that it was hard to imagine that there would not be enough for everyone (Hume 

1893). Commercial fishermen initially targeted spring-run Chinook adults, the superior canning 

variety (Lichatowich et al. 1996). Harvest pressure intensified in the 1860s. 

As the number of the spring-run adults diminished, commercial fishermen shifted to 

fall-run Chinook in 1890. Concurrently a significant reduction in the number of adults returning 

to spawn became apparent in 1890 in the Snake River basin (Evermann 1895). A one-month 

delay in the spawning time of mainstem Snake River fall-run adults also was observed 

consistently for several years (Evermann 1895). Evermann noted that the adult runs passing over 

Lower Salmon Falls Dam on the Snake River, which usually arrived in late July and early 

August, did not arrive until early September. Adult runs in the Payette and Salmon rivers in 

Idaho completed the upriver migration at least one month earlier than the Snake River run and in 

173
Salmon 

harvest 

began 

(1820)

Cannery and 

intensive 

fisheries 

(1866)

Harvest 

peak (1883)

Marked 

decline 

(1911)

1800 1820 1840 1860 1880 1900 1920 1940

Fall Chinook 

harvest 

began 

(1890)

Fall Chinook 

50% of 

cannery 

harvest 

(1920)

95% of 

cannery 

harvest 

(1892)

75% of 

cannery 

harvest 

(1912)

Spring and summer 

Sustained Fishery ( 1880 - 1920 )

Figure 80. Harvest timeline for Chinook salmon, 1800–1916 based on significant events presented by 

Oregon State Board of Fish Commissioners (OSBFC 1890 and 1892), Hume (1893), Craig and 

Hacker (1940), Fulton (1970), Beiningen (1976), Smith and Wahle (1981), and Lichatowich and 

Mobrand (1995). 

slightly higher numbers compared to other years. Fishing pressure was potentially affecting 

specific components of the Chinook salmon run in addition to the natural variability associated 

with populations. 

The temporal and spatial differentiation of the adult runs increased the vulnerability of 

each subbasin population to fishing pressure, which has further compounded their natural 

volatility. Rich and Holmes (1928) commented repeatedly that fishery managers must regulate 

harvest of the entire adult run and not target discrete segments to minimize the impact on any 

single population. The shift in harvest from spring- to fall-run stocks in the late 1800s could 

have redirected the fisheries impact onto the mainstem Snake River adult run while allowing the 

Payette and Salmon rivers adult runs to recover. By 1938, Rich (1943) reiterated his support of 

ecosystem-based harvest regulations after completing fish counts and noting the greater 

abundance of fall-run adults, which had recently received protection by the closure of the lower 

river fall-run fishery starting on 25 August 1938. The effects of the harvest pressure were 

obvious from the fish counts going over Bonneville Dam, since harvest was shifted back to 

spring-run Chinook salmon, and their abundance fell accordingly. 

One effect of harvest and other intensive selection pressures in the Columbia Basin may 

have been the development of a lesser number of relatively discrete salmon runs. Chinook 

salmon in the Columbia historically may have been composed of a broad continuum of spawning 

populations distributed across the entire habitat spectrum (Miller and Brannon 1981, Beaty 

1992). Multiple changes during the past century, including the effects of intensive fisheries, may 

have selectively eliminated components of this continuum while promoting others. 

174
Thompson (1951) suggested that the upriver bright stock, a distinct group of fall Chinook 

salmon that spawns in late August to September, may have developed from the late tail of the 

summer run, which was protected by a long-term fishery closure. Rapid growth of Columbia 

River brights may have been aided by additional habitat opportunities created by heavy 

exploitation on other stocks (Beaty 1992). Today a majority of the fall Chinook salmon run still 

passes Bonneville Dam during late summer (Figure 81). 

Because the early life history strategies of Chinook salmon are directly linked to the 

seasonal timing of the adult runs, changes in spawning populations during the past 80 years may 

have directly affected patterns of estuarine rearing. Rich (1925) analyzed scales from returning 

adults in the Columbia River and determined that the majority of the spring-run adults had 

stream-type life histories and the fall-run adults were dominated by ocean-type life histories. 

However, both types were present from May to September (Figure 82). Summer-run adults 

exhibited both life history types depending upon where in the basin the juveniles originated. 

Snake River basin summer-run adults typically are stream-type migrants, while mid-Columbia 

River summer-run adults (i.e., Hanford Reach spawners) are ocean-type juveniles. 

Fisheries that inadvertently targeted specific populations of returning adults reduced the 

production of the juvenile life histories associated with those populations. By decreasing the 

abundance of wild populations and replacing a broad continuum of spawning populations with a 

few discrete stocks, harvest and other selective pressures have diminished life history diversity in 

the Columbia River basin, including some subyearling life history types that may have used the 

estuary. 

Habitat loss 

Habitat degradation and its adverse effects on salmon were noted as early as 1894, when 

mining in the Snake River watershed destroyed Chinook salmon spawning beds and contributed 

to the collapse of a popular American Indian fishing site (Evermann 1895). Habitat loss and 

degradation has been and continues to be a major influence on the abundance and diversity of 

salmon in the Columbia River (Nehlsen 1995, Lichatowich et al. 1996, Lichatowich 1999). 

Chinook salmon populations from the upper Columbia River basin in British Columbia and 

Alberta, Canada; middle Snake River basin and above, and the greater part of the Deschutes 

River basin in Oregon have been extinct for at least 40 years because of impassable dams (Figure 

2). The blocking of upstream passage reduced basin-wide productivity and diversity of salmon. 

In the Snake River, ocean-type Chinook salmon now occupy only 17% of the historical 

habitat (Hassemer et al. 1997). The Deschutes River basin, now inaccessible above 161 RKm, 

encompassed a highly connected cold-water tributary system (Metolius River), an extremely 

large warm-water tributary system (Crooked River), and a mainstem system. It may have been 

one of the greatest contributors to Chinook salmon production in the Columbia River and 

probably included a wide variety of life history types associated with the diverse freshwater 

habitats (Burke et al. in prep.). 

175
Figure 81. The effect of seasonal protection of salmon runs in the Columbia River. Adult run timing 

(top) reconstructed from historical gill-net records for 1876 and adult escapement at Bonneville 

Dam, 1981–1990. Seasonal protection (bottom) of salmon runs, 1877–1963 (reprinted with 

permission from Beaty 1992). 

Loss and degradation of habitat throughout the Columbia River basin has reduced its 

productive potential and concentrated the remaining salmon into more limited and highly 

fragmented regions. Dam construction, together with temperature increases in the main stem and 

in lower subbasins, have diminished habitat opportunity upriver and substantially reduced the 

proportion of ocean-type migrants that are now produced in the Columbia (ISG 2000, Williams 

in press). 

Loss of subyearling migrant types from summer and spring spawners probably has 

occurred in many upriver areas that historically offered optimal growth opportunity, particularly 

in the warmer middle portions of Columbia subbasins (Lichatowich and Mobrand 1995, ISG 

2000, Williams in press). Because subyearling migrants typically reside in the estuary for longer 

periods and use different habitats than those with yearling life histories, such losses could have 

176
0%

20%

40%

60%

80%

100%

10 May

13 May

16 May

17 May

27 May

30 May

10 June

16 June

17 June

24 June

03 July

07 July

16 July

28 July

05 August

06 August

22 August

12 September

Ocean-type

0%

20%

40%

60%

80%

100%

Stream-type

Ocean-type

Stream-type

Figure 82. Interpretation of early life history behavior based on scale patterns from returning salmon 

adults collected in the Columbia River estuary, 10 May–12 September 1919 (Rich 1925). Sample 

dates are not equal time intervals. 

an important influence on contemporary patterns of estuarine rearing by Chinook salmon and 

could leave vacant various shallow-water estuarine habitats favored by smaller ocean-type 

juveniles. 

Habitat changes within the estuary (see the “Estuarine Habitat Opportunity” section, page 

89, and the “Estuarine Habitat Capacity” section, page 127), however, also could account for the 

loss of some subyearling life history types. Tidal marshes and swamps within the Columbia 

River estuary have been reduced by 65% (Thomas 1983). Use of these habitats by salmonids 

currently is being studied in the Columbia River estuary and results are not yet available, but 

tidal marshes and swamps are productive rearing areas for small Chinook and chum fry in other 

Northwest estuaries (Healey 1982, Levy and Northcote 1982). Additional wetland losses have 

not been quantified in the tidal freshwater region between 75 RKm and 235 RKm (Bonneville 

Dam). Losses of tidal riparian and floodplain habitats in this region from diking, filling, and 

railroad construction also appear to be significant. Other types of shallow habitat may have 

increased in the estuary (see the “Estuarine Habitat Opportunity” section, page 89), including an 

estimated 7% in the amount of shallows and flats, primarily because of the artificial creation of 

islands from disposal of dredged material (see the “Estuarine Habitat Capacity” section, page 

127). 

177
Yet these habitats do not provide the same functions as the marginal wetlands that have 

been removed, nor do they mitigate for the estimated 15% reduction in the estuary’s historical 

tidal prism (Sherwood et al. 1990). Regardless of other shallow-habitat gains, considerable 

diking of wetland and floodplain habitats may have reduced the capacity of the estuary to 

support ocean-type subyearling salmon and may contribute to the apparent underrepresentation 

of these life histories in recent studies relative to the period of Rich’s (1920) survey. 

Irrigation 

Cropland irrigation in the Columbia River basin withdraws more water than industrial, 

hydropower, and municipal sources with devastating effects on juvenile and adult salmonids 

(Lichatowich and Mobrand 1995, NRC 1996, Lichatowich et al. 1996). The construction of 

ditches and irrigation dams in Columbia River stream systems began in the mid-1800s, 

accelerated in the early 1900s, and continues today successfully converting arid lands to 

cultivated fields. In the early 1900s irrigation ditches diverted 90–97% of the Yakima River 

from April to late October, carrying juvenile salmonids into ditches and blocking the upstream 

migration of adults (Pacific Fisherman 1920). High rates of mortality occurred when juveniles 

were dispersed onto cultivated fields and became trapped when irrigation ceased and ditches 

dewatered (Pacific Fisherman 1920). A single watering event in a Yakima River valley 

sacrificed an estimated 4.5 million migrating juveniles (Pacific Fisherman 1920). 

Irrigation practices also have effectively blocked juvenile and adult salmon migrations. 

Temporary push-up dams and irrigation diversions left downstream channels with little or no 

water, hindering juvenile and adult passage and reducing water quality (NRC 1996, PFMC 

1999). Low flows from irrigation withdrawals also produced extreme water temperatures, 

rendering some streams lethal and impassable to salmonids (Lichatowich and Mobrand 1995, 

Lichatowich et al. 1996). We can only surmise the potential losses from diversions and dams 

since no quantified assessments are available (NRC 1996). Thermal barriers to the lower reaches 

of many Columbia River tributaries, however, may have effectively blocked the downstream 

migrations of ocean-type juveniles (ISG 2000, Williams in press). Thousands of unscreened 

diversions still remain in the basin today. 

Flow regime 

Diking and flow regulation have drastically altered the available habitat and flow regime 

encountered by salmon in the Columbia River and the estuary (see the “Changes in Hydrological 

Conditions” section, page 47, [Figure 28]). Diking of islands and margins of the estuary has 

eliminated refugia from high flows once available to juvenile salmon. At the same time, flow 

regulation has reduced spring-freshet levels and dams have created impoundments that alter the 

migratory habitat for juveniles traveling downstream. Prior to flow regulation, flow levels were 

greater and the variability within short time periods was higher (Sherwood et al. 1990). 

Floodwaters of the Columbia River historically inundated the margins and floodplains 

along the estuary, permitting juvenile salmon access to a wide expanse of low velocity 

marshland and tidal channel habitats. The greater seasonal variability of estuarine velocities and 

depths prior to flow regulation also may have allowed a greater diversity of estuarine rearing 

178
behaviors by juvenile salmon. Reduced habitat potential coupled with an altered flow regime 

probably has reduced the productive capacity of the estuary for juvenile salmon. 

The salmon data analyzed in this study encompass periods of a relatively free flowing 

river in 1916, a highly regulated river in the early 1970s, and the added effects of a volcanic 

eruption in 1980. Long-term river flow values are available at The Dalles gauge from 1878 to 

the present (USGS 2001). The relevant flow years are presented in Figure 83, including 

estimates for the Willamette River (see the “Changes in Hydrological Conditions” section, page 

47). The May 1980 eruption of Mount St. Helens, which added a huge quantity of silt and logs 

to the lower Columbia River estuary, hampered collection efforts until June (Dawley et al. 1986). 

Excluding the Mount St. Helens eruption, the sampling seasons of 1966 and 1980 were 

relatively benign, while the 1916 sampling season had one of the latest spring freshets on record, 

with flows on July 5 exceeding 20,000 m3

s

-1 (Figure 83). Although Rich (1920) made no 

mention of the river conditions, flows would have been between 10,000 m3s

-1 and 23,000 m3

s

-1

during Rich’s sampling (Figure 81). Flows in 1966 and 1980, however, probably were close to 

5,000 m3

s

-1 and 10,000 m3

s

-1, including the Willamette River’s contribution. 

The importance of shallow-water habitat as refugia for salmon fry is epitomized by the 

collection of juveniles less than 60 mm in the estuary during and after the peak freshet in 1916 

(Rich 1920). The mid-July sample of 1916 included subyearlings that had resided in the estuary 

for at least 8–57 days, which encompassed the peak flow period. Prior to major physical 

alterations, the marginal areas of the estuary would have extended outward, expanding the 

surface area of the estuary dramatically and increasing the area of shallow, low velocity habitat 

accessible to smaller juvenile salmon. To maintain their position within the estuary during 1916 

peak flows, the smaller subyearlings must have sought refuge in shallow peripheral marshes and 

other off-channel habitats that would have been flooded. 

Artificial propagation of salmon 

The capacity of the estuary to support juvenile salmon may be influenced by the timing 

of hatchery releases and the abundance of hatchery juveniles in the Columbia River estuary. 

Several studies suggest that wild Chinook salmon may have a much broader migration period to 

the estuary than that of hatchery fish. 

Reimers and Loeffel (1967) beach seined seven tributaries in the lower Columbia River 

subbasin until subyearlings were no longer captured. Their results showed considerable 

variability in the duration and completion of outmigration from each tributary into the estuary 

(Figure 82). The Klaskanine River population, for example, concluded their outmigration within 

one month and ended by the middle of June. The North Fork Lewis River population entered the 

estuary over a four-month period and did not complete their seaward migration until the middle 

of October (Figure 84). These results are consistent with McIsaac’s (1990) study of the North 

Fork Lewis River 1977–1979 brood, which similarly documented considerable variability in wild 

fish migration timing to Jones Beach between sample years (Figure 75). The prolonged period 

of fry emergence and variable timing of seaward migration in the North Fork Lewis River 

population indicates a variety of life histories among wild fish. 

179
0

5

10

15

20

25

1 January

31 January

1 March

31 March

30 April

30 May

29 June

29 July

28 August

27 September

27 October

26 November

26 December

Streamflow (1000 m3/s)

1916

1966

1980

July 5, 1916

Stream flow 1,000 (m3s-1

)

Figure 83. River flows (cubic meters per second) for 1916, 1966, and 1980. Arrows at base of graph 

represent sampling dates in the lower estuary by Rich (1920). Flows compiled from The Dalles 

gauge (USGS 2001) and estimates of Willamette River contribution at Salem, Oregon (see the 

“Changes in Hydrological Conditions” section, page 47). 

Several studies have found that hatchery-reared Chinook salmon migrate within a 

relatively narrow period. Dawley et al. (1986) correlated the estuarine abundance and time of 

entry of subyearling Chinook sampled at Jones Beach with their time of release from the 

hatchery (Figure 73). Using PIT tags to monitor downstream movement through Lower Granite 

Dam, Achord et al. (1996) found that wild spring Chinook migrated later, wild summer Chinook 

migrated earlier, and both types migrated over a more protracted period compared to their 

hatchery-reared counterparts. The combined effect of hatchery-reared juveniles arriving in the 

estuary within an abbreviated and artificial migration window and at elevated numbers increases 

the density of juveniles and may artificially limit the productive capacity of the estuary. 

Conclusions 

Our evaluation of past and present salmon size distributions and migrations are consistent 

with the hypothesis that life history diversity in the estuary has declined. Despite the obvious 

limitations of the available estuarine data, the results of several surveys from a similar estuary 

location provide a valid comparison before and after intensive development modified the 

Columbia River basin. These results reflect the kinds of changes that might be expected based 

on our conceptual framework (see the “Conceptual Framework for Evaluating Estuarine Habitat 

Conditions” section, page 21), large-scale changes in watershed conditions, and the results of 

180
0

20

40

60

80

9 May

29 May

18 June

8 July

28 July

17 August

6 September

26 September

16 October

5 November

25 November

Number of fish

Klaskanine River

Elochoman River

Toutle River

Kalama River

North Fork Lewis River

Washougal River (a)

Washougal River (b)

Figure 84. Time and relative duration of subyearling Chinook outmigration from six tributaries into the 

Columbia River estuary during 1963 (Reimers and Loeffel 1967). Two sites were sampled in the 

Washougal River, (a) was at the Highway 830 bridge and (b) was 10.8 miles upriver from the 

Highway 830 bridge. 

upriver assessments that also document reduced life history diversity in the basin (Lichatowich 

and Mobrand 1995, ISG 2000, Williams in press). The results suggest a more uniform size 

distribution among subyearling estuarine migrants, relatively constricted migration periods 

dictated by the timing of hatchery releases, and evidence of apparently shorter estuarine 

residence times compared to the early results of Rich (1920). 

The physical conditions of the watershed and the salmon populations when Rich (1920) 

studied estuarine use and residency already were modified by development and intensive 

fisheries. It is expected that greater diversity existed prior to his survey. Estuarine habitat for 

salmon has declined further since Rich (1920) sampled. We also have experienced a marked 

decline in wild populations, including the extinction of complete salmon runs, such that 

artificially propagated fish dominate present-day monitoring efforts and population-strength 

indicators. It is difficult to establish the importance and duration of estuarine residency by wild 

juvenile salmon under present conditions of reduced estuarine habitat and the predominance of 

hatchery-reared salmon. Multiple factors may account for the apparent reduction of small oceantype migrants in the estuary, including: 

• loss or deterioration of upriver and estuarine habitats that historically supported salmon 

with ocean-type life histories, 

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• flow modifications that have dampened established disturbance regimes and altered 

estuarine habitats, and 

• genetic selection associated with intensive fisheries (Figure 85). 

Such changes are further amplified by hatchery programs that concentrate the time of salmon 

entry into the estuary and further accentuate larger subyearling and yearling life histories. By 

releasing large batches of similarly sized fish over restricted time windows, hatcheries may limit 

the timing of estuarine migrations, narrow the range of habitats selected by juveniles, and 

artificially elevate fish densities within the estuary. 

A reduction of the life history diversity or the habitats that those life histories depend 

upon can have implications for the overall population. Anderson and Hinrichsen (1996) argued 

that a hatchery population with a concentrated migratory period in the estuary would succumb to 

greater fluctuations in abundance because of decreased chances of encountering conditions 

favorable for survival. In the Columbia River, wild Lewis River ocean-type juveniles 

epitomized the hypothetical scenario proposed by Anderson and Hinrichsen (1996) whereby the 

longer migration period of the wild juveniles through the estuary may contribute to higher 

survival rates than their hatchery-reared cohorts (McIssac 1990). This example demonstrates 

factors upriver influencing migration timing to the estuary potentially affecting survival. It is 

critical, therefore, to document the spatio-temporal complexity of a population’s life histories to 

understand its vulnerability and fluctuations in abundance. 

Estuarine restoration activities should not be planned independent of riverine restoration 

efforts since habitat opportunities, life history diversity, and spatial structure of juvenile salmon 

in riverine habitats largely determine estuarine patterns (Healey and Prince 1995, Wallace and 

Collins 1997). Salmon population management and recovery efforts should promote the 

expression of juvenile life histories by expanding habitat opportunities (Healey and Prince 1995) 

in riverine and estuarine habitats. Research in Oregon’s Salmon River estuary has demonstrated 

that marsh restoration can increase life history variation in a fall Chinook salmon population by 

allowing greater expression of estuarine-resident behaviors (Bottom et al. 2005). 

The most vulnerable life histories to estuarine habitat losses may be the smaller 

ocean-type migrants (i.e., fry) that depend primarily on the upper tidal freshwater reaches 

(Kjelson et al. 1982, Wallace and Collins 1997). Fry migrants less than 60 mm are just one of 

many ocean-type life histories that contributed to the returning adult population, and one of 

many that depend on estuarine habitats. The survival of juveniles has been linked to estuarine 

habitat conditions (Magnusson and Hilborn 2003). Thus restoration of estuarine habitats in 

conjunction with recovery of the life histories that use those habitats will play a critical role in 

wild salmon recovery. This may be particularly true in estuaries of unsheltered coastal basins in 

California, Oregon, and Washington where salmon require additional growth before migrating to 

the ocean compared with populations that can migrate to the protected bays of Washington’s 

Puget Sound and British Columbia river systems. 

Unfortunately, Chinook salmon life history timing and rearing patterns have been 

characterized in very few river systems, our understanding of estuarine habitat use is limited in 

scope, and relatively few studies have investigated estuarine residency. These data are clearly 

needed to support salmon monitoring, management, and recovery. 

182
Fish 

Re

c

reg

Irr

wit

River flow 

(volume, 

hydro period)

Salmon size 

and time 

 at estuary 

entry 

Wate

modif

(uprive

Hatchery influences 

Genetic 

composition 

Release 

schedule 

and locations 

Number 

and sizes of 

fish released

Spawner 

distribution

Spawner 

abundance

Size/age structure 

Salmon harvest 

Population 

structure/ 

life history 

(upriver 

genetic, life 

history, and 

geographic 

structure) 

Habitat 

capacity

(quality) 

Performance 

(estuarine foraging 

success, growth, 

diversity)

Habitat 

opportunity 

(access) 

Figure 85. Linkages to life history and geographic structure of salmon populations upriver affect salmon performance with

basin-wide geographic and genetic structure of populations may determine whether salmon can fully realize the hahabitat capacity in the estuary. 

183
These results reinforce a central theme of our conceptual approach: the life histories and 

performance of salmon in estuaries cannot be dissociated from those of other life stages. 

Restoration projects to improve estuarine habitat opportunities for ocean-type juveniles, for 

example, may require concomitant habitat or flow improvements that can also sustain these 

subyearling migrants upriver. Efforts to stabilize the environment to create optimum survival 

conditions for one salmon life stage, however, also may reduce the variety of rearing and 

migration behaviors present in the population, narrowing the temporal or spatial range of habitat 

opportunities that salmon can potentially exploit at subsequent stages. Ironically the 

member/vagrant hypothesis predicts that manipulations to maximize the production of one 

salmon life history type upriver also may limit the total productive capacity of the estuary. 

184
Synthesis: Review 

of the Conceptual Framework 

Introduction 

At the start of this review, we noted that traditional assumptions of natural-resource 

management have contributed to the decline of Columbia River salmon. More specifically, an 

agricultural tradition in fisheries conservation, which we described as production thinking, took 

for granted that salmon abundance could be maximized by eliminating mortality during critical 

early life stages perceived as bottlenecks to production. For every additional egg, fry, fingerling, 

or smolt that survived by controlling local predators, competitors, or other perceived constraints, 

production thinking assumed that another adult salmon would return to fishermen or the 

spawning grounds. Viewed through a production lens, the estuary became the last in a series of 

hazardous places—the lowermost end of a long river pipe—where judicious control was deemed 

necessary to ensure the safe and efficient flow of fish to sea. 

While efforts to remove production constraints unfortunately failed to restore Columbia 

River salmon, it also yielded little understanding of the conditions that salmon need to persist in 

their native habitats. We concluded that a comprehensive review of the estuary’s role in salmon 

decline and recovery must begin from a different conceptual framework. 

In the “Conceptual Framework for Evaluating Estuarine Habitat Conditions” section 

(page 21), we proposed an alternative framework based on the population thinking of Rich 

(1939) and the member/vagrant hypothesis of Sinclair (1988). This approach emphasizes the 

geographic structure of habitats, populations, and diverse salmon life histories that contribute to 

salmon resilience and productivity. Now we briefly summarize the evidence regarding the 

validity of the member/vagrant hypothesis as adapted to Pacific salmon and the implications for 

conservation of salmon and their habitats in the Columbia River estuary. 

Evidence 

Geographic Structure 

A central tenet of Sinclair’s (1988) member/vagrant hypothesis is that population pattern 

and richness depend on the number of geographic settings that each species can use to complete 

its life cycle. The geographic structuring in populations, for example, is most evident during 

adult and early juvenile stages, when populations of many pelagic marine species segregate into 

discrete spawning/larval retention areas, or adult salmon return to their natal streams to deposit 

their eggs in the gravel (Sinclair 1988). Beyond just the stream environment, we applied the idea 

of geographic structuring to the entire habitat chain that supports salmon life cycles and that 

allows expression of diverse life histories within salmon populations. Each life history 

185
represents an alternative habitat pathway in time and space (i.e., geographic setting) by which 

population members can complete their life cycles. 

Our results provide evidence that the Columbia River estuary affords a variety of 

alternative pathways that contribute to the geographic structure and diversity of salmon 

populations and life histories throughout the basin. Historic surveys indicate that Chinook 

salmon occurred in the estuary year-round and exhibited a wide range of times and sizes of 

downstream migration and periods of estuarine residency (Figure 79, Rich 1920). 

Patterns of habitat use within the estuary appear to be size-related, such that small salmon 

migrants often rear for extended periods in shallow, nearshore habitats while larger individuals 

and older-age migrants tend to frequent deeper channels. Although we identified multiple 

factors that might contribute to the apparent decline in the proportion of fry and small fingerlings 

in the estuary today relative to the early 20th century (Figure 79), the response is nonetheless 

consistent with expectations (of the member/vagrant hypothesis) following widespread removal 

of shallow estuarine wetlands that allow expression of estuarine-resident life histories. 

The geographic structure of spawning populations across the Columbia River basin and 

associated travel distances from natal streams contribute to the diverse sizes and times of 

juvenile migration, estuarine entry, and other life history traits in the estuary (Rich 1920). 

Among contemporary populations, a coarse geographic structure linked to estuarine rearing 

behaviors is apparent: individuals with stream-type life histories predominate in Columbia River 

headwaters and in Snake and Salmon rivers subbasins, while ocean-type migrants are abundant 

in lower Columbia River reaches. 

Yet this is an oversimplification of spatial structure based on observations made long 

after habitat and population losses had altered historic patterns. Even contemporary life history 

patterns reveal a much finer geographic structuring than simply upper versus lower Columbia 

River basin. A population within a single watershed, for example, may exhibit stream- and 

ocean-type life histories. Additional work is needed to understand the population-specific 

linkages of Chinook salmon to diverse rearing behaviors in the estuary. 

Habitat Linkages 

The member/vagrant hypothesis indicates that ecological processes regulating marine 

population dynamics become linked across distant environments through the physical transport 

and migrations of species with complex life cycles (Sinclair 1988). We found evidence of 

significant physical and biological linkages upriver that influence salmon performance within the 

Columbia River estuary. 

For example, flow regulation by mainstem dams controls the quantity and quality of tidal 

floodplain and wetland habitat accessible by young salmon; hatchery operations upriver regulate 

the arrival times, sizes, and patterns of habitat use by salmon within the estuary; and historic 

fisheries and loss of spawning and rearing habitat in freshwater determine the geographic 

structure of contemporary populations, which also affects the variety of migratory and rearing 

patterns that salmon potentially can express within the estuary. Thus we cannot interpret 

patterns of estuarine habitat use by salmon without accounting for physical and biological 

186
linkages upriver. The processes governing many such linkages today are dominated by 

hydropower, hatchery, and fishery management systems. 

Salmon performance downstream in the coastal ocean similarly may be linked to the 

cumulative effects of river flow, habitat opportunity, and population structure upriver and in the 

estuary. Evidence of strong density gradients and enhanced biological production in the plume 

and frontal zone (Fresh et al. 2005) suggests a strong connection between Columbia River flows 

and prominent habitat features of the coastal ocean. These linkages further raise the possibility 

that control of the Columbia River hydrograph (Figure 28) may affect salmon habitat conditions 

offshore. 

River and ocean circulation processes and the migrations of Columbia River salmon 

define a large and interconnected watershed-ocean ecosystem whose behavior is not adequately 

described by a few critical periods or habitats within the river, estuary, or nearshore ocean. Thus 

the general estuarine model proposed in Figure 10 can be viewed as a part of a larger system of 

habitat/life history interactions that regulates salmon populations (Figure 86). Salmon 

performance at one life stage and aquatic environment dictates the time, size, and physiological 

condition of surviving migrants and establishes broad limits for the potential performance of all 

survivors at each subsequent stage and environment. Salmon performance at all life stages is 

also regulated by large-scale disturbances that impose ecological constraints on the entire salmon 

ecosystem, including regional climate, flow regulation, and other anthropogenic effects (Figure 

86). The performance of the entire salmon ecosystem is indicated by the diversity of habitat 

opportunities for salmon, the spatial structure and life histories of populations (i.e., the filling of 

habitat-opportunity space), and the basin-wide productivity and resilience of salmon species. 

Spatial and Energetic Process 

The member/vagrant hypothesis holds that losses of individuals from marine populations 

with complex life cycles may result from spatial or energetics processes. Whereas energetics 

losses involve direct mortality from predation, disease, or starvation, spatial losses result from 

the inability of individuals to find a mate successfully at the appropriate time and place to remain 

in the population (Sinclair 1988). 

We defined spatial effects broadly as any factors that sever the link between habitat and 

salmon life history and cause population losses. These can result from habitat removal and 

genetic or phenotypic changes that prevent the individuals in a population from realizing existing 

habitat opportunities (Figure 9). 

Evidence from the Columbia River estuary supports the idea that spatial losses have 

played a significant role in the decline of Columbia River Chinook salmon, including: 

• loss of upriver habitats that historically supported populations with subyearling-migrant 

life histories, 

• elimination of tidal floodplain and peripheral-wetland habitats that allowed expression of 

subyearling-migrant life histories within the estuary, 

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Flow 

regulation

Regional 

climate 

Anthropogen

modification

Ecosystem capacity for salmon 

Figure 86. Linkages among salmon environments implied by the member/vagrant hypothesis (Sinclair 1998). Spatial and 

shape salmon populations at each ontogenetic stage and determine the performance (growth, foraging success, and of the individuals that survive to enter each subsequent environment. 

Stream/river

Population 

structure/ 

life history 

Habitat 

capacity 

Performance

Habitat 

opportunity

Estuary 

Population 

structure/ 

life history 

Habitat 

capacity 

Performance

Habitat 

opportunity

Plume/ocean 

Population 

structure/ 

life history 

Habitat 

capacity 

Performance

Habitat 

opportunity

188
• effects of flow regulation on potential patterns of downstream migration by juvenile 

salmon, and 

• genetic and phenotypic effects of hatchery programs that have concentrated the times and 

sizes of salmon entry into the estuary. 

We also found evidence that energetics processes in the estuary may contribute to losses 

from Columbia River populations, including interactions with nonindigenous species, predation 

by marine birds, and an apparent shift from macrodetrital to microdetrital food webs. The effects 

of energetic and spatial processes in the estuary, however, are not easily separated. 

Apparent energetic effects of recent increases in avian predation, for example, may be 

linked to spatial processes, including new habitat opportunities for marine birds in the lower 

estuary (i.e., artificial dredge-spoil islands) or changes in salmon life history linked to 

concentrated releases of large hatchery smolts or both. Similarly rapid increases in American 

shad populations could be linked to habitat changes and food-web shifts, including conversion of 

the free-flowing river to a series of reservoirs behind mainstem dams and related increases in 

microdetrital carbon sources from upriver. These examples reveal spatial-energetic interactions 

that are not fully depicted by the proposed conceptual model (Figure 10). Rather than 

independent linkages to performance, the results imply a more complex (nonlinear) dynamic 

among habitat opportunity, habitat capacity, and salmon life history. 

Implications 

Recognizing the geographic population structure within Columbia River salmon species, 

Rich (1939) argued for a new management approach based on the conservation of populations 

within their local habitats. Reviews of the Columbia River Fish and Wildlife Program (NRC 

1996, ISG 2000, Williams in press) have reinforced these ideas and offered recommendations to 

conserve diverse salmon populations and life histories. 

We conclude that the member/vagrant hypothesis offers a useful scientific framework to 

support such recommendations and to extend salmon recovery efforts downstream to encompass 

the estuarine and plume environments of salmon life cycles. This framework has significant 

implications for future salmon conservation and research as described in the following 

subsections. 

Conservation Programs Must Account for Diverse Estuarine Life Histories 

The results of this analysis demonstrate that neither the status of salmon populations nor 

the estuary’s contribution to population viability is sufficiently described by simple production 

measures of abundance, density, and survival. Similarly the concept of single limiting factors, 

including the idea of a density-dependent bottleneck in the estuary, ignores the importance of 

spatial processes, which can play a significant role in salmon production and resilience 

regardless of population densities. Because spatial effects involve lost opportunities for life 

history expression, they cannot be measured by counting the number of live or dead fish. 

Environmental fluctuations that regulate spatial processes, including interdecadal shifts in 

oceanic and climatic regimes, undermine production-based conservation approaches that assume 

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the salmon ecosystem can be managed for a steady optimum condition. Population assessments 

and recovery plans in the Columbia River basin must account for the geographic structure and 

diverse life histories that allow populations to persist in a variable environment. This includes 

life history variations in the estuary that contribute to the geographic structure and diversity of 

populations throughout the Columbia River basin. This expanded view of population status is 

consistent with the performance criteria recently proposed by NOAA Fisheries Service to 

determine salmon recovery needs: abundance, population growth rate, spatial structure, and 

diversity (McElhany et al. 2000, Fresh et al. 2005). 

Recovery Actions Should Expand Habitat Opportunity, Life History Variation 

Habitat losses, hydroelectric development, salmon harvest, and fish management 

activities have simplified the spatial structure and diversity of salmon populations in the 

Columbia River basin (ISG 2000, Williams in press). Traditional salmon management 

programs, for example, have targeted time periods or geographic areas of maximum abundance 

that presumably will yield the greatest economic return. Thus rearing and release schedules for 

hatchery salmon are prescribed to match an average or optimal run timing, size at release, or 

other conditions expected to maximize survival and adult returns. 

An inevitable consequence of this approach is the continued narrowing of population 

traits toward their mean or central tendency and an erosion of the presumably less productive 

tails of the distribution. In contrast, the member/vagrant hypothesis suggests that conservation 

programs should target the breadth of life history possibilities in an ecosystem (i.e., the full range 

of potential habitat/life history interactions). 

Among many factors that may erode life history variation within the Columbia River 

estuary is the intensive hatchery propagation of large fingerling and yearling salmon, which are 

released over a limited range of river-flow conditions and time periods dictated by the 

hydropower and hatchery systems. We concluded that hatchery production and widespread 

habitat losses probably have narrowed the size and age distribution of Chinook salmon (Figure 

79), decreasing the proportion of fry and small fingerling migrants adapted to utilize productive 

estuarine rearing habitats (Levy and Northcote 1982, Healey 1991). 

The member/vagrant hypothesis implies that a principal goal of salmon recovery should 

be to expand habitat opportunities and life history expression in naturally reproducing 

populations. Recovery of habitat opportunities that support life history variations in the estuary 

offers a cost-effective strategy toward this goal. All anadromous salmonids pass through the 

estuary, and recovery of some estuarine habitats could simultaneously benefit multiple 

populations with similar life histories. Restoration of emergent and forested wetlands may be 

particularly important to allow expression of estuarine-resident life histories among a variety of 

ocean-type Chinook populations. (Bottom et al. 2005). 

Reference Conditions Must Be Defined To Establish Recovery Goals 

The member/vagrant hypothesis implies that present salmon distribution or standing crop 

in the estuary may not indicate the true rearing potential of a particular habitat. Elimination of 

source populations or loss of habitats elsewhere along the salmon migration route can leave 

190
otherwise suitable areas of the estuary vacant. Habitats where salmon are now most abundant 

might not be the highest priorities to restore or protect, if present patterns of abundance are a 

symptom of historic population or ecosystem decline (Li et al. 1995). Contrary to 

production-based conservation approaches, the goal to restore habitat opportunity requires 

identification of salmon life histories that are presently underrepresented and otherwise might be 

considered unimportant. 

Long-term data sets are rarely available, and no single historic snapshot can characterize 

the full range of variability that existed before the estuary was intensively developed. Moreover, 

even if historic ecosystem conditions were known, this does not mean that all former estuarine 

habitats and salmon life histories can be restored. For example, increased water temperatures, 

stabilization of flows, or introductions of nonindigenous species might limit present habitat 

functions (including support of juvenile salmon) even if historic habitat form can be recreated. 

The purpose of reconstructing historic reference conditions is to understand the life 

history variations characteristic of the species and the habitat opportunities in the basin that may 

have contributed to this diversity. While it may be impossible to restore former conditions, 

alternatives can be sought to provide equivalent opportunities for expanding life history 

expression. 

The challenges of historical reconstruction only underscore the need to explicitly define 

the goals of restoration and to describe their scientific basis using whatever reference examples 

are available. In some situations lack of historic data may require comparisons with other, less 

altered populations and ecosystems to provide a benchmark for developing recovery goals. 

Conserving Habitat Linkages Requires Ecosystem-scale Planning 

The member/vagrant hypothesis implies that restoring selected segments of the salmon 

life cycle will not succeed if other links in the habitat chain are broken. Habitat assessments and 

salmon restoration activities in the Columbia River basin have focused primarily on the 

freshwater phase of the salmon life cycle. Maintaining habitat linkages throughout the salmon 

life cycle will require conservation planning and coordination at landscape and river-basin 

scales. 

The effects of intensive management activities in the Columbia River basin extend far 

beyond the area or life stage they are meant to influence and inadvertently may alter downstream 

linkages in the salmon-habitat chain. We have suggested that flow manipulations intended to 

maximize salmon survival in the main stem also influence habitat conditions for the same fish in 

estuarine and plume environments. Similarly, hatchery and fish transportation programs 

designed to promote rapid downstream migration and improved in-river survival may narrow 

phenotypic variation—estuarine arrival times, sizes, and residency, for example—and thereby 

limit alternative survival possibilities among individuals entering the estuary and ocean. 

Performance criteria for management programs should account for potential effects throughout 

the salmon life cycle. 

The member/vagrant hypothesis implies that subbasin plans also need to explicitly assess 

the contribution of estuarine and plume habitats to the geographic structure and diversity of 

191
upriver populations. Although the estuarine life histories of individual populations are poorly 

known, information for downstream migration times, sizes, and travel rates may offer clues 

about the estuarine habitats that are most likely to benefit local populations. Recovery plans 

should propose concomitant actions in freshwater, estuarine, and plume environments that are 

needed to support particular salmon life histories. 

Strategic planning also is needed to support restoration efforts within the estuary. Many 

new restoration projects have been undertaken to improve and increase estuarine habitat 

opportunities for salmon, but site selection decisions rarely consider local project connections to 

the broader salmon-habitat landscape. Projects usually are chosen and implemented 

independently based on ad hoc funding opportunities and local landowner interest rather than 

strategic planning to identify the areas of greatest biological potential across the estuary 

landscape. 

The spatial arrangement of estuarine habitats may be particularly important to salmon 

performance, because individuals must continually adjust their position as tidal fluctuations alter 

the distribution of wetted areas, depths, velocities, and chemical gradients. Access to productive 

estuarine wetlands, however, may require linkages to adjacent subtidal refugia so that fish can 

enter and exit intertidal marsh channels successfully twice daily with the tide. Restoring 

connections between the river and its floodplain may be particularly important throughout the 

tidal fresh zone of the estuary, where flow regulation and diking have eliminated access by 

downstream migrants. An estuary restoration plan should identify the priority areas where 

habitat opportunities and linkages should be restored to promote diverse estuarine life histories. 

Metapopulation theory has been proposed as a framework for understanding and 

conserving salmon-habitat linkages in the Columbia River basin (ISG 2000, Williams in press). 

The theory describes regional population dynamics as a function of the spatial organization of 

suitable habitats and the relative rates of dispersal (straying) and extinction among local 

populations (Hanski and Simberloff 1996). A few empirical studies have applied 

metapopulation models to several inland salmonids with localized breeding and rearing areas, 

but no single model could explain the dynamics of inland species (Rieman and Dunham 2000). 

Metapopulation models may be much more difficult to apply to anadromous salmon 

populations, because abundance and survival reflect processes far beyond the dispersal and 

extinction dynamics of local spawning and freshwater rearing habitats. While metapopulation 

concepts provide a valuable framework for conserving processes important to population 

persistence (e.g., dispersal and habitat connectivity, patch size requirements, phenotypic 

variation, etc., [Rieman and Dunham 2000]), the member/vagrant hypothesis may be a useful 

alternative to account for processes in estuarine environments that also affect the dynamics of 

local spawning populations. 

New Research Approaches Needed 

The member/vagrant hypothesis raises important scientific questions that traditionally 

were not deemed relevant for salmonid research in the Columbia River basin. Whereas 

production thinking measured salmon survival and sought methods to minimize mortality at 

critical life stages, Sinclair’s (1988) hypothesis seeks information about habitat opportunities that 

192
allow diverse salmon populations to persist. From this perspective the member/vagrant 

hypothesis defines a new estuarine research agenda based on a fundamental question: What 

estuarine habitat opportunities and qualities are necessary to conserve the characteristic life 

histories and geographic structure of Columbia River salmon populations? 

To answer this question, we recommend the following five types of estuarine habitat 

research: 

Reference conditions 

Historic reconstruction is needed to establish a benchmark for restoration planning in the 

estuary. Some historic habitat data already have been developed for the lower estuary (Thomas 

1983), but similar data have not been compiled for the extensive tidal fresh region between Puget 

Island and Bonneville Dam. Further life history reconstruction for Chinook and other salmon 

species also may be possible if scale collections or other archival materials become available. 

Contemporary habitat/life history associations 

Additional empirical data are needed to determine the variety of salmon life histories now 

expressed in the estuary and the habitats that support them. Past investigations in the Columbia 

River estuary have examined a limited array of estuarine habitats, and little is known about the 

physical factors that influence habitat selection, accessibility, and performance by salmon. 

Scale-pattern analysis and otolith microchemistry (Volk et al. 2000, Kennedy et al. 2002) offer 

techniques for interpreting variations in freshwater and estuarine life history among individuals 

sampled in the estuary. 

Habitat linkages at landscape scales 

Little is known about the landscape-scale patterns of salmonid migration through the 

estuary or the spatial and temporal arrangement of habitats that support them. New tagging and 

tracking technologies often used to estimate salmon survival could be adapted to study life 

history variations and habitat linkages in the estuary. Although incapable of tracking the 

smallest individuals and life history types, new tagging technologies (PIT tags and acoustic tags) 

may allow comparisons of habitat use, residency, and migration behavior among a variety of 

salmon size classes. 

Source populations for estuarine life histories 

The member/vagrant hypothesis implies that salmon recovery plans should account for 

estuarine habitat linkages to upriver populations. The identification of distinct genetic markers 

among populations from different geographic areas of the basin offers one possible tool for 

identifying upriver sources of individuals with various estuarine life histories. 

Dynamics of estuarine habitat opportunity 

Habitat opportunities in the estuary continually shift through the interaction of tidal 

forces and river hydrology and may be sensitive to any management decisions that modify 

physical conditions. The preliminary results in the “Estuarine Habitat Opportunity” section 

193
(page 89) demonstrate that physical modeling may be used to evaluate alternative management 

scenarios based on their potential effects on the dynamics of habitat opportunity. Additional 

research to understand salmon-habitat associations will be needed to refine the 

habitat-opportunity metrics chosen for physical modeling. 

Summary and Conclusions 

We conclude that the member/vagrant hypothesis is a valid conceptual approach to 

account for the geographic structure and diversity of salmon populations that is essential to 

population persistence in a variable environment. The Columbia River estuary contributes to the 

geographic structure and diversity of populations by providing alternative rearing opportunities 

for upriver populations whose members arrive in the lower river at a variety of sizes and times. 

The evidence suggests that spatial and energetics losses affecting estuarine life histories have 

contributed to the decline of Chinook salmon populations throughout the Columbia River basin. 

Salmon recovery programs should expand estuarine habitat opportunities to support 

diverse populations and life histories. This implies that multiple scales of conservation planning 

will be needed to account for: 

1) effects of upriver management decisions (i.e., flow management, hatchery, and harvest) 

on salmon habitats and life histories in estuarine and plume environments, 

2) estuarine habitats that support local populations or groups of populations (i.e., ESUs) 

throughout the basin; and 

3) restoration priorities within the estuary, including the key habitat types and their spatial 

organization, to accommodate diverse salmon rearing and migration behaviors. 

The member/vagrant hypothesis outlines a new research framework to support salmon 

conservation and recovery planning, including: 

1) historical reconstruction of estuarine habitats and salmon life histories to establish 

reference conditions, 

2) empirical studies to understand life history/habitat associations, to track the migrations 

and habitat-use patterns of various size classes of salmon, and to identify the source 

populations of individuals with diverse estuarine life histories; and 

3) physical modeling to evaluate habitat-opportunity responses to alternative management 

and restoration decisions that may affect the estuary. 

The member/vagrant hypothesis does not offer a specific model to define a minimum 

quantity or spatial arrangement of habitat that will maximize salmon abundance or ensure 

population viability. The complex interactions of the salmonid ecosystem described in this 

analysis (Figure 85 and Figure 86) demonstrate why such an optimum condition does not exist. 

Rather the results argue for restoring flexibility to the ecosystem by expanding habitat 

opportunities and life history variations and restoring the physical processes that support this 

diversity. 

194
Additional work is needed to develop applications of the member/vagrant hypothesis to 

salmon conservation. As suggested in a review of metapopulation theory (Rieman and Dunham 

2000), we conclude that the principal benefits of the hypothesis are conceptual rather than 

prescriptive. Applying the hypothesis to salmon recovery, regardless if its assumptions can be 

proven or predictive models can be developed, requires an understanding of the key processes 

and habitat linkages that will nudge the ecosystem in a more favorable direction toward 

population persistence. 

195
Conclusions and Recommendations 

Conclusions 

The principal objective of this analysis was to assess the potential impact of flow 

regulation of the Columbia River on juvenile salmon utilization of the estuary. The analysis of 

historical data and hydrodynamic model simulations identified potential influences of flow 

regulation and of climate on hydrology and sediment transport, with likely consequences for the 

estuarine physical environment. Yet with the extant data it was not possible to separate or rank 

these effects on juvenile salmon from these compounding factors: 

• anthropogenic changes to estuarine bathymetry and the tidal floodplain, 

• hatchery and harvest effects on the demographics and life history diversity of juvenile 

salmon inclined to use the estuary, 

• climate-induced variability, and 

• biotic changes in the estuarine flora, fauna, and food web. 

The analyses indicated that habitat and food-web changes within the estuary and other 

factors affecting salmon population structure and life histories have altered the capacity of the 

estuary to support juvenile salmon. Diking and filling activities in the estuary have likely 

reduced the rearing capacity for fry and subyearling life histories by decreasing the tidal prism 

and eliminating emergent and forested wetlands and floodplain habitats adjacent to shore. These 

habitats, which provide off-channel areas during peak flows, refuge from predators, and sources 

of macrodetrital production, probably serve different rearing functions from the other kinds of 

shallow habitats that model simulations suggest may have increased within the peripheral bays 

and other areas of the estuary. 

Effects of flow regulation on habitat opportunity for subyearling salmon based on the 

depth criterion remain equivocal because of uncertainties in the available bathymetric data. But 

regardless of these modeling results, significant loss of shoreline emergent and forested wetlands 

that were not incorporated in these simulations could be important in limiting the productive 

potential of the estuary for salmon. 

Despite the physical and ecological changes in habitat opportunity and capacity in the 

estuary, simplification of the population structure and life history diversity of salmon may be the 

most important factor affecting juvenile salmon performance. In the absence of data on 

present-day estuarine use by wild, subyearling ocean-type salmon, we concluded that patterns of 

salmon abundance, diversity, and residency in the modern estuary are influenced significantly by 

upriver habitat losses throughout the basin, harvest, and hatchery management practices. 

Regulation of river flow and habitat losses in the estuary cannot independently account 

for apparent changes in estuarine rearing patterns of juvenile salmon. Restoration of estuarine 

196
habitats, particularly diked emergent and forested wetlands, and flow manipulations to restore 

historical flow patterns and habitat dynamics might significantly enhance the productive capacity 

of the estuary for salmon. 

Regardless of the degree of habitat loss, we cannot eliminate the possibility that changes 

in population structure and life histories now prevent salmon from realizing the productive 

capacity of the estuary. Accordingly efforts to improve or to restore the estuary for salmon must 

be developed in concert with hatchery, harvest, and upriver habitat improvements to recover 

those life history types that can benefit from estuary restoration. 

The results also underscore the need to establish a sound historical and evolutionary 

context for interpreting modern estuarine habitat conditions and for developing salmon recovery 

strategies. In the absence of such a context, recovery actions may inappropriately target those 

few salmon life history types and habitats that are abundant today, further reinforcing the 

symptoms of salmon decline rather than expanding the productive capacity of the basin. 

Continued emphasis on improving survival of a few dominant types of Chinook salmon, 

particularly large hatchery yearlings and fed subyearlings with short estuarine residence times, 

may only further narrow the sizes, times, and rates of migration, concentrating salmonid use of 

the estuary and preventing salmon from realizing the estuary’s full productive potential. 

The historical analyses suggest that just the opposite strategy is needed to improve 

salmonid performance: recovery efforts should expand diversity of salmon life history and 

habitat opportunities to allow for the widest possible range of successful rearing behaviors. 

Therefore efforts to improve the productive capacity of the estuary significantly for salmon may 

require recovery of many habitats and life histories that are now rare or nonexistent rather than 

those few that have come to dominate as a consequence of industrial development of the basin 

and intensive selection pressures from harvest and hatchery influences. 

Recommendations 

While the risk of extinction of many Columbia River populations implies the need for 

immediate recovery action, the historical lack of salmon research in the estuary argues that 

further study may be necessary before we can define the appropriate restorative measures. We 

conclude that these concerns should be addressed by initiating carefully targeted restoration 

activities where there is reasonable confidence in their ecological benefits and at the same time 

by collecting new data to better understand salmon habitat requirements and restoration needs. 

The following recommendations are offered as potential means to promote salmon recovery and 

improve estuarine conditions, as well as to advance understanding of salmon rearing 

requirements: 

Adopt an Explicit Ecologically Based Conceptual Framework 

for Estuary Management and Restoration 

The lack of information about the estuarine-rearing requirements of juvenile salmon is 

because of a longstanding production approach to salmon management and research. This 

approach assumes the estuary is a simple migration corridor or bottleneck, where predation and 

other mortality factors must be controlled, rather than a productive nursery ground, where the 

197
varied habitat needs of diverse populations and life history types must be protected. We concur 

with the conclusions of the Independent Scientific Group (ISG 2000, Williams in press) that a 

fundamental impediment to recovery efforts in the Columbia River basin is the lack of an 

explicit ecological framework for salmon conservation. 

Such a framework is important particularly to direct recovery efforts in the estuary, where 

physical and biological interactions are complex and continually changing in response to tidal 

forces, river flows, and seasonal fluctuations in the composition of species assemblages. In 

addition the ecological requirements of salmon within the estuary must be placed in the broader 

context of factors at other life stages that shape population structure and life histories and thereby 

determine whether juvenile salmon can realize the full productive potential of the estuary. 

The conceptual framework (member/vagrant hypothesis) adapted for this assessment 

provides a valid ecological approach to account for life cycle linkages that influence salmon 

performance in the estuary. This framework should be applied to salmon conservation: 

• to identify and protect diverse salmon life histories, including variations in the estuarine 

rearing behaviors of subyearling migrants; 

• to identify and protect the full variety of geographic features and disturbance processes in 

the basin that allow for diverse salmon life histories, including different patterns of 

estuarine rearing; and 

• to establish performance criteria for evaluating whether management activities in the 

basin will impact salmon diversity and the productive capacity of the estuary. 

Protect and Restore Opportunity for Salmon to Access Emergent and Forested Wetlands 

in the Estuary and Riparian Wetlands in the Tidal Floodplain 

Historical losses of peripheral floodplain, wetland, and riparian habitats from diking and 

filling activities in the Columbia River estuary have reduced available rearing habitat for salmon 

with subyearling life histories. Such effects may not be limited to yearling, stream-type juveniles 

at present because hatcheries, harvest, and upriver habitat losses tend to favor these life histories. 

However, any effort to increase life history diversity will require reestablishment of important 

rearing habitats that have been substantially modified or removed from the estuary. 

Although fish use of tidal wetlands and floodplain habitats rarely has been investigated in 

the Columbia River, studies in other Northwest estuaries indicate that wetland restoration could 

offer a cost-effective method to improve salmonid rearing conditions. Reestablishment of more 

natural flow regimes in the basin might also diversify estuarine habitat opportunity and its 

associated variety of salmon rearing and migration behaviors. The following actions are needed 

to support and evaluate wetland recovery projects intended to benefit salmon: 

• Develop a comprehensive plan for wetland restoration throughout the tidal river and 

estuary, including habitat recovery objectives; criteria for site selection and restoration 

priorities; an inventory of diked, filled, and excavated lands; and a list of high priority 

sites most likely to benefit salmon recovery. 

198
• Evaluate information on hatchery, harvest, and habitat management practices that reduce 

salmon life history diversity, particularly diversity of subyearling, ocean-type migrants 

that are potentially most dependent on estuarine habitats. 

• Establish experimental restoration projects at a few representative wetland sites to 

evaluate the effectiveness of dike removal as a method of salmon recovery. Conduct a 

monitoring program at experimental and previously unaltered (undiked) reference sites to 

assess rates of habitat recovery, and identify conditions that affect salmonid use and 

performance. 

• Reconstruct the historical structure of mainstem and tributary shallow-water habitat in the 

predevelopment tidal floodplain and compare with contemporary conditions. Evaluate 

the potential habitat function of this extensive area for juvenile salmon rearing and 

migration, and its contribution to the estuary in terms of sediment accretion and erosion, 

large woody debris and food-web sources, and disturbance regimes. 

• Evaluate options for restoring more natural flow regimes to the estuary and assess their 

potential effects on estuarine habitat opportunity under a variety of different wetlandrecovery scenarios and on the distribution and extent of the Columbia River plume and 

frontal zone. 

Expand Phenotypic Diversity of Salmon, Including a Broader Range of Sizes, 

Times of Entry, and Duration of Residency in the Estuary 

Although increased genetic and life history diversity of salmon ultimately may require 

long-term expansion of habitat opportunity upriver and in the estuary, rapid progress in the use 

of existing or restored habitats could be made by expanding phenotypic diversity of salmon now 

heavily influenced by hatchery programs. Such improvements could require reductions in 

hatchery releases or changes in hatchery rearing practices. 

Any management changes to benefit salmonid use of the estuary, however, will require 

an improved accounting system and a greater degree of coordination of basin-wide hatchery 

programs than presently exists. For example, incomplete records of hatchery release groups, 

variations in rearing and release practices that confound interpretation of management effects, 

and difficulties in distinguishing the hatchery or wild origin of unmarked salmon preclude a full 

accounting of the influence of hatchery practices on salmon behavior and performance in the 

estuary. The following recommendations address these issues: 

• Evaluate effects of past hatchery rearing and release practices on the sizes and times of 

downstream migration, estuarine residence periods, and potential densities of juvenile 

salmon in the estuary. Propose hatchery management alternatives for expanding the 

diversity of estuarine rearing behaviors and reducing the risks of hatchery programs on 

salmonid performance in the estuary. 

• Improve accessibility of all hatchery data and accounting of all marked groups of salmon 

to allow future auditing of hatchery practices and their effects on the estuarine rearing 

patterns of juvenile salmon. 

199
• Expand marking programs or develop alternative techniques to improve discrimination of 

hatchery from wild fish in the estuary. These data are critical to discern differences 

between the estuarine rearing behaviors of hatchery and wild fish, and ultimately to 

evaluate whether basin-wide salmon recovery programs are succeeding. 

Monitor Variations in Life History Diversity, Habitat Use, and Performance 

of Juvenile Salmon in the Estuary 

Because the abundance and life histories of salmon in the estuary are linked to source 

populations and habitats upstream, changes in life history diversity and the relative proportions 

of wild juveniles in the estuary may indicate whether recovery efforts throughout the basin are 

having a positive effect. Unfortunately there has been no long-term monitoring program to 

describe trends in salmon rearing behaviors in the estuary. Neither salmon scales nor otoliths 

have been collected or archived routinely to evaluate changes in estuarine life history patterns 

since Rich’s survey in 1914–1916. 

Most contemporary estuarine studies are of short duration, including numerous local 

impact studies, and only rarely have studies sampled many of the shallow habitats typically 

preferred by smaller subyearling salmon. The most consistent monitoring in the estuary has 

emphasized the migration rates and survival of large, hatchery-tagged fish, and poorly represents 

wild, ocean-type species and life histories that are likely most dependent upon estuarine 

conditions. A more representative sampling program is needed to monitor variability in the 

estuarine life histories and performance of salmon. Such a program should include these 

objectives: 

• Monitor fish use of a variety of potential rearing habitats to assess variability and causal 

relationships affecting size characteristics, residence times, growth, and habitat use 

among hatchery-reared and wild salmonids. 

• Initiate intensive studies of the spatial and temporal distribution, abundance, and ecology 

of subyearling, ocean-type juvenile salmon in selected shallow-water habitats of the 

estuary. Document variability in life history diversity in their use of emergent and 

forested wetlands. 

• Identify upstream sources and freshwater histories of fish captured in the estuary through 

mark and tag recovery and DNA, scale, and otolith analyses. Initiate in-depth life history 

studies based on analyses of existing or new materials including scales or otoliths. 

• Investigate patterns of movement and migration through the estuarine gradient, from tidal 

freshwater through brackish and estuarine habitats in different regions of the estuary. 

• Compare patterns of estuarine wetland use by juvenile salmonids in the Columbia River 

with those in the Fraser River in British Columbia as a method for further evaluating flow 

regulation and hatchery influences, which are much greater in the Columbia system. 

Review the Scientific Basis for Proposed Habitat and Bathymetric Changes in the Estuary 

Relative to the Restoration Goals of the Columbia Basin Fish and Wildlife Program 

Habitat changes and economic activities within the estuary have been evaluated 

independently of management or restoration efforts that affect salmon and their habitats 

200
elsewhere in the Columbia River basin. The potential effects, for example, of ongoing or 

proposed estuarine dredging, spoil disposal, or habitat restoration activities on the Columbia 

Basin Fish and Wildlife Program have not been explicitly evaluated. 

Because all anadromous salmonids in the Columbia River pass through or rear in the 

estuary before migrating to the ocean, changes in estuarine conditions could determine the 

effectiveness of salmonid recovery efforts throughout the basin. Modeling results show that 

estuarine habitat opportunity for salmonids is sensitive to bathymetric change. In addition the 

response of predacious birds to dredge-spoil islands artificially created and maintained in the 

lower estuary illustrates that at least some estuarine habitat changes may have unexpected 

ecological consequences. 

Despite these risks, impact assessments associated with dredging and disposal activities 

usually have focused on localized impacts and have not considered salmonid responses to 

changes in habitat opportunity or capacity at a landscape scale. Nor have they considered the 

history of incremental change upon which each new project is superimposed or the broader 

responses of the ecosystem to physical habitat modifications. Thus an independent scientific 

review is recommended to evaluate the following: 

• the scientific assumptions of Columbia River dredging and disposal programs relative to 

the goals and conceptual framework of the Columbia Basin Fish and Wildlife Program; 

• the potential effects of historical changes in bathymetric profile on the distribution and 

availability of salmonid habitat and, in particular, the estuary’s capacity to support a 

diversity of salmon life histories; and 

• the significance of dredge disposal activities as a factor in estuarine habitat and 

ecosystem change that could affect the performance of juvenile salmon. 

Use Physical Observations and Hydrodynamic Modeling to Assess 

the Effects of Bathymetric Change, Flow Regulation, and Alternative 

Restoration Designs on Habitat Opportunity 

Our modeling methodology has proven to be a useful approach for evaluating the 

relative effects of flow modification and bathymetric change on habitat opportunity for salmon. 

Its present application, however, is limited by several critical data gaps, including the lack of 

present-day, high resolution bathymetric data and physical observations for shallow regions of 

the estuary. For example, the ability of the model to characterize physical habitat opportunity 

relative to the depth criterion (much more so than opportunity determined with respect to the 

velocity criterion) was very sensitive to assumed bathymetric configurations in the shallow areas 

of the estuary. This emphasizes the need to obtain accurate bank-to-bank bathymetric data for 

the lower river and estuary if there is to be an improved understanding of the impacts of river 

flow on physical habitat opportunity. The following activities are recommended: 

• Revise historical bathymetric data and acquire new data on present-day, shallow-water 

bathymetry and circulation processes to resolve the lack of confidence and robustness in 

model predictions of habitat opportunity, especially those based on the depth criterion. 

201
• Conduct new simulations that include three-dimensional modeling of salinity intrusion 

and stratification as a third environmental variable (in addition to depth and velocity) that 

is an important determinant of juvenile salmon distribution and residence time. Use the 

model to evaluate sensitivity of the estuary to incremental physical changes associated 

with diking, dredging, and flow regulation and the implications of these results for future 

management of the estuary. 

• Reexamine the results of hydrodynamic modeling to evaluate landscape connectivity and 

other spatial indices affecting salmon habitat opportunity between historical conditions 

and the modern estuary configuration. 

• Conduct simulations to evaluate changes in salmon habitat opportunity for alternative 

restoration scenarios and a range of flow conditions. 

Review Results of Estuarine Predation Studies in the Context 

of Salmon Population and Habitat Change 

It is unclear whether the high rates of salmon predation by Caspian terns and other 

marine birds in the estuary is a significant factor affecting salmon recovery or an ecological 

symptom of other changes, including alteration of estuarine habitats, simplification of the 

geographic structure of salmon populations, and reduced variation in salmon rearing and 

migration behaviors. 

High predation rates on juvenile salmonids, however, could result from replacing a broad 

continuum of salmon life history types with punctuated releases of large hatchery fish that are 

concentrated in relatively few estuarine habitats over reduced time periods. Hatchery-induced 

changes in surface-feeding behavior also could be a factor increasing the vulnerability of salmon 

smolts to predators. Emphasis on estimating predation rates alone may lead to inappropriate 

salmon recovery proposals unless these results are evaluated in a broader historical and 

ecological framework. Independent scientific assessments of salmon predation studies are 

needed in the Columbia River estuary to address the following objectives: 

• Examine the assumptions and results of ongoing predator studies in the context of 

historical and present-day estuarine habitat opportunity; salmon migration, rearing, and 

feeding behaviors; and fish densities in the estuary. 

• Review the effects of bird predators on rates of adult salmon return to the Columbia 

River basin. 

• Recommend methods for testing alternative hypotheses to explain high predation rates, 

and identify what, if any, recovery measures may be appropriate. 

Assess the Effects of Altered Habitats and Food Webs on the Capacity 

of the Estuary to Support Juvenile Salmon 

Results of this review indicate that a variety of ecological changes may have affected the 

capacity of the estuary to support wild subyearling Chinook salmon. These changes include loss 

of floodplain and other wetland habitats, the effects of climatic changes on physical processes 

and estuarine food webs, interactions with an increasing number of nonindigenous species, and 

shifts in the timing of established patterns of river flow and salmon migrations. Unfortunately, 

202
the direction or magnitude of these ecological changes cannot be assessed from the limited 

empirical data available. 

The effects of altering food-web sources through habitat modifications, for example, have 

not been directly evaluated. We also have little data to assess the effects of a two-week advance 

in the spring freshet because of flow regulation and a substantial delay in peak salmon 

migrations because of hatchery and other influences. If estuarine prey production cycles and 

salmon migration behaviors are adaptive, and linked to flow variations, then such changes could 

create a mismatch between salmon and their prey resources, reducing the productive capacity of 

the estuary. 

Changes in the coarse and fine sediment budgets, particularly the quality of organic 

matter input to the system, also are poorly understood. The following research activities are 

recommended to evaluate the effects of modifying estuarine habitats and food webs on the 

salmon-rearing capacity of the estuary: 

• Use natural stable isotope analyses or other methods to investigate potential food-web 

disruptions because of habitat loss and degradation. These losses also should be 

evaluated in terms of changes to estuarine physical processes, through numerical model 

investigations and analyses of historical and contemporary data. 

• Use field studies and modeling to evaluate the potential risk imposed on salmon recovery 

by nonindigenous species influencing estuarine habitats and food webs supporting 

juvenile salmon. This should include, but not necessarily be limited to, American shad, 

Asian clam, purple loosestrife (Lythrum salicaria), and other potential nonindigenous 

community dominants. 

• Evaluate historical and present-day relationships between flow variability, production of 

key salmonid prey species (e.g., Corophium spp.), and the timing of salmonid migrations 

to the estuary. 

• Assess long-term human and climatic effects on sediment budgets and inputs of organic 

matter. Evaluate the influence of potential climatic trends and rates of sea-level rise on 

the feasibility of salmon recovery actions that involve estuarine habitat restoration and 

river-flow modifications. 

• Review the scientific design and results of recent estuarine predation studies in the 

context of historical changes in salmon populations and estuarine habitat opportunity. 

203
204
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228
Appendix A: Timeline for 

the Columbia River Basin, 1775–2000 

Table A-1. Time line of historical, scientific, legal, and natural events affecting salmonids in the 

Columbia River basin. 

Date 

Historic/ 

scientific 

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events 

1775 Bruno de Heceta, 

aboard the Santiago, 

sights the Columbia 

River, naming it 

the Rio San Roque 

Estimated historic 

Columbia River 

salmon runs fluctuate 

between 11 and 

16 × 106 fish, of which 

Native North Americans 

may have captured 

4.5–6.3 × 106

 1776–

1787 

1788 John Mears, aboard the 

Felice, encounters 

breakers at the 

Columbia’s mouth 

1789 

1790 Britain gains rights to 

territory in treaty with 

Spain 

1791 

1792 American Captain Robert 

Gray, aboard the 

Columbia Rediva,

enters the estuary and 

names river; Broughton 

maps the estuary 

to Point Vancouver 

1793 De Heceta maps 

the estuary 

 1794–

1799 

229
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date 

Historic/ 

scientific 

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events 

1800 Major ash fall from 

Mount St. Helens

 1801–

1803

1804 Lewis and Clark 

departs St. Louis 

1805 Lewis and Clark 

arrive at estuary 

1806 Lewis and Clark 

spend winter at 

Fort Clatsop and 

return east 

1807 David Thompson starts 

mapping upper 

Columbia River 

 1808–

1809 

1810 John Jacob Astor forms 

the Pacific Fur Company, 

the first permanent 

fur-trading colony 

1811 Astor’s Tonquin

arrives; Fort Astoria 

constructed 

1812 

1813 North West Fur Co. buys 

Astoria 

 1814–

1817 

1818 Spring Chinook salmon 

harvest begins 

 1819–

1822 

1823 Astor Company exports 

pickled salmon to London 

1824 

230
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date 

Historic/ 

scientific 

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events 

1825 Hudson’s Bay Company 

establishes Fort 

Vancouver and Fort 

Coleville; disease 

reduces Lower Chinook 

Indian population to half 

of its historical level

1826

1827 Dr. John McLoughlin of 

Hudson’s Bay Co. builds 

first sawmill in Pacific 

Northwest at Vancouver 

1828 

1829 Capt. John Dominis 

brings the brig Owyhee

into the Columbia River 

to fish salmon and trade. 

During two summers in 

the area, they put up 50 

barrels of salted salmon 

that sold in Boston in 

1831 for $0.10 per 

pound. 

1830 

1831 Mount St. Helens ash fall 

1832 

1833 John Ball is first teacher 

at first school in the 

Pacific Northwest at 

Fort Vancouver 

 1834–

1835 

1836 The Beaver, first 

steamship on river, 

arrives at Fort Vancouver 

1837 M.C. Ewing, in 

USS W.A. Talcum, maps 

90 miles upriver 

231
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date 

Historic/ 

scientific 

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events 

1838

1839 Sir Edward Beecher 

conducts first official 

survey of bar conditions 

in HMS Sulphur

1840 Approximately 800 

Euro-American settlers 

in Oregon country

1841 Com. Charles Wilkes 

surveys estuary for the 

United States; USS 

Peacock wrecks on north 

(Peacocks) spit 

1842 W. W. Raymond builds 

first frame house in the 

region; extensive ash fall 

and pyroclastic eruptions 

from Mount St. Helens 

begin 

1843 Irrigation begins 

in watershed 

 1844–

1846 

1847 Oregon Territorial 

Legislature passes 

law creating pilot 

service; S. C. Reeves 

is first pilot 

1848 Oregon becomes a 

territory 

1849 Lt. Commander William 

P. McArthur and Lt. 

Washington A. Bartlett 

begin first survey of U.S. 

coast 

Second largest spring 

freshet on record, 

measured at 

31.1–34.0 × 103

 m3s

-1

at The Dalles 

1850 

1851 Tansey Pt. treaties with 

Lower Chinook Indians; 

only ≈8,000 native 

peoples survive in 

Columbia River basin 

232
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1852 

1853 Washington becomes 

a territory 

 1854–

1855 

1856 First Cape 

Disappointment 

Lighthouse is built: cost, 

$38,000 

1857 Mount St. Helens 

ash falls and pyroclastic 

eruptions cease 

1858 

1859 Oregon attains 

statehood 

24.6 × 103

 m3s

-1

spring freshet 

 1860–

1861 

1862 26.9 × 103

 m3s

-1

spring freshet; also 

1861–1862 winter 

flood on Willamette 

River largest on 

record, 8.5 × 103 

m3s

-1, with Portland 

inundated twice 

during the winter 

1863 

1864 Moderately strong 

spring freshet of 

>21.2 × 103

 m3s

-1

1865 

1866 First channel 

dredging 

George Hume and 

Andrew Hapgood build 

Northwest’s first cannery 

at Oak Point; first 

intensive fishery; 

272,000-lb Chinook catch 

Moderately strong 

spring freshet of 

>21.2 × 103

 m3s

-1

233
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1867 Hume and Hapgood can 

18,000 cases of Chinook; 

fishermen earn $.15 per 

fish 

 1868–

1869 

1870 10,200,000 lb 

Chinook catch 

1871 24.4 × 103

 m3s

-1

spring freshet 

1872 

1873 Four canneries operating 

1874 

1875 Point Adams 

Lighthouse is completed 

Oregonian reports 

on 3 March that 

U.S. Fish Commissioner 

Spencer Baird predicts 

Columbia River salmon 

fisheries will likely be 

depleted, like other U.S. 

and European fisheries, 

because of overfishing, 

dams, and habitat loss. 

1876 First scrape 

dredging of 

Columbia River 

entrance bar 

27.2 × 103

 m3s

-1

spring freshet 

1877 Oregon and Washington 

legislatures approve laws 

to temporarily close 

fisheries but provide no 

enforcement; 

Oregon/Washington Fish 

Propagating Co., 

Clackamas Hatchery 

begins production 

1878 Fort Canby near presentday Ilwaco, Washington, 

is site of first life-saving 

station 

234
Table A-1 continued. Time line of historical, scientific1, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1879 

1880 25.8 × 103 m3s

-1

spring freshet 

1881 Lt. Thomas W. Symons, 

USACE, maps estuary 

1882 24.9 × 103

 m3s

-1

spring freshet; large 

winter flood on 

Umatilla River 

1883 Transcontinental railroad 

is completed 

55 canneries operating in 

estuary, canning 629,400 

cases (catch of 42,799,000 

lb Chinook), which is 

peak Chinook harvest 

1884 

1885 South Jetty 

construction begins 

1886 Columbia River 

Fisherman’s Protective 

Union formed 

1887 T. M. Sullivan 

Dam, first dam of 

significant size in 

the system, is built 

on Willamette 

River 

First regulatory board 

(3 members) in Oregon 

attempts to supervise 

fishery; state Clackamas 

Hatchery production 

begins 

25.5 × 103

 m3s

-1

spring freshet 

1888 Last year that only 

Chinook were caught 

commercially; federal 

Clackamas Hatchery 

production begins 

1889 Washington 

attains statehood 

Sockeye (blueback), 

1,210,000 lb, and 

steelhead, 1,727,000 lb, 

begin appearing in catch; 

state Warrendale Hatchery 

begins production 

235
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1890 Fall Chinook harvest 

begins; fish commission is 

established in 

Washington; report 

to Oregon State Board 

of Fish Commissioners 

on juvenile loss in 

irrigation ditches 

Second largest winter 

flood on Willamette 

River 

1891 

1892 Spring and summer 

Chinook runs 95% of 

canneries; declining 

numbers of Chinook; first 

coho (283,000 lb) harvest 

1893 Snag Island dike 

is built; Cordell 

Channel flow is 

diverted to 

North Channel 

Salmon price is $1.15/lb; 

first chum (157,000 lb) 

harvest; U.S. Fish 

Commissioner Marshall 

MacDonald warns Oregon 

Governor of “disastrous 

outlook for the future of 

salmon fisheries of the 

Columbia” 

1894 Fishermen’s Protective 

Union affiliated 

with American 

Federation of Labor 

Largest spring freshet 

on record, measured 

24. × 103

 m3s

-1 at The 

Dalles 

1895 South Jetty is 

completed; rock 

ledge near 

Astoria is blasted 

30,254,000 lb Chinook 

catch; state hatcheries at 

Chinook and Kalama, and 

private hatchery on upper 

Clackamus, begin 

production 

1896 Columbia River Packers’ 

association formed 

Moderately strong 

spring freshet of 

>21.2 × 103

 m3 s-1

1897 Federal Little White 

Salmon and Upper 

Clackamus Hatcheries 

begin production 

Moderately strong 

spring freshet of 

>21.2 × 103

 m3s

-1

1898 North Head Lighthouse 

is completed 

236
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1899 7.6-m (25 feet) 

navigational 

channel from mouth 

to Portland gets OK 

State Wind, Wenatchee 

hatcheries begin 

production 

Moderately strong 

spring freshet of 

21.2 × 103

 m3s

-1

1900 American Indian 

population has declined 

by 95%, while EuroAmerican population 

has increased to 

1.1 × 106

2,000 km2 of 

Columbia River 

basin under 

irrigation 

1901 6.1 × 103

 m3s

-1

winter flood on 

Willamette River 

1902 Dredging across 

Upper Sands Shoal 

is completed; 

navigational 

channel is realigned 

1903 Dredge Grant arrives 

in estuary 

Moderately strong 

spring freshet of 

>21.2 × 103

 m3s

-1; 

6.6 × 103

 m3s

-1 

winter flood on 

Willamette River 

1904 Dredge Chinook arrives 

in estuary 

1905 River and Harbor 

Act of 1905 

approves Entrance 

Project, including 

South Jetty 

extension 

1906 Steamships Charles R. 

Spencer and Bailey 

Gatzert race from The 

Dalles to Portland; the 

Spencer runs the 

Cascades and wins 

1907 6.0 × 103

 m3s

-1 

winter flood on 

Willamette River 

1908 

237
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1909 Substantial dredging 

begins in estuary; 

Grays River 

channel obstructions 

are cleared 

State Bonneville Hatchery 

begins production 

5.5 × 103

 m3 s-1

winter flood on 

Willamette River 

1910 Lower Salmon and 

Swan Falls Dams 

(Snake River) is 

completed 

Hatcheries started rearing 

(feeding) fry 

1911 36,603,000 lb. 

Chinook catch, but 

marked decline noted 

1912 Spring and summer-run 

Chinook had dropped 

by 75% 

1913 Extension to South 

Jetty is completed; 

North Jetty 

construction begins; 

Cowlitz River, 

Oregon Slough, and 

Baker Bay channels 

are dredged 

1914 Rich’s first year 

sampling juvenile 

salmon 

South Jetty 

extension 

completed; 

extensive dredging 

and pile dike 

construction begins 

in river channel 

1915 

1916 Rich’s last year sampling 

juvenile salmon 

1917 North Jetty 

extension is 

completed; 9.1 m 

(30 feet) channel is 

authorized from 

mouth to Brookfield

 1918–

1919 

238
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1920 North Jetty 

extension 

completed; 9.1 m 

(30 feet) channel 

authorized from 

mouth to Brookfield

Harvest in obvious 

decline 

 1921–

1922 

1923 5.6 × 103

 m3s

-1 

winter flood on 

Willamette River 

1924 Clatskanie River 

channel is dredged 

State Klaskanine Hatchery 

begins production 

 1925–

1927 

1928 Deep River channel 

is cleared; 10.7 m 

(35 ft) river channel 

is recommended 

 1929–

1930 

1931 South Jetty 

rehabilitation 

begins; Lake River 

channel is dredged 

1932 USACE conducts current 

survey at entrance 

Chinook Island pile 

dike is constructed 

1933 Rock Island Dam is 

completed 

1934 U.S. Bureau of Fisheries 

begins comprehensive 

survey of Columbia 

River tributaries 

Ilwaco Channel is 

completed 

239
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1935 10.7 m (35 feet) 

Columbia River 

channel is 

completed; dikes 

along river are 

completed; 

Harrington Point, 

Multnomah, and 

Cathlamet channels 

is completed 

1936 Estimated 175 dams 

in Columbia River 

basin 

1937 Bonneville Power 

Administration (BPA) is 

established 

1938 Bonneville Dam is 

completed; 

Youngs Bay 

channel is cleared; 

North Jetty 

rehabilitation begins

1939 Jetty A, North Jetty 

rehabilitation and 

Sand Island pile 

dikes are 

completed; 

Skipanon Channel 

and Westport and 

Elochoman sloughs 

are dredged 

Fisheries biologist Rich 

predicts rapid 

“extermination of a large 

part of the remaining runs 

of Chinooks and 

bluebacks” 

1940 Chinook Channel 

and Astoria 

mooring basin and 

breakwaters are 

completed

1941 Grand Coulee Dam 

completed; concrete 

terminal added to 

South Jetty 

1942 

240
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1943 5.9 × 103 m3s

-1 

winter flood on 

Willamette River 

1944 Ilwaco Channel is 

completed 

1945 Lois Island is 

created with 

dredged material; 

routine annual is 

dredging of 

entrance begins 

5.2 × 103

 m3s

-1 

winter flood on 

Willamette River 

1946 USACE initiates research 

on radionuclides in-river, 

estuary, and coastal 

ocean 

1947 USGS bathymetric 

survey of estuary and 

river begins 

1948 Ilwaco and three 

pile dikes on Sand 

Island are 

completed 

Third largest spring 

freshet on record, the 

“Vanport Flood” 

measured 

28.3 × 103

 m3s

-1 

at The Dalles 

1949 Columbia River 

Advisory Group (CRAG) 

is formed to advise 

Hanford operations 

Bliss Dam is 

completed 

(Snake River) 

1950 Flood Control Act 

of 1950 

Astoria East 

Mooring Basin is 

completed 

1951 Desdemona Shoal 

Channel 

realignment begins 

1952 C. J. Strike Dam is 

completed 

(Snake River) 

1953 Fourth Sand Island 

pile dike is 

completed 

241
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1954 McNary Dam is 

completed; River 

and Harbor Act of 

1954 approves 

14.6-m (48 feet) 

entrance channel 

project 

1955 Chief Joseph Dam 

is completed 

1956 

1957 The Dalles Dam is 

completed; 

Warrenton Mooring 

Basin dredging and 

Ilwaco Channel 

deepening are 

completed 

1958 Brownlee Dam 

(Snake River) is 

completed; 

Westport Slough is 

cleared; Chinook 

breakwaters are 

extended; dredge 

disposal Site B 

becomes primary 

disposal area 

1959 Major USACE-supported 

circulation study begins 

Priest Rapids Dam 

is completed 

1960 Cowlitz River 

channel is dredged 

1961 Rocky Reach Dam, 

and Ice Harbor and 

Oxbow dams on 

Snake River, are 

completed; South 

Jetty and Jetty A are 

rehabilitated 

242
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date 

Historic/ 

scientific 

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events 

1962 Completion of USACEWES physical model of 

estuary; Working 

Committee for Columbia 

River Studies forms to 

probe Hanford 

radionuclides

12.2-m (40 feet) 

Columbia River 

channel to RKm 

169 and 18.5 km 

up Willamette River 

gets approval

1963 USACE-WES prototype 

physical measurements 

begin 

Wanapum Dam is 

completed 

1964 5.1 × 103

 m3 s-1

winter flood on 

Willamette River 

1965 Radionuclide studies of 

estuary sediments 

1966 Astoria-Megler Bridge 

completed; radionuclide 

studies of Columbia 

River 

1967 Haertel and Osterberg 

publish first major 

scientific paper on biota 

of the estuary (Ecology 

48:459–472) 

Wells Dam and 

Hells Canyon Dam 

completed 

(Snake River) 

1968 John Day and 

Arrow 

Lake/Keenleyside 

Dams completed 

1969 Haertel et al. publish first 

significant scientific 

treatise on nutrient and 

plankton dynamics 

(Ecology 50:962–978) 

1970 Little Goose Dam 

completed 

(Snake River) 

1971 

243
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1972 Pruter and Alverson’s 

“The Columbia River 

Estuary and Adjacent 

Ocean Waters: 

Bioenvironmental 

Studies” published as a 

compilation of USACE 

studies in the estuary and 

ocean since 1942 

1973 Mica Lake Dam and 

Lower Granite 

(Snake River) dams 

completed 

1974 

1975 USACE current meter 

studies 

1976 12.2 m (40 feet) 

river channel 

completed from 

entrance to 

Portland/ 

Vancouver; Oregon 

Slough deepened 

1977 15.9 m (52 feet) 

entrance project 

initiated 

1978 USACE current meter 

studies 

1979 Initiation of CREDDP 

investigations 

1980 Mount St. Helens erupts, 

massive mudflows run 

down Toutle River into 

the Cowlitz River and 

then into the Columbia 

River 

31,6000 km2

 

under irrigation 

1981 U.S. NOS current meter 

study 

1982 Coal port channel to 

Tongue Point proposed 

244
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1983 5–11 × 106 m3 

of material is 

dredged from the 

Cowlitz/Columbia 

confluence 

1984 Final CREDDP 

“Integration Report” 

published 

Revelstoke Dam is 

completed 

1985 Total annual water 

withdrawal of 

13,300 × 106

 m3

 1986–

1988 

1989 Deepening of 

13.1 m (43 feet) 

navigational 

channel is 

authorized 

1990 Five-year lower 

Columbia River Bi-state 

Water Quality Study 

begins

Snake River sockeye and 

Chinook are listed under 

Endangered Species Act

1991

1992 Snake River fall Chinook 

is listed as threatened 

under ESA

1993

1994 Feasibility study of 

dredging 

navigational 

channel to 13.1 m 

(43 feet) begins

1995 

1996 With completion of 

Lower Columbia River 

Bi-state Water Quality 

Study, lower river and 

estuary become National 

Estuary Program site 

(U.S. EPA) 

245
Table A-1 continued. Time line of historical, scientific, legal, and natural events affecting salmonids in 

the Columbia River basin. 

Date

Historic/ 

scientific

Hydropower, 

irrigation, 

and navigation Salmon Peak flow events

1997 Strongest spring 

freshet in 23 years, 

but only 

16.2 × 103

 m3s

-1

1998 Upper Columbia River 

spring-run Chinook and 

lower Columbia River 

steelhead ESU is proposed 

for listing as endangered, 

and several mid- and 

lower-Columbia River 

Chinook ESU stocks as 

threatened, under ESA 

1999 National Estuary 

Program completes 

comprehensive 

management plan for 

lower river and estuary 

USACE approves 

environmental 

impact statement to 

deepen the 

Columbia River 

navigation channel 

from 40 to 43 feet. 

10-23 × 106

 salmon 

smolts are estimated to be 

consumed by Caspian 

terns nesting on Rice 

Island, an artificial, 

dredged material disposal 

island in the middle of the 

estuary 

2000 

246
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-NWFSC67 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.

59 Sloan, C.A., D.W. Brown, R.W. Pearce, R.H. Boyer, J.L. Bolton, D.G. Burrows, D.P. Herman, and

M.M. Krahn. 2004. Extraction, cleanup, and gas chromatography/mass spectrometry analysis of

sediments and tissues for organic contaminants. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-59, 47 p. NTIS PB2004-105739.