Columbia River Estuary 

ESA Recovery Plan Module 

for Salmon and Steelhead

National Marine Fisheries Service

Northwest Region

January 2011

NOTE TO READERS: 

This Columbia River Estuary Recovery Plan Module will be the basis of estuary recovery actions 

for Endangered Species Act-listed salmon and steelhead in the Columbia River Basin. The 

module will be incorporated by reference into recovery plans for listed Columbia Basin 

salmon evolutionarily significant units (ESUs) and steelhead distinct population segments 

(DPSs). It is important to have a unified set of actions for the Columbia River estuary to 

address the needs of all listed Columbia Basin ESUs and DPSs. 

This Columbia River Estuary Recovery Plan Module was prepared for NOAA’s National 

Marine Fisheries Service (NMFS) by the Lower Columbia River Estuary Partnership, 

(contractor) and PC Trask & Associates, Inc. (subcontractor). 

DISCLAIMER: 

Recovery plans delineate such reasonable actions as may be necessary, based upon the best 

scientific and commercial data available, for the conservation and survival of listed species. 

Plans are published by the National Marine Fisheries Service (NMFS), sometimes prepared 

with the assistance of recovery teams, contractors, State agencies, and others. Recovery 

plans do not necessarily represent the views, official positions, or approval of any 

individual or agencies involved in the plan formulation, other than NMFS. They represent 

the official position of NMFS only after they have been signed by the Assistant 

Administrator. Recovery plans are guidance and planning documents only; identification of 

an action to be implemented by any public or private party does not create a legal obligation 

beyond existing legal requirements. Nothing in this plan should be construed as a 

commitment or requirement that any Federal agency obligate or pay funds in any one fiscal 

year in excess of appropriations made by Congress for that fiscal year in contravention of 

the Anti-Deficiency Act, 31 U.S.C. 1341, or any other law or regulation. Approved recovery 

plans are subject to modification as dictated by new findings, changes in species status, and 

the completion of recovery actions. 

LITERATURE CITATION SHOULD READ AS FOLLOWS:

National Marine Fisheries Service (NMFS). 2011. Columbia River Estuary ESA Recovery Plan 

Module for Salmon and Steelhead. NMFS Northwest Region. Portland, OR. January. Prepared 

for NMFS by the Lower Columbia River Estuary Partnership (contractor) and PC Trask & 

Associates, Inc., subcontractor.

Columbia River Estuary 

ESA Recovery Plan Module 

for Salmon and Steelhead

National Marine Fisheries Service

Northwest Region

Prepared for NMFS by the Lower Columbia River Estuary Partnership 

(contractor) and PC Trask & Associates, Inc. (subcontractor)

January 2011

iii

Contents

Acknowledgements......................................................................................................................... vii

Acronyms and Abbreviations .........................................................................................................xi

Glossary............................................................................................................................................ xiii

Executive Summary......................................................................................................................ES-1

1 The Columbia River Estuary and Plume ................................................................................1-1

Purpose and Development of the Estuary Recovery Plan Module..............................1-1

Formation and Current Characteristics of the Estuary ..................................................1-3

Estuary Reaches ...................................................................................................................1-4

Columbia River Plume .......................................................................................................1-8

Major Land Uses..................................................................................................................1-8

Two Centuries of Change...................................................................................................1-9

2 Salmonid Use of the Estuary and Plume.................................................................................2-1

Salmonid Species in the Columbia River Basin ..............................................................2-1

Life History Types and Strategies .....................................................................................2-2

Changes in Life History Diversity.....................................................................................2-3

Relationship of the Estuary to the Columbia River Basin .............................................2-5

Summary...............................................................................................................................2-8

3 Limiting Factors ...........................................................................................................................3-1

Determining Estuary Habitat Limiting Factors...............................................................3-1

Sources .....................................................................................................................3-1

Mortality Estimates ................................................................................................3-2

Density-Dependent Mortality...............................................................................3-3

Habitat-Related Limiting Factors......................................................................................3-4

Reduced In-Channel Habitat Opportunity.........................................................3-5

Reduced Off-Channel Habitat Opportunity.......................................................3-6

Reduced Plume Habitat Opportunity .................................................................3-8

Limiting Factor: Water Temperature...................................................................3-8

Limiting Factor: Stranding ..................................................................................3-10

Food Web-Related Limiting Factors ...............................................................................3-10

Food Source Changes...........................................................................................3-11

Competition and Predation.................................................................................3-13

Toxic Contaminants ..........................................................................................................3-15

Limiting Factor: Bioaccumulation Toxicity.......................................................3-18

Limiting Factor: Non-Bioaccumulative Toxicity..............................................3-18

Habitat Opportunity, Habitat Quality, and Synergistic Effects..................................3-21

Prioritization of Limiting Factors....................................................................................3-22

Summary.............................................................................................................................3-23

4 Threats to Salmonids ..................................................................................................................4-1

Flow-Related Threats ..........................................................................................................4-2

Threat: Climate Cycles and Global Climate Change.........................................4-4

Threat: Water Withdrawal ....................................................................................4-5

Threat: Flow Regulation ........................................................................................4-6
CONTENTS

iv

Sediment-Related Threats.................................................................................................. 4-6

Threat: Entrapment of Fine Sediment in Reservoirs ......................................... 4-7

Threat: Impaired Transport of Coarse Sediment............................................... 4-7

Threat: Dredging.................................................................................................... 4-7

Structural Threats................................................................................................................ 4-8

Threat: Pilings and Pile Dike Structures ............................................................. 4-8

Threat: Dikes and Filling....................................................................................... 4-9

Threat: Reservoir-Related Temperature Changes ........................................... 4-10

Threat: Over-Water Structures........................................................................... 4-10

Food Web-Related Threats .............................................................................................. 4-10

Threat: Reservoir Phytoplankton Production.................................................. 4-11

Threat: Altered Predator/Prey Relationships.................................................. 4-11

Threat: Ship Ballast Practices.............................................................................. 4-12

Water Quality-Related Threats ....................................................................................... 4-13

Threat: Agricultural Practices ............................................................................ 4-14

Threat: Urban and Industrial Practices............................................................. 4-14

Other Threats..................................................................................................................... 4-15

Threat: Riparian Practices ................................................................................... 4-15

Threat: Ship Wakes .............................................................................................. 4-16

Prioritization of Threats ................................................................................................... 4-16

Summary ............................................................................................................................ 4-20

5 Management Actions.................................................................................................................. 5-1

Identification of Management Actions ............................................................................ 5-1

Other Recommended Management Actions................................................................... 5-4

Evaluation of Management Actions: Constraints to Implementation......................... 5-6

Evaluation of Management Actions: Survival Improvement Targets...................... 5-33

Estimating Juvenile Mortality in the Estuary and Plume .............................. 5-33

Establishing Survival Improvement Targets ................................................... 5-34

Assigning Survival Improvement Targets to Recovery Actions................... 5-37

Uses of the Survival Improvement Targets...................................................... 5-38

Evaluation of Management Actions: Costs and Schedule........................................... 5-41

Summary ............................................................................................................................ 5-68

6 Research, Monitoring, and Evaluation .................................................................................... 6-1

RME Framework................................................................................................................. 6-2

Status and Trends Monitoring ............................................................................. 6-2

Action Effectiveness Research.............................................................................. 6-5

Critical Uncertainties Research............................................................................ 6-6

Implementation and Compliance Monitoring................................................... 6-7

Adaptive Management Approach....................................................................... 6-7

Coordination........................................................................................................... 6-8

Data and Information Management.................................................................... 6-9

Synthesis, Reporting, and Evaluation............................................................... 6-10

Existing Programs and Projects and Additional Monitoring Needs ......................... 6-10

Existing Programs and Projects ......................................................................... 6-10

RME Needs, Existing Project Coverage, and Recommended Projects ......... 6-11

Monitoring Recommendations .......................................................................... 6-11

Estimated Costs................................................................................................................. 6-11
CONTENTS

v

Summary.............................................................................................................................6-11

7 Perspectives on Implementation ..............................................................................................7-1

Putting the Estuary in Context ..........................................................................................7-1

Factors That Influence Decision Making..........................................................................7-2

Significance of Constraints to Implementation..................................................7-2

Management Actions Offering the Greatest Survival Benefits ........................7-4

Costs for Constrained Implementation of Management Actions....................7-7

Cost-Effectiveness of Management Actions .......................................................7-9

Improving Ecosystem Health ..........................................................................................7-11

Implementation Issues......................................................................................................7-15

Relationship of the FCRPS BiOp to the Estuary Module.............................................7-15

Preparation for Decision Making....................................................................................7-16

8 References .....................................................................................................................................8-1

Appendixes

A Selected Threats to Salmonids by Reach

B Development of Survival Improvement Targets

Tables

ES-1 Management Actions to Address Threats..................................................................... ES-7

ES-2 Management Actions Important for Survival of Ocean- and StreamType Salmonids .............................................................................................................. ES-10

2-1 Characteristics of Ocean- and Stream-Type Salmonids.................................................2-2

2-2 Life History Strategies and Their Attributes ...................................................................2-4

2-3 Linkage between Salmonid ESU, Dominant Life History Type, and Life History 

Strategy .................................................................................................................................2-5

3-1 Impact of Limiting Factors on Ocean- and Stream-Type Salmonids .........................3-24

3-2 Limiting Factor Prioritization ..........................................................................................3-25

4-1 Linkages Between Limiting Factors and Threats to Ocean- and Stream-Type 

Salmonids ...........................................................................................................................4-17

4-2 Prioritization of Threats to Ocean- and Stream-Type Salmonids...............................4-20

5-1 Management Actions to Address Threats........................................................................5-2

5-2 Constraints to Implementation of Management Actions ..............................................5-8

5-3 Summary of Constraints to Implementation of Management Actions......................5-31

5-4 Estimated Mortality Rates, Survival Rates, and Survival Improvement Targets for 

Wild, ESA-Listed Juveniles ..............................................................................................5-35

5-5 Survival Improvement Targets Allocated to Management Actions ..........................5-39

5-6 Estimated Cost and Schedule ..........................................................................................5-44

5-7 Summary of Costs of Management Actions ..................................................................5-67

6-1 Monitoring Plans Applicable to Estuary RME................................................................6-3

6-2 Ongoing Monitoring Programs Applicable to Estuary RME (as of July 2009).........6-13

6-3 Ongoing Projects Addressing Estuary RME (as of July 2009).....................................6-15

6-4 Management Actions, Associated Monitoring Needs, and Existing Coverage........6-17

6-5 Recommended New RME Projects .................................................................................6-20

6-6 Monitoring Guidance for Estuary Recovery Plan Module RME................................6-21
CONTENTS

vi

6-7 Estimated Cost and Schedule.......................................................................................... 6-27

7-1 Management Actions Sorted by Degree of Constraint.................................................. 7-3

7-2 Management Actions Sorted by Benefit to Stream-type Juveniles .............................. 7-5

7-3 Management Actions Sorted by Benefit to Ocean-type Juveniles ............................... 7-6

7-4 Management Actions Sorted by Estimated Cost............................................................ 7-8

7-5 Management Actions Sorted by Cost/Survival Index ................................................ 7-10

Figures

ES-1 Listed Pacific Northwest ESUs........................................................................................ES-2

1-1 The Columbia River Estuary and Its Major Tributaries ................................................ 1-4

1-2 Lower Columbia River Estuary Reaches ......................................................................... 1-5

1-3 Plume Front ......................................................................................................................... 1-9

2-1 Historical and Contemporary Early Life History Types of Chinook Salmon in the 

Columbia River Estuary..................................................................................................... 2-7

3-1 Diked Areas in the Columbia River Estuary................................................................... 3-7

3-2 Temperatures of Water Entering the Estuary ................................................................. 3-9

3-3 Conceptual Model of the Columbia River Estuary Food Web................................... 3-12

3-4 Concentrations of PCBs in the Stomach Contents of Subyearling Fall Chinook ..... 3-20

3-5 Concentrations of DDTs in the Stomach Contents of Subyearling Fall Chinook .... 3-20

3-6 Concentrations of Total Aromatic Hydrocarbons in the Stomach Contents of 

Subyearling Fall Chinook ................................................................................................ 3-21

4-1 Conceptual Model of the Columbia River Estuary........................................................ 4-2

4-2 Changes in the Annual Columbia River Flow................................................................ 4-3

4-3 Subtidal, Intertidal, and Above-Tidal Estuarine Wetland Zones................................. 4-9

6-1 NMFS Listing Status Decision Framework ..................................................................... 6-8
vii

Acknowledgements

Many agencies, organizations, and individuals contributed to this document through review 

and comment, technical input, communication, and collaboration. The following entities 

and individuals, in particular, offered input and advice at key points during development of 

the estuary recovery plan module. Their assistance is greatly appreciated. 

Project Development, Drafting Assistance, Review, and Oversight (alphabetical)

Catherine Corbett Lower Columbia River Estuary Partnership

Patty Dornbusch National Marine Fisheries Service, 

Northwest Region

Elizabeth Gaar National Marine Fisheries Service,

Northwest Region

Gary Johnson Pacific Northwest National Laboratories

Lyndal Johnson National Marine Fisheries Service,

Northwest Fisheries Science Center

Ann Sihler Ann Sihler Writing and Editing 

Cathy Tortorici National Marine Fisheries Service,

Northwest Region

Technical Review, Data, and Input on Issues such as Prioritization of Limiting Factors, Threats, 

and Survival Improvement Targets (alphabetical)

Jeff Breckel Lower Columbia Fish Recovery Board

Ed Casillas National Marine Fisheries Service,

Northwest Fisheries Science Center

John Ferguson National Marine Fisheries Service,

Northwest Fisheries Science Center

Steve Manlow (formerly) Washington Department of Fish 

& Wildlife

Scott McEwen (formerly) Lower Columbia River Estuary 

Partnership
AKNOWLEDGEMENTS

viii

Other Input and Technical Assistance (alphabetical)

Ray Beamesderfer Cramer Fish Sciences

Matt Burlin (formerly) Lower Columbia River Estuary 

Partnership

Tom Cooney National Marine Fisheries Service,

Northwest Fisheries Science Center

Garth Griffin National Marine Fisheries Service,

Northwest Region

Evan Haas Lower Columbia River Estuary Partnership

Tracey Hillman BioAnalysts, Inc.

Krista Jones (formerly) Lower Columbia River Estuary 

Partnership

Rob Jones National Marine Fisheries Service,

Northwest Region

Lynne Krasnow National Marine Fisheries Service,

Northwest Region

Larry Lestelle Northwest Biostream

Bridgette Lohrman National Marine Fisheries Service,

Northwest Region

Naomi Lundberg National Marine Fisheries Service,

Office of Protected Resources

Keith Marcoe Lower Columbia River Estuary Partnership

Deb Marriott Lower Columbia River Estuary Partnership

Phil Miller Washington State Governor’s Salmon 

Recovery Office

Oregon Lower Columbia River 

Recovery Plan Stakeholder and 

Planning Teams

Oregon Mid-Columbia Steelhead 

Sounding Board

Larissa Plants National Marine Fisheries Service,

Office of Protected Resources

Mark Plummer National Marine Fisheries Service,

Northwest Fisheries Science Center
AKNOWLEDGEMENTS

ix

Susan Pultz National Marine Fisheries Service,

Office of Protected Resources

Dan Roby U.S. Geological Survey

Upper Willamette Recovery Plan 

Stakeholder Team

xi

Acronyms and Abbreviations

BACI before-after-control-impact

BiOp Biological Opinion

BMP best management practice

BMPs best management practices

cfs cubic feet per second

CRE Columbia River estuary

CSMEP Collaborative Systemwide Monitoring and Evaluation Project 

DDT dichlorodiphenyltricholoroethane 

DEQ Oregon Department of Environmental Quality

DPS distinct population segment

EDT Ecosystem Diagnosis and Treatment

ENSO El Niño/Southern Oscillation

EPA U.S. Environmental Protection Agency

ERME estuary research, monitoring, and evaluation

ESA Endangered Species Act

ESU evolutionarily significant unit

ETM estuarine turbidity maximum

FCRPS Federal Columbia River Power System

GIS geographic information system

HUC hydrologic unit code

ISAP Independent Science Advisory Panel

ISRP Independent Science Review Panel

LCFRB Lower Columbia Fish Recovery Board

LCRANS Lower Columbia River Aquatic Nonindigenous Species Survey

LIDAR Light Detection and Ranging

MMPA Marine Mammal Protection Act

MR&E monitoring, research, and evaluation 

NASQAN National Stream Quality Accounting Network

NMFS National Marine Fisheries Service

NOAA National Oceanic and Atmospheric Administration

NPCC Northwest Power and Conservation Council

PAHs polycyclic aromatic hydrocarbons

PCBs polychlorinated biphenyls
ACRONYMS AND ABBREVIATIONS

xii

PDO Pacific Decadel Oscillation

PIT passive integrated transponder 

PNAMP Pacific Northwest Aquatic Monitoring Partnership

RM river mile

RME research, monitoring, and evaluation

TMDL total maximum daily load

VGP vessel general permit

WDF Washington Department of Fisheries

WDFW Washington Department of Fish and Wildlife
xiii

Glossary

Accretion: The accumulation of sediment 

deposited by natural fluid flow processes.

Alevins: Salmonids at the life stage between 

egg and fry.

Amphipods: Benthic invertebrates, 

particularly the amphipod Americorophium 

salmonis, which is found in intertidal and 

shallow subtidal habitats of the Columbia 

River estuary and is seasonally important in 

the diet of juvenile salmonids.

Ancient marshes: Marshes formed between 

6,000 and 10,000 years ago. 

Bar: A ridge or succession of ridges of sand or 

other substances, especially a formation 

extending across the mouth of a river or 

harbor that may obstruct navigation. 

Bathymetry: The measure of the depths of 

oceans, seas, or other large bodies of water.

Beach erosion: The carrying away of beach 

materials by wave action, tidal currents, 

littoral currents, or wind.

Beach nourishment: The process of 

replenishing a beach by artificial means, such 

as through deposition of dredged materials; 

also called beach replenishment or beach 

feeding. 

Bedload: Sand that rolls and bounces along 

the surface of the riverbed, usually 

downstream, although there may be a small 

displacement toward deeper water caused by 

the side slopes of the riverbed. In sandy 

riverbeds, bedload transport shapes the bed 

into a series of sand waves. 

Beneficial use: Placement or use of dredged 

material for some productive purpose. 

Examples of beneficial uses include habitat 

development, beach nourishment, 

aquaculture, parks and recreation, shoreline 

stabilization, and erosion control. 

Benthic: Of or relating to the bottom of a body 

of water.

Buffer area: A parcel or strip of land that is 

designed and designated to permanently 

remain vegetated in an undisturbed and 

natural condition to protect an adjacent 

aquatic or wetland site from upland impacts, 

to provide habitat for wildlife. 

Centennial marshes: Marshes formed over the 

last century. 

Continental shelf: The zone bordering a 

continent extending from the line of 

permanent immersion to the depth (usually 

about 100 to 200 meters) at which there is a 

marked or steep descent toward greater 

depths. 

Delta: An alluvial deposit, usually triangular, 

at the mouth of a river. It is normally built up 

only where there is no tidal or current action 

capable of removing the sediment as fast as it 

is deposited. 

Deposition: The deposit of sediment in an 

area through natural means, such as wave 

action or currents, or mechanical means. 

Detritus: A loose mixture of organic material 

(dead plants and animals) and inorganic 

material (rock fragments) that results directly 

from disintegration of the material. 

Dikes: Earthen walls constructed to contain 

water; sometimes constructed around dredged 

material disposal sites but more commonly 

constructed as flood protection.

Dredging: The removal or redistribution of 

sediments from a watercourse. 

Ecosystem: A community of organisms in a 

given area together with their physical 

environment and its characteristic climate. 

El Niño/Southern Oscillation: A shorter term 

climate effect that alternates between cold and 

warm phases approximately every 3 to 7 

years; is associated with a warm-water current 

that periodically flows southward along the 

coast of Ecuador, and the southern oscillation 
GLOSSARY

xiv

in the atmosphere; affects climatic and ocean 

conditions throughout the Pacific region. 

Emergent marsh: A wet, springy peatland that 

occurs along the edges of lakes and streams 

and is covered by grass-like sedges and fed by 

minerals washing in from surrounding lands.

Emergent vegetation: Rooted plants that can 

tolerate some inundation by water and that 

extend photosynthesis parts above the water 

surface for at least part of the year; emergent 

vegetation is intolerant of complete 

inundation over prolonged periods. 

Estuarine turbidity maximum (ETM): A 

circulation phenomenon in an estuary that 

traps particles and promotes biochemical, 

microbial, and ecological processes that 

sustain an important pathway in the estuary’s 

food web. 

Estuary: A semi-enclosed coastal body of 

water with a free connection to the open ocean 

in which sea water is diluted with runoff from 

the land. 

Exotic species: A non-native plant or animal 

deliberately or accidentally introduced into a 

habitat.

Fill: Sand, sediment, or other earth materials 

that are placed, deposited, or stockpiled. 

Fingerling: A juvenile salmonid less than 1 

year old.

Floodplain: A flat tract of land bordering a 

river, mainly in its lower reaches, and 

consisting of alluvium deposited by the river 

during flooding. 

Fluvial: Involving running water; usually 

pertains to stream processes.

Forested wetlands: Wetlands that occur in 

palustrine and estuarine areas and possess an 

over story of trees, an understory of young 

trees or shrubs, and a herbaceous layer.

Freshet: High stream flow caused by rains or 

snowmelt and resulting in the sudden influx 

of a large volume of freshwater in the estuary.

Fresh water: Water that is less than 0.5 part 

salt per thousand. 

Fry: Juvenile salmonids that have absorbed 

their egg sac. 

Genetic diversity: Variation at the level of 

individual genes (polymorphism); provides a 

mechanism for populations to adapt to their 

ever-changing environment.

Habitat: The physical, biological, and 

chemical characteristics of a specific unit of the 

environment occupied by a specific plant or 

animal; the place where an organism naturally 

lives.

Habitat capacity: A category of habitat 

assessment metrics, including “habitat 

attributes that promote juvenile salmon 

production through conditions that promote 

foraging, growth, and growth efficiency, 

and/or decreased mortality” (Fresh et al. 

2005). 

Habitat connectivity: A measure of how 

connected or spatially continuous habitats 

occur in a larger ecosystem. 

Habitat opportunity: A category of habitat 

assessment metrics that evaluate the capability 

of juvenile salmon to access and benefit from 

the habitat’s capacity (Fresh et al. 2005). 

High marsh: A wetland ecosystem influenced 

by a marsh surface elevation at approximately 

mean higher high water that is inundated by 

only the most extreme high tides and is 

characterized by salt-tolerant emergent 

vegetation. 

Intertidal: Of or relating to the substrate that 

is exposed and flooded by tides; includes the 

associated splash zone.

In-water disposal: Placement of dredged 

material along the riverbed in or adjacent to 

the navigational channel or in designated inwater sites; commonly referred to as flow-lane 

disposal.

Limiting factor: Physical, chemical, or 

biological features that impede species and 

their independent populations from reaching 

viability status. 

Littoral: Of, relating to, or situated or growing 

on or near a shore; especially of the sea.
GLOSSARY

xv

Littoral current: A current running parallel to 

the beach and generally caused by waves 

striking the shore at an angle. 

Low marsh: A wetland ecosystem 

characterized by salt-tolerant emergent 

vegetation and twice-daily inundation of high 

tides. 

Macroinvertebrates: Invertebrates that are of 

visible size, such as clams and worms. 

Marsh: An area of soft, wet, or periodically 

inundated land, generally treeless and usually 

characterized by grasses and other low 

growth. 

Mean high water: The average height of all 

high waters over 19 years. 

Mean higher high water: The average height 

of the higher of two unequal daily high tides 

over 19 years. 

Mean low water: The average height of all 

low waters over 19 years. 

Mean lower low water: The average height of 

the lower of two unequal daily low tides over 

19 years. 

Macrodetritus: Dead or dying matter from a 

plant or animal that is visible to the unaided 

eye; usually larger than 1 to 2 mm in diameter. 

Microdetritus: Dead or dying matter from a 

plant or animal; usually smaller than 1 to 2 

mm in diameter. 

Navigational channels: Channels in estuaries 

and other water bodies that are created, 

deepened, and maintained by dredging to 

enable vessels to navigate safely between, into 

and out of ports, harbors, and marinas 

without running aground.

Nearshore: An indefinite zone extending 

seaward from the shoreline well beyond the 

breaker zone. 

Ocean-type: Of or relating to salmonid 

juveniles that enter the estuary as fry or 

fingerlings and stay in the estuary for weeks 

or months before entering the ocean; examples 

are chum and subyearling Chinook. 

Oligohaline: Of or relating to water having 

low salinity.

Overbank flooding: Out-of-bank flooding 

resulting from flow events that exceed the 

bankfull.

Over-water structures: Human-made 

structures, such as a pier, that extend over all 

or part of the surface of a body of water. 

Pacific Decadal Oscillation: A longer term 

climate effect that alternates between cold and 

warm phases approximately every 30 years. 

Pelagic: Pertaining to the open ocean.

Pinnipeds: Seals, sea lions, and walruses that 

belong to the taxonomic suborder called 

Pinnipedia, or the “fin-footed.” Pinnipeds are 

carnivorous aquatic mammals that use 

flippers for movement on land and in the 

water. The pinnipeds referred to in this 

document are Pacific harbor seals, California 

sea lions, and Stellar sea lions.

Pier: A structure, usually of open 

construction, extending out into the water 

from the shore, to serve as a landing place, 

recreational facility, etc., rather than to afford 

coastal protection. 

Piling: A long, heavy timber or section of 

concrete or metal that is driven into the earth 

or bottom of a water body to serve as a 

structural support or protection. 

Pile dike: Two parallel rows of piling that are 

tied together and extend 300 to 500 feet into 

the river. 

Pile dike field: Several pile dikes spaced 

about 1,200 to 1,500 feet apart, typically built 

to concentrate flow and stabilize the channel; 

within the dike field, current velocities are 

slowed and flow is deflected away from the 

river bank. 

Plume: The layer of Columbia River water in 

the nearshore Pacific Ocean. 

Polychlorinated biphenyls (PCBs): A group 

of synthetic, toxic industrial chemical 

compounds that are chemically inert and not 

biodegradable; they once were used in making 

paint and electrical transformers.
GLOSSARY

xvi

Polycyclic aromatic hydrocarbons (PAHs): A 

group of more than 100 different chemicals 

that are formed during the incomplete 

burning of coal, oil and gas, garbage, or other 

organic substances like tobacco or charbroiled 

meat.

Population: A distinct breeding unit of a 

species that exhibits similar life history 

strategies. 

Redds: Spawning nests used by trout and 

salmon.

Revetment: A facing of stone, concrete, etc., to 

protect an embankment or shore structure 

from erosion by wave action or currents. 

Salmonid: Any member of the family 

Salmonidae, which includes the salmon, trout, 

char, whitefishes, and grayling of North 

America.

Salmonid population viability: Measure of 

the status of anadromous salmonids that uses 

four performance criteria: abundance, 

productivity, spatial distribution, and 

diversity. 

Sand: An unconsolidated mixture of inorganic 

soil (possibly including disintegrated shells 

and coral) consisting of small but easily 

distinguishable grains ranging in size from 

about 0.062 mm to 2.0 mm. 

Sand waves: Waves of sand on the bottom of 

a riverbed that move in response to river 

discharge and bedload transport. In the 

Columbia, sand waves cover the riverbed and 

are typically 4 to 8 feet high and 300 to 400 feet 

long. When the river discharge is less than 

300,000 cfs, sand waves move only a few feet 

per day; however, when discharge exceeds 

400,000 cfs, sand wave movement can reach 20 

feet per day or more. 

Scour: The removal of underwater material by 

waves and currents, especially at the base or 

toe of a structure. 

Sediment: Material in suspension in water or 

recently deposited from suspension; in the 

plural, all kinds of deposits from the waters of 

streams, lakes, or seas.

Sediment trapping: The capture of sediments 

behind structures such as dams and shoreline 

armoring, which restrict sediments from 

entering systems. 

Shallows and flats: Areas from the 6-foot 

bathymetric contour line up to the edge of 

tidal marsh or swamp vegetation, or to mean 

higher high water where vegetation is absent. 

Shoaling: A gradual decrease in water depth 

as the result of the accretion of sediments. 

Smolts: Juvenile salmonids that have left their 

natal stream and are headed downriver 

toward the ocean.

Stream-type: Of or relating to salmonid 

juveniles that rear in freshwater for a year or 

more before entering the ocean. 

Threat: A human action or natural event that 

causes or contributes to limiting factors; 

threats may be caused by past, present, or 

future actions or events.

Tidal marshes: Areas dominated by emergent 

vegetation and low shrubs; are typically found 

from mean lower low water to slightly above 

mean higher high water, although they are 

rare at the lowest elevations.

Tidal prism: The difference in the volume of 

water covering an area, such as a wetland, 

during low tide and the volume covering it 

during the subsequent high tide. 

Tidal swamps: Shrub- and forest-dominated 

wetlands that extend up to the line of nonaquatic vegetation (the line at which excess 

water ceases to be a factor controlling the 

composition of the vegetation); tidal swamps 

may be of sufficiently high elevation that they 

are inundated only during spring tides, but 

they may also extend down below mean 

higher high water. 

Tide: The periodic rising and falling of the 

water that results from gravitational attraction 

of the moon and sun acting on the rotating 

earth. 

Turbidity: A condition in bodies of water 

where high sediment loads cause clouding of 

the water to varying extents; turbidity is an 

optical phenomenon and does not necessarily 
GLOSSARY

xvii

have a direct linear relationship to particulate 

concentration. 

Viable salmonid population: An independent 

population of Pacific salmon or steelhead 

trout that has a negligible (generally ≤5 

percent) risk of extinction over a 100-year 

timeframe.

ES-1

Executive Summary

What is the Estuary Recovery Module?

This estuary recovery plan module is one element of a larger regional planning effort to 

develop recovery plans for Endangered Species Act-listed salmon and steelhead trout in the 

Columbia River basin. Recovery plans are being developed for each of the 13 listed 

evolutionarily significant units (ESUs) in the Columbia.1

This estuary recovery plan module complements other recovery plans in the region. The 

planning area for the module is all tidally influenced areas of the Columbia River. The

upstream boundary of this area is Bonneville Dam, at River Mile 146, and the downstream 

boundary includes the Columbia River plume.

Figure ES-1 shows the 13 listed 

ESUs in the Columbia River basin grouped by region. The regions include the Lower 

Columbia, Upper Willamette, Middle Columbia, Snake, and Upper Columbia River ESUs. 

Within each of the regions, the ESUs have unique geographical boundaries that are based on 

similarities among populations. 

2

This estuary recovery plan module is intended to help answer questions about the degree to 

which the estuary and plume can contribute to salmon and steelhead recovery efforts 

throughout the Columbia River basin. The state of the science surrounding the estuary and 

plume is such that quantitative answers to questions about estuarine ecology are not 

necessarily available at this time. This is true in part because of the complexity of the 

ecological processes in the estuary and plume. However, it is also true because the 

Columbia River estuary and plume are only now being studied at a level of detail that 

With few exceptions, the module’s focus is 

limited to habitat conditions and processes in the Columbia River estuary and plume, rather 

than hatchery or harvest practices, hydroelectricity production, or tributary habitats in the 

Columbia River basin. The goal of the module is to identify and prioritize management 

actions that, if implemented, would reduce the impacts of limiting factors, meaning the 

physical, biological, or chemical conditions that impede salmon and steelhead survival 

during their migration through and rearing in the estuary and plume ecosystems. To 

accomplish this, changes in the physical, biological, or chemical conditions in the estuary are 

reviewed for their potential to affect salmon and steelhead. Then, the underlying causes of 

limiting factors are identified and prioritized based on the significance of the limiting factor 

and each cause’s contribution to one or more limiting factors. These causes are referred to as 

threats and can be either human or environmental in origin. Finally, management actions 

are identified that are intended to reduce the threats and increase the survival potential of 

salmon and steelhead during estuarine rearing and migration. Costs are developed for each 

of the actions using an estimated level of effort to implement actions. 

 1 NOAA’s National Marine Fisheries Service (NMFS) has revised its species determinations for West Coast steelhead under 

the Endangered Species Act (ESA), delineating steelhead-only “distinct population segments” (DPSs). The former steelhead 

ESUs included both anadromous steelhead trout and resident, non-anadromous rainbow trout, but NMFS listed only the 

anadromous steelhead. The steelhead DPS does not include rainbow trout, which are under the jurisdiction of the U.S. Fish 

and Wildlife Service. In January 2006, NMFS listed five Columbia River basin steelhead DPSs as threatened (71 FR 834). To 

avoid confusion, references to ESUs in this estuary recovery plan module imply the steelhead DPSs as well.

2 See Figures 1-1 and 1-2 for a depiction of the planning area. 
EXECUTIVE SUMMARY

ES-2

allows knowledge about this portion of the Columbia River ecosystem to be integrated into 

the understanding of life history patterns that have been well documented in the upstream 

portions of the basin.

FIGURE ES-1

Listed Pacific Northwest ESUs

This estuary recovery plan module is a synthesis of diverse literature sources and the direct 

input of estuary scientists. The module was developed by the Lower Columbia Estuary 

Partnership and a private consultant, PC Trask & Associates, Inc. The primary author was 

PC Trask & Associates, Inc., with significant involvement from Lower Columbia River 

Estuary Partnership staff. The author used several key documents as a platform for the 

module. One of those documents is the “Mainstem Lower Columbia River and Columbia 

River Estuary Subbasin Plan,” which the Lower Columbia River Estuary Partnership 

developed, along with its supplement, for the Northwest Power and Conservation Council’s 

Columbia River Basin Fish and Wildlife Program (Northwest Power and Conservation Council 

2004). In 2005, the Northwest Fisheries Science Center of NOAA’s National Marine Fisheries 

Service (NMFS) produced two important technical memoranda for the estuary: Salmon at 

River’s End (Bottom et al. 2005) and Role of the Estuary in the Recovery of Columbia River Basin 

Salmon and Steelhead (Fresh et al. 2005). The author used these two memoranda extensively 

and consulted other sources as well, including many primary sources. Area experts from the 
EXECUTIVE SUMMARY 

ES-3

NMFS Northwest Fisheries Science Center and Northwest Regional Office, the Lower 

Columbia River Estuary Partnership, and the Lower Columbia Fish Recovery Board 

provided input and advice on scoring and evaluation processes. Additionally, the author 

briefed the Northwest Power and Conservation Council, Mid-Columbia Sounding Board, 

Upper Willamette Recovery Planning Stakeholder Team, and Lower Columbia River 

Recovery Planning Stakeholder Team and took their feedback into account when refining 

the module. Lastly, PC Trask & Associates, Inc., and Lower Columbia River Estuary 

Partnership staff worked with NMFS Northwest Regional Office staff to revise the module 

in response to comments received during the public comment period.

Why Are the Estuary and Plume Important?

The Columbia River estuary and plume represent one of three major stages in the life cycle 

of salmon and steelhead. In tributaries, adults spawn and juveniles rear in freshwater. In the 

ocean, juveniles grow to adults as they forage in food-rich environments. The estuary is 

where juveniles and adults undergo vast physiological changes needed to transition to and 

from saltwater. In addition, a properly functioning estuary provides high growth 

opportunities and refugia from predators. 

But why are the estuary and plume so important? The answer lies in the very reason that 

salmonids grew in numbers to an estimated 16 million over the past 4,000 years. Salmon and 

steelhead were successful because they exploited a wide array of the habitat niches available 

to them. They did this by employing a variety of strategies that allowed them to use many 

diverse habitats across a wide geographic space. In fact, the distribution of salmon and 

steelhead historically spanned thousands of river miles throughout the basin. 

If this were not remarkable enough, salmon and steelhead’s traits allowed them to use 

habitats at varying times, and this is one of the primary reasons the estuary and plume are 

so important. Every downstream-migrating juvenile salmon or steelhead must use the 

habitats of the estuary to complete its life cycle. If the progeny of the 16 million adult salmon 

and steelhead that historically made use of the estuary had converged on the estuary at one 

time, there likely would not have been enough habitat and food to sustain them. So they 

developed strategies to enter the estuary at different times, at different sizes, using unique 

habitats. In fact, it has been hypothesized that each individual population’s use of estuarine 

habitats is discrete in terms of time and location of use. The implication of this for the 

estuary and plume today is that the area’s habitats must be available through time and 

space and at sufficient quantities to support more than 150 distinct salmon and steelhead 

populations, which represent 13 ESUs that use many diverse life history strategies. 

The number of adult salmon and steelhead that return to the Columbia River basin each 

year varies, but in recent years, average returns have been about 1.7 million, with 

approximately 65 to 75 percent of those fish being of hatchery origin.3

 3 This is an informal estimate; determining the ratio of hatchery-origin fish with more certainty would require stock-by-stock run 

calculations averaged over many years. 

For 2006, scientists 

from the NMFS Northwest Fisheries Science Center estimated that about 168 million 

juveniles would enter the estuary (Ferguson 2006b). This suggests that only 1 percent of the 

juveniles entering the estuary will return as adults and 99 percent are lost as a result of all 

the limiting factors (human and natural) in the estuary, plume, nearshore, and ocean. 
EXECUTIVE SUMMARY

ES-4

Understanding the extent to which the estuary and plume contribute to these losses is 

essential to the ultimate recovery of salmon and steelhead ESUs throughout the basin. 

What Is the Condition of the Estuary Now?

Flows, Dikes and Filling, and Sediment

The estuary and plume are considerably degraded compared to 200 years ago. In terms of 

absolute size, the estuary tidal prism is about 20 percent smaller than it was when Lewis 

and Clark camped along the Columbia’s shore (Northwest Power and Conservation Council 

2004). This reduction in estuary size is due mostly to dike and filling practices used to 

convert the floodplain to agricultural, industrial, commercial, and residential uses. Instream 

flows entering the estuary also have changed dramatically—there has been a 44 percent 

decrease in spring freshets or floods, and the annual timing, magnitude, and duration of 

flows no longer resemble those that historically occurred in the Columbia River (Jay and 

Kukulka 2003). Changes to flow volume and timing are attributed to hydrosystem 

regulation; water withdrawal for agricultural, municipal, and industrial purposes; and 

climate fluctuations. Further alterations in flow are likely to occur during the next century as 

a result of global climate change, the effects of which are expected to include more 

precipitation falling as rain rather than snow, less snow storage, and—in the estuary—

higher peak flows and reduced late-summer/early-fall stream flows (Independent Scientific 

Advisory Board 2007). 

Flow alterations and dike and filling practices are significant to salmon and steelhead in 

several ways. Historically, vegetated wetlands within the floodplain supplied the estuary 

with its base-level food source: macrodetritus. The near elimination of overbank events and 

the separation of the river from its floodplain have altered the food web by reducing 

macrodetrital inputs by approximately 84 percent (Bottom et al. 2005). At the same time, 

phytoplankton detrital sources from upstream reservoirs now dominate the base of the food 

chain. The substitution of food sources likely has profound effects on the estuary ecosystem. 

In addition, access to and use of floodplain habitats by ocean-type ESUs (salmonids that 

typically rear for a shorter time in tributaries and a longer time in the estuary) have been 

severely compromised through alterations in the presence and availability of these critical 

habitats. 

The timing, magnitude, and duration of flows also have important ramifications to inchannel habitat availability and connectivity. Sand transport along the river bottom is 

highly correlated to flow. With reductions in the magnitude and duration of flows, erosion 

and accretion processes no longer function as they have for thousands of years. This may 

have far-reaching consequences to the estuary, plume, and nearshore lands north and south 

of the river’s mouth. At the same time, upstream dams have prevented sediments from 

entering the estuary, while dredging activities have exported sand and gravel out of the 

estuary. Studies have shown that sand is exported from the estuary at a rate three times 

higher than that at which it enters the estuary. The full impact of these changes is unknown; 

however, sediment transport is a primary habitat-shaping force that determines the type, 

location, and availability of habitats distributed in the estuary and plume. In addition, 

decreases in sediments have improved water clarity and increased the effectiveness of 

predators that consume juvenile and adult salmon and steelhead.
EXECUTIVE SUMMARY 

ES-5

Water Quality

Water quality in the estuary and plume has been degraded by human practices from within 

the estuary and also from upstream sources. Today, elevated water temperatures and toxic 

contaminants both pose risks to salmon and steelhead in the estuary. Summer water 

temperatures entering the estuary are on average 4° F (2.2° C) warmer today than they were 

in 1938 (Lower Columbia Fish Recovery Board 2004). The upper thermal tolerance range for 

cold-water fish, including salmon and steelhead, is about 20° to 24° Celsius (68° to 75° 

Fahrenheit). Temperatures exceeding this threshold have been occurring earlier in the year 

and more frequently since 1938 (as measured at Bonneville Dam). Degradation of tributary 

riparian habitat caused by forest, residential, commercial, and industrial practices, as well as 

reservoir heating and global climate change are responsible for increased temperatures. 

During the next century, it is likely that the expected effects of global climate change will 

continue to increase water temperatures.

Another important indicator of water quality degradation in the estuary is the presence of 

toxic contaminants. One study of contaminant impacts on juvenile salmon estimated 

disease-induced mortalities of 1.5 and 9 percent as a result of contaminant stressors for 

residencies in the Columbia River estuary of 30 to 120 days, respectively (Loge et al. 2005). If 

this estimate is accurate, threats from contaminants may exceed those from Caspian tern 

predation. 

Toxic contaminants are widespread in the estuary, both geographically and in the food 

chain, with the urban and industrial portions of the estuary contributing significantly to 

juvenile salmon’s toxic load (Lower Columbia River Estuary Partnership 2007). Some of 

these contaminants are water-soluble agricultural pesticides and fertilizers, such as 

simazine, atrazine, and diazinon. Industrial contaminants include polycyclic aromatic 

hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs). Also present are 

pharmaceuticals, personal care products, brominated fire retardants, and other emerging 

contaminants. Concentrations of toxic contaminants in the bodies of juvenile salmonids in 

the estuary sometimes are above levels estimated to cause health effects. In a 2007 study, 

this was the case for PCBs, PAHs, and DDT, and juveniles showed evidence of exposure to 

hormone-disrupting compounds (Lower Columbia River Estuary Partnership 2007). Salmon 

and steelhead experience both short-term exposure to toxic substances and long-term 

exposure to contaminants that accumulate over time and magnify through the food chain. 

Even when exposures are sublethal, they can cause significant developmental, behavioral, 

health, and reproductive impairments. Ocean-type ESUs are more susceptible to 

bioaccumulation than stream-type ESUs; however, both are equally vulnerable to acute 

exposures (stream-type ESUs are those ESUs that typically spend longer periods in 

tributaries and less time in the estuary). 

Food Web and Species Interactions

The Columbia River estuary represents a distinct ecosystem that is a unique expression of 

biological and physical interactions. As physical and biological changes occur in the estuary, 

the ecosystem responds to those changes. There is general agreement that the estuary 

ecosystem is degraded and no longer provides the same level of support to native species 

assemblages that it did historically. Unfortunately, this field of research is perhaps the least 

understood, and its impact on salmon and steelhead is not well documented or studied. 
EXECUTIVE SUMMARY

ES-6

Limiting factors related to the food web and species interactions can be thought of as the 

product of all the threats to salmon and steelhead in the estuary. Some examples of food 

web and species interactions-related limiting factors are easy to understand, but others are 

subtle and far-reaching. Caspian terns are a good example of an ecosystem shift that is easy 

to understand. New islands formed through the disposal of dredged materials attracted 

terns away from their traditional habitats, which may be being degraded. Reduced sediment 

in the river may have increased terns’ efficiency in capturing steelhead juveniles migrating 

to saltwater at the same time that the birds need additional food for their broods. The result 

is a predator/prey shift in the estuary that has increased mortality for steelhead juveniles. 

Double-crested cormorants also prey on juvenile salmonids, in similar numbers as terns. 

Other shifts in the ecosystem are more complex, and it can be difficult to understand 

whether or how they affect salmon and steelhead. For example, the shift in the food base of 

the estuary—from local macrodetrital sources to imported microdetrital sources such as 

phytoplankton—has fundamentally changed the food web and species relationships; 

however, what this means to salmon and steelhead—or, for that matter, to the entire 

estuarine ecosystem—is unknown. The introduction of exotic species is another poorly 

understood ecosystem alteration. Examples of exotic species thriving in the estuary include 

21 new invertebrates, such as Asian clams and copepods, plant species such as Eurasian 

water milfoil, and exotic fish such as shad. Shad in particular, because of the sheer tonnage 

of their biomass, undoubtedly play a large role in the degradation of the estuary ecosystem 

and may compete with juvenile salmonids for food resources. Natural-origin juvenile 

salmonids may compete with large pulses of hatchery fish for food and space in the estuary 

if they overlap in space and time. Given the decreases in habitat opportunity and capacity in 

the estuary, it may be that too many fish—both salmonids and other species—are competing 

for too few estuarine resources at key times, with the resulting stressors translating into 

reduced salmonid survival. It is likely that this density-dependent mortality is manifesting 

itself in the estuary through limiting factors such as reduced off-channel habitat availability, 

competition with other fish species, and predation by fish and birds.

Other Threats

The estuary also is influenced by a number of physical structures that contribute to its 

overall degradation, but the extent of their impacts to salmon and steelhead is poorly 

understood. Over-water and instream structures in the estuary number in the thousands

and alter river circulation patterns, sediment deposition, and light penetration; they also

form microhabitats that often benefit predators. In some cases, structures reduce juvenile 

access to low-velocity habitats. Examples of structures include jetties, pilings, pile dikes, 

rafts, docks, breakwaters, bulkheads, revetments, groins, and ramps. 

Ship wake stranding is an example of another threat to salmon and steelhead in the estuary. 

A study in 1977 by the Washington Department of Fisheries estimated that more than 

150,000 juvenile salmonids, mostly Chinook, were stranded on five test sites as a result of 

ship bow waves striking shorelines (Bauersfeld 1977). Additional studies since the 

Bauersfeld study have not documented the same level of mortality. Light Detection and 

Radar (LIDAR) analysis and results from a new study by the University of Washington and 

the Portland District of the U.S. Army Corps of Engineers may help characterize this threat 

in the near future. This threat is most detrimental to ocean-type juvenile fry that are less 

than 60 millimeters long and that rear inches from shore. 
EXECUTIVE SUMMARY 

ES-7

What Can We Do to Improve Salmon and Steelhead Survival?

Identification of Management Actions and Monitoring Activities

This estuary recovery module identifies 23 management actions to improve the survival of 

salmon and steelhead migrating through and rearing in the estuary and plume 

environments. Table ES-1 lists these management actions and shows their relationship to 

threats to salmonid survival; this information is presented by topic, rather than priority. 

TABLE ES-1

Management Actions to Address Threats

Threat Management Action

Flow-related threats

Climate cycles 

and 

global climate 

change2

CRE1

-1: Protect intact riparian areas in the estuary and restore riparian areas that are 

degraded.2

CRE-2: Operate the hydrosystem to reduce the effects of reservoir surface heating, or 

conduct mitigation measures.2

CRE-3: Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries.2

Water 

withdrawal

CRE-3: Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries

Flow regulation

CRE-4: Adjust the timing, magnitude, and frequency of hydrosystem flows (especially 

spring freshets) entering the estuary and plume to better reflect the natural hydrologic cycle, 

improve access to habitats, and provide better transport of coarse sediments and nutrients 

in the estuary and plume. 

CRE-3: Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries.

Sediment-related threats

Entrapment of 

fine sediment 

in reservoirs

CRE-5: Study and mitigate the effects of entrapment of fine sediment in reservoirs, to 

improve nourishment of the estuary and plume.

Impaired 

transport of 

coarse sediment 

CRE-6: Reduce the export of sand and gravels via dredge operations by using dredged 

materials beneficially.

CRE-8: Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health. 

CRE-4: Adjust the timing, magnitude, and frequency of hydrosystem flows (especially 

spring freshets) entering the estuary and plume to better reflect the natural hydrologic cycle, 

improve access to habitats, and provide better transport of coarse sediments and nutrients 

in the estuary and plume.

Dredging CRE-7: Reduce entrainment and habitat effects resulting from main- and side-channel 

dredge activities and ship ballast intake in the estuary.

1 CRE = Columbia River estuary.

2 Study of the impacts of global climate change is an evolving field, and additional research is needed to understand the 

phenomenon’s likely effects on estuarine habitats and processes with specificity. At this time, the Independent Scientific 

Advisory Board of the Northwest Power and Conservation Council expects that the regional effects of global climate change in 

the next century will include more precipitation falling as rain rather than snow, reduced snow pack, and late-summer/early-fall 

stream flows, and associated rises in stream temperature (Independent Scientific Advisory Board 2007). The climate-related 

management actions in Table ES-1 reflect these expected impacts. Although the management actions clearly would not 

change the threat of global climate change itself, they have the potential to lessen its impact on salmonids in the estuary. Even 

if climate cycles and global climate change have effects different from those assumed in this document, the management 

actions that Table ES-1 associates with climate would provide benefits to salmonids by addressing other threats, such as water 

withdrawal, urban and industrial practices, and reservoir heating. All three of the management actions associated with climate 

in Table ES-1 are associated with other threats listed in Table ES-1.

Note: Italics indicate an action’s second occurrence in the table, in connection with a different threat.
EXECUTIVE SUMMARY

ES-8

Threat Management Action

Structural threats

Pilings and 

pile dike 

structures

CRE-8: Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health. 

Dikes and 

filling

CRE-9: Protect remaining high-quality off-channel habitat from degradation and restore 

degraded areas with high intrinsic potential for high-quality habitat.

CRE-10: Breach, lower, or relocate dikes and levees to establish or improve access to offchannel habitats.

Reservoirrelated 

temperature 

changes

CRE-2: Operate the hydrosystem to reduce the effects of reservoir surface heating, or 

conduct mitigation measures.

Over-water 

structures

CRE-11: Reduce the square footage of over-water structures in the estuary.

Food web-related threats

Increased 

phytoplankton 

production

CRE-10: Breach, lower, or relocate dikes and levees to establish or improve access to offchannel habitats.

Altered 

predator/prey 

relationships

CRE-13: Manage pikeminnow and other piscivorous fish, including introduced species, to 

reduce predation on salmonids.

CRE-14: Identify and implement actions to reduce salmonid predation by pinnipeds.

CRE-15: Implement education and monitoring projects and enforce existing laws to reduce 

the introduction and spread of invasive plants.

CRE-16: Implement projects to redistribute part of the Caspian tern colony currently nesting 

on East Sand Island.

CRE-17: Implement projects to reduce double-crested cormorant habitats and encourage 

dispersal to other locations.

CRE-18: Reduce the abundance of shad in the estuary.

CRE-8: Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health. 

Ship ballast 

practices

CRE-19: Prevent new introductions of aquatic invertebrates and reduce the effects of existing 

infestations

CRE-7: Reduce entrainment and habitat effects resulting from main- and side-channel dredge 

activities and ship ballast intake in the estuary.

Water quality-related threats

Agricultural 

practices

CRE-20: Implement pesticide and fertilizer best management practices to reduce estuarine 

and upstream sources of nutrients and toxic contaminants entering the estuary.3

CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are 

degraded.

CRE-9: Protect remaining high-quality off-channel habitat from degradation and restore 

degraded areas with high intrinsic potential for high-quality habitat.

Urban and 

industrial 

practices

CRE-21: Identify and reduce terrestrially and marine-based industrial, commercial, and public 

sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.

CRE-23: Implement stormwater best management practices in cities and towns.3

CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are 

degraded.

CRE-9: Protect remaining high-quality off-channel habitat from degradation and restore 

degraded areas with high intrinsic potential for high-quality habitat.

Other 

threats

Riparian 

practices

CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are 

degraded.

Ship wakes CRE-12: Reduce the effects of vessel wake stranding in the estuary.

3 Unless otherwise noted, the term best management practices is used in this document to indicate general methods or 

techniques found to be most effective in achieving an objective. NMFS envisions that in implementation, specific best 

management practices would be developed or recommended.
EXECUTIVE SUMMARY 

ES-9

Research, monitoring, and evaluation (RME) needs related to the 23 management actions are 

discussed in Chapter 6. As noted there, some of these needs are addressed in an existing 

document, Research, Monitoring, and Evaluation for the Federal Columbia River Estuary Program

(Johnson et al. 2008), while others are identified as new needs specific to the management 

actions in the module. Together, the existing and new RME activities will provide crucial 

information on salmonid performance in the estuary, the effectiveness of actions that are 

implemented in the estuary, associated changes in the ecology of the estuary, and scientific 

uncertainties that affect implementation of the actions. 

Evaluating Management Actions: Relationship of Implementation Constraints to 

Cost and Survival Improvements

Identifying management actions that could reduce threats to salmon and steelhead as they 

rear in or migrate through the estuary is an important step toward improving conditions for 

salmonids during a critical stage in their life cycles. However, actual implementation of 

management actions is constrained by a variety of factors, such as technical, economic, 

public health and safety, and property rights considerations. In fact, in some cases it will be 

impossible to realize an action’s full potential because its implementation is constrained by 

past societal decisions that are functionally irreversible. For example, reclaiming off-channel 

habitats in the lower Cowlitz River floodplain is constrained by the development of the city 

of Longview decades ago. An important assumption of the estuary recovery plan module is 

that the implementation of each

The module makes another important assumption about implementation: although 

implementation of actions is constrained, even constrained implementation can make 

important contributions to the survival of salmonids in the estuary and plume. 

of the 23 management actions identified in the module is 

constrained in some manner. 

It is within the context of these two fundamental assumptions that recovery actions are 

evaluated in the module, in terms of their costs and potential benefits. The evaluation of 

survival benefits and costs is highly uncertain because it relies on estimates not only of what 

is technically feasible, but also of what is socially and politically practical. To help 

characterize survival improvements, the estuary recovery module uses a planning exercise 

that involves distributing a plausible survival target across the actions to hypothesize a 

potential amount of improvement that would result from each action. Costs then are 

developed by identifying projects for each action and units and per-unit costs for each 

project. Both the survival improvements and costs reflect assumptions about the constraints 

to implementation and the degree to which those constraints can be reduced given the 

technical, social, and political context in the Columbia River basin. 

Evaluation Results

The estuary recovery plan module estimates the cost of constrained implementation of all 

23 actions over a 25-year time period at $528.05 million. This represents an order-ofmagnitude increase over the current level of investment in the estuary and reflects a 

significant level of effort needed to improve ecosystem health in the estuary and plume over 

the next 25 years. An additional $64.1 million is identified in Chapter 6 for research, 

monitoring, and evaluation activities. This effort is necessary because (1) scientific 

understanding of the estuary and how salmonids respond to conditions there is not yet 
EXECUTIVE SUMMARY

ES-10

mature, and (2) the module proposes some innovative management actions whose 

effectiveness should be explored before they are fully implemented. Thus the total 

implementation costs for the module are $592.15 million.

Table ES-2 shows the most important management actions for ocean- and stream-type 

salmonids that emerged from the analysis and planning exercises in the estuary recovery 

plan module. Many of these key actions are the same for ocean and stream types. 

Implementing the suite of key actions in Table ES-2 for ocean-type salmonids would cost 

approximately $392 million and be expected to achieve approximately 88 percent of the 

survival target for ocean-type juveniles. (See Chapter 5 for a description of survival targets.) 

Implementing the suite of key actions for stream-type salmonids would cost approximately 

$408 million and be expected to achieve 90 percent of the survival target. Additionally, an 

estimated annual gain of about 1,000 adult salmon and steelhead is associated with the 

implementation of CRE-14, “Reduce predation by pinnipeds.” The lists of priority actions in 

Table ES-2 for ocean- and stream-type salmonids contain eight actions that are predicted to 

benefit both types of salmonids. Implementing this common set of actions would cost 

approximately $372 million and would be expected to yield survival improvements of 

roughly 3 million juveniles.

TABLE ES-2

Management Actions Most Important for Survival of Ocean- and Stream-type Salmonids

For Ocean Types For Stream Types

CRE-01: Protect/restore riparian areas.

CRE-04: Adjust the timing, magnitude, and frequency 

of hydrosystem flows.

CRE-08: Remove or modify pilings and pile dikes.

CRE-09: Protect/restore high-quality off-channel 

habitat.

CRE-10: Breach, lower, or relocate dikes and levees.

CRE-13: Manage pikeminnow and other piscivorous 

fish.

CRE-21: Identify and reduce sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.

CRE-02: Mitigate/reduce reservoir-related 

temperature changes.

CRE-01: Protect/restore riparian areas.

CRE-04: Adjust the timing, magnitude, and frequency 

of hydrosystem flows

CRE-08: Remove or modify pilings and pile dikes. 

CRE-09: Protect/restore high-quality off-channel 

habitat.

CRE-10: Breach, lower, or relocate dikes and levees.

CRE-13: Manage pikeminnow and other piscivorous 

fish.

CRE-21: Identify and reduce sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.

CRE-14: Reduce predation by pinnipeds.

CRE-16: Redistribute Caspian terns.

CRE-17: Redistribute cormorants.

Note: Bold-face italics indicate management actions that would benefit primarily ocean- or stream-type salmonids, rather than 

both types.

Other Implementation Considerations: Life History Diversity,

Cost-Effectiveness, and Achieving Maximum Benefit

It is tempting to pick and choose among the management actions, looking for the path of 

least resistance to achieve the desired survival improvements. For example, using the results 

of the Chapter 7 survival improvement planning exercise, it appears obvious that significant 

improvements in the survival of stream-type salmonids can be achieved by reducing threats 

associated with predators such as terns, cormorants, pikeminnow, and pinnipeds. However, 
EXECUTIVE SUMMARY 

ES-11

addressing these threats would improve survival primarily for the dominant life-history 

strategy displayed by stream-type salmonids; in terms of recovery of ESUs, less dominant 

stream-type life history strategies also must be addressed. This points to the need to 

implement additional management actions in the estuary not directly related to predation.

For ocean-type juveniles, management actions that improve the health of the estuarine 

ecosystem appear to be the linchpin. Ocean-type juveniles reside in the estuary longer than 

stream types do. As a result, they rely more heavily on a healthy estuarine ecosystem to 

provide them with food and habitat (Bottom et al 2005). Given the challenges of making 

wide-scale ecosystem change, significant improvements for ocean-type juveniles may 

depend largely on three of the most constrained actions: adjusting hydrosystem flows 

(CRE–4), establishing or improving access to off-channel habitats (CRE-10), and restoring 

contaminated sites (CRE-22). Although these are some of the most expensive actions, their 

effects could be far-reaching enough that their potential benefits would be at least 

commensurate with their high costs.

Finally, because the estuary recovery module (by design) takes an optimistic view about 

what is possible in terms of reducing the constraints to implementation of management 

actions, in actuality specific actions probably will not be implemented with the level of effort 

needed to elicit the desired response. In fact, the most important take-home message of the 

estuary plan module is that recovery of listed ESUs in the Columbia River may not be 

possible without properly functioning estuary and plume ecosystems. To achieve a 

meaningful boost in survival from these ecosystems, every ounce of an action’s potential 

benefit should be explored, and serious consideration should be given to implementing all 

of the 23 management actions to the fullest extent possible.

1-1

CHAPTER 1

The Columbia River Estuary and Plume

Purpose and Development of the Estuary Recovery Plan 

Module

This estuary recovery plan module is a planning document intended to complement other 

recovery plans in the region. With few exceptions, the module’s focus is limited to habitat 

conditions and processes in the Columbia River estuary and plume, rather than hatchery or 

harvest practices, hydroelectricity production, or tributary habitats in the Columbia River 

basin. The purpose of this estuary recovery plan module is to identify and prioritize habitatrelated management actions that, if implemented, would reduce threats to salmon and 

steelhead in the Columbia River estuary and plume.1

Chapter 2 provides background information on salmonid use of the estuary and plume 

within the context of the entire Columbia River basin. Chapter 3 identifies and prioritizes 

habitat-related salmon and steelhead limiting factors, and Chapter 4 links these limiting 

factors to the underlying environmental and human threats that have contributed to 

declines in abundance in the estuary. Chapter 4 also prioritizes threats based on the priority 

of the limiting factors they contribute to and their relative contribution to those limiting 

factors. Chapter 5 describes management actions that have the potential to reduce threats 

and evaluates the actions in terms of their implementation constraints, potential benefits, 

and costs. Chapter 6 describes research, monitoring, and evaluation needs, while Chapter 7 

integrates elements of the earlier chapters to help characterize scenarios for improving the 

survival of salmonids as they rear in and migrate through the estuary and plume. 

This estuary recovery plan module was developed by PC Trask & Associates, Inc., with 

participation of staff at the Lower Columbia River Estuary Partnership. The author also 

coordinated closely with staff at NOAA’s National Marine Fisheries Service (NMFS) 

Northwest Regional Office throughout the module development process and obtained 

additional guidance and input from NMFS Northwest Fisheries Science Center staff and 

other regional experts (see Acknowledgements). 

In drafting the module, the author reviewed and synthesized information from three main 

source documents:

Salmon at River’s End: The Role of the Estuary in the Decline and Recovery of Columbia River 

Salmon (Bottom et al. 2005)—Technical memorandum by the NMFS Northwest Fisheries 

Science Center

 

1 Although current scientific information on the effects of limiting factors and actions does not differentiate between hatcheryand natural-origin salmon and steelhead, or between salmon and steelhead that are listed under the Endangered Species Act 

(ESA) and those that are not, the intent of the module is to improve the survival of ESA-listed salmon and steelhead. ESA 

recovery is determined by the status of naturally produced salmon and steelhead.
THE COLUMBIA RIVER ESTUARY AND PLUME

1-2

Role of the Estuary in the Recovery of Columbia River Basin Salmon and Steelhead: An 

Evaluation of the Effects of Selected Factors on Salmonid Population Viability (Fresh et al. 

2005)—Technical memorandum by the NMFS Northwest Fisheries Science Center

“Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan” and its 

supplement—Northwest Power and Conservation Council (2004)

NMFS Northwest Regional Office staff considered these documents to be timely, 

comprehensive, and accurate summaries of existing scientific knowledge about the estuary; 

they proved particularly valuable in providing information about threats and limiting 

factors affecting salmonids in the estuary. 

To clarify key points or address topics that were not included in Bottom et al. (2005), Fresh 

et al. (2005), and Northwest Power and Conservation Council (2004), the author reviewed 

additional literature and contacted researchers whose findings were relevant but as yet 

unpublished; this included researchers at the NMFS Northwest Fisheries Science Center. 

Area experts (see Acknowledgements) reviewed and helped refine the author’s draft 

products; thus, the module relies heavily on expert opinion rather than an expert panel or 

“Delphi” process. The author also worked with NMFS Northwest Regional Office and 

Lower Columbia River Estuary Partnership staff to further revise the module based on 

comments received during a Federal Register public review period. In summary, the final 

module is a broader, more comprehensive document than the three key source documents 

and has evolved with input from a diversity of scientists, other specialists, and the public.

Although the estuary recovery plan module is scientifically based, it is primarily a planning 

document and has important relationships to other planning processes and documents in 

the region. In the context of Columbia River basin recovery planning, the estuary module 

provides information on how conditions in the estuary and plume affect the 13 listed 

Columbia Basin evolutionarily significant units (ESUs). It was distributed in draft form to 

recovery planning forums around the Columbia River basin, and presentations on the 

module were made to Oregon’s Mid-Columbia Sounding Board, the Upper Willamette 

Recovery Planning Stakeholder Team, and the Oregon Lower Columbia River Recovery 

Planning Stakeholder Team. 

In the context of lower Columbia River management plans, the estuary recovery plan 

module is consistent with information in the Northwest Power and Conservation Council’s 

“Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan” (in Columbia 

River Basin Fish and Wildlife Program, Northwest Power and Conservation Council 2004), the 

Lower Columbia River Estuary Partnership’s Comprehensive Conservation and Management 

Plan, and the Columbia River Estuary Study Taskforce’s Columbia River Estuary Data 

Development Program. In addition, information in the module was used in the Federal 

Columbia River Power System (FCRPS) 2008 Biological Opinion (BiOp) and later 

incorporated into the 2010 Supplemental BiOp; information from the module also was used 

in Washington’s Lower Columbia Fish Recovery Board planning process, Oregon’s Lower 

Columbia River recovery planning process, and other recovery planning efforts throughout 

the Columbia River basin. 

The process of identifying and prioritizing management actions in the estuary module has 

inherent difficulties. Although scientific knowledge about the estuary is advancing, it is still 
THE COLUMBIA RIVER ESTUARY AND PLUME 

1-3

incomplete. In addition, effective management solutions must acknowledge irreversible 

changes in estuary conditions over time, reflect the social and political will of the region, 

and focus on the biological and physical needs of the fish. In the final analysis, it is likely 

that science will never fully explain how every action affects the viability of fish. It will be 

up to current and future residents of the basin to determine how much they are willing to 

pay or do without in order to return salmon and steelhead to viable levels. 

Formation and Current Characteristics of the Estuary 

The geographic scope of the estuary recovery module encompasses areas from Bonneville 

Dam (River Mile [RM] 146; River Kilometer [RKm] 235) to the mouth of the Columbia River, 

including the Columbia River plume. The scope includes the lower portion of the 

Willamette River (from Willamette Falls, at RM 26.6 [RKm 42.6], to the Willamette’s 

confluence with the Columbia River), along with the tidally influenced portions of other 

tributaries below Bonneville Dam. (Tidal portions of tributaries entering the estuary also are 

addressed in the Lower Columbia Fish Recovery Board’s Washington Lower Columbia Salmon 

Recovery and Fish & Wildlife Subbasin Plan [2010] and Oregon’s Lower Columbia River 

Conservation and Recovery Plan for Oregon Populations of Salmon and Steelhead [ODFW 2010] in 

a manner consistent with the overall framework of this module.)

The Columbia River estuary is a former river valley that, during the last ice age, was carved 

to 110 meters (360 feet) below current sea level. As sea levels subsequently rose, the floor of 

the valley was submerged and began to fill with sediments—initially from eastern drainages 

and then from the Cascade Range. The Missoula Floods, which occurred roughly 15,000 to 

13,000 years ago, filled the valley with sand. This was followed by rapid sea level rise, which 

increased the size of the estuary and allowed further accumulation of mud and sand. By 

about 9,500 years ago, the rate of sea level rise had declined, the former river valley had 

filled with sediments, and most suspended sediment and bed load sand arriving from the 

Columbia River were being transported through the estuary to marine areas via the action 

of ebb tides and spring freshets, with some suspended sediment being deposited in 

floodplains and peripheral bays. This pattern continued to the historical period (Petersen et 

al. 2003).

The historical (circa 1880) total surface area of the Columbia River estuary has been 

estimated at up to 186 square miles (482 square kilometers) (Thomas 1983, Simenstad et al. 

1984 as cited in Northwest Power and Conservation Council 2004). The current estuary 

surface area is approximately 159 square miles (412 square kilometers) (Northwest Power 

and Conservation Council 2004). The Willamette River is the largest tributary to the lower 

Columbia River. Other major tributaries originating in the Cascade Mountains include the 

Sandy River in Oregon and the Washougal, Lewis, Kalama, and Cowlitz rivers in 

Washington. Coastal range tributaries include the Elochoman and Grays rivers in 

Washington and the Lewis and Clark, Youngs, and Clatskanie rivers in Oregon. The general 

geography of the estuary is shown in Figure 1-1. 
THE COLUMBIA RIVER ESTUARY AND PLUME

1-4

FIGURE 1-1

The Columbia River Estuary and Its Major Tributaries

(Reprinted from Bottom et al. 2005.)

Tidal impacts in water levels are observed as far upstream as Bonneville Dam at RM 146 

(RKm 235). During low flows, reversal of river flow has been measured as far upstream as 

Oak Point at RM 53 (RKm 84.8). The intrusion of saltwater is generally limited to Harrington 

Point at RM 23 (RKm 36.8); however, at lower daily flows saltwater intrusion can extend 

past Pillar Rock at RM 28 (RKm 44.8). 

Today, the lowest river flows occur during September and October, when rainfall and 

snowmelt are lowest (Northwest Power and Conservation Council 2004). The highest flows 

occur from April to June and result from snowmelt runoff. High flows also occur between 

November and March and are caused by heavy winter precipitation. Discharge at the mouth 

of the river typically ranges from 100,000 to 500,000 cubic feet per second (cfs). Historically, 

unregulated flows were both lower and higher—79,000 and 1 million cfs, respectively (Neal 

1972 and Lower Columbia River Estuary Partnership 2002 as cited in Northwest Power and 

Conservation Council 2004).

Estuary Reaches

For the purposes of this estuary recovery plan module, the estuary is broadly defined to 

include the entire continuum where tidal forces and river flows interact, regardless of the 
THE COLUMBIA RIVER ESTUARY AND PLUME 

1-5

extent of saltwater intrusion (Fresh et al. 2005, Northwest Power and Conservation Council 

2004). For planning purposes, the upstream boundary is Bonneville Dam and the 

downstream boundary includes the Columbia River plume. These two divisions—the 

estuary and plume—have been used extensively in this estuary recovery plan module as 

distinct zones. Further delineation of the estuary has occurred, including efforts by Thomas 

(1983), Johnson et al. (2003), and the Lower Columbia River Estuary Partnership (2005). 

In this estuary recovery plan module, limiting factors, threats, and management actions are 

identified at the finest reach level possible. In some cases, this may be as general as making 

a distinction between the estuary and plume. In other cases, additional definition is 

available at the reach scale. The Lower Columbia River Estuary Partnership, in conjunction 

with the University of Washington and U.S. Geological Survey, has developed and is 

continuing to refine several estuary landscape classifications. Of these overlaying 

classifications, the estuary recovery module uses the Level 3 Stratum, which organizes the 

estuary between the mouth and Bonneville Dam into eight lettered reaches (Lower 

Columbia River Estuary Partnership 2005). 

FIGURE 1-2

Lower Columbia River Estuary Reaches 

(Adapted from Northwest Power and Conservation Council 2004.)

Figure 1-2 shows these eight reaches, which can be described briefly as follows:

Reach A. This area includes the estuary entrance (Clatsop Spit and Trestle Bay), Bakers 

Bay, and Youngs Bay. The entrance is dominated by subtidal habitat and has the highest 

salinity in the estuary. Historically, the estuary entrance was a high-energy area of 

natural fluvial land forms with a complex of channels, shallow water, and sand bars. 
THE COLUMBIA RIVER ESTUARY AND PLUME

1-6

Reach A supports the Columbia River plume, which creates a unique low-salinity, highproductivity environment that extends well into the ocean. The dynamic nature of the 

entrance area has changed as a result of dredging and the construction of jetties. These 

activities have limited wave action and the marine supply of sediment. 

Historically, ocean currents and wave action made Bakers Bay a high-energy area, but 

both currents and wave action have been altered by dredging and jetty construction. The 

migration of mid-channel islands toward the interior of Baker Bay also has sheltered the 

area from wave action. As a result, tidal marsh habitat has recently started to develop in 

some areas, although much of the historical tidal marsh and tidal swamp habitat has 

been lost because of dike construction in the floodplain. Given its proximity to the river 

mouth, Baker Bay consists primarily of brackish water. 

Youngs Bay is characterized by a broad floodplain and historically was abundant in tidal 

marsh and swamp habitat. Diking and flood control structures have been used to convert 

floodplain habitat in the area to pasture. The remaining fragmented tidal marsh and tidal 

swamp habitats in Youngs Bay are thought to be different in structure and vegetative 

community than historical conditions of these habitats. 

Reach B. Reach B generally extends from the Astoria-Meglar Bridge upstream to the 

westernmost tip of Puget Island. This area includes what has been referred to as the 

mixing zone (Northwest Power and Conservation Council 2004), along with Grays Bay 

and Cathlamet Bay. The mixing zone is an area characterized by a network of midchannel shoals and flats, such as Desdemona and Taylor Sands. It also has the highest 

variation in salinity within the estuary because of the interactions between tide cycles 

and river flows. The estuarine turbidity maximum (see p. 3-8), which is created through 

these interactions, is often located within this area of Reach B. Many islands are found in 

Reach B, including Tenasillahe, Horseshoe, Marsh, Karlson, Russian, Svensen, Miller 

Sands, Rice, and Lois islands. 

Grays Bay is found on the Washington side of the river in Reach B. Historically, water 

circulation in this area was a result of interactions between river flow and tidal intrusion. 

Pile dike fields constructed adjacent to the main Columbia River navigation channel have 

decreased circulation in Grays Bay. This circulation change is suspected of causing 

flooding problems in the Grays and Deep River valley bottoms and may have promoted 

the beneficial development of tidal marsh habitat in the accreting bay. Dike construction, 

primarily for pasture conversion, has isolated the main channel from its historical 

floodplain and eliminated much of the historical tidal swamp habitat. 

Cathlamet Bay is located on the Oregon side of the river in Reach B. This area is 

characterized by some of the most intact and productive tidal marsh and swamp habitat 

remaining in the estuary, and a large portion of Cathlamet Bay is protected by the Lewis 

and Clark National Wildlife Refuge. The western edge of Cathlamet Bay contains part of 

the brackish oligohaline zone, which is thought to be important during the transition of 

juvenile anadromous fish from freshwater to saltwater. Portions of Cathlamet Bay have 

lost substantial acreage of tidal swamp habitat as a result of dike construction. 

Conversely, tidal marsh habitat has formed along the fringe of dredge disposal locations. 
THE COLUMBIA RIVER ESTUARY AND PLUME 

1-7

Reach C. This area, which includes deep channels and steep shorelines on the 

Washington side of the river, extends from the westernmost tip of Puget Island to the 

western edge of Longview. Historically, Reach C contained significant acres of tidal 

swamp dominated by sitka spruce. Dike construction and clearing of vegetation have 

resulted in a substantial loss of tidal marsh habitat on islands and floodplain in the 

Oregon portion of Reach C. Lord Walker, Hump Fisher, Crims, Wallace and Puget 

islands are located within Reach C. 

Reach D. This area begins west of Longview and ends north of the city of Kalama. 

Reach D is distinct from the downstream reaches in its geology, vegetation, and climate. 

It includes flows from the Cowlitz and Kalama rivers. Extensive diking and filling 

around Longview and the mouth of the Kalama River have significantly reduced access 

to the floodplain. Islands and shoreline have been extensively modified through the 

disposal of dredged material. Sediment loading from eruptions of Mount St. Helens have 

significantly altered hydrology and channel morphology in and downstream of the 

Cowlitz and Kalama rivers. Dredging and the disposal of sediment from Mount St. 

Helens have been extensive. The two primary islands in Reach D are Cottonwood and 

Howard. High levels of polychlorinated biphenyls (PCBs) have been detected in the 

Longview and Kalama industrial area. 

Reach E. This area includes the Columbia River south of the city of Kalama to the 

confluence with the Lewis River, adjacent to the city of St. Helens, Oregon. The Lewis 

River system, including the North Fork and East Fork, flows into the Columbia River in 

Reach E. Sandy, Goat, Deer, Martin, and Burke islands are included in Reach E. Several 

of these islands, including Sandy and Goat islands, were created through the placement 

of dredged materials). Extensive diking has occurred on Deer Island and around the city 

of Woodland, Washington. 

Reach F. This area includes the Columbia River south of the confluence with the Lewis 

River up to and including the mid-point of Hayden Island. Reach F also extends into the 

Willamette River, to the downstream tip of Ross Island. Reach F is generally rural in 

character; however, it is located immediately downstream of the most urban/industrial 

areas in the entire Columbia River. Reach F contains the largest historical floodplain lakes 

below Bonneville Dam: Sturgeon Lake, at about 3,600 acres, and Vancouver Lake, which 

is approximately 2,400 acres. The historical floodplain was very wide in Reach F relative 

to the narrow and constricted channel through the Columbia River Gorge. Islands 

included in this reach are Bachelor and Sauvie islands. Sloughs include the 13-mile Lake 

River system and the more than 20-mile-long Multnomah Channel. Scappoose Bay is 

relatively undiked; however, Sauvie Island and Bachelor Island have been extensively 

diked. Reach F also includes Portland Harbor, a heavily industrialized stretch of the 

Willamette River located north of downtown Portland that was listed as a Superfund site 

in December 2000. Sediments in the river at this site are contaminated with various toxic 

compounds, including metals, polycyclic aromatic hydrocarbons (PAHs), PCBs, 

chlorinated pesticides, and dioxin (Oregon Department of Environmental Quality 2008).

Reach G. This area includes the Columbia River west of Hayden Island and extends to 

just east of Reed Island. Major tributaries include the Washougal and Sandy rivers. The 

cities of Portland and Vancouver straddle the Columbia River in this reach. Islands 

included in this reach are Hayden Island, Government Island, Lady Island, and Reed 
THE COLUMBIA RIVER ESTUARY AND PLUME

1-8

Island. Extensive diking has reduced the floodplain throughout the reach. Smith and 

Bybee lakes represent a large floodplain lake system similar to that of Vancouver and 

Sturgeon lakes in Reach F. Significant numbers of industrial piers and over-water 

structures line the Columbia rivers in this reach. 

Reach H. This area includes the Columbia River from east of Reed Island to the 

Bonneville Dam. This reach receives flow from many small tributaries, including 

Gibbons, Duncan, Hamilton, Hardy, and Multnomah creeks. Notable islands in this 

reach include Ackerman and Skamania islands. Reach H includes the entrance to the 

Columbia River Gorge, which is characterized by steep slopes. Little diking has occurred 

in this area, primarily because the steep adjacent slopes on both side of the river have 

naturally constrained the floodplain. 

Lower Willamette Reach. This reach extends upstream from the northern tip of Ross 

Island to Willamette Falls at RM 26.6 (RKm 42.6). The Lower Willamette reach is highly 

urbanized, bisecting the city of Portland and flowing past the cities of Milwaukie, Lake 

Oswego, Gladstone, and Oregon City. Notable islands in the Lower Willamette reach

include Ross and Hardtack, Elk Rock, Hog, Cedar, and Goat islands. The primary 

tributary entering the Lower Willamette reach is the Clackamas River just downstream of 

Willamette Falls. Other smaller tributaries include Johnson, Tryon, Kellogg, Miller, and

Stephens creeks. The shoreline of the Lower Willamette reach has been highly modified 

for industry, flood control, and other uses. Twelve transportation bridges cross the 

Willamette River in this reach.

GIS maps of each of the reaches are presented in Appendix A. The maps show additional 

information such as the locations of pile dikes and some tide gates, the navigation channel, 

the historical floodplain, diked areas, and dredged material placement sites. 

Columbia River Plume

The Columbia River plume is generally defined by a reduced-salinity contour near the 

ocean surface of approximately 31 parts per thousand (Fresh et al. 2005). In high flows, the 

plume front is easily recognized by the sharp contrast between the sediment-laden river 

water and the clearer ocean (see Figure 1-3). The plume’s location varies seasonally with 

discharge, prevailing near-shore winds, and ocean currents. In summer, the plume extends 

far to the south and offshore along the Oregon coast. During the winter, it shifts northward 

and inshore along the Washington coast. Strong density gradients between ocean and 

plume waters create stable habitat features where organic matter and organisms are 

concentrated (Fresh et al. 2005). The Columbia River plume can extend beyond Cape 

Mendocino, California, and influences salinity in marine waters as far away as San Francisco 

(Northwest Power and Conservation Council 2000). For the purposes of this estuary 

recovery plan module, the plume is considered to be off the immediate coasts of both 

Oregon and Washington and to extend outward to the continental shelf. 

Major Land Uses

A variety of land uses are found adjacent to the Columbia River estuary. The area contains 

multiple cities and political jurisdictions, including Portland, which is Oregon’s largest city, 

and Vancouver, the fourth largest Washington city. Smaller cities include Astoria, 
THE COLUMBIA RIVER ESTUARY AND PLUME 

1-9

Cathlamet, Longview, Kalama, Woodland, and Camas. Approximately 2.5 million people 

live in the vicinity of the estuary, and more are coming. Five deep-water ports in the area 

support a shipping industry that transports 30 million tons of goods annually (Lower 

Columbia Fish Recovery Board 2004), worth $13 billion each year (Columbia River Channel 

Improvement Reconsultation Project). Timber harvest occurs throughout the basin—six 

major pulp mills contribute to the region’s economy. Until the early 2000s, aluminum plants 

along the river produced more than 40 percent of the country’s aluminum. Agriculture is 

widespread throughout the floodplain and includes fruit and vegetable crops along with 

beef and dairy cattle. Commercial and recreational fishing activity plays an important role 

in local economies, bringing in millions of dollars of revenue each year. Primary outdoor 

recreational activities include fishing, wildlife observation, hunting, boating, hiking, and 

windsurfing. 

FIGURE 1-3

Plume Front 

(Photo courtesy of NMFS.)

Two Centuries of Change

Before Euro-American settlement of the Pacific Northwest, the Columbia River estuary and 

plume served as a physical and biological engine for salmon. Juveniles from hundreds of 

populations of steelhead, chum, Chinook, and coho entered the estuary and plume every 

month of the year, with their timing honed over evolutionary history to make use of 

habitats rich with food. A beach seine survey during any month of the year would likely 

have yielded salmon of all species and many populations, with individuals of many sizes. 

This genetic variation in behavior was an important trait that allowed salmon and steelhead 
THE COLUMBIA RIVER ESTUARY AND PLUME

1-10

to occupy many habitat niches in time and space. It also guarded populations against 

catastrophic events such as volcanic eruptions (Bottom et al. 2005). 

Today the Columbia River estuary and plume are much different. Notably, the North and 

South jetties at the mouth of the river restrict the marine flow of nutrients into the estuary. 

Dikes and levees lining the Washington and Oregon shores prevent access to areas that once 

were wetlands. New islands have been formed by dredged materials, and pile dike fields 

reach across the river, redirecting flows. Less visible but arguably equally important are 

changes in the size, timing, and magnitude of flows that, 200 years ago, regularly allowed 

the river to top its banks and provide salmon and steelhead with important access to 

habitats and food sources. Flow factors, along with ocean tides, are key determinants of 

habitat opportunity and capacity in the estuary and plume. 

Salmon have thrived in the Columbia River for up to 1 million years (Lichatowich 1999). In 

the last 100 years, the entire Columbia River has undergone tremendous change as a direct 

result of people living and working in the basin. While the threats to salmon persistence are 

very diverse, at some level it is the increase in human population in the Northwest that 

underlies every human threat. There are an estimated 5 million people in the Columbia 

River basin today, and somewhere between 40 million and 100 million people are predicted 

to be living in the basin by the end of the twenty-first century (National Research Council 

2004). If we want healthy salmon runs at the same time that our population is multiplying, 

our interactions with land and water must pose fewer threats to salmonids than they have 

in the last 100 years. Before identifying management actions that could do just that, this 

document discusses which salmonids currently use the Columbia River basin, and how.
2-1

CHAPTER 2

Salmonid Use of the Estuary and Plume

The estuary and plume provide salmonids with a food-rich environment where they can 

undergo the physiological changes needed to make the transition from freshwater to 

saltwater habitats, and vice versa. Every anadromous salmonid that spawns in the 

Columbia River basin undergoes such a transformation twice in its lifetime—the first time 

during its first year of life (or soon after) when migrating out to sea, and the second time 

1 to 3 years later, as an adult returning to spawn. The transition zone where juvenile 

salmonids undergo this transformation is thought to extend from the estuary itself to the 

near-shore ocean and plume habitats and into rich upwelling areas near the continental 

shelf (Casillas 1999). 

The estuary and plume also serve as rich feeding grounds where juveniles have the 

opportunity for significant growth as they make the important transition from freshwater to 

seawater. Studies have shown that juvenile salmon released within the estuary and plume 

returned as larger adults and in greater numbers than juveniles released outside the 

transition zone (Emmett and Schiewe 1997 as cited in Casillas 1999). Thus, although juvenile 

salmonids face risks from a variety of threats in the estuary and plume (see Chapter 4), these 

environments can be highly beneficial. In the salmon life cycle, successful estuarine and 

plume residency by juveniles is critical for fast growth and the transition to a saltwater 

environment. 

Clearly, the Columbia River estuary and plume are uniquely important to salmonids, and 

conditions in the estuary and plume undoubtedly affect salmonid survival. Yet the estuary 

and plume represent just one in a series of ecosystems that salmon use in their complex life 

cycle. Exploring the connections among these ecosystems, the habitats they provide, the 

salmonid species that use them, and the variety of life histories those salmonids display 

sheds further light on the role of the estuary and plume in the salmonid life cycle. 

Salmonid Species in the Columbia River Basin

Before Euro-American settlement, the Columbia River basin was used extensively by six 

species of the family Salmonidae and the genus Oncorhynchus: Chinook, chum, coho, and 

sockeye salmon plus two trout species: steelhead and sea-run cutthroat (Lichatowich 1999). 

Within these six species, 13 ESUs,1 representing more than 150 populations of salmon and 

steelhead, have been listed as threatened or endangered under the Federal Endangered 

Species Act (Bottom et al. 2005). All 13 of the ESUs use the estuary and plume as an essential 

link in their far-reaching life cycles. 

 

1 NMFS has revised its species determinations for West Coast steelhead under the Endangered Species Act (ESA), 

delineating steelhead-only “distinct population segments” (DPSs). The former steelhead ESUs included both anadromous 

steelhead trout and resident, non-anadromous rainbow trout, but NMFS listed only the anadromous steelhead. The steelhead 

DPS does not include rainbow trout, which are under the jurisdiction of the U.S. Fish and Wildlife Service. In January 2006, 

NMFS listed five Columbia River basin steelhead DPSs as threatened (71 FR 834). To avoid confusion, references to ESUs in 

this estuary recovery plan module imply the steelhead DPSs as well. 
SALMONID USE OF THE ESTUARY AND PLUME

2-2

It is estimated that historically up to 16 million salmon from perhaps hundreds of distinct 

populations returned to the Columbia River each year (Lichatowich 1999). This contrasts 

markedly with recent returns of salmon and steelhead adults, which have averaged about 

1.7 million, with 65 to 75 percent of those fish being of hatchery origin.2 For 2006, scientists 

from the NMFS Northwest Fisheries Science Center estimated that about 168 million 

juveniles would enter the estuary (Ferguson 2006b).3 This suggests that only 1 percent of the 

juveniles entering the estuary will return as adults and 99 percent are lost as a result of all 

the limiting factors (human and natural) in the estuary, plume, nearshore, and ocean. 

Life History Types and Strategies

In discussing salmonids, fish scientists commonly refer to ocean type and stream type to 

distinguish two main freshwater rearing strategies. Ocean-type salmonids are characterized 

by migration to sea early in their first year of life, after spending only a short period in 

freshwater (Fresh et al. 2005). Ocean types may rear in the estuary for weeks or months, 

making extensive use of shallow, vegetated habitats such as marshes and swamps, where 

significant changes in flow and habitat have occurred (Fresh et al. 2005). Conversely, 

stream-type salmonids are characterized by migration to sea after rearing for more extended 

periods in freshwater, usually at least 1 year (Fresh et al. 2005). Table 2-1 shows the general 

characteristics of ocean-type and stream-type ESUs.

TABLE 2-1

Characteristics of Ocean- and Stream-Type Salmonids 

Attribute

Ocean-Type Fish:

fall Chinook, chum

Stream-Type Fish: 

coho, spring Chinook, steelhead

Residency time Short freshwater residence

Longer estuarine residence

Longer ocean residence

Long freshwater residence (>1 year)

Shorter estuarine residence

Shorter ocean residence

Size at estuary entry Smaller Larger

Primary habitat use Shallow-water estuarine habitats, 

especially vegetated ones

Deeper, main-channel estuarine habitats; use 

plume more extensively

Adapted from Fresh et al. 2005.

In the Columbia River estuary, both ocean- and stream-type salmonids experience 

significant mortality. However, because the two types typically spend different amounts of 

time in the estuary and plume environments and use different habitats, they are subject to 

somewhat different combinations of threats and opportunities. 

For ocean-type juveniles, mortality is believed to be related most closely to lack of habitat, 

changes in food availability, and the presence of contaminants, including persistent, 

bioaccumulative contaminants present in sediments in the shallow-water habitats where 

ocean-type juveniles rear in the estuary. Stream types are affected by these same factors, 

although presumably to a lesser degree because of their shorter residency times in the 

 

2 This is an informal estimate; determining the ratio of hatchery-origin fish with more certainty would require stock-by-stock run 

calculations averaged over many years. 

3 2006 was a normative year and is considered representative.
SALMONID USE OF THE ESTUARY AND PLUME 

2-3

estuary. However, stream types are particularly vulnerable to bird predation in the estuary 

because they tend to use the deeper, less turbid channel areas located near habitat preferred 

by piscivorous birds (Fresh et al. 2005), and they are subject to pinniped predation when 

they return to the estuary as adults (see Chapter 3). Also, scientists at the NMFS Northwest 

Fisheries Science Center now hypothesize that larger numbers of stream-type yearling 

juveniles are susceptible to predation by northern pikeminnow than was previously 

thought; this predation occurs as the juveniles move into the shallows behind structures 

such as pilings or pile dikes to forage (Casillas 2007); this and related hypotheses are in the 

process of being tested through a program initiated by the Federal action agencies (the U.S. 

Army Corps of Engineers, the U.S. Bureau of Reclamation, and Bonneville Power 

Administration) and the Lower Columbia River Estuary Partnership. Additionally, streamtype salmonids are thought to use the low-salinity gradients of the plume to achieve growth 

and gradually acclimate to saltwater. Changes in flow and sediment delivery in the plume 

may affect stream-type juveniles in a way similar to how estuary conditions affect oceantype juveniles; however, additional research is needed to determine more precisely how 

stream types use the plume (Casillas 2006). 

Fish scientists also describe salmonids in terms of the life history strategies they employ, 

meaning a population’s unique pattern of preferred spawning substrate, habitat use, 

migration timing, length of estuarine and marine residency, and so on. For thousands of 

years, Columbia River salmonids exhibited great diversity in life history strategies, 

exploiting a wide array of the habitat niches available to them. This rich diversity in life 

history strategies allowed salmonids to persist as species for millennia even when 

individual populations were wiped out by disease or natural disturbances such as volcanic 

eruptions. 

Table 2-2 identifies the six basic life history strategies used by salmon and steelhead in the 

Columbia River and their general attributes.

Changes in Life History Diversity

The 13 listed ESUs in the Columbia River express much less diversity in life history 

strategies now than they did historically. Formerly, both ocean- and stream-type salmonids 

entered the estuary and plume throughout the year, at a great variety of sizes, which 

reflected the various life history strategies in Table 2-2. Today juveniles tend to arrive in 

pulses and are more uniform in size. 

Table 2-3 shows losses in life history diversity in the Columbia River. The table identifies the 

dominant life history type (ocean vs. stream) and strategies for each ESU, the prevalence of 

each life history strategy, and whether that prevalence has changed from historical times to 

the present. The number of life history strategies employed by some ESUs, such as 

Columbia River chum, have not changed. But for other ESUs—notably the Lower Columbia 

River coho—several life history strategies that used to exist have been lost. In a research 

project studying outmigration of juvenile Chinook salmon in the lower Willamette River, 

results indicated the presence of fry and fingerling juveniles in all months of the year. 

Although the specific ESUs of these juvenile salmon have not been confirmed, the results 

indicate more contemporary life history stages present than indicated in Table 2-3 (Friesen 

et al. 2007). 
SALMONID USE OF THE ESTUARY AND PLUME

2-4

Losses in life history diversity can also be seen in Figure 2-1, which compares historical and 

current estuarine life history types for one brood year of Chinook salmon. The figure shows 

a reduction in the number of strategies available in the contemporary versus historical 

estimates.

Some of the losses in salmonid life history diversity are attributable to habitat alterations 

throughout the Columbia River basin that have eliminated entire populations of salmon and 

steelhead. In other cases, hatcheries and harvest impacts have reduced the health and 

genetic makeup of species. As a result, many of the populations currently using the estuary 

and plume are significantly different than the fish that historically used the various habitats 

available to them, and some existing habitats may not be being used by salmonids at all. 

TABLE 2-2

Life History Strategies and Their Attributes

Life History Strategy Attributes

Early fry Freshwater rearing: 0 - 60 days 

Size at estuarine entry: <50 mm

Time of estuarine entry: March - April

Estuarine residence time: 0 - 40 days 

Late fry Freshwater rearing: 20 - 60 days 

Size at estuarine entry: <60 mm

Time of estuarine entry: May - June, present through Sept.

Estuarine residence time: <50 days

Early fingerling Freshwater rearing: 60 - 120 days 

Size at estuarine entry: 60 - 100 mm

Time of estuarine entry: April - May

Estuarine residence time: <50 days

Late fingerling Freshwater rearing: 50 - 180 days 

Size at estuarine entry: 60 - 130 mm

Time of estuarine entry: June - October, present through winter

Estuarine residence time: 0 - 80 days

Subyearling (smolt) Freshwater rearing: 20 - 180 days 

Size at estuarine entry: 70 - 130 mm

Time of estuarine entry: April - October

Estuarine residence time: <20 days

Yearling Freshwater rearing: >1 year 

Size at estuarine entry: >100 mm

Time of estuarine entry: February - May

Estuarine residence time: <20 days

Adapted from Fresh et al. 2005.
SALMONID USE OF THE ESTUARY AND PLUME 

2-5

TABLE 2-3

Linkage between Salmonid ESU, Dominant Life History Type, and Life History Strategy in the Columbia River Estuary

ESU

Life 

History 

Type

Historical and Current Life History Strategies

Early Fry Late Fry

Early 

Fingerling

Late 

Fingerling

Subyearling Yearling

Columbia River 

chum salmon Ocean Abundant Abundant — — — —

Snake River sockeye 

salmon Stream — — — — Rare Abundant

Lower Columbia 

River coho salmon Stream

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Rare Abundant

Upper Columbia 

River steelhead Stream — — — —

Historically 

rare, 

currently 

absent

Abundant

Snake River 

steelhead Stream — — — —

Historically 

rare, 

currently 

absent

Abundant

Lower Columbia 

River steelhead Stream — — —

Historically 

rare, 

currently 

absent

Historically 

medium, 

currently 

rare

Abundant

Middle Columbia 

River steelhead Stream — —

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Historically 

medium, 

currently 

rare

Abundant

Upper Willamette 

River steelhead Stream — — — —

Historically 

rare, 

currently 

absent

Abundant

Snake River fall 

Chinook salmon Ocean — —

Historically 

medium, 

currently 

rare

Historically 

medium, 

currently 

rare

Abundant

Historically 

rare, 

currently 

medium

Upper Willamette 

River Chinook 

salmon

Ocean

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Historically 

medium, 

currently 

rare

Historically 

medium, 

currently 

rare

Historically 

rare, 

currently 

medium

Abundant

Lower Columbia 

River Chinook 

salmon

Ocean

Historically 

medium, 

currently 

rare

Historically 

medium, 

currently 

rare

Historically 

medium, 

currently 

rare

Historically 

medium, 

currently 

rare

Historically 

medium, 

currently 

abundant

Rare

Upper Columbia 

River spring Chinook 

salmon

Stream — —

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Rare Abundant

Snake River 

spring/summer 

Chinook salmon

Stream — —

Historically 

rare, 

currently 

absent

Historically 

rare, 

currently 

absent

Rare Abundant

“—“ = historically and currently absent.

Adapted from Fresh et al. 2005. 

Relationship of the Estuary to the Columbia River Basin

In 2005, scientists working at the NMFS Northwest Fisheries Science Center published a 

technical memorandum that establishes an ecologically based conceptual framework for 

understanding the estuary within the larger context of the Columbia River basin. In Salmon 
SALMONID USE OF THE ESTUARY AND PLUME

2-6

at River’s End: The Role of the Estuary in the Decline and Recovery of Columbia River Salmon, 

Bottom et al. (2005) hypothesize that Columbia River salmon’s resilience to natural 

environmental variability is embodied in population and life history diversity, which 

maximizes the ability of populations to exploit available estuarine rearing habitats. Bottom 

et al.’s conceptual framework is based on Sinclair’s (1988) member/vagrant theory, which 

proposes general principles for understanding marine species with complex life cycles. The 

member/vagrant theory serves as a useful tool for evaluating salmon’s specific needs in 

estuaries in relation to the entire continuum of their habitat needs throughout their complex 

life cycles (Bottom et al. 2005). 

Bottom et al. (2005) hypothesize that how an individual salmon or steelhead uses the 

ecosystems it encounters—when juveniles migrate, how big they are, what habitats they 

use, and how long they stay in a particular habitat—correlates directly to the discrete 

population of fish that individual is part of. In other words, different populations within 

ESUs employ different life history strategies. For example, two populations of steelhead 

within an ESU may produce juveniles of different sizes that enter the estuary at different 

times, and these juveniles may use distinct habitats that may be available only at that 

particular time.

Considering that the estuary is just one of three major ecosystems used by salmon and 

steelhead, the member/vagrant theory implies that how juveniles migrate and use estuarine 

habitat may depend as much on the status of upriver habitats and corresponding 

populations as on environmental conditions in the estuary itself (Bottom et al. 2005). In 

other words, if there is a close relationship between particular geographical features in the 

estuary and the life history of a discrete salmonid population, use of the estuary may reflect 

the abundance and life history strategy of the associated population, which is in part a 

function of upstream conditions. Thus, if salmonid migration and rearing behaviors in the 

estuary are linked to specific geographic features and those features are reduced or 

eliminated, mortality in the population that uses those features increases (Bottom et al. 

2005). By the same token, if salmonid populations are lost because of other factors (such as 

blockage by dams), habitats in the estuary may be left unoccupied.
SALMONID USE OF THE ESTUARY AND PLUME 

2-7

FIGURE 2-1

Historical and Contemporary Early Life History Types of Chinook Salmon in the Columbia River Estuary

(Reprinted from Fresh et al. 2005.)

The implication for salmon recovery in the Columbia River basin is that habitat use by 

salmonids must be considered from a multi-ecosystem perspective if we are to understand 

which components of each ecosystem—tributaries, mainstem, estuary, plume, nearshore, 

and ocean—are limiting the overall performance of salmon. 

Historical

Contemporary
SALMONID USE OF THE ESTUARY AND PLUME

2-8

Summary

Since 1991, 13 Columbia River ESUs have been listed as threatened or endangered under the 

Federal Endangered Species Act. During their complex life cycles, salmon and steelhead rely 

on many diverse ecosystems, from tributaries to ocean environments, that span hundreds or 

thousands of miles. For recovery efforts to be successful, it is necessary to understand 

salmonids’ requirements during all stages of their life cycles. Thus, although the estuary and 

plume represent important stages in the salmonid life cycle, these ecosystems must be 

considered within the context of other life cycle stages if management actions are to be 

effective. Perhaps most central to the recovery of listed ESUs is the importance of conserving 

biological diversity and the native ecosystems it depends on (Bottom et al. 2005).
3-1

CHAPTER 3

Limiting Factors

Chapter 3 identifies and prioritizes the key habitat-related physical, chemical, or biological 

features that scientific literature and area experts suggest are affecting the viability of ESUs 

and their component populations in the estuary. These features are referred to as limiting 

factors.1 The discussion of limiting factors in this chapter pertains to the estuary and plume; 

however, upstream limiting factors in some cases have a direct bearing on conditions in the 

estuary. Discussion of limiting factors in this chapter generally relates to specific factors that 

limit salmonid productivity; however, it is recognized that the effects of multiple limiting 

factors may have a compounding effect. The estuary module does not address this 

compounding effect because of a lack of technical information to address the topic. 

Determining Estuary Habitat Limiting Factors 

Sources

It would be desirable to know with certainty which factors are responsible for the highest 

losses of salmon and steelhead in the estuary so that recovery actions could be focused on 

activities to address those factors. But as described below, researchers have quantified 

salmonid mortality in the estuary for only a few limiting factors, and additional research on 

mortality is needed to understand which factor (or factors) is most limiting salmonid 

viability in the estuary. In the absence of more comprehensive mortality data, the estuary 

recovery module relies on expert opinion and available information in the literature to 

identify and prioritize limiting factors.

PC Trask & Associates, Inc., based this chapter on a thorough review and synthesis of 

pertinent literature, supplemented by input from staff at the NMFS Northwest Fisheries 

Science Center and Northwest Regional Office, the Lower Columbia River Estuary 

Partnership, and the Lower Columbia Fish Recovery Board. The following documents, 

among others, provided consistent guidance:

Salmon at River’s End: The Role of the Estuary in the Decline and Recovery of Columbia River 

Salmon (Bottom et al. 2005)—Technical memorandum by the NMFS Northwest Fisheries 

Science Center

Role of the Estuary in the Recovery of Columbia River Basin Salmon and Steelhead: An 

Evaluation of the Effects of Selected Factors on Salmonid Population Viability (Fresh et al. 

2005)—Technical memorandum by the NMFS Northwest Fisheries Science Center

“Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan” and its 

supplement—Northwest Power and Conservation Council (2004)

These three literature sources, and others, identified and evaluated limiting factors in a 

similar manner. But it should be noted that the three sources have separate goals, and this 

 

1 In this module, the term “limiting factors” is used to indicate the full range of factors that are believed to be affecting the 

viability of salmon and steelhead in the estuary and not to indicate the single factor that is most limiting.
LIMITING FACTORS

3-2

affects each document’s structure and content. Thus, the depth and breadth of information 

were not always consistent across documents. To develop a relatively comprehensive list of 

factors that are limiting ESUs’ viability in the estuary and to weigh the probable effect of 

each factor, the author had to synthesize information from multiple sources.

Mortality Estimates

Estimates of salmon and steelhead mortality in the estuary and mainstem are not well 

supported in the literature, especially in the case of indirect mortality. (There are more 

reliable estimates of direct impacts to salmonids populations than indirect or combined 

impacts.) However, some modeling efforts have made assumptions about estuary mortality. 

One example is Ecosystem Diagnosis and Treatment (EDT), a life-cycle model that accounts 

for the estuarine stage of salmon and steelhead in tributaries of the Columbia River. For 

lower Columbia River ESUs, EDT assumes 18 to 58 percent mortality for various 

populations. 

In addition, research is under way by NMFS, the U.S. Army Corps of Engineers, and Battelle 

Laboratories to estimate the survival rate of juvenile salmonids in the lower Columbia River. 

This research involves technologies for miniaturizing acoustic tags to a size capable of 

tracking yearling and subyearling juveniles. Current technology developed for the project 

allows for the tracking of subyearlings of sizes down to approximately 90 mm. Data from 

2005 indicated an approximate range of survival of 65 to 75 percent for subyearlings and 

yearlings during their residency in the estuary (Ferguson 2006a).2 It is probable that actual 

survival rates are lower than these estimates suggest because the research did not address 

mortality among juveniles smaller than 90 mm, mortality occurring in the plume and 

nearshore, or delayed mortality. 

There are reliable mortality estimates for a few limiting factors. For example, Caspian tern 

predation was estimated to be responsible for the mortality of about 5.5 million smolts in 

2007 (Roby et al. 2008)—up to 14.1 percent of in-river migrant steelhead smolts and 

7.7 percent of transported steelhead smolts (Roby et al. 2008). Double-crested cormorants 

appear to be consuming approximately 6 percent of steelhead, 6 percent of subyearling 

Chinook, 2 percent of yearling Chinook, and 1 percent of sockeye salmon entering the 

estuary (Fredricks 2010). 

Other limiting factors, such as pinnipeds (primarily affecting adult survival), ship wake 

stranding, and toxic contaminants, have incomplete mortality estimates associated with 

them. Toxic contaminants, for instance, can have lethal and sublethal impacts to salmonids, 

resulting in direct and indirect mortality, both of which are difficult to quantify. In most 

cases it is very difficult to point to a specific limiting factor and then estimate mortality. This 

is because of the inherent complexity associated with connecting the physical, chemical, and 

biological features that limit the productivity of salmon and steelhead. 

 

2 The mean yearling survival estimate for the years 2005 to 2009 is 75.8 percent (standard deviation = 5.4 percent), while the 

mean subyearling survival estimate for the same period is 67.6 percent (standard deviation = 9.0 percent) (Casillas 2010). 

Because these more current survival estimates are very close to the estimates used when the module was initially drafted, and 

because local recovery planners in the Washington and Oregon Lower Columbia region incorporated the 2005 estimates into 

their salmon recovery plans, the module was not updated with the most current numbers. In future revisions of the module and 

the Lower Columbia tributary plans, needed updates will be made.
LIMITING FACTORS 

3-3

Density-Dependent Mortality

In the Columbia River estuary, limiting factors such as off-channel habitat availability, 

competition with native and exotic fish for food and space, disease, and predation by 

piscivorous fish and native birds may in part be manifestations of density dependence. 

Density dependence refers to changes in the size of a population that are themselves a result 

of the size of the population, such as when a population declines because it has exceeded the 

amount of resources available to support it. Density-dependent mortality can occur through 

several mechanisms, such as direct competition for limited food and habitat and changes in 

the foraging activity of predators. With salmon and steelhead, density-dependent mortality 

can occur at any stage in the animal’s life cycle and may be exacerbated by the introduction 

of large numbers of hatchery fish released over a relatively short period of time, or by the

cumulative effects of such releases on natural-origin salmon.3

How much density-dependent mortality is taking place in the estuary compared to in the 

ocean is unclear. There is some evidence that density-dependent mortality is occurring in 

the open ocean. For example, during years when salmon are especially numerous in the 

ocean, their growth rates are reduced (Peterman 1984 as cited in Ford 2007). One study 

found that, during years when nearshore ocean productivity was low, survival of wild 

Snake River Chinook decreased as releases of hatchery Chinook increased (Levin et al. 2001 

as cited in Ford 2007). However, another study found no connection between ocean 

conditions and density-dependent mortality, which appeared to be occurring among wild 

Snake River Chinook as hatchery steelhead were released (Levin and Williams 2002 as cited 

in Ford 2007). The authors suggested that the apparent density-dependent mortality could 

be better explained by interactions in the tributaries or estuary than by interactions in the 

ocean. 

There is growing awareness among scientists studying the Columbia River estuary that 

mechanisms related to density dependence may limit salmon and steelhead while they are 

using estuary and plume habitats. Scientists studying Skagit River fall Chinook have 

documented density dependence-related mortality as a result of loss of habitat in the Skagit 

estuary and believe that such mortality can be attributed to a 75 percent loss of tidal delta 

estuarine habitat (Beamer et al. 2005). With similar habitat losses in the Columbia River 

estuary, it is possible that too many fish are competing for limited habitat and associated 

resources in the estuary at key times, and that the resulting stressors translate into reduced 

salmonid survival. The NMFS Northwest Fisheries Science Center currently is investigating 

potential density-dependent mortality in the estuary. The “Mainstem Lower Columbia 

River and Columbia River Estuary Subbasin Plan” raised the specter of density dependence 

in the estuary and recommended continued research to analyze conditions there (Northwest 

Power and Conservation Council 2004). Thus, although the occurrence of density 

dependence-related mortality in the Columbia River estuary has not been proven, given the 

dramatic changes in habitat opportunity and capacity in the estuary over the last 200 years, 

it is likely that some of the mortality associated with the limiting factors described in this 

chapter is related to increased density of juveniles in the estuary. 

 

3 It is also possible that inverse density dependence processes occur in some situations. For example, large numbers of adult 

salmon could swamp marine mammal predators at Bonneville Dam, and the adult survival rates could be higher than in 

scenarios with smaller numbers of adult fish.
LIMITING FACTORS

3-4

Consistent with this concern, the NMFS Northwest Region Salmon Recovery Division and 

Northwest Fisheries Science Center are working to better define and describe the scientific 

uncertainty associated with ecological interactions between hatchery-origin and naturalorigin salmon in freshwater, estuarine, and nearshore ocean habitats. Needs include an 

assessment of the state of the science to help identify priority research on the ecological 

interactions between hatchery-origin and natural-origin salmon in these habitats and to 

better define the ecological risks of such interactions. A conference on ecological interactions 

between hatchery-origin and natural-origin salmon held in May 2010 in Portland, Oregon, 

contributed to describing the state of the science on these interactions. Conference 

proceedings will be published and priority research needs identified. Follow-up workshops 

will help refine the assessment, develop specific research plans, and identify funding 

sources. 

The estuary recovery plan module assumes that density-dependent mortality that may be 

occurring in the estuary is manifested in part through limiting factors related to habitat 

availability, competition for food and space, disease, and predation. Given the uncertainty 

about the mechanisms and effects of density dependence in the estuary, density dependence 

itself is not included as a limiting factor in the module. Neither are the effects of hatchery 

fish. Although it is likely that hatchery fish influence the estuarine survival of naturally 

produced fish (possibly through mechanisms of competition, predation, and disease 

transfer), the focus of this estuary recovery plan module is the effects of habitat conditions 

and processes in the estuary and plume, rather than the effects of hatchery or harvest 

practices. But the degree of density-dependent mortality occurring in the estuary, the role of 

large releases of hatchery fish, and the cumulative impact of hatchery releases on densitydependent mechanisms are worth exploring through further research. 

Habitat-Related Limiting Factors 

Salmonid populations exhibit diverse strategies that guide them through various habitats 

and ecosystems in specific sequences and patterns. If those sequences and patterns are 

interrupted, increased mortality may result. Thus, mismatches between the needs of 

salmonid populations and the availability of habitats to meet those needs can limit salmonid 

performance in the estuary and plume. The member/vagrant theory discussed in Chapter 2 

underscores the need to consider relationships between ESUs’ life history strategies and the 

quality, quantity, and availability of habitats in the estuary and other ecosystems that are 

interconnected via the salmon and steelhead’s complex life cycle.

The habitats that salmonids occupy during their residency in the estuary and plume are 

formed through the interaction of ocean forces, land, and river flow (Fresh et al. 2005). 

Flows entering the estuary govern the general availability of habitats, along with sediment 

transport, salinity gradients, and turbidity, which are themselves aspects of habitat or 

habitat formation. Over the last 200 years, the magnitude, timing, and frequency of flows 

have changed significantly, with corresponding effects on the formation and availability of 

salmonid habitats. Some habitat has been removed, which has reduced the total acreage of 

the estuary by approximately 15 percent (Fresh et al. 2005). In other cases, particular habitat 

types have been transformed into other habitat types, and the resulting mosaic of habitats 

may not be meeting the needs of salmonids as well as the historical pattern of habitats did. 

For example, approximately 77 percent of historical tidal swamp has been lost (Northwest 
LIMITING FACTORS 

3-5

Power and Conservation Council 2004), while other shallow-water habitats have increased 

significantly. The loss of tidal swamps and other forested or vegetated wetlands represents a 

loss of habitat that ocean-type salmonids use during their estuarine residence. In short, 

habitat opportunity and capacity have been degraded in the estuary and plume, and 

alterations in flow have contributed significantly to losses in in-channel, off-channel, and 

plume habitat. An accurate accounting of specific habitat type changes from pre-European 

settlement to the present day has not been initiated estuarywide. This measurement of 

change is important to guiding restoration priorities and represents a significant data gap in 

the estuary. 

An important goal of this estuary recovery module is to describe the various habitats and 

limiting factors that both ocean- and stream-type juvenile salmonids encounter in the 

Columbia River estuary and plume. However, current scientific understanding of how 

stream-type juveniles use the various habitats they encounter in the estuary and plume is 

less robust than what is known about ocean types’ habitat use. To fill this important 

knowledge gap, the NMFS Northwest Fisheries Science Center and others are exploring 

how stream-type juveniles expressing all the different possible life history strategies use 

individual estuarine habitats. 

Affected salmonids: Because of their longer estuary residence times and tendency to use 

shallow-water habitats, ocean-type ESUs are more affected by flow alterations that structure 

habitat and/or provide access to wetland or floodplain areas than are stream-type ESUs. 

Stream types have relatively short estuary residence times and use the plume much more 

extensively than ocean types do. Thus stream-type salmonids are affected by habitat 

elements such as the shape, behavior, size, and composition of the plume (Fresh et al. 2005). 

Reduced In-Channel Habitat Opportunity

In-channel habitat opportunity in the estuary is a function of the size of river flows, the 

timing of river flows, incoming and outgoing tides, and the amount and patterns of 

sediment accretion. Together, tidal action, river flow, and sediment movement create a 

constantly changing mosaic of channel habitats as water levels rise and fall, sands shift, and 

salinity gradients move in response to tides. To support salmonids, the various habitats in 

the estuary need to be connected both spatially and in time. With twice-daily tidal 

fluctuations, areas that are accessible at one point during the day can be inaccessible 6 hours 

later or can trap salmonids, exposing them to higher water temperatures and lower 

dissolved oxygen levels that can result in stress or mortality. Changes in both flow and 

sediment transport have reduced in-channel habitat opportunity. 

Limiting Factor: Flow-Related Estuary Habitat Changes. The ability of juvenile salmon to 

access and benefit from habitat depends greatly on instream flow (Fresh et al. 2005). 

Changes in the quantity and seasonality of flows in the estuary have a direct bearing on 

whether key habitats are available to salmonids, when and how long those habitats are 

available, and whether and how they connect with other key habitats. In addition, juvenile 

salmonids have physiological or behavioral traits that set the timing for their transformation 

to saltwater, and changes in flows may interrupt this timing. 

Both the quantity and timing of instream flows entering the Columbia River estuary and 

plume have changed from historical conditions (Fresh et al. 2005). Jay and Naik (2002) 
LIMITING FACTORS

3-6

reported a 16 percent reduction of annual mean flow from 1878 to the present and a 

44 percent reduction in spring freshet flows. Jay and Naik also reported a shift in flow 

patterns in the Columbia to 14 to 30 days earlier in the year, meaning that spring freshets are 

occurring earlier in the season.4 In addition, the interception and use of spring freshets (for 

irrigation, reservoir storage, etc.) have caused increased flows during other seasons (Fresh et 

al. 2005). These changes in the volume and timing of Columbia River flow are limiting 

factors for salmon and steelhead and have affected habitat opportunity and capacity in the 

estuary and plume. It is likely that global climate change will contribute to further flowrelated changes in estuary habitat. However, changes in flow entering the estuary as a result 

of climate change are expected to be less than those caused by construction of the 

hydrosystem (Independent Scientific Advisory Board 2007). 

Limiting Factor: Sediment/Nutrient-Related Estuary Habitat Changes. The transport of 

sediment is fundamental to habitat-forming processes in the estuary through sediment 

deposition and erosion (Fresh et al. 2005). An estuary’s form is altered primarily through the 

deposition of sediment—either sediment that is reworked from other parts of the estuary or 

sediment that enters the estuary from the watersheds or ocean. Sediment moves among each 

of the components within the estuary, allowing the estuary as a whole to continually be 

adjusting toward some long-term equilibrium form in response to changes in physical or 

geomorphic processes (Philip Williams & Associates and Farber 2004). Sediment from the 

estuary and upstream sources also affects the formation of nearshore ocean habitats north 

and south of the Columbia River entrance. 

Since the late nineteenth century, sediment transport from the interior basin to the Columbia 

River estuary has decreased about 60 percent and total sediment transport has decreased 

about 70 percent (Jay and Kukulka 2003). This reduction in the amount of sediment 

transport in the Columbia River has affected habitat-forming processes in the estuary and 

plume (Bottom et al. 2005) and is presumed to be a limiting factor for salmon and steelhead 

because it limits the accretion of sediment and thus the formation of shallow-water habitats. 

Although the consequences of the reduced transport of sediment through the estuary and 

plume are not fully understood, the magnitude of change is very large compared to 

historical benchmarks (Fresh et al. 2005). 

Sediment also provides important nutrients that support food production in the estuary and 

plume. Microdetrital food particles adhere to sediment suspended in the water column, 

making different food sources available to different species than was the case historically. 

Currently, organic matter associated with fine sediments supplies the majority of estuarine 

secondary productivity in the food web (Simenstad et al. 1984 as cited in Northwest Power 

and Conservation Council 2004). 

Reduced Off-Channel Habitat Opportunity

Columbia River access to its historical floodplain is an important factor for rearing oceantype juvenile salmonids. Stream-type juvenile salmonids also are believed to benefit from 

access to off-channel habitats, which support less dominant stream-type life histories and 

provide food resources for stream types during downstream migration (Bottom et al. 2005). 

 

4 These analysis were calculated by comparing observed flow (data from a gauge), estimated adjusted flow (observed flow

corrected for reservoir manipulations), and estimated virgin flow (estimate of river flow without human alteration).
LIMITING FACTORS 

3-7

Historically, flows that topped the river’s bank provided juvenile salmonids with access to 

low-velocity areas in the lower river and estuary that juveniles used as refugia and for 

rearing; many of these areas were dominated by Sitka spruce tidal swamps, which were an 

integral component of the estuarine ecosystem. Overbank flows contributed key food web 

inputs to the ecosystem and influenced wood recruitment, predation, and competition in the 

estuary (Fresh et al. 2005). 

Today, mainstem habitat in the Columbia and Willamette rivers has, in many cases, been 

reduced to a single channel (Northwest Power and Conservation Council 2004), and 

channelization of the estuary has eliminated access to an estimated 77 percent of historical 

tidal swamps (Fresh et al. 2005). In fact, over the past 200 years the surface area of the 

estuary has decreased by approximately 20 percent (Fresh et al. 2005). 

The near elimination of overbank flooding is a function of both reductions in peak freshet 

flows (as a result of flow regulation for electricity generation, storage for irrigation and 

municipal use, and flood control) and increases in the bankfull level of the Columbia River 

(as a result of dikes and levees), among other factors. 

Figure 3-1 shows diked areas from the estuary mouth to Bonneville dam. This map was 

generated from a GIS database developed by the University of Washington, U.S. Geological 

Survey, and Lower Columbia River Estuary Partnership that provides statistics and maps 

depicting the historical floodplain, diked areas, dredged material disposal sites, over-water 

structures, contaminant monitoring sites, and other key features in the estuary. Some of 

these features are shown in GIS-based reach maps presented in Appendix A. 

FIGURE 3-1

Diked Areas in the Columbia River Estuary

(Source: Lower Columbia River Estuary Partnership 2005.)
LIMITING FACTORS

3-8

Limiting Factor: Flow-Related Changes in Access to Off-Channel Habitat. Reduced access to 

off-channel habitats is a limiting factor for salmon and steelhead because of impacts on food 

webs and the reduced availability of habitats preferred by fry and fingerlings. Typically, 

overbank flows were driven by spring freshets, which occurred at the time of year when 

there was the greatest variety of juvenile salmon and steelhead using the estuary (Fresh et 

al. 2005). Overbank flows occur much less frequently now than they did historically, in part 

because climate changes and human alterations have reduced the number of high flows in 

the Columbia (Jay and Kukulka 2003). 

Limiting Factor: Bankfull Elevation Changes. The construction of levees also has reduced the 

frequency of overbank flows because more river water is needed to cause overbank flow. 

Historically the bankfull level was 18,000 m3 s

-1, while today it is 24,000 m3 s-1—fully onethird more. Only five overbank events have occurred since 1948 (Jay and Kukulka 2003). 

The reduction in overbank events is a limiting factor because it reduces the availability of 

food and refugia for ocean-type juveniles rearing in the estuary. Less dominant stream-type 

juveniles are affected in the same manner.

Reduced Plume Habitat Opportunity

Evidence suggests that the plume supports ocean productivity by increasing primary plant 

production during the spring freshet period, distributing juvenile salmonids in the coastal 

environment, concentrating food sources such as icthyoplankton (megalopae, for example) 

and zooplankton, and providing refugia from predators in the more turbid, low-salinity 

plume waters (Fresh et al. 2005). Changes in the volume and timing of Columbia River flow 

have altered both the size and structure of the plume during the spring and summer months 

(Northwest Power and Conservation Council 2000). 

Limiting Factor: Flow-Related Plume Changes. For juvenile salmonids preparing for ocean 

life, the plume is believed to function as habitat, as a transitional saltwater area, and as 

refugia. As mentioned earlier, stream-type ESUs in particular are affected by the size, shape, 

behavior, and composition of the plume (Fresh et al. 2005). 

Over the past 200 years characteristics of the plume have been altered, and conditions 

caused by reductions in spring freshets and associated sediment transport processes may 

now be suboptimal for juvenile salmonids (Casillas 1999). Plume attributes affected by 

changes in flow include surface areas of the plume, the volume of the plume waters, the 

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

(Fresh et al. 2005). 

Limiting Factor: Sediment/Nutrient-Related Plume Changes. It is believed that the sediment 

and nutrients transported in the plume fuel salmon productivity in the ocean and provide 

relief from predation (Casillas 1999). This is particularly true for stream-type ESUs, who use 

the plume more extensively than ocean types do and thus are more affected when the 

amount of plume habitat is reduced. 

Limiting Factor: Water Temperature

Higher water temperatures have reduced habitat quality for salmonids that use the estuary 

during summer months. Since 1938, average summer water temperatures at Bonneville Dam 

have increased 4° F (2.2° C) (Lower Columbia Fish Recovery Board 2004). Among-year 
LIMITING FACTORS 

3-9

variability in temperature has been reduced by 63 percent since 1970 (Lower Columbia Fish 

Recovery Board 2004). As shown in Figure 3-2, temperatures entering the estuary (as 

measured at Bonneville Dam) have increased steadily since 1938. Temperatures also exceed 

20° C (68° F) earlier during the year and more frequently than they did historically (National 

Research Council 2004). 

FIGURE 3-2

Temperatures of Water Entering the Estuary

(Reprinted from Lower Columbia Fish Recovery Board 2004.)

(Water temperatures of 20° C (68° F) are considered the upper thermal tolerance limit for 

cold-water species such as salmonids (National Research Council 2004). Pacific salmon can 

suffer adverse physiological and behavioral effects as a result of persistent, intermittent, or 

cumulative exposure to high water temperatures, or from increased daily variation in water 

temperature (McCullough 1999). Temperatures above 18° C (64.4° F) can impair the 

metabolism, growth, and disease resistance of salmonids, as well as alter the timing of adult 

migrations, fry emergence, and smoltification (McCullough et al. 2001, Sauter et al. 2001). 

Other effects of high water temperatures include adult mortality, reduced pre-spawning 

survival of eggs and sperm, difficulty competing with non-salmonid fish, prevention or 

reversal of smoltification, and harmful interactions with certain other habitat stressors 

(Marine 2004, McCullough 1999, Dunham et al. 2001, Materna 2001, McCullough et al. 2001, 

and Sauter et al. 2001). For example, the toxicity of some contaminants increases at high 

water temperatures, and levels of dissolved oxygen go down. Adult sockeye have been 

known to suffer stress and disease as they are exposed to warm water in estuaries, waiting 

for cool runoff conditions in their natal stream (Independent Scientific Advisory Board 

2007). Warmer temperatures may also enhance conditions for warm-water fish that prey on 

or compete with juvenile salmonids (Independent Scientific Advisory Board 2007) and cause

other changes in the estuarine food web. 
LIMITING FACTORS

3-10

During the next century, it is likely that global climate change will contribute to continued 

water temperature rises in the Columbia River basin as precipitation increasingly falls as 

rain rather than snow, snow pack diminishes, peak flows increase, and late-summer/earlyfall flows are reduced (Independent Scientific Advisory Board 2007). (See Chapter 4 for 

more on the expected effects of global climate change in the Columbia River basin and 

estuary.)

Limiting Factor: Stranding

In the estuary, large ships passing through the navigational channel produce bow waves 

that crash against shorelines in Oregon and Washington. Small ocean-type fry and 

fingerlings rear within inches of shore and may become stranded as waves intersect the 

bank and recede (Ackerman 2002), although the extent of this problem is unclear. A 1977 

study by Washington Department of Fisheries (WDF) observed 2,397 juvenile salmonids—

mostly Chinook—stranded as a result of passage of 216 deep draft vessels (Bauersfeld 1977). 

A NOAA technical memorandum (Hinton and Emmett 1994) published in 1994 concluded 

that the problem was not as significant as documented in the WDF report. Hinton and 

Emmett found only five juvenile salmonids stranded after observing 145 vessels. A third 

study, conducted for the U.S. Army Corps of Engineers, observed 21 juvenile Chinook 

salmon stranded at two sites (Ackerman 2002). In one occurrence, 10 juveniles were 

stranded by one vessel. As part of the channel deepening project being conducted by the 

U.S. Army Corps of Engineers, a two-part study of stranding was initiated by the University 

of Washington and the Portland District of the Corps. The study is designed to measure 

differences in stranding events before and after channel deepening activities. The first study 

was published in February 2006 (Pearson et al. 2006). In general, the report documents 

mortality attributed to stranding events for three test sites; it also builds on other work to 

determine the conditions that increase the likelihood of stranding events. 

Early in 2008, the Port of Vancouver enlisted Entrix, Inc., to perform a spatial analysis of 

beach susceptibility for the stranding of juvenile salmonids by ship wakes (Pearson 2008). 

The study examined wave characteristics and the geomorphology of the lower river but did 

not examine nearshore fish density. The purpose of the study was to estimate the number of 

miles of shoreline that exhibit traits expected to potentially cause stranding. The study 

concluded that approximately 33 miles of shoreline between the mouth of the river and the 

city of Vancouver have shoreline characteristics consistent with stranding (Pearson 2008). 

Food Web-Related Limiting Factors

Energy released from the Columbia River and the ocean converges in the estuarine and 

plume environments where, combined with the biological energy of primary plant 

production, it forms the basis for life in the estuarine ecosystem. Ultimately, energy that is 

transferred through the estuarine food web begins with sunlight; sunlight, minerals, and 

nutrients lead to plant growth in primary production; plants are eaten by animals and 

animals are preyed upon by other animals in secondary production; and dead plants, 

animals, and their material are broken down and re-integrated into the base of the food 

web. Salmon and other native species have evolved together in response to the basic inputs 

of energy and their circulation through the ecosystem. The result has been the development 

of an intricately structured food web in the estuary that encompasses food sources, food 
LIMITING FACTORS 

3-11

availability, and inter- and intra-species relationships. Alterations in any one of the elements 

of the food web, such as food sources or availability, can ripple throughout the ecosystem, 

reducing habitat capacity and having potentially far-reaching effects on salmonids and 

other species. 

As part of the food web, decomposing materials known as detritus are consumed by 

juvenile salmonids, either directly or indirectly through other organisms that feed on the

detritus (Northwest Power and Conservation Council 2004). There is evidence that a shift in 

the food base of the estuary—from macrodetrital to microdetrital—has significantly 

changed the food web and that complex inter- and intra-species relationships have been 

permanently altered (Northwest Power and Conservation Council 2004). Microdetrital 

sources favor production of planktonic copepods and other deep-water organisms that are 

not typically consumed by juvenile salmon (Bottom et al. 2005). Juvenile salmon that rear 

extensively in the estuary preferentially consume invertebrates from shallow-water and 

vegetated habitats, where decomposing plant tissue from emergent plants in estuarine 

wetlands creates macrodetritus (Bottom et al. 2005). Reductions of wetland and foraging 

habitat, simplification of habitats, and altered sediment inputs have contributed to the 

changes in detrital sources in the estuary. By disrupting the food web, these conditions have 

increased competition and predation (Bottom et al. 2005).

Most studies of prey preferences of juvenile salmon using the estuary focus on stream-type 

fish, which are less likely than ocean types to rear in estuarine habitats for extended periods. 

Studies that focus on ocean-type salmonids demonstrate that juvenile salmon appear to feed 

selectively within particular regions of the estuary (Bottom et al. 2005). In freshwater and 

brackish habitats, juvenile salmon feed extensively on emergent insects such as chironomids 

(midges) and epibenthic crustaceans such as mysid shrimp and gammarid amphipods 

(Macneale et al. 2009 and Miller and Simenstad 1997). Farther downstream in higher salinity 

portions of the estuary, salmon consume epibenthic crustaceans such as gammarid 

amphipods and harpaticoid copepods (Bottom et al. 2005). According to a University of 

Washington master’s thesis that demonstrated the importance of midge insects in the diet of 

juvenile Chinook salmon occupying shallow-water habitats in the Columbia River estuary, 

emerging chironomids were the dominant prey for Chinook of all sizes (Lott 2004). 

Additionally, the Oregon Department of Fish and Wildlife found migrating yearling 

Chinook actively feeding on daphnia. The same study found subyearling Chinook and coho 

feeding on daphnia year-round in the lower Willamette River (Friesen 2005). 

Affected salmonids: Ocean-type ESUs are more likely than stream-type juveniles to be affected 

by food web alterations because of their use of estuary habitats and their longer residency 

times. Stream-type ESUs are more influenced in the plume environment because of reduced 

fine-sediment inputs leaving the estuary. 

Food Source Changes

As described below, changes in the detrital sources that form the base of the estuarine food 

web have been significant and represent a limiting factor for salmonids. Figure 3-3 shows a 

conceptual model of the estuary food web developed by the U.S. Army Corps of Engineers. 

The historical tidal marsh macrodetritus-based food web is displayed at the top of 

Figure 3-3, while the current food web, which is based on imported microdetritus, is shown 

at the bottom. 
LIMITING FACTORS

3-12

Limiting Factor: Reduced Macrodetrital Inputs. The estuarine food web formerly was 

supported by macrodetrital inputs that originated from emergent, forested, and other 

wetland rearing areas in the estuary (Northwest Power and Conservation Council 2004). 

Today, detrital sources from emergent wetlands in the estuary are approximately 84 percent 

less than they were historically (Bottom et al. 2005). The reduction of macrodetritus in the 

estuary reduces the food sources for juvenile salmonids. As a result, juveniles may have 

reduced growth, lipid content, and fitness prior to ocean migration or may need to reside 

longer in the estuary. 

Macrodetrital plant production has declined as a result of the construction of revetments 

along the estuary shorelines, the disposal of dredged material in what formerly were 

shallow or wetland areas where plant materials or insects could drop into the water, 

simplification of habitat through the removal of large wood, and reductions in flow. Flow 

reductions affect detrital sources by limiting the amount and availability of wetlands—areas 

that normally would be contributing macrodetritus to the food web—and cutting the 

number of overbank flows. Historically, much of the detrital inputs occurred during 

overbank events, which provided additional shallow-water habitat for juvenile salmonids 

and resulted in significant detrital inputs to the estuary. As mentioned earlier, overbank 

events occur much less frequently today than they did historically.

FIGURE 3-3

Conceptual Model of the Columbia River Estuary Food Web

Limiting Factor: Increased Microdetrital Inputs. The current food web is based on decaying 

phytoplankton delivered from upstream reservoirs and nutrient inputs from urban, 

industrial, and agricultural development. The amount of this microdetritus has increased 

dramatically (Bottom et al. 2005). The switch in the estuarine food web from a 
LIMITING FACTORS 

3-13

macrodetritus-based source to a microdetritus-based source has altered the productivity of 

the estuary (Bottom et al. 2005). 

The substitution of detrital sources in the estuary also has contributed to changes in the 

spatial distribution of the food web (Bottom et al. 2005). Historically the macrodetritusbased food web was distributed evenly throughout the estuary, including in the many 

shallow-water habitats favored by ocean-type salmonids. But the contemporary 

microdetrital food web is concentrated within the estuarine turbidity maximum in the 

middle region of the estuary (Bottom et al. 2005). This location is less accessible to oceantype ESUs that use peripheral habitats and more accessible to species such as American 

shad that feed in deep-water areas.

Pelagic fish such as shad may also benefit from the fact that the estuarine turbidity 

maximum traps particles and delays their transport to the ocean up to 4 weeks, compared to 

normal transport of around 2 days (Northwest Power and Conservation Council 2004). The 

estuarine turbidity maximum is thought to contain bacteria that attach to detritus. Together 

these represent the primary food source in the estuary today (Northwest Power and 

Conservation Council 2004). 

Competition and Predation

Predation and competition for habitat and prey resources limit the success of juvenile 

salmonids entering the estuary and plume. Both spatial and energetic losses can involve 

either density-dependent or density-independent processes (Bottom et al. 2005). Spatial and 

temporal losses of habitat and large pulses of hatchery juveniles may, under some 

conditions, result in density-dependent salmonid mortality (Bottom et al. 2005). 

Competition among salmonids and between salmonids and other fish may be occurring in 

the estuary (Lower Columbia Fish Recovery Board 2004), with the estuary possibly 

becoming overgrazed when large numbers of ocean-type salmonids enter the area. Food 

availability may be reduced as a result of the temporal and spatial overlap of juveniles from 

different locations (Bisbal and McConnaha 1998 as cited in Lower Columbia Fish Recovery 

Board 2004). 

Ecosystem-scale changes in the estuary have altered the relationships between salmonids 

and other fish, birds, and mammal species, both native and exotic. Some native species’ 

abundance levels have decreased from historical levels—perhaps to the point of extinction—

while others have increased to levels far exceeding those in recorded history, with 

associated changes in predation of salmon and steelhead juveniles. 

The presence of non-indigenous fish, invertebrates, and plants in species assemblages 

indicates major changes in aquatic ecosystems (Northwest Power and Conservation Council 

2004). Globally the introduction of such species is increasing, a fact that is attributable to the

increased speed and range of world trade, which facilitates the transport and release—

whether intentional or not—of non-indigenous species (Northwest Power and Conservation 

Council 2004). In the estuary, the introduction of exotic species has altered the ecosystem 

through competition, predation, disease, parasitization, and alterations in the food web. 

Non-native species affect ocean-type ESUs more than they do stream-type ESUs because of 

the ocean types’ longer juvenile estuary residency times and use of shallow-water habitats. 
LIMITING FACTORS

3-14

Limiting Factor: Native Fish. The northern pikeminnow is a native piscivorous fish that preys 

on juvenile salmonids in the estuary. Although pikeminnows have always been a significant 

source of mortality for juvenile salmonids in the Columbia River, changes in physical 

habitats may have created more favorable conditions for predation (Northwest Power and 

Conservation Council 2004). These changes include reduced flows and favorable microhabitats formed by pilings, pile dikes, and other over-water structures. The diet of 

pikeminnows varies with age, with the largest adults representing the biggest risk to 

juvenile salmonids. Both ocean-type ESUs and stream-type ESUs are affected, but for 

different reasons. Ocean-type juveniles are susceptible because of their longer estuary 

residency times and use of shallow-water habitats. Stream-type juveniles are susceptible 

because they are leaving faster, deeper water to forage for food in shallow areas that are 

frequented by pikeminnow. 

Limiting Factor: Native Birds. As a result of estuary habitat modifications, the number and/or 

predation effectiveness of Caspian terns, double-crested cormorants, and a variety of gull 

species has increased (Fresh et al. 2005). In 1997 it was estimated that avian predators 

consumed 10 to 30 percent of the total estuarine salmonid smolt production in that year 

(Northwest Power and Conservation Council 2004). The 2007 season summary of Research, 

Monitoring, and Evaluation of Avian Predation on Salmonid Smolts in the Lower and MidColumbia River (Roby et al. 2008) estimates that 5.5 million juvenile salmonids were 

consumed by terns in 2007. Stream-type juvenile salmonids are most vulnerable to avian 

predation by Caspian terns because the juveniles use deep-water habitat channels that have 

relatively low turbidity and are close to island tern habitats (Roby et al. 2008). Doublecrested cormorants are estimated to have consumed an average of 7 million juvenile 

salmonids annually over the years 2001 to 2009. Cormorant predation has increased in the 

past several years and has been as high as 11 million, in 2009 (Fredricks 2010). 

Limiting Factor: Native Pinnipeds. The abundance of native pinnipeds has steadily increased 

since passage of the Marine Mammal Protection Act in 1972. Harbor seals, Steller sea lions, 

and California sea lions all prey on salmon and steelhead in the estuary (Northwest Power 

and Conservation Council 2004). Diet studies indicate that pinnipeds consume both juvenile 

and adult salmonids. U.S. Army Corps of Engineers’ annual estimates of adult mortality 

that occurs at Bonneville Dam because of pinnipeds (primarily California sea lions) ranged

from 0.4 percent (2002) to 4.2 percent (2007) during the study period ending in 2010 (U.S. 

Army Corps of Engineers 2010).5 Other, radio telemetry-based studies suggest that annual 

pinniped predation on spring Chinook and winter steelhead at Bonneville Dam may be as 

high as 8.5 percent and 20 percent, respectively (NMFS 2008b, Appendix G). These estimates 

do not account for pinniped mortality occurring downstream of Bonneville Dam. There are 

no official estimates of downstream mortality on adult spring Chinook and winter steelhead 

(both of which are stream-type salmonids); however, unsubstantiated estimates are as high 

as 10 percent. 

Limiting Factor: Exotic Fish. At least 37 exotic fish species are now found in the Columbia 

River estuary (Northwest Power and Conservation Council 2004). American shad were 

introduced into the Columbia River in the 1880s, and adult returns now exceed 4 million in 

 

5 Estimated consumption of adult salmonids ranged from a low of 1,010 in 2002 to a high of 6,081 in 2010; the percent of run 

consumed varied among reporting years because of changes in run size.
LIMITING FACTORS 

3-15

a single year (Northwest Power and Conservation Council 2004). While shad do not eat 

salmonids, they exert tremendous pressure on the estuary food web given the sheer weight 

of their biomass. Some evidence suggests that planktivorous American shad have an impact 

on the abundance and size of Daphnia in Columbia River mainstem reservoirs (Haskell et al. 

2006 in Independent Scientific Advisory Board 2008), thereby reducing this important food 

source for subyearling fall Chinook. Other exotic fish in the estuary, such as smallmouth 

bass, walleye, and catfish, are piscivorous; however, their abundance levels are relatively 

small.

Limiting Factor: Introduced Invertebrates. Twenty-seven non-native invertebrate species have 

been observed in the estuary and documented by the Lower Columbia River Aquatic Nonindigenous Species Survey (Sytsma et al. 2004). Surveys have documented that the estuarine 

copepod community has changed from a system dominated by a single introduced species, 

Pseduodiaptomis inopinus, to a system dominated by two newly introduced Asian copepods: 

Pseudodiaptomis forbesi and Sinoclaanus doerri (Santen 2004). In some cases, the abundance of 

non-native invertebrates can alter food webs through their wide distribution and key role in 

the food chain (Northwest Power and Conservation Council 2004). 

Limiting Factor: Exotic Plants. The introduction of non-indigenous plant species also has 

altered the estuary ecosystem. Exotic plant species often out-compete native plants, which 

results in altered habitats and food webs (Northwest Power and Conservation Council 

2004). About 18 aquatic plants have been introduced into the estuary since the 1880s 

(Sytsma et al. 2004). Examples of non-indigenous plant species include purple loosestrife, 

Eurasian milfoil, parrot feather, and Brazilian elodea. In addition to out-competing native 

plants, introduced plant species can contribute to poor water quality and create dense, 

monospecific stands that represent poor habitat for native species (Northwest Power and 

Conservation Council 2004). In turn, these new plant communities may alter insect and 

detritus production in and around vegetated wetlands. 

Toxic Contaminants

The quality of habitats and the food web in the Columbia River estuary is degraded as a 

result of past and current releases of toxic contaminants (Fresh et al. 2005, Lower Columbia 

River Estuary Partnership 2007), from both estuary and upstream sources. Historically, 

levels of contaminants in the Columbia River were low, except for some metals and 

naturally occurring substances (Fresh et al. 2005). Today, contaminant levels in the estuary 

are much higher, as the estuary receives contaminants from more than 100 point sources 

and numerous non-point sources, such as surface and stormwater runoff from agricultural 

and urban sources (Fuhrer et al. 1996). With the cities of Portland, Vancouver, Longview, 

and Astoria on its banks, the Columbia River below Bonneville Dam is the most urbanized 

section of the river. In 2000, Portland Harbor was placed on the National Priorities List, 

which designates Superfund sites. Sediments in the river at Portland Harbor are 

contaminated with various toxic compounds, including metals, PAHs, PCBs, chlorinated 

pesticides, and dioxin (Oregon Department of Environmental Quality 2008). Work in recent 

decades has detected contaminants in aquatic insects, resident fish species, salmonids, river 

mammals, and osprey, reinforcing that contaminants are widespread throughout the 

estuary’s food web (Tetra Tech 1996, Fuhrer et al . 1996, Lower Columbia River Estuary 

Partnership 2007).
LIMITING FACTORS

3-16

Depending on concentration, exposure to toxic contaminants can kill aquatic organisms 

outright or have sublethal effects that compromise their health and behavior. Sublethal 

concentrations of contaminants affect the survival of aquatic species by increasing stress, 

decreasing fitness, predisposing organisms to disease, delaying development, and 

disrupting physiological processes such as reproduction and smoltification.

Acute lethal effects of toxic contaminants, such as fish kills in response to accidental 

discharges or spills, have been reported but are generally rare. However, research by the 

NMFS Northwest Fisheries Science Center has revealed some notable exceptions in which 

toxic contaminants may lead to the direct mortality of salmonids, such as the following 

situations:

Coho pre-spawn mortality. For the past several years, NMFS has been documenting 

the recurrent die-offs of adult coho salmon returning to spawn in restored lowland 

urban streams in the Puget Sound Basin, at rates ranging from 30 to 90 percent of 

local coho runs (McCarthy et al. 2008). The weight of evidence to date suggests that 

pollutants in runoff from urban landscapes are causing the fish kills, and the 

phenomenon is correlated with high densities of roads and vehicle traffic. Based on 

findings from Puget Sound, coho spawners are likely at risk in urbanizing 

watersheds in the greater Columbia Basin (particularly the lower Columbia River). 

Synergistic toxicity of pesticide mixtures. A study by NMFS, in collaboration with 

Washington State University, has shown that common current-use pesticides 

(organophosphate and carbamate insecticides) produce unexpectedly synergistic 

toxicity and death in juvenile salmon following short-term exposure (Laetz et al. 

2007). These agricultural pesticides are used in most of the major subbasins, and they 

reach rearing and migration habitats for salmon via spray drift, surface runoff, and 

irrigation return flows. In a 10-year study by the U.S. Geological Survey, Gilliom 

(2007) found that mixtures of pesticide compounds are prevalent in streams in 

watersheds that are dominated by agricultural, urban, or mixed land use.

Salmon egg mortality. Increased mortality has been observed in salmon eggs 

exposed to PAHs in oil, such as at sites in Alaska following the Exxon Valdez oil 

spill (Heintz et al. 1999, Carls et al. 2005). An unpublished study by NMFS suggests 

that salmon embryos incubated in urban stream water also show relatively high 

rates of developmental defects and mortality when compared to embryos raised in 

the same water passed though an in situ streamside filtration system. At this time, 

the contaminants in the urban stream water are unidentified contaminants that are 

toxic to salmon embryos and likely pose an important early life stage threat to 

salmon in urbanizing watersheds. 

Although the lethal effects described above are of concern, sublethal effects of contaminants 

are probably the greatest threat to juvenile salmon in the Columbia River. In juvenile 

salmonids, contaminant exposure can result in decreased immune function and generally 

reduced fitness (Northwest Power and Conservation Council 2004, Arkoosh and Collier 

2002). Exposure can also impair growth, development, and reproduction and disrupt 

olfaction; salmonids depend on olfaction for migration, imprinting on natal streams, 

homing, and detecting predators, prey, potential mates, and spawning cues. These sublethal 

effects of contaminant exposure may indirectly increase mortality from other factors like 
LIMITING FACTORS 

3-17

infectious disease, parasites, predation, exhaustion, and starvation by suppressing salmonid 

immune systems and impairing necessary behaviors such as swimming, feeding, 

responding to stimuli, and avoiding predators (Lower Columbia River Estuary Partnership 

2007). Contaminants that affect growth can have significant effects. Juvenile growth is 

necessary for ocean survival (Zabel and Williams 2002 as cited in Lower Columbia River 

Estuary Partnership 2007), and adult fish size has been correlated to reproductive success 

and egg size (Healey and Heard 1983, Beacham and Murray 1987). Low lipid content, which 

has been observed in outmigrating juvenile Chinook salmon in the Columbia River estuary 

(Johnson et al. 2007b, Lower Columbia River Estuary Partnership 2007), is another sign of 

poor growth that is correlated with an increased risk of juvenile mortality (Biro et al. 2004). 

Thus, toxic contaminants that impair salmonid growth can reduce juvenile survival, adult 

returns, and individual reproduction. Although many effects of contaminants require an 

exposure period of weeks to months, some impacts, especially those on behavior, can occur 

very quickly. For example, effects of pesticides and copper on the salmon olfaction system 

can be seen after exposure periods of only a few hours (Sandahl et al. 2004 and 2007, Hecht 

et al. 2007).

Toxic contaminants can also indirectly affect salmon via the food web, especially prey such 

as aquatic and terrestrial insects. Insect bodies accumulate contaminants, which salmon in 

turn ingest when they consume insects. Additionally, many toxic contaminants are 

specifically designed to kill insects and plants, reducing the availability of insect prey or 

modifying the surrounding vegetation and habitats. The availability of prey species is one of 

the primary determinants of salmonid growth, and reductions in the prey base can affect 

salmonid survival and productivity (Chapman 1966 and Mundie 1974 as cited in Lower 

Columbia River Estuary Partnership 2007). Changes in vegetative habitat can shift the 

composition of biological communities; create favorable conditions for invasive, pollutiontolerant plants and animals; and further shift the food web from macrodetrital to 

microdetrital sources. 

A study by Loge et al. (2005) in the Columbia River will likely bring more attention to the 

effects of contaminants on salmonids in the estuary. The study documents infectious disease 

in outmigrating juvenile salmonids attributed to abiotic stressors, such as chemicals, that 

influence host susceptibility to infection. The study estimates disease-induced mortalities in 

Chinook salmon related to exposure to contaminants at 1.5 percent and 9 percent for estuary 

residence times of 30 to 120 days, respectively (Loge et al. 2005). 

Other contaminants, including endocrine-disrupting substances such as synthetic 

hormones, are beginning to be characterized in the estuary, and these contaminants could 

have substantial effects on salmon and steelhead (Fresh et al. 2005). A study by the Lower 

Columbia River Estuary Partnership, aided by NMFS and the U.S. Geological Survey, found 

emerging contaminants such as caffeine, acetaminophen, and human and veterinary 

antibiotics in the water column of the estuary and evidence of exposure to estrogenic 

compounds in the blood of juvenile Chinook salmon (Lower Columbia River Estuary 

Partnership 2007). Several suspected hormone disruptors were detected in the water 

column, including bisphenol A (a plasticizer), HHCB (a synthetic musk), and 

polybrominated diphenyl ethers (PBDEs, which are synthetic flame retardants used in 

everyday products like plastic, cushions, and fabrics). Although some forms of PBDEs have 

been banned, PBDE concentrations in the environment have increased exponentially during 
LIMITING FACTORS

3-18

recent decades. In the Columbia River estuary, they have been found in the water column, 

on suspended sediment, and in the tissue and stomach contents of juvenile Chinook salmon, 

which indicates that salmon prey also are contaminated (Lower Columbia River Estuary 

Partnership 2007). PBDEs are similar to PCBs in their chemical structure and sublethal 

effects, such as neurotoxicity and hormone disruption. 

Affected salmonids: Contaminant exposure by stream-type and ocean-type salmon likely 

reflects contaminants present in rearing habitats. Stream-type salmon are apt to have 

contaminant loads that reflect conditions in the upper Columbia River and its tributaries, 

while ocean-type salmon are apt to have loads that reflect conditions in the lower river and 

estuary (Leary et al. 2006, Johnson et al. in prep, Dietrich et al in prep a). It is likely that both 

stream-type and ocean-type juvenile salmonids are affected by short-term exposure to 

waterborne contaminants such as organophosphate pesticides and dissolved metals that can 

have acute effects on salmon olfactory function and behavior (Fresh et al. 2005, Johnson et 

al. in prep a), and both types could be affected by bioaccumulative legacy pesticides, such as 

DDTs, that are present throughout the Columbia Basin. Additionally, ocean-type juveniles 

likely experience adverse effects and possibly mortality from urban and industrial 

bioaccumulative toxics such as PCBs and PBDEs that are present in the Columbia River 

estuary and are absorbed during longer estuarine residence times (Fresh et al. 2005). Both 

life history types could be affected by contaminant impacts on prey resources (Johnson et al. 

in prep). Preliminary data tend to support the hypothesis that contaminant body burdens 

are generally higher in ocean-type stocks than in stream-type stocks (Johnson et al. 2007a) 

and higher in outmigrating subyearling Columbia River Chinook than in yearlings, 

especially for industrial contaminants such PCBs and PBDEs that are present at higher 

concentrations in the Columbia River estuary (Lower Columbia River Estuary Partnership 

2007, Dietrich et al. 2008). However, more work is needed on contaminant uptake and 

impacts on salmon of different stocks and life history types.

Limiting Factor: Bioaccumulation Toxicity. Bioaccumulative and potentially toxic waterborne 

contaminants, trace metals, and chlorinated compounds have been observed in the estuary 

(Fuhrer et al. 1996, Fresh et al. 2005, Lower Columbia River Estuary Partnership 2007). DDT 

and PCBs have been detected in juvenile salmon from the estuary at concentrations above 

threshold levels for health effects, and in salmon stomach contents and water quality 

samples from sites throughout the estuary (Lower Columbia River Estuary Partnership 

2007). DDT, PCBs, and trace metals such as copper all bioaccumulate and concentrate in 

animals near the top of the food chain. 

Loge et al. (2005) estimated disease-induced, contaminant-related mortalities at 1.5 percent 

and 9 percent for juvenile Chinook residing in the Columbia River estuary for 30 to 

120 days, respectively (Loge et al. 2005). Figures 3-4 and 3-5 show concentrations of PCBs 

and DDTs found in the stomach contents of subyearling fall Chinook in several locations of 

the Columbia River estuary, other Pacific Northwest sites, and hatcheries. 

Limiting Factor: Non-Bioaccumulative Toxicity. A variety of organochlorines (including 

trichlorobenzene, the insecticides aldrin and dieldrin, and PAHs) in the estuary are above 

state and Federal guidance levels (Northwest Power and Conservation Council 2004). These 

contaminants tend not to bioaccumulate in salmon and steelhead (although PAHs do 

bioaccumulate in invertebrates), but they are readily absorbed and can have sublethal 
LIMITING FACTORS 

3-19

effects. Copper also was detected in juvenile salmon, at concentrations that can impair 

olfaction (Lower Columbia River Estuary Partnership 2007). In addition, copper can interact 

with other toxic contaminants—mercury, aluminum, iron, and certain pesticides—to cause 

synergistic effects, such that the combined toxicity is greater than the toxicity predicted 

based on the sum of the contaminants present (Eisler 1998 as cited in Lower Columbia River 

Estuary Partnership 2007). 

As mentioned above, sublethal concentrations of contaminants can affect the survival of 

aquatic species by increasing stress, predisposing organisms to disease, delaying 

development, and disrupting physiological processes (Northwest Power and Conservation 

Council 2004). Exposure to PAHs may be a particular problem for salmon in the urbanized 

portions of the estuary, as these contaminants are very common in stormwater as well as in 

industrial discharges. Although salmonids can break down PAHs, the metabolites of PAHs 

can be mutagenic and carcinogenic, especially in cases of chronic exposure. PAHs also can 

contribute to immune dysfunction in juvenile salmon (Arkoosh and Collier 2002, Bravo et al. 

2008) and cause alterations in growth and metabolism that could increase the risk of 

mortality (Meador et al. 2006 and 2008). Figure 3-6 shows concentrations of PAHs in the 

stomach contents of subyearling fall Chinook in various locations of the Columbia River 

estuary, other Pacific Northwest sites, and hatcheries.

One study detected numerous currently used pesticides present in water quality samples 

from sites throughout the estuary, with the most frequently detected pesticides being the 

suspected hormone disruptors atrazine, simazine, and metolachlor (Lower Columbia River 

Estuary Partnership 2007). Exposure to individual pesticides has sublethal effects on salmon 

behavior, interfering with predator avoidance, altering homing and migration, and reducing 

egg fertilization. Health effects include reduced olfactory function, impaired growth, and 

immune suppression. Pesticides also can be toxic to salmon prey.

Although the concentrations of the individual pesticides detected in the study were lower 

than threshold levels for health effects in juvenile salmonids, pesticides often were found in 

combination (Lower Columbia River Estuary Partnership 2007). This is of concern because 

some pesticides are known to have additive effects. For example, when common pesticides 

such as diazinon, chlorpyrifos, and carbaryl occur together, even if each is at a relatively low 

concentration, their combined concentration can have toxic effects on fish and wildlife 

(Scholz et al. 2006 as cited in Lower Columbia River Estuary Partnership 2007). Among 

salmonids, carbamate and organophosphate pesticides can have additive effects on 

olfactory function (Scholz et al. 2006 as cited in Lower Columbia River Estuary Partnership 

2007). Some studies suggest that synergistic effects may also be occurring when current-use 

pesticides occur together in the environment (Anderson and Zhu 2004 and Denton et al. 

2003 as cited in Lower Columbia River Estuary Partnership 2007). This is a reminder that the 

effects of toxic contaminants in the estuary may not be directly proportional to measured 

concentrations. 
LIMITING FACTORS

3-20

FIGURE 3-4

Concentrations of PCBs in the Stomach Contents of Subyearling Fall Chinook 

(From Johnson et al. 2007a and 2007b, Lower Columbia River Estuary Partnership, 

Olson et al. 2008, Stehr et al. 2000, and Lower Willamette Group 2007)

FIGURE 3-5

Concentrations of DDTs in the Stomach Contents of Subyearling Fall Chinook 

(From Johnson et al. 2007a and 2007b, Lower Columbia River Estuary Partnership, 

Olson et al. 2008, Stehr et al. 2000, and Lower Willamette Group 2007)
LIMITING FACTORS 

3-21

FIGURE 3-6

Concentrations of Total Aromatic Hydrocarbons (PAHs) in the Stomach Contents of 

Subyearling Fall Chinook 

(From Johnson et al. 2007a and 2007b, Lower Columbia River Estuary Partnership, 

Olson et al. 2008, Stehr et al. 2000, and Lower Willamette Group 2007)

Habitat Opportunity, Habitat Quality, and Synergistic Effects

A lack of habitat opportunity and reduced habitat quality both play a role in limiting the 

viability of salmon and steelhead in the Columbia River estuary. In terms of habitat 

opportunity, changes in the timing and volume of Columbia River flows, combined with 

higher bankfull elevations, have reduced the amount and accessibility of in-channel, offchannel, and plume habitat. Overbank flooding that normally would aid juveniles in 

accessing off-channel refugia and food resources has been virtually eliminated, and 

sediment transport processes that structure habitat have been impaired.

Meanwhile, the quality of the habitat available to salmon and steelhead in the estuary has 

been compromised. Water temperatures are relatively high for cold-water species such as 

salmon and steelhead and are expected to continue to climb. Researchers have found a 

variety of toxic contaminants in water, sediments, and salmon tissue in the estuary. With 

changes in vegetation and flow, juvenile salmonids’ traditional macrodetrital food sources 

have become scarcer and the food base has switched to a microdetritus-based source, thus 

altering the productivity of the estuary. Predation by northern pikeminnow, pinnipeds, 

Caspian terns, and cormorants has increased, and it is likely that the presence of native and 

exotic fish, introduced invertebrates, and invasive plant species is further altering food web 

dynamics. These and other changes in habitat quality make the estuary a very different 

place for salmon and steelhead than it was historically.

Habitat quality often is influenced by features that this analysis considers aspects of habitat 

opportunity, such as river flow and sediment processes. As one example, alterations in flow 
LIMITING FACTORS

3-22

have eliminated much of the vegetated wetlands that ordinarily would supply insect prey 

for juvenile salmonids and macrodetrital inputs to the estuarine food web. In some cases it 

may not be not be possible to improve habitat quality without reducing limiting factors 

related to habitat opportunity. Likewise, it may be necessary to address habitat quality 

issues, such as toxic contaminants, before increasing access to habitat that could be 

contaminated. 

This type of interplay between habitat opportunity and habitat quality is a reminder of how 

connected limiting factors in the estuary are, even though this chapter describes them 

discretely. It is possible that some of the limiting factors have synergistic effects, in which 

the cumulative negative impact of two or more limiting factors is greater than the sum of the 

impacts of the individual limiting factors. This likely is the case with flow reductions and 

increases in bankfull elevation, which combine to limit juveniles’ access to off-channel 

habitats. Although synergistic effects are difficult to identify and quantify, the estuary 

recovery plan module assumes that they exist and that they can be taken advantage of to 

enhance the beneficial impacts of management actions in the estuary. Chapter 7 addresses 

the implications of potential synergistic effects more directly.

Prioritization of Limiting Factors

This estuary recovery module uses a 1-to-5 rating system to prioritize limiting factors by 

ocean- and stream-type salmon and steelhead, at the estuary scale. PC Trask & Associates, 

Inc., performed an initial prioritization, based on a synthesis of the three main literature 

sources (Bottom et al. 2005, Fresh et al. 2005, and Northwest Power and Conservation 

Council 2004), supplemented by additional literature. (See the discussion of each limiting 

factors for specific source material.) Staff from the Lower Columbia River Estuary 

Partnership, NMFS Northwest Fisheries Science Center, NMFS Northwest Regional Office, 

and Lower Columbia Fish Recovery Board reviewed and provided input on the 

prioritization.

All three of the main literature sources used in this estuary recovery module identify flow, 

sediment, water quality, and food web alterations as limiting factors. Salmon at River’s End

(Bottom et al. 2005) analyzes each of the limiting factor categories in the context of habitat 

opportunity and capacity and how the limiting factor fits within the member/vagrant 

conceptual framework. The Fresh technical memorandum evaluates selected limiting factors 

(tern predation, toxics, habitat, and flow) for their impacts on ocean- and stream-type ESUs 

(Fresh et al. 2005). Finally, the “Mainstem Lower Columbia River and Columbia River 

Estuary Subbasin Plan” and its supplement (Northwest Power and Conservation Council 

2004) evaluate limiting factors for their impacts to salmonids and the level of certainty that 

the factor is limiting. Of the limiting factors identified in this module, the only one not 

identified in at least one of the three main documents is stranding, which the author 

researched at the suggestion of Washington Department of Fish and Wildlife staff.

In prioritizing limiting factors, the author considered the following: (1) how the three main 

literature sources evaluated and/or prioritized limiting factors, (2) the magnitude or 

severity of limiting factors as described in the source documents, (3) estimates of mortality 

caused by a limiting factor, which were available only for predation-related limiting factors, 

and (4) the frequency with which a limiting factor was identified in the source documents. 
LIMITING FACTORS 

3-23

Limiting factors were prioritized individually, without trying to account for potential 

negative synergistic effects, which are difficult to evaluate.

Table 3-1 shows the results of the limiting factor rating process. Each limiting factor received 

two scores—one for ocean-type salmonids and one for stream-type salmonids. One 

simplifying assumption in scoring is that both ocean- and stream-type salmonids express a 

diversity of life history strategies within ESUs and their constituent populations. Relative 

scores between ocean- and stream-type salmonids generally reflect the dominant life history 

stage by providing extra weight to the dominant life history strategy; however, less 

dominant strategies are considered. For example, reduced off-channel habitat is primarily a 

limiting factor for ocean-type juveniles because the dominant life history strategy is 

subyearlings that use shallow-water habitats extensively to feed and rear. However, some 

ocean-type populations and subpopulations also express a yearling strategy as part of the 

overall genetic makeup of the population. As a result, both ocean- and stream-type 

salmonids received scores (albeit lower) for other less dominant life history strategies. The 

far right-hand column of the table is the total score, which adds ocean- and stream-type 

impact scores into a single composite score. The assumption that within healthy ESUs there 

is expression of less-dominant life history strategies is central to Salmon at River’s End

(Bottom et al. 2005) and the Fresh technical memorandum. 

Table 3-2 organizes limiting factors into groups based on total score. Top-priority limiting 

factors are those that have the greatest impact on both ocean- and stream-type ESUs, while 

lowest priority limiting factors have the least combined impact to ocean- and stream-type 

ESUs. An important assumption in the rating system is that all limiting factors had an effect 

on one or both ESU types.

The prioritization of limiting factors in this module should be considered a working 

hypothesis to be tested and refined through research and evaluation (including a formal 

expert opinion, or “Delphi,” process). Future planning efforts would also be enhanced by a 

limiting factors analysis at the reach or sub-reach scale, although information is generally 

not available at this time to consistently identify limiting factors at these finer scales. (In 

Chapter 5, priority reaches are identified for the 23 management actions.)

Summary

The identification of limiting factors in the Columbia River estuary is well supported in a 

variety of literature sources, although additional research is needed to understand the 

relative impacts of the limiting factors and their interactions. Source documents take 

different approaches to lumping limiting factors together or splitting them apart for the 

purposes of evaluation, but all of the documents generally agree that channel confinement 

and alterations to flows and sediment have significantly degraded the estuary ecosystem in 

far-reaching ways. Water quality and food web limiting factors also are well documented. 

The interconnectedness of these limiting factors suggests the use of ecosystem-based 

analysis to understand more exactly their effects on salmonids; however, at this point 

modeling efforts cannot fully explain the complex relationships among limiting factors.

The next chapter examines human actions and natural events that cause or contribute to the 

limiting factors described in Chapter 3.
LIMITING FACTORS

3-24

TABLE 3-1

Impact of Limiting Factors on Ocean- and Stream-Type Salmonids

Limiting Factor

Level of Impact

Ocean 

Type*

Stream 

Type*

Total 

Score

Habitat-Related Limiting Factors

Reduced in-channel habitat opportunity

Flow-related estuary habitat changes 5 3 8

Sediment/nutrient-related estuary habitat changes 4 3 7

Reduced off-channel habitat opportunity

Flow-related changes in access to off-channel habitat 5 3 8

Bankfull elevation changes 5 2 7

Reduced plume habitat opportunity

Flow-related plume changes 3 5 8

Sediment/nutrient-related plume changes 2 3 5

Water temperature 5 3 8

Stranding 3 2 5

Food Web-Related Limiting Factors

Food Source Changes

Reduced macrodetrital inputs 5 3 8

Increased microdetrital inputs 3 2 5

Competition and Predation

Native fish 3 3 6

Native birds 2 5 7

Native pinnipeds 2 5 7

Exotic fish 2 2 4

Introduced invertebrates 2 2 4

Exotic plants 2 2 4

Toxic Contaminants

Bioaccumulation toxicity 4 2 6

Non-bioaccumulative toxicity 4 3 7

*Significance of limiting factor to life history strategy:

1 = No likely effects. 

2 = Minor effects on populations. 

3 = Moderate effects on populations. 

4 = Significant effects on populations. 

5 = Major effects on populations.
LIMITING FACTORS 

3-25

TABLE 3-2

Limiting Factor Prioritization

Limiting Factor Limiting Factor 

Scorea

Limiting Factor 

Priorityb

Flow-related estuary habitat changes 8

Top

Flow-related changes in access to off-channel habitat 8

Flow-related plume changes 8

Water temperature 8

Reduced macrodetrital inputs 8

Sediment/nutrient-related estuary habitat changes 7

High

Bankfull elevation changes 7

Native birds 7

Native pinnipeds 7

Non-bioaccumulative toxicity 7

Native fish 6

Medium

Bioaccumulation toxicity 6

Sediment/nutrient-related plume changes 5

Stranding 5 Low

Increased microdetrital inputs 5

Exotic fish 4

Lowest Introduced invertebrates 4

Exotic plants 4

a

From Table 3-1.

b

Limiting factors have been prioritized in groups, rather than individually,

to avoid a false sense of precision in this qualitative analysis.

4-1

CHAPTER 4

Threats to Salmonids

Chapter 4 identifies and prioritizes threats to ESUs in the Columbia River basin. Threats are 

the human actions or natural events, such as volcanic eruptions or floodplain development, 

that cause or contribute to limiting factors (Gaar 2005). Threats may be caused by past, 

present, or future actions or events. 

PC Trask & Associates, Inc., identified and prioritized threats using the same process and 

sources used to identify and prioritize limiting factors—that is, a thorough review and 

synthesis of pertinent literature (particularly Bottom et al. 2005, Fresh et al. 2005, and 

Northwest Power and Conservation Council 2004), supplemented with input from staff at 

the NMFS Northwest Fisheries Science Center and Northwest Regional Office, Lower 

Columbia River Estuary Partnership, and Lower Columbia Fish Recovery Board. The 

module’s three key source documents and a number of other sources document both 

limiting factors and threats. In most cases the literature addresses limiting factors and 

threats together, and it required substantial effort to separate them for the purposes of this 

estuary recovery plan module.

The one threat presented in this chapter that the three main source documents do not 

mention is ship wakes, which can cause stranding of juvenile salmonids. Although the topic 

of stranding was first raised in a 1977 report (Bauersfeld 1977), the extent of stranding 

remains unclear. Washington Department of Fish & Wildlife staff suggested that the topic 

be addressed in this recovery plan module. 

The relationship between limiting factors and threats is not necessarily one-to-one. A single 

threat can contribute to several limiting factors, and in many cases a limiting factor exists 

because of the effects of multiple and varied threats. (Table 4-1, which is presented later in 

this chapter, shows the linkages between the limiting factors in Chapter 3 and the threats 

described in Chapter 4.) For ease of understanding, this chapter organizes threats to 

salmonids into the following groupings: flow, sediment, structures such as dikes and jetties, 

ship wakes, food web (including species relationships), and water quality in the estuary. 

The presentation of threats as discrete activities or phenomena is an oversimplification of 

complex physical and biological relationships that affect salmon survival. The threats 

related to flow, sediment transport, and food webs are particularly difficult to tease apart 

and discuss discretely. Thus the reader should bear in mind that describing threats 

individually does not fully capture the dynamic interplay of forces that are currently 

putting salmonids in the estuary at risk. The complexity of these forces is illustrated in 

Figure 4-1, which is a representation of a conceptual model of the Columbia River estuary 

developed by the U.S. Army Corps of Engineers (Diefenderfer et al. 2005). The model 

provides in-depth detail on the relationships between limiting factors and threats.
THREATS TO SALMONIDS

4-2

FIGURE 4-1

Conceptual Model of the Columbia River Estuary

(Note: “Stressors” are equivalent to threats as defined in this module.)

(Figure provided courtesy of the U.S. Army Corps of Engineers.)

Most of the human threats described in this chapter are the result of the cumulative impacts 

of European Americans living in the Northwest. From an ecological perspective these 

impacts have taken place relatively quickly. Consider that in 1770, when American Robert 

Gray first crossed the Columbia River bar, about 100,000 Native Americans lived in the 

Columbia River basin (Oregon State University 1998). Today the population of the 

Columbia Basin is approximately 5 million (National Research Council 2004). In the early 

years of Euro-American settlement, the area’s abundant natural resources supported 

farming, mining, logging, fishing, and other activities that modified the landscape into 

productive uses for people. Later, the availability of cheap hydroelectric power helped fuel 

expanded agriculture, manufacturing, and development and the rise of urban centers such 

as Portland. The impacts of these activities on salmonids in the estuary have been 

substantial.

Flow-Related Threats

Over the last 4,000 years, salmon thrived in the Columbia River by adapting to habitats 

created by characteristics of the land and water flow (Fresh et al. 2005). Key attributes of 

flow include magnitude and timing, both of which have changed significantly in the 
THREATS TO SALMONIDS

4-3

Columbia River over the last two centuries. Today the mean flow to the estuary is about 

16 percent less than it was in the latter part of the nineteenth century (Jay and Kukulka 

2003), and spring freshet peak flows have declined about 44 percent in that same time 

period (Jay and Kukulka 2003). In addition, the timing of peak flows occurs about 14 to 

30 days earlier than it did historically (Jay and Kukulka 2003). Reductions in the spring 

freshet flows are shown in Figure 4-2, which presents simulated mean monthly discharge at 

Bonneville Dam before development of the hydrosystem and under current hydrosystem 

configurations and operations. 

FIGURE 4-2

Changes in the Annual Columbia River Flow

(Adapted from National Marine Fisheries Service 2000.)

Flow alterations, in connection with other factors, can increase or decrease salmonids’ 

ability to access habitats and the capacity of habitats to sustain salmonids (Bottom et al. 

2005). In the case of the Columbia River, alterations in the timing, magnitude, and duration 

of flows are responsible for dramatic changes in habitat opportunity and capacity in the 

estuary, including effects on groundwater recharge, cold-water upwelling, flooding, offchannel habitat quality and quantity, and water quality. Climate fluctuations, the 

withdrawal of water, and regulation of river flow have altered the amount and timing of 

instream flows entering the estuary and plume. 

Affected salmonids: Alterations in the magnitude and timing of Columbia River flows affect 

both ocean- and stream-type juvenile salmonids. Ocean-type juveniles spend more time in 

the estuary, where they rely on shallow vegetated marsh habitats and upland swamp 

habitats (Northwest Power and Conservation Council 2004). Chum salmon (ocean-type) also 

spawn in the mainstem and are affected by low flows during the spawning and egg 

incubation life stages. In extreme cases, redds may have been dewatered; however, a 

minimum flow now has been administratively set from November through April to reduce 

the potential for dewatering of chum redds located immediately below Bonneville Dam. 

Ocean-type salmonids also rely on seasonal overbank flows to access habitats and preferred 

food sources. 
THREATS TO SALMONIDS

4-4

Stream-type juveniles do not spend much time in the estuary, but research indicates that 

they may use the Columbia River plume habitat as they adjust to saltwater conditions (Fresh 

et al. 2005). Columbia River flows have a direct effect on the plume’s surface area, volume, 

frontal features, and extent offshore (Fresh et al. 2005). Flow alterations also affect sediment 

transport processes and water quality. 

Threat: Climate Cycles and Global Climate Change

Natural variations in Columbia River flow as a result of long- and short-term climate 

fluctuations have occurred throughout history. The Pacific Decadal Oscillation (PDO) 

alternates between cold and warm phases approximately every 30 years (Fresh et al. 2005). 

The cold, rainy phase is typical of the Northwest and increases flows, while the warm phase 

is drier and decreases flows (Fresh et al. 2005). The El Niño/Southern Oscillation (ENSO) is 

a shorter, 3- to 7-year phenomenon that similarly has cold and warm phases that may 

magnify or reduce the effects of the PDO. 

Climatic fluctuations have a significant effect on the amount and timing of water flowing to 

the estuary (Fresh et al. 2005). Since 1878, climatic changes have reduced Columbia River 

flows by 9 percent (Jay and Kukulka 2003). The NMFS Northwest Fisheries Science Center 

has observed changes in PDO and ENSO indicators that suggest that changes in ecosystem 

structure can be expected that are unfavorable for salmon and steelhead (Varanasi 2005). 

These changes may continue over the next several years. 

Scientists believe that the release of high levels of carbon dioxide as a result of human 

activities is contributing to global climate change. The source of these releases includes the 

use of fossil fuels to run cars, heat homes and offices, and power factories. Over the past 

century, global climate change has caused sea levels to rise about 4 to 5 inches (10 to 

13 centimeters), worldwide precipitation to increase by about 1 percent, and the frequency 

of extreme rainfall events to increase in much of the United States (U.S. Environmental 

Protection Agency 2005). Sea level rise is predicted to accelerate worldwide in the coming 

decades as a result of global climate change (Intergovernmental Panel on Climate Change 

2007). The Intergovernmental Panel on Climate Change has observed that sea levels rose at 

an average rate of 1.8 millimeters per year from 1961 to 2003 and may be 0.18 to 0.59 meter 

(0.6 to 1.9 feet) higher at the end of the 21st century than they were during the baseline 

period of 1980 to 1999 (Intergovernmental Panel on Climate Change 2007). 

The Independent Scientific Advisory Board for the Northwest Power and Conservation 

Council (2007) reports that the Pacific Northwest has warmed about 1° C (1.8° F) since 1900 

(this is about 50 percent more than the global average for the same time period) and is 

projected to warm at a rate of 0.1 to 0.6° C (0.18 to 1.1° F) per decade during the next 

century. Over the long term, winter precipitation is expected to increase, and summer 

precipitation is expected to decrease. Within the Columbia River basin, expected effects of 

rising temperatures include more precipitation falling as rain rather than snow, diminished 

snow pack, associated reductions in late-summer/early-fall flow, altered timing of flows, 

increased peak flows, and continued rises in water temperatures. In the estuary, these 

factors could lead to changes in flooding and ecosystem processes and conditions that 

already are considered limiting factors for salmon and steelhead—namely, flow-related 

habitat changes, sediment transport, food web dynamics, populations of non-native species, 

and water temperature (Independent Scientific Advisory Board 2007). Increasingly, water 
THREATS TO SALMONIDS

4-5

temperatures in the estuary are approaching the upper thermal limit for salmonids that use 

the estuary during summer months (National Research Council 2004). Further increases in 

water temperature could render some current estuarine habitat unsuitable for salmonids, 

enhance conditions for warm-water fish that prey on or compete with juvenile salmonids, 

and alter physiological processes such as growth and metabolism among juveniles 

(Independent Scientific Advisory Board 2007). Some evidence suggests that salmonid 

response to climate change varies among populations (Crozier and Zabel 2006 as cited in 

Independent Scientific Advisory Board 2007). Other potential impacts of global climate 

change in the estuary may include continued rises in sea level and associated effects on 

intertidal habitat formation and maintenance. 

Study of the impacts of global climate change is an evolving field, and additional research is 

needed to understand the phenomenon’s likely effects on estuarine habitats and processes 

with specificity. Although the estuary recovery plan module does not consider global 

climate change separately from other climate-related impacts in the estuary, the topic 

should receive increasing attention for its potential to affect fish management in the 

Columbia River basin as a whole. As additional scientific information on global climate

change becomes available, it will be incorporated into any updates of the estuary recovery 

plan module and implementation of associated management actions.

Limiting factors this threat contributes to: Flow-related estuary habitat and plume changes, flowrelated changes in access to off-channel habitat, water temperature, and reduced 

macrodetrital inputs.

Threat: Water Withdrawal

Reduction in the amount of instream flow in a river system is an important measure of 

alterations to the system (Fresh et al. 2005). Water withdrawals affect both the magnitude 

and timing of flows entering the estuary and plume.

Historically, flow conditions in the estuary were determined by seasonal climate effects 

(such as precipitation) and hydrology. Since the early 1900s and to a larger degree since the 

1960s, irrigation practices have reduced flows in the Columbia River. Water withdrawals as 

a result of agricultural irrigation and other water uses are estimated to have reduced flows 

of the Columbia River by 7 percent since the latter part of the nineteenth century (Jay and 

Kukulka 2003). 

Other human activities that reduce flows are the result of upstream use of surface water and 

groundwater for commercial, industrial, municipal, domestic, and other purposes (National 

Research Council 2004). 

Irrigation withdrawals of surface water account for approximately 96 percent of total water 

used, while municipal and other uses account for only 4 percent (National Research Council 

2004). On the other hand, about 75 percent of all groundwater withdrawals support 

irrigation and the remaining 25 percent are used for other purposes (National Research 

Council 2004). 

Limiting factors this threat contributes to: Flow-related estuary habitat and plume changes, flowrelated changes in access to off-channel habitat, and reduced macrodetrital inputs.
THREATS TO SALMONIDS

4-6

Threat: Flow Regulation

The timing and magnitude of spring freshets have been drastically altered by management 

of the Columbia River hydrosystem (Fresh et al. 2005). Jay and Kukulka (2003) estimate that

26 percent of the overall reduction of freshet season flow since the late nineteenth century is 

attributable to flow regulation. Together with irrigation storage and withdrawal, flow 

regulation has increased fall and winter flows (winter flows have increased because of prerelease before the freshet season), and much of the seasonal timing of flows in the estuary 

can be attributed to flood control and hydroelectric operations.

Flow regulation is a function of the hydrosystem in the United States and Canada. The first 

hydroelectric facility in the lower Columbia Basin—the T.W. Sullivan Dam in Oregon City—

was constructed in 1888. Since then, more than 450 dams have been built in the Columbia 

River basin (Columbia Basin Trust). These dams supply British Columbia with 50 percent of 

its electricity, while the American Northwest relies on hydropower for about two-thirds of 

its electricity (Columbia Basin Trust). Columbia River dams also provide flood control, 

enhance irrigation, and improve navigation. 

The total active storage of water in the Columbia River Basin is 42 million acre-feet 

(Northwest Power and Conservation Council 2001), with dams in Canada accounting for 

about half of the total storage (Northwest Power and Conservation Council 2001). Major 

Canadian dams include the Duncan, Arrow, and Mica dams. Major U.S. hydroelectric 

facilities with significant storage include the Grand Coulee, Dworshak, Hungry Horse, and 

Libby dams. In addition, the U.S. Bureau of Reclamation owns and operates dozens of water 

storage dams in the Snake and Yakima rivers. The U.S. Army Corps of Engineers also 

operates many large flood control projects in the Willamette River. 

Several recent changes in hydrosystem operations have been implemented to benefit 

salmonids throughout the basin. These include increasing flows by minimizing winter flood 

control drafts and reducing the amount of water needed to refill projects during the 

spring—measures that benefit spring juvenile salmonid migration in the mainstem Snake 

and Columbia rivers. Also, summer flows have been augmented to cool Snake River 

temperatures and assist migration of Snake River salmon and steelhead. Finally, a minimum 

flow has been administratively set from November through April to reduce the potential for 

dewatering of chum redds, primarily in Reach G in the estuary. 

Limiting factors this threat contributes to: Flow-related estuary habitat and plume changes, flowrelated changes in access to off-channel habitat, increased microdetrital inputs, and reduced 

macrodetrital inputs.

Sediment-Related Threats

Changes to seasonal flows, dredging, and the entrapment of sediment in reservoirs have 

altered those habitat-forming processes in the Columbia River estuary and plume that relate 

to sediment. 

As described in Chapter 3, the transport of sediment is fundamental to habitat-forming 

processes in the estuary. Sediment helps create and maintain and promote wetlands, which 

are important to carbon cycling in the estuary and provide habitat for juvenile salmonids. 

Sediment also provides important minerals and nutrients that support food production in 
THREATS TO SALMONIDS

4-7

the estuary and plume. And suspended sediments contribute to turbidity, which is 

important to salmonids because of the protection it provides from predators. Although the 

effects of impaired sediment processes on salmonids in the estuary are not fully understood, 

the magnitude of change and the key role that sediments play in habitat- and food-related 

processes are significant.

Entrapment of sediment in reservoirs, reduced downstream transport of sediment as a 

result of altered spring freshets, and dredging are the primary sediment-related threats to 

salmonids in the estuary. Ocean-type juvenile salmonids are affected by sediment-related 

changes in habitat in the estuary and by reduced turbidity (which can increase predation). 

Stream-type juveniles are affected by reduced turbidity in deeper waters in the estuary and 

plume. 

Threat: Entrapment of Fine Sediment in Reservoirs

Reduction in water velocity as a result of upstream reservoirs has altered the transport of 

organic matter associated with fine sediments such as silt and clay. Fine sediments entering 

the estuary originate in the upper watersheds of the Snake River (Northwest Power and 

Conservation Council 2004). Reduced velocities behind upstream reservoirs cause reservoirs 

to act as a sink to fine sediments and likely reduce amounts delivered to the estuary 

(Northwest Power and Conservation Council 2004). Currently, organic matter associated 

with fine sediments supplies the majority of estuarine secondary productivity in the food 

web (Simenstad et al. 1984 as cited in Northwest Power and Conservation Council 2004). 

Additionally, reductions in the quantity of fine sediments can increase water clarity and 

thus contribute to increased predation by piscivorous fish and birds.

Limiting factors this threat contributes to: Flow-related plume changes, sediment/nutrientrelated estuary habitat changes, native birds, native fish, and exotic fish.

Threat: Impaired Transport of Coarse Sediment

Historically, the force of spring freshets moved sand down the river and into the estuary, 

where it formed shallow-water habitats that are vital for salmonids, particularly ocean 

types. Today, alterations to spring freshet flows have reduced sand discharge in the 

Columbia River estuary to 70 percent of nineteenth-century levels (Jay and Kukulka 2003). It 

is likely that the magnitude of change in sand transport affects habitat-forming processes 

and reduces turbidity, which results in increased predation in the estuary and plume 

environments. 

Limiting factors this threat contributes to: Flow-related plume changes and sediment/nutrientrelated estuary habitat changes.

Threat: Dredging

Dredging and the disposal of sand have been a major cause of estuarine habitat loss over the 

last century (Northwest Power and Conservation Council 2004). Currently, three times more 

sand is dredged from the estuary than is replenished by upstream sources (Northwest 

Power and Conservation Council 2004). In addition to causing habitat loss, dredging may 

have impaired sediment circulation in nearshore ocean areas and resulted in impacts to 

benthic organisms through disturbance. Still other impacts include the entrainment of crab, 

juvenile salmonids, sturgeon, and other fish and wildlife species. 
THREATS TO SALMONIDS

4-8

Additional losses of vegetated wetlands in the Columbia River estuary are attributable to 

filling activities, with deposition of dredged materials accounting for most of the filling 

activities in the estuary (Fresh et al. 2005). Most dredged materials result from maintenance 

of the shipping channel. Dredged materials are disposed of in-water, along shorelines, or on 

upland sites; some dredged material disposal sites are shown in the reach maps in 

Appendix A. Annual maintenance dredging since 1976 has averaged 3.5 million cubic yards 

per year (Northwest Power and Conservation Council 2004). Significantly more dredged 

material has resulted from the U.S. Army Corps of Engineers’ 43-foot channel deepening 

project. Dredge fill and diking activities have significantly reduced the availability of 

wetlands to the river, while placement of dredged material in several areas has increased 

nesting habitat for Caspian terns and cormorants. 

Limiting factors this threat contributes to: Sediment/nutrient-related estuary habitat and plume 

changes and native birds.

Structural Threats

The development of instream and over-water structures has altered circulation patterns, 

sediment deposition, sediment erosion, and the formation of habitats in the estuary. 

Examples of instream and over-water structures include jetties, pile dikes, tide gates, docks, 

breakwaters, bulkheads, revetments, seawalls, groins, and ramps (Williams and Thom 

2001). Such structures create favorable conditions for predators such as northern 

pikeminnow and walleye, and they can reduce circulation in areas outside of the channel. 

Instream and over-water structures are found in all reaches of the estuary (for locations, see 

the reach maps presented in Appendix A). 

Another structural threat is reservoirs associated with the hundreds of dams in the 

Columbia River basin. The construction and operation of these reservoirs has contributed to 

changes in the temperature of water entering the estuary. 

Affected salmonids: Structural threats primarily affect ocean-type juvenile salmonids because 

of their longer residency time in the estuary and their wider use of off-channel habitats; 

however, scientists are now hypothesizing that stream-type juveniles forage outside of 

deeper channels in shallow-water habitats, where they may fall victim to predators that 

congregate near instream and over-water structures. 

Threat: Pilings and Pile Dike Structures

Construction of the North and South jetties has altered sediment accretion and erosion 

processes near the mouth of the Columbia River. Sediment accretion in the marine littoral 

areas adjacent to the mouth has decreased the inflow of marine sediments into the estuary 

(Northwest Power and Conservation Council 2004), while the extensive use of pilings, pile 

dikes, and other structures to maintain the shipping channel has affected natural flow and 

sedimentation patterns. Pile dikes maintain the navigation channel by reducing the cross 

section of the river, increasing the velocity of the river within the channel, and at times 

slowing velocities immediately downstream of the dike. Development of the navigation 

channel has reduced flow to side channels and peripheral bays (Northwest Power and 

Conservation Council 2004). In addition, pile dikes and similar structures may create 
THREATS TO SALMONIDS

4-9

conditions that increase predation on juvenile salmonids by northern pikeminnow and 

other piscivorous fish. 

Limiting factors this threat contributes to: Sediment/nutrient-related estuary habitat and plume 

changes and exotic fish. 

Threat: Dikes and Filling

Dikes and filling activities have significantly altered the size and function of the Columbia 

River estuary. Since the early 1900s, dikes have been built to allow agricultural and 

residential uses (Fresh et al. 2005). Dikes are thought to have caused more habitat 

conversion in the estuary than any other human or natural factor (Thomas 1983, as reported 

in Northwest Power and Conservation Council 2004). The effects of diking on estuarine 

habitats are directly proportional to elevation, with the greatest impacts on the highest 

elevation estuarine habitats: forested wetlands, followed by tidal swamps and tidal 

wetlands. Diking-related impacts to these habitats have reduced their availability to juvenile 

salmon and steelhead (Thomas 1983, as reported in Northwest Power and Conservation 

Council 2004). Figure 4-3 shows the various zones found in typical estuaries. The emergent 

vegetation, diked marsh, shrub wetlands, and forested wetlands are the zones most affected 

by dike and filling practices (reprinted from Thom 2001). Diked areas and the historical 

floodplain in the Columbia River estuary are shown in the reach maps presented in 

Appendix A. 

FIGURE 4-3

Subtidal, Intertidal, and Above-Tidal Estuarine Wetland Zones

Before development of the Columbia River hydrosystem and diking and filling, the estuary 

was dominated by macrodetrital inputs that originated from vegetated wetlands within the 

estuary. As a result of diking and filling practices and flow alterations (such as changes in 

the number and timing of spring freshets), emergent plant production in the estuary has 

decreased by 82 percent and macroalgae production has decreased by 15 percent 

(Northwest Power and Conservation Council 2004). The availability of insect prey for oceantype salmonids has been reduced as vegetation has been removed via diking and filling 

activities and associated dike vegetation maintenance. 

Limiting factors this threat contributes to: Reduced macrodetrital inputs, sediment/nutrientrelated estuary habitat and plume changes, bankfull elevation increases, and exotic plants. 
THREATS TO SALMONIDS

4-10

Threat: Reservoir-Related Temperature Changes

More than 450 dams have been built in the Columbia River basin (Columbia Basin Trust). 

The associated impoundment of water in upstream reservoirs increases the surface area of 

the Columbia River, allowing more solar heating of river water than occurs in free-flowing 

river stretches. This solar heating, combined with the reduced flows from upstream 

impoundments, has contributed to increased water temperatures in the Columbia River. 

Measurements at Bonneville Dam indicate that periods of increased temperatures are lasting 

longer than they did historically (National Research Council 2004). Currently, during 

summer months, average and maximum values of Columbia River water temperatures are 

often above 20° C (68°F), which approaches the upper limits of thermal tolerance for coldwater fishes such as salmon (National Research Council 2004). (For additional information 

on increases in water temperature in the lower Columbia River, see Figure 3-2 and the text 

that precedes the figure.)

The dynamics of reservoir-related temperature changes in the estuary are complicated and 

are affected by factors such as thermal inertia, which, among other things, contributes to 

delayed fall cooling and spring warming of downstream waters. Additional study is needed 

to better understand reservoir-related temperature changes and their effects on salmonids 

rearing in the estuary. 

Limiting factors this threat contributes to: Water temperature. 

Threat: Over-Water Structures

Over-water structures refer to docks, piers, transient moorage, log rafts, and other 

structures. These structures block sunlight, reduce flow, and trap sediments downstream of 

pilings (Kahler, Grassley, and Beauchamp 2000; Nightingale and Simenstad 2001). They also 

change circulation patterns and reduce edge habitats for ocean-type salmonids. Over-water 

structures contribute to predation on salmonids by altering habitat, creating microhabitats 

and favorable conditions for predators, especially the northern pikeminnow and non-native 

species such as small-mouth bass (Kahler, Grassley, and Beauchamp 2000; Nightingale and 

Simenstad 2001). 

Although the actual square footage of over-water structures in the Columbia River estuary 

has never been inventoried, the structures themselves number in the thousands. Some 

research has occurred on the effects of breakwaters and over-water structures in the context 

of marinas. Salmon fry tend to concentrate in higher densities around these structures, thus 

increasing the risk of predation (Williams and Thom 2001). 

Limiting factors this threat contributes to: Sediment/nutrient-related estuary habitat changes, 

and exotic fish. 

Food Web-Related Threats

As described in Chapter 3, changes in the estuarine food web can ripple through the 

ecosystem, altering energy pathways, feeding patterns, predator/prey relationships, and 

competition within and among species. As a result of increased nutrients, elevated water 

temperatures, slower passage of water through reservoirs, and entrapment of organic 

matter in reservoirs, concentrations of phytoplankton at the base of the food web in the 
THREATS TO SALMONIDS

4-11

estuary are higher than they were historically. The introduction of exotic species such as 

shad may have accelerated the pace of ecological change in the estuary by permanently 

altering food webs. Food webs also have been altered by sediment transport, in that 

microdetrital food particles adhere to sediment suspended in the water column, making 

different food sources available to different species than was the case historically. 

Affected salmonids: Both stream- and ocean-type salmonids are affected by energy-related 

threats—stream types primarily through increased predation in deep-water habitats and 

ocean types primarily through food web changes in the estuary. Ocean-type juveniles also 

are affected by reduced availability of insect prey as a result of the construction and 

maintenance of dikes. 

Threat: Increased Phytoplankton Production

A reduction in macrodetrital inputs has shifted the food base in the estuary to 

phytoplankton produced in and imported from upstream reservoirs (Northwest Power and 

Conservation Council 2004), or produced as a result of augmented levels of nutrients from 

urban, industrial, and agricultural development. Phytoplankton support a food web that is 

less accessible to ocean-type salmonids occupying shallow edge habitats than the historical 

food web (Northwest Power and Conservation Council 2004). A shift from a generally 

animal-based salmonid diet to a generally plant-based diet may impair caloric inputs 

(Garman 1991; Cloe and Garman 1996; Nakano, Miyasaka, and Kuhara, 1999; Henschel, 

Mahsberg, and Stumpf 2001), and thus the fitness of salmonids that rely on estuarine rearing 

habitats to grow and prepare for ocean migration. The shift in food sources from a 

macrodetrital base to a microdetrital base provides different food sources than salmonids 

historically were accustomed to, in different places within the estuary, and this may favor 

different species. Because this area of study is immature in the estuary, it is difficult to 

establish which species benefit more than others. 

Limiting factors this threat contributes to: Increased microdetrital inputs. 

Threat: Altered Predator/Prey Relationships

Although predation has always occurred in the estuary ecosystem, the cumulative effect of 

altered flows, changes in sediment transport processes and food sources, introduced species, 

hatcheries, upstream habitat impacts, hydroelectric impacts, and contaminants have recast 

estuary and plume environments such that predator/prey relationships have changed 

significantly. As a result, significant numbers of salmon are lost to fish, avian, and marine 

mammal predators during migration and residency in the estuary (Northwest Power and 

Conservation Council 2004). Fish predators include northern pikeminnow, walleye, 

smallmouth bass, and catfish; avian predators include Caspian terns, double-crested 

cormorants, and gull species; and marine mammal predators include Steller and California 

sea lions and harbor seals. 

Degraded conditions (loss of habitat and altered food web) in the Columbia River estuary 

and the timing of large hatchery releases have increased the likelihood that mortality from 

competition may occur under some circumstances (Northwest Power and Conservation 

Council 2004). Mortality from intra-species competition has been documented in the Skagit 

River estuary (Beamer et al. 2005), and there is speculation that it may be a factor in the 

Columbia River as well (Northwest Power and Conservation Council 2004). If inter-species 
THREATS TO SALMONIDS

4-12

competition is occurring, it is likely to have the greatest impact on ocean-type salmonids 

because of their longer residence time in the estuary (Northwest Power and Conservation 

Council 2004). If density dependence is affecting stream-type juveniles, it likely happens in 

the plume. 

As the result of human alterations of the estuary environment, native species such as 

Caspian terns and double-crested cormorants have significantly increased in number, with 

measurable impacts on stream-type salmonids (Bonneville Power Administration, U.S. 

Bureau of Reclamation, and U.S. Army Corps of Engineers 2004). These increases in 

population in the Columbia River estuary are attributed to the deposition of dredged 

materials in the estuary that represent high-quality habitat for the birds (Bottom et al. 2005) 

and predation opportunities for cormorants created through the placement of pilings, pile 

dikes, and other structures. The loss of habitat elsewhere has contributed to terns and 

cormorants effectively relocating to the Columbia River estuary, with the populations there 

now representing the largest nesting colonies in the world. 

Similarly, the new microdetritus-based food web in the estuary has benefited 

zooplanktivores, including American shad (an introduced species) (Northwest Power and 

Conservation Council 2004). Although shad do not appear to be in direct competition with 

salmonids, their biomass alone—more than 4 million returning adults a year—represents a 

threat to trophic relationships in the Columbia River. Future increases in water 

temperatures as a result of climate change may improve conditions for shad in the 

Columbia River Basin and lead to their continued expansion (Independent Scientific 

Advisory Board 2008). Other exotic fish species such as introduced walleye and catfish also 

have been able to capitalize on degraded conditions in the upper reaches of the estuary and 

altered food web dynamics through predation and competition for food resources 

(Northwest Power and Conservation Council 2004). 

Pinniped predation on adult spring Chinook and winter steelhead continues to increase. On 

the West Coast the total abundance of California sea lions is approximately 250,000; Stellar 

sea lions total about 31,000, and Pacific harbor seals total about 25,000 (Griffin 2006). Each 

spring about 1,000 Stellar sea lions, 3,000 Pacific harbor seals, and 800 California sea lions 

take up residence in the lower estuary (Griffin 2006). About 1,000 sea lions and harbor seals 

enter the freshwater portion of the estuary; of these, approximately 80 animals (primarily 

California sea lions) congregate at Bonneville Dam. The U.S. Army Corps of Engineers’ 

estimates that annual adult mortality at Bonneville Dam because of pinnipeds (primarily 

California sea lions) ranged from 0.4 percent (2002) to 4.2 percent (2007) during the study 

period ending in 2010 (U.S. Army Corps of Engineers 2010).1 Other, radio telemetry-based 

studies suggest that annual pinniped predation on spring Chinook and winter steelhead at 

Bonneville Dam may be as high as 8.5 percent and 20 percent, respectively (NMFS 2008b, 

Appendix G). There is a need for better estimates of the mortality caused by pinnipeds 

throughout the estuary and plume. Unsubstantiated estimates suggest a mortality rate of 

10 percent of the entire adult spring Chinook and steelhead runs in a given year. 

Non-native plant species have altered habitat and food webs in the Columbia River estuary. 

The rate of intentional and unintentional introductions has been increasing over the past 100 

 

1 Estimated consumption of adult salmonids ranged from a low of 1,010 in 2002 to a high of 6,081 in 2010; the percent of run 

consumed varied among reporting years in part because of changes in run size.
THREATS TO SALMONIDS

4-13

years, mostly as a result of horticultural practices and the increase in travel and commerce 

in the Columbia River. Four of those species—purple loosestrife, Eurasian water milfoil, 

parrot feather, and Brazilian elodea—are of particular concern. Each of these species, in its 

own way, alters habitat and food webs in the estuary. Purple loosestrife, for example, adapts 

easily to environmental changes and expands its ranges quickly. The primary ecological 

effect of purple loosestrife is that it disrupts wetland ecosystems by displacing native plants. 

Eventually, animals that rely on native flora for food, nesting, or cover also are displaced 

(Northwest Power and Conservation Council 2004). 

Limiting factors this threat contributes to: Native birds, native fish, native pinnipeds, introduced 

invertebrates, exotic fish, and exotic plants. 

Threat: Ship Ballast Practices

Ship ballast practices have been responsible for the introduction of at least 21 exotic species 

in the Columbia River estuary (Sytsma et al. 2004). When ships release ballast water, nonindigenous species can enter receiving waters. Most of the non-indigenous species in the 

estuary have originated from Asia (Sytsma et al. 2004). Populations of non-native copepods 

have established themselves in Reaches A and B (Youngs Bay, Cathlamet Bay, and Grays 

Bay), and the New Zealand mudsnail has colonized other estuary reaches. The Asian 

bivalve Corbicula fluminea has expanded its range in the estuary, with densities of 10,000 per 

m2 being recorded in Cathlamet Bay; however, densities of 100 to 3,000 m2 are more 

common (Northwest Power and Conservation Council 2004). These and other nonindigenous invaders disrupt food webs and out-compete juvenile salmonids’ native food 

sources. 

An emerging source of concern regarding ship ballast practices is the potential entrainment 

of juvenile salmonids when large ships take on ballast water as they leave ports unloaded. 

This issue is being evaluated in relevant Endangered Species Act (ESA) Section 7 

consultations (Tortorici 2008). 

Limiting factors this threat contributes to: Introduced invertebrates.

Water Quality-Related Threats

The release of toxic contaminants, nutrient loading, and reduced dissolved oxygen have 

altered the quality of salmonid habitats in the Columbia River estuary. Currently the 

estuary receives toxic contaminants or nutrients from more than 100 point sources and 

numerous non-point sources, such as surface and stormwater runoff from urban and 

agricultural areas (Fuhrer et al. 1996 as referenced in Fresh et al. 2005). In most areas, 

nonpoint sources such as agricultural, urban, industrial, and timber harvest practices 

contribute greater nutrient loads than point sources do (Wise et al. 2007). The Snake, 

Yakima, Deschutes, and Willamette rivers contribute most of the nutrient loads discharged 

to the Columbia River. Nutrient yields (loads normalized for basin size) are generally 

greater in basins west of the Cascade Range and are correlated with precipitation and pointsource loads (Wise et al. 2007). 
THREATS TO SALMONIDS

4-14

Threat: Agricultural Practices

The health of an aquatic ecosystem is substantially affected by agricultural, urban, and 

industrial practices and wastewater discharge (National Research Council 2004). Specific 

threats include increased nutrients (nitrogen and phosphorus), sediment, and organic and 

trace metals (National Research Council 2004). For example, Wise et al. (2007) found a 

significant correlation between total nitrogen yields in basins west of the Cascades and 

fertilizer and manure loads. Increased nutrient loads from anthropogenic sources can lead 

to increased phytoplankton concentrations, decreased water clarity, and depressed 

dissolved oxygen levels, especially in areas with longer residence times and warmer water 

temperatures. DDT, other banned pesticides that have persisted in the environment, and 

pesticides in current use are entering the estuary from agricultural runoff, some of which 

originates outside the lower Columbia River basin. The middle and upper Columbia are 

primary sources of DDT and other organochlorine pesticides in the estuary, as are 

tributaries such as the Yakima and Willamette rivers (Clark et al. 1998, Williamson et al. 

1998, Hinck et al. 2006, Johnson and Norton 2005, McCarthy and Gale 2001 as cited in Lower 

Columbia River Estuary Partnership 2007). A 2007 study confirmed the presence of the 

pesticides atrazine, simazine, metolachlor, EPTC, DCPA, and diuron at sites throughout the 

estuary, often in combination (Lower Columbia River Estuary Partnership 2007). The timing 

of detections suggests that precipitation events play an important role in transporting 

pesticides to the Willamette River, which is a primary contributor of both agricultural and 

urban/industrial contaminants to the Columbia River estuary. 

The U.S. Geological Survey’s National Stream Quality Accounting Network (NASQAN) 

program also reports detection of a wide range of commonly used pesticides at sampling 

sites near Bonneville Dam and at the confluence of the Willamette and Columbia rivers 

(Fresh et al. 2005). Detected pesticides include simazine, atrazine, chlorpyrifos, metolachlor, 

diazinon, and carbaryl. Arsenic and trace metals such as copper, iron, and manganese also 

have been detected. Although trace metals occur naturally, they also are introduced through 

human activities, such as the use of lead arsenate as an insecticide for apples (Fresh et al. 

2005). Water-soluble contaminants, trace metals, and chlorinated compounds have been 

detected in the estuary (Fresh et al. 2005), and DDT, PCBs, dioxins, and metals have been 

detected at elevated levels in tissue from fish in the estuary (Northwest Power and 

Conservation Council 2004). 

Limiting factors this threat contributes to: Non-bioaccumulative toxicity, bioaccumulation 

toxicity, and increased microdetrital inputs.

Threat: Urban and Industrial Practices

The Columbia River downstream of Bonneville Dam is the most urbanized stretch in the 

entire basin. The area has more than 100 point sources that are known to discharge directly 

into the Columbia River estuary; these include chemical plants, pulp and paper mills, 

hydroelectric facilities, municipal wastewater treatment plants, and seafood processors 

(Fuhrer et al. 1996 as cited in Lower Columbia River Estuary Partnership 2007). Potential 

nonpoint sources include hazardous waste sites, landfills, marinas and moorages, and 

overland surface runoff that transports nutrients, sediment, PAHs, metals, and pesticides 

from streets, yards, and industries. 
THREATS TO SALMONIDS

4-15

The largest sources of effluent in this area are the Portland and Vancouver sewage treatment 

plants (Fresh et al. 2005), with Portland’s wastewater treatment facility being the largest

point-source discharger in the Columbia Basin (Wise et al. 2007). The annual nutrient loads 

from this facility equal approximately 2 to 3 percent of the annual in-stream nutrient loads 

at the Beaver Army Terminal water quality sampling site, downstream of Longview, 

Washington (Wise et al 2007). Contaminants also are transported to the estuary from areas 

above Bonneville Dam, such as the Deschutes, Yakima, and Snake rivers. These rivers, 

together with the Willamette, contribute most of the nutrient loads discharged to the 

Columbia River (Wise et al. 2007).

An intensive study of sediments in Portland Harbor (the stretch of the Willamette River 

from Sauvie Island to Swan Island) has uncovered pesticides, PCBs, and other toxic 

chemicals. In general, studies have shown that PCB and PAH concentrations in salmon and 

their prey in the estuary are comparable to those in organisms in other moderately to highly 

urbanized areas (Fresh et al. 2005, Lower Columbia River Estuary Partnership 2007, Johnson 

et al. 2007b). Industrial contaminants such as PAHs have been detected in sediments from 

the lower Willamette River in Portland at levels that exceed state or Federal sediment 

quality guidelines. The U.S. Environmental Protection Agency identified PCB and DDT hot 

spots within the estuary, including near Longview, West Sand Island, the Astoria Bridge, 

and Vancouver (Fresh et al. 2005). Studies in the 1990s found that sediment contamination 

was highest near urban and industrial areas, with concentrations in excess of levels of 

concern for DDE (a breakdown product of DDT), PCBs, dioxins and furans, and PAHs 

(Tetra Tech 1996). Current studies find higher levels of flame retardants (PBDEs), PCBs, and 

DDT on bed sediment collected near Portland than in sediment collected from other sites in 

the estuary (Jones et al. 2008). 

In addition, emerging contaminants associated with urban development are beginning to be 

detected in the Columbia River estuary. These include PBDE flame retardants, which have 

been found in juvenile salmon tissue, their stomach contents, the water column, and on 

suspended sediment at sites throughout the estuary (Lower Columbia River Estuary 

Partnership 2007). Caffeine, human and veterinary antibiotics, synthetic musk, and the

plasticizer bisphenol A have also been detected in the water of the estuary (Lower Columbia 

River Estuary Partnership 2007). Although the effects of these compounds are not yet well 

understood, some of them are suspected hormone disruptors, and juvenile salmon collected 

from the estuary show evidence of exposure to estrogenic compounds (Lower Columbia 

River Estuary Partnership 2007). This could be the result of emerging contaminants or more 

familiar toxic contaminants in the estuary, such as certain pesticides. 

Limiting factors this threat contributes to: Non-bioaccumulative toxicity, bioaccumulation 

toxicity, and increased microdetrital inputs. 

Other Threats

Threat: Riparian Practices

Riparian practices along the estuary mainstem and in tributaries throughout the Columbia 

River basin have contributed to increases in water temperature in the estuary by changing 

hydrology and removing riparian habitats (National Research Council 2004) that—among 

other ecological functions—provide insects and macrodetrital inputs to the food web. 
THREATS TO SALMONIDS

4-16

Problematic practices include shoreline modifications, timber harvest, certain agricultural 

activities within riparian zones, and residential, commercial, and industrial land uses. These 

activities increase water temperatures, alter hydrology and macrodetrital inputs, and in 

some cases modify shoreline habitats used by salmonids, especially ocean types (Lower 

Columbia Fish Recovery Board 2004). 

Limiting factors this threat contributes to: Sediment/nutrient-related estuary habitat changes, 

reduced macrodetrital inputs, water temperature, and exotic plants. 

Threat: Ship Wakes

Ships traveling through the Columbia River estuary produce waves and an uprush which, 

under certain circumstances, causes juvenile salmonids and other fish to become stranded 

on shore (Bauersfeld 1977). Although Bauersfeld concluded that ship wake stranding was a 

significant cause of mortality in ocean-type Chinook salmon and other species, other studies 

have not confirmed the magnitude of this threat. As a part of the U.S. Army Corps of 

Engineers’ channel deepening project, a study is under way that may help characterize the 

magnitude of ship wake stranding. The purpose of the study is to document ship wake 

stranding before and after channel deepening. The first half of the study, published in 

February 2006, documented stranding events at three test sites. The second part of the study 

will begin after dredging is completed (Pearson et al. 2006). These results should be useful 

as partial basis for Light Detection and Ranging (LIDAR) analysis and extrapolation of test 

site mortality throughout the estuary for similar habitat types. Early in 2008, the Port of 

Vancouver enlisted Entrix, Inc., to perform a spatial analysis of beach susceptibility for the 

stranding of juvenile salmonids by ship wakes (Pearson 2008). The study examined wave 

characteristics and the geomorphology of the lower river but did not examine nearshore fish 

density. The purpose of the study was to estimate the number of miles of shoreline that 

exhibit traits expected to potentially cause stranding. The study concluded that 

approximately 33 miles of shoreline between the mouth of the river and the city of 

Vancouver have shoreline characteristics consistent with stranding (Pearson 2008). 

Limiting factors this threat contributes to: Stranding. 

Prioritization of Threats

This estuary recovery module establishes priorities for threats by linking them to pertinent 

limiting factors and estimating their relative contribution to those limiting factors. The 

threats identified above are well supported in a wide variety of literature sources, including 

Fresh et al. (2005), Bottom et al. (2005), the “Mainstem Lower Columbia River and Columbia 

River Estuary Subbasin Plan” (Northwest Power and Conservation Council 2004), and a 

variety of more topic-specific primary literature sources.2 The prioritization of threats, 

though, is not nearly as well supported, partly because of the limited understanding of how 

threats contribute to limiting factors and to what degree salmon and steelhead are affected 

by a given limiting factor. While it is attractive to assume that additional study will fully 

answer these questions, the biological response to environmental conditions will always be 

difficult to model because of the tremendous complexities of the physical, biological, and 

 

2 As with the limiting factors, most of the threats identified in this chapter are not supported by data at the reach or sub-reach 

scale.
THREATS TO SALMONIDS

4-17

ecological interplay that occurs in the environment. On the other hand, new interest in the 

estuary and its role in the recovery of listed species in the Columbia River has generated 

better understanding, and it is likely that uncertainty surrounding threats and limiting 

factors will continue to lessen. 

Table 4-1 demonstrates the relationship between limiting factors and threats by showing 

which threats are causing which limiting factors and estimating the contribution of each 

threat to each limiting factor. The presumed relative contribution of a threat to each limiting 

factor is indicated by the primary, secondary, or tertiary designation. The contribution of 

each threat to its associated limiting factor(s) is multiplied by the relative importance of that 

limiting factor to salmonids to yield the threat index score. This score expresses the relative 

priority of the threat in question. (The relative importance of limiting factors is taken from 

Table 3-2.)

PC Trask & Associates, Inc., developed the initial threat contribution scores for Table 4-1 by 

reviewing the extent to which the three main literature sources—and other sources—

described relationships between limiting factors and threats or evaluated the contribution of 

multiple threats to a single limiting factor. Although literature sources were useful in 

making connections between threats and limiting factors, in many cases the literature did 

not separate limiting factors from threats or did not attempt to identify and rank the full 

scope of threats that might be contributing to a particular limiting factor. In nearly all cases, 

authors discussed cause-and-effect relationships in qualitative language. In some cases, 

authors described quantitative relationships, as in the relationship between flow regulation 

and sediment transport. Only a handful of sources estimated priorities for threats. 

To supplement information gleaned from the literature, the author talked with regional 

experts (see Acknowledgements) to identify potential threat contributions not described in 

the literature. The author also refined the initial scores based on review and input by NMFS 

Northwest Fisheries Science Center, NMFS Northwest Regional office, Lower Columbia 

River Estuary Partnership, and Lower Columbia Fish Recovery Board staff. The author, in 

consultation with staff from the Lower Columbia River Estuary Partnership and NMFS, also 

made minor adjustments to the scores in response to comments received during the public 

review period.

TABLE 4-1

Linkages Between Limiting Factors and Threats to Ocean- and Stream-Type Salmonids

Limiting Factor Threat

Limiting Factor 

Priority & 

Numerical Scorea

Contribution of Threat 

to Limiting Factor, & 

Numerical Scoreb

Threat 

Indexc

Flow-related 

estuary habitat 

changes

Climate cycles and global 

climate change Top (5) Secondary (2) 10

Water withdrawal Top (5) Secondary (2) 10

Flow regulation Top (5) Primary (3) 15

Flow-related 

changes in access 

to off-channel 

habitat

Climate cycles and global 

climate change Top (5) Secondary (2) 10

Water withdrawal Top (5) Secondary (2) 10

Flow regulation Top (5) Primary (3) 15

Flow-related 

plume changes

Climate cycles and global 

climate change Top (5) Secondary (2) 10

Water withdrawal Top (5) Secondary (2) 10

Flow regulation Top (5) Primary (3) 15
THREATS TO SALMONIDS

4-18

Limiting Factor Threat

Limiting Factor 

Priority & 

Numerical Scorea

Contribution of Threat 

to Limiting Factor, & 

Numerical Scoreb

Threat 

Indexc

Impaired transport of coarse 

sediment Top (5) Secondary (2) 10

Entrapment of fine sediment in 

reservoirs Top (5) Tertiary (1) 5

Water 

temperature

Climate cycles and global 

climate change Top (5) Secondary (2) 10

Reservoir-related temperature 

changes Top (5) Secondary (2) 10

Riparian practices Top (5) Secondary (2) 10

Reduced 

macrodetrital 

inputs

Climate cycles and global 

climate change Top (5) Secondary (2) 10

Water withdrawal Top (5) Secondary (2) 10

Riparian practices Top (5) Secondary (2) 10

Flow regulation Top (5) Primary (3) 15

Dikes and filling Top (5) Primary (3) 15

Sediment/nutrientrelated estuary 

habitat changes

Impaired transport of coarse 

sediment High (4) Primary (3) 12

Entrapment of fine sediment in 

reservoirs

High (4) Secondary (2) 8

Dredging High (4) Secondary (2) 8

Pilings and pile dike structures High (4) Primary (3) 12

Dikes and filling High (4) Primary (3) 12

Over-water structures High (4) Tertiary (1) 4

Riparian practices High (4) Tertiary (1) 4

Bankfull elevation 

changes Dikes and filling High (4) Primary (3) 12

Native birds 

Entrapment of fine sediment in 

reservoirs High (4) Tertiary (1) 4

Dredging High (4) Secondary (2) 8

Altered predator/prey 

relationships High (4) Primary (3) 12

Native pinnipeds Altered predator/prey 

relationships High (4) Primary (3) 12

Nonbioaccumulative 

toxicity

Agricultural practices High (4) Primary (3) 12

Urban and industrial practices High (4) Primary (3) 12

Native fish

Entrapment of fine sediment in 

reservoirs Medium (3) Tertiary (1) 3

Altered predator/prey 

relationships Medium (3) Primary (3) 9

Bioaccumulation 

toxicity

Agricultural practices Medium (3) Primary (3) 9

Urban and industrial practices Medium (3) Primary (3) 9

Sediment/nutrientrelated plume 

changes

Dredging Low (2) Primary (3) 6

Pilings and pile dike structures Low (2) Secondary (2) 4

Dikes and filling Low (2) Secondary (2) 4

Stranding Ship wakes Low (2) Primary (3) 6

Increased 

microdetrital 

inputs

Agricultural Practices Low (2) Secondary (2) 4

Urban and industrial practices Low (2) Secondary (2) 4

Increased phytoplankton 

production Low (2) Primary (3) 6

Flow regulation Low (2) Tertiary (1) 2
THREATS TO SALMONIDS

4-19

Limiting Factor Threat

Limiting Factor 

Priority & 

Numerical Scorea

Contribution of Threat 

to Limiting Factor, & 

Numerical Scoreb

Threat 

Indexc

Exotic fish

Entrapment of fine sediment in 

reservoirs Lowest (1) Tertiary (1) 1

Over-water structures Lowest (1) Secondary (2) 2

Pilings and pile dike structures Lowest (1) Secondary (2) 2

Altered predator/prey 

relationships Lowest (1) Primary (3) 3

Introduced 

invertebrates

Altered predator/prey 

relationships Lowest (1) Tertiary (1) 1

Ship ballast practices Lowest (1) Primary (3) 3

Exotic plants

Dikes and filling Lowest (1) Primary (3) 3

Riparian practices Lowest (1) Secondary (2) 2

Altered predator/prey 

relationships Lowest (1) Primary (3) 3

a From Table 3-2.

b Indicates how important the threat is in perpetuating the limiting factor:

3 = Threat is a primary cause of the limiting factor. Addressing this threat would significantly improve salmonid 

performance.

2 = Threat is a secondary cause of the limiting factor. Addressing this threat would improve performance.

1 = Threat is a tertiary cause of the limiting factor. Addressing this threat would benefit performance, but by itself would 

result in only minor improvement.

c Product of the numerical scores for the limiting factor priority and the threat’s contribution to the limiting factor. A high threat 

index score means that the threat is a major contributor to one or more significant limiting factors. A low threat index score 

means the threat is a small contributor to a minor limiting factor. 

Table 4-2 organizes threats by their threat index score, in descending order. However, the 

state of the science is such that the differentiation of threat priorities in Tables 4-1 and 4-2 

should be viewed as reasonable guidance and a set of working hypotheses to be tested and 

refined through research and evaluation. Given uncertainties about estuarine ecosystems 

and how they function, some threats that are ranked relatively low in Table 4-2 may 

eventually prove to have large impacts to the estuary. For example, it is difficult to dispute 

the importance of flow regulation compared to ship ballast practices. But it is possible that 

the effects of exotic invertebrates introduced to the estuary through ship ballast practices 

will significantly degrade the overall health of the estuary ecosystem over time and that this 

threat will move up in the priority ranking. As another consideration, Tables 4-1 and 4-2 

reflect the prioritization of threats across the entire estuary; within each reach, threats could 

be prioritized differently. A reach-scale analysis of limiting factors and threats was beyond 

the scope of this document and, in some cases, beyond the limits of currently available 

science. But such an analysis would be useful as additional scientific information becomes 

available.
THREATS TO SALMONIDS

4-20

TABLE 4-2

Prioritization of Threats to Ocean- and Stream-Type Salmonids

Threat Threat Index* Threat Priority

Flow regulation 15

 HIGH

 LOW

Dikes and filling 15

Altered predator/prey relationships 12

Urban and industrial practices 12

Agricultural practices 12

Impaired transport of coarse sediment 12

Pilings and pile dike structures 12

Reservoir-related temperature changes 10

Riparian practices 10

Climate cycles and global climate change 10

Water withdrawal 10

Dredging 8

Entrapment of fine sediment in reservoirs 8

Ship wakes 6

Increased phytoplankton production 6

Over-water structures 4

Ship ballast practices 3

* From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that limiting factor. 

High numbers indicate threats that have a major contribution to high-priority limiting factors; lower numbers indicate threats that 

have a minor contribution to low-priority limiting factors. Numbers indicate the highest score per threat category and do not 

account for multiple limiting factor contributions.

Summary

Chapter 4 provides information on the underlying causes of the factors that influence the 

viability of ocean- and stream-type ESUs during their residency and migration in the 

estuary. Analysis of threats is challenging because a single threat often contributes to 

multiple limiting factors and may originate miles upstream from the estuary. In Chapter 4, 

threats were identified, described, linked to limiting factors, and prioritized. Chapter 5 turns 

to management actions, identifying actions that will address threats and thus help reduce 

risks to the 13 ESA-listed ESUs using the Columbia River estuary.
5-1

CHAPTER 5

Management Actions

Chapters 3 and 4 of this recovery plan module identify factors that currently limit 

salmonids’ biological performance in the estuary and the threats that contribute to those 

limiting factors. Chapter 5 presents 23 management actions that, together, address the range 

of threats salmonids in the estuary face, from altered habitat-forming processes to physical 

structures in the estuary, changes in the food web, and poor water quality. If implemented, 

the actions presented in this chapter would reduce the impacts of threats to salmonids 

during their migration and residency in the estuary and plume.

In addition to identifying the management actions, Chapter 5 evaluates them in terms of 

constraints to implementation, potential improvement in salmonid survival, and cost. More 

specifically, the chapter discusses each management action’s potential benefits and 

implementation constraints, hypothesizes how benefits could translate into increased 

survival of salmonids, breaks each action into component projects, and estimates the cost of 

each project, and thus of each action. Also included is a list of actions that would address 

threats to salmonids in the estuary but that would need to be implemented outside the 

estuary, either in estuary tributaries or in upstream areas of the Columbia River basin. 

As in other chapters of this recovery plan module, the analysis in Chapter 5 does not fully 

capture the subtleties of the ecological interactions that influence salmonid survival. Despite 

continuing research, many aspects of the salmonid life cycle are poorly understood, in part 

because of the sheer complexity of the ecosystems that salmonids transition into and out of 

during their lives. The actual relationships among threats and management actions are far 

more intricate than what is described here. Additionally, given the limits in scientific 

understanding, there is a degree of uncertainty at each step of the analysis in this chapter. 

Yet the categories, ratings, and associations presented here are useful tools for discussing 

complex ecological relationships and comparing possible outcomes of different 

management actions.

Identification of Management Actions

For the purposes of this recovery plan module, a management action is any action that has 

the potential to reduce the impact of human-caused or naturally occurring threats to 

salmonids while they migrate or rear in the estuary and plume. PC Trask & Associates, Inc., 

identified management actions using available literature and input from area experts (see 

Acknowledgements). Key documents used to identify management actions are the 

“Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan” (Northwest 

Power and Conservation Council 2004) and its supplement; Role of the Estuary in the Recovery 

of Columbia River Salmon and Steelhead (Fresh et al. 2005); Salmon at River’s End (Bottom et al. 

2005); and the 2004 FCRPS Biological Opinion on Remand (National Marine Fisheries Service 

2004). Table 5-1 lists threats to salmonids in the estuary and plume and management actions 

that would address those threats; this information is organized by topic and does not reflect 

the priority of either threats or management actions.
MANAGEMENT ACTIONS

5-2

TABLE 5-1

Management Actions to Address Threats

Threat Management Action

Flow-related threats

Climate cycles 

and 

global climate 

change2

CRE1-1: Protect intact riparian areas in the estuary and restore riparian areas that are 

degraded.2

CRE-2: Operate the hydrosystem to reduce the effects of reservoir surface heating, or conduct

mitigation measures.2

CRE-3: Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries.2

Water 

withdrawal

CRE-3: Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries

Flow regulation

CRE-4: Adjust the timing, magnitude, and frequency of hydrosystem flows (especially spring 

freshets) entering the estuary and plume to better reflect the natural hydrologic cycle, improve 

access to habitats, and provide better transport of coarse sediments and nutrients in the estuary 

and plume. 

CRE-3: Protect and/or enhance estuary instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and other water management actions in tributaries.

Sediment-related threats

Entrapment of 

fine sediment 

in reservoirs

CRE-5: Study and mitigate the effects of entrapment of fine sediment in reservoirs, to improve 

nourishment of the estuary and plume.

Impaired 

transport of 

coarse 

sediment 

CRE-6: Reduce the export of sand and gravels via dredge operations by using dredged 

materials beneficially.

CRE-8: Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health. 

CRE-4: Adjust the timing, magnitude, and frequency of hydrosystem flows (especially spring 

freshets) entering the estuary and plume to better reflect the natural hydrologic cycle, improve 

access to habitats, and provide better transport of coarse sediments and nutrients in the estuary 

and plume.

Dredging CRE-7: Reduce entrainment and habitat effects resulting from main- and side-channel dredge 

activities and ship ballast intake in the estuary.

Structural threats

Pilings and pile 

dike structures

CRE-8: Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health.

Dikes and filling

CRE-9: Protect remaining high-quality off-channel habitat from degradation and restore 

degraded areas with high intrinsic potential for high-quality habitat.

CRE-10: Breach, lower, or relocate dikes and levees to establish or improve access to offchannel habitats.

Reservoirrelated 

temperature 

changes

CRE-2: Operate the hydrosystem to reduce the effects of reservoir surface heating, or conduct 

mitigation measures.

Over-water 

structures

CRE-11: Reduce the square footage of over-water structures in the estuary.
MANAGEMENT ACTIONS

5-3

Threat Management Action

Food web-related threats

Increased 

phytoplankton 

production

CRE-10: Breach, lower, or relocate dikes and levees to establish or improve access to offchannel habitats.

Altered 

predator/prey 

relationships

CRE-13: Manage pikeminnow and other piscivorous fish, including introduced species, to 

reduce predation on salmonids.

CRE-14: Identify and implement actions to reduce salmonid predation by pinnipeds.

CRE-15: Implement education and monitoring projects and enforce existing laws to reduce the 

introduction and spread of invasive plants.

CRE-16: Implement projects to redistribute part of the Caspian tern colony currently nesting on 

East Sand Island.

CRE-17: Implement projects to reduce double-crested cormorant habitats and encourage 

dispersal to other locations.

CRE-18: Reduce the abundance of shad in the estuary.

CRE-8: Remove or modify pilings and pile dikes with low economic value when removal or 

modification would benefit juvenile salmonids and improve ecosystem health. 

Ship ballast 

practices

CRE-19: Prevent new introductions of aquatic invertebrates and reduce the effects of existing 

infestations

CRE-7: Reduce entrainment and habitat effects resulting from main- and side-channel dredge 

activities and ship ballast intake in the estuary.

Water quality-related threats

Agricultural 

practices

CRE-20: Implement pesticide and fertilizer best management practices to reduce estuarine and 

upstream sources of nutrients and toxic contaminants entering the estuary.3

CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are degraded.

CRE-9: Protect remaining high-quality off-channel habitat from degradation and restore 

degraded areas with high intrinsic potential for high-quality habitat.

Urban and 

industrial 

practices

CRE-21: Identify and reduce terrestrially and marine-based industrial, commercial, and public 

sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.

CRE-23: Implement stormwater best management practices in cities and towns.3

CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are degraded.

CRE-9: Protect remaining high-quality off-channel habitat from degradation and restore 

degraded areas with high intrinsic potential for high-quality habitat.

Other 

threats

Riparian 

practices CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are degraded.

Ship wakes CRE-12: Reduce the effects of vessel wake stranding in the estuary.

1 CRE = Columbia River estuary.

2 Study of the impacts of global climate change is an evolving field, and additional research is needed to understand the 

phenomenon’s likely effects on estuarine habitats and processes with specificity. At this time, the Independent Scientific 

Advisory Board of the Northwest Power and Conservation Council expects that the regional effects of global climate change in 

the next century will include more precipitation falling as rain rather than snow, reduced snow pack, and late-summer/early-fall 

stream flows, and associated rises in stream temperature (Independent Scientific Advisory Board 2007). The climate-related 

management actions in Table 5-1 reflect these expected impacts. Although the management actions clearly would not change 

the threat of global climate change itself, they have the potential to lessen its impact on salmonids in the estuary. Even if 

climate cycles and global climate change have effects different from those assumed in this document, the management actions 

that Table 5-1 associates with climate would provide benefits to salmonids by addressing other threats, such as water 

withdrawal, urban and industrial practices, and reservoir heating. All three of the management actions associated with climate 

in Table 5-1 are associated with other threats listed in Table 5-1.

3 Unless otherwise noted, the term best management practices is used in this document to indicate general methods or 

techniques found to be most effective in achieving an objective. NMFS envisions that in implementation, specific best 

management practices would be developed or recommended.

Note: Italics indicate an action’s second occurrence in the table, in connection with a different threat.
MANAGEMENT ACTIONS

5-4

Given the complexity of the riverine, estuarine, and marine ecosystems that salmon use 

during their lives, the actual relationships among threats and management actions are more 

complicated than Table 5-1 suggests. For example, several of the management actions in 

Table 5-1 are associated with more than one threat (italics indicate an action’s second 

occurrence in the table). This illustrates the complex interplay of ecological processes in the 

estuary, particularly processes related to flow, sediment, the food web, and water quality, 

all of which influence salmon survival. Later in this chapter actions are described and 

analyzed discretely. Some actions are interrelated, both in the problems they attempt to 

solve and their probable effects. As an example, CRE-2 through CRE-5 (reducing the effects 

of reservoir heating, protecting/enhancing instream flows influenced by withdrawals and 

other water management actions in tributaries, adjusting flow timing and magnitude, and 

addressing entrapment of fine sediments in reservoir) all deal with reservoir and 

hydrosystem operations. If implemented together, these actions could act in concert to 

significantly improve water temperature and sediment delivery in the estuary, potentially 

providing greater benefits through synergistic action than if they were implemented singly. 

The potential for synergistic effects of management actions is discussed in more detail in 

Chapter 7. 

The estuary recovery module also identifies specific monitoring, research, and evaluation 

activities appropriate to the 23 management actions. These activities will provide crucial 

information on the effectiveness of actions that are implemented in the estuary, associated 

changes in the ecology of the estuary, and scientific uncertainties that affect implementation 

of the actions. Monitoring, research, and evaluation activities are presented in Chapter 6. 

Some of these activities are part of the Research, Monitoring, and Evaluation for the Federal 

Columbia River Estuary Program (Johnson et al. 2008), while others are specific to the 

management actions in this recovery plan module.

Other Recommended Management Actions

In many ways, conditions in the estuary are the sum of ecological stressors that exist 

throughout the Columbia River basin. Although some threats to salmonids in the estuary 

originate exclusively in the estuary itself (Caspian tern predation is one example), others are 

the result of activities in estuary tributaries or in upstream areas; examples of such threats 

are riparian practices and upstream water withdrawals that reduce stream flow in the 

estuary. Still other threats, such as land use practices that contribute contaminants to the 

river, originate in all three areas—estuary, estuary tributaries, and upstream. Because of the 

geographic scope of these threats, fully addressing them will require effort not just in the 

estuary but throughout the basin. 

When it comes to management actions, though, the geographic scope of this estuary 

recovery plan module is limited. For the most part the module focuses on management 

actions that can be implemented within the estuary itself and that will address threats that 

either originate exclusively within the estuary itself or have a significant in-estuary 

component. The assumption is that threats originating from outside the estuary are affecting 

local conditions in tributary and upstream areas and that actions to address these threats 

will be included in recovery plans being developed for upstream salmonid populations. 
MANAGEMENT ACTIONS

5-5

Even so, the analysis in Chapters 3 and 4 of this recovery plan module and a review of 

contemporary literature yielded six management actions that would directly affect threats to 

salmonids in the estuary yet would need to be implemented almost exclusively outside of 

the estuary or are otherwise beyond the scope of this document:

• Implement hatchery actions as appropriate throughout the Columbia River basin to 

reduce the threat of density-dependent mortality as a direct result of ecological 

interactions (disease, predation, or competition for food or space) between hatchery and 

wild salmonid juveniles using reduced and/or impaired lower river habitats. The 

magnitude of the ecological interactions as a function of the cumulative effects of large 

hatchery releases on natural-origin salmonids, both spatially and temporally, is 

currently an important scientific uncertainty.

• Upgrade up-river irrigation structures to reduce evaporation and conveyance losses and 

improve estuary instream flows.

• Implement public and private best management and water system conservation 

practices to maximize the quantity and quality of instream flows entering the estuary.

• Incorporate water availability analysis in land use planning activities to ensure efficient 

use of water, improve tributary flows, and reduce stream temperatures. 

• Protect and restore riparian areas in tributaries to provide shade and future wood

sources.

• Reduce inputs of toxic contaminants originating from upstream tributary and mainstem 

sources. 

Because these six actions are outside the geographic scope of the estuary recovery plan 

module, they are not analyzed in this chapter. Nevertheless, implementation of these six

out-of-estuary actions is important to improving the survival of salmonids in the estuary, so 

it is recommended that the actions be included in recovery plans being developed for 

upstream areas of the Columbia River basin. 

One factor that is beyond the geographic scope of the estuary recovery plan module but is 

addressed in the module in a limited manner is hydrosystem operations, which affect water 

temperature, sediment transport, and various other habitat-forming processes and 

conditions in the estuary. Although actual operation of the hydrosystem occurs outside the 

estuary, the system’s effects are considered in the module because they are such significant 

determinants of habitat conditions for juvenile salmonids in the estuary. Also, unlike the 

recommended out-of-estuary actions listed above, hydrosystem operations that affect 

estuarine habitat are unlikely to be addressed in recovery plans being developed for 

upstream areas of the Columbia River basin. For these reasons, the estuary recovery plan 

module includes two management actions (CRE-2 and CRE-4) that focus specifically on 

hydrosystem operations. 

The recommendation of out-of-estuary actions to improve survival in the estuary is another 

reflection of the interconnectedness of the various ecosystems salmonids use during their 

life cycles, the power of the river as a connector, and how the effects of problematic 

upstream activities are manifested—and sometimes magnified—in the estuary. 
MANAGEMENT ACTIONS

5-6

Evaluation of Management Actions: Constraints to 

Implementation

Constraints to implementation are a key factor in evaluating management actions and their 

likely impacts on salmonids. No management action can benefit salmonids if it cannot be 

implemented, and in many cases the degree of benefit corresponds to the degree of 

implementation. For this reason, the 23 management actions identified above are evaluated 

in terms of the constraints to their implementation, which yields information about the 

actions’ likely outcomes and starts to provide a basis for comparing the probable 

effectiveness of different actions. 

PC Trask & Associates, Inc., performed an initial rating of management action constraints by 

qualitatively estimating the degree of difficulty in implementing each action, taking into 

account social, political, and technical factors, including the probable cost of 

implementation. Staff at the Lower Columbia River Estuary Partnership, NMFS Northwest 

Fisheries Science Center, NMFS Northwest Regional Office, and Lower Columbia Fish 

Recovery Board provided input into this process. PC Trask & Associates, Inc., and NMFS 

also revised some constraint scores in response to the Federal Register public comment 

process. Because the scientific literature generally falls short of prescribing discrete actions 

to address threats and is even less robust when it comes to evaluating constraints to 

implementation, the reader should view specific ratings as a qualitative estimate only, but 

one that is useful in comparing relative implementation constraints across the 

23 management actions.

For each management action, Table 5-2 summarizes the primary threat and limiting factors 

that the action addresses and expresses the significance of those threats and limiting factors 

in terms of a threat index. (The threat index indicates whether the threat is a major 

contributor to a significant limiting factor or a minor contributor to a minor limiting factor. 

The index is useful in distinguishing those actions that, even if they were successful, would 

affect a relatively small number of fish from those actions that, even if they were only 

partially implemented or partially successful, would have more profound benefits because 

they would affect a larger number of fish.) Table 5-2 also provides a score for the potential 

benefit to salmonids in the estuary if implementation of the action were completely 

unconstrained, plus a brief rationale for the score. 

Assigning a score for potential benefit with unconstrained implementation is just the first 

step in evaluating management actions. In fact, decisions about management actions will be 

made within a complex social and political context that includes a wide variety of interests, 

and it is likely that many of the actions will not be able to be implemented fully because of 

various technical, financial, political, or social obstacles. To address this issue, Table 5-2 

assigns an implementation constraints score to each management action and briefly explains 

how implementation of the action could be constrained by various factors. It then gives a 

score that represents the potential benefits of the action if implementation of the action is 

constrained. By design, the estuary recovery module takes a relatively optimistic view about 

what is possible in terms of reducing the constraints to implementation of management 

actions. This means that even the score in Table 5-2 for constrained implementation of an 

action may represent a higher degree of implementation than is likely to actually occur. 

However, some constraints may be reduced over time, such as through technology 
MANAGEMENT ACTIONS

5-7

advances or changes in economic sectors; as a result, some actions may have greater 

potential for implementation than is represented in this recovery plan module. 

The table concludes with a score for potential benefit of each action assuming that 

implementation of the action is constrained. This score is an attempt to identify more 

realistically what the results of an action would be given the social, political, and financial 

climate in which management actions will be decided on, but it also assumes that 

considerable effort is made to reduce constraints to implementation. Also, the difference in 

Table 5-2 between potential benefit with unconstrained implementation of an action and 

potential benefit with constrained implementation is helpful in identifying where it might 

be worthwhile to expend effort to reduce constraints because the benefits would be great. 

This topic is discussed more fully in Chapter 7. 

The threat index and scoring in Table 5-2 are for the estuary as a whole, instead of by reach, 

because in most cases the assessment information needed to do a reach-scale analysis 

currently is lacking. However, the severity of individual threats and limiting factors varies 

from reach to reach in the estuary, as do the potential benefits of the management actions. It 

is assumed that implementation of the management actions will involve dialogue and 

additional evaluation at the reach scale to aid in prioritizing actions and focusing them in 

the geographical areas where they would be most beneficial. 
MANAGEMENT ACTIONS

5-8

TABLE 5-2

Constraints to Implementation of Management Actions

Management Action CRE-1:

Protect intact riparian areas in the estuary and restore riparian areas that are degraded.

Primary threat

this action would address

Riparian Practices. Riparian areas provide key ecological functions 

that affect water temperature, the availability of insects, and 

macrodetrital inputs to the ecosystem. Riparian areas in the lower 

Columbia River have been degraded by a number of factors, 

including shoreline modifications, diking and dike maintenance 

practices, and activities related to the disposal of dredged material.

Associated limiting factors Water temperature, reduced macrodetrital inputs, and exotic plants. 

Threat index1 10 This threat is a secondary contributor to two top-priority limiting 

factors (water temperature and reduced macrodetrital inputs) and a 

tertiary contributor to one additional limiting factor.

Potential benefits with 

unconstrained 

implementation of 

action 2

4 Protecting intact riparian areas and restoring degraded riparian areas 

in priority reaches would provide significant benefits to salmonids by 

reducing water temperatures and increasing macrodetrital inputs to 

the system.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 3 Levels of protection vary across the lower Columbia region. In some 

cases, riparian areas in cities and counties are protected through 

regulatory mechanisms such as growth management or shoreline 

rules. Regulatory tools such as buffer zones along streams can be 

effective but require broad public support over time. Restoration 

projects are expensive and can take decades to provide their full 

benefit to tributaries directly entering the estuary.

Potential benefits with 

constrained 

implementation of 

action

2

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-9

Management Action CRE-2:

Operate the hydrosystem to reduce the effects of reservoir surface heating, or conduct mitigation measures.

Primary threat

this action would address

Reservoir-related temperature changes. Low-velocity flows and 

broad surface area exposure in reservoirs increase the temperature 

of flows in the estuary. Salmonids are cool-water fish that need 

stream temperatures of 20o C or lower for normal metabolism, 

growth, disease resistance, and timing of important life functions 

such as smoltification and adult migration. Salmonids in the estuary 

are experiencing water temperatures at the upper limit of their 

tolerance for longer periods and more frequently than they did 

historically. 

Associated limiting factors Water temperature. 

Threat index1 10 This threat is a secondary contributor to a top-priority limiting factor.

Potential benefits with 

unconstrained 

implementation of 

action 2

3 Given that at many times during the year water temperatures in the 

estuary are at or above the upper limits of salmonids’ thermal 

tolerance, any lowering of water temperature could provide 

significant survival benefits. Water temperatures of below 20o C 

throughout the year would aid salmonids in carrying out essential 

physiological processes and life functions.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 5 Elevated temperatures that result from reservoir heating are difficult 

to reduce. Temperatures may be influenced by the volume and 

speed of flows through the hydrosystem and the source of those 

flows (some impoundments have cooler water than others do). 

International treaties, conflicting fish management objectives 

systemwide, the need for flood control, power management, and 

other factors constrain management of the hydrosystem to allow 

cooler flows to enter the estuary. 

Potential benefits with 

constrained 

implementation of 

action

2

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-10

Management Action CRE-3:

Protect and/or enhance estuary instream flows influenced by Columbia River tributary/mainstem water withdrawals 

and other water management actions in tributaries.

Primary threats

this action would address

Water withdrawal and impaired transport of coarse sediment.

Instream flows in the estuary are important for salmonids because 

they maintain habitat-forming processes and conditions in the 

estuary and plume. Transport of sand and gravel from upstream and 

estuary sources during high flows helps establish and maintain 

salmonid habitats, contributes to turbidity that shelters salmonids 

from predation, and influences food sources in the plume. Some 

instream flows have been established in Columbia River basin 

tributaries, but others are needed, especially with human population 

growth in the basin. This action focuses on water withdrawals in 

tributaries and the mainstem and other tributary flow issues, 

including tributary hydropower. It complements CRE-4, which 

focuses on mainstem hydrosystem flow-related issues, such as 

hydrosystem regulation, to establish incremental flow improvements 

in the estuary within the context of power generation and flood 

control.

Associated limiting factors Flow-related estuary habitat changes, flow-related changes in access 

to off-channel habitat, flow-related plume changes, and reduced 

macrodetrital inputs.

Threat index1 12 This threat is a secondary contributor to four top-priority limiting 

factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

2 This action contributes incremental instream flow improvements that 

protect/enhance the flow regime in the estuary and plume and 

support associated habitat-forming processes.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings); stream-type salmonids in the plume. 

Implementation 

constraints3 5 Implementation of this action would require the involvement of 

multiple stakeholders, including irrigation, commercial, industrial,

hydrosystem, tribal, Federal, state, and local interests, plus 

significant public involvement. Establishing protected instream flows 

is challenging because of competing interests and often takes years.

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-11

Management Action CRE-4:

Adjust the timing, magnitude, and frequency of hydrosystem flows (especially spring freshets) entering the estuary 

and plume to better reflect the natural hydrologic cycle, improve access to habitats, and provide better transport of 

coarse sediments and nutrients in the estuary and plume.

Primary threats

this action would address

Flow regulation and impaired transport of coarse sediment. The 

magnitude, frequency, and timing of flows are an important 

determinant of habitat opportunity for salmonids in the estuary. 

Salmonids have adapted to historical flows and depend on them to 

complete their life cycles. The transport of sand and gravel from 

upstream and estuary sources helps maintain salmonid habitats, 

contributes to turbidity that shelters salmonids from predation, and 

influences food sources in the plume. Spring freshets are important 

habitat-shaping events for the estuary and plume. Improved flow 

regimes would help ecological processes (and salmonids) by making 

nutrients and other food sources, such as insects, available in the 

food web. 

Associated limiting factors Flow-related estuary habitat changes, flow-related changes in access 

to off-channel habitat, flow-related plume changes, reduced 

macrodetrital inputs in the estuary, and sediment/nutrient-related 

estuary habitat changes.

Threat index1 15 This threat is a primary contributor to several top-priority limiting 

factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

5 Return to a more natural flow regime would have significant 

ecosystem benefits and would affect all facets of salmonid life 

histories expressed in the estuary and plume. Adjustments to the 

timing, magnitude, and frequency of hydrosystem flows entering the 

estuary would be likely to have synergistic effects that would 

increase the benefit of many of the other actions. 

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies; stream-type juveniles rearing in the 

plume.

Implementation 

constraints3 5 Constraints on hydrosystem operations prevent the return to a 

natural flow regime in the estuary. Implementation of this action 

would be limited by international treaties, the need for flood control, 

fish management objectives systemwide, and power production. 

However, even slight modifications in the flow regime have the 

potential to provide significant ecosystem benefits. 

Potential benefits with 

constrained 

implementation of 

action

3

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-12

Management Action CRE-5:

Study and mitigate the effects of entrapment of fine sediment in reservoirs, to improve nourishment of the estuary 

and plume.

Primary threat

this action would address

Entrapment of fine sediment in reservoirs. Fine sediments 

originating from upstream sources are trapped in low-velocity 

impoundments in the Columbia River, and their movement into the 

estuary and plume has been reduced. This alters processes that 

form shallow-water habitats, affects food sources, and reduces 

turbidity that otherwise would shelter salmonids from predation.

Associated limiting factors Flow-related plume changes and sediment/nutrient-related estuary 

habitat changes.

Threat index1 8 This threat is a secondary contributor to several high-priority limiting 

factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

2 Fine sediment transport processes are important determinants of 

estuary and plume habitats. Effective mitigation of this threat would 

reduce predation of salmonids in the main channel and plume and 

strengthen habitat-forming processes. 

Affected salmonids Ocean- and stream-type salmonids.

Implementation 

constraints3 5 There are no apparent technical solutions to this threat at this time. 

Mitigation is recommended, but research is needed to identify the 

magnitude of the threat and potential solutions or mitigation 

measures.

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = significant potential for implementation.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-13

Management Action CRE-6:

Reduce the export of sand and gravels via dredge operations by using dredged materials beneficially.

Primary threat

this action would address

Impaired transport of coarse sediment. The transport of sand and 

gravel from upstream and estuary sources is a primary force that 

influences the creation, maintenance, and distribution of salmonid 

habitats in the estuary. While there are many potential beneficial uses of 

dredged materials—including enhanced nourishment of the littoral cell, 

land creation, property stabilization, and out-of-stream uses—there is 

also an important ecological need to retain coarse sediments in the 

estuary for habitat creation and maintenance. 

Associated limiting factors Sediment/nutrient-related estuary habitat changes and flow-related 

plume changes.

Threat index1 12 Although impaired transport of coarse sediment is a primary contributor 

to a top-priority limiting factor (flow-related plume changes), this 

management action is likely to have its greatest effect in addressing 

sediment/nutrient-related estuary habitat changes, a high-priority limiting 

factor; thus it has a threat index of 12. 

Potential benefits with 

unconstrained 

implementation of 

action 2

2 The beneficial use of sand resulting from dredge activities could play an 

important role in restoring habitat capacity and habitat opportunity in the 

estuary and plume. The beneficial use of dredged materials to provide 

sand nourishment could reduce the effects of ship wake stranding, 

improve habitat for Americorphium (a food source for salmonids), and be 

beneficial in the development of intertidal swamps and marshes and 

other salmonid habitat features. Sand entering the littoral cell could also 

have important ecological benefits.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less dominant 

life history strategies (e.g., early and late fingerlings and subyearlings). 

This particularly applies to ocean-type juveniles because of their 

significant use of shallow-water habitats and the nearshore environment. 

Implementation 

constraints3 3 Beneficial uses of dredged materials, such as through littoral cell sand 

nourishment and direct beach nourishment, are currently receiving 

significant attention, The most obvious constraint to implementation is 

identifying funding sources to pay for activities beyond the minimum 

required by law. 

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-14

Management Action CRE-7:

Reduce entrainment and habitat effects resulting from main- and side-channel dredge activities and ship ballast 

intake in the estuary.

Primary threat

this action would address

Dredging. Annual dredge operations maintain a navigational 

channel that concentrates flows, alters tidal influences, reduces 

circulation patterns around the estuary, and releases toxic 

contaminants from substrates. Dredging activities can result in 

deposited contaminants being disturbed and redistributed throughout 

the estuary. Dredging activities also result in the entrainment of 

juvenile salmonids and benthic organisms through the physical 

removal of sand via pipeline or clamshell dredging. Ship ballast 

intake may also result in the entrainment of juveniles as ships take 

on ballast water when exiting port facilities. 

Associated limiting factors Sediment/nutrient-related estuary habitat changes, native birds, and 

sediment/nutrient-related plume changes.

Threat index1 8 As it relates to this action, dredging is a secondary contributor to a 

high-priority limiting factor (sediment/nutrient-related estuary habitat 

changes) and thus has a threat index of 8. 

Potential benefits with 

unconstrained 

implementation of 

action 2

2 Continued dredge operations represent a physical change to the 

Columbia River estuary. However, reducing or mitigating the effects 

of dredging would improve habitat-forming processes that would 

benefit salmonids. Reduction of entrainment through new 

technologies or management practices for both dredging and ship 

ballast intake would reduce mortality of juveniles. 

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 2 Dredging activities have been occurring since the 1870s to provide 

sufficient draft for ships entering the Columbia River and will continue 

into the foreseeable future. Ongoing maintenance is needed to keep 

the channel to specifications for ships, and additional dredging will be 

conducted in the estuary as part of the channel deepening process. 

Maintaining the navigation channel requires dredging and disposal of 

large volumes of material (4 to 5 million cubic yards) each year. 

Changing dredging equipment, ballast water intake screens, and

practices to reduce entrainment and habitat effects would be 

expensive.

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that limiting factor. High 

numbers indicate threats that have a major contribution to high-priority limiting factors; lower numbers indicate threats that have a 

minor contribution to low-priority limiting factors. Numbers indicate the highest score per threat category and do not account for 

multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully implemented, with no 

constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-15

Management Action CRE-8:

Remove or modify pilings and pile dikes when removal or modification would benefit juvenile salmonids and improve

ecosystem health.

Primary threat

this action would address

Pilings and pile dike structures. Extensive use of pilings and pile 

dikes has altered sediment accretion and erosion processes and 

reduced flow circulation through shallow-water habitats in the 

estuary. Pile structures also have created favorable conditions for 

predators of salmonids and can reduce physical access to lowvelocity juvenile salmonid habitats. In some cases, treated pilings 

may release toxic contaminants, including PAHs, and it can be 

beneficial to remove these structures. In other cases, pile structures 

may protect riparian areas from erosion and wave energy, collect 

large wood to form complex habitat, and stimulate sediment accretion 

in the creation of habitat. In these cases, maintenance or modification 

of existing structures may be beneficial. 

Associated limiting factors Sediment/nutrient-related estuary habitat changes, sediment/nutrientrelated plume changes, exotic fish, native birds, and bioaccumulation 

toxicity. 

Threat index1 12 This threat is a primary contributor to a high-priority limiting factor 

(altered predator/prey relationships), a secondary contributor to a 

high-priority limiting factor (sediment/nutrient-related estuary habitat 

changes) and two low-priority limiting factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

4 Removing many instream structures would improve circulation in 

shallow-water habitats and eliminate some salmonid predator 

habitats. 

Affected salmonids Ocean-type salmonids; stream-type salmonids (yearlings) leaving the 

heavier flows to forage in shallow waters downstream of pilings and 

pile dikes; stream-type salmonids displaying less dominant life history 

strategies (e.g., early and late fingerlings and subyearlings);

Implementation 

constraints3 2 Only some of the thousands of pilings, pile dikes, and similar 

structures in the Columbia River estuary are necessary to maintain 

the shipping channel, protect property, or serve their intended 

economic use. Removal of superfluous structures generally is 

restricted only by cost and would be unlikely to affect property rights 

or the shipping industry. In cases where pile dikes that do aide in 

navigation are removed, constraints to implementation would include 

the cost for additional dredging to maintain the channel.

Potential benefits with 

constrained 

implementation of 

action

2

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that limiting factor. High 

numbers indicate threats that have a major contribution to high-priority limiting factors; lower numbers indicate threats that have a 

minor contribution to low-priority limiting factors. Numbers indicate the highest score per threat category and do not account for 

multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully implemented, with no 

constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-16

Management Action CRE-9:

Protect remaining high-quality off-channel habitat from degradation and restore degraded areas with high intrinsic 

potential for high-quality habitat.

Primary threat

this action would address

Dikes and filling. High-quality off-channel habitat provides crucial 

feeding, rearing, and refuge opportunities for juvenile salmonids and 

supplies macrodetrital inputs to the estuarine food web. Reduced 

floodplain inundation has limited juvenile salmonids’ access to 

historical wetland and swamp habitat, much of which has been 

converted to other land uses. Protecting remaining intact and 

accessible off-channel habitats and restoring accessible but 

degraded off-channel areas are critical to maintaining key habitats 

and food sources for juvenile salmonids. 

Associated limiting factors Reduced macrodetrital inputs, sediment/nutrient-related estuary 

habitat changes, bankfull elevation changes, sediment/nutrientrelated plume changes, and exotic plants.

Threat index1 15 This threat is a primary contributor to both top-priority and highpriority limiting factors. 

Potential benefits with 

unconstrained 

implementation of 

action 2

5 Protecting high-quality off-channel areas would help maintain 

important wetland habitats and supply macrodetrital inputs to the 

food web and insect food sources for juvenile salmonids—a main 

component of their diet. Restoring or enhancing accessible but 

degraded off-channel areas in the estuary represents a largely 

untapped strategy that could provide similar benefits. Benefits from 

this strategy likely would be realized more quickly than from the 

passive restoration associated with CRE-10.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 3 Regulatory programs often do not effectively protect floodplains from 

conversion to other uses. The acquisition of land for habitat 

protection remains controversial in the estuary. Rural county 

governments see land disappearing off tax rolls and also listen to 

citizen disapproval of public ownership of land. Land acquisition is 

expensive and depends on the willingness of landowners to sell. 

Restoring accessible off-channel habitat also depends on willing 

landowners .The fact that many habitats already have been 

converted to other land uses limits opportunities to protect highquality off-channel habitat. 

Potential benefits with 

constrained 

implementation of 

action

3

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that limiting factor. High 

numbers indicate threats that have a major contribution to high-priority limiting factors; lower numbers indicate threats that have a 

minor contribution to low-priority limiting factors. Numbers indicate the highest score per threat category and do not account for 

multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully implemented, with no 

constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-17

Management Action CRE-10:

Breach, lower, or relocate dikes and levees to establish or improve access to off-channel habitats.

Primary threat

this action would address

Dikes and filling. Many juvenile salmonids rely on off-channel 

habitats for feeding and refuge opportunities. Historically, insects and 

macrodetritus from these habitats were important inputs to the 

estuarine food web. Dikes, levees, tide gates, and filling have limited 

the amount and accessibility of key off-channel habitats by reducing 

floodplain inundation and allowing conversion of land to agricultural, 

residential, and industrial uses. This action would allow juvenile 

salmonids access to habitats and food sources that currently are 

unavailable to them and support improved habitat conditions over 

time. 

Associated limiting factors Reduced macrodetrital inputs, sediment/nutrient-related estuary 

habitat changes, bankfull elevation changes, sediment/nutrientrelated plume changes, and exotic plants. 

Threat index1 15 This threat is a primary contributor to both top-priority and highpriority limiting factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

5 Establishing or improving access to off-channel areas via dike 

breaching and similar activities would reclaim habitat that is 

important to salmonids. Over time, improved hydrology would 

support reestablishment of wetland vegetation and salmonid food 

sources in off-channel areas, through passive restoration. In most 

cases, project benefits would accrue over relatively long periods of 

time.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 3 Opportunities to establish or improve access to off-channel habitats 

are limited because many such habitats already have been filled with 

dredged materials. Breaching, lowering, or relocating dikes and 

levees or removing tide gates often requires the cooperation of 

multiple landowners and may fundamentally alter land uses. The 

associated habitat restoration is expensive. 

Potential benefits with 

constrained 

implementation of 

action

4

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-18

Management Action CRE-11:

Reduce the square footage of over-water structures in the estuary.

Primary threat

this action would address

Over-water structures. Over-water structures may provide habitats 

for predators and affect instream and shoreline plant communities. 

However, the total surface area of over-water structures in the 

estuary has not been quantified and the structures’ case-by-case 

functions have not been analyzed.

Associated limiting factors Sediment/nutrient-related estuary habitat changes and exotic fish.

Threat index1 4 This threat is a tertiary contributor to a high-priority limiting factor 

(habitat changes) and a secondary contributor to one of the lowest 

priority limiting factors (exotic fish).

Potential benefits with 

unconstrained 

implementation of 

action 2

3 Given the uncertainty about how much of a threat over-water 

structures actually pose to salmonids, the potential improvement in 

survival must be considered low pending additional research and 

analysis.

Affected salmonids Ocean-type salmonids (because of their preference for the shallowwater habitats where most structures are located); stream-type 

salmonids displaying less dominant life history strategies (e.g., early 

and late fingerlings and subyearlings).

Implementation 

constraints3 3 It is assumed that some over-water structures are more important 

than others and that removing superfluous or less useful structures 

would not have deleterious effects on adjacent land uses. Removal 

of over-water structures that are in currently use would likely require 

compensation. In some cases, structures such as log rafts could be 

relocated. 

Potential benefits with

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-19

Management Action CRE-12:

Reduce the effects of vessel wake stranding in the estuary. 

Primary threat

this action would address

Ship wakes. Wakes from deep-draft vessels traveling through the 

estuary wash subyearling salmonids onto shore, leaving them 

stranded. Factors that affect stranding include beach slope and time 

of day as well as vessel draft, speed, and hull design.

Associated limiting factors Stranding.

Threat index1 6 This threat is a primary contributor to a low-priority limiting factor. 

Potential benefits with 

unconstrained 

implementation of 

action 2

2 The extent of mortality caused by ship wake stranding is unknown. 

Studies in 1977 and 1994 (Bauersfeld 1977, Hinton and Emmett 

1994) reached different conclusions, using different approaches. A 

soon-to-be-released study by the University of Washington and U.S. 

Army Corps of Engineers may provide further clarification of the 

issue.

Affected salmonids Ocean-type salmonids (because of their longer estuarine residency 

times, their relatively small size, and the habitats they prefer); 

stream-type salmonids displaying less dominant life history strategies 

(e.g., early and late fingerlings and subyearlings).

Implementation 

constraints3 3 Options for reducing the effects of vessel wake stranding are limited, 

primarily because of the lost revenues that would result from slower 

ship travel. Ship traffic through the estuary will continue, ship hull 

design is unlikely to change, and the speed of ships traveling the 

estuary may be difficult to alter. Modification of some habitats may be 

necessary to reduce this threat and would likely be expensive.

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-20

Management Action CRE-13:

Manage pikeminnow and other piscivorous fish, including introduced species, to reduce predation on salmonids.

Primary threat

this action would address

Altered predator/prey relationships. Pikeminnows have always 

been a significant source of mortality for juvenile salmonids in the 

Columbia River, but changes in physical habitat, such as the addition 

of in-water structures, have created more favorable conditions for 

predation by pikeminnow. Introduced species such as smallmouth 

bass, walleye, and channel catfish also prey on juvenile salmonids, 

primarily in the freshwater reaches.

Associated limiting factors Native fish and exotic fish. 

Threat index1 12 This threat contributes to many limiting factors, although the 

management action addresses only the native and exotic fish limiting 

factors, which have threat indexes of 12 and 3, respectively.

Potential benefits with 

unconstrained 

implementation of 

action 2

4 Ecosystem alterations in the estuary as a result of pikeminnow, 

smallmouth bass, walleye, and channel catfish are uncertain. 

Scientists speculate that pikeminnow may be preying on both oceanand stream-type juveniles. Stream-type juveniles may be affected 

significantly more than previously thought because evidence 

suggests that they forage in shallow areas downstream of piling 

structures.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 2 Because of their abundance, pikeminnow appear to be a far greater 

threat to juvenile salmonids than bass, walleye, and channel catfish, 

at least at this time. Implementation activities to reduce pikeminnow 

predation are constrained by the challenge of reducing their 

preferred slack-water habitats. Bounty programs can be effective at 

removing older pikeminnow, which represent the largest threat to 

salmonids. Although the introduction of exotic fish to the estuary may 

be irreversible, there are viable tools for managing smallmouth bass, 

walleye, and channel catfish; these include habitat management and 

less restricted harvest management. It is likely that warm-water 

fishers would actively support maintaining the abundance of these 

species at current—rather than reduced—levels. 

Potential benefits with 

constrained 

implementation of 

action

2

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-21

Management Action CRE-14:

Identify and implement actions to reduce salmonid predation by pinnipeds.

Primary threat

this action would address

Altered predator/prey relationships. Pinniped predation on adult 

salmonids at Bonneville Dam has been estimated at between 

0.4 percent (2002) and 4.2 percent (2007) of the spring Chinook and 

winter steelhead runs, or possibly as high as 8.5 percent and 20 

percent, respectively (based on radio-telemetry studies). The extent 

of predation needs further study and documentation.

Associated limiting factors Native pinnipeds.

Threat index1 12 This threat contributes to many limiting factors, although the 

management action relates only to native pinnipeds.

Potential benefits with 

unconstrained 

implementation of 

action 2

3 Actions to reduce predation by pinnipeds would have moderate 

impacts on salmonid survival, depending on how many adults are 

actually being consumed by pinnipeds—a question that remains 

uncertain. 

Affected salmonids Ocean- and stream-type salmonids.

Implementation 

constraints3 4 Methods for reducing salmonid predation by pinnipeds are limited 

because pinnipeds are protected under the Marine Mammal 

Protection Act (MMPA). It could take years to amend the act to allow 

additional pinniped management tools. Non-lethal methods have 

been only minimally successful, although it is possible that additional 

testing would identify effective non-lethal methods. In 2008, NMFS 

granted Washington, Oregon, and Idaho authority to use and 

evaluate lethal methods of control under Section 120 of the MMPA. 

Potential benefits with 

constrained 

implementation of 

action

2

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-22

Management Action CRE-15:

Implement education and monitoring projects and enforce existing laws to reduce the introduction and spread of 

invasive plants.

Primary threat

this action would address

Altered predator/prey relationships. Exotic plants in the estuary 

often out-compete native plants and change the structure of plant 

communities. The resulting habitat frequently does not provide the 

same food or shelter that other species, including salmonids, have 

adapted to over time.

Associated limiting factors Exotic plants.

Threat index1 3 This threat contributes to many limiting factors, although the 

management action relates only to exotic plants, one of the lowest 

priority limiting factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

2 Preventing and controlling invasive plants would help maintain the 

estuarine food web and habitats that juvenile salmonids rely on.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 4 Controlling existing infestations of certain species is functionally 

impossible once the species are established. Although landowners

are the most important agents in preventing and controlling exotic 

plant infestations, landowner education is a significant task that 

requires a large effort.

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-23

Management Action CRE-16:

Implement projects to redistribute part of the Caspian tern colony currently nesting on East Sand Island.

Primary threat

this action would address

Altered predator/prey relationships. Caspian tern predation 

represents a significant source of mortality for stream-type juveniles 

migrating to saltwater. Stream-type salmonids are particularly 

vulnerable because of the timing of their out-migration (during tern 

nesting season) and their preference for deep-channel habitats near 

tern nesting sites.

Associated limiting factors Native birds.

Threat index1 12 This threat contributes to many limiting factors, although the 

management action relates only to Caspian terns.

Potential benefits with 

unconstrained 

implementation of 

action 2

5 Reducing tern predation could have significant effects on the survival 

of stream-type salmonids, as terns have been documented to 

consume as much as 3 percent of stream-type juveniles migrating 

through the estuary. 

Affected salmonids Stream-type salmonids; ocean-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 2 Management efforts have helped reduce mortality by relocating terns 

to nearby habitats. Long-term solutions will require habitat 

improvements elsewhere for Caspian terns.

Potential benefits with 

constrained 

implementation of 

action

3

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-24

Management Action CRE-17:

Implement projects to reduce double-crested cormorant habitats and encourage dispersal to other locations. 

Primary threat

this action would address

Altered predator/prey relationships. Predation by double-crested 

cormorants represents a significant source of mortality for streamtype juveniles migrating to saltwater.

Associated limiting factors Native birds.

Threat index1 12 This threat contributes to many limiting factors, although the 

management action relates only to double-crested cormorants. 

Potential benefits with 

unconstrained 

implementation of 

action 2

4 Studies indicate that double-crested cormorants prey on salmonid 

juveniles in the estuary at a rate equal to or greater than the rate by 

Caspian terns. Cormorants are estimated to have consumed an 

average of 7 million juvenile salmonids annually over the years 2001 

to 2009.

Affected salmonids Ocean- and stream-type juvenile salmonids are preyed upon by 

double-crested cormorants with some fluctuation from year to year. 

In 2009 double-crested cormorants consumed approximately 11 

million juvenile salmonids. 

Implementation 

constraints3 4 Double-crested cormorants are more difficult to relocate than 

Caspian terns. Techniques such as the use of decoys and audio 

playback have not been as effective compared to terns. Perch 

habitats are plentiful enough in the estuary that removal of pile dikes 

and other structures may not be an effective tool. 

Potential benefits with 

constrained 

implementation of 

action

2

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-25

Management Action CRE-18:

Reduce the abundance of shad in the estuary.

Primary threat

this action would address

Altered predator/prey relationships. Shad returns to the Columbia 

River number approximately 4 million annually. Shad’s effects on the 

estuary ecosystem and salmonids are poorly understood. However, 

shad are an introduced species and their biomass alone represents a 

threat to trophic relationships in the Columbia River.

Associated limiting factors Exotic fish.

Threat index1 3 This threat contributes to many limiting factors, although the 

management action relates only to shad. 

Potential benefits with 

unconstrained 

implementation of 

action 2

2 The impacts of shad in the estuary are unclear. However, it is likely 

that reducing shad numbers would have some benefits for 

salmonids.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 5 Shad are thought to have permanently altered the estuary 

ecosystem, and their complete removal from the estuary is neither 

practical nor feasible. Effective management tools to limit shad 

productivity in the Columbia River basin currently are not available. 

Research is needed in the near term to determine the significance of 

this threat and identify potential management actions to manage the 

abundance of shad. 

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-26

Management Action CRE-19:

Prevent new introductions of aquatic invertebrates and reduce the effects of existing infestations.

Primary threat

this action would address

Ship ballast practices. Ship ballast water is responsible for the 

introduction of non-native aquatic invertebrates in the estuary. The 

effects of these introductions are poorly understood, but it is likely 

that exotic invertebrates disrupt food webs and out-compete juvenile 

salmonids’ native food sources. 

Associated limiting factors Introduced invertebrates.

Threat index1 3 This threat is a primary contributor to one of the lowest priority 

limiting factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

2 Reducing the impacts of non-native aquatic invertebrates would help 

maintain traditional salmonid food sources and the trophic 

relationships that salmon have adapted to.

Affected salmonids Ocean-type salmonids; stream-type salmonids displaying less 

dominant life history strategies (e.g., early and late fingerlings and 

subyearlings).

Implementation 

constraints3 4 Improvements in ship ballast practices have already been 

implemented by the industry as a result of new regulations, and 

stricter regulations are currently being debated at the Federal level. 

However, there are inherent challenges in managing ballast water 

that contains organisms from other ecosystems. Also, once nonnative aquatic invertebrates have been introduced, they represent a 

permanent alteration of the ecosystem and opportunities to reduce 

their effects may be few. Current understanding of how the estuary 

ecosystem is affected by introductions of exotic invertebrates is very 

limited. 

Potential benefits with 

constrained 

implementation of 

action

1

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-27

Management Action CRE-20:

Implement pesticide and fertilizer best management practices to reduce estuarine and upstream sources of 

nutrients and toxic contaminants entering the estuary.1

Primary threat

this action would address

Agricultural practices. Fertilizers include different forms of nutrients 

that are important for plant growth. When fertilizers make their way to 

the estuary through overland runoff, they contribute nutrients to the 

estuary that increase phytoplankton production, alter the food web, 

and in some instances depress dissolved oxygen levels. Watersoluble contaminants such as simazine, atrazine, chlorpyrifos, 

metolachlor, diazinon, and carbaryl enter the estuary as a result of 

tributary and upstream agricultural practices. DDT and PCBs have 

been detected at elevated levels in the estuary. These and other 

agricultural contaminants can cause salmonid mortality through 

bioaccumulation or non-bioaccumulative toxicity.

Associated limiting factors Non-bioaccumulative toxicity, bioaccumulation toxicity, and increased 

microdetrital inputs. 

Threat index 2 12 This threat is a primary contributor to a high-priority limiting factor 

(non-bioaccumulative toxicity) and a medium-priority limiting factor.

Potential benefits with 

unconstrained 

implementation of 

action 3

3 Reducing the level of pesticides and herbicides in the estuary would 

improve survival by reducing ocean-type salmonids’ acute and 

chronic exposure to toxic contaminants and stream-type salmonids’ 

acute exposure. 

Affected salmonids Ocean- and stream-type salmonids.

Implementation 

constraints4 4 Impacts from pesticides and fertilizers have lessened dramatically 

since the 1950s as a result of new application technologies, new 

products, and better understanding and regulation of these toxins. 

More extensive compliance with existing regulations and usage 

guidelines, along with development of additional best management 

practices, could further reduce the impacts of pesticides and 

fertilizers. The integration of new practices can be expensive and 

time-consuming. 

Potential benefits with 

constrained 

implementation of 

action

1

1 The term best management practices is used here to indicate general methods or techniques found to be most 

effective in achieving an objective. NMFS envisions that in implementation, specific best management practices 

would be developed or recommended.

2 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

3 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

4

Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-28

Management Action CRE-21:

Identify and reduce terrestrially and marine-based industrial, commercial, and public sources of pollutants.

Primary threat

this action would address

Urban and industrial practices. The estuary has been affected by 

historical and current releases of toxic contaminants, including 

industrial and commercial pollutants such as PCBs and PAHs. These 

substances have been found near Portland, Vancouver, Longview, 

and Astoria. Studies have demonstrated significant juvenile mortality 

in the estuary as a result of toxic contaminants. In addition, urban 

and industrial effluent and stormwater runoff are principal sources of 

nutrients that can support increased phytoplankton levels.

Associated limiting factors Non-bioaccumulative toxicity, bioaccumulation toxicity, and increased 

microdetrital inputs. 

Threat index1 12 This threat is a primary contributor to high- and medium-priority 

limiting factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

4 Reducing sources of pollutants would lower water temperature, 

nutrient loading, and the amount of toxic contaminants in the estuary. 

This would improve both habitat capacity in the estuary and the 

fitness level of salmonids. 

Affected salmonids Ocean- and stream-type salmonids (particularly ocean types 

because of their longer residency in the estuary).

Implementation 

constraints3 4 While some discharges of industrial and commercial pollutants are 

permitted, others are not. Efforts to reduce industrial and commercial 

pollutants are already under way, and there is potential to reduce 

point-source emissions. Efforts to reduce sources of pollutants are 

expensive and time-consuming and often have a negative economic 

effect on operations. 

Potential benefits with 

constrained 

implementation of 

action

3

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-29

Management Action CRE-22:

Restore or mitigate contaminated sites.

Primary threat

this action would address

Urban and industrial practices. The estuary has been affected by 

historical and current releases of toxic contaminants, including 

industrial and commercial pollutants such as PCBs and PAHs. These 

substances have been found near Portland, Vancouver, Longview, 

and Astoria. Studies have demonstrated significant juvenile mortality 

in the estuary as a result of toxic contaminants. The action is 

intended to address the need to monitor the entire estuary for 

contaminants; however, actual restoration activities are feasible only 

in specific reaches. 

Associated limiting factors Non-bioaccumulative toxicity and bioaccumulation toxicity. 

Threat index1 12 This threat is a primary contributor to high- and medium-priority 

limiting factors.

Potential benefits with 

unconstrained 

implementation of 

action 2

5 Reducing toxic contaminants in the estuary would improve both 

habitat capacity and the fitness level of salmonids.

Affected salmonids Ocean- and stream-type salmonids (particularly ocean types 

because of their longer residency in the estuary).

Implementation 

constraints3 3 Monitoring activities are already occurring; however, actual 

restoration of contaminated sites is expensive and technically 

challenging in many cases. In cases where restoration is not 

feasible, the effects of contaminated sites should be mitigated.

Potential benefits with 

constrained 

implementation of 

action

3

1 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

2 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

3 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-30

Management Action CRE-23:

Implement stormwater best management practices in cities and towns.1

Primary threat

this action would address

Urban and industrial practices. Municipal stormwater runoff can 

convey nutrients and toxic contaminants to the estuary, reduce 

groundwater recharge, and increase the “flashiness” of stream flows. 

Although cities and towns in the Columbia River basin generally have 

programs to reduce the impacts of stormwater runoff, stormwater 

best management practices have not been universally accepted or 

implemented throughout the basin. 

Associated limiting factors Non-bioaccumulative toxicity, bioaccumulation toxicity, and increased 

microdetrital inputs. 

Threat index2 9 This threat is a secondary contributor to a medium-priority limiting 

factor as it relates to this management action.

Potential benefits with 

unconstrained 

implementation of 

action 3

2 Identifying and implementing stormwater best management practices 

throughout the Columbia River basin would improve conditions and 

provide a net benefit to salmonids in the estuary through a more 

normal flow regime, reduced exposure to contaminants, and lower 

water temperatures.

Affected salmonids Ocean- and stream-type salmonids (particularly ocean types 

because of their longer residency in the estuary).

Implementation 

constraints4 2 Some cities lack the resources or will to implement or enforce 

stormwater best management practices. The benefits of improved 

stormwater practices generally are associated only with new 

development and do not offset the full impact of the impervious 

surfaces in those developments, or the existing impervious surfaces 

in areas that have already been developed.

Potential benefits with 

constrained 

implementation of 

action

1

1 The term best management practices is used here to indicate general methods or techniques found to be most 

effective in achieving an objective. NMFS envisions that in implementation, specific best management practices 

would be developed or recommended.

2 From Table 4-1. Indicates the significance of the associated limiting factor and the threat's contribution to that 

limiting factor. High numbers indicate threats that have a major contribution to high-priority limiting factors; lower 

numbers indicate threats that have a minor contribution to low-priority limiting factors. Numbers indicate the highest 

score per threat category and do not account for multiple limiting factor contributions.

3 Estimate of the expected benefits to salmonids (ocean- and stream-types combined) if the action were fully 

implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

4 Indicates the feasibility of implementing the action.

1 = Current constraints to implementation are minimal.

5 = Current constraints to implementation are significant.
MANAGEMENT ACTIONS

5-31

Table 5-2 estimates the potential of each management action to benefit salmonids under two 

different implementation scenarios. Assuming that implementation of most actions is 

significantly constrained, which management actions would be likely to result in the 

greatest survival improvements? 

In partial answer to this question, Table 5-3 summarizes the potential benefits of each action 

under both unconstrained and constrained implementation scenarios. It is tempting to sort 

the actions in Table 5-3 by potential benefit with constrained implementation and view the 

sorted list as a prioritized list of management actions, with the actions at the top being those 

predicted to have the greatest benefits. Although Table 5-3 does provide insight into the 

relative benefits of the various management actions, it is perhaps most useful as a means of 

contrasting the benefits that might be achieved with unconstrained implementation of an 

action with the benefits that might be achieved under a more likely scenario of constrained 

implementation. 

To provide greater insight into the relative benefits of each management action, PC Trask & 

Associates, Inc., developed a second analysis based on survival improvement targets. This 

analysis, which is presented in the next section of the document, is more refined and specific 

than the analysis in Table 5-3. For instance, it focuses more on how the potential benefits of 

the 23 management actions would compare to each other and on the survival benefits that 

might be gained from each action. It also evaluates the benefits of each action to both oceanand stream-type salmonids.

TABLE 5-3

Summary of Constraints to Implementation of Management Actions

Number Action Description

Benefit with 

Unconstrained 

Implementation 

of Action1

Benefit with 

Constrained 

Implementation of 

Action2

CRE-01 Protect intact riparian areas in the estuary and restore 

riparian areas that are degraded. 4 2

CRE-02

Operate the hydrosystem to reduce the effects of 

reservoir surface heating, or conduct mitigation 

measures.

3 2

CRE-03

Protect and/or enhance estuary instream flows 

influenced by Columbia River tributary/mainstem water 

withdrawals and other water management actions in 

tributaries.

2 1

CRE-04

Adjust the timing, magnitude, and frequency of 

hydrosystem flows (especially spring freshets) entering 

the estuary and plume to better reflect the natural 

hydrologic cycle, improve access to habitats, and 

provide better transport of coarse sediments and 

nutrients in the estuary and plume.

5 3

CRE-05

Study and mitigate the effects of entrapment of fine 

sediment in reservoirs, to improve nourishment of the 

estuary and plume.

2 1

CRE-06 Reduce the export of sand and gravels via dredge 

operations by using dredged materials beneficially. 2 1
MANAGEMENT ACTIONS

5-32

Number Action Description

Benefit with 

Unconstrained 

Implementation 

of Action1

Benefit with 

Constrained 

Implementation of 

Action2

CRE-07

Reduce entrainment and habitat effects resulting from 

main- and side-channel dredge activities and ship 

ballast intake in the estuary.

2 1

CRE-08

Remove or modify pilings and pile dikes when removal 

or modification would benefit juvenile salmonids and

improve ecosystem health.

4 2

CRE-09

Protect remaining high-quality off-channel habitat from 

degradation and restore degraded areas with high 

intrinsic potential for high-quality habitat.

5 3

CRE-10 Breach, lower, or relocate dikes and levees to establish 

or improve access to off-channel habitats. 5 4

CRE-11 Reduce the square footage of over-water structures in 

the estuary. 3 1

CRE-12 Reduce the effects of vessel wake stranding in the 

estuary. 2 1

CRE-13

Manage pikeminnow and other piscivorous fish, 

including introduced species, to reduce predation on 

salmonids.

4 2

CRE-14 Identify and implement actions to reduce salmonid 

predation by pinnipeds. 3 2

CRE-15

Implement education and monitoring projects and 

enforce existing laws to reduce the introduction and 

spread of invasive plants.

2 1

CRE-16 Implement projects to redistribute part of the Caspian 

tern colony currently nesting on East Sand Island. 5 3

CRE-17 Implement projects to reduce double-crested cormorant 

habitats and encourage dispersal to other locations. 4 2

CRE-18 Reduce the abundance of shad in the estuary. 2 1

CRE-19 Prevent new introductions of invertebrates and reduce 

the effects of existing infestations. 2 1

CRE-20

Implement pesticide and fertilizer best management 

practices to reduce estuarine and upstream sources of 

nutrients and toxic contaminants entering the estuary.

3 1

CRE-21 Identify and reduce terrestrially and marine-based 

industrial, commercial, and public sources of pollutants. 4 3

CRE-22 Restore or mitigate contaminated sites. 5 3

CRE-23 Implement stormwater best management practices in 

cities and towns. 2 1

1

Estimate of potential benefit if action is fully implemented, with no constraints.

1 = very low benefits.

5 = very high benefits.

2

Estimate of potential benefit assuming that implementation is constrained.

1 = very low benefits.

5 = very high benefits.
MANAGEMENT ACTIONS

5-33

Evaluation of Management Actions: Survival Improvement 

Targets

The Columbia River estuary and plume are only two of many ecosystems that salmonids 

travel in their complex and lengthy journey from headwaters to ocean and back again. 

Mortality occurs at every stage of this journey. Each year, scientists from the NMFS 

Northwest Fisheries Science Center estimate the number of juvenile salmonids that enter the 

estuary from upstream of Bonneville Dam and from estuary tributaries. For 2006, scientists 

from NMFS estimated that about 168 million juvenile salmonids (both wild and hatchery) 

would enter the estuary (Ferguson 2006b). Some years later, the surviving fish return to the 

estuary in varying numbers, with the average return in the last 10 years being 

approximately 1.7 million fish; roughly 65 to 75 percent of those fish are of hatchery origin.1

Estimating Juvenile Mortality in the Estuary and Plume 

This means that less than 1 percent of the juveniles that enter the estuary are returning as 

adults. 

How much juvenile mortality is occurring in the estuary and plume? The answer to this 

question is fundamental to developing an understanding of the role the estuary will play in 

the recovery of salmonid populations basinwide. The answer also is critical in evaluating 

the benefits and costs of potential management actions because it helps establish the level of 

effort needed to offset threats to salmonids in the estuary. Unfortunately, determining how 

much juvenile mortality is occurring in the estuary and plume is challenging for scientists. 

Counting juveniles in the Columbia River estuary and plume is problematic because 

available tracking technologies are limited, and it is difficult to monitor juveniles—which 

tend to move in and out of saltwater—in large, high-energy sites such as the mouth of the 

Columbia River.

However, some efforts have been made to separate mortality that occurs in the estuary and 

plume from mortality that occurs in the ocean. One such effort has been the underlying 

assumptions in the Ecosystem Diagnosis and Treatment (EDT) model, which is used 

extensively throughout the Columbia River basin. For juveniles entering the estuary from 

tributaries to the lower Columbia River, EDT assumes mortality rates in the estuary and 

plume of between 18 and 58 percent, depending on the salmonid species and the amount of 

time juveniles spend in the estuary (Lower Columbia Fish Recovery Board 2004). In a study 

of juvenile mortality in the estuary, Schreck et al. (2006) estimated spring/summer Chinook

mortality at between 11 and 17 percent, largely from avian predation. 

In addition, research is under way by NMFS, the U.S. Army Corps of Engineers, and Battelle 

Laboratories to estimate the survival rate of juvenile salmonids in the lower Columbia River. 

This research involves new technologies for miniaturizing acoustic tags to a size capable of 

tracking yearling and subyearling juveniles. Current technology developed for the project 

allows for the tracking of subyearlings of sizes down to approximately 90 mm. Results for 

the first year (2005) indicated an approximate range of survival of 65 to 75 percent for 

subyearlings and yearlings during their residency in the estuary (Ferguson 2006a). It is 

probable that actual survival rates are lower than these preliminary estimates suggest 

 1 This is an informal estimate; determining the ratio of hatchery-origin fish with more certainty would require stock-by-stock run 

calculations averaged over many years.
MANAGEMENT ACTIONS

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because the research did not address mortality among juveniles smaller than 90 mm or 

mortality occurring in the plume and nearshore. The studies above have not been 

conclusive, and separating estuarine and ocean mortality for juvenile salmonids in the 

Columbia River remains significant challenge. 

Some specific estimates of salmonid mortality are known in the estuary; they include 

estimates for double-crested cormorants and Caspian terns. For other threats to salmonids, 

such as toxic contamination, ship wake stranding, and pinniped predation, information on 

mortality in the estuary is incomplete or relatively new in the literature. Still other threats, 

especially those related to the food web, are poorly understood and have no mortality 

estimates associated with them, although in some cases the change in conditions from the 

historical template to the present has been well documented. 

Establishing Survival Improvement Targets

An important goal of this estuary recovery plan module is to estimate the potential 

benefits—in terms of increased survival of salmonids in the estuary—that could result from 

the implementation of different management actions. To accomplish this goal, PC Trask & 

Associates, Inc., used available information about limiting factors, threats, and constraints to 

the implementation of management actions to assign benefits that could possibly result 

from different actions.

If scientific understanding of the relationships between ecological conditions and biological 

responses in estuarine systems were robust, it would be attractive to assign specific 

mortality rates to each of the factors limiting salmonids’ biological performance in the 

Columbia River estuary. Then one could follow a deterministic logic path that associates 

mortality rates with specific threats, relates the mortality rates to management actions, and 

ultimately arrives at an estimate of the survival improvement that would be likely to result 

from each action. This is not possible at this time, and it will likely not be possible until there 

have been significant advances in scientific understanding of the complex estuarine 

environment. 

To compensate for the lack of detailed information on mortality in the estuary, PC Trask & 

Associates, Inc., established targets for improved survival of wild ESA-listed salmonids 

rearing and migrating in the estuary and plume, assuming that the implementation of 

management actions is constrained to the degree indicated in Table 5-2. PC Trask & 

Associates, Inc., then allocated these survival targets to individual management actions. 

These targets are intended to serve as a planning tool useful in characterizing the potential 

results of actions and describing the level of effort needed to recover salmonids.

The primary purpose of the survival improvement targets is to help compare the potential 

benefits of different management actions, particularly actions that partially address major 

limiting factors versus actions that fully address minor limiting factors. In addition, the 

survival improvement targets provide insight into the specific survival benefits of each 

action and the differential benefits of each action to stream- and ocean-type salmonids. 

Numerically, the survival improvement targets in this chapter were based on an estimate of 

the number of naturally produced ESA-listed ocean- and stream-type juvenile salmonids 

entering the estuary. The total number of naturally produced ESA-listed juvenile salmonids 
MANAGEMENT ACTIONS

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estimated to enter the estuary in 2006 was approximately 39 million (Ferguson 2006b).2

To establish survival improvement targets, PC Trask & Associates, Inc., developed some 

assumptions about the overall mortality of juvenile salmonids during estuary and plume 

residency. Ocean-type juveniles were assumed to have an overall mortality rate of 

50 percent during their estuary residency; this includes the 35 percent mortality suggested 

by the unpublished micro-acoustic tagging research (Ferguson 2006a) plus an additional 15 

percent to account for juveniles too small to be tracked. Stream-type juveniles were assumed 

to have an overall mortality rate of 40 percent during estuary and plume residency. This rate 

was based on the 25 percent mortality found in the micro-acoustic tagging research 

(Ferguson 2006a) plus an additional 15 percent to account for mortality occurring in the 

plume, which was not part of study. These assumptions about estuary mortality are based 

on best professional judgment by PC Trask & Associates, Inc., after a review of pertinent 

literature and discussions with subject matter experts, including scientists at the NMFS 

Northwest Fisheries Science Center.

Of 

these, approximately 25 million were estimated to be ocean type and 14 million were 

estimated to be stream type. 

Table 5-4 shows the number of wild, ESA-listed ocean- and stream-type juveniles thought to 

be entering the lower Columbia estuary and plume, their estimated mortality and survival 

rates based on the assumptions above, and the number of juveniles estimated to survive 

their journey through the estuary and plume—again, based on the assumptions above.

TABLE 5-4

Estimated Mortality Rates, Survival Rates, and Survival Improvement Targets for Wild, ESA-Listed Juveniles

Type

Juveniles 

Entering 

Estuary*

Assumed 

Mortality 

Rate

Assumed 

Survival 

Rate

Estimated Number of 

Juveniles Exiting 

Estuary and Plume*

Survival 

Improvement Target 

(20 percent)**

Ocean Type 25 million 50% 50% 12.5 million 2.5 million***

Stream Type 14 million 40% 60% 8.4 million 1.68 million***

* = Wild, ESA-listed juveniles.

** = Twenty percent of the estimated number of juveniles exiting the estuary and plume; this target represents 

additional fish surviving their estuary and plume residency.

*** These numbers are used to characterize the potential, relative benefits of implementing various management 

actions and do not represent actual numbers of additional fish expected to survive.

Table 5-4 also presents survival improvement targets for ocean- and stream-type salmonids 

in the estuary and plume. For planning purposes only, this estuary recovery plan module 

selects 20 percent as a target for improvement in the survival rate of wild, ESA-listed oceanand stream-type juveniles in the estuary and plume. Twenty percent represents a 

hypothetical level of improvement that might be realized through the implementation of the 

management actions, assuming that considerable effort is expended to help offset 

constraints to implementation, such that threats and limiting factors are reduced. For ocean 

types, increasing survival by 20 percent would result in a total of 15 million juveniles exiting 

 2 Current scientific information on the effects of limiting factors and actions does not differentiate between hatchery- and 

natural-origin salmon and steelhead, or between salmon and steelhead that are listed under the ESA and those that are not. 

Because ESA recovery is determined by the status of natural-origin fish, the intent of the module is to improve the estuarine 

survival of naturally produced, ESA-listed salmon and steelhead. Naturally produced fish are the focus of the analysis of 

survival improvement targets because they are the focus of the module. 
MANAGEMENT ACTIONS

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the estuary and plume—2.5 million more juveniles than the current estimate of 12.5 million. 

For stream types, a 20 percent improvement would equal 10.08 million—1.68 million 

additional juveniles beyond the current 8.4 million that are estimated to exit the estuary and 

plume. Thus the survival improvement targets for ocean- and stream-type salmonids are 

2.5 million and 1.68 million, respectively, as shown in Table 5-4. Targets for both types were 

set at 20 percent to avoid the appearance of a false level of precision in establishing them. 

Ocean-type juveniles were assumed to incur more mortality in the estuary and nearshore 

compared to stream types. Stream types were assumed to incur less mortality in the estuary 

than ocean types but significantly more mortality in the plume. 

PC Trask & Associates, Inc., selected the 20 percent survival improvement number for 

ocean- and stream-type juvenile salmonids based on a qualitative analysis of the level of 

improvement that reasonably and plausibly might be expected if the 23 management actions 

were implemented. In establishing the 20 percent target, PC Trask & Associates, Inc., 

reviewed existing management plans, other literature sources, and the constraints analysis 

in Table 5-2. However, setting 20 percent as the target for improvement, rather than 15 or 

30 percent, is inherently subjective and relies in part on the following assumptions:

• That estuary mortality for juveniles (currently between 40 and 50 percent, depending 

on population) can be reduced by initiating restoration projects and reducing 

uncertainties through research and monitoring

• That mortality rates associated with certain threats, such as Caspian terns and 

cormorants, are well understood and will be lessened through actions specified in 

management plans that are reasonably likely to be implemented

• That all of the actions identified in this chapter are implemented to a reasonable 

degree and historical and current constraints to action implementation are 

thoroughly challenged

Actual improvements in survival will depend on which management actions are 

implemented, how fully they are implemented, and their efficacy—factors that at this point 

are open to interpretation and can be qualitatively estimated only. Although the 20 percent 

targets for ocean- and stream-type salmonids are intended to be reasonable and plausible 

given the information available to date, open technical, political, and social discussion could 

refine the targets until science can substantiate them. 

The survival improvement targets in Table 5-4 were developed using ocean- and streamtype life history strategies to characterize the 13 ESUs in the Columbia River basin. As a 

result, the survival improvement targets do not account for important variations found at 

the ESU, population, and subpopulation scales. For example, not all ocean-type ESUs in the 

Columbia River basin exhibit the same run timing, size at estuary entry, or use of particular 

habitats (Fresh et. al 2005). In fact, this variability in estuarine use by the ESUs is 

fundamental to the member/vagrant theory proposed by the NMFS Northwest Fisheries 

Science Center and a central premise of the estuary recovery plan module (see Chapter 2 for 

more information on the member/vagrant theory). Although genetic and spatial diversity 

are not explicitly accounted for in survival improvement targets, the suite of management 

actions identified in the estuary recovery plan module is intended to collectively address all 

life history strategies historically expressed in the estuary and plume. This further 
MANAGEMENT ACTIONS

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emphasizes that the survival improvement targets are best viewed as a planning tool only. 

In reality, there will be significant variability among ESUs, populations, and subpopulations 

in how much additional survival might result from improvements in estuary and plume 

habitat. 

Assigning Survival Improvement Targets to Recovery Actions

The usefulness of the 20 percent target lies not in the 20 percent number itself, but in the 

distribution of the targets (2.5 million ocean-type juveniles and 1.68 million stream-type 

juveniles) across the various management actions, as a way of characterizing the relative 

benefits of the various management actions.3 Table 5-5 shows this allocation of survival 

improvement targets to the 22 management actions for juvenile salmonids.4

Although the survival improvement targets in Table 5-5 are estimates only, they 

complement the analysis summarized in Table 5-3.

In cases where 

there is good scientific literature that supports the allocation of survival targets, as with 

terns and cormorants, PC Trask & Associates, Inc., used that information as a basis for the 

analysis in Table 5-5. In other cases, such as reservoir-related temperature changes, 

PC Trask & Associates, Inc., estimated survival improvements based on literature discussion 

of related limiting factors and threats. The reader should view the resulting survival 

improvement targets as the product of a planning exercise, not a representation of 

deterministically based estimates. (Appendix B presents more information on how PC Trask 

& Associates, Inc., allocated survival improvement targets to the different actions.)

5

A special case in assigning survival improvement targets to actions are those actions (CRE–

01 and CRE–09) that use land protection as a means of achieving the target. In theory, 

protection projects contribute only to maintenance of baseline conditions and not to 

recovery. However, the estuary recovery plan module does assign a portion of the survival 

improvement targets to protection projects. The reasoning here is that without protection of 

baseline environmental conditions, significantly more effort would be required in 

restoration projects to offset the continued loss of functioning habitat that would result from 

increases in the human population and corresponding conversion of habitats to 

economically beneficial land uses. Thus, assigning survival improvement targets to 

In addition, they provide a useful way 

to show the potential magnitude of juvenile survival at the action scale relative to other 

actions. The survival improvement targets illustrate how a small increment of 

implementation of a far-reaching action could offer significantly more potential for recovery 

than full implementation of an action that is more limited in scope. Comparison of Tables 

5-3 and 5-5 and the cost estimates that are developed in the next section form the basis for 

prioritization of actions in Chapter 7, “Perspectives on Implementation.”

 3 Although for the purposes of this analysis 20 percent is considered a hypothetical number, it is a plausible number. The 

20 percent figure is based on overall estimates of juvenile mortality in the estuary, known mortality that can be attributed to 

specific threats, and professional judgment regarding the efficacy of the different management actions and the likelihood that 

constraints to their implementation can be overcome. 

4 Although the survival improvement targets are expressed in terms of numbers of natural-origin ESA-listed fish, this is simply 

to illustrate the potential benefits of actions, not to analyze differential benefits to natural-origin listed fish versus unlisted or 

hatchery-origin fish; what is important is the allocation of relative benefits among the management actions.

5 Table 5-2 contrasts the difference between constrained and unconstrained implementation of an individual action, while 

Table 5-5 compares potential benefits across the entire set of actions. Given the two tables’ different purposes, there is not a 

mechanistic relationship between them. However, there is a rough correlation between the potential benefits of constrained 

implementation in Table 5-2 and where an action falls in the relative rankings presented in Table 5-5.
MANAGEMENT ACTIONS

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protection projects reflects the value of avoiding the additional effort that would be required 

to restore functioning habitats lost because they were not protected. 

Uses of the Survival Improvement Targets

The purpose of the survival improvement targets in Table 5-5 is to address a particular 

planning challenge in the estuary module: how to compare the potential benefits of 

management actions that are disparate in their scope and feasibility, especially when 

scientific information about the causes of salmonid mortality in the estuary is incomplete. In 

the absence of comprehensive scientific data, the targets provide a useful framework for 

evaluating the relative merits of different actions. However, survival improvement targets 

do not represent actual numbers of fish.

For example, it would be inappropriate to use the survival improvement targets to estimate 

total juvenile mortality in the estuary, attribute a level of mortality to a specific limiting 

factor or threat, or calculate “per-fish” costs of actions. Because the survival improvement 

targets are not scientifically derived, they have limited use for life-cycle modeling. On the 

other hand, the targets could serve as a starting point for life-cycle modeling in the absence 

of rigorous data.

It also would be unwise to predict specific outcomes of an action or suite of actions based 

solely on the survival improvement targets. Although it would be appropriate to use the 

targets to guide expenditures and the selection of individual projects that are consistent 

with the module’s management actions, monitoring should accompany any implementation 

of those projects—to evaluate their effectiveness, test the assumptions underlying the 

targets, and provide a basis for refining them.

Because the survival improvement targets are a tool for comparing the relative benefits of 

actions, they are particularly useful in weighing the trade-offs involved in implementing 

some actions but not others, or implementing actions only partially. For example, in theory, 

if a certain action were implemented partially or not at all, the potential 20 percent gain in 

the number of wild, ESA-listed juveniles leaving the estuary and plume could not be 

achieved unless other actions were implemented to a greater extent than envisioned in the 

module, to compensate. Survival improvement targets provide a way of evaluating various 

scenarios for implementation. This is critical because the implementation of every action 

already is constrained (often significantly) and, in most cases, the opportunities to remove 

constraints and implement actions more fully are limited. 
MANAGEMENT ACTIONS

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TABLE 5-5

Survival Improvement Targets Allocated to Management Actions1

Number Action Description

Survival Improvement Target1 with Constrained 

Implementation 

(numbers of wild, ESA-listed fish)

Ocean 

Type1

% of Total 

Improvement 

Target

Stream 

Type1

% of Total 

Improvement 

Target

CRE-01

Protect intact riparian areas in the estuary 

and restore riparian areas that are 

degraded.

150,000 6% 100,000 6%

CRE-02

Operate the hydrosystem to reduce the 

effects of reservoir surface heating, or 

conduct mitigation measures.

90,000 4% 20,000 1%

CRE-03

Protect and/or enhance estuary instream 

flows influenced by Columbia River 

tributary/mainstem water withdrawals and 

other water management actions in 

tributaries.

25,000 1% 20,000 1%

CRE-04

Adjust the timing, magnitude, and frequency 

of hydrosystem flows (especially spring 

freshets) entering the estuary and plume to 

better reflect the natural hydrologic cycle, 

improve access to habitats, and provide 

better transport of coarse sediments and 

nutrients in the estuary and plume.

225,000 9% 125,000 7%

CRE-05

Study and mitigate the effects of entrapment 

of fine sediment in reservoirs, to improve 

nourishment of the estuary and plume.

5,000 <1% 5,000 <1%

CRE-06

Reduce the export of sand and gravels via 

dredge operations by using dredged 

materials beneficially.

50,000 2% 15,000 <1%

CRE-07

Reduce entrainment and habitat effects 

resulting from main- and side-channel 

dredge activities in the estuary.

8,000 <1% 10,000 <1%

CRE-08

Remove or modify pilings and pile dikes 

when removal or modification would benefit 

juvenile salmonids and improve ecosystem 

health.

150,000 6% 100,000 6%

CRE-09

Protect remaining high-quality off-channel 

habitat from degradation and restore 

degraded areas with high intrinsic potential 

for high-quality habitat.

400,000 16% 150,000 9%

CRE-10

Breach, lower, or relocate dikes and levees 

to establish or improve access to offchannel habitats.

450,000 18% 100,000 6%

CRE-11 Reduce the square footage of over-water 

structures in the estuary. 25,000 1% 3,000 <1%

CRE-12 Reduce the effects of vessel wake stranding 

in the estuary. 55,000 2% 2,000 <1%
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Number Action Description

Survival Improvement Target1 with Constrained 

Implementation 

(numbers of wild, ESA-listed fish)

Ocean 

Type1

% of Total 

Improvement 

Target

Stream 

Type1

% of Total 

Improvement 

Target

CRE-13

Manage pikeminnow and other piscivorous 

fish, including introduced species, to reduce 

predation on salmonids.

140,000 6% 122,000 7%

CRE-14 Identify and implement actions to reduce 

salmonid predation by pinnipeds. N/A2 N/A 1,0342 N/A

CRE-15

Implement education and monitoring 

projects and enforce existing laws to reduce 

the introduction and spread of invasive 

plants.

20,000 <1% 15,000 <1%

CRE-16

Implement projects to redistribute part of the 

Caspian tern colony currently nesting on 

East Sand Island.

2,000 <1% 350,000 21%

CRE-17

Implement projects to reduce doublecrested cormorant habitats and encourage 

dispersal to other locations. 

2,000 <1% 250,000 15%

CRE-18 Reduce the abundance of shad in the 

estuary. 5,000 <1% 5,000 <1%

CRE-19

Prevent new introductions of aquatic 

invertebrates and reduce the effects of 

existing infestations.

8,000 <1% 2,000 <1%

CRE-20

Implement pesticide and fertilizer best 

management practices to reduce estuarine 

and upstream sources of nutrients and toxic 

contaminants entering the estuary.

50,000 2% 42,000 3%

CRE-21

Identify and reduce terrestrially and marinebased industrial, commercial, and public 

sources of pollutants.

275,000 11% 72,000 4%

CRE-22 Restore or mitigate contaminated sites. 300,000 12% 142,000 8%

CRE-23 Implement stormwater best management 

practices in cities and towns. 65,000 3% 30,000 2%

Total 2.5 

million

1.68 

million

1 Appendix B presents more information on how survival improvement targets were developed.

2 The survival improvement targets are assigned for juvenile salmonids only. Although CRE-14 relates specifically to adult 

salmonids, the survival numbers for CRE-14 are not included in the 20 percent survival improvement targets for juvenile 

salmonids. The stream-type survival number is based upon an estimated 17 percent reduction in adult fish mortality applied to 

2010 run-size information reported in U.S. Army Corps of Engineers (2010). Some mortality may be occurring as a result of 

pinniped predation on ocean-type juvenile salmon and steelhead. The extent to which this is occurring has not been established.
MANAGEMENT ACTIONS

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Evaluation of Management Actions: Costs and Schedule

Implementing recovery actions in the estuary will require a long-term commitment by many 

entities. In Tables 5-2 and 5-5, two approaches were used to portray the potential survival 

improvements associated with implementing actions. In Table 5-6, each action is broken 

down into one or more projects that can be considered elements of that action. 

For some management actions, the first project involves conducting a study or assembling 

existing technical information. There are several reasons for this. In some cases, existing 

information about how to reduce the associated threat to salmonids is limited, and 

additional study is needed to identify and pilot-test possible actions to determine which 

ones would be most effective. This is particularly important when funds for implementing 

management actions are limited. Additionally, conducting a study or assembling technical 

information involves stakeholders who may have local knowledge about the threat or will 

be responsible for implementing projects. Lastly, studies and information gathering provide 

an opportunity to understand the constraints of management actions, to reexamine 

assumptions about what is and is not possible, and to explore the lengths to which, as a 

society, we are willing to go to implement actions that will contribute to the recovery of 

salmon and steelhead in the Columbia River basin. The intent of including studies and 

information gathering in the management actions, when appropriate, is not to postpone 

taking on-the-ground action but to ensure that any actions that are taken are truly effective, 

that stakeholders are involved in the process, and that important dialogue occurs about the 

value of reducing constraints and implementing management actions as fully as possible, 

even in situations where implementation is highly constrained. 

The recovery plan module does not present a detailed list of projects waiting to be 

completed in the estuary. This is because in many cases, additional work is needed to 

develop complex, large-scale projects that will provide maximum benefit, or to work with 

landowners and other stakeholders to gain their support, or to understand the most 

effective avenue for implementation. 

Table 5-6 provides cost estimates for each of the 23 actions in the estuary recovery plan 

module and a timeframe for their implementation. Each project in Table 5-6 has a 

corresponding unit and cost, and the project costs are summed to produce a total cost for 

each action. The costs identified in this section do not represent a detailed economic 

analysis; in fact, they are not economic costs in that they have not been discounted across 

time. Instead, the cost estimates are in constant dollars over a 25-year period. A 25-year 

implementation period was selected for several reasons. Many of the actions identified in 

the estuary module include project types that have never been implemented in the estuary, 

and it will take time to establish or modify programs to implement these projects; some will 

require new research and monitoring to guide their effective implementation. In addition, a 

25-year implementation period will allow time to identify funding sources and build the 

landowner buy-in and project sponsor capacity needed to implement the 23 actions. 

In most cases the costs listed in Table 5-6 are direct, incremental costs, meaning that they are 

(1) out-of-pocket costs that a public or private interest would pay to initiate and complete a 

management action, and (2) costs in addition to the baseline costs for existing programs and 

activities, which may or may not be focused on salmon recovery. This approach is consistent
MANAGEMENT ACTIONS

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with NMFS Northwest Regional Office guidance on cost estimates for ESA recovery plans. 

In some cases, distinctions between baseline and incremental costs are clear. For instance, 

reducing the abundance of shad (CRE-18) is an action that includes only incremental costs 

because it is a new action that has yet to be implemented in the estuary. Other actions, such 

as breaching, lowering, or relocating dikes (CRE-10), have been implemented in the estuary 

at a relatively modest scale. For such actions, the estuary recovery plan module cost 

estimate is still entirely incremental in that it identifies an additional level of effort needed 

to achieve the survival improvement targets identified later in this chapter. 

Several of the 23 actions do contain some baseline costs, because in some cases these 

baseline costs represent a small fraction of the overall implementation cost of the action and 

it was deemed infeasible to separate out the incremental costs. In these cases, this fact is 

noted in Table 5-6 under the key assumptions for the individual management action. For 

example, Caspian tern management (CRE-16) is supported by an existing management plan, 

and some efforts are already under way to implement the action. The other two examples 

are managing pikeminnow and other piscivorous fish (CRE-13) and implementing 

stormwater best management practices (CRE-23). In these examples, programs are in place, 

but major portions of the estuary recovery plan module action have not been implemented 

to date. In addition, for one action—adjusting the timing, magnitude, and frequency of 

hydrosystem flows (CRE-4)—the primary costs are the costs of foregone power generation. 

Generally, recovery action cost estimates do not include such opportunity costs. We have 

included an estimate of such costs in this case because otherwise this action would have 

skewed the cost-effectiveness assessment in Chapter 7 (see Table 7-5) in a way that would 

preclude constructive dialogue about adjusting flows.

The cost estimates in Table 5-6 were developed by PC Trask & Associates, Inc., and 

reviewed by the Lower Columbia Fish Recovery Board, the Lower Columbia River Estuary 

Partnership, and NMFS. In addition, an economist at the NMFS Northwest Fisheries Science 

Center reviewed Chapter 5 and provided comments (although not a detailed evaluation of 

the costs). Lower Columbia River Estuary Partnership staff contributed substantively to cost 

estimates for actions for which the Estuary Partnership has some history of implementation. 

For example, the Estuary Partnership has funded multiple dike breaches (CRE-10), riparian 

protection projects (CRE-1), and off-channel protection/restoration projects (CRE-9). In 

other cases, where possible, experts knowledgeable about implementing similar actions 

were consulted. For example, staff from the NMFS Northwest Regional Office were 

consulted to estimate costs for managing pinnipeds (CRE-14).

In still other cases, a coarse estimate was established based on the component projects and 

assumptions about the feasibility of their implementation. These were generally cases in 

which the extent of on-the-ground actions could not be determined until certain scientific or 

technical questions have been answered more definitively through studies or information 

gathering (see, e.g., CRE-2, CRE-7, CRE-12, CRE-18). In these cases, costs of any assessment 

work were estimated, and then a coarse-scale, placeholder cost estimate was developed 

based on assumptions about the magnitude and nature of subsequent projects needed to 

implement the management action. It is expected that such cost estimates will be refined as 

more specific projects are defined. 

Thus the cost estimates in Table 5-6 attempt to establish a realistic cost for recovery, but the 

precision with which costs can be estimated at this time is limited, and there is considerable 
MANAGEMENT ACTIONS

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uncertainty in all the cost estimates. In Chapter 6, some additional costs are identified for 

research, monitoring, and evaluation activities (see Table 6-7).

The estuary recovery plan module addresses habitat conditions for all Columbia River basin 

ESUs during a single stage of their life cycle, but many additional management actions—

including actions in the tributaries—will be needed to achieve recovery of any particular 

ESU. Because the management actions in the module are only a subset of all the actions 

needed for recovery of an ESU, the costs in Table 5-6 do not reflect the total costs to achieve 

recovery. Total costs for recovery are more appropriately represented in the recovery plans 

for each ESU, as these plans deal with multiple life stages for a specific ESU. 

Each action in Table 5-6 includes a proposed schedule for implementation. The schedule is 

designed to place projects in a logical order and spread costs over a long period of time 

when possible. Costs are estimated over a 25-year span, with some projects being 

implemented once over a relatively short period and others continuing over the entire 

25 years. 

Other elements contained in Table 5-6 include the association of actions to specific 

geographical reaches, key assumptions about actions, a list of potential implementers,6

notes that help explain how costs were developed, and a brief summary of some of the 

existing programs that address limiting factors identified in this recovery plan module. The 

summaries of existing programs are not exhaustive and are intended to emphasize that 

opportunities exist to build on existing programs to improve salmon and steelhead survival 

in the estuary. The relationship of actions to the eight geographic reaches and the plume 

helps to define the breadth of the action and may also indicate which jurisdictions may 

implement actions in the future. Key assumptions relate primarily to implementation and 

provide insight into the level of effort reflected in the action costs. Notes are specific 

information that helps clarify a particular unit or cost. 

 6 The list of potential implementers is intended only to indicate entities that may have a role in implementation and to serve as 

a guide to begin discussion of implementation roles. It does not imply any budgetary, regulatory, or other responsibility for

implementation. 
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TABLE 5-6

Estimated Cost and Schedule

Management Action CRE-1:

Protect intact riparian areas in the estuary and restore riparian areas that are degraded. 

Project Unit Cost Schedule

1. Educate landowners about the ecosystem benefits of intact 

riparian areas and the costs of degraded riparian areas.1 20 years @ 

$50,000/year $1 million 2008 - 2028

2. Encourage and provide incentives for local, state, and Federal 

regulatory entities to maintain, improve (where needed), and 

enforce consistent riparian area protections throughout the 

lower Columbia region.2

10 years @ 

$500,000/year $5 million 2008 - 2018

3. Actively purchase riparian areas from willing landowners in 

urban and rural settings when the riparian areas cannot be 

effectively protected through regulation or voluntary or 

incentive programs and (1) are intact, or (2) are degraded but 

have good restoration potential. 

Rural: 

3,500 acres at 

$5,000/acre3

Urban:

100 acres at 

$75,000/acre

$25 million 2007 - 2031

4. Restore and maintain ecological benefits in riparian areas; this 

includes managing vegetation on dikes and levees to enhance 

ecological function and adding shoreline/instream complexity 

for juvenile salmonid refugia. 

28 miles @ 

$250,000/mile $ 7 million 2006 - 2031

Total costs: $38 million

Geographical priority: Reaches A-H and the Lower Willamette reach.

Key assumptions: (1) New homes, businesses, and industry will increase with population growth in the basin. 

(2) Some intact riparian areas are not adequately protected. (3) Protecting intact riparian areas would be cheaper than 

restoring degraded areas. (4) Some degraded riparian areas could be restored and gain ecological function, with 

associated downstream benefits. (5) Comprehensive protection and restoration of riparian habitats would occur 

concurrently with population growth, which will continue at a high rate.

Existing efforts: Protection of riparian areas relies heavily on local governments; the content and implementation of 

their land use plans specifically for shoreline and floodplain protection will be key to this action. Multiple Federal and 

state resource agencies provide funding for land acquisition and restoration, and multiple entities such as land trusts 

and watershed councils actively acquire and restore lands in the lower river. The Division of State Lands in Oregon and 

the Department of Natural Resources in Washington own and/or regulate submerged and submersible lands. The 

Natural Resource Conversation Service and conservation districts provide technical assistance to private landowners. 

Where water quality issues (such as toxic or conventional contaminants) are involved, agencies such as Washington’s 

Department of Ecology and Oregon’s Department of Environmental Quality may provide additional support. 

Potential implementers:

• U.S. Army COE

• BPA

• WA Dept. of Fish & Wildlife

• OR Dept. of Fish & Wildlife

• Cities\Counties

• Port districts

• Conservation districts 

• Columbia Land Trust

• The Wetlands Conservancy 

• The Nature Conservancy

• Ducks Unlimited

• Natl. Fish & Wildlife Foundation

• Tribes

• OR Watershed Enhance. Bd. 

• Salmon Recovery Fund. Bd.

• Lower Col. River Est. Partnership

• National Marine Fisheries Service

• Col. River Estuary Study Taskforce

• Utility districts

• Watershed councils

Notes:

1 Projects CRE-1.1 and CRE-9.1 both call for outreach efforts. Outreach efforts for these two actions will be combined 

in a single outreach program whose costs will be shared.

2 Projects CRE-1.2 and CRE-9.2 both call for incentives for local, state, and Federal entities to maintain, improve, and 

enforce regulatory protections. Given their similarities, activities for CRE-1.2 and CRE-9.2 could be coordinated or 

combined into one effort.

3 Acreage amounts are 25-year targets that depend on willing sellers and funding.
MANAGEMENT ACTIONS

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Management Action CRE-2:

Operate the hydrosystem to reduce the effects of reservoir surface heating, or conduct mitigation measures. 

Project Unit Cost Schedule

1. Conduct a reservoir heating study to determine the 

extent of the issue and identify hydrosystem 

operational changes (including design) that would 

reduce effects and/or mitigate downstream 

temperature issues. 

1 study $2.5 million 2007 - 2013

2. Implement hydrosystem operational changes to 

reduce temperature effects; if no change is possible, 

mitigate effects through restoration of tributary riparian 

areas.

25 years @ 

$700,000/year1

$17.5 

million 2010 - 2032

Total costs: $20 million

Geographical priority: Reaches A-H and the plume. 

Key assumption: (1) Either there is potential to alter management practices in the hydrosystem to reduce flow 

temperatures or a commensurate level of mitigation in tributaries would reduce temperatures in the estuary. (2) If 

temperatures continue to increase above 19° C, the estuary could become completely lethal for salmonids and 

other native species. 

Existing efforts: The U.S. Environmental Protection Agency (EPA) is concerned about water temperature 

issues in the Columbia and Snake River system and their impacts on ecosystem health, particularly in light of 

global climate change. Oregon and Washington have listed the Columbia River as impaired for temperature 

under the Clean Water Act Section 303(d). In 2003, EPA issued a Preliminary Draft Total Maximum Daily Load 

(TMDL) for the mainstem Columbia River, but the TMDL has not been finalized. EPA plans to work with the 

states of Oregon and Washington to revisit the TMDL and decide how to address mainstem Columbia River 

temperature issues.

Potential implementers:

• Bonneville Power Administration

• U.S. Army Corps of Engineers

• Utility districts

• Oregon Department of Environmental Quality

• Washington State Department of Ecology

Notes:

1 Assumes that some level of improvement is possible but that the level of possible improvement is likely to be 

minor because of complexities of the hydrosystem; assumes that mitigation will be needed to offset temperature 

increases.
MANAGEMENT ACTIONS

5-46

Management Action CRE-3:

Protect and/or enhance estuary instream flows influenced by Columbia River tributary/mainstem water 

withdrawals and other water management actions in tributaries.

Project Unit Cost Schedule

1. Explore technical options and develop policy 

recommendations on instream flows. 

5 years @ 

$1 million/year $5 million 2007 - 2015

2. Implement instream flow regulations in accordance 

with the policy recommendations in Project No. 1. 

5 years @ 

$1 million/year $5 million 2015 - 2023

Total costs: $10 million

Geographical priority: Reaches A–H and the plume.

Key assumptions: (1) Demand for water for human use will grow as the human population in the basin 

increases. (2) Additional instream flows in the Columbia River mainstem and tributaries could be established 

through the efforts of affected parties basinwide. (3) Establishing an instream flow regime would protect flows 

entering the estuary in the future. (4) An instream flow regime would help develop additional water conservation 

efforts and guide land use development in concert with water availability. (5) Protecting and/or enhancing estuary 

instream flows would require coordination with the Columbia River hydrosystem to achieve lasting results. 

Existing efforts: Resource agencies can request instream flows to support fish and wildlife, water quality, and 

recreational needs in tributaries entering the estuary. In Oregon, the Department of Environmental Quality, 

Department of Fish and Wildlife, and Department of Parks & Recreation are authorized to request instream water 

rights to support their statutory obligations. The Oregon Water Resources Department and Commission review 

these requests and establish instream water rights. In Washington, the Department of Ecology established 

instream flows in all of the major Washington tributaries entering the estuary. Tributary flows also are often 

addressed in the relicensing processes for hydropower facilities regulated by the Federal Energy Regulatory 

Commission. Over the past decade, many tributary hydropower facilities (e.g., the Cowlitz River Project and the 

Lewis River Hydroelectric Projects) have been relicensed. Establishing an instream flow regime for the estuary 

would involve many Federal and state agencies and would require an organizational framework that currently 

does not exist.

Potential implementers:

• States (Washington, Oregon, Idaho, Montana)

• Cities and counties

• Irrigators

• Tributary hydropower utilities

• U.S. Army Corps of Engineers

• Bonneville Power Administration

• U.S. Bureau of Reclamation
MANAGEMENT ACTIONS

5-47

Management Action CRE-4:

Adjust the timing, magnitude, and frequency of hydrosystem flows (especially spring freshets) entering the 

estuary and plume to better reflect the natural hydrologic cycle, improve access to habitats, and provide better 

transport of coarse sediments and nutrients in the estuary and plume.

Project Unit Cost Schedule

1. Conduct a flood study to determine the risks and 

feasibility of returning to more normative flows in the 

estuary.

2 years @ 

$500,000/year $1 million 2009 - 2010

2. Conduct a study to determine the habitat effects of 

increasing the magnitude and frequency of 

hydrosystem flows (i.e., how much access of river to 

off-channel habitats would increase).

3 years @ 

$500,000/year $1.5 million 2009 - 2011

3. Conduct additional studies to determine the extent of 

other constraints, including international treaties, 

systemwide fish management objectives, and power 

management.

4 years @ 

$500,000/year $2 million 2010 - 2014

4. Make policy recommendations to action agencies on 

flow, taking into consideration beneficial estuary 

flows, flood management, power generation, 

irrigation, water supply, fish management, and other 

interests. 

25 years @ 

$100,000/year $2.5 million 2010 - 2035

5. Implement modified estuary flow regime annually in 

concert with other interests, including hydroelectric, 

flood control, and water withdrawals. 

25 years @ 

$1.5 million/year1 $37.5 million 2011 - 2036

Total costs: $44.5 million

Geographical priority: All reaches (A-H) and the plume.

Key assumptions: (1) Even incremental changes in the magnitude and frequency of hydrosystem flows would 

improve salmonid habitat opportunity and food inputs, which would have benefits throughout the ecosystem. 

(2) Studies of flood risk and the effect of flow changes on estuarine habitat would provide data useful in 

modifying hydrosystem operations to benefit salmonids. (3) Studies of constraints to implementation would 

identify some obstacles that could be overcome. (4) Small to moderate changes in the magnitude, frequency, 

and timing of flows would improve sediment transport-related habitat opportunity in the estuary. (5) Increased 

spring freshets would yield greater sediment transport-related benefits than would other flow modifications.

Existing efforts: Large-scale efforts to adjust flows entering the estuary and return hydrology to more historical 

conditions have not yet begun because of the level of uncertainty regarding potential scenarios for adjusting the 

timing and volume of flow and the associated habitat benefits. Significant efforts have been undertaken by 

Bonneville Power Administration, the U.S. Army Corps of Engineers, and the U.S. Bureau of Reclamation to 

manage the hydrosystem for passage of juvenile salmonids. In addition, flows entering the estuary currently are 

managed to minimum seasonal flows to protect chum redds in the mainstem below Bonneville Dam. 

Potential implementers:

• Bonneville Power Administration

• U.S. Army Corps of Engineers

• U.S. Bureau of Reclamation

Notes:

1 Assumes $1.5 million per year cost of decreased hydrosystem generation revenues associated with minor and 

incremental adjustments to flows; also assumes that the flood risk associated with beneficial estuary flows does 

not increase significantly. The $1.5 million per year cost is included primarily as an indicator that there would be 

some foregone revenues even with minor changes in the flow regime. Specific costs will be evaluated during 

implementation as specific scenarios for modifying flows are developed and considered.
MANAGEMENT ACTIONS

5-48

Management Action CRE-5:

Study and mitigate the effects of entrapment of fine sediment in reservoirs, to improve nourishment of the 

estuary and plume. 

Project Unit Cost Schedule

1. Identify the effects of reservoir sediment entrapment 

on economic and ecological processes; this includes 

effects on ship channels, turning basins, port access, 

jetty activities, and habitat availability. 

1 study $2 million 2008 - 2011

2. Develop a regionwide sediment plan for the estuary 

to address salmonid habitat-forming processes. 

10 years @ 

$100,000/year $1 million 2006 – 2031 

3. Implement projects recommended in the plan to 

mitigate the effects of sediment entrapment. 

5 projects @ 

$1 million/project $5 million 2010 - 2020

Total costs: $8 million

Geographical priority: Reaches A-H and the plume.

Key assumptions: (1) Sediment entrapment in reservoirs will continue. (2) Sediment entrapment has negative 

effects, both ecologically and economically. (3) The extent of these effects warrants exploration and 

implementation of potential mitigation measures. (4) Studying potential mitigation measures would identify some 

actions that would be effective and could be implemented. (5) Synergistic ecological effects may be realized as a 

result of implementing CRE-5 and CRE-6, which could increase sediment inputs into the estuary (CRE-5) and 

optimize beneficial uses of dredged materials (CRE-6). 

Existing efforts: The Lower Columbia Solutions Group, a bi-state organization made up of local, state, and 

Federal governmental and non-governmental stakeholders, was formed by the governors of Washington and 

Oregon to address activities related to the disposal of dredged materials in the estuary. Developing a sediment 

budget is one of the activities of the Lower Columbia Solutions Group; it is likely that this sediment management 

budget will include the effects of reservoir sediment entrapment.

Potential implementers:

• U.S. Army Corps of Engineers

• Bonneville Power Administration
MANAGEMENT ACTIONS

5-49

Management Action CRE-6:

Reduce the export of sand and gravels via dredge operations by using dredged materials beneficially. 

Project Unit Cost Schedule

1. Develop a regionwide sediment plan for the estuary 

and littoral cell.

See

CRE-5.

See

CRE-5.

See

CRE-5.

2. Identify and implement dredged material beneficial 

use demonstration projects, including the notching 

and scrape-down of previously disposed materials 

and placement of new materials for habitat 

enhancement and/or creation. 

100 acres @ 

$10,000/ acres $1 million 2006 - 2012

3. Dispose of dredged materials using techniques 

identified through the demonstration projects and 

regionwide planning.

500 acres @ 

$10,000/acre1 $5 million 2008 - 2033

Total costs: $6 million

Geographical priority: Reaches A, B, C, and G, the Lower Willamette reach, and the plume and nearshore.

Key assumptions: (1) Dredging activities will continue or increase over time. (2) Opportunities to beneficially 

use dredged materials for habitat can be identified. (3) Beneficial use of dredged material would have a positive 

effect on sediment transport and habitat-forming processes in the estuary, plume, and littoral cell.

Existing efforts: Several agencies and organizations are actively engaged in the evaluation of dredged material 

for ecosystem-based beneficial uses. The Lower Columbia Solutions Group currently is focused on reducing the 

disposal of dredged materials in open waters off the mouth of the Columbia River in favor of supplementing the 

nearshore littoral cell with sediments. The Portland District of the U.S. Army Corps of Engineers is exploring tidal 

wetland development in the estuary based on an assessment of wetlands that have formed accidentally where 

dredged materials were placed historically. The Port of Portland also is exploring the use of dredged materials for 

potential development of subtidal habitats.

Potential implementers:

• U.S. Army Corps of Engineers

• Port districts

• Cities

• Lower Columbia River Solutions Group

• Oregon Department of Environmental Quality

• Oregon Department of State Lands

• Oregon Department of Fish and Wildlife

• Oregon Department of Land Conservation and Development

• Washington Department of Ecology

• Washington Department of Fish and Wildlife

Notes:

1

Unit cost is funding to pay for activities beyond the minimum required by law, to achieve regional-scale 

ecosystem benefits.
MANAGEMENT ACTIONS

5-50

Management Action CRE-7:

Reduce entrainment and habitat effects resulting from main- and side-channel dredge activities and ship ballast 

intake in the estuary.

Project Unit Cost Schedule

1. Identify and evaluate dredge operation techniques 

designed to reduce entrainment and other habitat 

effects. 

1 project $500,000 2008 - 2010

2. Initiate demonstration projects designed to test and 

evaluate dredge operations.

5 projects @ 

$200,000/project $1 million 2009 - 2012

3. Implement best management techniques. 10 years @ 

$250,000/year1 $2.5 million 2011 – 2036

4. Study the effects of entrainment of juvenile 

salmonids from ship ballast water intake. 1 study @ $250,000 $250,000 2009 – 2011

5. Implement a demonstration project to evaluate the 

feasibility of reducing entrainment of juvenile 

salmonids from ship ballast intake.

1 project @ 

$250,000 250,000 2012 -- 2015

Total costs: $4.5 million

Geographical priority: Reaches A, B, C, D, E, F, G, and the Lower Willamette reach. 

Key assumptions: (1) Improved best management practices can be identified that would help reduce the impact 

of dredging. (2) Mitigation activities would help offset changes to the estuary caused by dredging.

Existing efforts: The U.S. Army Corps of Engineers and ports in the lower Columbia River have studied the 

effects of entrainment on aquatic species and have implemented actions to reduce negative effects. Screening 

and other ship ballast activities to decrease entrainment of juvenile salmonids have been implemented.

Potential implementers:

• U.S. Army Corps of Engineers

• Port districts

• Private entities, such as ports and sand and gravel dredgers

• Counties and cities

Notes:

1

This is an estimate of the incremental cost above permitted dredge activities. Cost may vary significantly 

depending on site-specific conditions. 
MANAGEMENT ACTIONS

5-51

Management Action CRE-8:

Remove or modify pilings and pile dikes when removal or modification would benefit juvenile salmonids and

improve ecosystem health.

Project Unit Cost Schedule

1. Inventory, assess, and evaluate in-channel pile dikes 

for their economic value and their negative and 

positive impacts on the estuary ecosystem; develop 

working hypotheses for removal or modification. 

1 plan $250,000 2007 - 2009

2. Implement demonstration projects designed to test 

working hypotheses and guide future program 

priorities. 

4 pile dike removal 

projects @ 

$125,000/project

$500,000 2009 - 2010

3. Remove or modify priority pilings and pile dikes. 25 years @ 

$1 million/year $25 million 2008 - 2033

4. Monitor the physical and biological effects of pile dike 

removal and/or modification. 

10 years @ 

$150,000/year $1.5 million 2010 - 2020

Total costs: $27.25 million

Geographical priority: Reaches A – H and the Lower Willamette reach. 

Key assumption: (1) Many pilings, pile dikes, and similar structures could be removed or modified without 

compromising the shipping channel or protection of property. (2) Over time, the removal or modification of

superfluous pile dikes would improve conditions for salmonids and the ecosystem. 

Existing efforts: This action was incorporated into the 2008 Federal Columbia River Power System Hydropower 

Biological Opinion (BiOp) Remand as Reasonable and Prudent Alternative 38: Piling and Dike Removal 

Program. A project team composed of the Lower Columbia River Estuary Partnership, Bonneville Power 

Administration, and the U.S. Army Corps of Engineers is working to develop a strategic plan to remove, modify, 

or retain pile structures within the mainstem lower river. (Modification could include adding large wood to make 

complex habitat, for example.) The program currently is funded at a level of $1 million per year and is expected 

to be funded through 2018 if the program proves successful in providing benefits to salmonids.

Potential implementers:

• U.S. Army Corps of Engineers

• Bonneville Power Administration

• Washington Department of Natural Resources

• Washington Department of Fish and Wildlife

• Oregon Department of Fish and Wildlife

• Oregon Department of Lands

• Lower Columbia River Estuary Partnership

• Counties and cities

• Tribes
MANAGEMENT ACTIONS

5-52

Management Action CRE-9:

Protect remaining high-quality off-channel habitat from degradation and restore degraded areas with high 

intrinsic potential for high-quality habitat. 

Project Unit Cost Schedule

1. Educate landowners about the ecosystem benefits of 

protecting and stewarding intact off-channel areas 

and the costs of restoring degraded areas.1 (See CRE-1.1) $500,000 2008 - 2028

2. Encourage and provide resources for local, state, 

and Federal regulatory entities to maintain, improve 

(where needed), and consistently enforce habitat 

protections throughout the lower Columbia region.2

10 years @ 

$500,000 million/year $5 million 2008 - 2018

3. Actively purchase off-channel habitats in urban and 

rural settings that (1) cannot be effectively protected 

through regulation, (2) are degraded but have good 

restoration potential, or (3) are highly degraded but 

could benefit from long-term restoration solutions.3

Rural: 5,000 acres at 

$3,000/acre

Urban:150 acres at 

$100,000/acre

$30 million 2007 – 2031

4. Restore degraded off-channel habitats with high 

intrinsic potential for increasing habitat quality.

Rural: 6,000 acres at 

$5,000/acre

Urban: 500 acres at 

$5,000/acre

32.5 million 2007 - 2031

Total costs: $68 million

Geographical priority: Reaches A, B, C, and G and the Lower Willamette reach.

Key assumptions: (1) Protection opportunities can be increased over the next decade through public awareness, 

educational, regulatory, and acquisition programs. (2) Protection of off-channel habitats is less expensive than restoration. 

(3) High-quality off-channel habitats offer benefits to salmonids that cannot be provided in other ways. (4) Protection will be 

needed to offset increasing threats resulting from human population increases in the estuary and basin. (5) Restoring offchannel habitat function in the estuary is critical to ecosystem processes. (6) Restoring off-channel habitats enhances juvenile 

salmonid growth by increasing access to food sources and provides refugia from high flows and predation.

Existing efforts: Protection of off-channel habitats relies heavily on local governments; the content and implementation of 

their land use plans specifically for shoreline and floodplain protection will be key to this action. Multiple Federal and state 

resource agencies provide funding for land acquisition and restoration, and multiple entities such as land trusts and 

watershed councils actively acquire and restore lands in the lower river. The Division of State Lands in Oregon and the 

Department of Natural Resources in Washington own and/or regulate submerged and submersible lands. The Natural 

Resource Conversation Service and conservation districts provide technical assistance to private landowners. Where water 

quality issues (such as toxic or conventional contaminants) are involved, agencies such as Washington’s Department of 

Ecology and Oregon’s Department of Environmental Quality may provide additional support. The Lower Columbia River 

Estuary Partnership’s Habitat Restoration Program largely is directed toward this action, CRE-1, and CRE-10. Organizations 

such as the Columbia Land Trust and the Columbia River Estuary Study Taskforce are actively involved in off-channel 

restoration activities. 

Potential implementers:

• U.S. Army COE

• BPA

• Columbia Land Trust

• The Wetlands Conservancy

• Ducks Unlimited

• Col. River Est. Study Taskforce

• The Nature Conservancy

• Lower Col. River Est. Partnership 

• Watershed councils

• OR Watershed Enhancement Bd.

• OR Dept. of Fish and Wildlife

• WA Dept. of Ecology

• Port districts

• Cities

• Conservation districts

• Other special districts

• Tribes

Notes: 1 Projects CRE-1.1 and CRE-9.1 both call for outreach efforts. Outreach efforts for these two actions will be combined in a 

single outreach program whose costs will be shared.

2 Projects CRE-1.2 and CRE-9.2 both call for incentives for local, state, and Federal entities to maintain, improve, and enforce 

regulatory protections. Given their similarities, activities for 1.2 and 9.2 could possibly be coordinated or combined into a single 

effort.

3 Assumes purchases are made over a 25-year period with willing sellers. 
MANAGEMENT ACTIONS

5-53

Management Action CRE-10:

Breach, lower, or relocate dikes and levees to establish or improve access to off-channel habitats. 

Project Unit Cost Schedule

1. Breach, lower the elevation of, or relocate dikes and 

levees; create and/or restore tidal marshes, shallowwater habitats, and tide channels.

5,000 acres1 @ 

$10,000/acre $50 million 2006 - 2031

2. Remove tide gates to improve the hydrology between 

wetlands and the channel and to provide juveniles 

with physical access to off-channel habitat; use a 

habitat connectivity index to prioritize projects. 

2,000 acres1 @ 

$10,000/acre $20 million 2006 - 2031

3. Upgrade tide gates or perched culverts where (1) no 

other options exist, (2) upgraded structures can 

provide appropriate access for juveniles, and (3) 

ecosystem function would be improved over current 

conditions. 

1,000 acres1 @ 

$5,000/acre $5 million 2006 - 2031

Total costs: $75 million

Geographical priority: Reaches A, B, C, E, F, and G and the Lower Willamette reach. 

Key assumptions: (1) Additional opportunities to restore off-channel habitats can be developed through longterm outreach and improved landowner relationships. (2) Restoration of sites, including elevation restoration, 

would yield broad-scale ecosystem benefits over time. (3) A habitat connectivity index would help target efforts 

toward the projects that would provide the greatest benefits. (4) Restoration of highly degraded sites may be 

necessary to yield long-term benefits. 

Existing efforts: Multiple Federal and state resource agencies provide funding for restoration activities, including 

improving hydrologic conditions and access for juvenile salmonids. In the estuary, the U.S. Army Corps of 

Engineers, Columbia River Estuary Taskforce, and Columbia Land Trust have significant experience breaching 

dikes or retrofitting tide gates. Other entities, including watershed councils, conservation districts, and private 

firms, also have experience but sometimes lack sufficient technical and infrastructure capacity. Extensive 

community outreach and long-term relationship building will be needed to implement this action. The Lower 

Columbia River Estuary Partnership’s Habitat Restoration Program largely is directed toward this action, CRE-1, 

and CRE-9.

Potential implementers:

• U.S. Army Corps of Engineers

• Bonneville Power Administration

• U.S. Fish and Wildlife Service

• Oregon Watershed Enhancement Board

• Oregon Department of Fish and Wildlife

• Columbia Land Trust

• Columbia River Estuary Study Taskforce

• Salmon Recovery Funding Board

• Conservation districts

• Other districts

• Cities

• Counties

• Lower Columbia River Estuary Partnership

• Lower Columbia Fish Recovery Board

• Watershed councils

• Tribes

Notes:

1

Acreage equals amount of affected area. Costs include those associated with protecting other land uses from 

renovated hydrology (i.e., moving dikes and levees).
MANAGEMENT ACTIONS

5-54

Management Action CRE 11:

Reduce the square footage of over-water structures in the estuary. 

Project Unit Cost Schedule

1. Inventory over-water structures and develop a GIS 

layer with detailed metadata files. 2 projects @ 

$150,000/project $300,000 2007 - 2009

2. Initiate a planning process to evaluate existing and 

new over-water structures for their economic, 

ecological, and recreational value. 

2 phases1 @ 

$100,000/phase $200,000 2009 - 2013

3. Remove or modify over-water structures to provide 

beneficial habitats. 

10 projects @ 

$500,000/project2 $5 million 2012 - 2037

4. Establish criteria for new permit applications to 

consider the cumulative impacts of over-water 

structures.

1 project $300,000 2008 - 2010

Total costs: $5.8 million

Geographical priority: Reaches D and G and the Lower Willamette reach. 

Key assumptions: (1) Over-water structures pose some threat to salmonids. (2) A fair number of over-water 

structures are no longer in use or have relatively minor value to owners. (3) An inventory of over-water structures 

would aid in assessing individual structures’ economic, ecological, and recreational value.

Existing efforts: Over-water structures are regulated by specific sections of the Federal Clean Water Act, state 

statute, or both. These laws are administered by Federal agencies (U.S. Army Corps of Engineers, U.S. 

Environmental Protection Agency) or state agencies (Oregon Department of Environmental Quality, Oregon 

Division of State Lands, Oregon Department of Land Conservation and Development, Washington Department of 

Ecology, and Washington Department of Natural Resources). The Lower Columbia River Estuary Partnership 

created a shoreline condition inventory that maps all over-water structures using GIS. Currently, there are no 

targeted efforts to remove over-water structures in the estuary.

Potential implementers:

• U.S. Army Corps of Engineers

• Cities

• Washington Department of Natural Resources

• Oregon Department of Land Conservation and Development

• Oregon Department of State Lands

Notes:

1

The first phase is technical and the second phase is policy.

2

A project is defined as a set of structures that have been identified for removal; cost is level of effort. 
MANAGEMENT ACTIONS

5-55

Management Action CRE-12:

Reduce the effects of vessel wake stranding in the estuary. 

Project Unit Cost Schedule

1. Analyze factors contributing to ship wake stranding to 

determine potential approaches to reducing mortality 

in locations where juveniles are most vulnerable. 

Design and implement demonstration projects and 

monitor their results.

1 study @ $1 million $1 million 2007 - 2010

2. Implement projects identified in Project No. 1 that are 

likely to result in the reduction of ship wake stranding 

events. 

12 projects @ 

$1 million/project1 $12 million 2011 - 2026

Total costs: $13 million

Geographical priority: Reaches C, D, E, and F. 

Key assumptions: (1) Vessel wake stranding is a significant issue for ocean- and stream-type salmonids 

employing the fry life history strategy in the estuary. 

Existing efforts: The U.S. Army Corps of Engineers initiated a two-phase study on vessel wake stranding 

associated with the channel deepening project. Phase 1 was completed in 2006 as part of the channel 

deepening project. Results could be used to design follow-up studies analyzing factors that contribute to ship 

wake stranding. In addition, in 2008 the Port of Vancouver completed a study designed to estimate the total 

acres of estuary shoreline (downstream of the port) that may contribute to ship wake stranding. 

Potential implementers:

• U.S. Army Corps of Engineers

• Columbia River pilots

• Ports

• US Coast Guard

• River and bar pilots

Notes:

1 This is a level-of-effort cost approach that will require information generated in Projects No. 1 and 2. 
MANAGEMENT ACTIONS

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Management Action CRE-13:

Manage pikeminnow and other piscivorous fish, including introduced species, to reduce predation on salmonids.

Project Unit Cost Schedule

1. Monitor the abundance levels of pikeminnow, 

smallmouth bass, walleye, and channel catfish.

5 monitoring events 

@ $100,000/event

(every 5 years)

$500,000 2006 - 2031

2. Implement actions as necessary to prevent 

population growth (i.e., modify habitat)1; increase the 

northern pikeminnow bounty program in the estuary. 

25 years @ 

$500,000/year $12.5 million 2006 - 2031

Total costs: $13 million 

Geographical priority: Reaches D, E, F, G, and H and the Lower Willamette reach. 

Key assumption: Management techniques would maintain populations at levels that would maintain or reduce 

predation impacts to salmonids. A pikeminnow management plan exists and is being implemented. Costs 

associated with this action are partly covered as a baseline cost. Costs associated with managing other 

piscivorous fish, including smallmouth bass, walleye, and channel catfish, are entirely incremental costs. 

Existing efforts: Bonneville Power Administration funds the Northern Pikeminnow Sport Reward Fishery 

Program whereby anglers receive $4 to $8 for every qualifying northern pikeminnow 9 inches or longer returned 

to a registration station. Since 1990, more than 3.1 million northern pikeminnow have been removed from the 

Snake and Columbia rivers as a result of this program. The annual budget for the Northern Pikeminnow 

Management Program has varied from $2.0 to $6.4 million, with an average of about $3.0 million basinwide. 

Potential implementers:

• U.S. Army Corps of Engineers

• Washington Department of Fish and Wildlife

• Oregon Department of Fish and Wildlife

• Bonneville Power Administration

• National Marine Fisheries Service

Notes:

1 It is unknown whether projects will be needed to manage warm-water fish. In some cases, there may be warmwater habits close to juvenile habitat, in which case site-specific action would be required.
MANAGEMENT ACTIONS

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Management Action CRE-14:

Identify and implement actions to reduce salmonid predation by pinnipeds.

Project Unit Cost Schedule

1. Expand Federal and state activities at Bonneville 

Dam to test non-lethal and potentially lethal methods 

of reducing pinniped populations throughout the 

estuary. This includes efforts to manage pinnipeds 

through the Marine Mammal Protection Act.

5 years @ 

$500,000/year $2.5 million 2007 - 2011

2. Implement actions likely to reduce pinniped predation 

on adult salmonids.

25 years @ 

$500,000/year1 $12.5 million 2007 - 2032

Total costs: $15 million

Geographical priority: Reaches A-H (especially H).

Key assumptions: (1) Mortality from pinnipeds throughout the lower Columbia River may be a larger source of 

salmonid mortality than previously understood. (2) Further study would clarify the impact of pinniped predation on 

salmonids; studies by the U.S. Army Corps of Engineers at Bonneville Dam represent a good start on this task. 

(3) Mortality from pinniped predation could be reduced through non-lethal and lethal methods. (4) The Marine 

Mammal Protection Act could be modified over time to allow more tools for managing pinnipeds in the estuary. In 

2008, NMFS granted authority under Section 120 of the Marine Mammal Protection Act to the states of Oregon, 

Washington, and Idaho to intentionally take, by lethal methods, individually identifiable California sea lions that 

prey on Pacific salmon and steelhead at Bonneville Dam (Federal Register 2008).

Existing efforts: The National Marine Fisheries Service, Oregon and Washington, the U.S. Army Corps of 

Engineers, and Bonneville Power Administration have initiated efforts to manage pinnipeds, primarily at 

Bonneville Dam. As of 2010, efforts included both lethal and non-lethal methods sanctioned under Section 120 of 

the Marine Mammal Protection Act. 

Potential implementers:

• U.S. Army Corps of Engineers

• Bonneville Power Administration

• National Marine Fisheries Service

• Columbia River Inter-Tribal Fish Commission

• Oregon Department of Fish and Wildlife

• Washington Department of Fish and Wildlife

Notes:

1 Units are years; given the constraints to this action, it is likely that ongoing efforts to prevent predation will 

continue over the next 25 years. 
MANAGEMENT ACTIONS

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Management Action CRE-15:

Implement education and monitoring projects and enforce existing laws to reduce the introduction and spread of

invasive plants. 

Project Unit Cost Schedule

1. Increase public awareness of exotic plant species 

and proper stewardship techniques.1 10 years @ 

$100,000/year $1 million 2008 – 2018

2. Inventory exotic plant species infestations and 

develop a GIS layer with detailed metadata files. 

5 phases @ 

$200,000/phase $1 million 2007 – 2012

3. Implement projects to address infestations on public 

and private lands.

10,000 acres @ 

$1,000/acre $10 million 2008 – 2028

4. Monitor infestation sites. 20 years @ 

$25,000/year $500,000 2010 - 2030

Total costs: $12.5 million

Geographical priority: Reaches A-H and the Lower Willamette reach).

Key assumptions: (1) Aquatic invasive plants have a negative effect on the estuary ecosystem and affect 

juvenile salmonids by altering habitat and causing food webs to deteriorate. (2) Additional information is needed 

on the location, extent, and type of infestations and their effects on the estuary ecosystem. (3) Because 

introductions of invasive plants can permanently alter the estuary ecosystem, prevention activities are crucial. (4) 

Education, outreach, and monitoring would help prevent further introductions of invasive plants.

Existing efforts: The fish and wildlife departments of Oregon and Washington have management 

responsibilities for fish and wildlife, including the control of non-indigenous species. The Washington Department 

of Fish and Wildlife has developed an Aquatic Non-indigenous Species Management Plan. The Pacific States 

Marine Fisheries Commission promotes interstate communication and facilitates the coordination of aquatic nonindigenous species activities on the West Coast. The Oregon and Washington Sea Grant programs combined to 

form the Northwest Marine Invasive Species Team to raise the level of awareness about the threats of invasive 

species. The Invasive Alien Species Executive Order at the Federal level created the Invasive Species Council 

and directed development of an Invasive Species Management Plan. Multiple Federal and state resource 

agencies provide funding for restoration projects that remove exotic invasive plants, and entities such as land 

trusts and watershed councils actively eradicate exotic native plants and plant native species in the lower river. 

Noxious weed control entities exist in Oregon and Washington to help educate landowners and control invasive 

plants.

Potential implementers:

• U.S. Army Corps of Engineers

• Bonneville Power Administration

• US Fish and Wildlife Service

• State agencies

• Conservation districts

• Noxious weed districts 

• Counties

• Cities

• Tribes

• Watershed councils

• Lower Columbia River Estuary Partnership

• The Nature Conservancy

• Landowners

Notes:

1

This project is recommended for upstream mainstem and tributaries, but the costs presented here are for 

activities in the estuary only. Many exotic plants have established themselves upstream and represent a constant 

downstream threat to the estuary. 
MANAGEMENT ACTIONS

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Management Action CRE-16:

Implement projects to redistribute part of the Caspian tern colony currently nesting on East Sand Island. 

Project Unit Cost Schedule

1. Enhance or create tern nesting habitat at alternative 

sites in Washington, Oregon, and California.

3 sites @ 

$1 million/site $3 million 2008 - 2012

2. Reduce tern nesting habitat on East Sand Island 

from 6 acres to 1 to 1.5 acres.

1 project @ 

$4.5 million/project $4.5 million 2007 - 2010

3. Monitor the regional tern population. 25 years @ 

$100,000/year $2.5 million 2010 - 2035

Total costs: $10 million

Geographical priority: Reaches A and B. 

Key assumption: Ongoing and new management actions directed to Caspian tern nesting habitat would 

continue to reduce salmonid mortality from tern predation. A management plan exists and is being implemented. 

Costs associated with this action are partially covered as a baseline cost. 

Existing efforts: The U.S. Army Corps of Engineers has recently constructed alternative habitat for Caspian 

terns outside of the estuary. The Corps also funds studies assessing Caspian tern population levels and 

predation rates on juvenile salmonids. These studies track terns along the West Coast to determine whether 

management actions in the lower river result in redistribution of terns elsewhere along the West Coast. A 

predatory bird Web site (www.birdresearchnw.org) keeps the public and others informed on the status of 

management plans and research.

Potential implementers:

• U.S. Army Corps of Engineers

• U.S. Fish and Wildlife Service

• U.S. Geological Survey

• Oregon Department of Fish and Wildlife

• Washington Department of Fish and Wildlife
MANAGEMENT ACTIONS

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Management Action CRE-17:

Implement projects to reduce double-crested cormorant habitats and encourage dispersal to other locations. 

Project Unit Cost Schedule

1. Identify, assess, and evaluate methods of reducing 

double-crested cormorant abundance numbers. 1 multiphase study $1 million 2007 - 2011

2. Implement demonstration projects resulting from 

Project No. 1 (i.e., decoys and audio playback 

methods). 

5 pilot projects @ 

$500,000/project $2.5 million 2010 - 2015

3. Implement projects resulting in reduced predation by 

cormorants.1

10 years @ 

$700,000/year $7 million 2013 - 2023

Total costs: $10.5 million

Geographical priority: Reaches A and B.

Existing efforts: The U.S. Army Corps of Engineers funds studies assessing cormorant population levels and 

predation rates on juvenile salmonids. These studies track cormorants along the West Coast to determine 

whether management actions in the lower river result in redistribution elsewhere along the West Coast. A 

predatory bird Web site (www.birdresearchnw.org) keeps the public and others informed on the status of 

management plans and research.

Potential implementers:

• U.S. Army Corps of Engineers

• U.S. Fish and Wildlife Service

• U.S. Geological Survey

• Oregon Department of Fish and Wildlife

• Washington Department of Fish and Wildlife

Notes:

1

This is a level-of-effort cost estimate; efforts to manage cormorants in the estuary are significantly lagging 

Caspian tern management efforts and will likely be more difficult to implement.
MANAGEMENT ACTIONS

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Management Action CRE-18:

Reduce the abundance of shad in the estuary. 

Project Unit Cost Schedule

1. Organize existing technical information about shad 

and identify data gaps and potential control methods. 2 phases @ 

$250,000/phases $500,000 2007 - 2011

2. Implement demonstration projects to evaluate 

effective shad management methods.

4 projects @ 

$500,000/project $2 million 2008 - 2015

3. Implement shad population management techniques.1 10 years @ 

$250,000/year $2.5 million 2010 - 2015

4. Monitor and evaluate shad management techniques. 10 years @ 

$50,000/year $500,000 2011 - 2021

Total costs: $5.5 million

Geographical priority: Reaches A-H and the Lower Willamette reach. 

Key assumptions: (1) Shad have negative affects on salmonids in the estuary. (2) Additional research would 

shed light on how shad affect salmonids and suggest new management techniques. (3) New management 

techniques would be unlikely to cause significant change.

Existing efforts: The U.S. Geological Survey, with funding from Bonneville Power Administration, is studying the 

presence of American shad in the Columbia River throughout the year, assessing shad diet trends, and PIT 

tagging up to 1,000 adult pre-spawn shad in the estuary to examine their time of arrival at dams using PIT tag 

detection technologies in fishways.

Potential implementers:

• U.S. Army Corps of Engineers

• U.S. Geological Survey

• Oregon Department of Fish and Wildlife

• Washington Department of Fish and Wildlife

Notes: 1

This is a level-of-effort cost estimate; currently there are no plans to manage shad abundance levels in the 

Columbia River.
MANAGEMENT ACTIONS

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Management Action CRE-19:

Prevent new introductions of aquatic invertebrates and reduce the effects of existing infestations. 

Project Unit Cost Schedule

1. Assemble existing technical information on introduced 

aquatic invertebrates in the estuary and develop a 

plan for managing existing infestations and preventing 

new infestations. 

2 phases @ 

$250,000/phase $500,000 2007 - 2010

2. Implement recommendations from the plan for 

managing existing infestations and preventing new 

infestations (Project No. 1, above).1

5 projects @ 

$500,000/project $2.5 million 2008 – 2013

Total costs: $3 million

Geographical priority: Reaches A-H and the Lower Willamette reach.

Key assumptions: (1) Ship ballast practices could be improved to help prevent further degradation of the 

estuary ecosystem. (2) Additional research would help scientists understand the effects of exotic invertebrates 

on the ecosystem. (3) Because the effects of exotic invertebrates on the ecosystem usually cannot be reversed, 

it is important to prevent introductions when possible.

Existing efforts: Following the direction of the 2007 Oregon Legislature, the Shipping Transport of Aquatic 

Invasive Species Task Force was convened in 2008 to examine how Oregon can better handle aquatic invasive 

species coming into the state via shipping activities. The task force compiled a report outlining various aspects of 

preventing the introduction of aquatic invasive species from shipping-related pathways. The report also 

recommended steps that the Oregon Department of Environmental Quality, working with other agencies and the 

shipping industry, can take to bolster efforts to halt the arrival and spread of aquatic invasive species that 

degrade existing ecosystems and displace native species.

Likewise, the Aquatic Nuisance Species Unit of the Washington Department of Fish and Wildlife (WDFW) has 

implemented the Washington State ballast water program since 2000. This program receives state funds for 

program management, vessel report tracking, and vessel inspection efforts. Two vessel inspectors stationed in 

Puget Sound and the SW/Columbia River regions target high-risk vessels for boarding and ballast sampling. 

Washington established discharge standards that, as of 2009, had not yet been implemented.

In 2008, the Environmental Protection Agency issued a Vessel General Permit (VGP) as part of the National 

Pollutant Discharge Elimination System under the Federal Water Pollution Control Act. This permit is intended to 

regulate discharges resulting from the normal operation of all non-recreational vessels 79 feet or longer. In 

addition, the ballast water discharge provisions apply to any non-recreational vessel of less than 79 feet and 

commercial fishing vessels of any size discharging ballast water, and require adoption of best management 

practices for discharges. Currently, the VGP regulations adopt U.S. Coast Guard ballast water exchange 

requirements and coastal exchange requirements for domestic voyages along the West Coast but do not include 

ballast water treatment technology. Under the Clean Water Action Section 401 certification requirements, states 

can adopt more stringent conditions than the VGP in their certifications if so needed to meet requirements of 

either the Clean Water Act or state law.

Potential implementers:

• Port districts

• Oregon Department of Fish and Wildlife

• Washington Department of Fish and Wildlife

• U.S. Fish and Wildlife Service

• Oregon Department of Agriculture

• Washington State Department of Agriculture

• Portland State University

• Oregon State Marine Board

• Washington State Parks and Recreation 

Commission

• Oregon Department of Environmental Quality

Notes:

1

This is a level-of-effort cost estimate.
MANAGEMENT ACTIONS

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Management Action CRE-20:

Implement pesticide and fertilizer best management practices to reduce estuarine and upstream sources of 

nutrients and toxic contaminants entering the estuary. 

Project Unit Cost Schedule

1. Educate landowners, businesses, and other users 

about practices to reduce usage and the effects of 

pesticides and fertilizers.1

10 years @ 

$50,000/year $500,000 2008 - 2018

2. Implement pesticide, fertilizer, and nutrient best 

management practices to reduce contaminants 

entering the estuary.

10 years @ 

$1.15 million/year2 $11.5 million 2008 – 2018

3. Evaluate the adequacy of best management practices 

and update as needed.

2 reviews @ 

$250,000 $500,000 2012 and 

2017

Total costs: $12.5 million

Geographical priority: Reaches A-H and the Lower Willamette reach. 

Key assumptions: (1) Some users of pesticides and fertilizers are not adequately informed about best 

management practices for these toxic contaminants. (2) Additional benefits to salmonids could be realized 

through continued efforts by farmers, chemical manufacturers, and regulatory programs to reduce impacts from 

fertilizers and pesticides. (3) Benefits to salmonids would increase over a relatively long period of time as 

agricultural practices improve. Several of the projects identified in this action are being implemented and 

therefore could be considered baseline costs. The costs in this action are considered additive to baseline costs 

because of the significant effort needed to reduce nutrients and toxic contaminants entering the estuary. 

Existing efforts: Both Washington and Oregon produce and encourage implementation of best management 

practices (BMP) manuals to address non-point sources of pollution. In both states, load allocations and reduction 

strategies are identified through the total maximum daily load (TMDL) process. The Oregon Department of 

Environmental Quality is now conducting “pesticide stewardship partnerships” in five Oregon watersheds that 

eventually flow into the Columbia or Willamette rivers. These partnership programs work through outreach with 

the agricultural community to implement BMPs that will reduce pesticides in rivers and streams. The U.S. 

Department of Agriculture, through Senate Bill 1010 authorities, is developing plans to ensure BMPs on 

agricultural lands. The U.S. Environmental Protection Agency convened the Columbia River Basin Toxics 

Reduction Working Group in 2005 to coordinate monitoring, cleanup, and reporting efforts basinwide. In 

September 2010, the working group produced the Columbia River Basin Toxics Reduction Action Plan. 

Potential implementers:

• Washington Department of Agriculture

• Oregon Department of Agriculture

• Cities

• Conservation districts

• U.S. Environmental Protection Agency

• Washington Department of Ecology

• Oregon Department of Environmental Quality

• Lower Columbia River Estuary Partnership

• Natural Resources Conservation Service

Notes:

1Projects CRE-20.1 and CRE 21.1 both call for outreach efforts. Outreach efforts for these two projects will be 

combined into a single outreach program whose costs will be shared. 2 Unit cost includes estimates for the estuary and estuary tributaries only; the action recommends similar 

upstream activities. 
MANAGEMENT ACTIONS

5-64

Management Action CRE-21:

Identify and reduce terrestrially and marine-based industrial, commercial, and public sources of pollutants.

Project Unit Cost Schedule

1. Educate the industrial and commercial sectors and 

the general public on how to reduce the introduction 

of pollutants into the estuary and its tributaries.1

10 years @ 

$20,000/year $200,000 2008 - 2028

2. Identify sources, loads, and pathways of pollutants in 

the estuary. 

8 years @ 

$100,000/year

$800,000 2010 - 2018

3. Provide cost-share incentives for National Pollution 

Discharge Elimination System (NPDES) permit 

holders to upgrade effluent above their permit 

requirements.

10 years @ 

$1.5 million/year $15 million 2010 – 2020

4. Study and establish threshold treatment standards 

for pharmaceuticals and other unregulated substance 

discharges; update existing NPDES permits to reflect 

the new standards. 

5 years @ 

$2 million/year $10 million 2007 – 2012

5. Provide grants and low-cost loans to permit holders 

required to treat effluent to standards established in 

Project No. 3. 

10 years @ 

$2 million/year $20 million 2012 - 2017

Total costs: $46 million

Geographical priority: Reaches D and G and the Lower Willamette reach. 

Key assumptions: (1) Non-permitted discharges that currently are occurring would be identified and curtailed. 

(2) Financial incentives or support would motivate NPDES permit holders to raise their effluent treatment levels 

above permit requirements. (3) Releases of industrial and commercial pollutants into the estuary would be 

reduced over time. Several of the projects identified in this action are being implemented and therefore could be 

considered baseline costs. The costs in this action are considered additive to baseline costs because of the 

significant effort needed to reduce inputs of pollutants. 

Existing efforts: In both Oregon and Washington, pollutant load allocations and reduction strategies are 

identified through the total maximum daily load (TMDL) process. The Oregon Department of Environmental 

Quality’s (DEQ) Water Quality Program is developing a list of key, persistent bioaccumulative toxic contaminants 

that have a documented effect on human health, wildlife, and aquatic life. The Oregon Legislature has directed 

DEQ to report on where persistent bioaccumulative toxic contaminants are coming from and options to reduce 

their discharge. In addition, legislation required Oregon’s 52 largest municipal wastewater treatment plants to 

develop plans by 2011 to reduce priority persistent pollutants through pollution prevention and toxic reduction. 

Initial monitoring and reduction efforts are to focus on the Willamette River. The U.S. Environmental Protection 

Agency convened Columbia River Basin Toxics Reduction Working Group in 2005 to coordinate monitoring, 

cleanup, and reporting efforts basinwide. In September 2010, the working group produced the Columbia River 

Basin Toxics Reduction Action Plan. The Lower Columbia River Estuary Partnership has created a long-term 

monitoring strategy that calls for baseline conventional and toxic contaminant data along with data sufficient to 

assess trends and biological integrity. 

Potential implementers:

• U.S. Environmental Protection Agency

• Washington Department of Ecology

• Oregon Department of Environmental Quality

• Cities

• Trade groups such as the Oregon Association of Clean Water Agencies that represent wastewater 

dischargers

Notes:

1 Projects CRE-20.1 and CRE-21.1 both call for outreach efforts. Outreach efforts for these two actions will be 

combined into a single program whose costs are shared.
MANAGEMENT ACTIONS

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Management Action CRE-22:

Restore or mitigate contaminated sites.

Project Unit Cost Schedule

1. Develop criteria and a process for evaluating 

contaminated sites to establish their restoration 

potential.

1 phase @ 

$500,000/phase $500,000 2007 - 2017

2. Develop an integrated multi-state funding strategy to 

address contamination cleanup in the estuary from 

non-identifiable upstream sources. 

Out-of-Estuary1 n/a 2007 - 2012

3. Restore those contaminated sites that will yield the 

greatest ecological and economic benefits.

20 years @ 

$3 million/year $60 million 2007 - 2027

Total costs: $60.5 million

Geographical priority: Reaches A-H and the Lower Willamette reach. 

Key assumptions: (1) Monitoring will continue to provide vital data needed to understand the toxic contaminant 

problem and identify potential solutions. (2) Monitoring will identify hot spots of contamination. (3) Contamination 

sites will be identified for which responsible parties cannot be determined. (4) Additional analysis would identify 

contamination sites whose restoration would yield significant ecological and economic benefits. (5) Restoration of 

contaminated sites would benefit salmonids and the ecosystem over time. (6) The action will include improving 

the condition of habitats that have been impaired by the contaminants, not just removing pollutants. (7) Clean up 

will be to levels that support survival and recovery in both the short-term and long-term. Several of the projects 

identified in this action are being implemented and therefore could be considered baseline costs. The costs in 

this action are considered additive to baseline costs because of the significant effort needed to address 

contamination cleanup.

Existing efforts: The U.S. Environmental Protection Agency regulates cleanup of contaminated sites under 

Superfund and other programs, which include monitoring of these sites. The U.S. Environmental Protection 

Agency convened the Columbia River Basin Toxics Reduction Working Group in 2005 to coordinate monitoring, 

cleanup, and reporting efforts basinwide. In September 2010, the working group produced the Columbia River 

Basin Toxics Reduction Action Plan. The Lower Columbia River Estuary Partnership has created a long-term 

monitoring strategy that calls for baseline conventional and toxic contaminant data along with data sufficient to 

assess trends and biological integrity. The Estuary Partnership, U.S. Geological Survey, and NMFS completed a 

3-year study that compiled and analyzed monthly toxic and conventional pollutant data at five sites, primarily for 

PAHs, PCBs, estrogenic compounds, flame retardants, current-use pesticides, nutrients, and trace elements, 

Toxics monitoring of juvenile salmon also was conducted at six sites (for PCBs, PAHs, organochlorine 

pesticides, and flame retardants) (Lower Columbia River Estuary Partnership 2007). In addition, the Estuary 

Partnership and NMFS developed three models that describe the role that toxics play in a salmon’s life history: a 

conceptual model of the interactions between contaminants and endangered salmonid species, a contaminant 

transport and uptake model, and an ecological risk model to provide a quantitative measure of the impact of 

contaminant exposure on salmonid populations in the Columbia River basin (Spromberg and Johnson 2008, 

Leary et al. 2005, and Leary et al. 2006).

Potential implementers:

• Lower Col. River Est. Partnership

• Col. River Est. Study Taskforce 

• Cities

• Conservation districts

• OR Dept. of Env. Quality 

• WA State Dept. of Ecology 

• Port districts

• U.S. Geological Survey 

• Federal regulatory agencies 

such as the National. Marine 

Fisheries Service and U.S. 

Geological Survey 

Notes:

1 Cost is considered to be outside the purview of estuary-specific projects.
MANAGEMENT ACTIONS

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Management Action CRE-23:

Implement stormwater best management practices in cities and towns. 

Project Unit Cost Schedule

1. Monitor stormwater outputs to measure treatment 

compliance with existing local and state regulations 

throughout the basin; develop a network of monitoring 

sites and establish a data repository that includes data 

collected by permittees. 

10 years @ 

$200,000/year $2 million 2007 - 2015

2. Establish a fund source for regulatory agencies and 

local governments to use when insufficient resources 

are available to (1) access best available science, (2) 

develop standards beyond requirements, or 

(3) adequately enforce regulations. 

3 years @ 

$2 million/year $6 million 2009 –

2011

3. Evaluate the adequacy of best management practices 

and update as needed.

3 evaluations @ 

$500,000 $1.5 million 2010 –

2025

4. Provide incentives for low-impact development 

practices.

20 years @ 

$500,000/year $10 million 2010 - 2030

Total costs: $19.5 million

Geographical priority: Reaches D and G and the Lower Willamette reach. 

Key assumptions: (1) Population growth in the Columbia River basin will continue to influence the hydrology 

and water quality in the estuary. (2) Stormwater practices could be improved by monitoring and enforcing 

compliance with existing regulations, making best scientific information available, and developing higher 

standards. (3) The resulting improvements in hydrology and contaminant exposure in the estuary would occur 

slowly over time. (4) This action is protective in nature; costs are not associated with retrofitting existing 

stormwater facilities. Several of the projects identified in this action are being implemented and therefore could 

be considered baseline costs. The costs in this action are considered additive to baseline costs because of the 

significant effort needed to address stormwater-related water quality issues. 

Existing efforts: Both the Washington Department of Ecology and Oregon Department of Environmental Quality 

produce best management practices manuals to address certain non-point sources. Local governments develop 

and update land use plans that include stormwater practices and that guide future development. The Lower 

Columbia River Estuary Partnership has worked with three schools on Schoolyard Stormwater Projects and 

engaged corporate partners to design and construct stormwater facilities. 

Potential implementers:

• Cities and counties

• Washington Department of Ecology

• Oregon Department of Environmental Quality

• U.S. Environmental Protection Agency

• Lower Columbia River Estuary Partnership

Notes:

This action is recommended for upstream mainstem and tributaries, but the costs presented here are for 

activities in the estuary only.
MANAGEMENT ACTIONS

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Table 5-7 is a summary of costs for the 23 management actions. The total estimated budget 

for constrained implementation of the actions as described in Table 5-6 approaches is 

$528.05 million over 25 years. This number contrasts with the $1.1 billion estimated to help 

restore salmon in Puget Sound tributaries over a 10-year period. Other major ecosystem 

restoration efforts across the United States, including San Francisco Bay, Chesapeake Bay, 

the Everglades, and the Louisiana Coast, are estimated to cost several billion dollars apiece. 

TABLE 5-7

Summary of Costs of Management Actions

Number Action Description Cost for Constrained 

Implementation %*

CRE-01 Protect intact riparian areas in the estuary and restore 

riparian areas that are degraded. $38 million 7%

CRE-02

Operate the hydrosystem to reduce the effects of 

reservoir surface heating, or conduct mitigation 

measures.

$20 million 4%

CRE-03

Protect and/or enhance estuary instream flows influenced 

by Columbia River tributary/mainstem water withdrawals 

and other water management actions in tributaries.

$10 million 2%

CRE-04

Adjust the timing, magnitude, and frequency of 

hydrosystem flows (especially spring freshets) entering 

the estuary and plume to better reflect the natural 

hydrologic cycle, improve access to habitats, and provide 

better transport of coarse sediments and nutrients in the 

estuary and plume.

$44.5 million 8%

CRE-05

Study and mitigate the effects of entrapment of fine 

sediment in reservoirs, to improve nourishment of the 

estuary and plume.

$8 million 2%

CRE-06 Reduce the export of sand and gravels via dredge 

operations by using dredged materials beneficially. $6 million 1%

CRE-07

Reduce entrainment and habitat effects resulting from 

main- and side-channel dredge activities and ship ballast 

intake in the estuary.

$4.5 million 1%

CRE-08

Remove or modify pilings and pile dikes when removal or 

modification would benefit juvenile salmonids and

improve ecosystem health.

$27.25 million 5%

CRE-09

Protect remaining high-quality off-channel habitat from 

degradation and restore degraded areas with high 

intrinsic potential for high-quality habitat.

$68 million 13%

CRE-10 Breach, lower, or relocate dikes and levees to establish or 

improve access to off-channel habitats. $75 million 14%

CRE-11 Reduce the square footage of over-water structures in the 

estuary. $5.8 million 1%

CRE-12 Reduce the effects of vessel wake stranding in the 

estuary. $13 million 2%
MANAGEMENT ACTIONS

5-68

Number Action Description Cost for Constrained 

Implementation %*

CRE-13 Manage pikeminnow and other piscivorous fish, including 

introduced species, to reduce predation on salmonids. $13 million 2%

CRE-14 Identify and implement actions to reduce salmonid 

predation by pinnipeds. $15 million 3%

CRE-15

Implement education and monitoring projects and enforce 

existing laws to reduce the introduction and spread of 

invasive plants.

$12.5 million 2%

CRE-16 Implement projects to redistribute part of the Caspian tern 

colony currently nesting on East Sand Island. $10 million 2%

CRE-17 Implement projects to reduce double-breasted cormorant 

habitats and encourage dispersal to other locations. $10.5 million 2%

CRE-18 Reduce the abundance of shad in the estuary. $5.5 million 1%

CRE-19 Prevent new introductions of aquatic invertebrates and 

reduce the effects of existing infestations. $3 million 1%

CRE-20

Implement pesticide and fertilizer best management 

practices to reduce estuarine and upstream sources of 

nutrients and toxic contaminants entering the estuary.

$12.5 million 2%

CRE-21 Identify and reduce terrestrially and marine-based 

industrial, commercial, and public sources of pollutants. $46 million 9%

CRE-22 Restore or mitigate contaminated sites. $60.5 million 11%

CRE-23 Implement stormwater best management practices in 

cities and towns. $19.5 million 4%

Total $528.05 million

*Column shows the relative percentage of each action to the total cost. Percentages do not add up to 100 

percent because of rounding.

Summary

The estuary and plume ecosystems are especially vulnerable to threats because these 

ecosystems are affected by factors across a wide geographic range—from upstream to the 

estuary itself, and even well out in the Pacific Ocean. A set of actions has been identified to 

help reduce threats to salmonids in the estuary and plume. Other recovery venues must also 

address upstream threats to effectively improve degraded habitats in the estuary. This 

estuary recovery plan module uses survival improvement targets to help estimate the level 

of effort required and the costs of that effort.
6-1

CHAPTER 6

Research, Monitoring, and Evaluation1

Research, monitoring, and evaluation (RME) is a critical element of recovery planning 

for ESA-listed species (Crawford and Rumsey 2010). RME provides essential 

information for planners, implementers, and managers of recovery programs on the 

effectiveness of their programs, whether individual actions are improving the 

performance2

Monitoring plans for ESA-listed Columbia Basin salmonids have been or will be drafted 

for all domain recovery plans in the basin. These monitoring plans address the most 

basic question in recovery planning: Is the status of the listed population or ESU 

improving? Estuary RME will address other key questions, such as whether the 

performance of juvenile salmonids passing through and using the estuary is improving 

or worsening, and whether the limiting factors that affect the status of a population or 

ESU within the estuary are changing. Accordingly, estuary RME will complement 

monitoring for recovery plans for all domains in the Columbia River basin. Additional 

questions addressed by estuary RME are as follows:

of listed salmonids, and how limiting factors and threats are affecting 

salmonids. This chapter describes RME needed to assess juvenile salmonid performance 

in the estuary and to evaluate the effectiveness of the 23 management actions described 

in Chapter 5. It also describes existing monitoring plans, programs, and projects that 

relate to estuary module RME needs and identifies gaps and potential projects to fill 

those gaps. 

• Are the actions identified in the estuary recovery plan module being 

implemented correctly, in sufficient scope, and according to schedule?

• What are the effects of estuary management actions on juvenile salmonids and 

their habitat?

• Are additional actions needed?

• Are there additional or new threats and limiting factors within the estuary 

beyond those considered in the estuary recovery plan module?

• How will the monitoring data be managed, analyzed, interpreted, and 

disseminated?

• How will monitoring data be incorporated into management decisions to best 

allow an adaptive management approach? 

Monitoring for this estuary recovery plan module needs to build on ongoing efforts. In 

particular, Research, Monitoring, and Evaluation for the Federal Columbia River Estuary 

 1 Catherine Corbett of the Lower Columbia River Estuary Partnership and Gary Johnson of Pacific Northwest National 

Laboratories provided the principal input to this chapter.

2 Salmonid performance refers to life history diversity, foraging success, spatial structure, and growth (Bottom et al. 

2005).
RESEARCH, MONITORING, AND EVALUATION

6-2

Program (ERME) (Johnson et al. 2008) is an appropriate monitoring plan on which to 

base the estuary recovery plan module RME. The ERME monitoring plan is important 

because it formed the basis for estuary RME in the 2008 Federal Columbia River Power 

System (FCRPS) Biological Opinion (National Marine Fisheries Service 2008a and 

2008b), and was carried over into the 2010 FCRPS Supplemental Biological Opinion 

(National Marine Fisheries Service 2010). In addition, versions of the ERME monitoring 

plan have been reviewed by the Independent Scientific Review Panel of the Northwest 

Power and Conservation Council (Independent Scientific Review Panel 2006a and 

2006b), along with state and tribal fisheries management agencies. Finally, the ERME 

monitoring plan was initially developed and refined by an inter-agency estuary/ocean 

subgroup for Federal RME that included members from the Bonneville Power 

Administration, the U.S. Army Corps of Engineers, the Lower Columbia River Estuary 

Partnership, NMFS, and the Pacific Northwest National Laboratory. This chapter 

borrows greatly from the Johnson et al. (2008) ERME plan. 

In addition to the Research, Monitoring, and Evaluation Program for the Federal Columbia 

River Estuary (Johnson et al. 2008), nine other monitoring plans and guidance documents 

are applicable to a framework for estuary recovery plan module RME (see Table 6-1). 

The earliest planning document for estuary RME—Lower Columbia River Estuary Plan, 

Aquatic Ecosystem Monitoring Strategy for the Lower Columbia River and Information 

Management Strategy (Lower Columbia River Estuary Partnership 1998)—outlined a 

general monitoring strategy that addressed coordination and oversight, data 

management and quality assurance, conventional and toxic contaminants, habitat, exotic 

species, and primary production. This document continues to be germane today. More 

recently, NMFS produced a document for recovery plans called Guidance for Monitoring 

Recovery of Pacific Northwest Salmon and Steelhead Listed under the Federal Endangered 

Species Act (Crawford and Rumsey 2010). This chapter is consistent with the guidance 

provided in that document, especially regarding the monitoring framework and 

adaptive management approach. 

RME Framework 

The main elements of estuary RME are status and trends monitoring, action 

effectiveness research, critical uncertainties research, and implementation and 

compliance monitoring. These elements inform an adaptive management approach that 

includes synthesis, reporting, and evaluation of monitoring data and use of results to 

modify management actions and monitoring programs. The main elements of the 

estuary RME are described below. 

Status and Trends Monitoring

The overall objective of status and trends monitoring in the estuary is to determine the 

status of ESA-listed salmonids, determine environmental conditions that are ecologically 

significant to listed species, and track how the status changes over time. The results of 

status and trends monitoring should provide information on ambient environmental 

conditions and insight into the cumulative effects of existing and new management 

actions and anthropogenic impacts as they occur. 
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TABLE 6-1

Monitoring Plans Applicable to Estuary RME

Title Lead 

Agency(s) Description Application

Guidance for Monitoring 

Recovery of Pacific 

Northwest Salmon and 

Steelhead Listed under 

the Federal Endangered 

Species Act (Crawford 

and Rumsey 2010)

NMFS This document provides general guidance 

for monitoring and evaluation within an 

adaptive management framework for 

recovery plans for ESA-listed salmonids in 

the Pacific Northwest.

Estuary recovery plan module 

RME used the monitoring 

elements and adaptive 

management approach espoused 

in this work. 

Lower Columbia River 

Estuary Plan, Volume 2: 

Aquatic Ecosystem 

Monitoring Strategy 

(Lower Columbia River 

Estuary Partnership 1998)

Estuary 

Partnership

The Monitoring Strategy makes specific 

recommendations for monitoring oversight, 

data management, and monitoring and 

research on pollutants, toxics, habitat, 

exotic species, and primary production. 

Many of the recommendations in 

this strategy pertain to the 

management actions in the estuary 

recovery plan module and, thus, 

were inherently applied to module 

RME.

Columbia River Basin 

Research Plan (Northwest 

Power and Conservation 

Council 2006a)

NPCC This plan identifies key uncertainties that, if 

resolved, would support actions to 

conserve and recover fish and wildlife 

populations addressed in the BPA/NPCC’s 

Fish and Wildlife Program. There are three 

uncertainties listed for the estuary, one of 

the plan’s focal areas.

Research called for in this plan 

informs many of the management 

actions in the estuary recovery 

plan module.

Research, Monitoring, and 

Evaluation for the Federal 

Columbia River Estuary 

Program (Johnson et al. 

2008)

BPA/ NMFS/

NPCC/USACE

This plan for RME in the tidally influenced 

area, from Bonneville Dam to the ocean, 

including the plume, has specific goals and 

objectives, a conceptual ecosystem model, 

monitored indicators, method and 

protocols, and an action plan. This is a 

working document that is periodically 

updated based on new knowledge and 

program maturation.

Estuary recovery plan module 

RME relied on applicable content 

in this plan. 

Guidance for Developing 

Monitoring and Evaluation 

as a Program Element of 

the Fish and Wildlife Program (Northwest Power 

and Conservation Council 

2006b)

NPCC This report concerns monitoring and 

evaluation for the Fish and Wildlife 

Program. It develops monitoring and 

evaluation guidance at two levels: Council 

policy-makers and project implementers. 

The Council’s Fish and Wildlife Program 

was last approved in 2009.

The guidance in this report, 

although general, is basic to 

monitoring and evaluation planning 

and was applied as appropriate in 

estuary recovery plan module 

RME.

Lower Columbia Salmon 

Recovery and Fish and 

Wildlife Subbasin Plan 

(Lower Columbia Fish 

Recovery Board 2010)

LCFRB The plan includes an extensive section on 

monitoring and research designed to 

evaluate biological status of listed salmon 

and steelhead, tributary habitat status, 

implementation compliance, and action 

effectiveness.

Applicability to estuary recovery 

plan module RME is limited 

because the material focuses on 

tributary watersheds of the lower 

Col. R. and estuary.

Lower Columbia River 

Conservation and 

Recovery Plan for Oregon 

Populations of Salmon 

and Steelhead (ODFW 

2010)

ODFW This plan includes an extensive section on 

monitoring and research designed to 

evaluate biological status of listed salmon 

and steelhead, status of tributary habitat 

and other limiting factors, implementation 

compliance, and action effectiveness.

Applicability to estuary recovery 

plan module RME is limited 

because the material focuses on 

tributary watersheds of the lower 

Col. R. and estuary

FCRPS 2008 Biological 

Opinion and 2010 

Supplemental Biological 

Opinion (NMFS 2008 and 

NMFS 2010)

NMFS The Reasonable and Prudent Alternative in 

the 2008 BiOp includes estuary RME 

actions and subactions. These were 

incorporated by reference into the 2010 

Supplemental BiOp.

There is some overlap between 

the management actions in the 

estuary recovery plan module and 

the RPAs in the Biological 

Opinions. As appropriate, RME 

from the Biological Opinions was 

incorporated into estuary recovery 

plan module RME.
RESEARCH, MONITORING, AND EVALUATION

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Title Lead 

Agency(s) Description Application

Supplement to the 

Mainstem Lower 

Columbia River and 

Estuary Subbasin Plan

(Lower Columbia River 

Estuary Partnership 

2004b)

Estuary 

Partnership

This supplement clarifies and provides 

additional details about the key elements in 

the subbasin plan for the estuary. It does 

not, however, explicitly develop an RME 

plan.

The supplement supports estuary 

RME, although specific 

recommendations are not 

provided.

Upper Columbia 

Monitoring and Evaluation 

Plan

(Upper Columbia 

Technical Recovery Team 

2007)

Upper Columbia 

Technical 

Recovery Team

This working draft provides a 

comprehensive plan for tributary RME. 

Many of the monitoring concepts are 

consistent with those used in the estuary.

Estuary recovery plan module 

RME used the monitoring 

guidance categories in this plan.

The U.S. Environmental Protection Agency (2000) developed 15 guidelines for 

developing environmental indicators that provide this type of information, including the 

following:

• Relevance to the assessment. Monitored indicators should be responsive to an 

identified question and provide information useful for management decisions.

• Linkage to management action. An indicator is useful only if it can provide 

adequate information to support management decisions or quantify the success 

of past decisions.

• Temporal variability across years. Although an indicator may show inter-annual 

variability, the indicator should reflect true trends in environmental conditions 

for the assessment question. To determine variability across years, monitoring 

must proceed for several years at relatively stable sites. Having a long time series 

of data is particularly important in the estuary, where the benefits of habitat 

restoration could be masked by salmonid population changes that are due to 

variable ocean conditions. 

Examples of indicators include direct measurements (such as nutrient concentrations), 

indices, and multimetrics (fish assemblage, for example) (U.S. Environmental Protection 

Agency 2000). 

There are two major objectives for status and trends monitoring in the estuary: (1) assess 

habitat conditions and limiting factors and threats as described in the estuary recovery 

plan module and (2) assess juvenile salmonid performance in the estuary. Johnson et al. 

(2008) list the following status and trends objectives for the estuary:

1. Status and Trends Monitoring (STM): Habitat Conditions – Determine the status and 

trends of monitored indicators for estuary/ocean conditions that are ecologically 

significant to listed salmonids in the lower river, estuary, plume, and nearshore 

ocean.

STM 1. Map bathymetry and topography of the estuary as needed for RME. 
RESEARCH, MONITORING, AND EVALUATION

6-5

STM 2. Establish a hierarchical habitat classification system based on 

hydrogeomorphology, ground-truth it with vegetation cover monitoring data, 

and map existing habitats. 

STM 3. Develop an index of habitat connectivity and apply it to each of the eight 

reaches of the study area. 

STM 4. Monitor habitat conditions periodically, including water surface 

elevation, vegetation cover, plant community structure, substrate characteristics, 

dissolved oxygen, temperature, conductivity, and primary and secondary 

production at representative locations in the estuary and plume. 

2. Status and Trends Monitoring: Juvenile Salmonid Performance – Determine the 

status and trends of monitored indicators for juvenile salmonid performance in the 

estuary and plume.

STM 5. Evaluate migration characteristics, including juvenile salmonid 

abundance, residence times, growth rates, diets, and prey resources at 

representative locations in the estuary and plume to understand habitat usage 

and relative ecological importance of various habitats to juvenile salmonids.

STM 6. Monitor and evaluate juvenile salmonid survival from Bonneville Dam 

through the estuary into the plume. 

STM 7. Develop an index and monitor and evaluate life history diversity of 

juvenile salmonid populations at representative locations in the estuary. 

STM 8. Monitor and evaluate temporal and spatial species composition, 

abundance, and foraging rates of juvenile salmonid predators at representative 

locations in the estuary and plume.

Johnson et al. (2008) also provide guidance on potential indicators that can be monitored 

to provide information relevant to these objectives. Additional information about status 

and trends monitoring objectives can be found in the Research, Monitoring, and Evaluation

for the Federal Columbia River Estuary Program (Johnson et al. 2008).

Action Effectiveness Research

The overall objective of action effectiveness research in the estuary is to provide 

information about the effects of management actions. Using a representative set of 

management actions, such as specific types of habitat restoration, researchers monitor a 

suite of variables to evaluate the effects of individual actions on juvenile salmon and 

their estuarine habitats and provide feedback on potential methods for improving 

techniques, locations, or other aspects of the action. Action effectiveness research usually 

involves project-scale monitoring of site-specific conditions to determine whether 

implemented actions were effective in creating the desired change and whether projector program-specific performance goals were met. This type of monitoring also can 

include long-term post-project implementation monitoring to see whether the actions 

continue to function as they were designed or intended. In some cases the information 

needed for action effectiveness monitoring may be provided by status and trends 

monitoring, but action effectiveness research generally requires focused evaluations of 

more specific parameters directly associated with actions. 
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6-6

The intent of action effectiveness research (AER) is to use quantitative studies to 

demonstrate how habitat restoration actions affect factors controlling ecosystem 

structures and processes at site and landscape scales and produce changes in juvenile 

salmonid performance. The following sub-objectives are from Johnson et al. (2008): 

Using a representative set of projects, monitor and evaluate the effects of habitat 

restoration actions in the estuary, as follows:

AER 1. Develop a limited number of reference sites for typical habitats, e.g., tidal 

swamp, marsh, island, and tributary delta, to use in action effectiveness 

evaluations.

AER 2. Evaluate the effects of selected individual habitat restoration actions at 

project sites relative to reference sites and evaluate post-restoration trajectories 

based on project-specific goals and objectives. ("Effectiveness Monitoring") 

AER 3. Develop and implement a methodology to estimate the cumulative effects 

of habitat conservation and restoration projects in terms of cause-and-effect 

relationships between ecosystem controlling factors, structures, and processes 

affecting salmon habitats and performance. ("Validation Monitoring")

Critical Uncertainties Research

The overall objective of critical uncertainties research in the estuary is to investigate 

uncertainties in the state-of-the-science that are pivotal to understanding fish 

performance within the estuary. Uncertainties include cause-and-effect relationships 

among fish, limiting factors, threats, and activities meant to protect or enhance fish 

performance. The following three critical uncertainties were identified as particularly 

relevant to this module:

• Extent of density dependence mortality in the estuary and the role of large 

releases of hatchery fish in density dependence

• Effects of climate cycles and global warming on salmonid performance in the 

estuary

• The amount of increased juvenile survival in the estuary that could reasonably be 

expected if all 23 management actions in the module were implemented, and the 

proportion of that increased survival that could be attributed to each action

Critical uncertainties were also identified in Johnson et al. (2008). The following subobjectives pertain to critical uncertainties research (CUR):

CUR 1. Continue work to define the ecological importance of the tidal 

freshwater, estuary, plume and nearshore ocean environments to the viability 

and recovery of listed salmonid populations in the Columbia Basin.

CUR 2. Continue work to define the causal mechanisms and migration/behavior 

characteristics affecting survival of juvenile salmon during their first weeks in 

the ocean.

CUR 3. Investigate the importance of the early life history of salmon populations 

in tidal freshwater of the lower Columbia River.
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CUR 4. Investigate the effects of hatchery fish on wild (naturally produced) fish 

in the estuary. 

CUR 5. Understand the wetting and drying of the floodplain habitats caused by 

complex hydrodynamic interactions of tides, mainstem and tributary flows, and 

the effect of the FCRPS on river conditions. 

By testing assumptions related to these and other critical uncertainties, recovery 

program planners, implementers, and managers can refine the foundation, 

implementation, and effectiveness of the management actions described in Chapter 5 to 

incorporate the best available science as it becomes accessible. 

Implementation and Compliance Monitoring

The overall objective of implementation and compliance monitoring is to determine 

whether projects that address management actions are being implemented correctly, in 

sufficient quantities, and according to schedule. This monitoring is important for 

evaluating whether recovery programs are meeting objectives and performance 

measures, such as the number of estuary habitat acres conserved or restored annually.

Objectives and performance measures for implementation and compliance monitoring 

are specific to the programs they evaluate; thus, in this case, performance measures and 

the resulting implementation monitoring would need to reflect targets derived from the 

23 management actions in Chapter 5. Johnson et al. (2008) identified the following 

implementation and compliance monitoring (ICM) objectives:

ICM 1. Determine whether restoration projects were carried out as planned, i.e., 

whether specified project criteria were met ("Implementation Monitoring").

ICM 2. Total the amount of estuary habitat conserved and restored annually by 

habitat type.

Adaptive Management Approach 

Estuary recovery plan module RME will employ an adaptive management approach. 

Adaptive management is the process of adjusting management actions based on new 

information. Management actions must be taken in an adaptive, experimental manner 

because ecosystems are inherently variable and highly complex (Independent Scientific 

Review Panel 2007). The process works by coupling decision making with the collection 

and evaluation of performance data and offering an explicit process through which 

alternative strategies to achieve the same ends can be proposed, prioritized, and 

implemented when necessary (Crawford and Rumsey 2010).

Figure 6-1 shows the role of RME and adaptive management in NMFS decisions 

regarding listing salmonids under the Endangered Species Act. The estuary recovery 

plan module addresses limiting factors and threats, which led to the management 

actions listed in Chapter 5. The RME described in this chapter will result in new 

information for use in evaluating the status of statutory listing factors and limiting 

factors and adjusting management actions as needed.
RESEARCH, MONITORING, AND EVALUATION

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FIGURE 6-1

NMFS Listing Status Decision Framework (Crawford and Rumsey 2010)

The adaptive management approach in the estuary recovery plan module is intended to 

achieve effective management actions in the Columbia River estuary ecosystem. For the 

estuary recovery plan module, adaptive management entails the following:

• Management actions

• Research, monitoring, and evaluation actions

• Coordination and implementation

• Data and information management

• Synthesis, reporting, and evaluation

• Decisions

Estuary-scale adaptive management will benefit from adaptive management planning 

by individual organizations (such as the Lower Columbia River Estuary Partnership and 

the U.S. Army Corps of Engineers) for their habitat restoration projects and programs 

(see Thom et al. 2007).

Coordination 

Coordination is critical in implementing RME for the Columbia River estuary, where 

multiple entities collect data for numerous individual projects with various objectives 

and potentially different monitoring protocols. Successful implementation and 
RESEARCH, MONITORING, AND EVALUATION

6-9

evaluation of estuary recovery plan module RME will require that ongoing and future 

RME efforts be coordinated and carried out within an adaptive management framework. 

An estuary RME information-sharing forum should be established that includes 

technical representatives of Federal, state, and local government agencies; the Lower 

Columbia River Estuary Partnership; and other entities involved in research, 

monitoring, and implementation of recovery actions. This forum would be a valuable 

mechanism for fulfilling the coordination need and would complement corresponding 

groups of policy representatives responsible for implementation.

Data and Information Management 

Data and other information pertinent to estuary RME are collected by many parties for a 

wide variety of applications. Data analysis and management are performed at a project 

and sometimes agency level, but not often at the estuary-wide level. It is neither 

desirable nor feasible to centrally manage or analyze all data within the Columbia River 

estuary. However, data should be managed so that synthesis and evaluation occurs 

through a coordinated, communal information network that includes the following 

elements:3

• Incorporation of data produced by existing programs and information systems to 

avoid duplication of effort.

• Integration with other basinwide and regional RME groups, including the Pacific 

Northwest Aquatic Monitoring Partnership.

• Regular written project-level reporting by RME partners within a coordinated 

system for peer review of project plans and reports.

• Periodic estuary RME workshops to present new data, discuss findings, and 

exchange information on future plans.

• A system for tracking implementation of RME projects throughout the estuary.

• Establishment of a central, Web-accessible repository and library for estuary data 

and references.

• Guidelines for metadata standards to facilitate data exchange and application.

• Centrally facilitated program-level review for comprehensive synthesis and 

evaluation of pertinent information relative to the goals and objectives of this plan.

• Periodic program-level summary reports.

• Communication and information exchange with other West Coast estuary and 

adaptive management programs, such as the Puget Sound Partnership.

• Consistent participation and funding commitments by partners.

A data management program for the estuary should build on existing efforts, such as the 

Lower Columbia River Estuary Partnership’s monitoring and data management 

activities. The Estuary Partnership’s science work group (and board of directors) 

 3 Adapted from Johnson et al. (2008) and Lower Columbia River Estuary Partnership (2004a).
RESEARCH, MONITORING, AND EVALUATION

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includes technical representatives of Federal, state, and local government agencies and 

other entities involved in restoration, monitoring, and implementation of recovery 

programs. This work group complements corresponding groups of policy 

representatives.

Synthesis, Reporting, and Evaluation 

The information from status and trends monitoring, action effectiveness research, critical 

uncertainties research, and implementation and compliance monitoring should be 

synthesized and integrated in periodic reports for decision makers and other interested 

parties. The intent is to “roll up” project-specific data into program-level information. 

Annual reporting at the project level should be a key mechanism for data dissemination; 

biennial reporting at the program level should be key to disseminating results of 

evaluations. The estuary RME information-sharing forum described above could guide 

the synthesis and roll-up in the biennial report. In an adaptive management process, 

program evaluation includes adjusting program objectives and methodologies based on 

new information. As Noon (2003) stated, monitoring programs “must be constantly 

revisited and revised as scientific knowledge is acquired.” Procedures should be 

established that link decision makers to estuary RME monitoring overseers and data 

managers. To conclude, Johnson et al. (2008) recommended the following synthesis and 

evaluation activities:

SE 1. Upload, compile, manage, and disseminate project-level data at the Estuary 

Program level.

SE 2. Synthesize the data and periodically report it to the region.

SE 3. Use the synthesized data to evaluate the Estuary Program and refine the 

estuary RME effort as necessary.

Existing Programs and Projects and Additional Monitoring 

Needs 

Activities conducted as part of the ERME program (Johnson et al. 2008) and other efforts 

do not fully address all of the monitoring needs associated with the 23 management 

actions identified in the module. The following sections describe (1) existing monitoring 

programs and projects and their applicability to the 23 management actions identified in 

the module; (2) gaps between existing monitoring efforts and needed monitoring for the 

management actions; (3) additional monitoring activities to fill those gaps and ensure 

monitoring to support all of the 23 management actions; (4) recommended indicators 

and protocols; and (5) estimated costs of estuary module RME. 

Existing Programs and Projects

Estuary recovery plan module RME will take advantage of ongoing monitoring 

programs and the projects implemented within them wherever possible to avoid

duplication of effort. At least 21 ongoing programs include projects that address aspects 

of research and monitoring in the estuary (see Table 6-2). The largest RME programs are 

the Columbia Basin Fish and Wildlife Program, which is funded by Bonneville Power 

Administration via the Northwest Power and Conservation Council, and the 
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Anadromous Fish Evaluation Program, which is funded by the U.S. Army Corps of 

Engineers. These two programs address estuary RME explicitly. The other programs 

exist for purposes other than estuary RME, but are applicable in a limited fashion. 

The research and monitoring effort in the estuary includes at least 42 projects (see 

Table 6-3). This project list was derived from data in Johnson et al. (2008), the Estuary 

Partnership’s RME inventory (conducted by K. Jones), and the Pacific Northwest 

Aquatic Monitoring Partnership’s RME Project Inventory (database provided by 

M. Banach, Pacific States Marine Fisheries Commission). The projects include status and 

trends monitoring, action effectiveness research, and critical uncertainties research. 

RME Needs, Existing Project Coverage, and Recommended Projects 

Table 6-4 identifies monitoring needs for each of the 23 management actions in the 

estuary recovery plan module (see Tables 5-2 and 5-6), lists existing projects and 

programs that help address the needs, and identifies gaps. Table 6-5 identifies potential 

new projects to fill the RME gaps identified in Table 6-4. In addition, all of the 

management actions will require implementation and compliance monitoring. 

Monitoring Recommendations

Table 6-6 provides recommendations specific to each need identified in Table 6-4. 

Recommendations include sampling design, spatial and temporal scale, measured 

variables, measurement protocols, derived variables, analysis, possible funding entities, 

and potential entities for implementation and coordination. Many of the measured 

variables and measurement protocols were obtained from Johnson et al. (2008). Specific 

monitoring methods will developed on a project basis. Habitat restoration monitoring 

protocols for the Columbia River estuary have been developed and disseminated in 

Roegner et al. (2009) (Table 6-3, Project J15). Mention of possible funding entities in 

Table 6-6 does not imply a funding commitment of any kind.

Estimated Costs

Table 6-7 presents estimates of costs and implementation schedules for estuary recovery 

plan module RME. These cost estimates were developed by Gary Johnson of Pacific 

Northwest National Laboratories, Catherine Corbett of the Lower Columbia River 

Estuary Partnership, and Phil Trask of PC Trask & Associates, Inc., by researching 

existing programs and estimates. The costs identified in this section do not represent a 

detailed economic analysis; in fact, they are not economic costs, in that they have not 

been discounted across time. Instead, the cost estimates are in constant dollars over a 25-

year period. As mentioned previously, some module actions included specific RME 

projects and associated cost estimates (see Table 5-6). In those cases, Table 5-6 is 

referenced. Other costs in Table 6-7 ($64.1 million) were estimated by evaluating the 

monitoring needs in Table 6-6. The total cost of the RME projects identified in the 

estuary recovery plan module is $85.1 million.

Summary

Monitoring, research, and evaluation elements identified in Guidance for Monitoring 

Recovery of Pacific Northwest Salmon and Steelhead Listed under the Federal Endangered 
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Species Act (Crawford and Rumsey 2010) and Research, Monitoring, and Evaluation for the 

Federal Columbia River Estuary Program (Johnson et al. 2008) provide a consistent 

methodology that supports the RME detailed in this chapter for the estuary recovery 

plan module. As management actions identified in the module are implemented, it will 

be important that monitoring and research data are returned to the managers of the 

recovery effort to determine whether the management actions in the estuary recovery 

plan module are achieving the desired results. 
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TABLE 6-2

Ongoing Monitoring Programs Applicable to Estuary RME (as of July 2009). The program “ID” number was invented for the purpose of this module to provide linkages 

to Table 6-3.

ID Program Lead Entity Description More Information

P1 National Stream Quality 

Accounting Network (reported in 

National Streamflow Information 

Program)

USGS (and OHSU) Monitoring at Beaver Terminal (RM54); includes water quality 

and discharge measurements. Water quality components 

enhanced by OHSU collaboration since summer 2009.

NASQAN: http://water.usgs.gov/nasqan/

Water quality (as of summer 2009): 

http://columbia.loboviz.com/loboviz/

Columbia River Factsheet: 

http://water.usgs.gov/ 

nasqan/progdocs/factsheets/ 

clmbfact/clmbfact.html

P2 National Water-Quality 

Assessment Program

USGS Routine water quality monitoring nationwide; it includes the 

Willamette basin, but not the estuary.

NAWQA: http://water.usgs. gov/nawqa/

Willamette page: http://or.water.usgs.gov/

projs_dir/pn366/ nawqa.html

P3 Columbia Basin Fish and Wildlife 

Program

BPA/ NPCC Contains a measure addressing the question, “Is the Columbia 

River estuary improving or deteriorating relative to desired 

conditions?” BPA/NPCC implements estuary RME projects 

here.

http://www. nwcouncil.org/ library/2000/

P4 Columbia River Channel 

Improvements Project

USACE Monitoring occurs as required for ESA concerns. https://www.nwp. usace.army.mil/ 

issues/crcip/

P5 Mouth of the Columbia River 

Project

USACE/ Ports Monitoring occurs as required for ESA concerns. https://www.nwp. usace.army.mil/op/n/ 

projects/

P6 Anadromous Fish Evaluation 

Program (AFEP)

USACE Implements the Columbia River Fish Mitigation Project designed 

to improve survival through the hydrosystem. The USACE does 

estuary research in AFEP.

https://www.nwd. usace.army.mil/ps/

P7 NOAA General Funds Program NOAA Provides funds for specific estuary/ocean research projects by 

NOAA.

Unknown

P8 Oregon Dept. of Environmental 

Quality/106/General Funds

ODEQ Focus is on Willamette, including its confluence with the 

Columbia River.

http://www.deq.state. or.us/lab/ 

wqm/watershed.htm

P9 Total Dissolved Gas Monitoring 

Program 

USACE/ USGS Routine monitoring. USGS: http://or.water.usgs.gov/ 

projs_dir/pn307.tdg/

USACE: http:// 137.161.202.92/TMT/ 

WQ/2001/ MonitorPlan/ tdgmgt01.pdf

P10 Washington Dept. of Ecology 

Ambient Monitoring Program

WDE Usually includes at least one mainstem site, in addition to 

tributary water quality monitoring.

Monitoring Home: http://www.ecy.wa.gov/ 

programs/eap/ fw_riv/rv_main.html
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ID Program Lead Entity Description More Information

P11 Water Resources Development 

Act – Ecosystem Restoration 

Programs

USACE USACE conducts monitoring of specific restoration actions 

conducted under these authorities; monitoring maximum cost is 

3% total project cost.

https://www.nwp. usace.army.mil/pm/lcr/

P12 Lower Columbia River 

Ecosystem Restoration General 

Investigations Feasibility Study 

(GI Study)

USACE The purpose of the GI Study is to “investigate and recommend 

appropriate solutions to accomplish ecosystem restoration in the 

lower Columbia River and estuary, including wetland/riparian 

habitat restoration, stream and fisheries improvement, water 

quality, and water-related infrastructure improvements.”

https://www.nwp.usace.army.mil/

pm/cr/envres.asp

P13 Portland Harbor Superfund 

Assessment Program

EPA Implements cleanup at the Superfund site in Portland harbor. EPA: http://yosemite.epa.gov/R10/ 

CLEANUP.NSF/sites/ ptldharbor

P14 Estuary Partnership Ecosystem, 

Action Effectiveness and Pile 

Structure Monitoring Programs

Estuary Partnership Implements an Ecosystem Condition Status and Trends 

Monitoring Strategy, Restoration Actions Effectiveness 

Research and Pile Structure Modification action effectiveness 

research and critical uncertainties. Funding by BPA/NPCC, 

EPA, NOAA, and others.

http://www.lcrep.org

P15 NOAA Tides and Currents NOAA Geodetic monitoring http://tidesandcurrents.noaa.gov/

P16 Surface Water Data Collection 

Program

USGS Water quality monitoring (at Beaver Terminal combined with 

OHSU as of summer 2009)

http://columbia.loboviz.com/loboviz/

P17 Volunteer Water Quality 

Monitoring Program

Will. River Keeper Volunteer water quality monitoring

P18 Zebra Mussel Monitoring 

Program

Portland State Univ. Monitoring of zebra mussels, an invasive species Contact: Steven Wells

P19 National Fish and Wildlife 

Foundation, Columbia River 

Estuarine Coastal Fund

National Fish and 

Wildlife Foundation 

(NFWF)

The Columbia River Estuarine Coastal Fund was established in 

2004 to receive community service payments ordered by court 

settlements resulting from violations of Federal pollution laws. 

http://www.nfwf.org/

P20 Ship-wake program Port of 

Vancouver/NOAA 

Spatial analysis of beach susceptibility for stranding of juvenile 

salmonids by ship wakes

P21 (Untitled) City of Portland Monitoring of project effectiveness, fish and wildlife, water 

quality, and stormwater within Portland’s waterways, including 

the lower Willamette River. The City is in the process of revising 

its monitoring approach, modeling the design on EPA’s 

Environmental Monitoring and Assessment Program.

http://www.portlandonline.com/bes/

Kaitlin.Lovell@bes.ci.portland.or.us
RESEARCH, MONITORING, AND EVALUATION

6-15

TABLE 6-3 

Ongoing Projects Addressing Estuary RME (as of July 2009)

The project “ID” number (e.g., J4) was invented for the purpose of this module to provide linkages to Table 6-4. Project numbers (e.g., 2000-012-00) are specific to the respective 

program. Program numbers (e.g., P3) correspond to the program ID numbers in Table 6-2.

ID Title Project No. Program Monitoring Entity

J1 ODEQ Ambient Water Quality Monitoring Unknown P8 OR Dept. of Env. Quality

J2 WDOE Ambient Water Quality Monitoring Unknown P10 WA Dept. of Ecology

J3 USGS Discharge and Water Quality Monitoring Unknown P1 USGS

J4 Ives Is. Chum Salmon Monitoring 2000-012-00 P3 USFWS

J5 Lower Columbia River and Estuary Ecosystem Monitoring Project 2003-007-00 P14 + P3 Estuary Partnership/ 

NOAA/PNNL/UW/USGS

J6 Total Dissolved Gas Monitoring PNAMP#409 P9 USGS

J7 Avian Predation on Juvenile Salmonids 1997-024-00 P3 OSU

J8 Tenasillahe Is. Monitoring Unknown P11 USFWS

J9 Canada-US Shelf Salmon Survival Study 2003-009-00 P3 DFO

J10 Life History, Habitat Connectivity, and Survival Benefits of Restoration EST-P-09-01 P6 PNNL/UW

J11 Estimation of Salmon Survival Using Miniaturized Acoustic Tags EST-P-02-01 P6 NMFS/ PNNL

J12 Tidal Fluvial Habitats and Juvenile Salmon – Current and Historical Linkages EST-P-10-01 P6 NMFS

J13 Sampling PIT Tagged Juvenile Salmonids Migrating in the Estuary BPS-W-00-11 P6 NMFS

J14 Survival and Growth of Juvenile Salmonids in the Columbia River Plume 1998-014-00 P3 NMFS

J15 Evaluation of Cumulative Ecosystem Response to Restoration EST-P-02-04 P6 PNNL/ NMFS/ CREST

J16 Action effectiveness research on habitat restoration projects EST-P-09-02 P6 USFWS

J17 Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon 2003-010-00 P3 NMFS/ OHSU/ PSU/ UW

J18 Acoustic Tracking for Survival (POST) 2003-114-00 P3 Kintama

J19 Relationship Among Time of Ocean Entry, Physical, & Biological Characteristics of Estuary/Plume EST-P-02-03 P6 NMFS

J20 Effectiveness Monitoring at Sites in Young’s Bay Unknown P19 CREST

J21 Habitat Restoration Program – Habitat GIS, Reference Sites, Restoration Actions Effectiveness 

Research and Pile Structure Modification Critical Uncertainties

2003-011-00 P14 + P3 Estuary Partnership

J22 Monitoring at Smith and Bybee Lakes Unknown Unknown Ducks Unlimited
RESEARCH, MONITORING, AND EVALUATION

6-16

ID Title Project No. Program Monitoring Entity

J23 Ramsey Lake Restoration Project Monitoring Unknown 14 City of Portland

J24 Impact of American Shad 2007-275-00 P3 USGS

J25 Caspian Tern Management 2006-002-00 P3 OSU

J26 Tidal Freshwater Monitoring of Juvenile Salmonids 2005-001-00 P3 PNNL/ODFW/UW/NMFS

J27 Effects of Total Dissolved Gas on Chum Fry SPE-P-07-01 P6 PNNL

J28 CORIE Unknown P3+ OHSU

J29 Pile Structure Removal and Modification Study Unknown P14 Estuary Partnership/BPA/ USACE

J30 Julia Butler Hansen Tide Gate Replacement Unknown P11 USFWS

J31 Comparison of Juvenile Salmonid Stranding Before and After Channel Improvements Unknown P4 PNNL/UW

J32 Bonneville Sea Lion Exclusion Study ADS-02-16 P6 USCAE Fisheries Field Unit

J33 Sea Lion Deterrent System BPA/NPCC P3 Smith Root

J34 Caspian Tern Management Measures AVS-P-08-01 P6 OSU

J35 Double-Crested Cormorant Management Measures AVS-P-08-02 P6 OSU

J36 Impact of Avian Predation on Smolts AVS-W-03-01 P6 NMFS

J37 Tides and currents Unknown P15 NOAA

J38 Northern Pikeminnow Surveys 1990-077-00 P3 ODFW

J39 Effectiveness Monitoring in the Lower Grays R. PNAMP#529 P3 CREST

J40 Ives Island – Adult Chum Salmon Monitoring PNAMP#277 P3 ODFW

J41 Volunteer Water Quality Monitoring PNAMP#575 P17 Willamette River Keeper

J42 Zebra Mussel Monitoring PNAMP#425 P18 PSU
RESEARCH, MONITORING, AND EVALUATION

6-17

TABLE 6-4

Management Actions, Associated Monitoring Needs, and Existing Coverage

Existing projects with “J” prefixes refer to projects listed in Table 6-3.

Management Action Type Monitoring Need Existing Projects and 

Gaps

CRE-1: Protect intact riparian areas in the 

estuary and restore riparian areas that are 

degraded.

STM Periodic mapping and areal 

measurement of riparian 

habitats and their condition 

using aerial photography to 

inform prioritization efforts

J5 and J21, although the 

projects do not do this at this 

time, but eventually could. 

CRE-2: Operate the hydrosystem to reduce 

the effects of reservoir surface heating, or 

conduct mitigation measures.

STM Water temperature 

monitoring in the estuary to 

establish baseline

J1, J2, J28

AER Monitoring during the 

hydrosystem temperature 

experiment

At dams, the US Army Corps of 

Engineers (USACE) monitors 

water temperature; revive 

hydrodynamic modeling

UR Reservoir heating study and 

downstream effects

No existing projects. 

CRE-3: Protect and/or enhance estuary 

instream flows influenced by Columbia River 

tributary/mainstem water withdrawals and 

other water management actions in 

tributaries.

STM Continuous monitoring of Col. 

River discharge at Beaver 

Terminal in the estuary

J3 USGS National Streamflow 

Information Program

CRE-4: Adjust the timing, magnitude and 

frequency of hydrosystem flows (especially 

spring freshets) entering the estuary and 

plume to better reflect the natural hydrologic 

cycle, improve access to habitats, and 

provide better transport of coarse sediments 

and nutrients in the estuary and plume.

STM/

AER

Continuous monitoring of Col. 

River discharge at Beaver 

Terminal in the estuary and 

at Bonneville dam

Plume turbidity monitoring 

using remote sensing

J3 USGS National Streamflow 

Information Program; J36 

NOAA Tides and Currents

UR Flood, habitat, and 

constraints study(s)

No existing projects; revive 

modeling, e.g., Jay and 

Kukulka 2003

CRE-5: Study and mitigate the effects of 

entrapment of fine sediment in reservoirs, to 

improve nourishment of the estuary and 

plume.

UR Effects of reservoir sediment 

entrapment

No existing projects; the 

USACE measured sediment 

entrapment previously.

CRE-6: Reduce the export of sand and 

gravels via dredge operations by using 

dredged materials beneficially.

UR Evaluate the long-term 

trajectory of beneficial use of 

shallow- water habitat 

creation sites

No existing projects; the 

USACE applies dredged 

material for beneficial uses 

when possible

CRE-7: Reduce entrainment and habitat 

effects resulting from main- and side-channel 

dredge activities and ship ballast intake in the 

estuary.

UR Dredge technique and 

operations study

No existing projects; the 

USACE studied crab 

entrainment previously 

(Pearson et al. 2006).

CRE-8: Remove or modify pilings and pile 

dikes when removal or modification would 

benefit juvenile salmonids and improve 

ecosystem health. 

STM Periodic mapping and length 

and density measurements of 

pile structures using the 

Estuary Partnership’s estuary 

GIS system

J29, J21

AER Monitor physical and 

biological effects of pile 

removal

J29, J21

UR Study fundamental physical 

and biological characteristics 

to understand where removal 

or modification would be 

advantageous

No existing projects.
RESEARCH, MONITORING, AND EVALUATION

6-18

Management Action Type Monitoring Need Existing Projects and 

Gaps

CRE-9: Protect remaining high-quality offchannel habitat from degradation and restore 

degraded areas with high intrinsic potential 

for high-quality habitat.

STM Periodic mapping and areal 

measurement of off-channel 

habitat types to inform 

prioritization and monitoring 

efforts

J5 and J21

CRE-10: Breach, lower, or relocate dikes and 

levees to establish or improve access to offchannel habitats.

STM Periodic mapping and length 

measurements of dike 

structures using the Estuary 

Partnership’s estuary GIS 

system.

J21 GIS map of dikes and tide 

gates

AER Effectiveness monitoring 

studies of tidal reconnections

J30 JBH study, J15 Cumulative 

effects, J20 Young’s Bay

UR Ecological importance of tidal 

reconnections

J15 Cumulative effects 

J17 Habitat linkages

CRE-11: Reduce the square footage of overwater structures in the estuary.STM Periodic mapping and areal 

measurements of over-water 

structures using the Estuary 

Partnership’s estuary GIS 

system.

Track permits for construction 

of shoreline structures

J21 GIS map of over-water 

structures – needs to be 

expanded to areal extent, not 

just linear extent

UR Study fundamental physical 

and biological characteristics 

to understand where removal 

would be advantageous

No existing projects in the 

estuary.

CRE-12: Reduce the effects of vessel wake 

stranding in the estuary.

STM Total stranding estimate for 

entire estuary

No existing projects.

UR Factors and stranding 

reduction study

J31 Before/after CRCIP 

addresses factors

CRE-13: Manage pikeminnow and other 

piscivorous fish, including introduced 

species, to reduce predation on salmonids.

STM Monitor trends in predator 

abundance

J38

CRE-14: Identify and implement actions to 

reduce salmonid predation by pinnipeds.

STM Pinniped predation 

monitoring

J32

AER Effectiveness of actions. 

Monitor actions under 

Section 120 of the Marine 

Mammal Protection Act

J32, J33

Section 120 monitoring

UR Magnitude of pinniped impact 

in the estuary

J32 (at BON) - expand to 

include magnitude of impact 

throughout estuary

CRE-15: Implement education and 

monitoring projects and enforce existing laws 

to reduce the introduction and spread of 

invasive plants.

STM Inventory and map invasive 

plants

No existing projects; revive 

Sytsma et al. 2004

AER Effectiveness monitoring Wahkiakum. Community 

Foundation Columbia Estuary 

Environmental Education 

Program (LCEEEP) 

identification and treatment of 

invasive weeds on Julia Butler 

Hansen Wildlife Refuge

CRE-16: Implement projects to redistribute 

part of the Caspian tern colony currently 

nesting on East Sand Island.

STM Tern monitoring J25, J34 Tern monitoring

AER Effectiveness of habitat shift J25, J34 Tern management

CRE-17: Implement projects to reduce 

double-crested cormorant habitats and 

encourage dispersal to other locations.

STM Cormorant monitoring J35

AER Methods to reduce cormorant 

abundance

J35 Cormorant management
RESEARCH, MONITORING, AND EVALUATION

6-19

Management Action Type Monitoring Need Existing Projects and 

Gaps

CRE-18: Reduce the abundance of shad in 

the estuary.

STM Monitor passage of adult 

shad at Bonneville Dam

USACE Fish counting 

AER Evaluate effectiveness of 

control methods

No existing projects.

UR Assess ecological effects of 

shad

J24 Shad impact study

CRE-19: Prevent new introductions of 

aquatic invertebrates and reduce the effects 

of existing infestations.

STM Monitor trends in abundance, 

distribution, and species 

composition of invertebrate 

invasives

No existing projects; revive 

Sytsma et al. 2004

CRE-20: Implement pesticide and fertilizer 

best management practices to reduce 

estuarine and upstream sources of nutrients 

and toxic contaminants entering the estuary.

STM WQ/toxics monitoring 

downstream of Bonneville 

Dam

No existing projects.

AER Pre- and post-project 

monitoring

No existing projects.

UR Source tracking; fish health; 

sublethal and lethal 

thresholds

No existing projects; J5; no 

existing projects.

CRE-21: Identify and reduce terrestrially and 

marine-based industrial, commercial, and 

public sources of pollutants.

STM WQ/toxics monitoring No existing projects; minimal 

WQ in J1, J2, J3, J5

AER Pre- and post-project 

monitoring

No existing projects.

UR Source tracking; fish health; 

sublethal and lethal 

threshold.

No existing projects; J5; none

CRE-22: Restore or mitigate contaminated 

sites.

STM WQ/toxics monitoring No existing projects; minimal 

WQ in J1, J2, J5

AER Pre- and post-project 

monitoring

No existing projects.

UR Source tracking; fish health; 

sublethal and lethal 

thresholds

No existing projects; J5; none

CRE-23: Implement stormwater best 

management practices in cities and towns.

STM Stormwater monitoring No existing projects; limited 

monitoring with NPDES permit 

requirements

AER Directed stormwater 

monitoring

No existing projects.

UR Source tracking; improve 

BMPs and regulations

No existing projects.
RESEARCH, MONITORING, AND EVALUATION

6-20

TABLE 6-5

Recommended New RME Projects or New Objectives in Existing Projects

These projects would fill gaps where “no existing projects” were noted in Table 6-4.

Action Type Project

CRE-2 UR Water temperature monitoring and modeling for a reservoir heating study

CRE-4 UR Flood, habitat, and constraints study(s) of the effects of “more normative” flows in the 

estuary

CRE-5 UR Measurement of sediment entrapment in mainstem Columbia River reservoirs

CRE-6 UR Demonstration study of beneficial use of dredged material to create shallow-water 

habitat

CRE-7 UR Dredging technique and operations to minimize entrainment of juvenile salmonids

CRE-8 UR Study fundamental physical and biological characteristics to understand where 

removal would be advantageous

CRE-11 UR Assessment of impacts and benefits of removing over-water structures

CRE-12 STM Total, estuary-wide stranding estimates by species of juvenile salmonid

CRE-15 STM Routine monitoring of percent cover and distribution of invasive plants by species

CRE-18 AER Effectiveness study of shad control methods

CRE-19 STM Routine monitoring of percent cover and distribution of invasive aquatic invertebrates 

by species

CRE-20, 

21, 22, 23

STM Water quality, stormwater, and toxic contaminants monitoring below Bonneville Dam

CRE-20, 

21, 22, 23

AER Pre- and post-project implementation water quality, stormwater and toxic contaminants 

monitoring below Bonneville Dam

CRE-20, 

21, 22, 23

UR Determine sources, concentrations, timing, types, and pathways of water quality and 

toxic contaminant pollutants; sublethal and lethal thresholds in fish and food web
RESEARCH, MONITORING, AND EVALUATION

6-21

TABLE 6-6

Monitoring Guidance for Estuary Recovery Plan Module RME. Adapted from Appendix C, Johnson et al. (2008).

Mngt. 

Action

Monitoring 

Need1 Sampling Design

Spatial/ 

Temporal 

Scale

Measured 

Variables

Measurement 

Protocols

Derived 

Variables

Analysis Possible 

Funding 

Entities

Possible 

Implementation & 

Coordination

CRE-1 Periodic mapping 

and areal 

measurement of 

riparian habitats 

and their 

condition

Complete 

census with 

groundtruthing

Estuary-wide 

every 5 years

Length of 

riparian habitat 

by type of habitat

GIS-linked aerial 

photography, 

Landsat imagery

and videography 

(Evans et al. 

2006)

Proportions for 

each riparian 

habitat type

Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership

CRE-2 Water 

temperature 

monitoring in the 

estuary to 

establish 

baseline

Stratified 

random 

sampling by 

reach

At 

representative 

sites 

throughout the 

estuary

essentially 

continuously

Water 

temperature

Data loggers 

(Callaway et al. 

2001)

Maximum 

daily/weekly 

maximum, 

seasonal 

averages

Trend analysis BPA/NPCC, 

USGS

BPA/NPCC Fish and 

Wildlife Program 

Hydrosystem 

temperature 

experiment

Modeling Estuary-wide Water 

temperature

Hydrodynamic 

model

Maximum 

daily/weekly 

maximum, 

seasonal 

averages

Compare/ 

contrast

BPA/NPCC, 

EPA, USGS

Ibid.

Reservoir heating 

study and 

downstream 

effects

Systematic 

sampling and 

modeling

At 

representative 

sites 

throughout the 

estuary 

essentially 

continuously

Water 

temperature

Data loggers 

(Callaway et al. 

2001)

Maximum 

daily/weekly 

maximum, 

seasonal 

averages

Compare/ 

contrast

BPA/NPCC Ibid.

CRE-3 Continuous 

monitoring of 

Columbia River 

discharge at 

Beaver Terminal 

in the estuary

Systematic 

sampling

Hourly 

sampling at 

Beaver 

Terminal

Stream 

discharge (cfs)

USGS gauging 

station

Annual 

maximum and 

minimum, 

seasonal 

averages

Trend analysis USGS USGS program
RESEARCH, MONITORING, AND EVALUATION

6-22

Mngt. 

Action

Monitoring 

Need1 Sampling Design

Spatial/ 

Temporal 

Scale

Measured 

Variables

Measurement 

Protocols

Derived 

Variables

Analysis Possible 

Funding 

Entities

Possible 

Implementation & 

Coordination

CRE-4 Continuous 

monitoring of 

Columbia River 

discharge at 

Beaver Terminal 

in the estuary 

and at Bonneville 

Dam 

Systematic 

sampling

Hourly 

sampling at 

Beaver 

Terminal and 

BON

Stream 

discharge (cfs)

USGS gauging 

station

Annual 

maximum and 

minimum, 

seasonal 

averages

Trend analysis USGS, 

USACE

USGS program (See 

CRE-3); also USACE

O&M program for 

mainstem dams

Plume turbidity 

monitoring using 

remote sensing

Complete 

census with 

groundtruthing

Plume-wide 

every 5 years

Turbidity GIS-linked aerial 

photography 

Time series of 

turbidity maps

Trend analysis BPA/NPCC, 

NOAA

BPA/NPCC Fish and 

Wildlife Program (See 

CRE-2)

Flood, habitat, 

and constraints

effects study(s)

Modeling 

effort

Estuary-wide Inundation Hydrodynamic 

model

Cumulative 

inundation 

curves

Compare/ 

contrast

BPA/NPCC, 

NOAA

USACE’s AFEP

CRE-5 Effects of 

reservoir 

sediment 

entrapment

Complete 

census

All 13 mainstem Snake 

and Columbia 

dams every 

5 years

Thickness of 

reservoir 

sediment

Acoustic bottom 

typing (multibeam 

sonar)

Sediment 

maps

Trend analysis USACE USACE’s AFEP (See 

CRE-4)

CRE-6 Evaluation of 

beneficial use of 

dredged material 

– create shallowwater habitat

Before-aftercontrolimpact (BACI)

Site-specific, 1 

year before and 

5 years after

Vegetation, 

bathymetry

Roegner et al. 

2009, bathymetry

Percent cover, 

shallow-water 

habitat

Effectiveness 

evaluation

USACE USACE’s Sediment 

Management 

Program

CRE-7 Dredge technique 

and operations 

study

Focused field 

experiments

TBD Crab entrainment Pearson et al. 

2006

Entrainment 

rates

Statistical 

analysis

USACE USACE’s Sediment 

Management 

Program (See CRE-6)

CRE-8 Periodic mapping 

and length and 

density 

measurements of 

pile structures 

Complete 

census with 

groundtruthing

Estuary-wide 

every 5 years

Length of pile 

structure

GIS-linked 

videography 

(Evans et al. 

2006)

Length and 

locations of pile 

structure

Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1)

Monitor physical 

and biological 

effects of pile 

removal

BACI Site-specific, 

1 year before 

and 3 years 

after

Water velocity, 

fish species 

composition and 

abundance

Data loggers 

(Callaway et al. 

2001), fish by 

Roegner et al. 

2009

Annual max 

and min 

velocity, fish 

species 

composition 

proportions

Effectiveness 

evaluation

USACE Ibid.
RESEARCH, MONITORING, AND EVALUATION

6-23

Mngt. 

Action

Monitoring 

Need1 Sampling Design

Spatial/ 

Temporal 

Scale

Measured 

Variables

Measurement 

Protocols

Derived 

Variables

Analysis Possible 

Funding 

Entities

Possible 

Implementation & 

Coordination

Study 

fundamental 

physical and 

biological 

characteristics to 

understand 

where removal 

would be 

advantageous 

Systematic 

sampling

Selected sites 

for all four 

seasons over 3 

years

Ibid. Ibid. Ibid. Ecological 

characterization

Ibid. Ibid.

CRE-9 Periodic mapping 

and areal 

measurement of 

off-channel 

habitat types 

Complete 

census with 

groundtruthing

Estuary-wide 

every 5 years

Length of 

riparian habitat 

by type of habitat

GIS-linked aerial 

photography

Amount of offchannel habitat Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8)

CRE-10 Periodic mapping 

and length 

measurements of 

dike structures 

Complete 

census with 

groundtruthing

Estuary-wide 

every 5 years

Length of 

dike/levee 

structures

GIS-linked aerial 

photography 

Length of 

dike/levee 

structures

Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8, 9)

Effectiveness 

monitoring 

studies of tidal 

reconnections

BACI Site-specific, 1 

year before and 

5 years after

Hydrology, 

vegetation, fish

Roegner et al. 

2009

Water surface 

elevation, 

percent cover, 

fish species 

comosition 

proportions

Statistical 

comparison

BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8, 9), 

BPA/NPCC Fish and 

Wildlife Program (See 

CRE-2, 4), USACE’s 

AFEP (See CRE-4,5)

Ecological 

importance of 

tidal 

reconnections

BACI Site-specific, 1 

year before and 

5 years after

Prey availability, 

fish diet, fish 

residence time, 

fish stock

Roegner et al. 

2009

Diet 

composition 

charts

Ecological 

characterization

BPA/NPCC, 

USACE, 

NOAA

Ibid.

CRE-11 Periodic mapping 

and areal 

measurements of 

over-water 

structures

Complete 

census with 

groundtruthing

Estuary-wide 

every 5 years

Length of overwater structuresGIS-linked aerial 

photography and 

videography

Length of overwater 

structures

Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8, 9, 10)

Track 

construction 

permits for 

shoreline 

structures

Census Estuary-wide 

annually

No. and location 

of shoreline 

structures

Contact permitting 

agencies

Map of 

structures 

planned or 

under 

construction

Trend analysis USACE USACE Regulatory 

Program
RESEARCH, MONITORING, AND EVALUATION

6-24

Mngt. 

Action

Monitoring 

Need1 Sampling Design

Spatial/ 

Temporal 

Scale

Measured 

Variables

Measurement 

Protocols

Derived 

Variables

Analysis Possible 

Funding 

Entities

Possible 

Implementation & 

Coordination

Study 

fundamental 

physical and 

biological 

characteristics

Systematic 

sampling

Selected sites 

for all four 

seasons over 3 

years

Water velocity, 

light, fish species 

composition and 

abundance

Data loggers 

(Callaway et al. 

2001), fish by 

Roegner et al.

2009

Annual max 

and min 

velocity and 

light levels, fish 

species 

composition 

proportions

Ecological 

characterization

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8, 9, 10), 

BPA/NPCC Fish and 

Wildlife Program (See 

CRE-2, 4, 10), 

USACE’s AFEP (See 

CRE-4, 5, 10)

CRE-12 Total stranding 

estimate for 

entire estuary

Stratified 

random 

sampling by 

reach

Estuary-wide 

over all four 

seasons of 1 

year

Number of 

juvenile 

salmonids 

stranded

Direct counts Extrapolation 

to total no. 

stranded; map 

of stranding 

densities

Correlation 

analysis of 

factors 

associated with 

stranding

USACE USACE’s Channel 

Improvement Project

Factors and 

stranding 

reduction study

BACI Selected sites Ibid. Ibid. Average no. 

stranded w/ 

and w/o the 

reduction 

device

Statistical 

comparison

USACE Ibid.

CRE-13 Monitor trends in 

piscivorous 

predator 

abundance

Stratified 

random 

sampling by 

reach

Estuary-wide 

annually

Catch per unit 

effort

Electrofishing Predator 

densities by 

location

Trend analysis BPA/NPCC, 

USACE, 

NOAA

USACE’s AFEP (See 

CRE-4, 5, 10, 11)

CRE-14 Pinniped 

predation 

monitoring

Systematic 

sampling

At BON during 

spring and 

summer

Number of 

pinnipeds

Observers Weekly 

average 

abundance

Trend analysis BPA/NPCC, 

USACE

USACE’s AFEP (See 

CRE-4, 5, 10, 11, 13)

Effectiveness of 

actions (monitor 

actions under 

Sec. 120)

BACI Ibid. Ibid. Ibid. Average 

abundance

Statistical 

comparison

USACE Ibid.

Magnitude of 

pinniped impact

Stratified 

random 

sampling by 

reach

Estuary-wide 

annually

Number of 

pinnipeds; 

number of 

salmon and 

steelhead 

consumed per 

predator; 

sampling rate

Observers, scat 

analysis

Estimate of the 

total number of 

salmon and 

steelhead 

consumed

Trend analysis NOAA Ibid.
RESEARCH, MONITORING, AND EVALUATION

6-25

Mngt. 

Action

Monitoring 

Need1 Sampling Design

Spatial/ 

Temporal 

Scale

Measured 

Variables

Measurement 

Protocols

Derived 

Variables

Analysis Possible 

Funding 

Entities

Possible 

Implementation & 

Coordination

CRE-15 Inventory and 

map invasive 

plants

Stratified 

random 

sampling by 

reach

Estuary-wide 

every 5 years

Species 

composition, 

abundance, 

distribution

Site surveys 

(Sytsma et al. 

2004)

Percent cover, 

maps

Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8, 9, 10,

11)

Effectiveness 

monitoring

BACI At selected 

sites over 3 

years

Ibid. Ibid. Average 

percent cover

Statistical 

comparison

Ibid. Ibid.

CRE-16 Tern monitoring Systematic 

sampling

Reach A during 

April-August 

annually

Number of birds Observers Number of 

mating pairs, 

total local 

population size

Trend analysis BPA/NPCC, 

USACE, 

NOAA, 

USFWS

USACE’s AFEP (See 

CRE-4, 5, 10, 11, 13, 

14)

Effectiveness of 

habitat shift

BACI Reach A during 

April-August for 

3-5 years

Ibid. Ibid. Ibid. Statistical 

comparison

Ibid. Ibid.

CRE-17 Double-crested 

cormorant 

monitoring

Systematic 

sampling

Reach A during 

April-August 

annually

Number of birds Observers Number of 

mating pairs, 

total local 

population size

Trend analysis BPA/NPCC, 

USACE, 

NOAA, 

USFWS

USACE’s AFEP (See 

CRE-4, 5, 10, 11, 13, 

14, 16)

Methods to 

reduce cormorant 

abundance

Site 

experiments

Reach A over 

1-3 years

Ibid. Ibid. Ibid. Compare/ 

contrast

Ibid. Ibid.

CRE-18 Monitor passage 

of adult shad at 

BON

Census Continuous 

monitoring at 

BON

Number of adult 

shad

Observers Total number 

per year, 

weekly and 

monthly 

averages

Trend analysis USACE BPA/NPCC Fish and 

Wildlife Program (See 

CRE-2, 4, 10, 11), 

USACE’s AFEP (See 

CRE-4, 5, 10, 11, 13, 

14, 16, 17)

Evaluate 

effectiveness of 

control methods

Site 

experiments

Selected sites Ibid. Seine, sonar Number of 

shad by 

treatment

Statistical 

comparison

BPA/NPCC, 

USACE, 

NOAA

Ibid.

Assess 

ecological effects 

of shad

Systematic 

sampling

Selected sites 

for summer 

over 3 years

Number of shad, 

diet, distribution, 

sex ratio

Various Total 

population 

size, fecundity, 

etc.

Ecological 

characterization

BPA/NPCC Ibid.
RESEARCH, MONITORING, AND EVALUATION

6-26

Mngt. 

Action

Monitoring 

Need1 Sampling Design

Spatial/ 

Temporal 

Scale

Measured 

Variables

Measurement 

Protocols

Derived 

Variables

Analysis Possible 

Funding 

Entities

Possible 

Implementation & 

Coordination

CRE-19 Monitor trends in 

abundance, 

distribution, and 

species 

composition of 

invasive 

invertebrates 

Stratified 

random 

sampling by 

reach

Estuary-wide 

every 5 years

Species 

composition, 

abundance, 

distribution

Site surveys 

(Sytsma et al. 

2004)

Density 

distribution 

maps

Trend analysis BPA/NPCC, 

USACE, 

NOAA

Estuary Partnership 

(See CRE-1, 8, 9, 10, 

11, 15)

CRE20, 21, 

22, 23

Water quality and 

toxics monitoring 

downstream of 

BON

Stratified 

random 

sampling by 

reach, 

directed 

source and 

load tracking

Estuary-wide 

annual

Concentrations

and loads of 

pollutants, 

contaminants by 

source and type

Various Maps of 

distribution of 

pollutant 

concentration

loads, 

pathways, and 

sources by 

type

Every 3 years -

trend analysis; 

concentration 

loads, and yields 

by tributary and 

source

EPA, NOAA, 

USGS, 

ODEQ, 

WDOE

Estuary Partnership 

(See CRE-1, 8, 9, 10, 

11, 15, 19)

Fish health, 

sublethal and 

lethal thresholds

Focused 

experiments

Laboratory Fish health/ 

mortality

Ibid. Dose response 

curves

Statistical 

analysis

Ibid. Ibid.

1

Monitoring needs are those identified in Table 6-4.
RESEARCH, MONITORING, AND EVALUATION

6-27

TABLE 6-7

Estimated Cost and Schedule for Monitoring Needs (includes ongoing projects in some cases)

Management Action Monitoring Need Unit Est. Cost Schedule

CRE-1: Protect intact riparian areas in the estuary and restore 

riparian areas that are degraded.

Periodic mapping and areal 

measurement of riparian habitats 

and their condition using aerial 

photography to inform prioritization 

efforts

Every 5 years, base flyover for data 

acquisition @ $250K and analysis for 

riparian zones @ $200K

$1M base plus 

$800K riparian 

2007-2022

CRE-2: Operate the hydrosystem to reduce the effects of 

reservoir surface heating, or conduct mitigation measures.

Water temperature monitoring in 

the estuary to establish baseline

Continuous monitoring at four sites 

(Bonneville Dam, Beaver, St. Helens, 

and Astoria) for 3 years @ $20K per 

year and one retrospective study of 

temperature

$60K (new data 

from Beaver, St. 

Helens) plus 

$50K study

2007-2009

Monitoring during the hydrosystem 

temperature experiment

Continuous monitoring at four sites 

(Bonneville Dam, Beaver, St. Helens, 

and Astoria) for 5 years @ $20K per 

year

$100K 2010-2014

Reservoir heating study and 

downstream effects

see Table 5-6 see Table 5-6 see Table 5-6

CRE-3: Protect and/or enhance estuary instream flows 

influenced by Columbia River tributary/mainstem water 

withdrawals and other water management actions in tributaries.

Continuous monitoring of 

Columbia River discharge at 

Beaver Terminal in the estuary

Data collection and dissemination are 

routine and ongoing.

$0 (already 

covered)

2007-2035

CRE-4: Adjust the timing, magnitude and frequency of 

hydrosystem flows (especially spring freshets) entering the 

estuary and plume to better reflect the natural hydrologic cycle, 

improve access to habitats, and provide better transport of 

coarse sediments and nutrients in the estuary and plume.

Continuous monitoring of 

Columbia River discharge at 

Beaver Terminal in the estuary 

and at BON dam

Plume turbidity monitoring using 

remote sensing (satellite)

See CRE-3

3 years @ $100K/year

$0 (already 

covered)

$300K

2007-2035

2009-2011

Flood, habitat, and constriant

study(s)

see Table 5-6 see Table 5-6 see Table 5-6

CRE-5: Study and mitigate the effects of entrapment of fine 

sediment in reservoirs, to improve nourishment of the estuary 

and plume.

Effects of reservoir sediment 

entrapment

see Table 5-6 see Table 5-6 see Table 5-6

CRE-6: Reduce the export of sand and gravels via dredge 

operations by using dredged materials beneficially.

Evaluate the beneficial use of 

dredged material – create shallowwater habitat

see Table 5-6 see Table 5-6 see Table 5-6

CRE-7: Reduce entrainment and habitat effects resulting from 

main- and side-channel dredge activities and ship ballast intake 

in the estuary.

Dredge technique and operations 

study

see Table 5-6 see Table 5-6 see Table 5-6
MONITORING, RESEARCH, AND EVALUATION

6-28

Management Action Monitoring Need Unit Est. Cost Schedule

CRE-8: Remove or modify pilings and pile dikes when removal 

or modification would benefit juvenile salmonids and improve 

ecosystem health. 

Periodic mapping and length and 

density measurements of pile 

structures using the Estuary 

Partnership’s estuary GIS system

One assessment every 5 years @ 

$200K per assessment

$800K 2007-2022

Monitor physical and biological 

effects of pile removal

see Table 5-6 see Table 5-6 see Table 5-6

Study fundamental physical and 

biological characteristics to 

understand where removal would 

be advantageous

One study for 3 years @ $250K/year $750K 2007-2009

CRE-9: Protect remaining high-quality off-channel habitat from 

degradation and restore degraded areas with high intrinsic 

potential for high-quality habitat.

Periodic mapping and areal 

measurement of off-channel 

habitat types to inform 

prioritization and monitoring efforts

See CRE-1 cost for base flyover, plus 

analysis of off-channel habitats every 

5 years @ $200K per assessment

$800K 2007-2022

CRE-10: Breach, lower, or relocate dikes and levees to 

establish or improve access to off-channel habitats.

Periodic mapping and length 

measurements of dike structures 

using the Estuary Partnership’s 

estuary GIS system.

See CRE-9; additional analysis @ 

$50K per assessment every 5 years

$200K 2007-2022

Effectiveness monitoring studies 

of tidal reconnections

Two case studies each in Reaches 

A-E and one study each in Reaches 

F-H with samplings in Years 0, 1, 4, 7 

@ $100K per sampling-year

$5.2M 2007-2035

Ecological importance of tidal 

reconnections

Building on the data from the 

effectiveness monitoring, one study 

for 5 years @ $400K per year

$2M 2007-2011

CRE-11: Reduce the square footage of over-water structures in 

the estuary.

Periodic mapping and areal 

measurements of over-water 

structures using the Estuary 

Partnership’s estuary GIS system.

Track permits for construction of 

shoreline structures

Assessments every 5 years @ $250K 

per assessment

Annual compilation and reporting 

@ $60K per year

$1M

$1.5M

2007-2022

2007-2031

Study fundamental physical and 

biological characteristics to 

understand where removal would 

be advantageous

One study for 3 years @ $250K/year $750K 2008-2010

CRE-12: Reduce the effects of vessel wake stranding in the 

estuary.

Total stranding estimate for entire 

estuary

One study with sampling three 

seasons per year at eight sites for 2 

years @ $1M per yr

$2M 2009-2010
MONITORING, RESEARCH, AND EVALUATION 

6-29

Management Action Monitoring Need Unit Est. Cost Schedule

Factors and stranding reduction 

study

see Table 5-6 see Table 5-6 see Table 5-6

CRE-13: Manage pikeminnow and other piscivorous fish, 

including introduced species, to reduce predation on salmonids.

Monitor trends in predator 

abundance

see Table 5-6 see Table 5-6 see Table 5-6

CRE-14: Identify and implement actions to reduce salmonid 

predation by pinnipeds.

Pinniped predation monitoring One study estuary-wide for 5 years 

@ $250K per year

$2.5M 2008-2012

Effectiveness of actions. Monitor 

actions under Sec. 120

Study every 5 years for 20 years 

@ $200K (see above)

$0 (already 

covered)

2013-2032

Magnitude of pinniped impact in 

estuary

See pinniped predation monitoring 

above

$0 (already 

covered)

2008-2012

CRE-15: Implement education and monitoring projects and 

enforce existing laws to reduce the introduction and spread of 

invasive plants.

Inventory and map invasive plants see Table 5-6 see Table 5-6 see Table 5-6

Effectiveness monitoring see Table 5-6 see Table 5-6 see Table 5-6

CRE-16: Implement projects to redistribute part of the Caspian 

tern colony currently nesting on East Sand Island.

Tern monitoring see Table 5-6 see Table 5-6 see Table 5-6

Effectiveness of habitat shift see Table 5-6 see Table 5-6 see Table 5-6

CRE-17: Implement projects to reduce double-crested 

cormorant habitats and encourage dispersal to other locations.

Cormorant monitoring see Table 5-6 see Table 5-6 see Table 5-6

Methods to reduce cormorant 

abundance

see Table 5-6 see Table 5-6 see Table 5-6

CRE-18: Reduce the abundance of shad in the estuary. Monitor passage of adult shad at 

Bonneville Dam

Data collection and dissemination are 

routine and ongoing.

$0 (already 

covered as part 

of adult fish 

counts)

2007-2035

Evaluate effectiveness of control 

methods

see Table 5-6 see Table 5-6 see Table 5-6

Assess ecological effects of shad One study for 3 years @ $300K per 

year

$900K 2008-2010

CRE-19: Prevent new introductions of aquatic invertebrates and 

reduce the effects of existing infestations.

Monitor trends in abundance, 

distribution, and species 

composition of invasive 

invertebrates 

Recurring study every 3 years for 30 

years @ $500K per year

$5M 2008-2037
MONITORING, RESEARCH, AND EVALUATION

6-30

Management Action Monitoring Need Unit Est. Cost Schedule

CRE-20: Implement pesticide and fertilizer best management 

practices to reduce estuarine and upstream sources of nutrients 

and toxic contaminants entering the estuary.

WQ/toxics monitoring downstream 

of Bonneville Dam

Annual ambient and directed 

sampling for 25 years @ $1M/year

$25M 2008-2032

Pre- and post-project monitoring Twice annual upstream + 

downstream sites @ $10K per project 

@ one project per year for 25 years

$250,000 2008-2032

Source tracking, fish health, 

sublethal and lethal thresholds

One study for 5 years @ $500K; fish 

health @ 5-6 sites per year @ $250K 

for 25 years; one study for eight 

priority toxics @ $1.5M for 3 years

$8.25M 2008-2032

CRE-21: Identify and reduce terrestrially and marine-based 

industrial, commercial, and public sources of pollutants.

WQ/toxics monitoring See CRE-20 See CRE-20 See 

CRE-20

Pre- and post-project monitoring Ibid. Ibid. Ibid.

Source tracking, fish health, 

sublethal and lethal thresholds

Ibid. Ibid. Ibid.

CRE-22: Restore or mitigate contaminated sites. WQ/toxics monitoring See CRE-20 See CRE-20 See 

CRE-20

Pre- and post-project monitoring Ibid. Ibid. Ibid.

Source tracking, fish health, 

sublethal and lethal thresholds

Ibid. Ibid. Ibid.

CRE-23: Implement stormwater best management practices in 

cities and towns.

Stormwater monitoring see Table 5-6 see Table 5-6 see Table 5-6

Directed stormwater monitoring Twice annual @ 5 cities @ $24K per 

site for 25 years

$3M 2008-2032

Source tracking, improve BMPs 

and regulations

1 study for 5 years @ $500K (see 

CRE-20); 1 study for 3 years @ 

$1.5M

$2M 2008-2013
7-1

CHAPTER 7

Perspectives on Implementation

Substantial investment is being made in the Columbia River basin to recover listed Chinook, 

coho, steelhead, and chum. How much of this investment should be made in the estuary? 

How much do the estuary and plume environments contribute to the survival of upstream 

ESUs, and is recovery of upstream ESUs possible without a healthier estuary ecosystem? If 

not, what does the information in Chapters 3, 4, and 5 tell us about which management 

actions to implement in the estuary?

Chapter 7 explores issues related to the selection of management actions to be implemented 

in the estuary and how those choices will shape future conditions for salmonids in the 

estuary and plume. It also suggests next steps in implementation and identifies 

implementation challenges.

Putting the Estuary in Context

This recovery plan module reflects current scientific understanding that the Columbia River 

estuary and plume provide habitat that wild salmonids need to complete their life cycles. 

Historically, juveniles from hundreds of distinct salmonid populations, at various life 

history stages, used the estuary for refuge and rearing as they prepared physiologically for 

life in the ocean. Over evolutionary time populations developed life history strategies in 

which juveniles from different populations staggered their use of the estuary throughout the 

year, exploiting estuarine habitats in different ways for different lengths of time. Although 

the estuary posed risks to juvenile salmonids, the diversity in life history strategies allowed 

salmon and steelhead to take maximum advantage of estuarine resources, which offered 

tremendous opportunities for refuge and growth. Unlike an upstream tributary, through the 

year the estuary provided habitat for all of the salmonid populations in the Columbia River 

basin during a critical stage in their life cycles.

Over the last 200 years the ability of the Columbia River estuary to meet the needs of salmon 

and steelhead has been seriously compromised. There is no question about the extent of 

changes in the estuary: the timing, magnitude, and duration of flows do not resemble those 

of historical flows, access to the estuary floodplain has been virtually eliminated, sediment 

transport processes that depend on flows and upstream sediment sources are radically 

different than they were historically, water quality has degraded as a result of 

contamination, temperatures are approaching and sometimes exceeding lethal limits, and 

there have been fundamental changes at the base of the estuarine food web, with associated 

alterations in inter- and intra-species relationships. A central premise of this recovery plan 

module is that although the estuary ecosystem is degraded, it can be improved, and that a 

healthier estuary ecosystem would contribute meaningfully to the basinwide recovery of 

ESA-listed salmonids. 
PERSPECTIVES ON IMPLEMENTATION

7-2

Factors That Influence Decision Making

Decisions about implementation would be easy if protecting and restoring salmonids were 

the only consideration. However, as much as we value healthy native fish runs, as a society 

we also value a stable economy, financial opportunity for individuals and businesses, public 

safety, and property rights. These values will play into decisions about which management 

actions to implement, as will the three factors used to evaluate the management actions in 

Chapter 5: cost, constraints, and potential benefits to salmonids. 

Also affecting choices about implementation is scientific uncertainty. Although fisheries 

science has matured over the last 100 years, how salmonids interact in complex ecosystems 

is not well understood; this is especially true in the estuary and plume. Yet we cannot wait 

until uncertainty has been eliminated before taking action. In the face of scientific 

uncertainty, then, decisions about implementing management actions will have to be made 

using the most current scientific information available, combined with best professional 

judgment. Historically, it has been a mix of science and policy choices that have guided 

decisions that affected the estuary; it is likely that these same forces will also determine the 

effectiveness of science-driven recovery efforts. 

Significance of Constraints to Implementation

Not a single management action identified in Table 5-1 will be easy to implement. In one 

way or another, implementation of each of the 23 actions is constrained, in some cases 

greatly. Understanding the nature and magnitude of constraints to the implementation of 

management actions is important for several reasons. First, it grounds the actions in the real 

world and tempers expectations for results. Second, it provides insights into the level of 

effort that would be required for an action to have a sizable impact on salmonid 

populations. Third and most important, it reveals that every proposed action in this 

recovery plan module has significant obstacles to implementation. 

Because it will be difficult to implement any single action fully and gain all of its potential 

benefit to salmonids, it will be important to implement a relatively large number of the 

proposed management actions. In other words, if each management action in the estuary 

has significant constraints, it may take partial implementation of all or most of the actions to 

improve the health of the estuary ecosystem to the point that the ecosystem provides the 

benefits that salmonids need to recover. 

To illustrate the relative constraints of different actions, Table 7-1 presents management 

actions by degree of constraint to implementation, in descending order.
PERSPECTIVES ON IMPLEMENTATION 

7-3

Table 7-1 

Management Actions Sorted by Degree of Constraint

# Action Degree of 

Constraint

CRE-02 Operate the hydrosystem to reduce reservoir heating. 5

CRE-03 Protect/enhance instream flows influenced by water withdrawals and other water 

management actions in tributaries. 5

CRE-04 Adjust the timing, magnitude, and frequency of hydrosystem flows. 5

CRE-05 Mitigate entrapment of fine sediment in reservoirs. 5

CRE-18 Reduce shad abundance. 5

CRE-19 Prevent aquatic invertebrate introductions. 5

CRE-14 Reduce predation by pinnipeds. 4

CRE-15 Reduce invasive plants. 4

CRE-17 Redistribute cormorants. 4

CRE-21 Identify and reduce sources of pollutants. 4

CRE-20 Implement pesticide/fertilizer BMPs. 4

CRE-9 Protect/restore high-quality off-channel habitat 3

CRE-10 Breach, lower, or relocate dikes and levees. 3

CRE-12 Reduce vessel wake stranding. 3

CRE-22 Restore or mitigate contaminated sites. 3

CRE-11 Reduce over-water structures. 3

CRE-01 Protect/restore riparian areas. 3

CRE-06 Use dredged materials beneficially. 3

CRE-16 Redistribute Caspian terns. 2

CRE-07 Reduce entrainment/habitat effects of dredging and ballast. 2

CRE-13 Manage pikeminnow and other piscivorous fish. 2

CRE-23 Implement stormwater BMPs. 2

CRE-08 Remove or modify pilings and pile dikes 2

Another useful table when considering implementation constraints is Table 5-3, which 

shows the differences in potential benefit to salmonids if implementation of actions is 

unconstrained, versus constrained, which represents a more realistic scenario. However, 

although Table 5-3 demonstrates the size of the gap between unconstrained and constrained 

implementation of actions, it does not adequately characterize the magnitude of response 

that might be expected from constrained implementation. The next section of this document 

is intended to help show the potential benefit from constrained implementation of actions.
PERSPECTIVES ON IMPLEMENTATION

7-4

Management Actions Offering the Greatest Survival Benefits

If we were to increase our investment in restoration of the Columbia River estuary by an 

order of magnitude, what would the ecological return on that investment be? Our ability to 

answer that question is limited by a lack of understanding of how much mortality actually 

occurs in the estuary and plume. Still, we do have some information about potential gains 

that reasonably could be expected as a result of such investment.

Juvenile Survival Improvement. In Chapter 5, survival improvement targets were developed 

as a tool for comparing the potential benefits of implementing different management 

actions. This planning exercise used the best available information about estuary mortality 

for wild, ESA-listed stream- and ocean-type juveniles and then established a 20 percent 

survival improvement target for the 22 management actions that would affect the survival 

of juveniles. The survival improvement targets were then allocated across the various 

management actions to help characterize where survival gains might occur. The results are 

not intended to represent a deterministically based analysis; however, they do reflect 

information in the scientific literature, especially about mortality resulting from terns, 

cormorants, ship wake stranding, contaminants, and pinnipeds. 

Tables 7-2 and 7-3 summarize the results of this planning exercise, sorting actions by their 

potential to improve survival of stream- and ocean-type juveniles, respectively, assuming 

that implementation of the actions is constrained. This ordering is simply an exercise to 

hypothesize where survival improvements equal to 20 percent of the number of juveniles 

exiting the estuary and plume might be expected for stream-type and ocean-type juveniles. 

For stream-type salmonids, the following observations can be made from Table 7-2:

Approximately 60 percent of the survival improvements are assigned to the top five 

actions, which include adjusting flow, protecting or restoring off-channel habitat, 

restoring or mitigating contaminated sites, and managing birds that prey on salmonids. 

Approximately 30 percent of the survival improvements are assigned to establishing or 

improving access to off-channel habitat, protecting and restoring riparian areas, 

reducing sources of pollutants, managing piscivorous fish, and removing or modifying 

pilings and pile dikes. 

Approximately 10 percent of the survival improvements are assigned across the 

remaining actions, with varying degrees of improvements. 

For ocean-type salmonids, the following observations can be made from Table 7-3:

Approximately 65 percent of the survival improvements are assigned to the top five 

actions, which include adjusting flows, establishing or improving access to off-channel 

habitat, protecting or restoring off-channel habitat, and addressing issues of 

contamination. 

Approximately 30 percent of the survival improvements are assigned to protecting and 

restoring riparian areas, reducing reservoir heating, removing or modifying pilings and 

pile dikes, reducing vessel wake stranding, using dredged materials beneficially, 
PERSPECTIVES ON IMPLEMENTATION 

7-5

managing piscivorous fish, and implementing pesticide, fertilizer, and stormwater 

BMPs. 

Approximately 5 percent of the survival improvements are assigned across the 

remaining actions, with varying degrees of improvements. 

Table 7-2 

Management Actions Sorted by Benefit to Stream-type Juveniles

# Action

Survival Target 

(Stream Types)

Percentage of 

Target 

Improvements

CRE-16 Redistribute Caspian terns. 350,000

~60%

CRE-17 Redistribute cormorants. 250,000

CRE-09 Protect/restore high-quality off-channel habitat. 150,000

CRE-22 Restore or mitigate contaminated sites. 142,000

CRE-04 Adjust the timing, magnitude, and frequency of 

hydrosystem flows. 125,000

CRE-13 Manage pikeminnow and other piscivorous fish. 122,000

~30%

CRE-10 Breach, lower, or relocate dikes and levees. 100,000

CRE-01 Protect/restore riparian areas. 100,000

CRE-08 Remove or modify pilings and pile dikes 100,000

CRE-21 Identify and reduce sources of pollutants. 72,000

CRE-20 Implement pesticide/fertilizer BMPs. 42,000

~10%

CRE-23 Implement stormwater BMPs. 30,000

CRE-02 Operate the hydrosystem to reduce reservoir 

heating. 20,000

CRE-03

Protect/enhance instream flows influenced by water 

withdrawals and other water management actions in 

tributaries. 20,000

CRE-06 Use dredged materials beneficially. 15,000

CRE-15 Reduce invasive plants. 15,000

CRE-07

Reduce entrainment/habitat effects of dredging and 

ballast. 10,000

CRE-05 Mitigate entrapment of fine sediment in reservoirs. 5,000

CRE-18 Reduce shad abundance. 5,000

CRE-11 Reduce over-water structures. 3,000

CRE-19 Prevent aquatic invertebrate introductions. 2,000

CRE-12 Reduce vessel wake stranding. 2,000

Total: 1.68 million
PERSPECTIVES ON IMPLEMENTATION

7-6

TABLE 7-3

Management Actions Sorted by Benefit to Ocean-type Juveniles

# Action Survival Target 

(Ocean Types)

Percentage of 

Target 

Improvements

CRE-10 Breach, lower, or relocate dikes and levees. 450,000

~65%

CRE-09 Protect/restore high-quality off-channel habitat. 400,000

CRE-22 Restore or mitigate contaminated sites. 300,000

CRE-21 Identify and reduce sources of pollutants. 275,000

CRE-04

Adjust the timing, magnitude, and frequency of hydrosystem 

flows. 225,000

CRE-01 Protect/restore riparian areas. 150,000

~30%

CRE-08 Remove or modify pilings and pile dikes 150,000

CRE-13 Manage pikeminnow and other piscivorous fish. 140,000

CRE-02 Operate the hydrosystem to reduce reservoir heating. 90,000

CRE-23 Implement stormwater BMPs. 65,000

CRE-12 Reduce vessel wake stranding. 55,000

CRE-20 Implement pesticide/fertilizer BMPs. 50,000

CRE-06 Use dredged materials beneficially 50,000

CRE-03 Protect/enhance instream flows influenced by water withdrawals 

and other water management actions in tributaries. 25,000

~5%

CRE-11 Reduce over-water structures. 25,000

CRE-15 Reduce invasive plants. 20,000

CRE-07 Reduce entrainment/habitat effects of dredging and ballast. 8,000

CRE-19 Prevent aquatic invertebrate introductions. 8,000

CRE-05 Mitigate entrapment of fine sediment in reservoirs. 5,000

CRE-18 Reduce shad abundance. 5,000

CRE-16 Redistribute Caspian terns. 2,000

CRE-17 Redistribute cormorants. 2,000

Total: 2.5 million
PERSPECTIVES ON IMPLEMENTATION 

7-7

While many of the actions are highly constrained, the planning exercise summarized in 

Tables 7-2 and 7-3 assumes that, even with incremental changes associated with constrained 

implementation, certain actions could yield significant results, especially when coupled 

with complementary actions. For example, ocean-type juveniles rely heavily on off-channel 

habitats for food sources and rearing opportunities. The two primary actions intended to 

improve access to off-channel habitats are CRE-10, “Breach, lower, or relocate dikes and 

levees,” and CRE-4, “Adjust the timing, magnitude, and frequency of hydrosystem flows.” 

Implementation of both of these actions is highly constrained, yet they could have 

synergistic effects and their joint implementation—even if only partial—could result in 

significant survival improvements for ocean-type salmonids. In contrast, if only one of these 

actions were implemented (or, worse yet, neither), other actions would need to be 

implemented as fully as possible in an attempt to compensate for the foregone opportunity 

to address one of the main factors limiting juvenile salmonid performance in the estuary. 

Adult Survival Improvement. Because CRE-14, “Reduce predation by pinnipeds,” is the only 

action that directly addresses the adult life history stage of salmonids, this action is treated 

separately and is not included in Tables 7-2 and 7-3. In 2010, which saw the largest spring 

Chinook and steelhead runs from 2002 to 2010, pinniped predation on spring Chinook and 

steelhead (both of which are stream types) at Bonneville Dam was estimated to be 

2.2 percent. This equates to 6,081 spring Chinook and steelhead out of a run size of 267,194 

fish (U.S. Army Corps of Engineers 2010). Projects to reduce pinniped predation have had 

limited success, and more stringent management techniques are constrained by protections 

afforded by the Marine Mammal Protection Act. Although the act does provide for lethal 

control, the process for implementing that provision is challenging. In 2008, NMFS granted 

authority under Section 120 of the Marine Mammal Protection Act to the states of Oregon, 

Washington, and Idaho to intentionally take, by lethal methods, individually identifiable 

California sea lions that prey on Pacific salmon and steelhead at Bonneville Dam, but the 

effectiveness of this approach is unknown. Given these constraints, PC Trask & Associates, 

Inc., in consultation with NMFS Northwest Regional Office staff, estimated that CRE-14 

might result in a 17 percent reduction in pinniped-related mortality of adults at Bonneville 

Dam each year (approximately 1,034 fish annually as applied to 2010 run returns).

Costs for Constrained Implementation of Management Actions

As discussed in Chapter 5, estimating the cost of the management actions in this module is 

inherently difficult and involves significant uncertainties. This is partly because in many 

cases, the constraints to implementation have not yet been explored in enough detail to be 

able to determine what is and is not possible, and key scientific and technical questions 

about the estuary have not yet been answered. In Chapter 5, Table 5-6 established cost 

estimates for constrained implementation of actions by assuming an optimistic view—that 

constraints can be reduced through focused effort and that positive changes in the estuary 

can be made. A more pessimistic view would likely yield a significantly lower cost estimate, 

with correspondingly smaller survival improvements. Costs were assigned at the project 

scale to help identify possible components to actions, with the expectation that future 

refinements would yield a more sophisticated estimate. Finally, project costs were estimated 

over a 25-year time horizon. 
PERSPECTIVES ON IMPLEMENTATION

7-8

Table 7-4 organizes management actions by total estimated cost (from Table 5-6). The 

following observations can be made: 

Costs for the top six actions total $332 million, or about 63 percent of the entire budget. 

The actions include restoring contaminated sites, modifying flows, reducing sources of 

pollutants, establishing or improving access to off-channel habitats, protecting or 

restoring off-channel habitats, and protecting and restoring riparian areas. 

Costs for the next six actions on the list equal $108 million, or about 20 percent of the 

budget. This group of actions consists of reducing reservoir-related temperature 

changes, implementing stormwater BMPs, addressing vessel wake stranding, removing 

or modifying pilings and pile dikes, and managing fish and pinnipeds that prey on 

salmonids. 

The final 11 actions on the list equal $88 million, or about 17 percent of the budget.

TABLE 7-4

Management Actions Sorted by Estimated Cost

# Action Cost of 

Action

Cost per 

Group of 

Actions

CRE-10 Breach, lower, or relocate dikes and levees. $75 million

~$332 million,

or 63% of 

total

CRE-09 Protect/restore high-quality off-channel habitat. $68 million

CRE-22 Restore or mitigate contaminated sites. $60.5 million

CRE-21 Identify and reduce sources of pollutants. $46 million

CRE-04 Adjust the timing, magnitude, and frequency of hydrosystem flows. $44.5 million

CRE-01 Protect/restore riparian areas. $38 million

CRE-08 Remove or modify pilings and pile dikes $27.25 million

~$108 million,

or 20% of 

total

CRE-02 Operate the hydrosystem to reduce reservoir heating. $20 million

CRE-23 Implement stormwater BMPs. $19.5 million

CRE-14 Reduce predation by pinnipeds. $15 million

CRE-13 Manage pikeminnow and other piscivorous fish. $13 million

CRE-12 Reduce vessel wake stranding. $13 million

CRE-15 Reduce invasive plants. $12.5 million

~$88 million,

or 17% of 

total

CRE-17 Redistribute cormorants. $10.5 million

CRE-20 Implement pesticide/fertilizer BMPs. $12.5 million

CRE-03 Protect/enhance instream flows influenced by water withdrawals 

and other water management actions in tributaries. $10 million

CRE-16 Redistribute Caspian terns. $10 million

CRE-05 Mitigate entrapment of fine sediment in reservoirs. $8 million

CRE-06 Use dredged materials beneficially. $6 million

CRE-11 Reduce over-water structures. $5.8 million

CRE-18 Reduce shad abundance. $5.5 million

CRE-07 Reduce entrainment/habitat effects of dredging and ballast. $4.5 million

CRE-19 Prevent aquatic invertebrate introductions. $3 million

Total: $528.05 

million
PERSPECTIVES ON IMPLEMENTATION 

7-9

As also discussed in Chapter 5, there is significant uncertainty in these cost estimates 

because of the ambiguity about the degree to which constraints to implementation can be 

overcome, the level of effort that would be required to achieve a measurable result, and how 

new information could change current understanding about the cost and effectiveness of 

management actions. However, it is assumed that if restoring the ecosystem of the 

Columbia River estuary were established as a goal, this would require financial investment 

on a par with that for other major ecosystem recovery efforts around the United States. 

Cost-Effectiveness of Management Actions

Cost-effectiveness is an important consideration when attempting to achieve large goals 

with limited resources, and the more limited the resources with respect to the goal, the more 

important it is that the maximum benefit be obtained from each expenditure. In the case of 

the Columbia River estuary, improving conditions for salmonids is likely to be an expensive

and long-term effort—one that will require careful consideration of the survival benefits and 

costs of possible actions.

The linkage between the survival benefits and costs in this recovery plan module is difficult 

to characterize accurately because of the margin of error that, at this point, exists in both the 

estimated costs and the survival targets. Because the survival improvement targets were 

allocated across the set of actions as a planning exercise rather than as results of a scientific 

analysis, it is the allocation that is most important, not the target numbers themselves. In the 

case of costs, estimates were made assuming that constraints to implementation of actions 

could be partially overcome; this assumption served as a way to explore the degree of 

constraints and the level of effort that would be required to bring about significant benefits 

to salmonids. The resulting costs should be viewed as preliminary numbers useful in 

starting critical discussions about decisions that will shape the future of the estuary. 

Understanding that, as outlined above, there are limitations governing the survival 

improvement targets and cost estimates, these sets of numbers can be compared to provide 

clues about which management actions might be the most cost-effective. Table 7-5 makes 

such a comparison, using cost information from Table 7-4 and target survival improvements 

from Table 7-3 to estimate the cost-effectiveness of each action, expressed as a cost/survival 

index. The actions are sorted in ascending order to show the most cost-effective actions first. 

Table 7-5 is intended as a general indication of cost-effectiveness to help frame the 

discussion about implementing management actions. Also, some actions were assigned very 

conservative survival improvement numbers because of the level of uncertainty about 

underlying ecological processes. This is the case with several actions related to the food web 

because the connection between food web changes and effects on juveniles is not fully 

defined. As a result, the cost-effectiveness ratings of these actions appear high.
PERSPECTIVES ON IMPLEMENTATION

7-10

TABLE 7-5

Management Actions Sorted by Cost/Survival Index

# Action

Survival 

(Ocean 

Types)

Survival 

(Stream 

Types)

Total 

Survival

Cost of 

Action

Cost/ 

Survival 

Index

CRE-16 Redistribute Caspian terns. 2,000 350,000 352,000 $10 million 28

CRE-17 Redistribute cormorants. 2,000 250,000 252,000 $10.5 million 42

CRE-13 Manage pikeminnow and other 

piscivorous fish. 140,000 122,000 262,000 $13 million 50

CRE-06 Use dredged materials beneficially. 50,000 15,000 65,000 $6 million 92

CRE-08 Remove or modify pilings and pile 

dikes 150,000 100,000 250,000 $27.25 million 109

CRE-09 Protect/restore high-quality offchannel habitat. 400,000 150,000 550,000 $68 million 124

CRE-04 Adjust the timing, magnitude, and 

frequency of hydrosystem flows. 225,000 125,000 350,000 $44.5 million 127

CRE-21 Identify and reduce sources of 

pollutants. 275,000 72,000 347,000 $46 million 133

CRE-20 Implement pesticide/fertilizer 

BMPs. 50,000 42,000 92,000 $12.5 million 136

CRE-10 Breach, lower, or relocate dikes 

and levees. 450,000 100,000 550,000 $75 million 136

CRE-22 Restore or mitigate contaminated 

sites. 300,000 142,000 442,000 $60.5 million 137

CRE-01 Protect/restore riparian areas. 150,000 100,000 250,000 $38 million 152

CRE-02 Operate the hydrosystem to reduce 

reservoir heating. 90,000 20,000 110,000 $20 million 182

CRE-23 Implement stormwater BMPs. 65,000 30,000 95,000 $19.5 million 205

CRE-11 Reduce over-water structures. 25,000 3,000 28,000 $5.8 million 207

CRE-03

Protect/enhance instream flows 

influenced by water withdrawals 

and other water management 

actions in tributaries.

25,000 20,000 45,000 $10 million 222

CRE-12 Reduce vessel wake stranding. 55,000 2,000 57,000 $13 million 228

CRE-07 Reduce entrainment/habitat effects 

of dredging and ballast. 8,000 10,000 18,000 $4.5 million 250

CRE-19 Prevent aquatic invertebrate 

introductions. 8,000 2,000 10,000 $3 million 300

CRE-15 Reduce invasive plants. 20,000 15,000 35,000 $12.5 million 357

CRE-18 Reduce shad abundance. 5,000 5,000 10,000 $5.5 million 550

CRE-05 Mitigate entrapment of fine 

sediment in reservoirs. 5,000 5,000 10,000 $8 million 800
PERSPECTIVES ON IMPLEMENTATION 

7-11

The following observations can be made from Table 7-5:

The median of all assigned cost/survival index numbers is 144. (The median is the 

middle number of a group of numbers, with half the numbers having values greater 

than the median and half having values less than the median). 

Some of the actions that appeared most cost-prohibitive in Table 7-4, such as 

establishing or improving access to off-channel habitat (CRE-10), adjusting flows (CRE04), and restoring or mitigating contaminated sites (CRE-22), emerge as cost-effective 

when viewed in the context of the survival improvements they could bring about. All 

three of these actions have a cost/survival index value that is less than the median and 

that puts them in the top—or more cost-effective—half of Table 7-5.

Several actions, including redistributing terns (CRE-16), redistributing cormorants 

(CRE-17), and managing piscivorous fish such as pikeminnow (CRE-13), appear to be 

very cost-effective. 

In this planning exercise, the total survival improvement of actions listed above the median 

is 3.5 million juveniles (2.0 million ocean type and 1.5 million stream type), or about 

17 percent of the total number of juveniles currently thought to be exiting the estuary. 

Improving Ecosystem Health

The Columbia River estuary and plume ecosystems are degraded compared to historical 

conditions. One hypothesis of this recovery plan module is that if the estuary and plume 

remain in their degraded state, recovery of all 13 ESUs may not be possible. The remainder 

of this section is intended to help characterize choices that will ultimately govern the health 

of the estuarine ecosystem in the Columbia River. 

Is there really a problem for salmonids in the estuary? Sources such as Salmon at River’s 

End (Bottom et al. 2005), and emerging micro-acoustic tagging studies make clear that the 

mortality rate in the estuary is very high and almost certainly approaches 50 percent for 

some ESUs. This alone argues for discarding the old paradigm of the estuary as primarily a 

transportation corridor for salmonids on their journey to the ocean. Stream- and ocean-type 

salmonids clearly rely on estuary and plume habitats for crucial rearing and refuge 

opportunities during one of the stages in their life cycles. Chapters 3 and 4 of this estuary 

recovery module describe the mechanisms by which a degraded estuarine ecosystem puts 

juvenile salmonids at risk.

Is ecosystem restoration necessary in the estuary, or can we surgically reduce specific 

threats to improve salmonid survival? Ecosystem health in the estuary and plume is the 

cumulative result of many stressors that originate within the estuary and also outside of the 

estuary. The level of constraint observed in each of the management actions identified in 

this estuary recovery module is high, and it is extremely unlikely that one or more actions 

could be implemented to the degree that they would essentially eliminate a threat to 

salmonids. Thus each management action should be implemented to the greatest degree 

practical, unless it is proven that to do so would seriously undermine public safety, the 

economy, or property rights. 
PERSPECTIVES ON IMPLEMENTATION

7-12

What suite of actions is most important to implement for ocean-type salmonids? There is 

no single correct answer to this question. In the long term, ecosystem restoration will 

provide the most stable, self-supporting conditions for salmonids and other native species. 

Ocean-type juvenile salmonids rear longer in the estuary than stream types do and therefore 

would benefit the most from improved ecosystem health. 

The analysis and planning exercises in this recovery plan module suggest that the following 

actions are most important for ocean-type salmonids:

CRE-01: Protect/restore riparian areas.

CRE-02: Operate the hydrosystem to reduce reservoir heating.

CRE-04: Adjust the timing, magnitude, and frequency of hydrosystem flows.

CRE-08: Remove or modify pilings and pile dikes.

CRE-09: Protect/restore high-quality off-channel habitat.

CRE-10: Breach, lower, or relocate dikes and levees.

CRE-13: Manage pikeminnow and other piscivorous fish.

CRE-21: Identify and reduce sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.

Implementing this suite of actions would cost approximately $392.3 million and would be 

expected to yield survival improvements of roughly 2.2 million wild, ESA-listed ocean-type 

juveniles, or 88 percent of the survival target for ocean-type salmonids. In other words, for 

ocean-type juveniles, 88 percent of the gain to be had from the management actions could be 

achieved by implementing these nine actions.

What suite of actions is most important to implement for stream-type salmonids? Streamtype salmonids prefer deeper waters with higher velocities than ocean-types do. They also 

reside in the estuary for shorter periods of time, but they tend to use the plume more 

extensively than do ocean-type salmonids. Stream-type juveniles are thought to actively 

feed in the estuary; information indicates that stream types travel out of the channel to 

forage and may encounter predators such as the northern pikeminnow (Casillas 2006). For 

stream types, it is very important to reduce Caspian tern and double-crested cormorant 

predation. In addition, predation by pinnipeds on adult spring Chinook and winter 

steelhead is a significant threat. 

The analysis and planning exercises in this recovery plan module suggest that the following 

actions are most important for stream-type salmonids:

CRE-01: Protect/restore riparian areas.

CRE-04: Adjust the timing, magnitude, and frequency of hydrosystem flows. 

CRE-08: Remove or modify pilings and pile dikes.

CRE-09: Protect/restore high-quality off-channel habitat.

CRE-10: Breach, lower, or relocate dikes and levees.

CRE-13: Manage pikeminnow and other piscivorous fish.

CRE-14: Reduce predation by pinnipeds.

CRE-16: Redistribute Caspian terns.

CRE-17: Redistribute cormorants.

CRE-21: Identify and reduce sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.
PERSPECTIVES ON IMPLEMENTATION 

7-13

Implementing this suite of actions would cost approximately $407.8 million and would be 

expected to yield survival improvements of roughly 5,000 stream-type adults (ESA-listed 

and non-listed adults) and 1.51 million wild, ESA-listed stream-type juveniles, or 90 percent 

of the survival target for stream-type juveniles. In other words, for stream-type juveniles, 

90 percent of the gain to be had from the management actions could be achieved by 

implementing these 11 actions.

How cost-effective are the top actions for ocean- and stream-type salmonids? Of the top 

11 priority actions for stream- and ocean-type salmonids, nine are listed at or above the 

median cost/survival index.

What would be gained by implementing actions that benefit both ocean- and stream-type 

salmonids? The lists of priority actions identified above for ocean- and stream-type 

salmonids contain eight actions that are predicted to benefit both types of salmonids. These 

actions are as follows:

CRE-01: Protect/restore riparian areas.

CRE-04: Adjust the timing, magnitude, and frequency of hydrosystem flows.

CRE-08: Remove or modify pilings and pile dikes.

CRE-09: Protect/restore remaining high-quality off-channel habitat.

CRE-10: Breach, lower, or relocate dikes and levees.

CRE-13: Manage pikeminnow and other piscivorous fish.

CRE-21: Identify and reduce sources of pollutants.

CRE-22: Restore or mitigate contaminated sites.

Implementing this set of actions would cost approximately $372.25 million and would be 

expected to yield survival improvements of roughly 3 million wild, ESA-listed juvenile 

salmonids (ocean- and stream-types combined). Although the majority of these would be 

ocean types, there is an argument to be made for favoring actions that would benefit both 

salmonid types—namely, that implementing such actions would be likely to provide 

benefits across the spectrum of life history strategies that juvenile salmonids of both types 

employ in the estuary. Many of the actions that benefit stream-type salmonids would also 

benefit ocean types displaying less dominant life history strategies, while many actions 

benefiting ocean-type salmonids would also benefit stream types displaying less dominant 

life history strategies. Actions that benefit both ocean and stream types, then, presumably 

would affect a wide range of less dominant life history strategies and thus would help 

preserve the diversity that contributes to salmonids’ ability to persist in the face of changing 

environmental conditions. 

However, this is not to suggest implementation only of those actions that would benefit 

both ocean- and stream-type juveniles because there are limitations to this approach. For 

instance, avian and pinniped predation actions, which would primarily benefit stream 

types, are cost-effective and critical to improving the survival of stream-type salmonids. 

Will management actions have synergistic effects? Many of the management actions could 

have far-reaching effects if they were implemented together, either because they address 

multiple interrelated threats, such as flow regulation and impaired sediment transport, or 

because their effects could amplify the benefits of other, complementary management 

actions. An example would be the two actions of improving flows and establishing access to 

off-channel habitat by breaching dikes or levees. Although each action by itself would 
PERSPECTIVES ON IMPLEMENTATION

7-14

increase salmonid access to off-channel habitat, implementing both actions has the potential 

to offer exponentially greater access, as well as contribute macrodetrital inputs to the food 

web and offer other ecosystem benefits. Although such benefits are difficult to quantify, the 

potential for synergistic effects of complementary actions is real and should be taken into 

consideration when management actions are selected. 

The U.S. Army Corps of Engineers currently is studying the cumulative effects of various 

combinations of restoration activities in the estuary; results of the study are expected to 

provide valuable data on the potential synergistic effects of the management actions 

presented in the estuary recovery plan module. Meanwhile, several actions have the 

potential to be complementary in their effects, at the very least, and possibly to offer 

significant synergistic benefits. While it is not possible to identify all such actions, examples 

include using dredged materials to reduce vessel wake stranding (CRE-6 and CRE-12) or 

improving access to off-channel habitats by breaching dikes and adjusting flows (CRE-10 

and CRE-4). At the same time, management actions need to be sequenced to avoid possible 

negative synergistic effects, such as by restoring contaminated sites (CRE-22) in off-channel 

habitat before restoring access to that habitat through dike breaching and flow 

modifications (CRE-10 and CRE-4). Considering the possible complementary, cumulative, 

or synergistic effects of management actions and sequencing actions for maximum benefit 

will be important aspects of implementing the estuary recovery plan module.

What about the lower ranking actions? In many ways, the lower ranking actions are the 

most difficult to characterize in terms of survival improvements and costs. Low ratings may 

be due more to a lack of scientific information than a lack of effectiveness. For example, 

basic changes to the food web in the estuary as a result of increased phytoplankton 

production or the introduction of aquatic invertebrates may have profound effects on the 

estuary, but the degree of impact is unknown. These threats must be more fully understood 

if their contribution to overall ecosystem health is to be determined with accuracy. 

What planning tasks remain? The process of developing this estuary recovery plan module 

pointed to several areas where recovery planning for the estuary could be refined. 

Additional scientific information about juvenile mortality in the estuary would clarify the 

ecological significance of the estuary relative to tributaries and the middle and upper 

mainstem Columbia River. A finer scale analysis of limiting factors, threats, and the benefits 

of management actions would aid in prioritizing actions and focusing them in the 

geographical areas where they would be most beneficial. Testing the assumptions 

underlying the allocation of benefits across management actions would increase the value of 

survival improvement targets as a planning tool, as would further evaluation of the 

constraints to implementation of the management actions. Lastly, understanding the 

potential cumulative or synergistic effects of management actions could lead to 

implementation decisions that would enhance the benefits of actions. Obtaining more 

information about these topics—mortality in the estuary, biological effects at a finer level, 

potential benefits of management actions, and synergistic effects—could represent the next 

level of planning for salmon recovery in the estuary. 
PERSPECTIVES ON IMPLEMENTATION 

7-15

Implementation Issues

Implementation of the 23 actions in the module will require the efforts of a variety of 

Federal, state, and local agencies, organizations, private enterprises, and citizens. (Some 

potential implementers have been identified in Table 5-6.) While many of these entities have 

already been working to identify, prioritize, and implement salmon and steelhead recovery 

actions, effective implementation of all module actions will require additional coordination. 

Goals of coordination include using existing processes, programs, and forums efficiently; 

ensuring the appropriate scale, scope, and sequencing of projects; coordinating funding; 

tracking and reporting on implementation progress; coordinating monitoring efforts; and 

providing data management. In addition, implementing the module will require further 

evaluation of the constraints associated with the 23 actions as well as consideration of 

potential cumulative and synergistic effects. Also, implementers of module actions will need 

to remain abreast of current scientific information and ensure that it is continually 

incorporated into implementation decisions. Although some elements of these larger 

processes are in place, additional organizational capacity is necessary if these needs are to 

be adequately addressed.

Table 5-6 includes a rudimentary schedule for implementing each of the 23 management 

actions described in Chapter 5, but this schedule will need to be refined as the 

considerations mentioned above are addressed. The first step in coordinated 

implementation of the module will be a conversation among all relevant entities and 

stakeholders to discuss near-term implementation priorities, with a goal of developing a 5-

year implementation plan that provides specificity and certainty regarding near-term 

actions and that identifies lead entities for implementation of specific actions or projects. 

Given the complexities involved in implementing the full suite of module actions, this 

conversation also will be an opportunity to explore options for and recommend an 

organizational structure for coordinating and overseeing implementation of the module. 

The Lower Columbia River Estuary Partnership, a National Estuary Program established to 

bring about collaboration, would be an appropriate convener of this discussion. 

Education and outreach are important aspects of module implementation. Threats to 

salmonids in the estuary are likely to continue unabated unless resource users in the 

Columbia River basin make different choices about consumption and development—

choices that may be socially and politically challenging. In the face of social and political 

obstacles, education is one way of garnering support for implementation of the 

management actions; in fact, education about stewardship and the ecosystem benefits that 

implementation would provide is an essential component of the management actions in the 

module; to the extent possible, these education efforts should be coordinated to create 

efficiencies.

Relationship of the FCRPS BiOp to the Estuary Module

Drafts of this module were available during the Federal Columbia River Power System 

(FCRPS) Biological Opinion (BiOp) remand collaborative process, which led to the 2008-

2018 FCRPS Biological Opinion and Supplemental Comprehensive Analysis (National 

Marine Fisheries Service 2008a and 2008b). Among the provisions of the 2008 FCRPS 

Biological Opinion (2008 BiOp) were requirements for the Federal action agencies to 
PERSPECTIVES ON IMPLEMENTATION

7-16

implement habitat improvement and predation control actions in the estuary. Estimates of 

the survival benefits that would be gained from those actions were included in the 2008 

BiOp, and those survival estimates were derived from the allocation of survival 

improvements among actions in this module. 

In February 2010, NMFS issued the 2010 Supplemental BiOp for the FCRPS (National 

Marine Fisheries Service 2010), which integrated elements from the 2008 BiOp and Adaptive 

Management Implementation Plan (AMIP). The AMIP included accelerated and enhanced 

actions to protect Columbia Basin salmon and steelhead, including (1) commitments to 

additional estuary actions under an agreement with the state of Washington, and (2) efforts 

to control native predators and invasive species. The AMIP also included enhanced research 

and monitoring and incorporated specific biological triggers for contingencies linked to 

unexpected declines in the abundance of listed fish. 

The 2010 Supplemental BiOp retained the estimates of survival improvements from estuary 

habitat and predation control actions that had been incorporated into the 2008 BiOp and 

that were based on a draft version of this estuary module. The 2010 Supplemental BiOp also 

summarized and assessed relevant new information that had become available since the 

2008 BiOp was issued, including information on climate change, juvenile salmonid use of 

the estuary and plume, predation, toxics, and ecological interactions between hatchery- and 

natural-origin fish. The new information summarized in the 2010 BiOp will be useful in 

informing implementation decisions regarding actions in the module. 

Actions in the 2008 BiOp and its 2010 Supplement that relate to estuarine habitat, predation, 

and flow will contribute to implementation of actions in this module. The module, however, 

identifies habitat, predation, and flow actions that are larger in scope than the actions that 

will be implemented under the 2008 BiOp and its 2010 Supplement. NMFS projects that the 

2008 BiOp actions related to estuarine habitat, flow, and predation will yield only a portion 

of the total survival improvements that the estuary module hypothesizes are possible for 

actions in those categories. The intent of the estuary module was to lay out the full suite of 

limiting factors and threats affecting the estuary; to identify actions or assessments needed 

to address—or inform the potential to address—those limiting factors and threats; and to 

provide a basis for future discussions and societal decisions about recovery efforts in the 

Columbia River estuary.

Preparation for Decision Making

Chapter 7 is intended to help organize a much-needed conversation about recovery efforts 

in the estuary, plume, and other ecosystems that salmonids depend on to complete their life 

cycles. While there are many decisions to be made, perhaps the most important is what our 

level of effort and commitment will be to improving conditions in the estuary. This boils 

down to deciding how much we are willing to do to recover salmon and steelhead in the 

Columbia River basin and how comfortable we are with the sacrifices that will be necessary.

The planning exercises in Chapters 5 and 7 were based on the best available science 

pertaining to limiting factors and threats. However, although science can help inform the 

key analyses in these chapters (the identification of management actions, constraints 

evaluation, survival improvement targets, and cost estimates), it cannot tell us which 

management actions to implement. This is so partly because of the gaps in our 

understanding of the physical and biological world of the estuary but also because other 
PERSPECTIVES ON IMPLEMENTATION 

7-17

decision-making processes come into play when we make choices about the future and what 

we most value. Ultimately, the degree to which the estuary module is implemented will be 

determined by the social and political will of the region, and what current and future 

residents of the basin are willing to pay for—or do without—in order to return salmon and 

steelhead to viable levels.

Perhaps the single most important conclusion that can be made about the prioritization of 

management actions is that threats remain threats to salmonids because tough choices have 

yet to be made—choices that are difficult because of the myriad conflicting goals of the 

various public, private, individual, and organizational interests within the Columbia River 

basin. The variety and extent of those interests are reflected in the high degree of constraint 

for each of the 23 management actions identified in the recovery plan module. The takehome message from this is that the estuary and plume are crucial to ocean- and stream-type 

salmonids and that achieving a meaningful boost in survival from these ecosystems will 

require a major investment and implementation of all 23 management actions, to the extent 

possible.

8-1

CHAPTER 8

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APPENDIX A 

Selected Threats to Salmonids by Reach 
APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 

APPENDIX A 
APPENDIX B

Development of Survival Improvement Targets
DEVELOPMENT OF SURVIVAL IMPROVEMENT TARGETS

B-2
B-1

APPENDIX B

Development of Survival Improvement Targets

The survival improvement targets in Table 5-5 are a planning tool intended to help initiate a 

comprehensive discussion about salmonid mortality in the estuary and plume. This tool is 

an important first step in setting recovery targets for salmonids in the estuary and also for 

the Columbia River basin. PC Trask & Associates, Inc., developed the survival improvement 

targets because, in many cases, estimates of mortality resulting from individual limiting 

factors and of the effectiveness of management actions in reducing threats and limiting 

factors do not exist. On the other hand, there are reliable estimates of mortality resulting 

from several of the predators, ship wake stranding, and toxic contamination, and emerging 

acoustic wire tagging studies are helping to estimate the extent of mortality that juvenile 

salmonids experience during residency in the estuary. 

PC Trask & Associates, Inc., took the following steps to develop the survival improvement 

targets:

1. Determined the abundance of wild, ESA-listed ocean- and stream-type juveniles 

entering the estuary using Ferguson (2006b), which estimated 25 million ocean-type 

juveniles and 14.3 million stream-type juveniles for 2006. 

2. Assumed a 50 percent overall juvenile mortality rate for ocean-type salmonids in the 

estuary and a 40 percent mortality rate for stream-type juveniles. PC Trask & Associates, 

Inc., reached the 50 percent mortality estimate for ocean type juveniles by taking the 

35 percent rate from 2005 micro-acoustic tagging results (Ferguson 2006b) and adding an 

additional 15 percent to account for smaller ocean-type juveniles not tracked by the 

study. PC Trask & Associates, Inc., reached the 40 percent mortality estimate for streamtype juveniles by taking the 25 percent rate from the same micro-acoustic tagging study 

and adding 15 percent to account for presumed deaths occurring in the plume. 

Continued annual study results will help refine these estimates over time. 

3. Used a survival improvement target of 20 percent for both ocean- and stream-type 

juveniles. The 20 percent number is not scientifically based; instead, it represents a 

planning target that will require refinement as the extent to which actions are 

implemented and effective becomes clearer. Survival improvement numbers attempt to 

reflect wild, ESA-listed fish only. In most cases, known mortality to salmonids (such as 

from terns) does not break out wild fish from hatchery fish or ESA-listed fish from nonlisted fish. 

4. Allocated the two targets described above across 22 actions (CRE-14, “Reduce predation 

by pinnipeds,” was treated separately for adult mortality), based on an extensive 

literature review and personal communication with various agency staff. PC Trask &

Associates, Inc., evaluated each action using limiting factor information from Chapter 3, 

threat information from Chapter 4, and action evaluations from Chapter 5. As a result, 

the allocation takes into consideration a combination of factors, including the magnitude 

of the limiting factor, the degree of the associated threat(s), how well the action 
DEVELOPMENT OF SURVIVAL IMPROVEMENT TARGETS

B-2

addresses the threat, how constrained implementation of the action is likely to be, and 

the assumption that a considerable level of effort will be applied to implementing each 

action. 

5. Assigned survival improvement targets on a relative scale across all of the actions. The 

reader should not view the survival improvement targets as an absolute numerical 

result for each action, but rather a relative indication of the importance of each action. In 

cases where the scientific community has determined the mortality associated with a 

particular limiting factor and developed a management plan with mortality reduction 

goals, such as with predation by Caspian terns, PC Trask & Associates, Inc., used these 

numbers to the degree possible. 

Survival improvement targets are intended to be correlated with cost estimates presented in 

Table 5-6 for constrained implementation of the management actions. The resulting 

cost/survival estimates (see Table 7-5) are intended to initiate discussions about the validity 

of cost estimates and potential survival improvement targets; the cost/survival index values 

in Table 7-5 are highly uncertain because of the gross assumptions on both sides of the 

equation. 

Disclaimer: Survival improvement numbers are for illustration only and are intended to 

demonstrate social choices in the face of significant uncertainty.

Literature sources generally do not prescribe actions, and relatively few actions 

have been specifically evaluated for associated survival estimates. 

Table B-1

Notes on Development of Survival Improvement Targets

Action Notes

CRE-1: Protect/restore 

riparian areas.

Estimate is unsupported in the literature.

Estimate was assigned a high value in recognition of its importance 

relative to food sources and shoreline habitats.

This is a protection action that is intended to reduce the potential for 

increased threat over time. 

CRE-2: Operate the 

hydrosystem to reduce 

reservoir heating.

Estimate is unsupported in the literature.

Estimate was assigned a relatively high value because temperatures 

commonly exceed 19 degrees Celsius and are doing so more 

frequently and for longer periods of time. (Nineteen degrees Celsius is 

considered the upper range of survival for salmonids).

Estimate is based on a relatively large level of effort to reduce the 

threat. It is likely that mitigation will be required in tributaries to 

implement the action.

CRE-3: Protect/enhance 

instream flows influenced by 

withdrawals and other water 

management actions in 

tributaries.

Estimate is unsupported in the literature.

This is a protection action that is intended to reduce the potential for 

increased threat.

Estimate is closely aligned with CRE-4 and probably has overlapping 

benefits.
DEVELOPMENT OF SURVIVAL IMPROVEMENT TARGETS

B-3

CRE-4: Adjust the timing, 

magnitude, and frequency of 

hydrosystem flows.

Estimate is unsupported in the literature.

The action affects nearly every facet of estuary ecosystem health.

Estimate is intended to demonstrate that changes to the hydrograph are 

possible and that small increments of change may produce a significant 

survival improvement.

This action is worthy of further analysis that may help support a more 

defensible survival estimate.

CRE-5: Mitigate entrapment 

of fine sediment in 

reservoirs.

Estimate is unsupported in the literature.

Estimate was assigned a low survival improvement because of the high 

degree of uncertainty about its potential to improve salmonid survival. 

Entrapment of sediment may have significantly larger effects.

CRE-6: Use dredged 

materials beneficially.

Estimate is unsupported in the literature.

Estimate was assigned a low survival improvement because of the high 

degree of uncertainty about its potential to improve salmonid survival.

Currently, beneficial uses are most often associated with nearshore 

erosion management, and little is known about potential benefits to 

salmonids in the nearshore. 

CRE-7: Reduce 

entrainment/ habitat effects 

of dredging and ballast.

Estimate is unsupported in the literature.

Estimate is relatively low because of the uncertainty and lack of 

mortality documentation associated with entrainment.

CRE-8: Remove or modify 

pilings and pile dikes

Estimate is unsupported in the literature.

Estimate is relatively high because of the number of pile dikes in the 

estuary and the suspected predation effects that result from the threat, 

including predation by cormorants, pikeminnow, bass, walleye, and 

catfish. Altered flow circulation and reduced juvenile access to lowvelocity habitats may also be a threat. 

CRE-9: Protect/restore 

high-quality off-channel 

habitat.

Estimate is unsupported in the literature.

This is a protection action that is intended to reduce the potential for 

increased threat.

The high estimate reflects the magnitude of importance that off-channel 

habitats represent to juveniles, especially ocean types. Because 

restoration activities are highly constrained, it is vital not to lose 

additional functioning habitats.

Protection alone will only help preserve the status quo.

CRE-10: Breach, lower, or 

relocate dikes and levees.

Estimate is unsupported in the literature.

Estimate is intended to demonstrate that dike or levee breaching is one 

of the top few actions that will increase ocean-type survival in the 

estuary. If substantial improvements for ocean-type life histories in the 

estuary are to occur, this is one of a handful of actions that must be 

implemented. 

Estimate assumes a significantly higher level of implementation than 

what is currently occurring.

CRE-11: Reduce over-water 

structures.

Estimate is unsupported in the literature.

Estimate is relatively high because of the number of over-water 

structures in the estuary and the suspected predation effects that result 

from the threat, including predation by cormorants, pikeminnow, bass, 

walleye, and catfish.

Other effects, such as decreased light penetration, are not well 

understood. 
DEVELOPMENT OF SURVIVAL IMPROVEMENT TARGETS

B-4

CRE-12: Reduce vessel 

wake stranding.

Mortality estimates for test sites have demonstrated a wide range of 

confirmed mortality. In Bauersfeld (1977), an assessment of five test 

sites estimated approximately 150,000 stranded juveniles (on those 

sites). No estuary-wide estimates have been developed. 

The emerging availability of LIDAR imagery for the estuary may provide 

for analysis to extrapolate confirmed site-specific information to estuarywide predictions. 

Estimate is relatively high within the range of study estimates.

CRE-13: Manage 

pikeminnow and other 

piscivorous fish.

Estimate is unsupported in the literature.

Some information exists about predation rates.

The threat does not currently appear to be on the increase.

Estimate is relatively high based upon conjecture by the NMFS 

Northwest Fisheries Science Center regarding pikeminnow predation 

rates, but the threat should be studied further and monitored over time.

CRE-14: Reduce predation 

by pinnipeds.

An estuary-wide mortality estimate is unsupported in the literature.

Estimates are for adults only.

Annual counts at Bonneville Dam indicate between 0.4 percent and 3.4 

percent mortality of spring Chinook and winter steelhead.

A 500-pound Stellar sea lion consumes about 40 to 60 pounds of fish 

each day.

An unsubstantiated estimate of all pinniped predation in the estuary of 

approximately 10 percent of spring Chinook and winter steelhead is 

probably reasonable. 

CRE-15: Reduce invasive 

plants.

Estimate is unsupported in the literature.

Noxious weeds alter food webs and habitat and work at the ecosystem 

scale.

Very little is understood about the connection between noxious weeds 

and juvenile salmonid survival.

Estimate is relatively high for noxious weeds compared to other 

ecosystem-scale threats because, although associated actions are 

difficult, they have a greater likelihood of success than do actions to 

address other similar threats, such as invertebrate infestations.

CRE-16: Redistribute 

Caspian terns.

Estimate is supported by the literature.

Recent successes in relocating terns have been documented.

Efforts to implement the action are under consideration.

Estimated mortality attributed to Caspian tern predation is 

approximately 3.6 million juveniles in 2005. 

Current planning calls for a two-thirds reduction in the East Sand Island 

nesting. 
DEVELOPMENT OF SURVIVAL IMPROVEMENT TARGETS

B-5

CRE-17: Redistribute 

cormorants.

Estimate is supported by the literature.

Efforts to manage cormorants are not nearly as mature as efforts to 

manage terns.

There is less certainty about implementation potential because 

cormorants have not responded to management efforts to the degree 

that terns have.

Estimated mortality attributable to predation by double-crested 

cormorants is considered to be comparable to that of predation by 

terns.

Assignment of the target survival improvement was lower than for terns 

because cormorants may be harder to manage than terns. 

CRE-18: Reduce shad 

abundance.

Estimate is unsupported in literature.

Estimate is low because of the high degree of uncertainty about the 

relationship between shad, salmonids, and ecosystem health.

Estimate is also low because the literature does not identify potential 

actions to reduce shad abundance levels. 

CRE-19: Prevent aquatic 

invertebrate introductions.

Estimate is unsupported in the literature.

Extent of the threat is well-documented; however, invertebrate 

infestations occur at the ecosystem scale, and the degree of mortality 

that occurs because of food web changes at this scale is unknown.

Estimate is relatively low because of the uncertainty of the threat and 

the inherent challenges of reducing the threat.

CRE-20: Implement 

pesticide/fertilizer BMPs.

Emerging literature (Loge et al. 2005) hypothesizes that mortality 

resulting from estuary contamination ranges from 1.5 percent to 9 

percent, depending on the amount of time juveniles spend in the 

estuary. 

Estimates for CRE-21, CRE-22, and CRE-23 form the basis for survival 

improvements (using estimates from Loge et al. 2005).

CRE-21: Identify and reduce 

sources of pollutants.

Emerging literature (Loge et al. 2005) hypothesizes that mortality 

resulting from estuary contamination ranges from 1.5 percent to 9 

percent.

Estimates for CRE-20, CRE-22, and CRE-23 form the basis for survival 

improvements (using estimates from Loge et al. 2005).

CRE-22: Restore or 

mitigate contaminated sites.

Emerging literature (Loge et al. 2005) hypothesizes that mortality 

resulting from estuary contamination ranges from 1.5 percent to 9 

percent.

Estimates for actions CRE-20, CRE-21, and CRE-23 form the basis for 

survival improvements (using estimates from Loge et al. 2005).

CRE-23: Implement 

stormwater BMPs.

Estimate is unsupported in the literature.

This is a protection action that is intended to reduce the potential for 

increased threat.

This action does not assume retrofitting of existing stormwater function.