DRAFT

Module for the Ocean Environment

Prepared for the NOAA Fisheries, Northwest Regional Office

Prepared by the Northwest Fisheries Science Center

June 2014
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Contents

1. Introduction................................................................................................................................. 4

2. Why Include the Ocean as Part of Recovery Planning and Implementation.............................. 5

3. Ocean Environments and Salmon: An Overview...................................................................... 8

3.1 Columbia River Estuary........................................................................................................ 8

3.2 Columbia River Plume........................................................................................................ 10

3.3 Northern California Current................................................................................................ 11

3.4 North Pacific Ocean............................................................................................................ 12

3.5. Ocean Conditions and Salmon........................................................................................... 13

3.5.1 Physical Processes ....................................................................................................... 13

3.5.2. Biological Processes. .................................................................................................. 16

4. Estuary/Ocean Life Histories of Listed Snake River Anadromous Species............................. 17

4.1 Snake River Spring/Summer Yearling Chinook Salmon. .................................................. 18

4.1.1. Estuary ........................................................................................................................ 18

4.1.2. NCC ............................................................................................................................ 19

4.1.3. North Pacific Ocean.................................................................................................... 21

4.1.4 Summary...................................................................................................................... 22

4.2 Snake River Steelhead ........................................................................................................ 24

4.2.1 Estuary ......................................................................................................................... 24

4.2.2. NCC ............................................................................................................................ 25

4.2.3. North Pacific Ocean.................................................................................................... 26

4.2.4 Summary...................................................................................................................... 27

4.3 Snake River Fall Chinook Salmon...................................................................................... 28

4.3.1 Estuary ......................................................................................................................... 28

4.3.2. NCC ............................................................................................................................ 29

4.3.3 Pacific Ocean ............................................................................................................... 30

4.4.4 Summary...................................................................................................................... 31

4.4 Snake River Sockeye Salmon ............................................................................................. 33

4.4.1. Estuary ........................................................................................................................ 33

4.4.2. NCC ............................................................................................................................ 33

4.4.3. North Pacific Ocean.................................................................................................... 34
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4.4.4. Summary..................................................................................................................... 34

5. Ocean Ecology.......................................................................................................................... 36

5.1 Food Habits......................................................................................................................... 36

5.2. Growth ............................................................................................................................... 39

5.3. Ecological Interactions....................................................................................................... 44

5.3.1. Competition................................................................................................................. 44

5.3.2. Predation ..................................................................................................................... 46

5.3.3. Pathogens and Parasites.............................................................................................. 49

5.4. Mortality ............................................................................................................................ 51

5.5 Habitat Use.......................................................................................................................... 56

5.6 Habitat Connectivity ........................................................................................................... 58

6. Anthropogenic Risks to Salmon During Estuarine/Ocean Life................................................ 59

6.1. General............................................................................................................................... 59

6.2 Climate Change................................................................................................................... 61

6.2.1 Estuary Effects............................................................................................................. 61

6.2.2. Ocean Effects.............................................................................................................. 64

6.2.3. Integrated Effects........................................................................................................ 66

6.3. Summary............................................................................................................................ 68

7. Ocean Ecology Snake River ESUs- Key Information Needs................................................... 69

8. Recovery Strategies .................................................................................................................. 72

8.1 Manage for Diversity .......................................................................................................... 73

8.2 Physical and Biological Connectivity- Spatial Structure.................................................... 75

8.3 Harvest ................................................................................................................................ 76

8.4 Improving survival in the ocean. ........................................................................................ 77

9. Adapting Recovery Actions Based on Ocean Conditions........................................................ 78

9.1 Forecasting.......................................................................................................................... 78

10. Implementation ....................................................................................................................... 80

10.1 Information Needs: Monitoring and Research................................................................. 80

11. Literature Cited ....................................................................................................................... 81
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1. Introduction

This document is the “Module for the Ocean Environment” that has been developed to support 

integrated recovery plans for four anadromous species that spawn in the Snake River and its 

tributaries that are listed under the Federal Endangered Species Act (ESA). These species are: 

• Snake River spring/summer Chinook salmon (an ESU or Evolutionarily 

Significant Unit)

• Snake River steelhead (a DPS or Distinct Population Segment)

• Snake River fall Chinook salmon (an ESU)

• Snake River sockeye salmon (an ESU)

Specifics on the listing of each species are provided in the individual recovery plans. The intent 

of the recovery plans is to identify recovery actions that will restore viability of the species, 

identify key information needs, define an adaptive management strategy for the plan, and 

describe plan implementation. In support of these recovery plans, several modules have been 

developed that present detailed and specific information on a particular subject to inform 

recovery planning (NMFS 2008; NMFS 2011). 

The purpose of this Module is to use the latest science to: 

1. Synthesize what we know about how each of the four listed species uses ocean 

ecosystems.

2. Identify major uncertainties regarding their use of the ocean environment

3. Define the role of the ocean in recovery planning and implementation of each species. 

The document is organized in ten sections. Following the introduction (section one), section two 

discusses why the ocean should be part of recovery planning while section three provides a 

general description of the estuary/ocean environments salmonids occupy. Section four presents a 

description of the ocean life history of each listed species and section five presents a description 

of the ecology of the listed stocks in the estuary and ocean (e.g., growth and predator-prey 

interactions). Section six discusses risks to the salmon during their ocean life, including climate 

change; the seventh section presents key information needs. The final three sections describe 

recovery strategies involving the ocean, adaptive management, and implementation, respectively.
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2. Why Include the Ocean as Part of Recovery 

Planning and Implementation

The ocean should be a part of recovery planning and implementation for listed Snake River 

anadromous species. In the mid-1990s, the Northwest Power and Conservation Council 

recognized the need to include the ocean environment in the management of Columbia River 

Basin salmonids. They adopted an approach to directly obtain explicit, quantitative information 

on marine recruitment success that could be used by salmon managers. Importantly they 

extended the definition of the Columbia River basin to include the North Pacific Ocean as "a 

geographic unit (of the Columbia River basin)” and that this “unit” should be considered in 

research, monitoring, and evaluation actions.

There are a number of compelling reasons why the ocean should be included in recovery 

planning for the listed Snake River ESUs. First, it has become increasingly clear that ocean 

mortality of salmon can be very high (> 95% depending on population- Bradford 1995) and 

highly variable. Further, variability in marine ecosystem productivity can drive much of the 

variability in adult salmon returns (Pearcy 1992; Welch et al. 2000; Peterson and Schwing 2003; 

Scheuerell and Williams 2005; Petrosky and Schaller 2010; Haeseker et al. 2012; Thomson et al. 

2012; Burke et al. 2013a). For example, for Snake River yearling hatchery spring Chinook 

salmon, tidal freshwater/estuary/plume/ocean survival is highly correlated with the overall SAR 

(smolt-to-adult ratio) but not with in-river survival from outmigration year 2000 to 2009 (Figure 

1). It is noteworthy for this yearling group of Chinook salmon that in-river survival varied by 

approximately 2.5-fold while ocean survival varied by about 25-fold. Another example of the 

importance of ocean conditions to the survival of Columbia River basin salmonids is provided by 

Williams et al. (2014) who found that changes in ocean conditions in the Northern California 

Current appeared to have a strong influence on variability in SARs of Columbia River sockeye 

salmon. 
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Figure 1. Smolt-to-adult survival information for several groups of Snake River salmonids during several time 

periods in their life histories. 

Although the ocean is clearly a major driver of salmon productivity, we want to emphasize that 

freshwater life stages such as egg incubation or overwintering by juveniles are very important in 

overall productivity of salmon and steelhead (Beechie et al. 2003). One of the lessons of 100+

years of anadromous salmonid research and management is that anadromous salmon are a life 

cycle animal that depend on a set of inter-connected habitats that differ considerably in their 

characteristics (e.g., ocean vs. spawning streams) (NRC 1996). Thus, all life stages of salmon

are important and cannot be discounted in recovery efforts (Bisbal and McConnaha 1998; 

Beechie et al. 2003; Good et al. 2007). 

A second reason why the ocean should be considered in recovery planning is that the effects of 

variability in ocean productivity can mask, enhance, or even override underlying trends in 

freshwater habitat productivity and lead to a misinterpretation of the proximate causes of 

variability in survival or adult returns. As the ISRP stated in its review of the Ocean Synthesis 

report (ISRP 2012), “[t]he effectiveness of restoration as estimated from adult returns must 

account for all sources of mortality, including ocean mortality. Ideally, this partitioning will be 

accomplished for wild and hatchery stocks, in-river vs. barged, individual ESUs, and different 
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life histories to help determine in-river, estuarine, or ocean responses to the 4-Hs.” In their 2009 

Fish and Wildlife Program, the Council noted (page 31) that “......accurate monitoring and 

evaluation of inland efforts depends on the ability to isolate the effects of the ocean from the 

effects of inland actions. Without the ability to distinguish ocean effects from other effects, the 

Council may be tempted to correlate large salmon returns with successful mitigation practices. 

Likewise, poor returns of adult fish may lead the Council to abandon mitigation actions that are 

highly beneficial but which are overshadowed by the effects of poor ocean conditions unless the 

Council can determine the poor returns are in spite of, and not because of, the mitigation 

actions.” The National Research Council (NRC 1996- page 3) also identified the potential 

masking effect of ocean conditions in their evaluation of the plight of anadromous salmon -

“Variations in ocean conditions—especially in water temperature and currents and the associated 

biological communities—also contribute to the rise and fall of salmon abundance, often 

thwarting the interpretation of events in freshwater and surrounding terrestrial systems.” 

A third reason to include the ocean in recovery efforts is because there are strong atmospheric, 

oceanographic, and biological connections between freshwater, the estuary and the ocean. 

Examples of these connections are numerous. Physical connectivity includes tidal action that 

can push saltwater well upstream and change salinity regimes in the estuary as well as freshwater 

discharged into the Pacific Ocean that creates the plume environment (Horner-Devine et al. 

2009). The influence of the plume is not strictly local and limited to the area near the mouth of 

the Columbia River but extends over broad areas off the Washington and Oregon Coasts (Hickey 

1989). Another example of physical connectivity is climate-induced changes to precipitation 

patterns can alter the proportion of freshwater that enters the Columbia River via snow-pack vs 

rainfall. This change in water supply can affect what is discharged into the ocean which may 

change the physics and ecology of the coastal ocean environment.

Freshwater, estuary, and ocean ecosystems are also connected biologically. One example is the 

transport of nutrients from the ocean back to freshwater by spawning adults (NRC 1996). In 

addition, humans both directly and indirectly affect the performance of salmonids while they are 

at sea (Bisbal and McConnaha 1998). For instance, management actions in freshwater have the 

ability to effect fish size, timing of ocean entry, density of salmonids in the estuary and ocean, 

and condition of the fish which can affect growth and survival of the salmonids during later life

stages (Scheuerell et al. 2009; Tomaro et al. 2012). For example, mean body size at ocean entry 

and early marine growth in yearling Chinook salmon are positively correlated with adult returns 

(Claiborne et al. 2011), body condition of sub-yearling Chinook salmon is correlated with adult 

returns (Miller et al. 2013), and time and size at which salmon are released from hatcheries can 

affect adult return rates (Bilton et al. 1982). 
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3. Ocean Environments and Salmon: An 

Overview

For purposes of this Ocean Module, we have divided the ocean environments used by salmon 

into the following major ecosystems: Columbia River estuary, Columbia River plume, Northern 

California Current, and Pacific Ocean (including the Gulf of Alaska and Bering Sea) (Figure 2). 

We do not include waters south of the Oregon/California border because so few Columbia River 

fish are found in this area. In addition, although there are species specific patterns of vertical 

distribution of salmon in the water column, we have not considered these here and how they may 

change in different ocean regions (Emmett et al. 2004).

NN

Figure 2. Map of ocean domains over which salmon and steelhead from the Columbia River Basin occur.

Gulf of Alaska

Northwestern Pacific Northcentral Pacific Northeastern Pacific

Northern California Current

Bering Sea
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3.1 Columbia River Estuary

For the Ocean Module, we have defined the Columbia River estuary based upon tidal conditions. 

By this definition, the estuary extends 235 km (146 miles) from the river’s mouth to the base of 

Bonneville Dam which is the upstream extent of tidal influence. It also includes tidally 

influenced portions of its tributary rivers, such as the lower 41 km of the Willamette River, the 

largest river entering the estuary. 

The estuary has been considered separately in an Estuary Module from the perspective of 

recovery actions. However, we consider use of the estuary by the listed ESU’s in this Module 

because how the fish use the estuary and what happens to them in the estuary may have a 

significant effect on their subsequent survival in the ocean (e.g., Weitkamp et al. In Review). 

Holsman et al. (2012) found a relationship between the temperature difference between the 

estuary and ocean that was correlated to survival of Columbia River Chinook salmon; larger 

temperature differences were associated with lower survival. Scheuerell et al. (2009) reported 

that timing of ocean entry was related to survival of Columbia River basin Chinook salmon and 

steelhead, with earlier migrating fish generally performing better that later migrating fish. 
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3.2 Columbia River Plume 

From the estuary, juvenile salmonids enter the Columbia River plume, the zone where recentlydischarged freshwater interacts with surrounding ocean water (Horner-Devine et al. 2009). The 

size, shape, volume and depth of the plume are very dynamic, even over short time scales, and 

are controlled by the amount of freshwater flowing out of the Columbia River, local winds, tides,

and ocean currents (Hickey 1989; Jay and Smith 1990; Horner-Devine et al. 2009). In the 

absence of upwelling winds, the freshwater from the Columbia River moves north along the 

coast (Horner-Devine et al. 2009). The plume can break apart and pieces can be found hundreds 

of miles from the mouth of the river (Hickey 1989). Figure 3 shows the simulated (modeled) 

dynamic nature of the plume over a very short time scale, six days in May 2011. 

Figure 3. Changes in the location and shape of the Columbia River plume over one week in May 2011. The color 

scale is salinity with the freshest water in the dark blue.
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3.3 Northern California Current

Once salmon leave the plume, they enter the Northern California Current (NCC). The California 

Current (CC) is an eastern boundary current that flows south along the coasts of Vancouver 

Island, Washington, Oregon, and California (Figure 4) and ends off southern Baja California. 

Here, we will refer to the NCC as the portion of the CC that occurs off Oregon, Washington, and 

Vancouver Island. In winter, southerly winds create “downwelling” conditions that result in 

transport of water northward and shoreward as the Davidson Current. In summer, northerly 

winds can transport water southward and offshore, generating “upwelling.” It is this upwelling 

that helps make the coastal branch of the CC periodically cool, nutrient-rich, and highly 

productive. 

A major feature of coastal areas is the continental shelf, which extends from the coastline of the 

continent out to the “shelf break” where the bathymetry begins to steepen rapidly. The width of 

the shelf varies considerably along the coast. Off of Washington, for example, the shelf is 

relatively flat and can be 50-80 km wide while off much of California, the shelf is steep and may

be only several km wide. 

Figure 4. Schematic representation of the major current systems in the Eastern Pacific. These are the major currents 

salmon from the Columbia River interact with.
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3.4 North Pacific Ocean 

For the Ocean Module, the North Pacific will be defined as the Pacific Ocean north of 

approximately 45 N. This region can be loosely subdivided into the Northeastern, North Central, 

and Northwestern Pacific Ocean regions and the Gulf of Alaska (GOA) (Figure 2). The northern 

boundaries of each Pacific region are defined by land, while the southern boundaries are 

imprecise. 
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3.5. Ocean Conditions and Salmon

We define ocean conditions, in the context of salmon ecology, as that set of factors that affect

ocean survival of salmonids. In general, survival in the ocean is a result of bottom up (i.e., food 

web related) and top down (e.g., predation) biological processes which are controlled by 

different types of physical/chemical processes (Figure 5). Both physical and biological 

processes that are important to salmon survival operate at multiple scales of space and time.

Figure 5. Schematic representation of the inter-relationships of physical and biological processes (both top down 

and bottom up) that affect salmon survival.

3.5.1 Physical Processes

Physical processes include climate, winds, stratification, current eddies and large-scale 

circulation that control to varying degrees bottom-up and top-down biological processes. In 

general, processes operating at larger scales constrain and at least partially regulate processes 

operating at smaller scales (Figure 5). 

At the largest spatial scale is the Pacific Decadal Oscillation (PDO) (Mantua et al. 1997), a very 

large-scale circulation pattern that results in major shifts in oceanographic conditions such as 

ocean temperature. The PDO index is calculated based on patterns of variation in sea surface 

temperature (SST) of the North Pacific Ocean from about 1900 to the present (Mantua et al. 

1997). The PDO generally occurs in one of two phases with shifts in the phase of the PDO 

Salmon
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linked with changes in salmon production (Beamish et al. 1996; Mantua et al. 1997; Francis et al. 

1998; Welch et al. 2000). There is generally a warm phase and a cold phase to the PDO (Figure 

6), with shifts between phases caused by changes in wind speed and direction. When winds are 

predominantly from the north or north-northwest in the Gulf of Alaska in winter, the ocean cools 

and is said to be in the “cool phase” of the PDO; this is considered to be good for Columbia 

River salmon (Figure 6). When winds are predominantly from the southwest, the ocean warms 

and is said to be in the “warm phase” of the PDO and less good for salmon from the Columbia 

River basin. Shifts between phases historically occurred at a frequency of decades or longer (20-

30 years), but in recent years shifts between PDO phases have occurred more frequently (at 

about five-year intervals) (Figure 7).

Figure 6. Illustration of how the two major phases of the PDO occur. The cold phase is the good phase for salmon 

while the warm phase is not as good.

Although the PDO is more-well known within the context of Pacific salmon trends, the North 

Pacific Gyre Oscillation (NPGO) is another wind driven, large scale circulation process. Recent 

studies suggest it can account for oceanographic variation not explained by the PDO such as low 

frequency variability in nutrients, chlorophyll and oxygen (DiLorenzo et al. 2008; Peterson et al. 

2013). 
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Figure 7. Fluctuations in the PDO index showing the changes from cold phase (blue) to warm phase (red) upper 

graph and the northern copepod index bottom graph. The upper graph illustrates how shifts between PDO phases 

are occurring more rapidly now. Blue in the bottom graph represents a more favorable zooplankton community for 

salmon. (Data Source- Bill Peterson, NWFSC, Newport, Oregon).

At a regional scale and generally operating at seasonal-to-annual temporal scales is wind-driven 

coastal upwelling (Hsieh et al. 1995; Macias et al. 2012). Upwelling is a dominant physical 

factor affecting production in coastal waters of the CC. It occurs primarily from April through 

September when winds blow from the north and transports nutrient rich bottom water into 

surface waters; this in turn fuels the rapid growth of phytoplankton resulting in high secondary 

productivity. The ecosystem effects of upwelling are complex, can vary spatially and 

temporally, depend upon the sign of the PDO, the length of the upwelling season and timing of 

the upwelling (e.g., Bograd et al. 2009). 

Upwelling can be disrupted by El Niño events (Hsieh et al. 1995), the consequences of which are 

well-known and include significant reductions in biological productivity in this region. El Nino 

events can result in high mortality of many pelagic fishes, salmon, and seabirds. It is a 

disruption of the ocean-atmosphere system in the Tropical Pacific that is characterized by 
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unusually warm ocean temperatures in the Eastern Pacific. The opposite of El Nino events are La 

Niña’s, which are characterized by unusually cold ocean temperatures in the Eastern Pacific. El 

Niño conditions generally result in warmer and more nutrient poor ocean waters throughout the 

eastern Pacific, and are considered ‘bad’ for salmon in the Pacific Northwest (Peterson et al. 

2002; DiLorenzo et al. 2010; McPhayden et al. 2010). La Nina events generally produce cooler 

more nutrient rich water and are generally considered ‘good’ for salmon from this region. In 

recent years, the El Niño’s of 1983, 1998 and 2010 have been especially strong, but impacts on 

salmon are also seen in weaker events such as the prolonged series of events in 1992-1996 and 

2003-2006. 

At smaller spatial and temporal scales (hours to weeks), a number of different physical processes 

occur. An example of a process occurring at a smaller scale is the Columbia River plume. 

Physical aspects of the plume such as volume, size and shape, are highly dynamic and can shift 

daily. 

3.5.2. Biological Processes 

Bottom up processes

Bottom-up processes are those that provide food to salmon and include both estuary and ocean

food webs. In the ocean, large scale shifts in ocean food webs generally occur as a result of

shifts between cold and warm phases of the PDO (Keister et al. 2011). During the cold phase of 

the PDO in the NCC, the amount of cold water transported from the sub-arctic domain relative to 

warmer waters from the subtropical domain or offshore waters of the central North Pacific Ocean

appears to increase. During colder years, more lipid rich zooplankton occur in the NCC 

ecosystem than during warm years because they are transported south from the sub-arctic (Bi et 

al. 2011). This means that the food chain leading to salmon has a higher lipid content when “cold 

ocean conditions” prevail (Hooff and Peterson 2006). This may result in higher quality food, 

which may be beneficial to the salmon. 

Top-Down Processes

In general, top down, biological processes that can potentially affect salmon are predation, 

parasites and disease. There are a wide variety of fish, birds, and mammals that prey on juvenile 

and adult salmon and numerous pathogens and parasites that can infect salmon. And, the 

magnitude of predation mortality by a predator and the effects of a pathogen or parasite are a 

function of a number of factors (e.g., Fresh 1997). The same large shifts in PDO can affect both 

predation and parasites/diseases. For example, predation on juvenile salmon by Pacific hake 

(Merluccius productus) varies inter-annually and spatially, suggesting top down control by this 

species is mediated in part by variation in physical conditions in the NCC. 

Competition for food is another controlling biological process but is not truly a top down or 

bottom up process. Therefore, we have put it into its own category. Competition occurs when 

resources are limiting which in estuarine and marine systems is food. 
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4. Estuary/Ocean Life Histories of Listed Snake 

River Anadromous Species

In this section, we describe the ocean life history of the four listed Snake River ESUs. Our focus

here is on defining when fish occur in different ocean ecosystems, where they occur, and how 

long they may be present in particular regions. 

Ideally, we would construct ocean life histories focusing on wild (naturally spawning) fish since 

that is the focus of conservation and recovery efforts in the Snake River basin. However, our 

ability to do this is limited. First, naturally spawning fish from Snake River ESUs, especially 

Snake River sockeye, are at low levels of abundance. Thus, these fish are rare in samples 

obtained during ocean sampling. Second, there are also technical issues with identifying some 

Snake River ESUs in any sample of salmon. For example, there has been incomplete baseline 

information against which to compare unknowns for steelhead (e.g., from ocean caught fish in 

the NCC). Third, few naturally spawning juveniles are marked or tagged because there are 

considerable challenges associated with marking or tagging wild juvenile salmon including 

simply catching the fish to tag them. Conversely, hatchery fish can be more easily obtained and 

tagged. As a result, most juvenile salmonids that are marked or tagged from the listed Snake 

River species are the hatchery components of listed ESUs.

Given these limitations in our ability to identify wild Snake River species during their ocean life, 

surrogates for the wild fish are needed. The use of surrogates in species recovery planning is not 

without precedent but requires validation (Murphy et al. 2011). There are two possible 

surrogates for wild fish that can be used. First, hatchery-origin fish from the same ESUs can be 

used. The use of hatchery-origin fish as surrogates to draw inferences about life history and 

ecology of wild fish is, however, controversial (e.g., Levings et al. 1986; Fresh 1997; Weitkamp 

and Neely 2002). Some studies suggest that hatchery-origin and wild salmon have similar 

performance (e.g., survival), behavior and ecology when such factors as size can be accounted 

for; under these conditions, hatchery-origin fish could represent reasonable surrogates of wild 

fish (e.g., Sweeting and Beamish 2009; Weitkamp 2010; Daly et al. 2012; Woodson et al. 2013). 

Other studies suggest there can be behavioral or survival differences (e.g., differences in survival 

between hatchery and wild fish within an ESU) that can make use of hatchery fish as surrogates

problematic (Buchanan et al. 2012). 

A second surrogate for naturally spawning Snake River ESU’s are more abundant ESUs from the 

Columbia River basin with similar life histories to Snake River ESUs. For example, Upper 

Columbia River summer/fall Chinook salmon can potentially be a surrogate for the Snake River 

fall Chinook salmon ESU while Upper Columbia River sockeye salmon can inform our 

understanding of the ocean life history of the Snake River sockeye salmon ESU.

Our discussion of ocean ecology of listed Snake River species will be as specific as possible with 

respect to species, ESU, and life history type. Life history type is an especially important 

determinant of many life history features such as habitat use and migration behavior. While 
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there are many ways salmonids can express life history diversity, we will primarily use how long 

fish rear in freshwater to distinguish life history types. The term yearling will refer to fish that 

rear for one or more years in freshwater before migrating to sea while the term sub-yearling will

refer to fish that rear for less than a year in freshwater and then migrate to the ocean. Both 

yearling or sub-yearling life history types can occur within the same ESU (and within a 

population within an ESU) with the proportion of each life history type varying by species, 

population, and year (Fresh et al. 2005). Although the differentiation of yearling and subyearlings is generally associated with Chinook salmon, other species can express juvenile life 

history diversity as well. For example, the amount of time sockeye salmon spend in their nursery 

lake can vary from 1 to 3 years. In addition, while the majority of steelhead migrate to the ocean 

after rearing in freshwater for two years, some steelhead rear for up to five years in freshwater 

before migrating to the ocean (Busby et al. 1996). 

One other expression of life history diversity that we will use in the Module is when adult fish 

enter the Columbia River. The words spring, summer, winter or fall associated with a species, 

ESU, or population refer to when the adult fish enter freshwater to spawn but not when they 

spawn. For example, spring run Chinook salmon may hold for many months in freshwater 

before spawning in the fall, despite entering the Columbia River from April to June. 

4.1 Snake River Spring/Summer Yearling Chinook Salmon. 

The Snake River spring/summer Chinook salmon ESU (abbreviated hereafter as SRSS Chinook

salmon) includes all naturally spawning populations of spring/summer Chinook salmon in the 

mainstem Snake River and in the Tucannon River, Grande Ronde River, Imnaha River, and 

Salmon River sub-basins. It also includes 15 artificial propagation programs. Most juvenile 

Chinook salmon in this ESU rear in freshwater for about a year before migrating to sea and so 

are yearlings at the time they migrate. There are some sub-yearling life history types (i.e.,

migrating to sea in within their first year following emergence) within this ESU although their 

contribution to adult returns are unknown (Copeland and Vendetti 2009). In this discussion, we 

focus only on the yearling life history type.

4.1.1. Estuary 

Detections of PIT tags from this ESU passing Bonneville Dam provide a means of estimating 

when fish enter the estuary. Most PIT tagged yearling SRSS Chinook salmon pass Bonneville 

Dam from late April through early June with most fish from this ESU passing the dam in a 

narrow time window that varies little between years. The average date of 50% passage (from 

2003 to 2012) through Bonneville Dam was May 18 for all fish (wild fish plus hatchery-origin 

fish) and May 17 (range May 11 to May 22) for wild fish only 

(http://www.cbr.washington.edu/http://www.cbr.washington.edu/dart). The mean date for 90% 

of the fish (combined hatchery and wild) to pass Bonneville Dam was June 6 for these 10 years.
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Available evidence suggests that the residence time of most juvenile SRSS Chinook salmon in 

the estuary is short and on the order of days. Weitkamp et al (2012) and Weitkamp et al. (In 

Review) estimated that the mean date of passage for hatchery and wild origin fish at the purse 

seine site at Rkm 15 using a combination of genetics analysis and tag recoveries (both PIT and 

CWT). Passage time at Rkm 15 was almost identical to the mean date of passage at Bonneville 

Dam (May 17 and 18, respectively). Based upon detections of PIT tags made in trawl collections 

at Rkm 70, SRSS Chinook salmon take only 1 to 2 days to migrate the 165 km from Bonneville 

Dam to this point in the river. McMichael et al. (2013) also reported rapid migration rates in the 

estuary using acoustically tagged yearling spring Chinook salmon (no stock identification was 

available, however); they found that most yearling Chinook salmon traveled from Rkm 153 to 

Rkm 8 in less than two days. 

Yearling spring Chinook salmon also appear to spend only a short period of time in the “plume”. 

McMichael et al. (2013) found that most yearling Chinook salmon (68.3%) that were tagged with 

acoustic transmitters (no stock origin was provided) remained in the vicinity of the river’s mouth 

(defined as the area downstream of Rkm 8 out about 15 km from the river’s mouth and north and 

south about 15 km) for less than a day; the average amount of time spent at the mouth of the 

river was 2.2 days with fish early in the year (May 5 to 18) tending to spend less time holding in 

this area (mean=0.7 days) compared to later in the year (mean=3.3 days) (May 19 to July 6). 

Another study using acoustic tags found that fish remained in the plume for an average of 7 days 

(Brosnan et al. 2014). This study, however, defined the plume as the Astoria-Megler Bridge 

(about Rkm 22.0) to nearly the mouth of Willapa Bay. 

Because on average, the time spent in the estuary and plume is short, passage date at Bonneville 

Dam probably provides a reasonable, general estimate of ocean entry timing. Although average 

time spent in the estuary and plume is short, there is considerable variation in travel times and 

timing of estuarine and ocean entry among individual fish. For example, residence time at the 

mouth of river ranged from 0.1 days to 34.7 days for individual acoustically tagged yearling 

spring Chinook salmon (McMichael et al. 2013). Differences in ocean entry date of days to 

weeks for individual fish may not be unimportant and could affect their survival in the ocean 

(Scheuerell et al. 2009; Holsman et al. 2012). 

4.1.2. NCC

Once the yearling SRSS Chinook salmon enter the NCC, they can initially disperse in any

direction. An acoustic telemetry study by McMichael et al. (2013) found that yearling spring 

Chinook salmon (stock specific information was not provided) dispersed in all directions from 

the river mouth with fish early in the spring more likely to be found south of the river’s mouth 

while later in the spring they were more likely to the north. The direction of movement once the 

fish leave the estuary appears to be a function of season and local environmental conditions 

including wind and currents (McMichael et al. 2013). 
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Trawl catches also suggest that yearling Chinook salmon disperse in all directions after ocean 

entry. In May, yearling Chinook salmon from the Columbia River (origin not known) are found

in the coastal ocean off Northern Oregon and Washington, with most fish found off of 

Washington (Bi et al. 2007, 2008; Yu et al. 2012) (Figure 8a); few Columbia River fish move 

south of Newport, OR based on trawl catches conducted in this area (Brodeur et al. 2004). 

Figure 8a. Average yearling Snake River spring Chinook salmon Catch Per Unit Effort (CPUE) by station at ocean 

sampling stations for May 2006 – 2012 and June 1998 – 2012. (Jacobson et al. 2012)

Trawl samples collected in the NCC by US and Canadian investigators have found that in May, 

most yearling SRSS Chinook salmon are found on the Continental Shelf off Washington (Figure 

8a. By June-July in the NCC, they are found from Northwest Washington to SE Alaska. During 

this time period, they occur in low numbers off Washington, and are most abundant off the 

WCVI and east of the Queen Charlotte Islands (Figure 8a). By September most yearling SRSS 

Chinook salmon have left the NCC. 

It is clear from results of trawl catches that regardless of their initial dispersal behavior in the 

NCC, yearling SRSS Chinook salmon soon migrate northwards. Burke et al. (2013b), Yu et al. 

(2012), and Bi et al. (2011) used different modeling approaches to evaluate factors affecting 

early marine migration behavior of yearling spring Chinook salmon in the NCC. Modeling work 

by Yu et al. (2012) and Bi et al. (2011) suggested that environmental factors had the most 

influence on migration behavior while the model by Burke et al. (2013b) suggested geospatial 
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factors were more critical in determining migration pathway. As a result, in Burke et al.’s 

(2013a) model, fish could occupy sub-optimal environmental conditions. 

4.1.3. North Pacific Ocean

Once SRSS Chinook salmon leave the NCC and are still in their first year of ocean life, they 

distribute over wide area of the NE Pacific Ocean, including along the continental shelf off 

Central BC, Central Alaska, SE Alaska and the GOA (Trudel et al. 2009; Tucker et al. 2011; 

Sharma and Quinn 2012; Fisher et al., 2014). Some yearlings from this ESU have moved as far 

north as Kodiak Island and can be found along coastal areas of BC and AK by the June-August 

time period (Trudel et al. 2009; Tucker et al. 2011; Fisher et al. 2014). During summer, Snake 

River yearlings are one of the most abundant stocks in the GOA. From July-September 2012, 

45% of the Chinook salmon present in the GOA at this time (first ocean fish) were SRSS

Chinook salmon (Teel et al. 2014). By fall and winter of their first ocean year, some SRSS 

Chinook salmon are still in shelf areas along the British Columbia coast (Tucker et al. 2011). By 

the end of their first year in the ocean (beginning of their second spring at sea), most SRSS 

yearlings have left the shelf (Tucker et al. 2011; Fisher et al. 2014) and are in the deeper waters 

of the GOA. 

Fisher et al. (2014) found that dispersal or migration rates of SRSS Chinook salmon during their 

first year in the ocean averaged 8 km/day, one of the fastest rates for any Columbia River 

Chinook salmon stock. Otolith analysis suggests mean northward migration rates of interior 

Columbia River yearling Chinook during their first months at sea are faster during years of poor 

ocean conditions, suggesting juveniles may modify their migratory behavior based on ocean 

conditions (Jacobson et al. 2012).

Once fish enter their second year of ocean life, little is known about their ocean life history and 

ecology. The lack of older ages of Chinook salmon in ocean sampling (Myers et al. 1996) and 

lack of information on the origin of captured fish in some ocean surveys makes it impossible to 

conclude much about the ocean life of older SRSS Chinook salmon (e.g., 2 or 3 years at sea). For 

example, it is not clear if and how ocean ecology varies with age of the fish. SRSS Chinook 

salmon probably spend most of their ocean lives in the GOA (Myers et al. 1996) until they begin 

to migrate back to their stream of origin. 

When fish (and from where) begin their return migrations and how this might vary with age is 

unclear. The life history of jack Chinook salmon (one year of ocean life before returning to 

spawn) is particularly relevant because jack salmon are used in forecasting adult returns of spring 

Chinook salmon (e.g., to Bonneville Dam). Understanding where fish that returns as “jacks” 

occur and when they return could help explain some of the discrepancies in forecasts made using 

jacks and those made using indicators of ocean conditions (Burke 2014). A modeling study by 

Bracis and Anderson (2013) suggested that jack Chinook salmon have a different spatial 

distribution in the ocean than older fish. Clairborne et al. (2011) found that age at maturity in 

hatchery-origin Willamette spring Chinook salmon was related to their size at release; younger 

returning fish were those that were larger after their first year of ocean growth. 
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Maturing Chinook salmon (i.e., two years or more in the ocean and destined for a spawning 

river) typically arrive off of coastal Washington beginning in March and April based upon 

fishery interceptions that have occurred in this area. It is unclear when adults first enter the 

estuary but spring Chinook salmon are abundant in the lower Columbia River estuary in April

and May (but present in March and June as well) where they have been tagged (Wargo-Rub et al. 

2011, 2012). Adult SRSS Chinook salmon tagged in the estuary took an average of 18.1 days to 

reach Bonneville Dam in 2011 and 15.4 days in 2010; travel times of individual fish from 

tagging location to Bonneville Dam ranged from 7 to 57 days (Wargo-Rub et al. 2011, 2012). 

At Bonneville Dam where the fish leave the estuary, passage of SRSS Chinook salmon varies as 

a function of river of origin (i.e., destination in the Snake River system). From 1996 to 2001, 

median date of passage at Bonneville Dam ranged from April 23 for fish destined for the 

Tucannon River to May 29 for fish destined for the Imnaha River (Keefer et al. 2004). Keefer et 

al. (2004) also found that fish destined for the Clearwater drainage arrived earlier at Bonneville 

Dam than fish destined for the Salmon River drainage. More recently (Hess et al. (2014) found 

that median, annual date of passage at Bonneville Dam for 2004-2007 ranged from about April 

30 to May 20 for fish destined for the Clearwater River and Lower Snake River, to about May 20 

to June 10 for fish destined for the Salmon River. Median passage date can vary up to 20 days 

depending on the destination of the fish (Hess et al. 2014) and appears to be strongly related to 

discharge, with fish passing earlier at lower flows (Keefer et al. 2004). 

4.1.4 Summary 

Average date of estuary entry (as measured at Bonneville Dam with PIT tag data) varies little 

from year to year (mid-May). Based primarily upon PIT tag data, average residence time of 

SRSS yearling Chinook salmon in the estuary appears to be a week or less and average residence 

time in the plume also appears to be short and on the order of hours to days. However, there is 

considerable variation in residence times in different habitats and timing of estuarine and ocean 

entry among individual fish. Such variation may not be unimportant, as it may affect survival at 

later life stages and help provide resilience to the ESU (McElhaney et al. 2000; Holsman et al. 

2012).

Once yearling SRSS Chinook salmon enter the NCC, they can initially disperse in any direction 

but they quickly begin to migrate along the coast to the north. Migration to the north appears to 

be controlled by a combination of environmental and geospatial factors. As the fish migrate 

north they distribute over a broad area of the NE Pacific Ocean, including coastal areas of 

Washington and British Columbia and Alaska, the continental shelf off Central BC, Central 

Alaska, SE Alaska and the GOA. In summer, yearlings SRRS Chinook salmon are abundant in 

the GOA. Some yearlings from this ESU move as far north as Kodiak Island by the June-August 

time period. SRSS have largely vacated coastal areas of Washington and British Columbia by 

September. By the end of their first year of ocean life, most fish are in the GOA. Little is known 

about the ocean life history of SRSS Chinook salmon after they have passed their first year in the 

ocean until arrive in coastal waters of Washington in March and April. Adult SRSS Chinook 

salmon tagged in the estuary took an average of 18.1 days to reach Bonneville Dam in 2011 and 
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15.4 days in 2010. Passage date of adults at Bonneville Dam varies with destination of the fish 

(where the fish ultimately spawn). 
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4.2 Snake River Steelhead

The Snake River steelhead DPS (Distinct Population Segment) occupies the Snake River Basin 

of southeast Washington, northeast Oregon and Idaho and includes all naturally spawning

populations of steelhead in the Snake River and its tributaries. Several artificial propagation 

programs are considered part of the DPS as well. Snake River steelhead are known to spawn and 

rear in all tributaries used by Snake River spring/summer Chinook, as well as many additional 

tributaries.

Unlike Chinook salmon, stock specific information on steelhead after they leave the Columbia 

River is very limited. In part, this is because development of steelhead genetic baselines have 

lagged those of other species. The genetic baseline is reasonably complete in the Columbia 

River basin but is not yet complete outside the basin. Until the genetic baseline is in place, the 

origin of ocean-caught fish can only be reliably determined with the use of PIT and CWT tags, 

most of which are of hatchery-origin. 

4.2.1 Estuary

Detections of PIT tags passing Bonneville Dam provide a means of estimating timing of 

estuarine entry. Based upon these PIT tag detections, the majority of Snake River steelhead pass 

Bonneville Dam from mid-April through early June, with most fish passing in a narrow time 

window that varies little between years. The average date of 50% passage (from 2003 to 2012) 

at Bonneville Dam was May 16 for all fish (hatchery-origin plus wild fish) and May 19 for wild 

fish only (HTTP://WWW.CBR.WASHINGTON.EDU/DART). The range for 50% passage of 

juvenile steelhead (hatchery and wild origin fish) over the 10 years was May 9 to May 31. The 

mean date for 90% of the Snake River steelhead (hatchery-origin plus wild fish) to pass 

Bonneville Dam was June 6. 

Available evidence suggests that the residence time of most juvenile SR steelhead in the estuary

is short and on the order of days, which suggests that passage date at Bonneville Dam for SR 

steelhead probably provides a reasonable, general estimate of ocean entry timing. Based upon

purse seine collections in the lower estuary (sampling occurred at approximately Rkm 15),

Weitkamp et al. (In Review) found that the timing of PIT tag detections of steelhead at 

Bonneville Dam was almost identical to the detection dates of known origin steelhead at the 

lower estuary purse seine site at Rkm 15 (Weitkamp et al. In Review). For example, the mean 

date of passage for Snake River steelhead in the lower estuary at Rkm 15 was May 21 for wild 

steelhead (all years combined) compared to May 19 at Bonneville Dam. Also, the average time 

for fish to migrate from Bonneville Dam to the trawl based PIT tag detection array at Rkm 70 

was about two days and to migrate from Rkm 70 to Rkm 15 was also about two days (Weitkamp 

et al. In Review). Average migration rates reported by McMichael et al. (2013) for acoustically 

tagged steelhead (stock origin was not reported) were also very rapid as they found that most 

steelhead traveled from Rkm 153 to Rkm 8 in less than two days. 

McMichael et al. (2013) also reported that most steelhead remained in the vicinity of the river’s 

mouth (below Rkm 8) for only a matter of hours; 83% of the juvenile steelhead they tagged spent 
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less than a day near the mouth of the river. Fish tended to hold at the mouth of the river for a 

shorter period early in the year (Mean=0.3 days, May 5 to 18) compared to later in the year 

(Mean=0.8 days, May 19 to July 6).

4.2.2. NCC

After they leave the estuary, steelhead can disperse in all directions (McMichael et al. 2013) with 

the proportion of fish moving in any direction a function of time of year. McMichael et al. 

(2013) reported that in early spring most fish initially dispersed south and west while later in the 

spring fish mostly were dispersing north and west. The authors speculate that this difference in 

dispersal patterns is a function of local ocean currents. Regardless of direction the fish initially 

go, information from ocean trawl catches indicate steelhead migrate rapidly through the plume 

and near coastal region and are beyond the continental shelf in a matter of days. Daly et al. 

(2014) estimated that individual Columbia River steelhead were present in shelf waters for an 

average of 10 days (an offshore distance of about 80 km). Because of this rapid migration over

shelf waters, steelhead are present in the NCC trawl catches off Washington and WCVI only in 

May and have completely vacated the NCC by June (Daly et al. 2014) (Figure 8b) (note that no 

April samples have been collected in the NCC and based upon passage data at Bonneville Dam, 

some steelhead are likely in the ocean in April). 
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Figure 8b. Average juvenile steelhead Catch Per Unit Effort (CPUE) by station at ocean sampling stations for May 

2006 – 2012 and June 1998 – 2012. (Jacobson et al. 2012).

4.2.3. North Pacific Ocean

 Once the steelhead exit the coastal area, there is little known about their life in the ocean other 

than where they are generally found. Steelhead are the most migratory of all anadromous 

salmonids on the west coast of North America (Quinn and Myers 2004) and can be found over 

much of the North Pacific Ocean and GOA, from SE Alaska to nearly the Kuril Islands, Japan 

(Myers et al. 1996; Atcheson et al. 2012a). Tagged Snake River steelhead have been recovered 

in a broad band across the North Pacific between 40°N and 50°N latitude and from the North 

American Coast to 165°W (west of the date line) (Myers et al. 1996). In general, this 

distribution appears to be highly dependent on temperature (Welch et al. 1998; Atcheson et al. 

2012a). Myers et al (1996) found 10, immature steelhead from the Columbia River in this 

latitude range in the western part of the Pacific Ocean. Fourteen maturing Columbia River 

steelhead were also reported in high seas sampling but most of these fish were caught in the 

eastern part of the Pacific Ocean and were north of 44°N. Forty-eight coded-wire tagged 

steelhead from Idaho showed this same ocean distribution with most fish found in the Pacific 
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Ocean between 40°N and 50°N latitude and from the North American Coast to 165°W. 

Recoveries of hatchery-origin Snake River steelhead (McKinnell et al. 1997) with CWTs have 

been made during high seas sampling. These recoveries of Snake River steelhead were made 

during their first two years in the ocean, primarily in the Aleutians and southern GOA. They are 

the dominate stock in these two areas during their first year in the ocean but not in their second 

year (McKinnell et al. 1997). Few steelhead have been found in the Bering Sea, probably 

reflecting the lack of anadromous trout (O. mykiss and O. clarki) spawning in Western Alaska. 

Arrival timing of adult steelhead in coastal waters of Washington is unknown as is arrival timing 

and residence time in the estuary. Steelhead adults are divided into an A and B run. Both runs 

are summer steelhead that return in summer and spawn the following spring. B-run fish are 

generally 2-ocean fish from the Clearwater/Selway basin in Idaho that are larger than A-run fish 

which are 1-ocean and smaller. Freshwater entry is reported to be June-August for the A-run and 

August -November for the B-run (Busby et al. 1996). Robards and Quinn (2002) evaluated 

timing of passage of summer run steelhead at Bonneville Dam from 1935 to 2000 and found that 

passage of steelhead has been changing. They found that peak passage of the “late” portion of 

the run had remained about September 1 for the 60 year record of the data. However, the peak 

passage of the earlier portion had shifted by about 2 weeks from late July to early August 

(Robards and Quinn 2002). They attributed this shift to warming temperatures and reduced 

flows in the river over this time period. 

4.2.4 Summary

Most steelhead migrate very rapidly (<5 days) through the estuary and into the ocean and are 

present in the immediate mouth of the river for a very short period (hours to days). Residence 

time at the mouth of the river is very short and increases slightly as the season progress. 

However, there is considerable variation in travel times and timing of estuarine and ocean entry 

between individual fish. For example, residence time of juvenile steelhead at the mouth of river 

ranged from 0.1 days to 10.8 days (McMichael et al. 2013). Differences in ocean entry date of 

days to weeks may not be unimportant and could affect survival of fish in the ocean (Scheuerell 

et al. 2009; Holsman et al. 2012). 

Once steelhead leave the estuary they migrate rapidly to the west and leave the NCC off 

Washington by mid-June. Residence time in the NCC off of Washington appears to be around 

10 days on average. Once the fish have departed coastal areas, Snake River steelhead distribute 

themselves in a broad band across the North Pacific, with most fish found between 40°N and 

50°N latitude and from the North American Coast to 165°W (west of the date line) (Myers et al. 

1996). In general, ocean distribution appears to be highly dependent on temperature. There is 

not much else known about ocean life of steelhead. Once fish enter the estuary, their timing of 

upstream migration at Bonneville Dam varies with age, size and distribution of the fish. Most 

wild fish pass the dam earlier than hatchery fish. The peak passage of the earlier portion of the 

returning steelhead has shifted by about 2 weeks from late July to early August, probably in 

response to warming temperatures and reduced flows in the river.
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4.3 Snake River Fall Chinook Salmon

The Snake River fall Chinook salmon (SRF) ESU includes all naturally spawning fall-run 

Chinook salmon (adults are often referred to as “brights”) in the mainstem Snake River below 

Hells Canyon Dam; fish spawning in the Clearwater, Tucannon, Grande Ronde, Imnaha, and 

Salmon rivers; and four artificial production programs. While the SRF Chinook salmon ESU is 

referred to as a sub-yearling group, it also contains significant numbers of yearlings. Many of 

the yearlings are juveniles that overwinter in the reservoirs and migrate downstream as yearlings, 

especially from the Clearwater River basin. Yearling migrants contribute substantially to the 

population as a whole in that juveniles that survive the summer and winter return at very high 

rates compared to the traditional sub-yearling migrants of this ESU (Connor et al. 2005). Here, 

we will distinguish the ocean ecology of the two life history types.

4.3.1 Estuary

For all SRF Chinook salmon (regardless of origin or life history type), the mean date for 50% of 

the ESU (based on PIT tag detections) to have passed Bonneville Dam over the last 10 years was 

June 10; for wild fish only, the mean date was July 9 

(HTTP://WWW.CBR.WASHINGTON.EDU/DART). However, combining all fish 

oversimplifies timing of estuarine entry as the timing of passage of PIT tagged fish of this ESU 

at Bonneville Dam is bimodal. The peak of the first mode (10 year average), which are likely the 

yearlings, has been early to mid-May while the peak of the second mode, which are likely the 

sub-yearlings, has been late June to early July. 

SRF Chinook salmon sub-yearlings and yearlings have different migration behaviors through the 

estuary ranging from rapid migration to extended rearing. Yearlings of this ESU migrate 

downstream rapidly and typically use main channels and large distributaries during their 

migration (Weitkamp et al. In Review). SRF yearling Chinook salmon had an average migration 

rate of 24.6 km/day which was more comparable with juveniles from the SRSS Chinook salmon 

ESU. Based upon sampling in shallow habitats such as wetlands, there is little evidence of 

extended rearing (weeks to months) by many SRF yearlings in the estuary. 

In contrast, sub-yearlings, exhibit a diversity of migration behaviors. Like many other subyearling dominated ESUs (e.g., West Cascade Fall Chinook), some sub-yearlings use shallow,

nearshore, and off channel areas (including wetland and floodplain areas) below Bonneville Dam 

for rearing and for migrating (Fresh et al. 2005). SRF Chinook salmon juveniles can be present 

in estuarine areas in winter, as fry in March – May, and fingerlings throughout the summer and 

fall (Roegner et al. 2012; Teel et al. 2014). SRF Chinook salmon sub-yearling juveniles occur in 

these habitats in low numbers compared to some of the other sub-yearling dominated ESUs (Teel 

et al. 2014). 

Other sub-yearling SRF Chinook salmon make a more directed migration through the estuary 

and into the ocean and use main channel large distributary channels during their migration. 

Some of these fish can migrate rapidly through the estuary to the ocean. Of the various Columbia 

River basin stock groups captured in purse seining in the lower estuary at Rkm 15 for which 
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there was sufficient sample sizes, sub-yearling SRF Chinook salmon had the fastest average 

migration rate from release point to the estuary (35.2 km/day) (Weitkamp et al. In Review). The 

telemetry studies by McMichael et al. (2013) found that migration rate of sub-yearling Chinook 

salmon (all stocks considered) from Rkm 153 to Rkm 8.3 was about 70km/day, indicating they 

could reach the ocean from this point in the mid estuary in about 2 days. Because of the 

protracted time during which SRF juvenile Chinook salmon pass Bonneville Dam, the inability 

to determine life history type of the fish as they pass Bonneville, and the extended time some fish 

from this ESU spend rearing in the estuary, the date of passage at Bonneville Dam based on PIT 

tag detections does not represent a reasonable estimate of ocean entry time for this ESU. 

Because sub-yearlings and yearlings have different habitat use patterns, an analysis of both beach 

seine (most representative of sub-yearlings) and purse seine (most representative of yearlings) 

catches is needed to derive a complete picture of timing of passage of SRF Chinook salmon 

through the estuary. The estuary purse seining at Rkm 15 and beach seining at several estuarine 

sites near the mouth of the river (Bottom et al. 2011; Roegner et al. 2012) indicates sub-yearling 

Chinook salmon (all Columbia River stocks combined) have a year-round presence but a broad 

peak of occurrence in the estuary from mid-April through July. In some years, there is no real 

peak or even multiple peaks in abundance, perhaps reflecting passage of different stock groups.

The peak occurrence of hatchery-origin SRF Chinook yearlings in purse seine catches at Rkm 15 

in the lower estuary is about May 1, which is earlier than SRSS Chinook and steelhead. The 

mean date of passage of identifiable sub-yearling SRF Chinook salmon at Rkm 15 is about July 

15 for wild fish and June 15 for hatchery-origin fish (Weitkamp et al. In Review); this pattern

more closely corresponds with the second peak of PIT tagged fish passing Bonneville Dam. 

There is no data specifically on residence time of SRF sub-yearlings at the mouth of the river. 

The only data available is from telemetry but is not specific to stock. Sub-yearling juvenile 

Chinook salmon (no stock identifications were made) were present in the plume area at the 

mouth of the river for an average of 3.6 days, which is longer than yearling juvenile Chinook 

salmon. But like the other ESU’s there was considerable variation between individual fish in 

residence time (McMichael et al. 2013). 

4.3.2. NCC

Based upon McMichael et al.’s (2013) telemetry studies, initial dispersal of fish originating from 

this ESU varies with life history type. As we discussed for SRSS yearling Chinook salmon, 

yearling Chinook salmon in general (stock specific information was not provided) disperse in all 

directions from the river mouth with fish early in the spring more likely to be found south of the 

river’s mouth while later in the spring, yearlings were more likely to be found to the north. 

Based upon telemetry studies, the initial ocean dispersal of SRF Chinook salmon sub-yearlings 

that enter the ocean June 19 to August 7 is primarily to the north (McMichael et al. 2013). The 

direction of movement of the fish after they leave the estuary was considered to be a function of 

season and local environmental conditions including winds and currents (McMichael et al. 

2013). 
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Once in the NCC ecosystem, results of trawl surveys suggest that yearlings from the SRF 

Chinook salmon ESU do not disperse as far or as quickly from the river as do the yearlings from 

the SRSS Chinook salmon ESU (Trudel et al. 2009; Tucker et al. 2011; Fisher et al. 2014). In 

contrast, SRF Chinook salmon sub-yearlings first appear in ocean catches in June and primarily 

to the north of the Columbia River; some fish have reached the WCVI by June (Trudel et al. 

2009) (Figure 8c). By September in the NCC, trawl catches show that SRF sub-yearlings are 

widely dispersed from central Oregon to WCVI (Tucker et al. 2011). By the end of their first 

year in the ocean, SRF sub-yearlings have not dispersed much farther to the north than the 

northern tip of the WCVI and thus are still in the NCC. Fisher et al. (2007) reported that subyearling Chinook salmon were most abundant from California to British Columbia and in 

shallower coastal areas during their first ocean year.

Figure 8c. Average subyearling Snake River fall Chinook salmon Catch Per Unit Effort (CPUE) by station at ocean 

sampling stations for May 2006 – 2012 and June 1998 – 2012. (Jacobson et al. 2012)

4.3.3 Pacific Ocean

Although some SRF yearling Chinook salmon can be found in the GOA by fall, most of these 

fish move only as far north as SE Alaska during their first ocean year. At the beginning of their 

second ocean year, most fish move off the shelf and into oceanic habitats. Sub-yearlings in 

general (independent of origin) migrate slower, are found closer to shore in shallower water, and 

do not disperse as far north as yearlings (Trudel et al. 2009; Tucker et al. 2011; Sharma and 
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Quinn 2012; Fisher et al. 2014) (Figure 8). Sub-yearling SRF Chinook salmon had the fastest 

ocean dispersal rate of any Columbia River fall Chinook stock, averaging 4 km/d (Fisher et al. 

2014).

From the end of the first ocean year, and until they return to Columbia River as mature adults, 

there is little stock specific information on the ocean life of this ESU. An analysis by Norris et al. 

(2000) of ocean distribution of upriver bright (fish that spawn in the fall) stocks indicated that 

these stocks move further north as they get older. However, they did not distinguish Snake River 

fish from other stocks or sub-yearlings and yearlings. 

Small numbers of maturing jack males (jack salmon are maturing male salmon that return after 

one year or less in the ocean which is a life history tactic common in Chinook salmon) can be 

found off the Washington coast in May and June of the year they enter the ocean (Beckman 

2014). The ocean migration behavior of these fish is unknown. 

Generally, adult fall run fish are found in the lower river in August and September with passage 

at Bonneville Dam occurring from mid-August to the end of September

(HTTP://WWW.CBR.WASHINGTON.EDU/DART). An indication of passage timing of SRF 

Chinook salmon adults can be obtained from timing of the Interior Columbia River summer/fall 

group which includes Snake River falls (Hess et al. 2014). Median date of passage of this 

reporting group was mid-September from 2004-2007 (Hess et al. 2014). Passage timing of 

adults from the Interior Columbia River summer/fall reporting group used by Hess et al. (2014) 

is, however, quite broad with adults passing Bonneville from mid-June to early October. It is not 

clear if there is a difference in timing of adult passage through the estuary or past Bonneville 

Dam for SRF Chinook salmon yearlings and sub-yearlings.

4.4.4 Summary

The SRF Chinook salmon ESU is comprised of both a yearling and sub-yearling component. 

The estuary and ocean life history of each of these life history types is distinct. Fish from this 

ESU enter the estuary (based upon passage of PIT tagged fish at Bonneville Dam) in two peaks 

over a long time period. The peak of the first mode, which are likely the yearlings, is early to 

mid-May while the peak of the second mode, which is likely the sub-yearlings, has been late 

June to early July. In the estuary, the two life history types have distinct readience times. The 

yearlings spend an average of around a week (similar to yearling SRSS yearling Chinook 

salmon). In contrast, some sub-yearlings can rapidly migrate through the estuary while others 

can rear for an extended period of up to several months in the estuary. Habitat use varies with 

migrating fish more associated with the mainstem and larger distributaries and rearing subyearlings often associated with shallow water areas such as wetlands and shoreline areas. 

Initial dispersal of subyearlings in the NCC is different than yearlings (in general, independent of 

origin) with most fish tending to move north. Yearling SRF Chinook do not move as far north as 

yearling SRSS Chinook salmon but by the beginning of their second year at sea they appear to 

move off the shelf and into the GOA. SRF Chinook salmon sub-yearlings first appear in ocean 
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catches in June that are primarily to the north of the Columbia River and some fish have reached 

the WCVI by June. By September in the NCC, trawl catches show that SRF sub-yearlings are 

widely dispersed from central Oregon to WCVI. By the end of their first year in the ocean, SRF 

sub-yearlings have not dispersed much farther to the north than the northern tip of the WCVI and 

thus are still in the NCC. Sub-yearlings in general (independent of origin) migrate slower, are 

found closer to shore in shallower water, and do not disperse as far north as yearlings. 

Generally, adult fall run fish are found in the lower river in August and September with passage 

at Bonneville Dam occurring from mid-August to the end of September. Based upon the Interior 

Columbia River summer/fall group which includes Snake River falls, median date of passage of 

this reporting group was mid-September from 2004-2007. 
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4.4 Snake River Sockeye Salmon

The Snake River sockeye salmon ESU is currently found only in lakes high in the Salmon River 

drainage of the Snake River basin, primarily in Redfish Lake. Snake River sockeye salmon are

similar to many other sockeye salmon populations in that fry emerge from spawning areas and 

immediately move into lake habitats where they rear for 1 to 3 years. Because Snake River 

sockeye salmon were nearly extirpated by the mid-1990’s and currently are at very low 

abundance levels, they are rarely detected in any ocean surveys using any sampling method. As 

a result, ocean migrations and distribution of this ESU are largely unknown. We have used

information on sockeye salmon from other populations, including other Columbia River ESUs,

to draw inferences about the estuarine and marine life history of the Snake River sockeye salmon 

ESU. 

4.4.1. Estuary

While pre-dam reports indicate that sockeye salmon smolts passed through the lower Snake 

River in May and June, PIT-tagged smolts from Redfish Lake recently passed Lower Granite 

Dam on the lower Snake River from mid-May to mid-July. Based upon PIT tag detections at 

Bonneville Dam, peak passage of juvenile sockeye from this ESU at Bonneville Dam is 

generally in late May (HTTP://WWW.CBR.WASHINGTON.EDU/DART). This is about two 

weeks later than peak passage of sockeye juveniles from all populations combined (using the 

sockeye smolt index- HTTP://WWW.CBR.WASHINGTON.EDU/DART). Catches of sockeye 

salmon juveniles (origins unknown) in the estuary peak in early June, with most fish caught 

between May 15 and June 15 (Weitkamp et al. 2012). There is relatively little annual variation 

in migration timing through the estuary with peak catches occurring on June 1 in 2007, on June 5 

in 2008, and on June 10 in 2010 (no real peak occurred in 2009) (Weitkamp et al. 2012). Two 

PIT tagged sockeye salmon migrated from Redfish Lake to the estuary purse seine sampling site 

(Rkm 15) in 15 and 21 days. The one fish detected at Bonneville Dam and in sampling at Rkm 

15, took three days to migrate from Bonneville Dam to the lower estuary purse seine site. 

4.4.2. NCC

Sockeye salmon enter the ocean and immediately began migrating north, as no sockeye from the 

Columbia River have been caught south of the river’s mouth in 16 years of sampling in the NCC. 

In May and June, Columbia River sockeye salmon are most abundant off of Washington but 

some fish have migrated as far north as North and Central BC (Tucker et al. 2009) by June. A 

comparison of May, June, and September catches off of coastal Washington from 2006 to 2011 

found that 65% of all sockeye caught during this time period were caught in May, 35% in June, 

and none in September (Teel 2013). The few fish genetically identified as from the Snake River 

ESU were found South of Quillayute River in May and North of Grays Harbor in June. The lack 

of sampling in July and August makes it problematic to determine when Columbia River sockeye 

salmon leave Washington coastal waters but clearly by September, all sockeye have left 

Washington waters. 
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4.4.3. North Pacific Ocean

Once Columbia River sockeye salmon leave the NCC, they likely move north into the GOA, 

Bering Sea, and up the coast into Alaska. By winter, sockeye salmon have clearly disappeared 

from coastal areas and have entered the GOA (Tucker et al. 2009). In general, maturing sockeye

salmon are distributed in the GOA and into the Bering Sea but are migratory within this region

(Burgner 1991; Myers et al. 1996). Water temperatures affect the distribution of fish in the GOA 

with warmer temperatures pushing fish further. The study by Myers et al. (1996) found six 

maturing sockeye salmon from the Columbia River in the GOA. In summer 2009, Beacham et 

al. (2011) sampled sockeye in the Bering Sea and found that most fish (86%) were of Alaska 

origin with the rest from British Columbia, including the Fraser system; no sockeye from the 

Columbia River were identified in this study.

As fish mature in the GOA and Bering Sea region, they eventually begin their return migration to 

their rivers of origin. The body size when sockeye salmon begin their return migration can be 

related to temperatures in the last months of ocean residence with warmer temperatures leading 

to a smaller body size (Pyper and Peterman 1999). Water temperatures affect the distribution of 

fish in the GOA with warmer temperatures pushing fish further north, thereby increasing the 

distance fish migrating south to the Columbia River have to travel. The date when sockeye 

salmon begin their return migration is apparently a population specific trait that is independent of 

where the fish are at sea (Hodgson et al. 2006). Water temperature plays an important role in 

determining when stocks arrive back to coastal areas near spawning rivers. 

Quinn and Adams (1996) examined timing of passage of adult sockeye salmon (all stocks) at 

Bonneville Dam from 1949 to 1993 and concluded that timing had shifted from early July at the

beginning of the time series to late June; this shift in migration timing was attributed to changes 

in flow and temperature regimes in the river (Quinn et al. 1997). Over the last 10 years, peak 

passage at Bonneville Dam of all sockeye salmon has been late June 

(HTTP://WWW.CBR.WASHINGTON.EDU/DART) and is consistent with the timing in the

later part of the Quinn and Adams (1996) time series. More recent data shows that these trends 

towards shifts to earlier migration timing have continued (Crozier et al. 2008).

4.4.4. Summary

Of the four species considered in this Module, Snake River sockeye are at the lowest abundance 

levels and so are rarely detected in any ocean surveys using any sampling method. Based upon 

PIT tag detections at Bonneville Dam, peak passage of juvenile sockeye from this ESU at 

Bonneville Dam is generally in late May. Too few sockeye juveniles form the Snake River ESU 

have been sampled to draw any conclusions about length of estuary residence although there is 

relatively little annual variation in migration timing of juveniles (all sockeye stocks combined) 

through the estuary with peak catches occurring in early June.

Based upon trawl samples, sockeye juveniles from the Columbia River do not disperse south of 

the Columbia River and have left the NCC by September. Fish enter the GOA/Bering Sea by the 

end of their first ocean year. Water temperatures affect the distribution of fish in the GOA with 
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warmer temperatures pushing fish further north. The body size when sockeye salmon begin their 

return migration can be related to temperatures in the last months of ocean residence with 

warmer temperatures leading to a smaller body size. Water temperatures affect the distribution 

of fish in the GOA with warmer temperatures pushing fish further, thereby increasing the 

distance fish migrating south (such as to the Columbia River) have to travel. The date when 

sockeye salmon begin their return migration is apparently a population specific trait that is 

independent of where the fish are at sea. Water temperature plays an important role in 

determining when stocks arrive back to coastal areas near spawning rivers. 
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5. Ocean Ecology

This section describes ecological aspects of the ocean life of the four listed Snake River species,

focusing specifically on: 

1. Food habits

2. Growth

3. Ecological interactions (predation, competition, disease, and parasites)

4. Mortality

5. Habitat use

6. Habitat connectivity 

Despite decades studying the ocean ecology of salmon and steelhead, there are still major gaps in 

our knowledge of their ocean ecology. In particular, we still have a poor understanding of the 

mechanisms that affect growth and survival of the fish during ocean life. This is partly due to the 

large size and dynamic nature of the coastal and open ocean environments, but it is also likely 

due to underlying differences between ESUs and DPSs, juvenile life-history strategies, species, 

and the experiences and biology of hatchery-origin versus natural-origin fish. We will present 

information in this section at the most relevant biological scale as possible (i.e., an individual 

Snake River ESU or DPS or particular life history type). Our goal in this section is to present the

information as it exists and not to argue for a particular point of view. On some issues, this 

means we will present information both for and against a particular hypothesis and will use this 

as a way to highlight some of the Key Information Needs presented in Section 7. 

5.1 Food Habits

There are few diet studies in either the estuary or ocean that are specific to ESU/DPS or life 

history type. In general, all three salmon species eat a mix of invertebrates and fish during their 

tenure in estuary and ocean habitats (e.g., LeBrasseur 1966; Brodeur 1990; Brodeur et al. 2007). 

Chinook salmon and steelhead are the most piscivorous and sockeye salmon the least

piscivorous. While there is only limited information on the Snake River sockeye salmon ESU, 

sockeye diets in the ocean have been analyzed from many other sources. And, regardless of 

when and where sockeye are captured, they always feed almost entirely on invertebrates 

(Peterson et al. 1982; Burgner 1991; Healey 1991; Quinn 2005; Brodeur et al. 2007; Price et al. 

2013). The species of invertebrate present in sockeye salmon stomachs depends on where and 

when samples are collected but krill is often a major diet item of sockeye salmon, especially in 

the GOA and Bering Sea (Peterson et al. 1982; Brodeur 1990; Myers et al. 1996).
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In both the estuary and NCC, invertebrates tend to be more numerically dominant and more 

frequently occurring in juvenile Chinook salmon diets whereas fish typically represent most of 

the biomass of prey consumed. In the estuary Americorophium spp., crustaceans, and insects are 

the most abundant insects in juvenile Chinook salmon diets (Bottom et al. 2011; Weitkamp et al. 

In Review) while in the NCC, invertebrates present in juvenile Chinook salmon diets include

copepods, amphipods, decapods, and euphausiids (Brodeur 1991; Daly et al. 2009, 2012). Fish 

found in Chinook salmon diets in the estuary and in the NCC include northern anchovy

(Engraulis mordax), rockfish (Sebastes spp.), Pacific sand lance (Ammodytes hexapterus), and 

smelt (Osmeridae) (Brodeur 1991; Daley et al. 2009). In the ocean, Chinook salmon eat mostly 

fish and squid (Loligo spp.) (Brodeur 1990; Myers et al. 1996).

In estuarine and NCC habitats, steelhead have a diet that is similar to juvenile Chinook salmon

but is not as heavily oriented towards fish (Brodeur 1990; Daly et al. 2014). But, similar to 

Chinook salmon, once steelhead leave the NCC region, their diet is comprised almost entirely of 

fish and squid (squid are rarely seen in diets in the NCC or off WCVI) (Brodeur 1990; Myers et 

al. 1996; Atcheson et al. 2012a, 2012b). Atcheson et al. (2012a) reported that steelhead diets 

varied by age group, region of capture and year of capture but that squid provided the highest 

energy content. 

Diets of all three species vary in response to a number of factors associated with: 1) the prey the 

fish consume (e.g., prey size), 2) the fish consumers themselves (e.g., predator size), and 3) the 

environment (e.g., temperature). Of these, body size of the salmonid predators is especially 

important. Generally, predators eat larger prey as their body size increases (Fresh 1997; Duffy et 

al. 2010). For some salmonid species, as body size increases, the amount of fish prey consumed

increases. For example, Brodeur (1991) found that Chinook salmon and steelhead ate more fish 

in the NCC as their body size increased. Recently, Daly et al. (2009) looked at ontogenetic shifts 

in diet of juvenile Chinook salmon in the NCC and found that diet shifted as a function of fish 

size in the size range 100 mm to 375 mm. In particular, the proportion (by weight) of fish in the 

diet of juvenile Chinook salmon increased as the salmon increased in size to nearly 100% of the 

diet (by weight) in the largest size classes examined (Daly et al. 2009). 

Another factor affecting diet is prey availability, which is a function of the foraging habitat being 

used, time of year, year and environmental conditions (Brodeur et al. 2007; Daly et al. 2009; 

2013). Due to life history and reproductive cycles of prey items, some prey may be abundant at 

one time of year (e.g., spring) but then all but disappear after several months. Shifts in prey 

availability can also occur at longer temporal scales (e.g., years to decades) to changing ocean 

conditions such as temperature and currents. Prey availability can also vary vertically in the 

water column, between day and night (due to diel vertical migration of prey species), and across 

the continental shelf. Shifts in diet in response to food availability can affect marine survival 

(Quinn 2005). Daly et al. (2013) found that winter icthyoplankton that was comprised of earlier 

life stages of many of the food items eaten in the spring by juvenile salmon, could help predict 

changes in ocean conditions and subsequent adult returns two years after the fish entered the 

ocean. Atcheson et al. (2012b) established that steelhead diets in the GOA and Pacific Ocean 

varied with ocean conditions with the amount of squid (the highest quality food item for
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steelhead) that was eaten declining during warm ocean years. For Central Valley Chinook 

salmon, Wells et al. (2012) found that the abundance of returning adult Chinook salmon was 

related to condition of the juvenile Chinook salmon of the same cohort the year before they 

returned to the Sacramento River to spawn. The condition of these salmon was related to the 

proportion of krill in their diets. 

Origin of the fish (hatchery vs. wild) is another factor that can potentially affect diet. There is a 

large amount of literature comparing diets of hatchery-origin and wild salmonids (e.g., Fresh 

1997). In general, when such factors as time and fish size are accounted for, hatchery and wild 

origin salmon of the same species typically have similar diets during their marine life (Daly et al. 

2012; Sweeting and Beamish 2009). For example, in the NCC, Daly et al. (2012) found that 

hatchery origin and wild juvenile Chinook salmon had similar diets during their early marine life 

and that both types of fish tracked seasonal and inter-annual changes in the prey base. While 

hatchery origin and wild Chinook salmon and steelhead had similar marine diets, wild fish 

consumed more food on average and were in better condition and had higher growth rates than 

hatchery origin salmon (Daly et al. 2012; Daly et al. 2014).

In summary, most food habits studies in the estuary and ocean are conducted at the species (e.g., 

sockeye vs. steelhead) level. All three salmon species eat a mix of invertebrates and fish during 

their tenure in estuary and ocean habitats. While there is only limited information on the Snake 

River sockeye salmon ESU, sockeye diets in the ocean have been analyzed from many other 

sources. These studies demonstrate that sockeye salmon always feed almost entirely on 

invertebrates with krill often a major invertebrate diet item of sockeye. In the estuary both 

juvenile Chinook salmon and steelhead eat a mix of different invertebrates and small fish prey. 

By the time Chinook salmon and steelhead are in the NCC and ocean, they eat mostly fish and 

some squid; squid appears to be more important in steelhead diets than in Chinook salmon. Diets 

of all three species vary in response to characteristics of the prey the fish consume (e.g., prey 

size), the fish consumers themselves (e.g., predator size), and the environment (e.g., 

temperature). Of these, body size of the salmonid predators is especially important with 

predators eating larger prey as their body size increases. Prey availability (what the salmon have 

to eat) is also an important factor affecting diet and can vary with the foraging habitat being 

used, time of year, year (e.g., reflecting El Niño’s and PDO changes), and environmental 

conditions.
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5.2. Growth

Growth is the outcome of what the fish eats (both quantity and quality), its basic physiology 

(e.g., metabolism), activity level, environmental conditions, genetic effects, maternal effects, and 

abundance and distribution of competitors. Growth is a key attribute of ocean salmon ecology 

since it is often strongly related to survival with high growth rates often correlated with high 

survival or adult return rates (Pearcy 1992; Mortensen et al. 2000; Beamish et al. 2004; Moss et 

al. 2005; Quinn 2005; Cross et al. 2008; Woodson et al. 2013, Friedland et al. 2014).

Growth rates vary between species, populations and life history types. For example, Figure 9 

illustrates how short term growth measured with the hormone IGF-1 in May and June in the 

NCC can vary between stock groups. The Willamette Spring Chinook salmon grew fastest. 

Wells et al. (2008) examined growth rates in spatially distinct (based on their distributions along 

the west coast of North America) Chinook salmon populations and concluded that growth rates 

were strongly related to the environment the fish occupied and that this was specific to both 

region and life history type. In the NCC, not all yearling Chinook salmon stock groups grow at 

the same rates (Figure 9). Sub-yearling and yearling Chinook salmon have different growth rates 

during their first months in the NCC. In particular, SRSS Chinook yearlings grew more slowly 

than SRF yearlings while SRF sub-yearlings grew more slowly than yearling SRF (Weitkamp et 

al. In Review). In both May and June in the NCC off Oregon and Washington, Willamette 

spring Chinook salmon had the highest growth rates of any of the stocks measured (Beckman 

2014; Figure 9). This may be because Willamette spring Chinook salmon typically enter marine 

waters nearly a month earlier than upper Columbia or Snake River stocks. The lowest percent 

weight gain from time of release to capture in May in the ocean was for SRSS yearling Chinook 

salmon (Beckman 2014).
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Figure 9. IGF-1Sadj levels of six yearling Chinook salmon genetic stocks captured in the ocean in May and June. 

Individual bars show annual means of IGF-1 levels (2006-2011, left to right). Grand means of all years within a 

genetic stock are indicated by black triangles to the right of the bars. Error bars show standard error of the mean.

Significant differences between stocks are indicated in lowercase letters above the bars (Repeated measures 

ANOVA; p < 0.05). Stocks for which n < 5 in a majority of years were not analyzed, indicated by “n/a”. No 

significant differences are abbreviated “nsd”. (Beckman 2014).

Figure 10. Growth of Spring Chinook salmon for two groups of yearling Chinook salmon from the Columbia River) 

using IGF-1 hormone showing variations between years and the relationship between growth and adult returns 2 

years later. (Beckman 2014).

In general, growth is directly correlated to survival with higher growth rates leading to higher 

survival. However, the time period and location over which growth can affect salmon survival 

can vary between populations. Growth that occurs early in ocean life is often positively 

correlated to survival but the specific ocean period over which this early marine growth occurs 

can vary considerably between species and population (Mortensen et al. 2000; Mueter et al. 

MA

a a

c b c n/

JUN

ns
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2002; Farley et al. 2007; Wells et al. 2008; MacFarlane 2010; Tomaro et al. 2012; Friedland et 

al. 2014). For example, Beckman (2014) found that levels of a hormone called IGF that 

measures growth over an 8-10 day period in May after the fish had just entered the ocean varied 

between years and were positively correlated to survival in two groups of yearling spring 

Chinook salmon originating from the Columbia River (Figure 10). Friedland et al. (2014) 

concluded that sustained growth during the summer and fall months after steelhead from the 

Keough River, British Columbia, had entered the ocean had a significant effect on survival. 

Woodson et al. (2013) found evidence that Central California Valley Chinook salmon 

experienced size and growth rate selective mortality early in their marine life near San Francisco 

Bay, but only during years of poor ocean conditions. Individuals that were larger and growing 

faster during freshwater and estuarine rearing were more likely to survive to summer and fall.

Beamish et al. (2004) found that growth of Coho salmon over the late fall and winter of their first 

year in the ocean was related to survival to adulthood while Duffy and Beauchamp (2011) found 

that growth in summer in Puget Sound was strongly related to survival of Puget Sound Chinook 

salmon. 

Higher growth rates result in greater survival as a result of several mechanisms. First, they can 

lead to a larger size at age which reduces vulnerability to size selective predators (Mortensen et 

al. 2000; Moss et al. 2005; Duffy and Beauchamp 2011; Friedland et al. 2014). Studies with a 

variety of salmonid stocks (including Columbia River spring Chinook salmon) have found that 

body size and survival are positively related (Bilton et al. 1982; Holtby et al. 1990; Henderson 

and Cass 1991; Mortensen et al. 2000; Duffy and Beauchamp 2011; Tomaro et al. 2012; 

Woodson et al. 2013). In a study of SRSS Chinook salmon by Miller et al. (2014), marine 

growth and size at capture were positivity correlated to survival (Miller et al. 2014). Second, in 

addition to reducing vulnerability to predators, a larger body size at age can increase 

reproductive success (e.g., through larger egg size and higher fecundity in larger females) (Quinn 

2005). 

Growth rates can also affect age of maturation and size at return during some specific life stages 

in the ocean (Clairborne et al. 2011; Martins et al. 2012). Wells et al. (2007) found that faster 

growth by Klamath River Chinook salmon during the year before they returned to spawn was

related to earlier maturation and larger return size.

Given that growth and mortality can be related during some phases of ocean life, biological and 

environmental factors that reduce growth rates will be especially relevant to recovery planning

(see also following section for discussion of competition effects on growth). One important 

environmental factor that can affect growth is changes in ocean conditions (shifts from good 

ocean years to bad ocean years). In general, good conditions for salmon are cooler ocean 

conditions (such as cool phase of the PDO) or with strong and early upwelling while poor ocean 

conditions for salmon occur in warmer years or in years with weak upwelling. El Nino events 

also result in poor ocean conditions for salmon in the NCC. 

Martinson et al. (2008) found evidence of density dependent ocean growth in all life stages of 

Karluk Lake sockeye salmon that varied as a function of ocean conditions. Growth was 
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negatively related to sockeye salmon abundance during the cool regime and positively related to 

sockeye salmon abundance during the warm regimes. Woodson et al. (2013) found that growth 

rate selective mortality in Central Valley Chinook salmon only occurred during years of poor 

ocean conditions and not during years of good environmental conditions. In general in the NCC, 

food quantity and quality can be affected by large scale environmental changes such as those 

resulting from shifts in the PDO or upwelling. In particular, cold phases of the PDO generally 

lead to higher growth rates (Jacobsen et al. 2012). 

Another factor that can affect growth rates is water temperatures because temperature directly 

affects metabolism of the fish and can affect the quantity and quality of prey available to the 

salmon (e.g., Mackas et al. 2007; Brodeur et al. 2008; Daly et al. 2013). Temperature affects are 

complex and are relevant to all ages of fish in the ocean, as Wells et al. (2007) suggested for 

Klamath River Chinook salmon. It is logical to assume that warmer temperatures can lead to

higher growth rates of salmon because of bioenergetics issues. However, temperatures that are 

too warm can reduce growth rates by impacting the quantity and quality of food that is available; 

when temperatures reach high enough levels they can also stress the fish which can reduce 

growth rates (MacFarlane 2010). 

The effect of higher water temperatures on growth can vary with species and life history stage 

(Martins et al. 2012). This is illustrated by the contrast between sockeye salmon and steelhead. 

In their review of climate effects on sockeye salmon growth and survival, Martins et al. (2012) 

found that warm water temperatures experienced by smolts in the ocean could increase growth 

and survival for some stocks (Alaskan) and decrease it in others (Fraser River). Hinch et al. 

(1995) concluded that warmer water temperatures would depress growth of Fraser River sockeye 

salmon by increasing metabolic costs in the warmer water temperatures and by reducing the food 

supply of the sockeye salmon in the areas they occupied. Friedland et al. (2014) found that the 

return rate of one steelhead population in Canada was negatively correlated with sea surface 

temperatures in the areas occupied by the steelhead. They suggested that this was due to either 

temperature effects on growth directly or on food webs on which the steelhead depended. The 

importance of temperature to steelhead growth and survival is also indicated by the work of 

Atcheson et al. (2012a) who found that steelhead trout in the North Pacific Ocean had a very 

narrow range of temperatures in which to achieve optimal growth and were thus sensitive to even 

small changes in temperature.

In summary, growth is a key attribute of the ocean ecology of salmon and is often strongly 

related to survival; high growth rates are usually correlated with high survival or adult return 

rates. The time period over which growth can influence survival rates can vary as a function of 

species, stock and life history type. The early ocean period is often a critical period for a number 

of salmon populations. Early ocean growth is often positively correlated to survival but the 

specific early ocean period over which this early marine growth occurs can vary considerably 

between species and population. In general, high growth rates are related to survival because 

they lead to a larger size at age which reduces vulnerability to size selective predators and 

because they can affect age of maturation and size when the fish return to spawn. Ocean 

conditions that affect growth can have an important effect on survival. For example, temperature 
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can affect growth rates by directly affecting metabolism of the fish and the quantity and quality 

of prey available to the salmon.
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5.3. Ecological Interactions

There are three primary ecological interactions that can affect the ocean growth and survival of 

Chinook salmon, steelhead or sockeye salmon: 

1. competition for food

2. predation

3. parasites/disease

All three are natural processes that salmon have evolved with for millennia. Of particular 

interest about these interactions is not that they occur, but how has our management of the 

system and the salmon altered these interactions and can we minimize or reduce their impacts to 

help recover depressed salmon populations. 

5.3.1. Competition

Competition for food can be intraspecific (within a species or ESU) or interspecific (between 

species or ESUs); both can occur at the same time. From the perspective of this module, 

competition involving the Snake River ESUs can potentially occur during any space/time 

window after the fish pass Bonneville Dam and until they return to the river as adults and cease 

feeding. The main concern with competition is that it will reduce growth rates which in turn can 

affect size at age and survival; as noted previously, smaller fish generally survive less well than 

larger fish. Relationships between growth, body size/condition, survival, environmental 

conditions, and competition can be complex, however. For example, in a study of upper 

Columbia River sub-yearling Chinook salmon in the NCC, Miller et al. (2013) found (counter 

intuitively) that body condition declined in years that oceanographic conditions were favorable 

(i.e., there was abundant food). They speculated that this could have occurred for two reasons. 

(1) When survival was high, competition was occurring and depressing growth rates because fish 

(i.e., competitors) were abundant. (2) Selective mortality was greater during years of lower 

survival (i.e., relatively more of the smaller, slower growing individuals die in poor survival 

years, leaving proportionately more faster growing fish in good condition).

There is a large accumulation of evidence that demonstrates that competition involving 

anadromous Pacific salmonids occurs under some conditions in both estuarine and ocean 

ecosystems (Quinn 2005). However, most of this information on competition is not specific to 

the Snake River ESU’s. One of the indicators of competition involving salmon in estuarine and 

ocean habitats is the occurrence of density dependent growth and survival for co-occurring

stocks of salmonids in a particular region. Many studies of density dependent growth and 

survival in ocean ecosystems are typically correlative. While correlative studies suggest a 

relationship exists, they do not demonstrate cause and effect. In general, these types of 

correlative studies find that at high enough abundance/density levels in a particular region

(including the estuary), growth declines (i.e., changes in growth are negatively correlated with 

changes in density or abundance); interspecific or intraspecific competition are the presumed 
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mechanism explaining the decline in growth as abundance increases (Fukuwaka and Suzuki 

2000; Bugaev et al 2001; Ruggerone and Goetz 2004; Beamer et al. 2005; Ruggerone et al. 2005; 

Martinson et al. 2008). 

Correlative studies of density-dependent growth and survival form the basis for much what we 

know regarding competition involving salmon in ocean habitats. In part, this reflects the fact 

that it is difficult to establish competition empirically because of challenges associated with 

measuring such things as abundance of competitors and their prey in the ocean. Martinson et al. 

(2008) found evidence of density dependent ocean growth in Karluk Lake sockeye salmon that 

varied with climatic regime; growth was negatively related to sockeye salmon abundance during 

the cool regime and lower abundance levels and positively related to sockeye salmon abundance 

at higher abundances during the warm regimes. Brodeur et al. (1992) suggested that when ocean 

conditions were unfavorable during the 1983 El Nino, the amount of several key prey taxa were 

insufficient to sustain the total population of salmon; under these conditions of prey limitation, 

salmon would be competing. Using growth and abundance data, Pyper and Peterman (1999) 

concluded that intraspecific competition for food resources in sockeye salmon occurred in the 

North Pacific Ocean. Bugaev et al.’s (2001) observation that the size of sockeye salmon 

returning to the Ozernaya River of Russia is reduced in years when sockeye salmon are abundant

in the marine environment suggests intraspecific competition was occurring in marine waters. 

Much of the evidence involving density dependent effects in ocean habitats is based upon studies 

involving pink salmon (which are planktivorous) because they undergo large, inter-annual 

fluctuations in abundance. Welch and Parsons (1993) used isotope analysis and suggested that 

high overlap and hence competition is most likely to occur between sockeye, pink and coho

salmon. Ruggerone and Goetz (2004), however, found that all 13 populations of Puget Sound 

Chinook salmon appeared to be affected by fluctuations in the abundance of pink salmon.

Several studies suggest that sockeye salmon marine growth and survival is reduced in years of 

high pink salmon abundance (Bugaev et al 2001; Ruggerone et al. 2003). Atcheson et al. 

(2012b) found that steelhead diets in the Pacific Ocean and GOA varied with abundance of wild 

pink salmon stocks from Kamchatka. Indicators of good steelhead diets such as a high 

proportion of squid were negatively correlated with the abundance of pink salmon.

One potential source of competitors for the listed ESU’s of the Snake River is the large 

production of hatchery fish in the Columbia River. The arrival of large numbers of fish in the 

estuary and NCC within narrow time windows could create conditions whereby hatchery fish 

might compete with and reduce growth rates of listed populations. If the overall consumptive 

demand (a function of both fish abundance and fish size) of hatchery fish was sufficient (i.e., 

how much prey do the hatchery fish eat relative to what is present), growth rates of listed 

populations could be reduced. This could depend upon environmental conditions, species being 

considered, relative amount of prey available in the environment, and habitat where the 

interaction occurred.

Levin et al. (2001) found a strong negative relationship between the survival of SRSS Chinook 

salmon and numbers of hatchery fish released, suggesting negative effects of hatchery fish were 
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occurring. Similar effects of hatchery fish on wild fish were suggested by Nickelson (2003) for 

Oregon coastal Coho salmon. Many diet studies suggest that juvenile hatchery-origin and wild 

salmon of the same species often have similar diets and high spatial overlap (Daly et al. 2009; 

Sweeting and Beamish 2009). Thus, if food was limiting in these situations, the likelihood that 

competition would occur is high. For example, Daly et al. (2012) evaluated a number of 

parameters associated with hatchery-origin and wild yearling spring Chinook salmon during 

early marine life to evaluate the potential for competition between these two types of fish. They 

found that both hatchery and wild Chinook had high dietary and spatial overlap during early 

marine life as well as similar growth rates. Most importantly, the overlaps in diet and spatial 

occurrence; size; condition; and growth appeared to change at the same time for both wild fish

and hatchery-origin fish and suggested fish were responding synchronously to changes in 

environmental conditions.

In summary, competition can occur throughout the life cycle of salmon in estuarine and ocean 

habitats. One of the major indicators of competition involving salmon in estuarine and ocean 

habitats is the occurrence of density dependent growth and survival for co-occurring stocks of 

salmonids. These density dependent relationships have been established for a number salmon 

stocks during ocean life and often involve pink salmon because they undergo large inter-annual 

changes in abundance. Most evidence that density dependent relationships are occurring are 

correlative. In general, correlative studies have found that changes in growth are correlated with 

changes in density or abundance; interspecific or intraspecific competition are the presumed 

mechanism explaining the decline in growth. One potential source of competitors for the listed 

ESU’s of the Snake River is the large production of hatchery fish in the Columbia River. The 

arrival of large numbers of fish in the estuary and NCC within narrow time windows could create 

conditions whereby hatchery fish might compete with and reduce growth rates of listed 

populations. 

5.3.2. Predation

In general, although predation is considered to be a major driver of salmon mortality throughout 

their entire life cycle, relatively little is known about predator prey interactions in the ocean. 

While factors such as disease or poor feeding conditions may be the proximate cause of 

mortality, predation probably represents the ultimate disposal of most salmon. For example, fish 

that are diseased or starving are more likely to be eaten by a predator. Potential estuarine and 

ocean predators of salmon include many species of fish, birds, and mammals (Fresh 1997), as 

well as several invertebrates such as Humboldt squid (Field et al. 2013). 

For Columbia River salmonids, considerable attention has focused on effects of predation by 

birds nesting on islands in the estuary. Caspian terns, several species of gulls, and doublecrested cormorants forage on salmon smolts in the Columbia River Estuary (Collis et al. 2001). 

The effects of these species on anadromous salmon in the Columbia River basin has also

increased in recent years as a result of the northern expansion of breeding colonies, especially 

Caspian terns. Ryan et al. (2003) estimated minimum predation losses in the Columbia River 

estuary by terns and cormorants of 11.6% for steelhead and 2.6% for yearling Chinook salmon. 
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Sebring et al. (2013) estimated losses of upper basin sub-yearlings (a mix of stocks including 

Snake River fish) to be about 2%. These percentages are not trivial and translate into millions of 

salmon consumed per year by birds from a single rookery. 

Although tern and cormorant predation in the estuary have been a primary management concern 

for Columbia River origin salmon, predation by birds also occurs beyond the estuary and in the 

plume and ocean. Avian predation outside the estuary is not as well studied. Potential bird 

predators outside the estuary include common murres, rhinoceros auklets, and shearwaters (Ogi 

and Tsjita 1973; Lance and Thompson 2005). Near the mouth of the Columbia River, common 

murres and shearwaters may be especially important predators as both are very abundant during 

the salmon outmigration and will eat salmon. Salmon were found in 11% of the stomachs of 

common murres sampled (n = 30) in one year near the mouth of the Columbia River (Zamon 

2013). Remains of Chinook salmon, Coho salmon, and steelhead were identified in the murres 

using genetic markers. Salmon have yet to be found in any of the available samples of 

shearwater stomachs (n = 37), but a Columbia River steelhead PIT tag was recovered from a 

shearwater stomach collected in 2007. Zamon (2013) found a significant linear relationship 

between the density of birds in May of a given year and adult returns at Bonneville Dam for

Coho salmon that migrated as juveniles during that year (R2 = 0.56; P = 0.05). No such 

relationship has been detected for Chinook salmon, or using bird densities in other months. 

Indirect evidence that avian predation might be significant near the mouth of Columbia River 

comes from a study of acoustically tagged fish that found that mortality rates of salmon in this 

region were high and residence times of the fish were short. These observations are consistent 

with predation, especially by birds, as the primary cause of the high mortality. Similar to any 

predator-prey interaction, actual predation losses are a result of the complex interactions of a 

number of factors such as river flow, salinity, tidal phase, and the distribution of non-salmonid 

prey species such as northern anchovy (Zamon et al. 2013) (Figure 11). 
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Figure 11. Conceptual diagram showing how changes in the availability of alternate prey can affect consumption of 

salmon by predators. (Zamon 2013).

Other than avian predators, all salmon species are preyed on at all life stages by a multitude of 

species such as sablefish (Sturtevant et al 2009), Pacific hake (Emmett et al. 2005), pinnipeds 

(McKenzie and Wynne 2008), and killer whales (Ford et al. 2006). There may be particular 

space/time windows, however, where predation levels are especially high. For example, 

Friedland et al. (2014) concluded that size mediated predation was the most likely explanation 

for the relationship between ocean growth of steelhead in summer and fall of their first year and 

their survival. Also, predation is believed to be especially high during estuarine and early marine 

life (Parker 1968; Pearcy 1992). 

Predation rates on salmon will depend on characteristics of predators, their prey and the 

environment they are occupying (Fresh 1997). For example, faster growing salmon can outgrow 

their predators more rapidly while larger salmon have a greater chance of out swimming a 

predator. In the ocean, human induced climate change has the potential to affect predation losses 

of all populations of salmon juveniles. Environmental conditions in some years can drive 

predation by particular species such as Pacific hake, mackerel, and Humboldt squid in the NCC 
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off the coast of Washington and Oregon (Emmett et al. 2006; Emmett and Sampson 2007; Litz et 

al. 2011). Studies suggest that abundance of these predators is often (but not always) higher in 

the coastal NCC during warm years of the PDO as these predators move onto the Continental 

Shelf in warm years where overlap with salmon increases. In colder years, overlap is reduced 

and abundance of predators declines as piscivores occupy deeper habitats. Given that we can 

expect a greater frequency of warmer years as a result of climate change, perhaps predation will 

become a recurring problem, unrelated to the phase of the PDO.

Once adults enter the Columbia River estuary, predation can occur during their upstream 

migration. The major source of predation in the estuary is harbor seals and sea lions and while 

predation probably occurs in the entire lower river, it is especially high around Bonneville Dam

because fish are concentrated in a smaller area and so more vulnerable to the predators. Stansell 

et al. (2010) estimated that pinnipeds consumed 4,000-6,000 salmonids per year in the tailrace of 

Bonneville dam since 2008, equivalent to 2.2 to 2.9% of the salmon run during spring (1 January 

to 31 May). Wargo-Rub (2011, 2012) provided estimates of adult Chinook salmon mortality

during migration through the estuary to Bonneville Dam and although they did not study causes 

of mortality, losses are most likely due to marine mammal predation.

In summary, predation is considered to be a major driver of salmon mortality throughout their 

entire life cycle. However, relatively little is known about predation in the estuary and the 

ocean. Predation rates on salmon will depend on characteristics of predators, their prey and the 

environment they are occupying. Predation may be especially high during certain space/time 

windows such as during estuarine and early marine life. In the Columbia River estuary, for 

example, high predation rates by birds nesting on islands in the estuary have been documented. 

Factors such as disease or poor feeding conditions may be the proximate cause of mortality, but 

most salmon that die, probably end up being eaten by a predator. Faster growing salmon can 

outgrow their predators more rapidly while larger salmon have a greater chance of out swimming 

a predator. Human induced climate change has the potential to affect predation losses of all 

populations of salmon juveniles through such mechanisms as changes in temperature regimes. 

5.3.3. Pathogens and Parasites

Similar to predators, pathogens can have a significant effect on the survival of juvenile salmon 

during their estuarine and marine residence (Jacobson et al. 2008). The outcome of an infection 

by a pathogen or parasite is mediated by interactions among the pathogen, its host, and the 

environment. A number of pathogens have been reported to affect juvenile salmon during the 

freshwater migration (Fryer and Sanders 1981; Bartholomew et al. 1992; Ferguson et al. 2011), 

but little is known about the effects of pathogens on juvenile salmon during early marine 

residence. The freshwater trematode, Nanophyetus salmincola, encysts in all tissues and organs 

of Pacific salmon. In the NCC, a decline of highly infected Coho salmon was observed between 

early and late summer (Jacobson et al. 2008). These results suggested that approximately 20% 

of Coho salmon mortality during the first months at sea was associated with this parasite. 

Abundances of this parasite are much lower in yearling and sub-yearling Chinook salmon, 

probably due to differences in freshwater residence and exposure to the infective stages of the 
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parasite. In steelhead, intensities can be similar, if not higher than in Coho salmon. Preliminary 

data from steelhead from the lower estuary collected in 2010 had a mean intensity of 1163 cysts 

in the posterior kidney (from a prevalence of 27%) (Jacobson 2014). 

Renibacterium salmoninarum, the causative agent for Bacterial Kidney Disease, has been highly 

prevalent in Chinook salmon at hatcheries (VanderKooi and Maule 1999), and during migration 

through the Columbia River estuary (Elliott et al. 1997, Pascho et al. 1993). Infected yearling 

Chinook salmon collected off of Oregon and Washington from 1999 – 2004 had lower weight 

residuals (less weight than expected for size) and plasma IGF-1 than uninfected yearlings in all 

years except 2000 (Sandell et al. In Press). As mentioned above any factors that affect growth 

and condition of juvenile salmon are ultimately contributing to mortality. Chinook salmon from 

Snake River stocks were too few in number to analyze separately. In 2008 sample sizes of Snake 

River fall Chinook salmon were large enough to compare the prevalence of R. salmoninarum

infection between June and September catches off Oregon and Washington. There was a 

decrease in prevalence from approximately 60% infected in June to less than 20% infected in 

September suggesting a loss of infected fish during the first months of ocean residence or of 

those fish leaving the Columbia River and estuary later in the summer (Jacobson 2014).
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5.4. Mortality

In general, mortality rates of salmonids after they leave freshwater can be as high as 95% but

vary considerably from year-to-year and between different populations (Parker 1968; Bradford 

1995; Moss et al. 2005; Scheuerell and Williams 2005; Williams et al. 2005). Within the 

estuary, overall mortality rates of salmonids are unknown but an examination of avian predation 

losses provides some perspective on levels of mortality of salmon in this area (Table 1). Clearly, 

if predation from other sources were considered (e.g., pikeminnow predation below Bonneville 

Dam- Zimmerman 1999), mortality in the estuary would be much higher than if only avian 

predators are considered. Ryan et al. (2003) estimated that tern and double-crested cormorant 

predation from birds nesting on Rice and East Sand islands in the estuary, ranged from 11.5% to 

2.6%, depending on the prey species. In a subsequent study, Sebring et al. (2013) found that 

predation on Upriver Bright stock groups (a mix coming from above Bonneville Dam that 

includes Snake River sub-yearlings), by terns and cormorants was low (about 2%). Good et al. 

(2007) concluded that eliminating even some of the predation mortality from Caspian tern 

predation in the estuary would assist recovery of Snake River steelhead trout. These benefits 

were comparable to reducing mortality through the hydropower system. 

Table 1. Predation rates on juvenile salmon in the estuary (Zamon 2013).

Group Caspian tern 2012 Double-crested cormorant 

2012

Snake River sockeye 2.1% (1.1%-3.2%) 4.0% (2.2-6.1%)

Snake River spring/summer 

Chinook

2.2% (1.8%-2.7%) 4.2% (3.4%-5.2%)

Snake River fall Chinook 0.7% (0.5%-0.9%) 3.0% (2.3%-3.8%)

Snake River steelhead 10.0% (8.4%-11.9%) 5.4% (4.0%-7.0%)

Once salmonids enter the ocean, evidence suggests that natural mortality is highly variable and 

that early marine life is a period of critical mortality for many (but not all) salmonid stocks 

(Bradford 1995; Scheuerell and Williams 2005; Williams et al. 2005). By critical mortality we 

mean that mortality is not necessarily the highest at this time but that mortality is highly variable 

and thus helps set year class strength. Evidence from a wide variety of salmonid stocks, 

including a number from the Columbia River basin, strongly supports the hypothesis that early 

marine life is a critical period that can largely determine the strength of adult returns years in the 

future; and this critical period can range from the first weeks to months the fish are at sea

(Beamish et al. 2004; Mueter et al. 2002; Farley et al. 2007; Wells et al. 2008; MacFarlane 2010; 

Moore et al. 2010; Duffy and Beauchamp 2011; Thomson et al. 2012; Tomaro et al. 2012; Miller 

et al. 2013; Burke et al. 2013a; Trudel and Hertz 2013). Thus, the condition and size of salmon 

as they leave the estuary and first enter the ocean may be a prime determinant of subsequent 

survival. What constitutes early marine life can vary with species, stock, and life history type. 

Using acoustically tagged fish, Brosnan et al. (2014) found that survival in the “plume” (Astoria 

Bridge to near the mouth of Willapa Bay) ranged from 0.13 to 0.86 for yearling Chinook salmon 
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of several different stocks. Because residence times in the plume were so short (an average of 7 

days), they concluded that predation was the most likely mechanism explaining this loss. In 

contrast, Friedland et al. (2014) concluded that the period of critical mortality of Keogh River 

steelhead was much longer and occurred during the summer and fall of their first year in the 

ocean. 

Most of this “early marine” mortality is thought to occur during two critical periods within the 

first year of ocean life. The first period is thought to be predation-based mortality that occurs 

during the first few weeks to months of ocean life (e.g., Brosnan et al. 2014; Friedland et al. 

2014). The second period occurs during and following the first winter at sea and is thought to 

occur as a result of starvation (Beamish and Mahnken 2001; Moss et al. 2005). The hypothesis 

for the second period is that the fish have to consume enough food during their first spring and 

summer at sea to achieve a critical size with enough accumulated energy reserves that allows 

them to successfully survive the winter. Although there is strong evidence that early marine life 

is a critical period for survival of many salmon stocks, substantial mortality can still occur later 

in ocean life and more distant from the river of origin (Welch et al. 2011). 

Two interrelated factors that can be important determinants of mortality are fish size and growth

(Figure 12 and 13). As we noted, mortality can be a function of growth rates and size 

(MacFarlane 2010; Duffy and Beauchamp 2011). Faster growing fish are less likely to die than 

slower growing fish although this effect may vary with environmental conditions in the ocean 

(Woodson et al. 2013). Studies with a variety of salmonid stocks (including Columbia River 

spring Chinook salmon) have found that body size and survival are often positively related 

(Bilton et al. 1982; Holtby et al. 1990; Henderson and Cass 1991; Mortensen et al. 2000; Duffy 

and Beauchamp 2011; Tomaro et al. 2012; Woodson et al. 2013). In general, larger bodied fish 

are less likely to die than smaller bodied fish although this relationship may not be true under all 

ocean environmental conditions (Irvine et al. 2013). Healey (1982) showed that significant size 

selective mortality occurred in chum salmon during their first weeks at sea. Fish size can affect

both predation- and starvation-based mortality (Willette et al. 2001). 
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Figure 12. Relationship between adult returns and mean annual size and growth characteristics for juvenile midupper Columbia River spring Chinook salmon. Ln-transformed adult returns to Priest Rapids Dam (-2 yr.) versus 

mid-upper Columbia River mean (±SE) juvenile size at freshwater emigration (a), size at capture (b), and marine 

growth rate (c). Lines represent linear or polynomial fit. Juvenile collections occurred in 1999-2000, 2002-2004, and 

2006-2008. (Jacobson et al. 2012)

Figure 13. Relationship between Ln-transformed adult returns to Priest Rapids Dam (-2 yr) and mean annual size 

(±SE) at capture for juvenile mid-upper Columbia River spring Chinook salmon versus (left); and relationship 

between survival (back-transformed SAR) and size at capture of juvenile Snake River sp/su Chinook salmon. 

Juvenile collections occurred in 1999-2000, 2002-2004, and 2006-2008. (Jacobson et al. 2012).

Salmon size can be important to mortality because swimming speed is related to fish size which 

in turn is related to a fish’s ability to evade predation. Also, high growth rates allow fish to 

outgrow their predators: get large enough such that predators cannot grasp, handle and eat the 

salmon. Thus, ocean conditions that lead to slower growth would be expected to reduce fish size 

and increase mortality during early marine life (Pearcy 1992; Beamish et al. 2004; Cross et al. 

2008; Woodson et al. 2013). 

Salmon and steelhead mortality can be affected by a number of environmental and biological 

factors (Fresh 1997), including factors associated with freshwater. One hypothesis is that 

passage through the hydroelectric dams can result in mortality that is delayed until well after the 

fish leave the Columbia River basin (Reichisky et al. 2014; Schaller and Petrosky 2007; Schaller 

et al. 2014). In addition, how the fish get to the estuary and migrate through the estuary may be 

important as well. In particular, some research suggests that salmon that are transported through 
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the hydrosystem perform less well than fish that freely migrate (e.g., Muir et al. 2006; Reichisky 

et al. 2014; Haeseker et al. 2012; Schaller et al. 2014). How the fish migrate through the 

complex system of channels in the estuary can affect survival. Harnish et al. (2012) used 

acoustic transmitters to evaluate mortality and travel times in different reaches for sub-yearling 

and yearling Chinook salmon and steelhead. They found differences in mortality were a function 

of pathway used; fish using the fastest pathways (the main channel) did not necessarily have the 

highest survival. 

Interestingly, some evidence suggests flow may have an influence on marine mortality rates. 

Studies by Petrosky and Schaller (2010) and Haeseker et al. (2012) suggest that flow during 

seaward migration can affect marine survival of Snake River steelhead and SRSS Chinook 

salmon with lower flows correlated with reduced marine survival; however, it is not clear what 

the mechanism is explaining this result. Flow can also influence arrival timing in the estuary, as 

can transportation, which can both affect subsequent mortality (Scheuerell et al. 2009; Tomaro et 

al. 2012). Flow also affects plume characteristics (Burla et al. 2010) which can affect salmonid 

survival. Miller et al. (2013) found that returns of upper Columbia sub-yearling Chinook salmon 

to Priest Rapids Dam were related to plume volume at the time of emigration in most years 

studied. 

During estuarine and marine life, fluctuations in environmental conditions can affect mortality 

rates. As noted previously, mortality can vary between good and bad ocean years (Cross et al. 

2008; Woodson et al. 2013). In their review of climate effects on sockeye salmon growth and 

survival, Martins et al. (2012) found that warm temperatures could increase survival for some 

stocks (Alaskan) and decrease it in others (Fraser River). They speculated that temperature 

might be a proxy for regional mechanisms affecting marine survival (Mueter et al. 2002). 

Although most studies have focused on mortality in juvenile and sub-adult life stages, adult

mortality due to marine mammal predation can occur throughout ocean life and in the estuary. 

Wargo-Rub et al. (2012) estimated stock specific mortality of spring Chinook salmon in the 

lower river (to Bonneville Dam) and found that for Snake River spring Chinook salmon, survival 

to Bonneville Dam in 2011 was 86% for the season but varied over time with higher mortality 

occurring in the middle part of the run. Stansell et al. (2010) examined mortality specifically in 

the tailrace of Bonneville Dam and estimated that pinnipeds consumed 4,000-6,000 salmonids 

per year in the tailrace of Bonneville dam since 2008, equivalent to 2.2 to 2.9% of the salmon 

run during spring (1 January to 31 May). 

In summary, salmon experience high (up to 95%) and variable mortality from the time they pass 

Bonneville Dam until they return as adults. Mortality rates vary as a function of species, stock, 

life history type, ecosystem the fish occupy, characteristics of the salmon such as fish size, and 

environmental characteristics. For example, warm ocean temperatures can increase survival for 

some sockeye stocks (Alaskan) and decrease it in other sockeye (Fraser River). Fish size and 

growth are often correlated with mortality with large size and fast growth related to high 

survival. Early marine life appears to be a critical period of mortality for many groups of 

salmon, especially yearling groups of Chinook salmon. By critical mortality we mean a period 
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where mortality is not necessarily the highest is highly variable and thus helps set year class 

strength. Depending on the species and origin, the period defined as early marine life can vary 

from the first days the fish are in the ocean to months later. Significant mortality for some 

species/stocks can occur, however, later in ocean life, such as for steelhead and sockeye. 
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5.5 Habitat Use 

In the estuary, fish can potentially occupy a wide range of habitat types that range from shallow, 

vegetated wetland areas to the deep, more open waters of the main channels. Habitat use varies 

as a function of species and life history type and is strongly related to fish size; species and life 

history type are all interrelated, however. In general, the smaller fish (typically sub-yearling 

Chinook salmon) are more closely associated with either shallow open beaches or wetlands 

(Roegner et al. 2012) while most of the larger bodied fish (including steelhead, sockeye and 

yearling Chinook salmon) are associated with deeper channel areas (such as the main navigation 

channel). Many of the larger bodied fish appear to primarily use the lower river/estuary as a 

migration corridor as evidenced by their very rapid migration through the estuary. Travel times 

of < 7 days from Bonneville to Rkm 15 are not uncommon for steelhead and yearling spring 

Chinook salmon. However there is considerable variability in migration rates of individual fish 

and there are some yearlings found in wetland habitats. Variable migration rate and use of 

alternate habitats contribute to the diversity and spatial structure of the populations, which are

important elements of recovery. In addition, the compressed migration window demonstrated by 

most yearling migrants means use of shallow water habitat may have been unappreciated when 

fish sampling periods and migration timing were not synchronized (Roegner et al. In Prep). 

For yearling Chinook salmon and steelhead, feeding intensity (relative amount of food in 

stomachs) increased as the fish migrated downstream from Bonneville Dam and into the estuary 

(Weitkamp et al. In Review). Similarly, for steelhead, feeding intensity increased as the fish 

moved from the estuary and into the NCC with steelhead in the estuary consuming fewer types 

of prey and having less full stomachs than fish captured in the NCC (Daly et al. 2014).

The long period of residence of sub-yearling fish in the estuary and diversity of sizes that are 

present (Weitkamp et al. In Review) suggests the sub-yearlings in the estuary are probably a mix 

of fish actively migrating to the ocean and fish that are rearing for some period in shallow water 

habitats (Roegner et al. 2012). Sub-yearling sized Chinook salmon dominate catches in shallow, 

open beach areas and shallow tidal channels in different types of wetlands (Bottom et al. 2011; 

Roegner et al. 2010; 2012). 

Within any part of the ocean, there is habitat structure with respect to such factors as depth of the 

bottom, distance to shore, water quality conditions (temperature and salinity), currents and 

eddies. How fish respond to these factors is poorly understood but depends upon their species 

and population, fish size, ocean entry time and other factors. Close to the estuary, the plume 

provides strong habitat features with respect to temperature and salinity. The potential benefits 

of inhabiting the plume have not been quantified for juvenile salmon, although work by Burla et 

al. (2010) suggests that under some conditions, the plume may benefit steelhead. We know that 

for spring Chinook salmon from the upper Columbia River, plume volume at the time of 

emigration is correlated with size at capture which is strongly related to adult returns two years 

later (Tomaro et al. 2012). It is not clear, however, why plume volume is important to salmon or 

if it is a surrogate for something else that the fish are responding to. The turbid, low-salinity 

water masses may provide shelter from many marine predators, aid in the physiological 
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transition from smolt to fully seawater adapted animal, and may create favorable feeding habitats 

in areas where plume water converges with shelf water to form highly dynamic turbidity fronts. 

Previous studies have shown that relatively high numbers of Coho and Chinook salmon smolts 

are present in the Columbia River plume off Oregon and Washington (Fisher and Pearcy 1995). 

Studies in other river plumes have demonstrated that elevated levels of potential prey items can 

occur in frontal regions (Grimes and Finucane, 1991; Grimes and Kingsford 1996).

Outside the plume, habitat factors that can be important to the salmon depend on species and life 

history. Yu et al. (2012) used a modeling approach to suggest that Chinook salmon yearling 

distribution (no stock assignments were done) was primarily a function of environmental factors 

such as temperature and chlorophyll in addition to long shore currents. They also concluded that 

different habitat factors affected fish north and south of the Columbia River. Although 

associations with habitat characteristics were probably not spurious, this approach oversimplifies 

the dynamics of fish in the midst of a migration. In a follow-up study, Burke et al. (2013a) used 

a different modeling approach and concluded that geospatial factors were more important than 

environmental factors. In essence, they found that fish were not selecting particular types of 

habitat per se but were migrating first and then responding to what they encountered second. 

There may be differences between the species in habitat use. Sub-yearlings may respond 

differently to environmental factors since they tend to not migrate as far north and are associated 

with the shelf area longer. Tomaro et al. (2012) showed that juvenile salmon moved slower off 

the coast of Washington when growth conditions were good than when they were bad. 

In the North Pacific, temperature appears to be an especially important habitat factor. The 

importance of temperature is especially true for steelhead who have a narrow range of optimum 

temperatures (Atcheson et al. 2012b) and appear to be primarily restricted in the their 

distribution to surface waters in a narrow north-south band across the Pacific Ocean (Welch et al. 

1998). 
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5.6 Habitat Connectivity

Although we often consider each habitat the salmon occupy in isolation, it is clear that there are 

physical and biological connections between habitats and the fish that occupy them. Physical 

connectivity includes tidal action that can push saltwater well upstream and change salinity 

regimes in the estuary which can have physical and biological manifestations. Freshwater 

discharged into the Pacific Ocean in combination with coastal winds creates the plume 

environment (Horner-Devine et al. 2009). The influence of the plume is not limited to the area 

near the mouth of the Columbia River but it can extend over broad areas off the Washington and 

Oregon Coasts because the plume can break apart and pieces can be found hundreds of miles 

from the mouth of the river (Hickey 1989). A significant portion of the plume volume (67%-

Baptista 2013) is a function of river flow. The plume does not simply affect the area near the 

river’s mouth but can affect much of coastal Washington depending on its volume, winds, and 

other physical factors (Hickey et al. 2009). We know that for spring Chinook salmon from the 

upper Columbia River, plume volume at the time of emigration is correlated with size at capture 

which is strongly related to adult returns two years later (Tomaro et al. 2012). Similarly, Miller 

et al. (2013) found that returns of a population of unlisted mid-upper Columbia sub-yearling 

Chinook salmon to Priest Rapids Dam were related to plume volume at emigration, in most 

years. 

Another example of physical connectivity is climate processes such as El Nino and La Nina 

events and the PDO which can affect both ocean and terrestrial processes. Ocean and land 

temperatures can both be affected at large spatial scales by the same climate processes such as 

the PDO (see following section). On land, climate-induced changes can alter the proportion of 

freshwater that enters the Columbia River via snow-pack vs rainfall. This change in water 

supply can affect what is discharged into the ocean which may change the physics and ecology 

of the coastal ocean environment, which in turn can affect the behavior, growth, and survival of 

the salmon (Bisbal and McConnaha 1998; Burla et al. 2010; Miller et al. 2013).

Freshwater, estuary, and ocean ecosystems are also connected biologically. One example is the 

transport of nutrients from the ocean back to freshwater by spawning adults (NRC 1996). 

Humans both directly and indirectly affect the performance of salmonids while they are at sea 

(Bisbal and McConnaha 1998) by controlling fish size, timing of ocean entry, density of 

salmonids in the estuary and ocean, and condition of the fish. Changes in all these parameters 

can influence growth and survival of the salmonids during later life stages (Scheuerell et al. 

2009; Tomaro et al. 2012). For example, mean body size at ocean entry and early marine growth 

in yearling Chinook salmon (hatchery-origin) was positively correlated with adult returns 

(Claiborne et al. 2011) while body condition of sub-yearling Chinook salmon has been correlated 

with adult returns in some Columbia River Chinook salmon (Miller et al. 2013). A number of 

studies have shown that manipulations of the time and size at which salmon enter the ocean 

(most obviously with hatchery origin fish) can affect adult return rates (Bilton et al. 1982; Holtby 

et al. 1990). 
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6. Anthropogenic Risks to Salmon During 

Estuarine/Ocean Life 

6.1. General

Salmon populations are subject to a wide variety of risk factors that can diminish their viability

or ability to persist over time. Many of these factors are naturally occurring while others result 

directly or indirectly from the actions of people. Further, risk factors operate at various spatial 

and temporal scales, can have cumulative effects, and will differ in their implications for 

population viability of an ESU, DPS, or population. We use the definition of viability developed 

by McElhaney et al. (2000) to guide recovery as encompassing four population attributes: 

abundance, productivity, spatial structure, and diversity. 

While naturally occurring risk factors (e.g., PDO) are important determinants of population 

viability, we focus this discussion on anthropogenic factors. While harvest can clearly affect 

population viability, it’s implications to listed Snake River salmonids are covered in other parts 

of the recovery planning process and are not considered further here. We also do not consider 

effects of the hatchery program as this is again part of other analyses. The effects of many 

potential risk factors are still not well understood. For example, while we have surveys of where 

toxics occur in some areas, we do not fully understand at what concentrations they are an issue 

for fish. We have focused much of this discussion of risk factors on climate change because of 

the potential of this factor to have broad scale impacts throughout the salmon life cycle and 

because recent analyses highlight the threat posed by climate change on our marine and estuarine 

ecosystems (e.g., Halpern et al. 2009).

Although our focus here is on climate change, we note that several large scale analyses of risk 

factors affecting salmonid populations have recently been conducted. In the estuary, Fresh et al. 

(2005) considered the effects of four estuarine risk factors on different Columbia River basin 

ESUs- flow, predation, habitat and toxics/contaminants. The estuary module further summarized 

the work of Fresh et al. (2005) who selected their four risk factors from a larger list because they 

met four criteria: 1) the factor could be linked to the hydropower system, 2) there was 

quantitative data, 3) a significant change in the factor was evident from historical conditions, and 

4) the factor could be linked to population viability of salmonids. Several important factors, 

notably temperature changes were not considered in this analysis. This analysis concluded that 

for yearling dominated populations, flow and habitat had a high ability to affect population 

viability. In contrast, none of the four factors were considered to have a high ability to affect 

viability of sub-yearling dominated populations (Fresh et al. 2005). More recent studies (since 

Fresh et al. 2005 was published) suggest that for yearling ESUs, predation by birds in the estuary 

may be a higher risk factor than previously considered (Sebring et al. 2013) given the high 

predation rates found in these studies. Habitat remains a high risk factor. Recently published 

studies of contaminant/toxic effects found that fish may acquire high levels of some pollutants in 

the upper river before they enter the estuary (Strickland et al. 2011). Johnson et al. (2013) found 
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the greatest uptake of pollutants in ESUs dominated by sub-yearlings, likely because individuals 

from these ESUs tend to have a longer residence time in the estuary. 

In the California Current, analyses of risk factors have been conducted by Halpern et al. (2009) 

and the Integrated Ecosystem Assessment program of NOAA. None of these analyses have been 

specific to salmon at this time. Halpern et al. (2009) evaluated cumulative effects of 25 human 

activities in 19 types of marine ecosystems and concluded that factors associated with human 

population centers and the continental shelf were of the most concern. 
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6.2 Climate Change

The effects of changing climate conditions on salmon and their ecosystems, especially those 

associated with anthropogenic drivers, are of considerable interest to salmon managers and 

ecosystem scientists. In this section, we consider some of the implications of climate-driven

changes occurring in the Columbia River estuary and the ocean on anadromous salmonids. 

Although our focus here is on effects in the ocean and estuary, the overall effect of climate 

change on any anadromous stock must consider all habitats and life stages simultaneously and 

cumulatively (Crozier et al. 2008; Healey 2011; Wainwright and Weitkamp 2013). The scope 

and magnitude of any affect experienced by salmon will be a function of how the climate 

actually changes (e.g., rate and magnitude), how these changes ultimately affect physical and 

biological processes, and the stock/population being considered (Tolimieri and Levin 2004). 

Many of these processes interact, making predicting effects of climate change especially 

problematic (Crozier et al. 2008). 

Although there is only a limited amount of information specific to climate change effects on the 

Snake River ESU’s (but, see Columbia River basin review by Independent Scientific Advisory 

Board [ISAB] 2007), there is a large and expanding literature on climate change effects in 

general on salmon (e.g., Schindler et al. 2008; Crozier et al. 2008) and ecosystems (e.g., see 

review by Griffis and Howard 2013 for a nation-wide perspective and King et al. 2011 for a 

‘California Current’ perspective). Wainwright and Weitkamp (2013) summarized the potential 

physical changes that could potentially result from the effects of climate change on Oregon coast 

Coho salmon; although developed for Coho salmon, this synopsis provides useful guidance for 

considering climate change effects on Snake River salmonids. Table 2 summarizes the major 

physical trends in estuaries and oceans that are likely to affect Snake River salmon. There is 

considerable published work on the effects of climate change on salmon in freshwater 

environments (reviewed by ISAB 2007 and Crozier et al. 2008), and these are not detailed here. 

We first review effects in estuaries, then in the ocean.

6.2.1 Estuary Effects

Within the Columbia River estuary, changes in temperature, flow, and sea level (water level in 

the estuary) are the primary physical factors responsive to a changing climate. The water 

temperatures in the estuary will increase both as a result of continued increases in water 

temperature in the Columbia River basin and because of increases in ocean water entering the 

estuary. Over the last 60 years, there has been a steady increase in temperature of water entering 

the estuary as a result of such basin scale changes as precipitation increasingly falling as rain 

rather than snow in higher elevations, snow pack decreasing, peak flows increasing, and latesummer/early fall flows diminishing (ISAB 2007). 
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Table 2. Physical and chemical climate trends in estuaries and the ocean that may affect Snake River salmon (from 

ISAB 2007; Wainwright and Weitkamp 2013).

Region Climate Trend Certainty of 

Change

Estuary

Increasing sea level High

Increasing water temperature Moderate

Changing seasonal freshwater flows Moderate

Changing saltwater intrusion limit Low

Ocean

Increasing water temperature High

Intensifying upwelling Moderate

Later spring transition Low

Intensifying stratification Moderate

Increasing acidity High

Temperature changes can potentially affect all ESU’s and life stages. First, we can expect 

changes in the amount of time juvenile salmon (primarily sub yearling Chinook salmon) occupy 

certain shallow water wetland habitats (i.e., tidal fluvial habitats) due to increases in temperature. 

What is especially critical is the amount of time temperatures will exceed sublethal and lethal 

thermal limits the Chinook salmon have. There are already time periods during summer and fall 

that juvenile salmon are not present in some estuarine habitats due to temperatures exceeding 

stressful thresholds. Roegner et al. (2012) found that at temperatures over 19 C, juvenile 

Chinook salmon tended to avoid estuarine wetlands. Thus, we can expect the duration of time 

juvenile salmon spend in these wetlands to decrease as temperatures increase. 

Second, before temperatures exceed thermal limits, we can expect other thermal responses to 

occur. In particular, all species and life stages will respond bioenergetically. For example, 

yearling size fish will encounter elevated temperatures during their migration through the estuary 

that can affect their metabolic rates while sub yearling Chinook salmon can encounter elevated 

but not stressful temperatures in wetlands. At more modest temperature increases, growth rates 

of salmon may actually increase, assuming food resources do not diminish. Roegner and Teel 

(In Press) found that the condition of sub-yearlings was higher at summer temperatures > 19°C 

than during cooler temperatures in spring. High food levels may have offset the negative effects 

of temperature induced metabolic demands. By contrast, many salmon stocks, particularly 

yearling migrants, moved through the estuary before temperatures reached stressful levels. It is 

unclear how migration and rearing timing will adapt to changes in the estuarine temperature 

regime.

Third, we can expect some temperature mediated changes to occur in the food web of the 

estuary. There may be changes in the community structure of invertebrates available to the 
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salmon to feed on as well as in the plant communities in the estuary. It is not clear what these 

temperature related changes will be and the net effect of thermal changes on the estuarine food 

web. There are many uncertainties associated with this type of change such as how tolerant 

different organisms are to temperature changes. 

The second major type of physical change that will impact the Columbia River estuary is sea 

level rise. As the level of the sea rises a number of changes can be expected. For example, tidal 

wetlands may become submerged or have longer periods of inundation than they do currently, 

and nearby terrestrial habitats will be flooded (Kirwan et al. 2010). In other cases, shallow water 

habitats such as wetlands may erode as sea levels rise. Diking and other barriers may prevent 

wetlands from expanding and keeping up with erosion impacts. The net effect of these processes 

on estuarine habitats depends on the rate of sea level rise, the rate of vegetation growth and 

sedimentation, and the land contours in and adjacent to the estuary (Roessig et al. 2004; Kirwan 

et al. 2010). The global rate of sea level rise is currently faster than the colonization rate for new 

wetlands (Roessig et al. 2004). The Chesapeake Bay has already experienced massive wave 

induced erosion of marsh areas due to a rising sea level (Stevenson et al. 2002). These types of 

change will clearly depend upon the rate and magnitude of sea level rise with effects varying 

with season and flow patterns. 

The biological characteristics of affected wetlands and other shallow water habitats will be

altered by climate change (Stevenson et al. 2002). Because Bonneville Dam acts as a barrier to 

the propagation of upstream increases in sea level, it is likely that the physical and water 

characteristics of the mouths of rivers below Bonneville Dam will change. Rising sea levels will 

push the saline portion of the estuary upstream into freshwater areas and change the location of 

freshwater-saltwater ecotones (Flitcroft et al. 2013). Such changes will affect how these 

estuarine habitats function for salmon. For example, the head of tide in tributaries to the 

Columbia River such as the Lewis and Cowlitz rivers will move upstream in these tributaries 

with accompanying changes in physical structure of the estuary (due to changes in the tidal 

prism) and biological characteristics of these river mouth systems. This type of change is 

expected to be slow as at the present rate of rise of 3 mm per year, it will be 50 years before a 

rise of 150 mm (6”) is seen. 

A third type of change that can affect salmon in the estuary (and the coastal plume) is flowrelated changes below Bonneville Dam which can occur as a result of changes in precipitation 

patterns and water management practices. Climate forecasts for the Pacific Northwest suggest 

that there will be a reduction in precipitation that occurs as snowfall and an increase in rainfall, 

which would increase winter flow levels and diminish summer flows. Coupled with increased 

temperatures, such a scenario could critically limit salmon migration periods. In the estuary, 

there is a relationship between flow, tides, and salinity at any point. Changes in salinity (e.g., 

either the upstream extent of measurable salinity or the regime at any particular place) will 

depend on freshwater flow, tides, and basic sea level rise (polar and glacial melting). As we 

noted, changes in salinity or water levels in the estuary will alter the biological community 

structure as well as accessibility of these locations to salmon. Flow changes are also important 

in terms of downstream fish migration rates through the estuary. Reduced flows during the time 
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salmon are outmigrating, for example, could slow the downstream migration of salmon and 

affect their timing of ocean entry. Given the rapid migration of larger, yearling sized fish, it is 

not clear if flow related delays of hours or days would result in changes to growth and survival. 

6.2.2. Ocean Effects

Salmon can potentially be affected by climate driven changes in the ocean’s physical (e.g., 

temperature, circulation, stratification, upwelling), chemical (e.g., acidification, nutrient input, 

oxygen content), and biological (e.g., primary production, species distributions, phenology, 

foodweb structure, community composition and ecosystem functions/services) components and 

processes (Griffis and Howard 2013; Doney et al. 2014). The major physical changes in the 

ocean that are of concern from the perspective of climate change are higher ocean temperatures, 

intensified upwelling, delayed spring transition, intensified stratification, and increased ocean 

acidity (Wainwright and Weitkamp 2013). Although these are variables of concern, there is little 

direct information on if and how changes in these physical factors would impact salmon. This is 

due in part because global climate models continue have such coarse resolution that the 

California Current is not well resolved by these models, thus we cannot yet draw inferences from 

the global models. In addition and perhaps most importantly, the key physical drivers of 

productivity in the California Current, the NPGO, the PDO, the ENSO and coastal upwelling are 

not resolved by the current generation of climate models, so we have little idea how these drivers 

will change in the future. Sydeman et al. (2013) examined recent variations in the NPGO, PDO, 

and ENSO in relation to biological variables in the California Current. They found no changes in 

variability of PDO or ENSO, but an increase in variability in the NPGO, as well as an increased 

importance of the NPGO in explaining biological variation.

The effects of temperature changes in the ocean on salmon have received the most attention from 

scientists. Water temperature has a strong effect on fish physiology, development, distribution, 

and behavior (e.g., Marine and Cech 2004; Richter and Kolmes 2005). As ocean temperatures 

warm a number of things will occur that will ultimately reduce survival rates of some 

anadromous populations. Effects of ocean warming are suggested for a number of different 

salmon and steelhead stocks including Snake River steelhead and Chinook salmon (Petrosky and 

Schaller 2010), Fraser River sockeye salmon (Hinch et al. 1995), Central Valley Chinook salmon 

(MacFarlane 2010), and steelhead in general (Welch et al. 2000). In particular, we can expect 

metabolic rates to increase such that growth will be impacted (Hinch et al. 1995). This will also 

affect adult size at age and age at maturity, which in turn may have consequences for fecundity, 

migration ability, and ability to dig spawning redds.

One of the mechanisms by which warming water temperatures will affect salmon is by changing 

bioenergetics of the fish. Diet information on yearling Chinook salmon from 19 years of ocean 

research indicates that during warmer ocean years, juvenile salmon consume 20-29% more food 

than in the colder ocean years and are in significantly lower body condition (Daly and Brodeur 

2014). Research also suggests that the biomass of fish prey is reduced during warmer ocean 

conditions at the same time that the salmon are consuming more food (Daly et al. 2013; Daly and 

Brodeur 2014). This food stress, along with direct effects of temperature on physiology, can shift 
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competitive responses and increase predation risk for salmonids (Reeves et al. 1987; Marine and 

Cech 2004).

Increasing ocean temperatures will also change food web relationships involving salmon, 

especially as ranges shift for predators, competitors, and prey (e.g. Murawski 1993; Hays et al. 

2005; Cheung et al. 2009). For one, as ocean temperatures warm, the quantity and quality of 

salmon food will change. Locally, Francis et al. (2012) predict that changes in marine 

zooplankton community structure will occur as climate changes. In general, when water 

temperatures are warmer in the NCC (e.g., a warm phase of the PDO), food quantity and quality 

are diminished and salmon growth declines. Thus, one effect of warming in the NCC could be 

lower early marine growth of salmon which can in turn reduce survival of some ESUs. Another 

temperature related response associated with the food web is expected to be changes in predator 

distribution and abundance. For example, hake tend to be more abundant in shelf wasters when 

water temperatures are warmer (Emmett and Brodeur 2000). As water temperatures warm, hake 

may become prevalent in more years on the Shelf and increase their predation on salmon. The 

critical factor here is not necessarily if hake are on the shelf, but when they arrive in shelf waters 

relative to when juvenile salmon enter the ocean. Cleary, if juvenile salmon migrate to the ocean 

in late-April/early-May and if hake arrive in June, there is a mismatch which favors salmon. 

Global warming may result in salmon leaving the rivers earlier (because the rivers will warm 

faster than will the ocean) and migrating at a different rate that they did historically. The 

potential problems associated with ‘hake-salmon’ interactions may actually diminish in the 

future if fish enter the ocean earlier and/or migrate faster from the region. 

Overall, the combination of these temperature effects will result in changes in the range of the 

species. Temperature is a main factor determining the northern and southern limits of fishes in 

the California Current (Horn and Allen 1978). Climate-driven range shifts in marine fishes have 

been observed (Hsieh et al. 2009) and predicted for the future (Cheung et al. 2009). Such range 

shifts for Pacific salmon have been observed in past periods of climate change (Ishida et al. 

2009) and are occurring now (Irvine et al. 2009). For the future, Abdul-Aziz et al. (2011) 

illustrate this point for Pacific Northwest salmon by showing how climate scenarios can result in 

a dramatic contraction (30-50% by the 2080s) of the summer thermal range suitable for chum, 

pink, Coho, sockeye and steelhead in the marine environment. They predict an especially large 

contraction (86-88%) of Chinook salmon summer range under two commonly-used IPCC (2007) 

greenhouse gas scenarios. Previous analyses focusing on sockeye salmon (Welch et al. 1998) 

came to similar conclusions. 

A consequence of northward shifts of suitable salmon marine habitats is that populations near the 

southern limit of their species’ range will be more susceptible to climate change than those near 

the species’ center of distribution. The Columbia River Basin supports the most southerly 

populations of sockeye salmon, which suggests that Snake River sockeye salmon may be more 

susceptible to these effects than either Chinook salmon or steelhead. Maintaining Snake River 

sockeye salmon under future climate conditions may require greater improvements in freshwater 

habitat and the river migration corridor than other Snake River ESUs.
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Beyond water temperature, other climatological changes in the California Current are also likely 

to affect Snake River salmon. The timing and intensity of upwelling has an important but 

complex relationship to salmon production (section 3.5). There have been observed increases in 

upwelling intensity (Bakun 1990) and shifts in timing of spring transition and the total length of 

the upwelling season (Bograd et al. 2009), but analyses using climate models find little 

agreement on future changes in upwelling, largely because current models do not have 

sufficiently fine scale to resolve coastal wind and circulation processes (Diffenbaugh 2005). 

Upwelling of nutrient-rich water is also limited by the degree of water-column thermal 

stratification (Kosro et al. 2006), which is expected to increase as surface waters warm (e.g., Di 

Lorenzo et al. 2005). A final major issue for coastal waters is acidification as a consequence of 

increasing atmospheric CO2; increasing acidity is already being observed in the California 

Current System (Hauri et al. 2009). Acidification will likely have little direct effect on salmon, 

with the exception of some possible biochemical stress (Fabry et al. 2008). However, it may have 

a dramatic impact on invertebrates that are important in salmon food webs (Fabry et al. 2008); 

the consequences for salmon depend on potentially complex shifts in prey availability and 

abilities of salmon to shift diets.

It should be noted, however, that biological effects of climate change, whether in estuarine or 

ocean environments, are extremely difficult to predict. The rapid expansion of Humboldt 

squid—a voracious predator-- along the West Coast of North America in recent years and their 

population explosion in 2009 (Field et al. 2013), remind us that although physical processes are 

more straightforward to predict, the response of biological systems to physical changes are much 

more difficult to predict.

Finally, there is a potential for complex salmon life-history changes in response to a changing 

climate. Many stocks of salmon have evolved to migrate long distances in the marine 

environment. Presumably, this is because the high metabolic cost of migration was offset by 

better growing conditions in more northern habitats. If productivity near the destination of a 

migration decreases due to an altered climate, the “expected” benefit in terms of growth may not 

be achieved, and the high cost of migration may not pay off in terms of an evolutionary strategy. 

Moreover, if warmer temperatures results in a larger predator population in northern latitudes 

survival for migrating individuals could decline, again resulting in long marine migrations

becoming less productive.

6.2.3. Integrated Effects

So far, we have discussed a number of individual climate factors that affect salmon in certain 

habitats or specific parts of their life cycle. In order to fully assess the consequences of climate 

change, we need to consider the interactions of all the individual effects as they multiply across 

life stages within generations and across generations within populations (Wainwright and 

Weitkamp 2013). While many of the effects described above are difficult to project with much 

certainty, most are more likely than not to have negative effects on salmon growth and survival. 

Thus, the overall consequences of climate change for Snake River salmon are likely to be 
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negative, and will require management strategies that increase resiliency of these ESUs over the 

foreseeable future.
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6.3. Summary

In summary, salmon populations are subject to a wide variety of risk factors during their 

estuarine and ocean life that can diminish their viability or ability to persist over time. Many of

these factors are naturally occurring while others result directly or indirectly from the actions of 

people. Further, risk factors operate at various spatial and temporal scales, can have cumulative 

effects, and will differ in their implications for population viability of an ESU, DPS, or 

population. OF these risk factors, climate change effects in the estuary and ocean have received 

considerable attention. Within the Columbia River estuary, changes in temperature, flow, and 

sea level (water level in the estuary) are the primary physical factors responsive to a changing 

climate. In the ocean, salmon can potentially be affected by climate driven changes in the 

ocean’s physical (e.g., temperature, circulation, stratification, upwelling), chemical (e.g., 

acidification, nutrient input, oxygen content), and biological (e.g., primary production, species 

distributions, phenology, foodweb structure, community composition and ecosystem 

functions/services) components and processes. Most of these risk factors are very poorly 

understood. Temperature changes have received the most attention. The scope and magnitude of 

any affect experienced by salmon will be a function of how the climate actually changes (e.g., 

rate and magnitude), how these changes ultimately affect physical and biological processes, and 

the stock/population being considered. It is important to keep in mind that the overall effect of 

climate change on any anadromous stock must consider all habitats and life stages 

simultaneously and cumulatively.
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7. Ocean Ecology Snake River ESUs- Key 

Information Needs

From the perspective of recovery planning for listed Snake River ESUs and estuary and ocean 

ecology, we propose the following as key information needs:

1. Improve our ability to discriminate listed ESU’s in the estuary and ocean, and detect 

rare stocks such as Snake River sockeye. In order to be able to understand the life 

history and ecology of the listed ESUs in the ocean, we have to be able to identify the 

origin of a fish caught anywhere in the ocean. We are limited in our ability to do this. 

Expected improvements in the ability to use genetic identification methods for 

steelhead in the ocean will improve this situation for steelhead. In several other areas, 

such as the Gulf of Alaska, genetic stock identification methods have only been 

applied recently.

2. Improve our ability to identify wild fish within listed ESUs. We are currently limited 

in our ability to identify the wild fish components of listed ESUs. This is due in part 

to the low production of the wild parts of each ESU. Clearly, this is especially true of 

Snake River sockeye where the number of outmigrants leaving the Central Idaho 

lakes is very small. A second issue in identifying wild fish since some genetic 

identification are not made with high certainty and adipose clip rates are always less 

than 100%. If Parental Based Tagging or other large-scale marking can be 

implemented in hatcheries in the Columbia River Basin, then our ability to 

discriminate hatchery-origin from wild fish would dramatically improve.

3. Better understand the role of the estuary in productivity of yearling sized fish

(steelhead, Chinook salmon, sockeye salmon). In particular, for yearling sized fish, it 

is important to evaluate where the prey consumed by these fish are coming from. In 

particular, we should determine how important prey are that are exported from 

wetlands are to yearlings. A small sample of stomachs from these large fish has 

found prey derived from wetlands (Weitkamp et al. In Review), suggesting either the 

fish are foraging in or near wetlands or prey is being transported out into the main 

migratory routes.

4. Further understand density dependent growth and survival, especially as it relates to

hatchery fish impacts on wild fish. Detecting density dependent effects of hatchery 

fish on wild fish will continue to be challenging. We suggest that some additional 

analytical approaches could be taken with existing information (e.g., bioenergetic 

analyses) to help further refine under what conditions density dependent interactions 

are likely occurring and how management approaches in terms of release timing can 

help mitigate effects.

5. Continue to study bottlenecks or critical periods in survival. Most attention has 

focused on early marine survival in coastal waters off the Pacific Northwest as the 

primary bottleneck to survival. However, there are several other spatial/temporal 
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windows we should consider as noted for steelhead (e.g., Friedland et al. 2014). First, 

we still do not fully understand mortality processes in the plume but some evidence 

suggests substantial mortality occurs during this period (Reichisky et al. 2013). 

Second, there has been almost no sampling during winter, with the exception of work 

by DFO off the WCVE. Winter mortality is likely critical in some years and so 

understanding morality processes in winter would be useful. Third, we lack an 

understanding of salmon ecology close to shore (within several km). Because of 

depth considerations for the sampling vessels, most ocean sampling work does not get 

close to shore. However, we know that sub-yearlings are most abundant in the most 

inshore stations when sampled by trawl and purse seine sets in the ocean reveal large 

numbers of sub-yearlings in this area. So, it seems likely that we are under-sampling 

the Snake River fall Chinook ESU during early ocean life in the NCC. Fourth, we 

should increase our understanding of mortality processes occurring in the Gulf of 

Alaska and North Pacific during the first summer the salmon are at sea.

6. Better understand the physical and biological relationships between the river, estuary 

and ocean habitats. We know there are close physical connections between the river, 

estuary and ocean that can affect biological processes, but these relationships can be 

complex and how they affect salmon survival is still unclear. 

a. We know that river flow affects plume and estuary conditions (e.g., for the 

estuary, salinity; for the plume, plume volume and plume surface area). Where 

are less clear about linkages to biological processes. In particular, one set of 

relationships that merits further investigation are the connections between river 

flow, plume, estuary, forage fish distribution and abundance and predation by 

birds on salmonids. 

b. Another set of relationships that merits further investigation are between time and 

size of ocean entry and growth and survival in the ocean. The effects on overall 

growth and survival of when the fish enter the ocean and their size are complex 

(Scheuerell et al. 2009; Muir et al. 2006; Tomaro et al. 2012) and further research 

is needed to resolve these issues. We know that fish size can be important to 

survival, but how the fish attain this size may also be important (e.g., relative 

amounts of growth in the estuary and ocean). An important question is do

changes in growth rate, size and condition of juvenile salmon and steelhead that 

occur between the estuary and the NCC are related to their early marine survival.

7. Develop a better understanding of the mechanisms that link climate variability with 

salmon survival, especially as it relates to human caused climate change.

8. Continue to develop and refine indicators of ocean conditions that are relevant to 

salmon performance. This work would continue to refine the suite of ocean indicators 

for each stock group that provide the best predictive ability for early marine survival 

and adult returns and eventually transition to monitoring a core set of those indicators 

for each stock group. New indicators should be evaluated. This could include 

residence time and feeding in the estuary as predictor variables in an effort to track 
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the value of estuary habitat improvements on subsequent fish performance (e.g., 

growth and survival). 

9. Determine at what time scale survival processes operate. At present, current study 

efforts are sufficient to understand annual patterns but we do not know if and how 

processes operating at finer time scales affect the salmon. But, we do not know if 

factors affecting survival are operating at daily, weekly or monthly scales. For 

example, is a delay of a day or a week entering the ocean significant (i.e., have a 

measurable effect on survival) for a fish that only takes five days to migrate from 

Bonneville Dam to the ocean? We also do not know how ocean conditions fluctuate 

at smaller temporal scales and if this predictable, e.g., if survival is high this week, is 

it also likely to be good next week or next month. 

10. Determine the spatial and temporal distribution of all ESUs in the ocean following 

their first ocean year. Much of the focus of sampling efforts has been on the first year 

of ocean life when the fish are in coastal waters. We do not have a good 

understanding of where the fish go and how long they are present in different places 

after they have passed their first year at sea. As these are older and larger fish, this 

would likely require different types of sampling methods than have been used in 

coastal areas. For example, older fish of some ESU’s such as the SRSS and SRF 

Chinook salmon ESU’s might be less surface oriented. Our lack of understanding of 

what happens to the fish after their first year at sea is of concern because recent data 

strongly indicates that at least in some years and some stocks, critical mortality occurs 

after the fish leave the NCC (Welch et al. 2000; Burke 2013). These mortality 

processes are largely unstudied because of the minimal work that has occurred on 

older life stages.

11. Increase our understanding of anthropogenic risk factors. In general, we have little 

information on effects of most potential risk factors either in general (e.g., ecosystem 

effects) or specifically for salmonids. Several notable exceptions are effects of flow, 

habitat, and avian predation in the estuary. Even for climate change which is the 

subject of considerable interest and many studies, we lack explicit understanding of 

strength, magnitude, and timing of climate change effects. 

12. Better understand effects of predation. Much of what we know about biological 

processes affecting salmon in the ocean is related to bottom-up processes or what 

occurs at the lower trophic levels. We have a very limited understanding of predation 

during ocean life both in the NCC and beyond. 
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8. Recovery Strategies

Most of the direct actions that will be directly taken to recover the listed Snake River ESUs will 

occur above Bonneville Dam. They will be designed to increase survival through the 

hydrosystem, improve egg-to-fry survival, improve upstream migration of adults above 

Bonneville Dan, and so on. Actions will of course vary by ESU and have been laid out in each 

recovery plan. 

The overall objective of recovery efforts is to improve viability. The framework for recovering 

viability in listed populations was originally proposed by McElhaney et al. 2000) and the Interior 

Columbia River Basin Technical Recovery Team (ICTRT, see ICTRT website for further 

details) further developed and refined this explicitly for the listed Snake River ESUs. There are 

four components to viability: abundance, productivity, spatial structure and diversity. All four 

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

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

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

which typically assessed the status of anadromous salmonids from a production perspective 

using numbers of harvested fish or reproducing adults as the metric. Defining population status 

using the NOAA Fisheries VSP criteria incorporates a much broader view of how to define 

population status. This perspective recognizes that factors affecting salmon populations vary 

widely, so using a variety of metrics can provide insight into what types of actions are needed to 

help populations and ESUs recover.

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

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

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

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

lot of members and a positive population growth rate are more likely to persist then populations 

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

can be measured at different and multiple time scales. 

Although conservation of diversity and spatial structure are emerging paradigms in recovery and 

management of Pacific Salmon (McElhany et al. 2000, Waples et al. 2001), their application to 

salmon recovery remains a considerable challenge. Spatial structure refers to the geographic 

distribution of individuals in the population and the processes that generate that distribution. 

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

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

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

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

channels, mudflats, and emergent marshes can be simultaneously occupied by members of one 

population. Distributing members of a population through an array of habitats helps reduce the 

vulnerability of the population to shifts in environmental conditions (McElhany et al. 2000). 

Diversity consists of the variability in life history and discrete genetic traits exhibited by 
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members of a population. In the ocean module and recovery plans, diversity is manifested and 

considered explicitly in recovery planning in a variety of ways, including differentiating 

yearlings from sub-yearlings and spawning timing (spring, summer, and fall). Many other traits, 

such as age at return, fecundity, migration behavior, and so on, follow from whether a fish is a 

yearling or sub-yearling and when they spawn. 

8.1 Manage for Diversity

One element of viability is diversity. One of the characteristics of salmonids, but especially 

Chinook salmon and sockeye, is that they exhibit considerable life history diversity within a 

stock (Fresh et al. 2005). Clearly, a major part of this diversity is in how the fish use ocean 

ecosystems. For example, freshwater recovery actions should consider the mix of life history 

types they are generating and how they will perform in the ocean. We have shown that different 

life history types use the ocean differently and that ocean condition can vary greatly over the vast 

region salmon occupy. A year that is “good” for yearlings may not be “good” for sub-yearlings. 

Another example of diversity based recovery strategies is timing of ocean entry (Scheurell et al. 

2009). We know that timing of ocean entry is complex within any ESU and can vary within a 

year and between years. Within year variability in when the fish enter the ocean (during periods 

of high or low productivity) can affect their survival (Chittenden et al. 2010). While the 

interaction of arrival timing in the estuary and fish size can be complex (e.g., Tomaro et al. 

2012), both factors can potentially affect ocean survival (e.g., Muir et al. 2006). While further 

research on this subject is needed, some general principles of when fish should enter the ocean 

should be developed. 

Because of uncertainty in how ocean entry timing might affect a particular group of fish, we also 

suggest that fish should also be spread out within these windows, especially if ocean conditions 

look unfavorable, to reduce risks of competition occurring (i.e. do not put all eggs in one 

basked). Further, the transportation of some populations through the hydrosystem in barges 

makes it especially challenging to manage for some optimal range of ocean entry timing. It 

seems as if a bet hedging approach would be useful that recognizes that although each stock has 

a general time and size range when they enter the ocean, considerable variability exists within 

each ESU in their life history approach. 

One potential opportunity to affect viability of Snake River ESU’s is in how we rear and release 

hatchery fish because of the potential for competition between listed ESUs and hatchery fish 

from multiple sources. The arrival of large numbers of fish in the estuary and NCC could create 

conditions whereby unlisted, hatchery fish might compete with and reduce growth rates of listed 

populations. If the overall consumptive demand (a function of both fish abundance and fish size) 

of hatchery fish was sufficient (i.e., how much prey do the hatchery fish eat relative to what is 

present) growth rates of listed populations could be reduced. This could depend upon 
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environmental conditions, species being considered, relative amount of prey available in the 

environment, and habitat where the interaction occurred. 

Given the accumulation of evidence that density dependent interactions are occurring under 

some circumstances, it seems that managing to reduce risks associated with the occurrence of 

this interaction seems prudent. For example, it seems prudent to spread out hatchery releases to 

reduce the likelihood of density dependent effects on naturally reproducing fish. Clearly, while 

this might be effective in managing density dependence in the estuary and NCC, it may be less 

likely to work as the fish from the Snake River mix in the ocean with stocks from other regions.
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8.2 Physical and Biological Connectivity- Spatial Structure

Although we tend to examine each habitat the salmon occupy in isolation, it is clear that there are 

physical and biological connections between these habitats and the fish that occupy them and 

that management of the river and its salmon resources should account for these connections. 

Connectivity is one element of spatial structure (McElhaney et al. 2000). One example of 

connectivity between the ocean and estuary is via the plume. We know that the amount of flow 

can affect salinity regimes in the estuary and characteristics of the plume. Studies show that that 

a significant portion of plume volume (67%- Baptista 2013) is a function of river flow and that 

the plume does not simply affect the area near the river mouth but can affect much of coastal 

Washington depending on its volume, winds, and other physical factors (Hickey et al. 2009). 

Characteristics of the plume can affect biological characteristics near the mouth of the river such 

as food webs and it can affect salmon survival. Spring Chinook salmon from the upper 

Columbia River, plume volume at the time of emigration is correlated with size at capture which 

is strongly related to adult returns two years later (Tomaro et al. 2012). Similarly, Miller et al. 

(2013) found that returns of a population of unlisted Upper Columbia sub-yearling Chinook 

salmon to Priest Rapids Dam were related to plume volume at the time of emigration in most 

years. 

From the perspective of biological connections, it is reasonable to hypothesize that ocean growth 

and survival, especially in the NCC, relate to characteristics of the fish (e.g., size, timing, 

condition) during their estuary and plume residence. We do not fully understand these biological 

connections, such as how growth and fish size and condition in the estuary is related to 

subsequent growth in the plume and ocean. But, it seems reasonable to hypothesize that such 

relationships exist. 
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8.3 Harvest

Columbia River salmon are harvested at a number of points in their life histories with the most 

important U. S. fisheries targeting fish near the mouth of the river and in the river. An important 

part of the fishery management cycle is forecasts of the numbers of returning adults. Accurate 

forecasts are of course highly desirable since they can reduce risks of overharvesting and can 

help ensure adequate escapement to spawning grounds which is a consequence of 

overharvesting. 

One of the more important salmon ocean science advances in recent years in the NCC, has been 

an increase in our understanding of the mechanisms affecting salmon ocean survival. From this 

mechanistic understanding of salmon ocean survival, indicators have been developed that seek to

predict adult returns and survival. As illustrated by Burke et al. (2013a) these indicators can 

accurately forecast adult returns of some stock groups. Accurate forecasts of adult returns two 

years into the future can provide an early warning about when we should be concerned about low 

returns of stocks that comprise such a group. This could provide advance warning of at risk 

fisheries, where the low returns would have economic impacts on fisherman. 
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8.4 Improving survival in the ocean. 

As we have noted, we have the ability to affect growth and survival of anadromous species in the 

ocean. First, a number of studies suggest that timing of ocean entry and size at ocean entry can

effect growth and survival (Tomaro et al. 2012). Chittenden et al. (2010) found that timing of 

ocean entry of hatchery and wild Coho salmon was important to their subsequent survival with 

fish entering the ocean during periods of high productivity (within a year) having higher survival 

than those entering the ocean during periods of lower ocean productivity. Although these 

relationships are complex, studies suggest that in general Snake River spring Chinook and 

steelhead that arrive earlier in the ocean survive better. For wild fish, timing of ocean entry will 

be a function of when the fish begin their downstream migrations (which will depend 

considerably on flow) and how long it takes them which will be primarily driven by flow. 

However, there is considerable variability in the effects of timing between years, making it 

impossible (at least currently) to predict when the optimum time of ocean entry is each year. For 

example, in three of the four years examined by Scheuerell et al. (2009), fish that passed 

Bonneville Dam in early May performed best but in one year, fish that passed Bonneville in June 

performed best. Thus, it seems prudent with this uncertainty to ensure fish arrive in the ocean 

within a time frame window rather than on a particular date.

In addition, larger fish in general will perform better than smaller fish (Holtby et al. 1990) but it 

is clear time of ocean entry and size are related but that this relationship can be complex (e.g., 

Bilton et al. 1982; Beamish and Mahnken 2001). For example, in a study of hatchery-reared 

Coho salmon, Irvine et al. (2013) found that the effects of fish size at release varied between year 

and between hatchery location. In some years, being larger at release did not confer a survival 

advantage. It also may not the size of the fish per se but the difference in size between their 

arrival in the estuary and their first days/weeks in the ocean. Thus, small fish arriving in the 

ocean may be able to compensate for their small size if ocean conditions are favorable. In 

addition, the most important aspect of timing is likely not so much timing relative to calendar 

date but timing relative to ocean conditions such as the available food supply. Biologically 

important events do not occur on the same calendar date every year; thus, differences of days to 

weeks may be important. 

Clearly, one factor that can affect survival is numbers of fish entering each ecosystem. In their 

comments on the Ocean Synthesis report, the ISRP suggested that “it may be worthwhile to 

investigate whether hatchery salmon growth and natural salmon production in freshwater can be 

adjusted to the extent possible, for example in the hydrosystem, to enhance survival of both 

hatchery and natural populations during anticipated years of poor ocean productivity.” For 

example, during years of poor ocean productivity, adjustments might be appropriate in terms of 

the numbers, sizes and timing of fish entering the ocean in order to optimize their survival 
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9. Adapting Recovery Actions Based on Ocean 

Conditions

Here we discuss how we can adapt freshwater and estuary recovery actions to help reduced risks 

to listed ESUs using ocean information. 

9.1 Forecasting

One of the more important salmon ocean science advances in recent years, especially in the 

NCC, has been an increase in our understanding of the mechanisms affecting ocean survival. An 

example of a mechanistic understanding is the linkages between the PDO, zooplankton, 

icthyoplankton, early marine growth, and survival. We can then use our understanding the topdown and bottom up mechanisms affecting early marine life of specific populations to develop 

indicators that accurately predict adult returns and survival.

Using ocean indicators for forecasting reflects a shift in application or use of ocean information. 

Typically, we have used ocean indicators such as PDO in correlative, retrospective types of 

analyses (e.g., Petrosky and Schaller 2010; Scheuerell et al. 2009); the focus has been on using, 

readily available off the shelf ocean indicators (i.e., off the internet) such as PDO and ocean 

surface temperatures, because they match with the long-term biological data (e.g., salmon 

abundance). However, over the last several years, it has become clear that some of these broad 

ocean indicators (PDO, for example) are becoming less correlative with salmon performance and 

that using other approaches (e.g., multivariate models) is needed. 

Recently, we have begun using ocean indicators of physical and biological conditions developed 

from in situ sampling for forecasting survival and adult returns (Burke et al. 2013a). These 

indicators have been developed based upon our understanding of the mechanisms affecting early 

marine life. Forecasting has multiple purposes but within the context of recovery planning, 

forecasts can clearly be used within a harvest management context to manage both in-river and 

ocean fisheries. With accurate forecasting, harvest managers can decrease the risk of 

overharvesting and increase the probability of having adequate escapement to spawning areas. 

In addition, forecasts can be used for conservation purposes. Presently, forecasts are being 

evaluated that use coarse scale or far field indicators like the PDO because they match the 

biological time series; however, “near-field” metrics may be better related to adult returns. As 

we have noted, in the last several years, there is evidence that the relationship between PDO and 

salmon performance during early marine life might be breaking down. Thus, there is a need to 

investigate the predictive power of the near-field metrics in the context of the early warning 

indicator, to understand the mechanisms underlying the statistical relationships, and to 

understand how these relationships vary by genetic stock group and natural versus hatchery 

origin. Examples here could include plume area/volume and indicators of ocean conditions that 
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focus on the time preceding when salmon are entering the ocean (March/April) or when they are 

entering the ocean (April/May). 

In some cases, adult returns two years into the future can be forecast using ocean indicators. 

Although these forecasts are coarse in that they are not stock specific at this time, they do 

provide an early warning about when we should be concerned about low returns of stocks that 

comprise such a group. If specific stocks or groups of stocks could be identified where low 

returns are expected, adaptive management actions might be possible that could target stocks 

where low returns are expected. Examples of adaptive management actions that could be 

implemented would be to further restrict harvest, accelerate the timing of freshwater restoration 

measures, and implement captive broodstock programs. 

A third application of accurate forecasts would be to incorporate the indicators that are most 

important (highest predictive power) in those forecasts in life cycle models. Life cycle models 

represent a more complete analysis of the factors affecting survival for a particular stock. The 

ability to accurately model the effect of future management actions in freshwater life stages 

depends on an adequate understanding of trends in and ties to ocean survival. Inadequate 

representation of variability in ocean survival can create a bias in the other stages of a life cycle 

model, which can lead to a misunderstanding of how both freshwater and marine habitats affect 

salmon.

We have found that some of the indicators we are collecting can be incorporated into life cycle 

models to make them more accurate because of the strong relationships between these indicators 

and fish survival in the ocean. Initial development of models typically relies on the longest data 

sets that are available. This is a weakness of some of the ocean data sets we have been collecting 

as they are limited to less than 15 years while other data sets such as PDO and SST are much of 

longer duration. It is currently unclear when the benefits of higher quality information outweigh 

a longer time series in terms of forecasting returns and understanding the ecology of salmon. 
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10. Implementation

Successful implementation of the overall recovery plans requires a process to refine direction 

and adjust course appropriately based upon information obtained from monitoring and research 

results. We have identified some of the key information needs that should be part of any 

research program. 

10.1 Information Needs: Monitoring and Research

While the focus of recovery actions for Snake River ESU’s is in freshwater and the estuary, it is 

very clear that we must continue to monitor and evaluate ocean conditions the fish experience in 

order to understand how well recovery actions are working. We must continue to provide the 

context for recovery actions. In the extreme, if certain freshwater recovery actions fail, we will 

need monitoring of ocean conditions to understand why these actions failed. We do not want to

incorrectly attribute low returns to dam passage when it was in fact due to ocean effects. 

Thus, we must monitor conditions of the fish themselves as well as conditions of the receiving 

environment (i.e. both fish and environmental indicators). While the focus regionally has been 

on the NCC, we must also consider information from other places the fish occupy (Gulf of 

Alaska).

We must also look for ways to improve collection of information. For instance, although 

collaboration and cooperation exists among different research groups, ocean studies of salmon

ecology have not been coordinated. Studies have been organized and led in different regions by 

different entities, largely as a function of available funding and regional drivers of information 

needs. Methods have varied between regions, such as in the timing of sampling. Not all 

programs use the same nets sampled in the same way and not all programs have collected 

comparable information (e.g., the same type of growth measurement or accompanying 

oceanographic information). In addition, some areas and times of year have been nearly 

unstudied, such as the deep oceanic waters beyond the continental shelf off Oregon and 

Washington. Also, most marine areas have not been sampled during winter and most of the nets 

used to sample salmon are most effective for the smaller size classes of fish and much less 

effective at sampling distribution patterns of larger fish (> 1 year in the ocean).
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