National Marine Fisheries Service September 24, 2008 

Recovery Plan Module

Mainstem Columbia River Hydropower Projects

1.0 Purpose

This module summarizes the general effects of Columbia River mainstem hydropower projects 

on all 13 Endangered Species Act (ESA)-listed anadromous salmonids in the Columbia basin, 

including the limiting factors and threats and expected actions (including site-specific 

management actions), or strategy options, to address those threats. The area to be addressed by 

the module includes the accessible mainstem habitat in the upper Columbia (i.e., to the tailrace of 

Chief Joseph Dam) and Snake (i.e., to the tailrace of Hells Canyon Dam) rivers, respectively, 

downstream to the tailrace of Bonneville Dam.1

 This module supports plans for the Snake River, 

Upper Columbia, Middle Columbia, Lower Columbia, and Upper Willamette River species, 

replacing the previous version provided as guidance to regional recovery planners, dated 

September 25, 2006. The material that follows is a synthesis of information that has undergone 

public processes for review, including, but not limited to, the Federal Columbia River Power 

System (FCRPS) 2008 Biological Opinion, Federal Energy Regulatory Commission (FERC) 

licensing proceedings, and Habitat Conservation Plans (HCPs). This module may, however, be 

updated as additional information becomes available. 

1.1 How Salmon and Steelhead Use the Mainstem 

All 13 ESA-listed species of salmon (Oncorhynchus spp.) and steelhead (O. mykiss) in the 

Columbia basin use the mainstem Columbia River (and Snake River for Snake River species) for 

migration to and from freshwater natal areas to the Pacific Ocean, where they grow from 

juveniles to mature adults. Most of the ESA-listed species spawn and incubate in tributaries, but 

Snake River (SR) fall Chinook, some populations of Lower Columbia River (LCR) fall Chinook, 

and Columbia River (CR) chum salmon spawn and incubate redds in the mainstem itself. 

Historically, the peak period for migration to the ocean has been spring and early summer, 

corresponding with snowmelt in the upper basin and high seasonal flows. However, individual 

juveniles from one species/population or another can be found in the system throughout the year. 

Downstream travel has been shown to be active rather than passive; in addition to water velocity, 

the rate of travel is affected by date, temperature, the location where the fish begin their 

migration, fish size, and the extent of the parr-smolt transformation. Survival through the 

migration corridor declines with distance traveled, whether due to natural hazards (including 

predation), mortality due to passage at hydroelectric projects, or other factors associated with 

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Mainstem Columbia River Hydropower Projects 1 

                                                           

1

 A separate module (the Mainstem Columbia River Estuary Recovery Plan Module) provides the same types of 

information for the lower river below Bonneville, in the estuary and the ocean plume. 
National Marine Fisheries Service September 24, 2008 

development (exotic predators, habitat conditions that make native predators more efficient, 

water quality, etc.). 

Based on emigration and rearing strategies, Connor et al. (2005) described two juvenile life 

history types for Snake River fall Chinook. At the time of the ESA listing (June 28, 2005; NMFS 

2005), it was assumed that all juveniles of this species were ocean-type fish, characterized by 

entering saltwater at age 0 and spending their first winter in the ocean. However, some of the 

smaller, later-migrating fall Chinook salmon from the Snake River basin delay seaward 

movement, wintering in the lower Snake River reservoirs before resuming their seaward 

movement the following spring at age 1. According to Connor et al. (2005), although the 

condition of reservoir-type juveniles decreased over winter compared with ocean-type juveniles, 

the mean condition factor of the former always exceeded 1.0 in the single year of study. 

After growth and maturation, whether in freshwater or the ocean, adult salmonids and steelhead 

generally return to their natal spawning areas for reproduction, though some straying into other 

basins is natural. As described in ISG (1996), the timing of adult entry and movement in rivers 

and tributary streams, and even the size, shape, and strength of adult fish represent adaptations to 

the physical and biological challenges presented by the upstream route to a specific spawning 

area. For example, waterfalls and similar physical barriers may be passable only at the range of 

flows that typically occurs during one month of the year, and then only by fish that have the 

physical ability to jump over or otherwise ascend the barrier. For fall-spawning fish, warm water 

conditions in late summer often present thermal barriers to movement and there may be little 

suitable habitat for resting (Berman and Quinn 1991, cited in ISG 1996). Therefore, at the adult 

life stage, population-specific behavioral patterns, closely attuned to the available habitats, 

appear to be critical for survival and successful reproduction. 

Preferred spawning habitat is determined by the incubation needs of embryos, i.e., high flow of 

oxygenated water through the interstitial spaces in the streambed (Quinn 2005). Salmon usually 

avoid both the slowest water (where fine sand and silt accumulate) and the fastest water. Salmon 

lay their eggs in nests called redds. In areas where winter freezing can destroy embryos, salmon 

often build redds at sites with upwelling groundwater, which is warmer than river water. In the 

Columbia basin, two of the listed species, Snake River fall Chinook and Columbia River chum 

salmon, spawn both in tributaries and in the mainstem. In the vicinity of Ives Island (downstream 

of Bonneville Dam), chum spawn in shallow areas where it appears that river water is warmed 

by its transit through the gravel (Geist et al. 2002). At both Ives Island and in the Hanford Reach, 

fall Chinook salmon select upwelling sites in preference to non-upwelling sites (Geist 2000; 

Arntzen et al. 2005), but in other locations, fall Chinook prefer to spawn in downwelling areas at 

the heads of riffles (Healey 1991). At both Ives Island and the Hanford Reach, fall Chinook 

salmon select redd sites containing the highest dissolved oxygen concentrations in the river and 

riverbed, which is consistent with the requirements for incubating relatively large eggs (Healy 

1991). 

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Mainstem Columbia River Hydropower Projects 2 
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2.0 Habitat Limiting Factors and Threats Related to Mainstem Hydropower 

Projects and Operations

This section identifies the past and continuing effects of dams and reservoirs located in the 

mainstem Columbia and Snake River migratory corridors on listed species of salmon and 

steelhead and their designated critical habitat. The mainstem migratory corridor extends from the 

base of Hells Canyon Dam on the Snake River, and from Chief Joseph Dam on the Columbia 

River, to the tailrace of Bonneville Dam on the Columbia River. 

Columbia River Basin anadromous salmon and steelhead have been affected by the development 

and operation of dams. Mainstem dams have extirpated anadromous fish from their predevelopment spawning and rearing habitats. Dams and reservoirs, within the currently accessible 

migratory corridor, have altered the river environment and have affected fish passage and 

survival. The operation of water storage projects has altered the natural hydrograph of the Snake 

and Columbia Rivers. Water impoundment and dam operations also affect downstream water 

quality characteristics, including water temperatures, which are important to the survival of 

anadromous fish. Detailed descriptions of these effects are provided in Williams et al. 2005 and 

Ferguson et al. 2005 (NOAA Technical Memoranda NMFS-NWFSC-63 and 64) and 

summarized in NMFS 2008a (Supplemental Comprehensive Analysis of the Federal Columbia 

River Power System and Mainstem Effects of the Upper Snake and other Tributary Actions – 

Section 5.1). 

2.1 Blocked and Inundated Habitat 

The construction of Grand Coulee Dam in 1939 – River Mile 597 (and later Chief Joseph Dam in 

1961 – RM 545) blocked access to important historical production areas for Upper Columbia 

River (UCR) spring Chinook salmon and steelhead (NRC 1996; ICTRT 2003) upstream of River 

Mile 597 (and RM 545). In addition to mainstem production areas, the Sanpoil, Spokane, 

Colville, Kettle, Pend Oreille, and Kootenai rivers each may have supported one or more 

populations of Chinook and/or steelhead. 

In the Snake River, the construction of Swan Falls Dam in 1901 blocked access to important 

historical production areas of salmon and steelhead in the Snake River basin upstream of RM 

424.2

 The construction of the Hells Canyon Dam complex (1958–1967) cut off access to the 

remaining historical habitat upstream of river RM 248, including seven major tributaries that had 

historically been important for spring/summer Chinook salmon and steelhead (and to sockeye 

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Mainstem Columbia River Hydropower Projects 3 

                                                           

2

 The area downstream of RM 578 (near the present location of Upper Salmon Falls Dam) was especially important 

to Snake River fall Chinook salmon, which Evermann (1896) identified as the “... largest and most important salmon 

spawning ground of which we know in Snake River.” 
National Marine Fisheries Service September 24, 2008 

salmon in the Payette River system): Boise, Burnt, Malheur, Owyhee, Payette, Powder, and 

Weiser rivers (Fulton 1968; Fulton 1970; Gustafson et al. 1997). 

Between 1938 and 1971, the construction of Bonneville, The Dalles, John Day, and McNary 

dams inundated mainstem habitat in the lower Columbia River between Bonneville Dam (RM 

146) and the confluence of the Snake River (RM 324). Between 1933 and 1967, the construction 

of Priest Rapids, Wanapum, Rock Island, Rocky Reach, and Wells dams inundated mainstem 

habitat in the middle Columbia River between the Snake River confluence (RM 324) and Chief 

Joseph Dam (545). Another 147 miles (RM 0 to RM 147) of mainstem habitat was inundated in 

the Snake River with the construction of Ice Harbor, Lower Monumental, Little Goose, and 

Lower Granite dams between 1962 and 1975 (Groves and Chandler 1999). Upstream from 

Bonneville Dam, the 41-mile stretch of the Columbia River known as the Hanford Reach 

between the head of Lake Wallula (McNary Dam pool – RM 356) and the tailrace of Priest 

Rapids Dam (RM 397), and the approximately 101-mile stretch of the Snake River, often 

referred to as the Hells Canyon reach (RM 147 to 248), provide the longest remaining 

unregulated reach of the mainstem ecosystem between Bonneville Dam and Chief Joseph Dam 

on the Columbia River and Hells Canyon Dam on the Snake River. 

2.2 Mainstem Habitats & the Migratory Corridor 

The Columbia and Snake Rivers (mainstem habitat) serve as corridors for migrating salmon and 

steelhead between the Pacific Ocean and their freshwater spawning and rearing habitats. Features 

of migration habitat important to these fish generally include: substrate, water quality, water 

quantity, water temperature, water velocity, cover/shelter, food (prey), riparian vegetation, space, 

and safe passage. For fall Chinook salmon, and to a lesser extent chum salmon, mainstem habitat 

also serves as important spawning and rearing habitat. Features of spawning and rearing habitat 

that are important to these fish generally include: spawning gravel, water quality, water quantity, 

water temperature, food, riparian vegetation, and access to spawning and rearing areas. 

Current conditions within much of the mainstem Columbia and Snake Rivers are altered 

compared to historical conditions. The development of mainstem hydropower projects have 

resulted in the inundation of many mainstem spawning and shallow-water rearing areas (loss of 

spawning gravels and access to spawning and rearing areas); altered water quality (reduced 

spring turbidity levels), water quantity (seasonal changes in flows and consumptive losses 

resulting from use of stored water for agricultural, industrial, or municipal purposes), water 

temperature (including generally warmer minimum winter temperatures and cooler maximum 

summer temperatures), water velocity (reduced spring flows and increased cross-sectional areas 

of the river channel), food (alteration of food webs, including the type and availability of prey 

species), and safe passage (increased mortality rates of migrating juveniles) (Williams et. al 

2005; Ferguson et. al 2005). 

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Within the migratory corridor, both dams and their associated reservoirs influence the current 

status of Columbia Basin salmon. To a greater or lesser extent specific to each dam, the dams 

present fish passage hazards, causing passage delays and varying rates of injury and mortality. 

2.2.1 Adult Passage 

Unlike downstream migrating juveniles, there is no indication that reservoirs substantially delay 

adult upstream migration (Ferguson et al. 2005). While the upstream migration of adults can be 

slowed as fish search for fishway entrances and navigate through the fishways themselves, they 

migrate more quickly through the relatively slow reservoirs. 

Adult fish passage, in the form of fish ladders, is provided at the eight mainstem projects in the 

lower Snake and lower Columbia rivers and the five mainstem FERC-licensed projects in the 

middle Columbia reach. In general, adult passage facilities are highly effective. Nonetheless, 

salmon may have difficulty finding ladder entrances, and fish also may fall back over the dam, 

either voluntarily (e.g., adults that “overshoot” their natal stream and migrate downstream 

through a dam on their own volition), or involuntarily (entrained in spillway flow after exiting a 

fish ladder). Some adults that fall back or migrate downstream pass through project turbines and 

juvenile bypass systems. Adult mortality rates have been estimated at between 22% and 59%, 

depending on the species and size of the individual fish (larger fish are more likely to contact a 

turbine blade, etc.) (Ferguson et al. 2005). There is even less data on the survival of adults 

through juvenile bypass systems. It seems logical to assume that survival rates would be much 

higher through these systems than through turbine units, and indeed, with the possible exception 

of passage through the 14 to 16” gatewell orifices, conditions within these systems should be 

easily navigable by adults. 

However, in spite of these potential hazards, average survival estimates using known origin PITtagged fish indicate that, after adjusting for known harvest and “natural” straying, survival 

through the mainstem Snake and Columbia River projects is relatively high (see Table 1 and 

discussion in Section 4 below). 

Steelhead Kelts 

Unlike other Pacific salmonids, a large fraction of the adult steelhead does not die after spawning 

and instead attempts to migrate back to the Pacific Ocean. Termed kelts, very few post-spawn 

adult steelhead survive downstream passage through the hydrosystem and so do not return and 

spawn again. Estimates of FCRPS passage survival ranged from 4.1 to 6.0% in the low flow year 

2001 to 15.6% in 2002 and 34% in 2003 (Boggs and Peery 2004; Wertheimer and Evans 2005). 

At present, juvenile collection and bypass systems are not designed to safely pass adult fish 

including kelts. In addition to injury and mortality, kelt downstream migrations are delayed by 

the mainstem projects (Wertheimer and Evans 2005) in a manner similar to that previously 

described for juveniles. 

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Mainstem Columbia River Hydropower Projects 5 
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The fraction of repeat spawning kelts in steelhead populations varies widely, from 1 to 51% 

(Wertheimer and Evans 2005). Boggs and Peery (2004) cite an estimated 2% kelt rate for the 

Clearwater River in 1954. It is estimated that 17 to 25% of the steelhead that pass Lower Granite 

Dam return downstream as kelts (Boggs and Peery 2004; Wertheimer and Evans 2005). Thus, 

while there is a relatively large number of kelts present, their relatively poor survival through the 

FCRPS (and potentially through the Middle Columbia PUD projects) may limit the contribution 

that they can make to steelhead populations. 

Predation 

Additionally, at Bonneville Dam, marine mammals (both the more common California sea lion 

and ESA-listed Stellar sea lion) are increasingly using the Bonneville Dam tailrace as a foraging 

area, presumably because the adult Chinook, steelhead, and lamprey upon which they feed are 

concentrated and delayed in this area as they seek entrance to the dam’s adult fishways. 

2.2.2 Juvenile Passage

Delay 

Prior to the development of mainstem dams (c. 1938–1975), the mainstem migratory corridor 

was free-flowing with high velocities and a broad complex of habitats including rapids, short 

chutes, falls, riffles, and pools. It is not known how long it took juvenile salmon and steelhead to 

traverse the free-flowing river. Today, median travel times for yearling Chinook from the Lower 

Granite Dam on the Snake River to Bonneville Dam range from 14 days to 31 days depending on 

flow conditions, an increase of 40 to 50% over travel times measured in 1966 (Raymond 1968 

and 1979), when fish encountered only the four mainstem dams (Williams et al. 2005). 

This increased travel time (migration delay) presents an array of potential survival hazards to 

migrating juvenile salmon and steelhead: increasing their exposure to potential mortality vectors 

in the reservoirs (e.g. predation, disease, thermals stress), disrupting arrival timing to the estuary 

(which likely affects predator/prey relationships),3

 depleting energy reserves, potentially causing 

metabolic problems associated with smoltification (smoltification is the process of metabolic 

changes required to allow juvenile fish to convert from freshwater to saltwater environments), 

and for some steelhead and all Chinook salmon, contributing to residualism (a loss of migratory 

behavior). 

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Mainstem Columbia River Hydropower Projects 6 

                                                           

3

 During the spring and summer a series of changes occur in the composition of biotic communities the estuary and 

near-shore ocean environment. The assemblages of species change through time and disrupting arrival timing may 

increase the exposure of juvenile salmon to predators and/or diminish the availability of prey species to which the 

fish are adapted. 
National Marine Fisheries Service September 24, 2008 

Migration delays and biological effects of a similar magnitude have likely also occurred in the 

middle Columbia River as a result of the construction of the middle Columbia PUD projects. 

Dam Passage

A substantial proportion of juvenile salmon and steelhead can be killed while migrating through 

dams, both directly through collisions with structures and abrupt pressure changes during 

passage through turbines and spillways, and indirectly, through non-fatal injury and 

disorientation, which leave fish more susceptible to predation and disease and result in delayed 

mortality. Some juvenile mortality and injury is associated with any route of dam passage, but 

turbine passage generally has the highest direct mortality rate—8 to 19 percent. Juveniles passing 

through project spillways, sluiceways and other surface routes generally suffer the lowest direct 

mortality rates, 2% or less. However, substantially higher mortality rates have been measured 

through spillways at several mainstem FCRPS projects (Ferguson et al. 2005, NOAA Technical 

Memoranda NMFS-NWFSC-64).4 

Additionally, a significant rate of juvenile mortality (approximately 3 to 5%) can occur in project 

forebays, just upstream of the dams (Axel et al. 2003; Ferguson et al. 2005; Hockersmith 2007), 

if fish are substantially delayed (median of 15-20 hours) before passing through the dam (Perry 

et al. 2007).5 Forebay delay increases the exposure of juveniles to fish and avian predators and 

increases their exposure time to adverse water quality conditions (e.g. elevated total dissolved 

gas levels and high water temperatures), where present. (See discussion in NMFS 2008a—

Supplemental Comprehensive Analysis, Section 5.1.2.1 for additional information regarding 

improvements made at the mainstem hydroelectric dams to improve passage since the mid1990s, including some discussion of how the newly developed surface passage routes are 

proving effective at reducing forebay delay.) 

Predation

The altered habitats in project reservoirs reduce smolt migration rates and create more favorable 

habitat conditions (increased growth rates, increased consumption rates, and enhanced foraging 

opportunities) for fish predators (see Dam Passage), including northern pikeminnow 

(Ptychocheilus oregonensis), and non-native walleye (Sander vitreus) and smallmouth bass 

(Micropterus dolomieu). 

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Mainstem Columbia River Hydropower Projects 7 

                                                           

4

 The route-specific mortality rate values given here are averages across several investigations. Higher and lower 

moralities have been observed and measured route-specific mortality is influenced by an array of factors ranging 

from the health and species of the test fish to study methods, the performance characteristics and working condition 

of the system being studied, and environmental conditions. 

5

 This study was conducted at McNary Dam; estimates of delay for individual fish ranged from 0 to 172 hours in this 

study. 
National Marine Fisheries Service September 24, 2008 

Dams also enhance conditions for avian predators - primarily Caspian terns, double-crested 

cormorants, and several gull species – because these species can more effectively forage in the 

forebays and tailraces of the mainstem projects than in a more riverine system. 

Transportation Program 

Following a decade of research that led to the conclusion that in most cases, the average adult 

return rates of predominantly stream-type salmonids (spring/summer Chinook and steelhead) that 

were transported as juveniles exceeded the return rates of fish that migrated inriver, the Corps 

began large-scale juvenile transportation as a management measure in 1975 (Ebel 1980; Ebel et 

al. 1973; Mighetto and Ebel 1994). Currently, fish collection and transportation systems are 

operated seasonally at Lower Granite Dam, Little Goose Dam, and Lower Monumental Dam 

(and at McNary Dam for summer migrating fall Chinook salmon). Most transported fish are 

barged to release points downstream from Bonneville Dam. When collection numbers become 

too small for barging to be cost-effective, collected fish are transported via truck. Approximately 

60 to 90% of spring migrating smolts (spring/summer Chinook and steelhead) in the Snake River 

basin have been transported annually (Williams et al. 2005). Higher proportions (>95%) of 

Snake River migrants are likely to be transported during low water year conditions (defined as 

years in which spring flows are expected to be less than 65,000 cubic feet per second at Lower 

Granite Dam). With the addition of surface passage routes at the Snake River dams, far fewer 

fish may be transported – especially early in the migration season when adult returns from 

Chinook salmon smolts left to migrate inriver are relatively high (compared to transported fish) 

[see discussion below] – than has been possible in the past. For example, in 2007 transport rates 

were estimated to be much lower than previously estimated (approximately 25% for wild and 

hatchery yearling Chinook salmon and about 41% for wild and hatchery steelhead) (Smith 2008). 

Recent data show that the effectiveness of transportation, in terms of the ratio of returning adults 

to transported juveniles (termed smolt-to-adult return ratio or SAR) from the Snake River, varies 

among species, season, and collection location (Williams et al. 2005; Scheuerell and Zabel 

2007). In general, the SARs of both transported and inriver migrating Snake River 

spring/summer Chinook salmon and steelhead tend to decrease once the day of arrival below 

Bonneville Dam passes early May. For steelhead, SARs of transported fish are typically equal to 

or higher than those of the surviving inriver migrants arriving downstream of Bonneville Dam 

(transport-to-in-river SAR ratios > 1.0). For spring/summer Chinook salmon, SARs of surviving 

inriver migrating fish often are substantially higher in early to mid May than those of transported 

migrants (transport-to-in-river SAR ratios < 1.0). However, in late May and June, the differences 

are generally diminished such that SARs are nearly equal (transport-to-in-river ratios ≈1.0).6

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6

 The ISAB (2008) recently reviewed this information and generally agreed with NOAA Fisheries’ assessment of 

the currently available data regarding the relative returns of adult Chinook and steelhead that were either transported 

or left inriver to migrate as juveniles. However, they advised NOAA Fisheries, the federal Action Agencies, and 

other regional managers to continue a “spread the risk” approach to spill and transport management to determine if 
National Marine Fisheries Service September 24, 2008 

2.3 Mainstem Hydrologic Conditions 

Flow regulation, water withdrawal, and climate change have reduced the Columbia River’s 

average flow, altered its seasonality, and reduced sediment discharge and turbidity (NRC 1996; 

Sherwood et al. 1990; Simenstad et al. 1982 and 1990; Weitkamp 1994). Annual spring freshet 

flows through the Columbia River estuary are about one-half of the pre-development levels that 

flushed the estuary and carried smolts to sea (Figure 1). 

Flow affects juvenile travel time and the distribution of individuals among the various routes of 

dam passage. In general, the lower the flow through the FCRPS reservoirs, the longer the travel 

time of juveniles that migrate inriver.7

 The longer juveniles remain in project reservoirs, the 

greater their exposure to predation, elevated temperatures, disease, and other sources of mortality 

and injury. 

Combined with the influence of reservoirs in the migration corridor, reductions in spring and 

early summer flows slow juvenile fish emigration, increase their exposure to injury and mortality 

factors within the reservoirs (e.g. predation, temperature stress, disease, and others), and change 

the timing of ocean entry. 

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these patterns have been altered by recent structural improvements and operations at the mainstem dams and out of 

concern for potential effects of spring spill and transport operations [proposed in the 2008 FCRPS biop (NMFS 

2008b)] on sockeye and lamprey. 

7

 At lower river flows a higher proportion of individuals is collected and transported for some ESUs, thereby 

avoiding the delay associated with inriver hydrosystem passage. 
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Figure 1. Simulated mean monthly Columbia River flows at Bonneville Dam under current 

conditions (black columns) versus flows that would have occurred without reservoir management 

(gray) (water years 1929 –1978. Source: Current Condition Flows – Bonneville Power 

Administration, HYDSIM model run FRIII_07rerun2004biop.xls; Pre-Development Flows – USBR 

(1999) Cumulative Hydrologic Effects of Water Use: An Estimate of the Hydrologic Impacts of 

Water Resource Development in the Columbia River Basin. (In NMFS’ (2008a) Supplemental 

Comprehensive Analysis, Section 5.1.3.) 

0

100000

200000

300000

400000

500000

600000

Columbia River discharge in cfs

Current 113017 128641 149403 189076 175921 172150 225689 293948 313930 218523 157935 109020

Natural 87115 91029 99387 99496 106033 128580 231047 450040 545561 334238 172430 104310

OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP

2.4 Mainstem Water Quality 

Water quality characteristics of the mainstem Snake and Columbia Rivers are affected by an 

array of land and water use developments. Water quality characteristics of particular concern are: 

water temperature, turbidity, total dissolved gas, and chemical pollutants. 

2.4.1 Water Temperature 

Changes in water temperatures can have significant implications for anadromous fish survival. 

Dams and reservoirs influence water temperatures through storage, diversion, and irrigation 

return flows. Comparisons of long-term temperature monitoring in the migration corridor before 

and after impoundment reveal a fundamental change in the thermal regime of the Snake and 

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Columbia rivers. As shown in Figure 2, there are three notable differences between the current 

and the unimpounded river:8

• the maximum summer water temperature has been slightly reduced, 

• water temperature variability has decreased, and 

• post-impoundment water temperatures stay cooler longer into the spring and warmer later 

into the fall. The latter phenomenon is termed thermal inertia. 

Figure 2. Median daily Snake River water temperatures (°C) at Ice Harbor Dam before and after 

development of the four lower Snake River projects (20°C denotes Washington Department of 

Ecology standard). Source: Perkins and Richmond 2001 in NMFS 2008a. 

 

High water temperatures stress all life stages of anadromous fish, increase the risk of disease and 

mortality, affect toxicological responses to pollutants, and can cause migrating adult salmon to 

stop or delay their migrations and juvenile steelhead to residualize. Warm water temperatures 

also increase the foraging rate of predatory fish thereby increasing the consumption of smolts. 

Though the duration and magnitude of high water temperatures in the migratory corridor is 

generally less under current, developed conditions than prior to water development, some 

juvenile fish are exposed to these conditions for a longer period of time due to the adoption of 

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Mainstem Columbia River Hydropower Projects 11 

                                                           

8

 NOTE: Significant land use practices, including the development of a large number of water storage and diversion 

projects had already occurred by the 1960s. Therefore, the unimpounded river scenario in this graphic does not be 

equate to the pre-development condition. 
National Marine Fisheries Service September 24, 2008 

alternative life histories (i.e, juvenile fall Chinook that over-summer in the mainstem reservoirs) 

or increases in migration travel time. 

Coincident with and possibly due to climate change, average annual Columbia Basin air 

temperatures have increased by about 1 degree C over the past century and water temperatures in 

the mainstem Snake and Columbia rivers have been affected similarly (ISAB 2007). The 

influence of this and other large-scale environmental variations are discussed in NMFS 2008a – 

Supplemental Comprehensive Analysis, Section 5.7. 

Also, due to the thermal inertia of the reservoirs (both mainstem and upstream storage projects), 

atmospheric cooling of water temperatures is delayed in the fall and warming is delayed in the 

early spring. This can affect Snake River fall Chinook by increasing the exposure of adults to 

elevated temperatures prior to spawning, resulting in an increased potential of pre-spawning 

mortality, reduced gamete viability, and subsequent impacts to the development and survival of 

fish through the egg to fry life stages. 

2.4.2 Turbidity 

Flow regulation and reservoirs reduces turbidity in the Columbia and Snake rivers. Reduced 

turbidity can increase predator success through improved prey detection, increasing the 

susceptibility of smolts to predation. Predation is a substantial contributor to juvenile salmon 

mortality in reservoirs throughout the Columbia and Snake River migratory corridors. 

2.4.3 Total Dissolved Gas 

Spill at mainstem dams (either as a means to pass fish or involuntarily in response to overgenerational flows) can cause downstream waters to become supersaturated with dissolved 

atmospheric gasses. Supersaturated total dissolved gas (TDG) conditions can cause gas bubble 

trauma (GBT) in adult and juvenile salmonids resulting in injury or death. Biological monitoring 

shows that the incidence of GBT in both migrating smolts and adults remains between 1-2% 

when TDG concentrations in the upper water column do not exceed 120% of saturation in 

FCRPS project tailraces and 115% in project forebays. When those levels are exceeded, there is 

a corresponding increase in the incidence of GBT symptoms. 

However, the effects of total dissolved gas (TDG) supersaturation on aquatic organisms are 

moderated by depth due to hydrostatic pressure. Each meter of depth compensates for about 10% 

of gas supersaturation as measured at the water surface. Thus, if the dissolved gas concentration 

is 120% of supersaturation at the surface, then the condition that the aquatic organism actually 

experiences at a depth of 2.0 meters is reduced to about 100% (i.e., the fishes tissues will be in 

equilibrium with the surrounding water and it will not develop gas bubble disease or trauma; 

Weitkamp 2003). 

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2.4.4 Pollutants 

Background or ambient levels of pollutants in inflows from upstream areas are variable and 

generally unquantified. Growing population centers throughout the Columbia and Snake River 

basins and numerous smaller communities contribute municipal and industrial waste to the 

rivers. Mining areas scattered around the basin deliver higher background concentrations of 

metals. Highly developed agricultural areas of the basin also deliver fertilizer, herbicide, and 

pesticide residues to the river. While these pollutants are not caused by the mainstem Snake and 

Columbia rivers projects, they are transported through them to the estuary. 

Current environmental conditions in the Columbia River estuary indicate the presence of 

contaminants in the food chain of juvenile salmonids including DDT, PCBs, and polyaromatic 

hydrocarbons (PAH) (NMFS 2001). This data also indicates that juvenile salmonids in the 

Columbia River estuary have contaminant body burdens in the range where sublethal effects can 

occur. The sources of exposure are not clear, but may be widespread. Several pesticides and 

heavy metal contaminants have been detected in Columbia River sediments (ODEQ 2007). In 

field studies, juvenile salmon from sites in the Pacific Northwest have demonstrated 

immunosuppression, reduced disease resistance, and reduced growth rates associated with 

contaminant exposure during their period of estuarine residence (Arkoosh et al. 1991, 1994, 

1998; Varanasi et al. 1993; Casillas et al. 1995a, 1995b, and 1998). Some impacts may be 

occurring within the mainstem Columbia and Snake Rivers, to the extent that juvenile fish are 

rearing in areas that are contaminated to similar levels as in the estuary. 

3.0 Current Recovery Strategies and Actions 

Current hydropower programs and operations are the result of completed or ongoing ESA 

section 7 consultations, Habitat Conservation Plans (HCPs) pursuant to section 10 of the ESA; 

FERC relicensing proceedings and other regulatory processes. In most cases, hydropower 

programs and operations are intended to avoid jeopardy and contribute to recovery. There is no 

distinction between the hydropower actions intended to meet ESA regulatory requirements and 

those intended purely for recovery.9

 

 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 13 

                                                           

9

 Recovery cost estimates do not include costs for implementing mainstem actions, first, because of their basinwide 

scope and applicability to all 13 Columbia Basin salmonid species listed as threatened or endangered, and second, 

because they are considered "baseline actions," a term that NMFS’ NWR ESA recovery plans use for actions 

already incorporated into other processes, such as section 7 consultations, FERC licensing agreements, and Habitat 

Conservation Plans, and these costs would occur regardless of the recovery plans. 
National Marine Fisheries Service September 24, 2008 

3.1 Federally Owned and Operated Projects in the Columbia Basin 

3.1.1 Federal Columbia River Power System 

The Federal Columbia River Power System (FCRPS) consists of 14 projects, each composed of 

dams, powerhouses, and reservoirs, that are operated as a coordinated system for power 

production and flood control (while also effectuating other project purposes) on behalf of the 

Federal government under various Congressional authorities. These projects are: Dworshak, 

Lower Granite, Little Goose, Lower Monumental, and Ice Harbor dams, power plants, and 

reservoirs in the Snake River basin; Albeni Falls, Hungry Horse, Libby, Grand Coulee and 

Banks Lake (features of the Columbia Basin Project), and Chief Joseph dams, power plants, and 

reservoirs in the upper Columbia River basin; and McNary, John Day, The Dalles, and 

Bonneville dams, power plants, and reservoirs in the lower Columbia River basin. 

The plan for operation of the FCRPS through 2018 is described in U.S. Army Corps of Engineers 

(USACE) et al.’s Comprehensive Analysis Document (USACE et al. 2007a) and Biological 

Assessment (USACE et al. 2007b) and in NMFS’ Supplemental Comprehensive Analysis 

Document (NMFS 2008a) and Biological Opinion (NMFS 2008b). The following is a general 

summary of the performance standards, metrics, and targets required in the 2008 Biological 

Opinion to maintain or improve salmon and steelhead survival in the mainstem migration and 

rearing corridor and the strategies that will be pursued to achieve these metrics (see RPA 51 in 

NOAA Fisheries’ Reasonable and Prudent Alternative Table of Actions – NMFS 2008b). These 

actions are intended to address the needs for survival and recovery of all 13 species of ESAlisted salmon and steelhead in the Columbia basin. 

• Adult Passage Performance Standards. The Actions Agencies must track and confirm 

that the relatively high levels of adult survival currently observed are maintained or 

increased through 2018 (see Table 7 of NOAA Fisheries’ Reasonable and Prudent 

Alternatives Table of Actions – NMFS 2008b). These survival rates, which are based on 

known-origin fish PIT tagged as juveniles, after accounting for known harvest and 

“natural” rates of straying, range from 81.2% for Snake River fall Chinook salmon up to 

91.0% for Snake River spring/summer Chinook salmon (BON to LGR); and from 84.5% 

for Upper Columbia River steelhead up to 90.1% for Upper Columbia River spring 

Chinook (BON to MCN).10

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 14 

                                                           

• Juvenile Dam Passage Performance Standards. The Action Agencies must achieve an 

average Juvenile Dam Passage Performance Standards of 96% survival across Snake 

10 The discrepancy between adult survivals for Upper Columbia River versus Snake River species in the lower 

Columbia River is recognized and is the subject of directed research, monitoring, and evaluation programs. The 

objectives of these programs are to determine why the differences exist and what actions might be effective at 

increasing the survival of the Upper Columbia River species in the lower Columbia River. 
National Marine Fisheries Service September 24, 2008 

River and Lower Columbia River dams for spring Chinook and steelhead and an average 

of 93% survival across Snake River and Lower Columbia River dams for Snake River 

sub-yearling fall Chinook. 

• Achieve Juvenile Inriver Survival Performance Metrics. The Action Agencies must 

annually measure the survival of inriver migrating fish and compare these numbers with 

COMPASS model estimates, which will be based on the conditions actually experienced 

and the expected benefits of completed hydro actions, to assure that survival 

improvements are occurring as expected. 

• Juvenile System Survival Performance Targets. The Action Agencies must achieve 

the expected increase in juvenile fish survival through the hydrosystem (survival to below 

Bonneville Dam of both transported and inriver migrating fish) that are associated with 

the proposed hydrosystem actions. 

To achieve these metrics, the Action Agencies will pursue the following general objectives and 

strategies (see NOAA Fisheries’ Reasonable and Prudent Alternatives Table of Actions, NMFS 

2008b, for specific details): 

• Continue collaboration with States and Tribes in the implementation of RPA actions, 

progress reporting, and adaptive management using fora such as the Regional 

Implementation Oversight Group. 

• Operate the FCRPS to provide flows and water quality to improve juvenile and adult fish 

survival.11

• Modify Columbia and Snake river dams to maximize juvenile and adult fish survival.12

• Implement spill and juvenile transportation improvements at Columbia and Snake River 

dams. 

• Operate and maintain facilities at Corps mainstem projects to maintain biological 

performance. 

• Implement piscivorous predation control measures to increase survival of juvenile salmonids 

in the lower Snake and Columbia rivers. 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 15 

                                                           

11 This includes the operation of storage reservoirs to increase the likelihood of achieving seasonal flow objectives: 

Spring \ 85 – 100 kcfs at Lower Granite dam, 135 kcfs at Priest Rapids dam, and 220 – 260 kcfs at McNary dam; 

Summer \ 50-55 kcfs at Lower Granite dam and 200 at McNary. It also includes the continued release of cool water 

from Dworshak dam during the summer to reduce and maintain temperatures in the lower Snake River. 

12 This includes the design, construction, and testing of structures and operations to provide surface oriented routes 

of passage which should be beneficial to juvenile migrants and downstream migrating adults (overshoots, fallbacks, 

or steelhead kelts). 
National Marine Fisheries Service September 24, 2008 

• Implement avian predation control measures to increase survival of juvenile salmonids in the 

lower Snake and Columbia rivers. 

• Implement marine mammal control measures to increase survival of adult salmonids at 

Bonneville Dam. 

• Provide information needed to support planning and adaptive management and demonstrate 

accountability related to the implementation of FCRPS ESA hydropower actions for all ESUs 

(i.e., implement research, monitoring, and evaluation programs for hydropower actions and 

predator control actions). 

In addition to these objectives, the 2008 FCRPS Reasonable and Prudent Alternative Action 

Table articulates site-specific management actions that will benefit interior Columbia species 

(see NOAA Fisheries’ Reasonable and Prudent Alternatives Table of Actions, NMFS 2008b, for 

specific details). 

3.1.2 U.S. Bureau of Reclamation Projects in the Upper Snake Basin above Brownlee Reservoir 

The USBR’s proposed actions in its August 2007 Biological Assessment (USBR 2007) 

addressed operations at 12 projects in the upper Snake River basin: Baker, Boise, Burnt River, 

Little Wood River, Lucky Peak, Mann Creek, Michaud Flats, Minidoka, Owyhee, Palisades, 

Ririe, and Vale (collectively, the Upper Snake Project). The proposed actions encompassed 

USBR’s future operations and routine maintenance, including storage and delivery of water, 

hydropower generation, and releasing water to augment flows for migrating salmonids. NMFS 

(2008c) prepared a biological opinion on this proposal and concluded that the action would not 

jeopardize the listed species nor result in the destruction or adverse modification of their 

designated critical habitat. 

The site-specific action of providing salmon flow augmentation is intended to address the needs 

for survival and recovery of all 13 species of ESA-listed salmon and steelhead in the Columbia 

basin. Although the physical project operations take place upstream of the migration barrier at 

Idaho Power Company’s Hells Canyon Complex, water released from the upper Snake River 

project reaches the lower Snake and Columbia rivers where it benefits juvenile salmon and 

steelhead migrants. 

The USBR provides salmon flow augmentation by acquiring water through rental pools and 

leasing or acquiring natural flow rights. The Nez Perce Water Rights Settlement and the Idaho 

law that implemented the settlement provide that up to 487,000 acre-feet may be provided for 

flow augmentation.

 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 16 
National Marine Fisheries Service September 24, 2008 

3.2 Federal Energy Regulatory Commission-licensed Projects 

The Federal Energy Regulatory Commission (FERC) licenses five hydroelectric dams in the 

middle Columbia reach (i.e., between Chief Joseph Dam and the confluence of the Snake and 

Columbia rivers): Wells (owned and operated by Douglas County Public Utility District (PUD)), 

Rocky Reach and Rock Island (Chelan County PUD), and Wanapum and Priest Rapids (Grant 

County PUD). FERC also licenses Idaho Power Company’s (IPC) Hells Canyon Complex in the 

Snake River basin. 

3.2.1 Hydropower Projects Owned and Operated by Chelan and Douglas PUDs 

NMFS (2002) entered into three site-specific 50-year anadromous fish agreements and habitat 

conservation plans (HCPs), one for each of the three mainstem Columbia River hydroelectric 

projects owned by Chelan (Rocky Reach and Rock Island) and Douglas (Wells) County PUDs, 

pursuant to section 10 of the Endangered Species Act. The HCPs were developed to protect the 

five species of Columbia River steelhead and salmon (spring-run Chinook salmon; summer/fallrun Chinook salmon; sockeye salmon, steelhead, and coho salmon, two of which (Upper 

Columbia River spring-run Chinook salmon and steelhead) were listed as endangered at that 

time.13 They satisfied the PUDs’ regulatory obligations with respect to anadromous salmonid 

species under the Federal Power Act, Fish and Wildlife Coordination Act, Pacific Northwest 

Electric Power Planning and Conservation Act, the essential fish habitat provisions of the 

Magnuson-Stevens Fishery Conservation and Management Act, and Title 77 RCW, as well as 

the ESA. The agreements set a “no net impact” standard to protect salmon and steelhead at the 

Wells, Rocky Reach, and Rock Island projects, and provide some degree of certainty for the 

long-term operation of these projects.14

Each of the three HCPs established a standard of 91% combined adult and juvenile passage 

survival at each project (Wells, Rocky Reach, and Rock Island) (NMFS 2002).15 The combined 

survival standard is composed of 93% juvenile and 98% adult project passage survival for all 

anadromous salmonids. At the time the Incidental Take Permits were issued (August 20, 2003), 

NMFS estimated that the HCPs represented a 22 to 45% survival improvement potential over the 

survival levels observed under the historical operations at these projects. 

 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 17 

                                                           

13 NMFS (2006) revised its listing of Upper Columbia River steelhead from “endangered” to “threatened” on 

January 5, 2006. 

14 The HCPs are intended to help prevent conditions that would lead to the need to list additional species of Upper 

Columbia River salmon and steelhead in the future. 

15 The HCPs allowed the PUDs to compensate for up to 9% project passage mortality through up to 7% hatchery 

production and up to 2% funding of tributary habitat enhancement projects. That is, the mitigation is intended to 

match the level of impact. 
National Marine Fisheries Service September 24, 2008 

3.2.2 Hydropower Projects Owned and Operated by Grant County PUD 

Grant County PUD’s new FERC license includes survival standards required in NMFS (2004) 

for the Priest Rapids Project (Priest Rapids and Wanapum dams and reservoirs) that are identical 

to those described above for the HCPs. Furthermore, the following site-specific measures are 

also included in the new FERC license and are being implemented to ensure that the standards 

are met: 

• Downstream passage measures, including spill through existing and top spill through 

future units; turbine operations and the installation of advanced turbines; total 

dissolved gas abatement; avian predator control; and a northern pikeminnow 

(Ptychocheilus oregonensis) removal program 

• Continued operation and maintenance, and where needed, improvements to adult 

fishways at both Priest Rapids and Wanapum dams 

• Design and construction of an off-ladder trap and fish-handling facilities at Priest 

Rapids Dam 

• Sluiceway operations for steelhead fallbacks (kelts) 

The FERC has completed consultation with NMFS on the terms of a new, 44-year license for the 

Priest Rapids Project. With respect to site-specific actions for mainstem facilities and operations, 

FERC adopted the hydro actions in the Reasonable and Prudent Alternative in NMFS’ Biological 

Opinion on Grant County PUD’s Interim Protection Plan (NMFS 2004) and in NMFS’ February 

1, 2008, Biological Opinion (NMFS 2008d) for listed salmon and steelhead, described above. 

3.3 Idaho Power Company’s Hells Canyon Project 

The relicensing of the Hells Canyon Hydroelectric Project is the subject of ongoing 

administrative proceedings before FERC involving its owner, IPC; Federal, state, and tribal 

agencies; and other stakeholders. At present, IPC voluntarily operates the project to protect 

habitat used by fall Chinook salmon for spawning (i.e., by eliminating flow fluctuations), and 

incubation (i.e., by providing enough flow to prevent the dewatering of redds downstream of the 

project). As part of an interim settlement agreement in the license proceedings, IPC has agreed to 

release about 237 thousand acre-feet (kaf) of water – primarily during July - to improve 

downstream migration conditions (flow) for juvenile fall Chinook salmon (Tucker 2005). 

 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 18 
National Marine Fisheries Service September 24, 2008 

4.0 Survival Rates at Mainstem Federal and Non-Federal Hydro Projects 

4.1 Adult Survival 

Adult survival estimates presented in this document are based primarily on a simple, straightforward “conversion rate” method which relies upon the detection and subsequent re-detection of 

PIT-tagged “known-origin” adults16 as they migrate upstream through the fishways (some fitted 

with PIT tag detectors) at the mainstem hydro projects. Detection rates are typically > 99% for 

an individual PIT tag detector and, because there are typically two or three detectors in series 

within each of the key fishways –virtually every PIT-tagged adult fish migrating upstream 

through a mainstem fishways is detected.17 

Minimum adult survival estimates (or conversion rates) can be calculated as the number of fish 

re-detected at an upstream project divided by the number of fish initially detected at the 

downstream project of interest. Estimates of “natural” straying rates and of known harvest are 

also factored in and the resulting number is the proportion of fish that survived between the two 

projects. For details regarding this method and how “natural” stray rates and harvest rates were 

used in these analyses, the reader is advised to read the Adult Survival Estimate Appendix of 

NOAA’s Supplemental Comprehensive Analysis (NMFS 2008a). Otherwise, these estimates 

capture all sources of mortality manifested within the identified reaches, including those 

resulting from the existence and operation of the FCRPS, as well as unquantifiable levels of 

mortality from other potential sources (e.g., unreported or delayed mortality caused by fisheries, 

marine mammal predator attacks, etc.) and unquantifiable levels of “natural” mortality (i.e., 

levels of mortality in the migratory corridor that would have occurred “naturally” without human 

influence). 

Adult Survival – Federal Projects 

Under the 2008 FCRPS Biological Opinion (NMFS 2008b), the federal action agencies are 

responsible for ensuring that the relatively high rates of survival currently observed in the 

Bonneville Dam to Lower Granite Dam (7 dams) reach for Snake River species and Bonneville 

Dam to McNary Dam (3 dam) reach for Upper Columbia River spring Chinook and steelhead is 

maintained or increased through 2018. Snake River species, for which the most information is 

available, were used as surrogates for Middle Columbia River steelhead, and Lower Columbia 

River species. The average survival estimates, annual estimates (ranges), and additional 

                                                           

16 “Known-origin” means that the release locations for all PIT tagged juvenile fish are available in the PITAGIS data 

base – and the general area to which these fish are attempting to migrate as adults is also known. 17 It should be noted that some adults may avoid detection by migrating past the dams via the locks at the federal 

projects. This is evidenced by individuals not being detected at a particular dam, but being detected at another dam 

upstream.

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 19 
National Marine Fisheries Service September 24, 2008 

information are provided in Table 1 (Column 3 titled “Adult Surv. – FCRPS”) and the 

information for Snake River and Upper Columbia River species is also summarized in the text 

below. 

The average survival estimate for Snake River fall Chinook salmon between Bonneville Dam 

and Lower Granite Dam was 81% for those that migrated inriver as juveniles and approximately 

75% for those that were transported as juveniles, equating to a per project survival (7 dams) of 

97% and 96%, respectively.18 

The average survival estimate for Snake River spring/summer Chinook salmon between 

Bonneville Dam and Lower Granite Dam was 91% for those that migrated inriver as juveniles 

and about 84% for those that were transported as juveniles, equating to a per project survival (7 

dams) of 99% and 98%, respectively. 

The estimated average survival of Snake River sockeye salmon between Bonneville Dam and 

Lower Granite Dam was 81% equating to a per project survival (7 dams) of about 97%. No 

estimate can be made with the available data for those fish transported as juveniles (see Table 1, 

footnote 3). 

The average survival estimate for Snake River steelhead between Bonneville Dam and Lower 

Granite Dam was 90% for those that migrated inriver as juveniles and approximately 83% for 

those that were transported as juveniles, equating to a per project survival (7 dams) of 99% and 

97%, respectively. 

The average survival estimate for Upper Columbia River spring Chinook salmon between 

Bonneville Dam and McNary Dam was 90% (all of these fish migrate inriver as juveniles), 

equating to a per project survival (3 dams) of approximately 97%. 

The average survival estimate for Upper Columbia River steelhead between Bonneville Dam and 

McNary Dam was 85% (all of these fish migrate inriver as juveniles), equating to a per project 

survival (3 dams) of 95%.19

 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 20 

                                                           

18 Average per project survival estimates are calculated as Average Survival Estimate ^ 1/n. Average per project 

survival estimates are useful because they allow for a comparison between species that migrate past different 

numbers of dams. 

19 Note: The apparent discrepancy between the survival rates of Upper Columbia River spring Chinook salmon and 

steelhead through a 3 dam reach and Snake River spring/summer Chinook salmon and steelhead through a 7 dam 

reach is noted in the 2008 FCRPS biological opinion. Reasonable and Prudent Alternative Action 52 requires an 

investigation into the possible causes of this apparent discrepancy (NMFS 2008b). Once a likely cause is identified, 

the Action Agencies, NOAA Fisheries and co-managing agencies will develop appropriate corrective actions and a 

monitoring plan to ensure that the differential survival is minimized or eliminated. 
National Marine Fisheries Service September 24, 2008 

Adult Survival – Non-Federal Projects 

Under the terms of the Middle Columbia Habitat Conservation Plans for the Wells, Rocky 

Reach, and Rock Island projects; and under the 2008 biological opinion for the Priest Rapids 

Project (Wanapum and Priest Rapids dams, NMFS 2008d), the Public Utility Districts must meet 

or exceed a per project survival of 98% for all adult migrants. At this time, it appears that the 

average per project survival between Priest Rapids and Wells Dam is 98.7% and 98.2% for 

Upper Columbia River spring Chinook salmon and steelhead, respectively. The average 

survival estimates, annual estimates (ranges), and additional information for Upper Columbia 

River species are provided in Table 1 (Column 4 titled “Adult Surv. – Mid-Columbia” and 

Column 5 titled “Adult Surv. - Total) and also summarized in the text below. 

The average survival estimate for Upper Columbia River spring Chinook salmon migrating 

between Priest Rapids and the Wenatchee, Entiat, and Methow rivers is approximately 95%, 

96%, and 97%, respectively. This survival multiplied by the Bonneville to McNary survival 

estimate20 yields a Bonneville to Wenatchee, Entiat, and Methow river survival estimate of about 

85%, 87%, and 88%. 

The average survival estimate for Upper Columbia River steelhead migrating between Priest 

Rapids and the Wenatchee, Entiat, and Methow rivers is approximately 93%, 95%, and 96%, 

respectively. This survival multiplied by the Bonneville to McNary survival estimate19 yields a 

Bonneville to Wenatchee, Entiat, and Methow river survival estimate of about 79%, 80%, and 

82%. 

4.2 Juvenile Survival 

Juvenile survival levels are estimated for two periods (See Tables 2 and 3). The “Current” 

scenario generally translates to survivals recently observed or estimated (modeled using 

COMPASS) to have occurred due to operational and configuration changes at the mainstem 

hydroelectric projects through about 2006. The “Prospective” scenario generally translates to 

attaining survival levels (if not already attained or exceeded) that are required by the Habitat 

Conservation Plans for the Wells, Rocky Reach, and Rock Island projects; the 2008 biological 

opinion for the Priest Rapids project (Wanapum and Priest Rapids Dam) (NMFS 2008d); or 

modeled using COMASS for the 2008 FCRPS biological opinion (NMFS 2008b). Full 

attainment of these standards is expected when the FCRPS biological opinion is fully 

implemented from 2015 to 2018. 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 21 

                                                           

20 A McNary to Priest Rapids (Hanford Reach) survival estimate has not yet been calculated, but is likely less than 

100%.
National Marine Fisheries Service September 24, 2008 

Juvenile survival through the federal projects under both the “Current” and “Prospective” cases 

was estimated using NOAA Fisheries’ COMPASS model. The COMPASS model was 

populated with the best empirically derived estimates of route-specific passage and survival rates 

available for juvenile Chinook or steelhead to reflect the “Current” configuration of the 

hydrosystem. The Federal Action Agencies assessed the likely benefits (specific survival 

improvements) that should result from additional dam configuration actions required in the 2008 

FCRPS biological opinion and these improvements were included in the modeling runs of the 

“Prospective” scenario. Both the “Current” and “Prospective” configurations and operations 

were modeled across a 70-year (1928 through 2000) historical water record. 

The model provides estimates of survival to below Bonneville Dam for inriver (and transported, 

if applicable) migrants, proportion of the migrants that would likely be transported (if 

applicable), and the arrival timing of migrants to the Bonneville dam tailrace for ESA-listed 

spring and summer Chinook salmon and steelhead from the Snake River, Upper Columbia River, 

and Middle Columbia River populations.21 For the purpose of this module, the most relevant 

pieces of information are likely the survival estimates. 

4.2.1 Juvenile Survival – Current 

Estimates of “Current” juvenile survival through the federal projects, ranges of expected 

survival, and proportion of juveniles expected to be transported are provided in Table 2 (Column 

3 - Juv. Survival – FCRPS). These results are broken into two categories (expected average 

flows at Lower Granite Dam of less than 65 kcfs or greater than >65 kcfs) for Snake River 

populations to display the likely effect of the “full transport” operation that would occur in the 

low flow years – which occurs in about 19% (13 of 70) of the years modeled. Estimates of 

survival for juveniles migrating from the Methow, Entiat and Wenatchee rivers are provided in 

Column 4 – Juv. Survival – Mid-Columbia; and combined survival estimates are provide in 

Column 5 – Juv. Survival – Total. A brief summary of this information is provided for spring 

migrating Snake River and Upper Columbia River Chinook salmon and steelhead populations in 

the text below. 

The average juvenile survival estimate for Snake River spring/summer Chinook salmon is 56% 

in the LGR > 65 kcfs years and 37% in the LGR < 65 kcfs years. Estimates of the proportion 

transported are about 64% and 95% in these flow conditions, respectively. 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 22 

                                                           

21 Insufficient data, primarily resulting from the multiple life-history strategies exhibited by Snake River fall 

Chinook salmon, was available to populate the COMPASS model to estimate juvenile fall Chinook survival through 

the FCRPS projects. Instead, NOAA Fisheries derived survival estimates from Fish Passage Center data (see NMFS 

2008a and 2008b). 
National Marine Fisheries Service September 24, 2008 

The average juvenile survival estimate for Snake River steelhead is 39% in the LGR > 65 kcfs 

years and 8% in the LGR < 65 kcfs years. Estimates of the proportion transported are about 79% 

and 94% in these flow conditions, respectively. 

The average juvenile survival estimate for Upper Columbia River spring Chinook salmon is 67% 

through the four FCRPS dams in the lower Columbia River, and 68%, 71%, and 77% for 

juveniles migrating from the Methow, Entiat, and Wenatchee rivers through the three to five 

Middle Columbia projects. The total survival estimate for these populations to below Bonneville 

Dam is 45%, 47%, and 51%, respectively. 

The average juvenile survival estimate for Upper Columbia River steelhead is 48% through the 

four FCRPS dams in the lower Columbia River, and 69%, 72%, and 75% for juveniles migrating 

from the Methow, Entiat, and Wenatchee rivers through the three to five Middle Columbia 

projects. The total survival estimate for these populations to below Bonneville Dam is 33%, 

34%, and 36%, respectively. 

4.2.2 Juvenile Survival – Prospective 

Estimates of “Prospective” juvenile survival through the federal projects, ranges of expected 

survival, and proportion of juveniles expected to be transported are provided in Table 3 (Column 

3 - Juv. Survival – FCRPS). These results are broken into two categories (expected average 

flows at Lower Granite Dam (LGR) of less than 65 kcfs or greater than >65 kcfs) to display the 

likely effect of the “full transport” operation that would occur in the low flow years – which 

occurs in about 19% (13 of 70) of the years modeled. Estimates of survival for juveniles 

migrating from the Methow, Entiat and Wenatchee rivers are provided in Column 4 – Juv. 

Survival – Mid-Columbia; and combined survival estimates are provide in Column 5 – Juv. 

Survival – Total. A brief summary of this information is provided for spring migrating Snake 

River and Upper Columbia River populations in the text below. 

The average juvenile survival estimate for Snake River spring/summer Chinook salmon is 63% 

in the LGR > 65 kcfs years and 52% in the LGR < 65 kcfs years. Estimates of the proportion 

transported are about 64% and 95% in these flow conditions, respectively. 

The average juvenile survival estimate for Snake River steelhead is 45% in the LGR > 65 kcfs 

years and 9% in the LGR < 65 kcfs years. Estimates of the proportion transported are about 74% 

and 89% in these flow conditions, respectively. 

The average juvenile survival estimate for Upper Columbia River spring Chinook salmon is 73% 

through the four FCRPS dams in the lower Columbia River, and 72%, 75%, and 81% for 

juveniles migrating from the Methow, Entiat, and Wenatchee rivers through the three to five 

Middle Columbia projects. The total survival estimate for these populations to below Bonneville 

Dam is 53%, 55%, and 59%, respectively. 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 23 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 24 

The average juvenile survival estimate for Upper Columbia River steelhead is 53% through the 

four FCRPS dams in the lower Columbia River, and 75%, 78%, and 81% for juveniles migrating 

from the Methow, Entiat, and Wenatchee rivers through the three to five Middle Columbia 

projects. The total survival estimate for these populations to below Bonneville Dam is 40%, 

41%, and 43%, respectively. 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 25 

Table 1: Recent Adult Survival Estimates for ESA-listed Columbia River Basin Salmon and Steelhead 

Populations Migrating Past Mainstem Hydroelectric Projects Based on PIT-tagged, Known-Origin Adults.1

Species Population Adult Surv.2 – 

FCRPS 

Reach 

Average 

Range

Special Info. 

Adult Surv. – 

Mid-Columbia5 

Reach 

Average 

Range

Special Info.

Adult Surv.2 – 

Total 

Average 

Range

Special Info.

SR fall 

Chinook3

Single Pop. BON – LGR 

Inriver: 

81.0 

(58.8 – 98.6) 

Transported: 

74.9 

(62.4 – 94.7) 

BON – LGR 

Inriver: 

81.0 

(58.8 – 98.6) 

Transported: 

74.9 

(62.4 – 94.7) 

SR spr/sum 

Chinook3

All Pops. BON – LGR 

Inriver: 

91.0 

81.6 – 97.9 

Transported: 

84.1 

73.7 – 88.0 

BON – LGR 

Inriver: 

91.0 

81.6 – 97.9 

Transported: 

84.1 

73.7 – 88.0 

SR sockeye3 Single Pop. BON – LGR 

Inriver: 

81.1 

79.1 – 83.2 

Transported: 

(No Est. Available) 

BON – LGR 

Inriver: 

81.1 

79.1 – 83.2 

Transported: 

(No Est. Available) 

SR 

steelhead3

All Pops. BON – LGR 

Inriver: 

90.1 

85.6 – 93.8 

Transported: 

83.3 

78.2 – 89.8 

(BON – LGR) 

BON – LGR 

Inriver: 

90.1 

85.6 – 93.8 

Transported: 

83.3 

78.2 – 89.8 

(BON – LGR) 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 26 

Species Population Adult Surv.2 – 

FCRPS 

Reach 

Average 

Range

Special Info. 

Adult Surv. – Adult Surv.2 – 

Mid-Columbia5 Total 

Reach 

Average Average 

Range Range

Special Info. Special Info.

UCR spring 

Chinook6

Methow 

Entiat 

Wenatchee 

BON - MCN 

Inriver: 

90.1 

86.1 – 96.1 

PRD - WEL 

94.7 

PRD - RRE 

96.2 

PRD – RIS 

97.4 

BON – WEL 

85.3 

BON – RRE 

86.7 

BON – RIS

87.8 

UCR 

steelhead6

Methow / 

Okanogan 

Entiat 

Wenatchee 

BON - MCN 

Inriver: 

84.5 

77.6 – 90.7 

PRD - WEL 

93.0 

PRD - RRE 

94.7 

PRD – RIS 

96.4

BON - WEL 

78.6 

BON - RRE 

80.0 

BON – RIS 

81.5

MCR 

steelhead4,7

Yakima / 

Walla Walla 

Umatilla / 

John Day 

Deschutes and 

BON pool 

BON - (MCN, JDA, and 

TDA) 

Inriver: 

95.6 

93.5 – 97.3 

97.0 

95.6 – 98.2 

98.5 

97.8 - 99.1 

BON-(MCN, JDA, and 

TDA) 

Inriver: 

95.6 

93.5 – 97.3 

97.0 

95.6 – 98.2 

98.5 

97.8 - 99.1 

LCR 

Chinook4

Spring-run 

adults 

Fall-run adults 

BON Pool 

Inriver: 

98.6 

97.1 – 99.7 

96.9

92.7 – 99.8 

BON Pool 

Inriver: 

98.6 

97.1 – 99.7 

96.9

92.7 – 99.8 

LCR 

steelhead4,8

BON pool BON Pool 

>98.5 

>97.8 - >99.1 

BON Pool 

>98.5 

>97.8 - >99.1 

CR coho4 BON pool BON Pool 

96.9

92.7 – 99.8 

BON Pool 

96.9

92.7 – 99.8 

CR chum4 BON pool BON Pool 

96.9

92.7 – 99.8 

BON Pool 

96.9

92.7 – 99.8 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 27 

Sources: NMFS’ 1) Supplemental Comprehensive Analysis Document (May 5, 2008a); and 2) Biological Opinion – 

Consultation on Remand for Operation of the Federal Columbia River Power System, 11 bureau of Reclamation Projects in 

the Columbia Basin and ESA Section 10(a)(1)(A) Permit for Juvenile Fish Transportation Program (May 5, 2008b). 

1 Key to Dams: BON = Bonneville Dam, TDA = The Dalles Dam, JDA = John Day Dam, MCN = McNary Dam, PRD = 

Priest Rapids Dam, WAN = Wanapum Dam, RIS = Rock Island Dam, RRE = Rocky Reach Dam, WEL = Wells Dam, IHR = 

Ice Harbor Dam, LMN = Lower Monumental Dam, LGS = Little Goose Dam, and LGR = Lower Granite Dam. 

2

 These estimates are based on detections of known origin fish returning to the Columbia River, detected passing Bonneville 

Dam, and redetected at upstream locations. These estimates have been adjusted to account for estimated harvest and 

“natural” straying rates of adults within the FCRPS migration corridor, but otherwise capture all other sources of mortality 

manifested within the identified reaches, including those resulting from the existence and operation of the FCRPS, 

unquantifiable levels of mortality from other potential sources (e.g., unreported or delayed mortality caused by fisheries, 

marine mammal predator attacks, etc.), and unquantifiable levels of “natural” mortality (i.e. levels of mortality in the 

migratory corridor that would have occurred “naturally” without human influence). 

3

 Adult survival rates for SR fall Chinook, SR spr/sum Chinook, and SR steelhead are reported separately as either inriver or 

transported (via barge or truck) to properly reflect their migration history as juveniles. Survival estimates for adult SR 

sockeye are primarily based on unknown origin (though likely from the Lake Wenatchee or Okanogan River sockeye 

populations) adults PIT tagged at Bonneville Dam and detected at McNary Dam. The average per dam survival is expanded 

to a seven dam reach (Bonneville Dam to Lower Granite Dam). 

4

 The estimates for these ESUs only apply to those adults migrating to tributaries entering the reservoir upstream of 

Bonneville Dam, or in the case of MCR steelhead, the adult populations migrating to tributaries entering the Columbia River 

between Bonneville Dam and McNary Reservoir. 

5

 Recent adult survival estimates from Priest Rapids to Wells dam are reported in Anchor Env. and Douglas PUD (2008): 

93.0% and 94.7% for summer steelhead (2004-2007) and spring Chinook salmon (2003-2007), respectively. The average per 

project survival estimates (1/4th root of the reach survival estimate) are 98.2% for steelhead and 98.7% for spring Chinook. 

6

 NOTE: A separate estimate for the McNary Dam to Priest Rapids Dam reach has not yet been generated. This will be 

addressed in the next update of the Recovery Planning Hydro Module. 

7

 Within the Bonneville pool, Klickitat River and 15 Mile Creek populations of steelhead are part of the Mid Columbia River 

steelhead Distinct Population Segment. 

8

 Within the Bonneville pool, Hood River and Wind River populations of steelhead are part of the Lower Columbia River 

steelhead Distinct Population Segment.
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 28 

Table 2. “Current” (2002-2009) Juvenile Survival Estimates for ESA-listed Columbia River Basin Salmon 

and Steelhead Populations Migrating Inriver Past Mainstem Hydroelectric Projects.1

Species Population Juv. Survival - FCRPS 

Reach 

Average (Range) 

Special Info. 

Juv. Survival3 – 

Mid-Columbia Reach 

Average (Range) 

Special Info. 

Juv. Survival – 

Total 

Average (Range) 

Special Info. 

SR fall 

Chinook 

Single Pop. LGR - BON

18.7 - 55.4 

(12.4 – 71.7) 

≈ 52% of the juveniles 

would be transported 

LGR - BON

18.7 - 55.4 

(12.4 – 71.7) 

≈ 52% of the juveniles 

would be transported 

SR spr/sum 

Chinook 

All Pops. LGR – BON 

LGR >65 kcfs 

56.3 (47.5 – 60.8) 

≈ 64% of the juveniles 

would be transported

LGR <65 kcfs 

37.3 (33.8 – 51.3)

≈ 95% of the juveniles 

would be transported 

LGR – BON 

LGR >65 kcfs 

56.3 (47.5 – 60.8) 

≈ 64% of the juveniles 

would be transported

LGR <65 kcfs 

37.3 (33.8 – 51.3)

≈ 95% of the juveniles 

would be transported 

SR sockeye4 Single Pop. LGR - BON 

LGR >65 kcfs 

36.4 (19.9 – 57.0) 

≈ 64% of the juveniles 

would be transported 

LGR <65 kcfs 

8.2 (Unknown) 

≈ 95% of the juveniles 

would be transported 

LGR - BON 

LGR >65 kcfs 

36.4 (19.9 – 57.0) 

≈ 64% of the juveniles 

would be transported 

LGR <65 kcfs 

8.2 (Unknown) 

≈ 95% of the juveniles 

would be transported 

SR steelhead All Pops. LGR – BON

LGR >65 kcfs 

38.9 (20.3 – 56.9) 

≈ 79% of the juveniles 

would be transported

LGR <65 kcfs 

7.5 (3.3 – 23.1)

≈ 94% of the juveniles 

would be transported

LGR – BON

LGR >65 kcfs 

38.9 (20.3 – 56.9) 

≈ 79% of the juveniles 

would be transported

LGR <65 kcfs 

7.5 (3.3 – 23.1)

≈ 94% of the juveniles 

would be transported 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 29 

Species Population Juv. Survival - FCRPS 

Reach 

Average (Range) 

Special Info. 

Juv. Survival3 – Juv. Survival – 

Mid-Columbia Reach Total 

Average (Range) Average (Range) 

Special Info. Special Info. 

UCR spring 

Chinook 

Methow 

Entiat 

Wentachee 

MCN – BON 

66.7 (60.9 – 72.9) 

WEL – PRD 

67.9 

RRE – PRD 

70.6 

RIS – PRD

76.7 

WEL – BON 

45.3 

RRE – BON 

47.1 

RIS – BON 

51.2 

UCR 

steelhead 

Methow / 

Okanogan 

Entiat 

Wentachee 

MCN – BON 

47.9 (16.8 – 67.4) 

WEL – PRD 

68.9 

RRE – PRD 

71.7 

RIS – PRD

74.8

WEL – BON 

33.0 

RRE – BON 

34.3 

RIS – BON 

35.8 

MCR 

steelhead2,5

Yakima / 

Walla Walla 

Umatilla / 

John Day 

Deschutes 

BON pool 

(MCN, JDA, TDA) – 

BON 

47.6 (17.2 – 67.1) 

53.6 (23.2 – 72.1) 

73.0 (61.5 – 77.6) 

90.0 (80.6 – 93.0)

(MCN, JDA, TDA, 

BON Pool) – BON 

47.6 (17.2 – 67.1) 

53.6 (23.2 – 72.1) 

73.0 (61.5 – 77.6) 

90.0 (80.6 – 93.0)

LCR 

Chinook2

BON pool BON Pool 

95.1 (94.4 – 95.9) 

BON Pool 

95.1 (94.4 – 95.9) 

LCR 

steelhead2,6

BON pool BON Pool 

90.6 (80.3 – 94.7) 

BON Pool 

90.6 (80.3 – 94.7) 

CR coho2 BON pool BON Pool 

95.1 (94.4 – 95.9) 

BON Pool 

95.1 (94.4 – 95.9) 

CR chum2 BON pool BON Pool 

95.1 (94.4 – 95.9) 

BON Pool 

95.1 (94.4 – 95.9) 

Sources: NMFS’ 1) Supplemental Comprehensive Analysis Document (May 5, 2008a); and 2) Biological Opinion – 

Consultation on Remand for Operation of the Federal Columbia River Power System, 11 bureau of Reclamation Projects in 

the Columbia Basin and ESA Section 10(a)(1)(A) Permit for Juvenile Fish Transportation Program (May 5, 2008b). 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 30 

1 Key to Dams: BON = Bonneville Dam, TDA = The Dalles Dam, JDA = John Day Dam, MCN = McNary Dam, PRD = 

Priest Rapids Dam, WAN = Wanapum Dam, RIS = Rock Island Dam, RRE = Rocky Reach Dam, WEL = Wells Dam, IHR = 

Ice Harbor Dam, LMN = Lower Monumental Dam, LGS = Little Goose Dam, and LGR = Lower Granite Dam. 

2

 The estimates for these ESUs only apply to those juveniles migrating from tributaries entering the reservoir upstream of 

Bonneville Dam, or in the case of MCR steelhead, the juvenile populations migrating from tributaries entering the Columbia 

River between Bonneville Dam and McNary Reservoir. 

3

 Current reach survival estimates for the Mid-Columbia projects are based on the following: 

• Wells (96.2% for spring Chinook and steelhead) - average of the 1998 (99.7%) Chinook study, and 1999 (94.3%) 

and 2000 (94.6%) steelhead studies as reported in NMFS 2002; 

• Rocky Reach (92.1% for spring Chinook) – average of 2004-2005 studies (93.0% and 91.1%, respectively) as 

reported in Skalski et al (2006), and (95.8% for steelhead) - average of 2004-2006 studies (98.3%, 93.0%, and 

96.0%, respectively) as reported in Anchor Env. and Chelan PUD (2007) and Skalski et al (2006); 

• Rock Island (93.4% for spring Chinook) – average of 2002-2004 studies (95.6%, 93.4%, and 91.4%, respectively) 

as reported in Anchor Env. and Chelan PUD (2004) and Skalski et al (2006), and (94.1% for steelhead) – average of 

2004-2006 studies (96.6%, 91.6%, and 94.0%, respectively) as reported in Anchor Env. and Chelan PUD (2007) and 

Skalski et al (2006); 

• Wanapum and Priest Rapids (82.0% for spring Chinook) – estimated using data from PIT tag studies conducted by 

Chelan PUD in 1998, 2001, 2002, and 2003 as reported in NMFS 2004 – Table A-2 (90.5% per project); and (79.5% 

for steelhead) - estimated using data from PIT tag studies conducted by Chelan PUD in 1999 and 2000 as estimated 

in NMFS 2004 – Table A-2 (89.1% per project). 

4

 Williams et al. 2005 provided estimated survival rates ranging for PIT tagged SR sockeye migrating from Lower Granite to 

McNary Dams in 2000 to 2003. Of these years, 2001, is most representative of the <65 kcfs flow condition – though still 

conservative because little spill was provided at the mainstem dams for passage in that year. Survival in this year was 

estimated at 23.9 percent. The remaining years are representative of the >65 kcfs flow condition. Survival rates ranged from 

39.7% to 72.5% (average of 56.1%) in these years. An average per project survival was estimated for this reach (LGR to 

MCN survival ^ (1/4) = 86.5% per project) and then expanded to a Lower Granite to Bonneville Dam (7 project) reach 

survival estimate (LGR to BON (per project survival estimate ^ 7 = 36.4%). 

5

 Within the Bonneville pool, Klickitat River and 15 Mile Creek populations of steelhead are part of the Mid Columbia River 

steelhead Distinct Population Segment. 

6

 Within the Bonneville pool, Hood River and Wind River populations of steelhead are part of the Lower Columbia River 

steelhead Distinct Population Segment.
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 31 

Table 3: “Prospective” (approximately 2014 and beyond) Juvenile Survival Estimates for ESA-listed 

Columbia River Basin Salmon and Steelhead Populations Migrating Inriver Past Mainstem Hydroelectric 

Projects.1

Species Population Juv. Survival - FCRPS 

Reach 

Average (Range) 

Special Info. 

Juv. Survival3 – 

Mid-Columbia Reach 

Average (Range) 

Special Info. 

Juv. Survival – 

Total 

Average (Range) 

Special Info. 

SR fall 

Chinook 

Single Pop. LGR - BON

18.7 - 55.4 

(12.4 – 71.7) 

≈ 52% of the juveniles 

would be transported

LGR - BON

18.7 - 55.4 

(12.4 – 71.7) 

≈ 52% of the juveniles 

would be transported 

SR spr/sum 

Chinook 

All Pops. LGR – BON 

LGR >65 kcfs 

62.8 (58.0 – 67.8) 

≈ 64% of the juveniles 

would be transported

LGR <65 kcfs 

51.9 (46.7 – 57.2)

≈ 95% of the juveniles 

would be transported

LGR – BON 

LGR >65 kcfs 

62.8 (58.0 – 67.8) 

≈ 64% of the juveniles 

would be transported

LGR <65 kcfs 

51.9 (46.7 – 57.2)

≈ 95% of the juveniles 

would be transported 

SR sockeye4 Single Pop. LGR - BON 

LGR >65 kcfs 

42.8 (23.5 – 64.6) 

≈ 64% of the juveniles 

would be transported 

LGR <65 kcfs 

9.8 (Unknown) 

≈ 88% of the juveniles 

would be transported

LGR - BON 

LGR >65 kcfs 

42.8 (23.5 – 64.6) 

≈ 64% of the juveniles 

would be transported 

LGR <65 kcfs 

9.8 (Unknown) 

≈ 88% of the juveniles 

would be transported 

SR steelhead All Pops. LGR – BON

LGR >65 kcfs 

45.3 (23.9 – 64.5) 

≈ 74% of the juveniles 

would be transported

LGR <65 kcfs 

9.1 (4.0 – 20.7)

≈ 89% of the juveniles 

would be transported

LGR – BON

LGR >65 kcfs 

45.3 (23.9 – 64.5) 

≈ 74% of the juveniles 

would be transported

LGR <65 kcfs 

9.1 (4.0 – 20.7)

≈ 89% of the juveniles 

would be transported 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 32 

Species Population Juv. Survival - FCRPS 

Reach 

Average (Range) 

Special Info. 

Juv. Survival3 – Juv. Survival – 

Mid-Columbia Reach Total 

Average (Range) Average (Range) 

Special Info. Special Info. 

UCR spring 

Chinook 

Methow 

Entiat 

Wentachee 

MCN – BON 

72.6 (65.4 – 79.6) 

WEL – PRD 

72.3 

RRE – PRD 

75.1 

RIS – PRD 

80.8 

WEL – BON 

52.5 

RRE – BON 

54.5 

RIS – BON 

58.7

UCR 

steelhead 

Methow / 

Okanogan 

Entiat 

Wenatchee 

MCN – BON 

52.8 (17.3 – 73.8) 

WEL – PRD 

75.0 

RRE – PRD 

78.0 

RIS – PRD 

81.4 

WEL – BON 

39.6 

RRE – BON 

41.2 

RIS – BON 

43.0

MCR 

steelhead2,5 Yakima / 

Walla Walla 

Umatilla / 

John Day 

Deschutes 

BON pool 

(MCN, JDA, TDA) – 

BON 

52.4 (17.9 – 73.3) 

57.9 (23.9 – 77.7) 

76.8 (64.5 – 82.2) 

90.3 (80.3 – 93.2)

(MCN, JDA, TDA, 

BON Pool) – BON 

52.4 (17.9 – 73.3) 

57.9 (23.9 – 77.7) 

76.8 (64.5 – 82.2) 

90.3 (80.3 – 93.2)

LCR 

Chinook2

BON pool BON Pool 

95.5 (94.6 – 96.2) 

BON Pool 

95.5 (94.6 – 96.2) 

LCR 

steelhead2,6

BON pool BON Pool 

90.8 (79.9 – 94.8) 

BON Pool 

90.8 (79.9 – 94.8) 

CR coho2 BON pool BON Pool 

95.5 (94.6 – 96.2) 

BON Pool 

95.5 (94.6 – 96.2) 

CR chum2 BON pool BON Pool 

95.5 (94.6 – 96.2) 

BON Pool 

95.5 (94.6 – 96.2) 

Sources: NMFS’ 1) Supplemental Comprehensive Analysis Document (May 5, 2008a); and 2) Biological Opinion – 

Consultation on Remand for Operation of the Federal Columbia River Power System, 11 bureau of Reclamation Projects in 

the Columbia Basin and ESA Section 10(a)(1)(A) Permit for Juvenile Fish Transportation Program (May 5, 2008b). 
National Marine Fisheries Service September 24, 2008 

Recovery Plan Module 

Mainstem Columbia River Hydropower Projects 33 

1 Key to Dams: BON = Bonneville Dam, TDA = The Dalles Dam, JDA = John Day Dam, MCN = McNary Dam, PRD = 

Priest Rapids Dam, WAN = Wanapum Dam, RIS = Rock Island Dam, RRE = Rocky Reach Dam, WEL = Wells Dam, IHR = 

Ice Harbor Dam, LMN = Lower Monumental Dam, LGS = Little Goose Dam, and LGR = Lower Granite Dam. 

2

 The estimates for these ESUs only apply to those juveniles migrating from tributaries entering the reservoir upstream of 

Bonneville Dam, or in the case of MCR steelhead, the juvenile populations migrating from tributaries entering the Columbia 

River between Bonneville Dam and McNary Reservoir. 

3

 Prospective reach survival estimates for the Mid-Columbia projects are based on the following: 

• Wells (96.2% for spring Chinook and steelhead) - average of the 1998 (99.7%) Chinook study, and 1999 (94.3%) 

and 2000 (94.6%) steelhead studies as reported in NMFS 2002; 

• Rocky Reach (93.0% for spring Chinook) – assumes that the minimum survival requirement of the Rocky Reach 

Habitat Conservation Plan will be met (NMFS 2002), and (95.8% for steelhead) - average of 2004-2006 studies 

(98.3%, 93.0%, and 96.0%, respectively) as reported in Anchor Env. and Chelan PUD (2007) and Skalski et al 

(2006); 

• Rock Island (93.4% for spring Chinook) – average of 2002-2004 studies (95.6%, 93.4%, and 91.4%, respectively) 

as reported in Anchor Env. and Chelan PUD (2004) and Skalski et al (2006), and (94.1% for steelhead) – average of 

2004-2006 studies (96.6%, 91.6%, and 94.0%, respectively) as reported in Anchor Env. and Chelan PUD (2007) and 

Skalski et al (2006); 

• Wanapum and Priest Rapids (86.5% for spring Chinook and steelhead) – assumes the minimum survival standard 

(93.0% per project) for these species will be achieved (NOAA 2004). 

4

 Williams et al. 2005 provided estimated survival rates ranging for PIT tagged SR sockeye migrating from Lower Granite to 

McNary Dams in 2000 to 2003. Of these years, 2001, is most representative of the <65 kcfs flow condition – though still 

conservative because little spill was provided at the mainstem dams for passage in that year. Survival in this year was 

estimated at 23.9 percent. The remaining years are representative of the >65 kcfs flow condition. Survival rates ranged from 

39.7% to 72.5% (average of 56.1%) in these years. An average per project survival was estimated for this reach (LGR to 

MCN survival ^ (1/4) = 86.5% per project) and then expanded to a Lower Granite to Bonneville Dam (7 project) reach 

survival estimate (LGR to BON (per project survival estimate ^ 7 = 36.4%). To estimate the expected increase in survival 

between the “current” and “prospective” conditions, these estimates were adjusted by the estimated survival improvement of 

SR steelhead in the >65 kcfs flow year condition (45.3% [Prospective] - 38.9% [Current] = 6.4%) resulting in an estimate of 

42.8% (36.4% + 6.4%). This was also done for the <65 kcfs flow year condition (9.1% [Prospective] – 7.5% [Current] = 

1.6%) resulting in an estimate of 9.8% (8.2% + 1.6%). 

5

 Within the Bonneville pool, Klickitat River and 15 Mile Creek populations of steelhead are part of the Mid Columbia River 

steelhead Distinct Population Segment. 

6

 Within the Bonneville pool, Hood River and Wind River populations of steelhead are part of the Lower Columbia River 

steelhead Distinct Population Segment. 
National Marine Fisheries Service September 24, 2008 

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Mainstem Columbia River Hydropower Projects 34 
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