The Role of the Estuary in the Decline and Recovery of Columbia River salmon

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Civil and Environmental Engineering
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January 2005
Salmon at River's End: Te Role of the Estuary in the Decline and
Recovery of Columbia River salmon
Daniel L. Botom
Portland State University
Charles A. Simenstad
Portland State University
Jennifer Burke
Antonio M. Baptista
David A. Jay
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Citation Details
Botom, 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.
Tis Technical Report is brought to you for free and open access. It has been accepted for inclusion in Civil and Environmental Engineering Faculty
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Authors
Daniel L. Botom, Charles A. Simenstad, Jennifer Burke, Antonio M. Baptista, David A. Jay, Kim K. Jone,
Edmundo Casillas, and Michael H. Schiewe
Tis technical report is available at PDXScholar: htps://pdxscholar.library.pdx.edu/cengin_fac/24
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
U.S. DEPARTMENT OF COMMERCE
National Oceanic and Atmospheric Administration
National Marine Fisheries Service
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 infor-
mal scientific and technical publications when com-
plete formal review and editorial processing are not
appropriate or feasible due to time constraints. Docu-
ments 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
1 University of Washington
School of Aquatic and Fishery Sciences
Seattle, Washington 98195
2 Oregon Health and Science University
OGI School of Science and Engineering
Department of Environmental and Biomolecular Systems
Beaverton, Oregon 97006
3 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
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 (
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