I N D EP EN D EN T SCI E N TI FI C ADV IS OR Y BO AR D

851 SW 6th Avenue, Suite 1100, Portland, OR 97204

9 June 1998

Letter / Memorandum (ISAB 98-4) 

To: The Northwest Power Planning Council

 The National Marine Fisheries Service

Re: The Scientific Basis for Juvenile Fish Passage 

Improvements In the Federal Columbia River Power System: 

John Day Dam Extended Length Turbine Intake Screens and 

Bonneville Dams Bypass System Outfalls

 First Report: 

 The ISAB Corps Capital Construction Project 

Review

Peter A. Bisson, Ph.D.

Charles C. Coutant, Ph.D.

Dan Goodman, Ph.D

.

James A. Lichatowich, M.S.

William J. Liss, Ph.D.

Lyman McDonald, Ph.D.

Phillip R. Mundy, Ph.D.

Brian Riddell, Ph.D.

Richard R. Whitney, Ph.D.

Richard N. Williams, Ph.D.
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 2

Table of Contents

INTRODUCTION.........................................................................................................................................................2

Definition of the Assignment.....................................................................................................................................2

Preparation of the Response ......................................................................................................................................3

JOHN DAY EXTENDED-LENGTH SCREENS .........................................................................................................4

Council Questions on John Day Extended Length Screens.......................................................................................4

John Day Conclusions .............................................................................................................................................11

John Day Recommendation:....................................................................................................................................12

BONNEVILLE FISH-BYPASS OUTFALL RELOCATION.....................................................................................13

Council Questions on Bonneville Hydroelectric Projects Bypass Outfall Relocation.............................................13

Bonneville Outfall Relocation Discussion...............................................................................................................21

Bonneville Recommendation...................................................................................................................................22

REFERENCES ............................................................................................................................................................23

INTRODUCTION

Definition of the Assignment

This report responds to a request for assistance from the Northwest Power Planning 

Council (Council) dated January 7, 1998 on issues related to the planned capital construction 

projects of the U. S. Army Corps of Engineers (Corps or COE) (i.e., the Corps’ Columbia River 

Fisheries Mitigation Program, or CRFM Program).

The U.S. Congress, in its appropriations bill for FY 98 directed the Council, with 

assistance from the Independent Scientific Advisory Board (ISAB), to review the mainstem 

Columbia River capital construction program of the Corps. The review is to evaluate the 

technical need for costly fish passage strategies at mainstem dams. The Northwest Power 

Planning Council document of January 7, 1998, identified sets of general and specific questions 

that Council staff initially felt would help focus the review by the ISAB (Appendix A). 

Subsequent discussions with the ISAB narrowed the focus at the outset to near-term and 

long-term assignments. The three near-term assignments are: 

1. Role of mainstem fish bypass measures in an ecosystem approach for the 

Columbia/Snake rivers;

2. Review of the scientific basis for future investment in extended-length bar screens at 

John Day Dam;

3. Review of the scientific basis for juvenile fish passage improvements at Bonneville 

Dam.

Long term assignments to be completed in December include reviews of the COE’s programs for 

surface bypass and dissolved gas abatement (tentatively scheduled for completion in September 

1998) and a comparative evaluation of multiple technologies for aiding downstream passage of 

salmonids. 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 3

The Council established a policy context for the review of the CRFM Program 

concerning possible major alternatives for future configuration of mainstem hydroelectric dams 

presently under consideration in the region. The following four future alternative system 

configuration scenarios provided sideboards for the review:

1. All existing mainstem dams, including dam modifications, remain in place and 

operational for the foreseeable future.

2. All dams remain in place except that the four lower Snake River projects are 

breached to provide a natural river condition in the Snake River within the next 

5-10 years.

3. All dams remain in place except that a lower Columbia River project, such as John 

Day Dam, is breached or lowered within the next 10 years.

4. Dams remain in place except that the four lower Snake River projects are breached 

to provide a natural river condition in the Snake River and John Day Dam is 

breached or lowered in the Columbia River within the next 5-10 years.

During 1999, the region will receive additional guidance on operational scenarios. The National 

Marine Fisheries Service is scheduled to issue a longer term Biological Opinion on the operation 

of the federal Columbia River hydroelectric system in 1999. 

Preparation of the Response

The ISAB used the Council’s scoping document (Ruff 1998) as a guide for its review. 

Each of the Council’s questions was adapted to the specific circumstances of the project being 

reviewed. We attempted to provide a direct answer to each of the Council’s question, with an 

explanation. 

Information for the review was derived from a number of sources. The ISAB received 

both oral presentations and written documents for its review. The COE staff briefed the ISAB 

on January 20 and February 17. Each briefing was attended by representatives of other 

organizations in the Columbia River basin, who also were offered time to provide their views 

and documents. Lists of the agencies participating and the documents tendered are available on 

request from Erik Merrill at the Council.

The full ISAB initially discussed the scope of the review and the desired product. A 

subcommittee of the ISAB reviewed documents and prepared the initial draft report. The draft 

was reviewed and modified by other ISAB members. This final report is a consensus document 

of the Board. 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 4

JOHN DAY EXTENDED-LENGTH SCREENS

The Corps of Engineers proposes to install extended-length submersible bar screens, 

ESBS, in the turbine intakes at John Day Dam as a replacement for the standard-length 

submersible traveling screens now in place. The purpose of the proposed operation is to 

increase the percentage of the juvenile emigrant salmonids guided into the bypass system for the 

powerhouse, thereby decreasing the complementary percentage of the emigrants passing through 

the turbines. This is expected to increase the survival of the emigrants passing John Day Dam 

based on the theory that emigrants passing through the bypass have higher survivals than 

emigrants passing through the turbines.

Council Questions on John Day Extended Length Screens

1. How does the concept of John Day turbine intake screening fit within the context of 

restoration of normative conditions to the Columbia River ecosystem?

The proposal for installation of the John Day extended length screens does not 

accommodate the natural ecological processes and juvenile salmonid migratory behaviors needed 

to sustain salmonids in the Columbia River basin, as explained in reviews such as Upstream

(National Research Council (NRC), 1996) and Return to the River (Independent Scientific Group 

(ISG), 1996). 

Screens at turbine intakes at John Day and elsewhere in the Columbia River mainstem 

inherently run counter to the behavioral characteristics of emigrating of juvenile salmon and 

steelhead. During periods of active downstream migration, juvenile salmonids characteristically 

are concentrated in the highest velocity regions of a river, which occur in the thalweg and upper 

third of the water column. Being drawn into or actively sounding into deep turbine intakes is not

a normal behavior of downstream migrants, with the result that many fish are delayed at dam 

forebays. Delay in the forebay increases risk of mortality for juvenile salmon and steelhead 

through predation, exposure to high temperatures and communicable diseases. 

One aspect of screening turbine intakes that could be considered consistent with natural 

ecological processes and juvenile salmonid migration behaviors are the location of the screens in 

the upper portions of the turbine intakes, and diversion to the gatewells. These aspects take 

advantage of the natural tendency of migrating juvenile salmonids to return to the surface after 

diving into the turbine intake.

On the other hand, these factors are not likely to apply equally to all species and 

populations. Due to inherent differences in size, swimming abilities and behavioral responses to 

bar screens, some populations, species and life history types may experience increases in 

survival while others may be harmed. Management actions that favor normal ecological 

processes and support of the typical juvenile salmonid migratory behaviors, such as surface spill 

and surface bypass, may provide benefits to a broader variety of populations, species and life 

history types than do remedies such as turbine intake screens.
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ISAB 98-4: First Report on the COE Capital Construction Project Review 5

2. What is the record of effectiveness of John Day turbine intake screening to mitigate for the 

mortality that would otherwise be inflicted by mainstem hydroelectric dams, and how would the 

implementation of extended length screens contribute to improving this record? Please address 

the following specifics in answering this question: a. How has John Day turbine intake screening 

contributed toward meeting salmon recovery goals? b. What are the positive impacts of John 

Day turbine intake screening facilities? c. What negative impacts have the facilities incurred?

Definition of terms: Fish guiding efficiency, FGE, is the proportion or percentage of 

juvenile salmon entering the turbine intakes that are diverted into the bypass system. Fish 

passage efficiency, FPE, is the proportion or percentage of juvenile salmon passing the 

hydroelectric project by routes other than turbines. When all of the river’s flow is going into the 

powerhouse there is no spill, and the FGE is equal to the FPE. At times when not all of the 

river’s flow is entering the powerhouse, FGE is less than FPE. Neither FGE nor FPE taken 

alone is a measure of survival experienced by juvenile salmon or other emigrants during 

hydroelectric project passage. Hydroelectric project survival is the proportion or percentage of 

the juveniles that pass the dam alive during a specified time interval, such as the migration 

season. The term, “nominal”, is given to a numerical survival value when it is applied to a route 

of passage at a hydroelectric project other than the project at which the survival was actually 

estimated empirically.

The record of effectiveness of turbine intake screens is uncertain. Large incremental 

improvements in FGE have been steadily made over the last 20 years at the mainstem dams 

operated by the COE, as well as at dams operated by other parties. For example, during the 17 

years of service at John Day Dam, before standard traveling screens were installed, COE staff 

estimated that only 2% of juveniles entering the turbine intakes exited via orifices into the 

"gatewell salvage systems". When standard screens were installed in 1985, FPE for wild yearling 

chinook improved to about 64% (Table 4 in Anderson et al., 1998). [Note that in the absence of 

spill at John Day, FGE is equal to FPE]. Similar fish passage efficiency improvements were 

also realized at other projects during the 1980s when turbine screens were installed. Despite 

these dramatic improvements in fish passage efficiency, no corresponding improvement in the 

return rates of wild adult stream type salmon and steelhead above Bonneville Dam has occurred 

and the downward trend in salmon abundance has continued (National Research Council, 1996; 

Whitney et al. 1997). Either survival in passing dams was not improved or the improvement 

was masked by changes in survival elsewhere (often suggested to occur in the estuary or ocean).

The interim objective in both the Fish and Wildlife Program of the Northwest Power 

Planing Council (FWP) and National Marine Fishery Services’ (NMFS) Proposed Recovery Plan 

is 80% FPE and 95% survival of juveniles past each project (i.e., 95% project survival). The 

COE expected with the installation of extended-length submersible bar screens (ESBS), to 

achieve 55%-84% improvement of FGE or 3% project survival improvement for spring migrants 

and 20-60% improvement of FGE or 4% project survival improvement for summer migrants (IT 

Briefing Summary). These improvements, if actually achieved, would contribute to the goal of 

95% project survival. Installation of ESBS was estimated to increase FGE relative to standard 

length submersible bar screens (SBS) for yearling spring chinook (58% to 84%), steelhead (86% 

to 94%), sockeye (41% to 79%), and subyearling chinook (32% to 60%) (Fredericks and Graves 

memo to Hydro Files, April 9, 1997; Brege et al., 1997; Krcma et al., 1986; Brege et al., 1992; 

Whitney et al. 1997). 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 6

Interpretation of the record of effectiveness of John Day turbine intake screening to 

mitigate for the mortality that would otherwise be inflicted by turbine passage would depend on 

how many of the juveniles were passed by the primary non-turbine alternative route, spill. Spill 

can occur during the migration season either involuntarily when river discharge exceeds the 

turbine capacity of the dam or voluntarily when spill is used as a management tool to pass 

juveniles. To evaluate the effectiveness of ESBS, the ISAB sought to verify expected 

improvements under operational scenarios that included or excluded passage of juvenile salmon 

by spill. Our efforts to match calculations of effectiveness of ESBS by the Corps and NMFS 

have highlighted many uncertainties, which are discussed in the answer to Question 3 below. 

Our calculations suggest that 80% FPE possibly could be achieved with ESBS for yearling 

chinook, steelhead, and perhaps for sockeye, but probably not for ocean type chinook over the 

course of an entire annual migratory season. The ISAB calculated that, assuming no juveniles are 

passed by spill, the reduction in nominal total project mortality of yearling chinook with 

extended-length screens relative to the standard screens might be 3.1%. The calculation used 

average numbers that were provided in agency documents for FGE of both screens, mortality in 

turbines, and mortality in the bypass systems (principally the Fredericks and Graves memo, 

Anderson et al., 1998, and summaries in Whitney et al., 1997). Reduction in mortality of 

subyearling chinook with the new screens relative to the standard screens was taken to be 3.0%. 

These figures are comparable to those of the COE. 

Spill decreases the relative improvement in survival of juvenile salmon due to the ESBS. 

For example, ISAB calculations suggest that when fifty percent or more of the emigrants are 

spilled, the difference in nominal survivals between standard and extended-length screens is 

1.5% or less. A question for fisheries managers is whether there is a greater increase in survival 

by voluntarily spilling water or by minimizing spill and depending on screens and fish bypasses 

to protect fish from turbines.

However, the more important question is whether a putative improvement in project 

survival of a few percent following installation of extended-length screens will contribute in a 

meaningful way to recovery of stocks at risk of extinction or to protection of healthy stocks. The 

answer to this question needs to be weighed relative to the costs of the installation and the 

alternative costs of lost power generation if survival is managed by voluntary spill. Analysis that 

addresses this question quantitatively and currently is not available. The analysis will require 

thoughtful collaboration between biologists and economists.

When considering species other than juvenile salmon and steelhead, the application of 

ESBS is indeed uncertain. Any changes in the FPEs generated by addition of the ESBS for other 

anadromous species, such as Pacific lamprey, and other migratory species, such as the 

catostomids, are unknown. Impingement of juvenile Pacific lamprey has been demonstrated for 

the John Day ESBS, but the proportion of migrants affected is not known.

3. What are the major uncertainties or research questions associated with increasing the ability of 

John Day turbine intake screens to divert juvenile emigrants to the bypass system?

a. The 80% fish passage goal and the 95% survival goal at each hydroelectric project are policy 

decisions. It is uncertain how these goals might relate to an expected improvement in the 

relationship between the numbers of downstream migrants and numbers of returning adults.
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ISAB 98-4: First Report on the COE Capital Construction Project Review 7

b. A major uncertainty regarding the effectiveness of turbine-intake screens (both conventional 

and extended-length) is highlighted by the fact that dramatic improvements in FGE over the 

last 20+ years at most Columbia basin mainstem dams have not been matched by dramatic 

improvements in returns of adult salmon and steelhead to spawning grounds above 

Bonneville Dam. In addition, there is no documented evidence that installation of screens has 

slowed the decline of salmonid stocks. However, documentation of improvements in 

numbers of returning adults is complicated by the difficulty of separating the mortality that 

occurs during dam passage from the mortalities experienced in other parts of the life cycle 

(especially in the estuary and ocean). Furthermore, evaluations of smolt to adult survival in 

Columbia River salmon generally lack statistical power sufficient to have a reasonable 

chance of detecting the effects of small, incremental increases in downstream survival of 

juveniles at a project such as John Day Dam. 

c. The following uncertainties involve the estimation of FPE and project survival. These 

uncertainties render estimates of FPE and project survival at John Day Dam problematic.

 There is an uncertainty with respect to the number used for downward adjustment of the estimates 

of FGE for standard screens. In calculating project survival, a downward adjustment of 20% in 

measured FGEs for screens in the Snake and lower Columbia rivers was made, due to the location 

of the fyke net array directly below the screens. The fyke array is thought to have pushed more 

water and fish upward than would have occurred in its absence (Anderson et al., 1998). The basis 

for this adjustment is tenuous. If the unadjusted FGE number is used, the expected improvement 

in survival due to installation of ESBS is lowered. For example, if the unadjusted FGE figure for 

yearling chinook is used (69%, Anderson et al., 1998), the estimated total mortality would be 

5.4%, giving a 1.6% improvement in survival with extended screens, compared to the 3.1% 

improvement estimated with the adjustment. 

 The estimate of bypass mortality (2%) used in calculating project survival may be too 

conservative. Bypass survival studies have not been conducted at John Day Dam. Numerous 

uncertainties are associated with bypass survival studies at other dams, which influence their 

applicability to John Day. Furthermore, NMFS studies at Snake River dams indicate that bypass 

mortality can be highly variable (0.6-7%; Bill Muir, NMFS, personal communication). Analysis 

of the sensitivity of project survival to variation in bypass mortality was not available, but it is 

likely that small changes in bypass mortality could lead to large changes in benefits ascribed to 

ESBS.

 Recent empirical studies of project survival of species and life history types at John Day Dam for 

standard length screens are lacking. Thus, project survival for standard-length bypass screens at 

John Day must be extrapolated from other sources or earlier studies for determination of expected 

improvement in survival with ESBS. The use of actual estimates of survival is preferred over the 

use of nominal figures.

 Estimation of improvement in project survival is complicated by difficulties in selecting the 

appropriate FGEs from among those that have been measured (Anderson et al. 1998; Fredericks 

and Graves memo to Hydro Files April 9, 1997; Whitney et al., 1997). Moreover, the use of 

average FGEs in determining project survival may bias survival estimates. Measured FGEs vary 

not only among species and life history types, but also with time of year, degree of smoltification, 

time of day, and other factors. (Whitney et al 1997). Analysis of the sensitivity of project survival 

estimates to variation in FGE was not available. 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 8

 Detecting effectiveness of small increases in downstream survival of juveniles at John Day on 

adult returns will be difficult. Rigorous modeling studies were not available to assess the 

probability of detecting effects of small increases in survival at John Day Dam on smolt to adult 

return rates (SARs), given variability in survival due to fluctuations in freshwater and ocean 

conditions.

d. Increased gatewell turbulence is a consequence of extended-length screens. During orifice 

blockages, fish in the gatewell cannot exit as intended and smolts would be subjected to 

increased turbulence for extended periods of time. The actual effects on salmon and other 

species of prolonged exposure to these higher levels of turbulence have not been measured, 

however the effects are likely to be harmful. Even in the absence of orifice blockages, 

turbulence may lead to higher levels of descaling than current designs of standard screens. 

Knowledge of the effects on survival of juvenile salmon and other species of prolonged 

exposure to high turbulence, and the effects of descaling on survival of juvenile salmon are 

uncertainties relevant to understanding the effects of extended length screens at John Day 

Dam. 

e. There are uncertainties of the effects on fish of increased debris loads in the bypass systems. 

An unintended consequence of extended screens is their ability to guide more debris into 

gatewells where it then travels into the bypass system. Although there are programs to 

check and clean orifices at each project, much of the increased debris goes into bypass 

systems. Bypass systems have not been specifically designed to minimize the effects of 

increased debris load on juvenile emigrant salmonids. John Day Dam has an open flume 

system that makes handling of debris problems easier, nonetheless experience in coping with 

debris from extended length screens is limited. Debris in dams can pose a serious mortality 

problem for juvenile emigrant salmonids (Matthews 1992). 

f. There are uncertainties in the development of the engineering criteria. Options for 

engineering features include angle of deployment of the screen, porosities of backing plates, 

configurations of vertical barrier screens, location and diameter of orifices, and numerous 

other features of a complete bypass system. Prototype tests are designed to help select the 

best combination for the particular project, but these are not necessarily the final features of 

the full system, as evaluation continues once it is in place. 

g. The following uncertainties are associated with the spill alternative (necessary for a 

comparative evaluation of ESBS):

 The mix of species included in spill is not known. This is important for measuring the true effects 

of using spill as a supplement to the FGE of intake screens for achieving the 80% fish passage 

goal.

 Spill passage efficiency curves (percentage of emigrants passed as a function of percentage of 

river flow spilled) are not available for John Day Dam. Because we do not have the spill passage 

efficiency curve, it is not possible to evaluate the feasibility of passing a particular percentage of 

emigrants under the operational scenarios posed by the Council. The assumption of a 1:1 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 9

relation between proportion of flow spilled and the proportion of the emigrants passed via spill is 

unlikely to be universally valid at all spill levels (Whitney et al. 1997). Relating levels of spill 

with levels of adult returns, and smolt to adult survivals will be difficult, just as it has been with 

evaluation of the effectiveness of bypass systems.

4. How does the existing level of scientific uncertainty affect the use and management of John 

Day turbine intake screening?

Scientific uncertainty about the effect of the turbine intake screening on the recovery of salmon 

populations makes use and management of the John Day turbine intake screens difficult to 

objectively evaluate in terms of long-term population viability. The use of turbine intake 

screening at John Day needs to be approached with substantial caution in view of the uncertainty. 

5. How does the existing level of scientific uncertainty affect the question of whether or not to 

proceed with increasing the ability of John Day turbine intake screening to facilitate entrainment 

of juvenile emigrants to the bypass system?

The small nominal increase in survival from installation of ESBS and the existing level of 

scientific uncertainty concerning the actual magnitude of the nominal increase make it difficult 

to justify proceeding with installation of ESBS at John Day dam at any cost. The high cost of 

ESBS makes justification even more dubious, but must be tempered by costs of spill as an 

alternative. Economic uncertainty (beyond the scope of the ISAB review) needs to be 

considered. 

6. What is the relative likelihood that increasing the ability of John Day turbine intake 

screening to facilitate diversion of juvenile emigrants to the bypass system will contribute to 

achievement of the goals of the NMFS Biological Opinion, the Council's Fish And Wildlife 

Program, or the tribes' 1995 Anadromous Fish Restoration Plan, Wy-Kan-Ush-Mi Wa-Kish-Wit –

Spirit of the Salmon?

There are a number of goals that could be identified in the three documents referenced. 

We highlight three of them for our purposes here, the 80% fish passage and 95% survival goal 

(which are related), an increase in numbers of adult salmon or recovery (which in theory is 

related to the preceding two), and maintenance of diversity of the salmon stocks. 

a) FPE and project survival goals may not be met for some species and life history types. The 

80% FPE goal probably would be achieved by ESBS for yearling chinook, steelhead and 

coho, and perhaps for sockeye, but it would not be achieved for subyearling chinook. It is 

difficult to discern whether any increases in project survival would result in increased adult 

returns.

b) Biodiversity may not be protected. Ample evidence is available to demonstrate that the 

collection efficiency of each bypass system varies by species, life history type and 

population. The FPE goal, if implemented over the long term, could increase survival of 

some stocks/life histories that pass through the existing system at an optimal time, while the 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 10

survival of other stocks/life history types that pass through the system at other times could be 

unaffected or adversely affected. The FPE goal should reflect the need to achieve high 

passage efficiency and survival for all stocks and/or species throughout the entire seasonal 

migration period. Each of the individual stocks must pass through the selective mortality 

bottleneck imposed by the mainstem dams. There is a critical clash between the upper-river 

salmon restoration programs and Corps mainstem passage programs. Upper river programs, 

such as many ESA-driven actions, employ performance criteria focused on individual stocks 

or spawning populations, while the Corps uses a seasonal average FPE criterion that ignores 

biodiversity at the stock level. Nearly all evidence for the effectiveness of turbine intake 

screens has been presented as composite numbers that average across the migration season, 

for a species (i.e. steelhead) or a life history type of a species (i.e. yearling chinook). These 

averages are insufficient for ensuring that changes in downstream survival (if detected) 

would preserve biodiversity. 

7. What scientific information is available to compare the John Day fish passage strategies, 

standard length turbine intake screens versus extended length screens? 

a. Are there significant limitations in the scientific information used to evaluate the different 

John Day turbine intake fish passage strategies? If so, how can the region best fill these 

information gaps?

The following are significant limitations in scientific information used to evaluate the different 

John Day turbine intake fish passage strategies. Please refer also to the uncertainties discussed 

above.

 There is a substantial likelihood that the screening and bypass system selectively favors some life 

history types/populations/species over others. A constant (average) FGE for each species/life history 

type was used to estimate seasonal FPE and project survival. FGE can vary with time of year, degree 

of smoltification, time of day, and other factors that would cause differences in project survival of 

individual populations emigrating at different times of the year (Whitney et al. 1997). 

 We lack rigorous modeling of juvenile survival at a project level. We also lack modeling of the 

overall life cycle survival. Inferences from these modeling efforts are essential to support the 

decision to install ESBS. It would have been useful to see model projections pertaining to the 

sensitivity of juvenile survival at a project as well as life cycle survival. These models should 

address variability in important factors such as in FGE and bypass mortality. Such models, although 

imperfect, are available for comparative analyses.

 The use of nominal survival figures creates substantial uncertainty. The nominal increase in juvenile 

survival through John Day Dam following installation of ESBS is an extrapolation from experience in 

other localities. Each hydroelectric project is different, hence the concern that experience in other 

localities does not necessarily apply to John Day. The lack of empirical data pertaining to survival of 

juveniles at John Day to support installation of ESBS, the uncertainties of bypass survival studies, 

and potential variability of bypass mortality all lead us to seriously question the magnitudes of the 

projected benefits of John Day ESBS. Detecting effectiveness of small increases in survival and the 

lack of data make it difficult to undertake rigorous modeling studies that assess the resulting influence 

on smolt to adult return rates. This problem is exacerbated by the relatively large variability in 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 11

survival due to fluctuations in freshwater and ocean conditions. In short, estimated increases in 

project-specific survival are so small that even if they occur we may never be able to evaluate their 

effects on adult returns. Given that we presently have no estimates that apportion adult returns to the 

effects of turbine intake screens at any single hydroelectric project, it is unlikely that estimates of the 

cumulative effects of ESBS installed over multiple projects on smolt to adult return rates will be 

forthcoming. 

 We lack empirically demonstrated benefits in SARs from installation of standard length screens, or 

analytical evidence that installation of screens has slowed decline of some salmon stocks.

 The lack of rigorous comparison (via modeling or other studies) of alternative scenarios to extended 

length screens such as improved spill efficiency and surface bypass, for achievement of not only 80% 

FPE and 95% survival but also significantly greater SARs, is a significant limitation in scientific 

information.

b. Within the constraints of the four operational scenarios provided by the Council, is the 

effectiveness of John Day standard length turbine intake screens adequate to achieve the interim 

performance objective of 80% fish passage efficiency and 95% juvenile fish survival at each dam

Under all scenarios, we believe that, with the existing levels of uncertainties, there is inadequate 

scientific justification to conclude that the objectives will be achieved. 

c. Does the proposed implementation of extended length turbine intake screens at John Day 

Dam have a high probability of achieving the expected biological benefit (salmon survival 

improvement) without undue risk to other anadromous and/or resident fish populations?

The ESBS likely will favor some species, life history types, and stocks over others and could be 

detrimental to some species such as Pacific lamprey. The extent of the effects on different stocks 

is unknown.

d. Does the proposed implementation of extended length turbine intake screens at John Day 

Dam provide potentially interim (within the next 10 years) biological benefits, or is it consistent 

with longer-term increasingly normative system configuration strategies? 

Improvements in FGE of turbine intake screening are not consistent with longer-term 

increasingly normative system configuration strategies. Existing turbine intake screening may 

be used in conjunction with a program to implement normative strategies. However the search 

for effective means of improving survival of the full diversity of salmon and steelhead 

populations needs to be expanded. 

John Day Conclusions

The incremental approach to salmon restoration embodied in the John Day Dam extended 

length bypass screen program involves activities that (1) rely on expensive technology and (2) 

focus on very narrow segments of the life history of the species/population, without linking the 

segments to the entire life cycle. Incremental approaches often are fragmentary and lack a 

unifying conceptual foundation and a context in a well-defined restoration strategy. Each 

incremental activity is acknowledged to bring about only a small increase in survival but the 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 12

cumulative increase in survival from all incremental activities is assumed to lead to significant 

survival advantages for the target species. Reliance on small-scale incremental approaches stems 

in part from reluctance to make larger-scale, longer-term changes that could have a higher 

probability of measurable success. Extended-length screens are an incremental technology that 

provides improvement in average, seasonal FGE over standard screens at diverting migrants 

from the turbine intake. However, there is uncertainty over whether increased FGE, if achieved, 

will translate into increased measurable project survival and increased adult returns.

John Day Recommendation: 

Implementation of the COE program to install extended-length screens at John Day Dam 

does not appear to be justified. Instead, the ISAB recommends pursuing existing surface spill 

alternatives and funding research toward possible deployment of a surface-flow bypass system. 

Where conventional or extended-length screens are already deployed, integrate their continued 

use with future installations of new facilities designed to mimic natural processes. Mitigation 

measures need to improve survival of the full range of diversity in salmon and steelhead 

populations, while taking into account impacts on other species. We are aware that with the 

existing screens spill is required in order to supplement the FGE of the screens and move toward 

the 80% fish passage goal. We are also aware that gas supersaturation restricts the amount of 

spill so that the 80% goal can not be achieved (Fish Passage Center, 1994; Whitney et al., 1997). 

Nonetheless we are recommending that strategies other than extended length screens that offer to 

achieve the 80% goal within gas supersaturation guidelines be pursued. 
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ISAB 98-4: First Report on the COE Capital Construction Project Review 13

BONNEVILLE FISH-BYPASS OUTFALL RELOCATION

The COE proposes to relocate outfalls of the bypass systems at both powerhouses in 

order to move bypassed juvenile salmonids away from known concentrations of predators. In 

addition to relocation of the outfall for the juvenile bypass system, planned alterations scheduled 

at Bonneville Dam to the juvenile fish passage facilities include increasing FGE of intake screens 

at both powerhouses, replacing the existing bypass conduits at the powerhouses, joining the two 

conduits to a common outfall, investigating surface bypass, and implementing gas abatement 

strategies (COE briefing to the ISAB). The ISAB has focused its work in this report primarily 

on evaluating the proposed bypass outfall relocation. However, the concerns expressed over the 

future of mechanical bypass in the portion of this report dealing with John Day extended length 

screens also apply to Bonneville.

Council Questions on Bonneville Hydroelectric Projects Bypass Outfall Relocation

1. How does the concept of Bonneville outfall relocation fit within the context of restoration of 

normative conditions to the Columbia River ecosystem?

The existing bypass outfalls artificially concentrate the juveniles and deliver them to 

locations where they are highly vulnerable to predation. Concentration of the juveniles into a 

relatively small volume of relatively slow moving water at a hazardous location is not preferable 

to alternative means of passage designed to recognize and take into account the natural 

ecological processes and migratory behaviors needed to sustain salmonids in the Columbia River 

basin, as explained in reviews such as Upstream (NRC, 1996) and Return to the River (ISG, 

1996). Avenues of passage, such as spill, more closely mimic natural situations and processes 

that emigrating juvenile salmonids encountered in their evolutionary history. Consequently, 

such means of passage should be less selective over the entire range of stocks and life history 

types than foreign or unnatural passage routes. Identifying and implementing more natural 

passage routes would increase normative conditions at Bonneville and should result in a decrease 

in juvenile mortalities. (See also the response to Question 1, John Day extended length 

screens.) 

Outfalls are an integral part of bypass systems. The access of emigrants to these bypass 

systems differs among populations, species, and life history type, artificially altering the 

individual fitness of emigrants, and ultimately the fitness of populations that comprise the total 

annual emigration. This is particularly true for later and smaller emigrants that are more 

vulnerable to predation than are the earlier, larger emigrants. For the long-term, additional and 

more substantial commitments to normative conditions, such as may be possible with surface 

bypass collection and spill (with reduced gas concentration), are expected to be required for 

further improvement of survival of juvenile salmon and steelhead. To the extent that bypass 

relocation can reduce mortalities for those juvenile salmon and steelhead that may enter the 

powerhouses, outfall relocation would be supportive of recovery of endangered salmon stocks, 

and it should reduce artificial selection against later and smaller emigrants. Relief from the 

present situation, where high outfall mortalities are known to be occurring, through relocation of 

the combined bypass outfall to deeper, swifter water more typical of the riverine migration 

pathway would contribute to restoration of normative conditions, at least in the short-term. 

Although Bonneville outfall relocation should help reduce artificial selection against later and 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 14

smaller emigrants, relocation is not supportive of restoring normative conditions to the extent

that the turbine-intake screening and bypass systems, including outfalls, continue to concentrate 

the juveniles. As a longer term consideration, any advantage of relocation of the outfall might 

be expected to decrease with time as the current type of predator alters its behaviors in response 

to relocation of the prey, or as other types of predators are able to take advantage of the 

concentrated prey. 

2. What is the record of effectiveness of Bonneville bypass outfalls to mitigate for the mortality 

that would otherwise be inflicted, and how would the relocation of the outfalls contribute to 

improving this record? 

Apparent survival rates of subyearling chinook salmon passing through either bypass 

systems were about the same, or lower, than those of fish passing through turbines of either 

powerhouse. Ledgerwood et al. (1994) evaluated survival through the bypass system and turbine 

at the first powerhouse. Survival was lowest through the bypass system, followed by the 

turbine, and downstream release. Petersen et al. (1993) documented that predatory cyprinid fish 

(Ptychocheilus oregonensis), commonly known as northern squawfish, are abundant near shore 

in the tailrace at the first powerhouse, and that fish of this species on both sides of the river 

actively fed on juvenile salmonids that were released at the present bypass outfall. [Note: Some 

Native Americans find the standardized common name for this predator published by the 

American Fisheries Society (Robins et al. 1980) to be offensive (Keith Hatch, Columbia River 

Inter-Tribal Fish Commission, personal communication). Given the current dispute over the 

standardized common name, we chose to use only the generally accepted form of the binomial, 

P. oregonensis, to refer to this species.]

There have been numerous studies of mortality rates of juvenile salmon (subyearling 

chinook) in and below the bypass system at the second powerhouse (Dawley et al., 1988; 1989; 

1996; Ledgerwood et al., 1990; 1991; Gilbreath et al., 1993; summarized by Whitney et al., 

1997). For two experimental lots of subyearling chinook, one passing through the turbines and 

the other through the bypass, downstream recovery rates of turbine fish were similar to, or 

slightly higher than, those of the bypassed fish. Recovery rates of subyearlings passing via spill 

were higher than those for subyearlings passing by either turbine or bypass. Excessive delay of 

fish in the bypass system has been documented, although these studies did not find exhaustion to 

be a factor in the delay. The excessive delay may have been due to the use of fish taken directly 

from a hatchery (unsmolted) for the evaluations. A summary of the results from 1987 - 1990 

provided by Gilbreath et al. (1993) can be used to estimate mortality in the tailrace below the 

outfall as 6.8%. Note that Gilbreath et al. (1993) made this estimate by comparing the 

recoveries of an experimental lot of bypassed juveniles to those of a downstream release 

(Whitney et al., 1997). Ledgerwood et al., (1994) reported that at the second powerhouse there 

appeared to be back eddies or shore areas where predator numbers concentrate. 

At the first powerhouse, the present bypass outfall is located in the tailrace near the north 

shore in low velocity water where P. oregonensis are concentrated. At the second powerhouse, 

the present bypass outfall is located in mid-channel, in the type of location advised by Shively et 

al., (1996), however, the support structure for the outfall itself provides refuge for P. oregonensis

that can dart out to take juveniles in passing. In addition, the outfall is below the surface, 

requiring that the conduit be pressurized. Current criteria for conduits require open, 

non-pressurized systems (NMFS/NOAA 1994 - Appendix D).
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 15

a. How have Bonneville bypass outfalls contributed toward meeting salmon recovery goals?

So far, the existing outfalls appear to have negated whatever benefits may have accrued 

to subyearling emigrants from the bypass system because of high mortalities experienced at and 

below the outfalls. Contributions toward other salmon emigrants’ recovery is unknown, but it is 

probably reasonable to conclude that whatever benefits may have accrued from the bypass 

system are probably negated for emigrants of size equal to or smaller than subyearling chinook 

with somewhat similar timing. For larger, earlier emigrants, such as spring chinook and 

steelhead, the negative effects of the outfalls could have been less than that observed for 

subyearling emigrants. The new location for a combined outfall should decrease predation, based 

on environmental characteristics of the site and experimental characterization of P. oregonensis

predation (several studies by the USGS/BRD, Cook, Washington). 

b. What are the positive impacts of Bonneville bypass outfalls?

There are no positive impacts of existing Bonneville bypass outfall locations for

emigrants of size equal to or smaller than subyearling chinook with somewhat similar timing, 

and the expected benefits of the bypass for other species and life history types are highly 

uncertain. 

c. What negative impacts have the facilities incurred?

Total rates of mortality for subyearling chinook emigrants passing through the bypass 

system (including mortality at and immediately below the current bypass outfalls) is comparable 

to that experienced with passage through the turbines. For larger, earlier emigrants, even if the 

outfalls are not a negative factor, the fish passage efficiencies at Bonneville Dam have been 

historically poor.

3. What are the major uncertainties or research questions associated with increasing the ability 

of Bonneville bypass outfalls to facilitate survival of juvenile emigrants? 

There are uncertainties with the potential adverse effects on juvenile salmonids of transit 

through a flume that would be about 1.7 miles long (CRITFC submission at the ISAB briefing), 

including uncertainties with respect to stress and physical injury that might be added during 

transit. The adverse impacts, if any, of the pipeline will be added to those of the existing screen 

guidance systems (CRITFC, 1998). 

As for effects of the release location on predation, information indicates that though 

juveniles will be released in higher velocity river flow, they will be more concentrated and some

of them simply may swim to lower velocity shoreline water to recover from stress associated 

with the bypass, and predators may follow (Oregon State University telemetry studies cited in 

CRITFC, 1988). On the other hand, the juvenile salmon exiting the re-located outfall are 

expected to have more time to re-orient and recover before encountering predators near shore 

than at the present outfalls. There is additional uncertainty with respect to the length of time 

positive effects may exist, because it is possible that existing types of predators may alter 

behavior in response to changing prey density, and other types of predators may be attracted to 

the new outfalls. 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 16

Although an attempt has been made to consider all features of the new outfall that would 

reduce predation on the juveniles that exit, please note that their effectiveness cannot be 

predicted with certainty. Post construction evaluations will be required as uncertainty and 

unanticipated results are common factors to be considered and evaluated in the implementation 

of new technologies. 

4. How does the existing level of scientific uncertainty affect the use and management of the 

Bonneville bypass outfalls?

For subyearling chinook, the bypass system cannot be trusted as a mitigation measure at 

present due to the nature of the outfall problem (Ledgerwood et al., 1991; Dawley et al., 1992; 

Gilbreath et al., 1993; Ledgerwood et al. 1994; Dawley et al. 1996). Demonstration of benefits 

is necessary because outfall relocation may not work as intended. Uncertainties also exist for 

other stocks and species. The use of mechanical bypass at Bonneville Dam needs to be 

approached with substantial caution in view of the uncertainty regarding the effect of outfall 

location on survival of emigrants that pass through it. 

5. How does the existing level of scientific uncertainty affect the question of whether or not to 

proceed with increasing the ability of Bonneville bypass outfalls to facilitate survival of juvenile 

emigrants?

There is no doubt that the present bypass locations cause artificially elevated levels of 

mortality (Ledgerwood et al., 1991; Dawley et al., 1992; Gilbreath et al., 1993; Ledgerwood et 

al. 1994; Dawley et al. 1996). The need for relief is certain. The degree to which salmon and 

steelhead are dependent on the bypass for improved survival is a matter of decisions about 

developing proposed alternative passage routes for fish. None of the passage routes except intake 

screens and spill have been shown to be feasible at this time. Surface bypass systems are under 

development elsewhere in the basin for possible general deployment, but would probably still 

require a bypass outfall. We presume that the proposed outfall would be used if surface 

collection replaces or augments screening of turbine intakes at Bonneville.

Increased efficiency of turbines might improve the rate of survival of juvenile salmon 

passing through the powerhouse (Whitney et al., 1997). As is the case with outfall relocation, 

changes in turbine efficiency as they relate to decreased juvenile salmonid mortality would 

require a number of years to implement, evaluate and fine tune. The potential benefits of 

increased turbine efficiencies would depend on the size of the emigrant, to name one key stockand life history-specific variable. 

6. What is the relative likelihood that increasing the ability of Bonneville bypass outfalls to 

facilitate survival of juvenile emigrants will contribute to achievement of the goals of the NMFS 

Biological Opinion, the Council’s Fish And Wildlife Program, or the tribes’ 1995 Anadromous 

Fish Restoration Plan, Wy-Kan-Ush-Mi Wa-Kish-Wit – Spirit of the Salmon?

There are a number of goals that could be identified in the three documents referenced. 

We highlight three of them for our purposes here, the 80% fish passage and 95% survival goal 

(which are related), an increase in numbers of adult salmon or recovery (which are also related), 

and maintenance of diversity of the salmon stocks. 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 17

Passage Goal. 

The 80% fish passage goal of the three entities (Council, NMFS and Tribes) can not be 

achieved at Bonneville Dam with the existing bypass systems (Whitney et al., 1997). The 

existing intake screens have been judged to be unsatisfactory in performance. The FGE for 

screens at the first powerhouse is thought to be 38% for fish migrating in the spring (Anderson et 

al., 1998) and 10% in summer (Fredericks memo), while at the second powerhouse, FGE is 

thought to be 44% in spring (Anderson et al., 1997) and 40% in summer (Fredericks memo). 

The existing dam configuration does not permit spill to be provided in amounts sufficient to 

achieve the goals, because of limits on the amount of gas supersaturation and negative effects on 

upstream passage of adults created by spill. Other measures, such as surface bypass, have yet to 

be demonstrated effective in achieving fish passage around the turbines (Whitney et al., 1997), 

but relatively little effort has gone into development of alternatives to date. Improvements in 

the intake screen systems called for by NMFS and the Council will be counterproductive without 

modifications of the outfalls to reduce predation, because the expected result would simply be 

more fish released into the areas of high predation with mortality rates comparable to those that 

occur in passing through turbines. 

Survival Goal. 

As a rule, the 95% survival goal is expected to be achieved if the 80% passage goal is 

achieved (Whitney et al., 1997). This assumes no extraordinary mortalities are associated with 

bypass passage, as has been the case at Bonneville Dam. Simultaneous efforts are underway to 

explore alternative measures for improving survival of juvenile salmon at Bonneville Dam. All 

but spill are in the developmental stages, and while they have the potential for improving fish 

passage and survival, their actual effectiveness is unknown at this time. An integrated plan for 

fish passage at Bonneville is needed that goes beyond piecemeal additions to technology such as 

relocating the outfall, even though that incremental improvement appears valuable. 

Other measures that might improve survival at the project are as follows: 

Spill. 

At present, in order to meet the 80% fish passage and 95% survival goal, spill is provided 

to supplement the FGE of the turbine intake screens. In practice, the 80% fish passage goal can 

not be achieved at Bonneville Dam because of the need to limit spill amounts below those that 

would lead to excess levels of gas saturation (Whitney et al., 1997). In 1995, as an example, only 

55% to 62% of the fish were estimated to have passed at Bonneville Dam through combinations 

of spill and the turbine intake bypass system (Fish Passage Center, 1995; Whitney et al., 1997). 

The remainder passed through the turbines. Mortality in turbines at the first powerhouse was 

estimated to range from 11 to 15% by Holmes (in Whitney et al., 1997), and about 4% by Weber 

(1954) and 2 to 3% by Ledgerwood (1993). Holmes estimates may have been high since some 

releases were made in the forebay instead of directly into the turbine (Iwamoto and Williams 

1993).

Simultaneous efforts are underway by the COE to develop engineering solutions at the 

spillway and tailrace that should make possible release of larger volumes of spill without 

producing gas supersaturation that now limits the amount of spill. For evaluating potential 

benefits of these options, the COE has developed some preliminary projections of improvements 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 18

in survival that might be achieved at the project. Until tests are conducted, these must be 

regarded as speculations. (Bonneville Fish Passage, Presentation Team to ISAB, February 17, 

1998). Under most flow conditions, it is unlikely, even with these modifications that spill alone 

could be provided in sufficient amounts to achieve the 80% or 95% goals without substantially 

exceeding gas supersaturation limits. 

Improved spill effectiveness. 

Spill effectiveness is assumed to be represented by the ratio 1:1 at Bonneville Dam (J. 

Ferguson, COE, briefing to ISAB), i.e. the percentage of river flow that is spill is equal to the 

percentage of fish that are passed in spill. Spill effectiveness has been improved at projects 

where it has been tried, either by modifying spill to draw water from nearer the surface, or by 

spreading the same volume over a 24 hour period (Whitney et al., 1997). There are no direct 

measurements of spill effectiveness at Bonneville Dam, however, the 1:1 ratio is unlikely to be 

realized at all spill levels (Whitney et al., 1997).

Extended-length Screens at Bonneville Dam. 

The COE began testing a prototype extended-length screen at Bonneville Dam in April 

1998 (John Ferguson personal communication). The proposed Recovery Plan calls for 

installation of a prototype extended-length screen at the second powerhouse in 1999. Any 

estimate of possible improvement in FGE for juvenile salmonids that might result from 

installation of extended-length screens would have to wait for results of prototype tests. The poor 

performance of standard screens at the second powerhouse, installed without prototype tests, 

underscores this conclusion. Forecasting survival benefits resulting from increased FGE would 

be purely speculative and unwarranted, given past problems with bypass systems at Bonneville.

Development of a Surface Bypass System 

Development of a surface bypass is called for by the Biological Opinion. The COE has 

ongoing feasibility studies, that have included model studies, and there are plans for a prototype 

test in 1998 (SCT Measures Work Sheet, 17 Dec 97).

Predator control 

With predators acting as a major source of mortality for juvenile emigrants (Riemann et 

al. 1991), changes in predator abundance and distribution through control efforts and changes in 

system operations have the capacity to influence the efficacy of all mainstem passage measures, 

including ESBS and bypass outfall relocation. Since 1990 a program of controlling P. 

oregonensis at known feeding stations below the COE dams has been conducted (Vigg et al. 

1990; Parker et al. 1993). In particular, predation is thought to be the principal source of 

mortalities experienced by juvenile emigrants at the Bonneville bypass outfall (Dawley et al. 

1996). Nominal catch rates for the predators below Bonneville have declined by a half to two 

thirds during the history of the program. Indicators of predator abundances in other nearby 

locations below Bonneville, such as tailrace density and boat restricted zone (BRZ) density have 

also declined (Vigg et al., 1990: Parker et al., 1993). 

In the longer term, designing routes of juvenile passage that do not artificially enhance 

the ability of native predators to catch smolts is desirable as a move toward normative 

conditions. For example, spill has been shown to disrupt concentrations of predators below 

dams. High rates of predation by Caspian terns on juvenile salmon and steelhead at a dredge 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 19

spoil island (Ken Collis, CRITFC, personal communication) downstream near the mouth of the 

Columbia River were recently discovered. We note that the degree to which the apparent 

savings of smolts due to removal of fish predators may have been offset by the bird predation is a 

matter of some concern. 

Maintenance of Diversity. 

As we pointed out in our transportation review (ISAB 98-2), the bypass systems are 

inherently selective with respect to species and stocks, due to differences among species and 

stocks in their response to intake screens and bypass systems. This results in species and stock 

differences in FGE. Because one mechanism by which the outfalls increase mortality is 

predation, the outfalls necessarily add another element of artificial selection, since rates of 

predation are controlled by size of the prey and the water temperature. Smaller, later emigrants 

are much more highly vulnerable to the effects of the present outfall location than are larger 

earlier emigrants. Such selectivity, as pointed out above, has the potential of narrowing the 

phenotypic variability of the stocks, thereby reducing the population fitness (Kapuscinski and 

Lannan 1986).

7. What scientific information is available to compare the present and proposed Bonneville 

bypass outfalls to each other, and to other fish passage strategies such as turbines and spill? 

Whether or to what degree the relocation will provide relief from the presently 

extraordinarily high levels of bypass mortality cannot actually be determined until after the 

bypass outfalls are relocated. However existing information indicates that relocation could 

provide some relief by releasing the juveniles in areas that are less favorable to predators. There 

is a considerable volume of research that has established the following information: 

First, predation at or directly below the outfall of the second powerhouse leads to losses that may 

be similar to losses in passing through the turbines, (Dawley et al., 1992; Gilbreath et al., 1993; 

Ledgerwood et al., 1991). While these studies demonstrated that mortality of juveniles within the 

conduit itself was low, there remained a question whether their transit through the system might 

have increased their vulnerability to predation (Dawley, NMFS, personal communication). 

Mortality of subyearling chinook juveniles associated with the bypass at the first powerhouse 

(either in transit or after exiting) is high enough to counteract any positive effects of diversion 

from the turbine intakes (Ledgerwood et al. 1994). It is clear that predator abundance is high at 

the present outfall locations (Petersen et al., 1993), so that mortality at the outfalls and in the 

tailraces is an integral component of overall bypass mortalities. 

Secondly, water velocity and depth criteria for locating bypass outfalls to minimize predation 

by P. oregonensis are well established and documented (Poe et al., 1993; Faler et al., 1988; 

Shively et al., 1996; NMFS/NOAA, 1994 - Appendix D). They have been developed by 

laboratory studies of the swimming ability of P. oregonensis at various velocities of flow (Mesa 

and Olson, 1993), and by observations of radio tagged P. oregonensis in the river (Faler et al., 

1988; Shively et al., 1996).
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 20

a. Are there significant limitations in the scientific information used to evaluate the Bonneville 

fish passage strategies (outfall relocation)? If so, how can the region best fill these information 

gaps?

Studies at Bonneville first powerhouse do not distinguish mortality rates of salmon 

experienced in passage at the outfall, or in the tailrace below it, from mortalities in the rest of the 

bypass system. Estimates of mortality of subyearling chinook salmon passing through the entire 

first powerhouse bypass relative to downstream release groups have been made (Ledgerwood et 

al. 1994). However, circumstantial evidence on the presence and behavior of P. oregonensis in 

the vicinity suggests that losses in the vicinity of the first powerhouse outfall are probably high. 

On the other hand, there is no direct evidence of the effectiveness of the new release location or 

of the ability of migrants to tolerate a 1.7-mile-long pipe. Both will be evaluated in 

post-construction monitoring. There is a lack of information on the differential effects of the 

outfall on survival of different species and life history types, by size and season. The degree to 

which research is warranted to fill these information gaps depends on the role and purpose of 

mechanical bypass, as determined by the overall salmon recovery strategy.

b. Within the constraints of the four operational scenarios provided by the Council, is the 

effectiveness of the new Bonneville bypass outfalls to facilitate survival of juvenile emigrants 

strategies adequate to achieve the interim performance objective of 80% fish passage efficiency 

and 95% juvenile fish survival at each dam?

The four policy operational scenarios do not appear to affect the situation at Bonneville 

Dam. While this question is not relevant to the relocation of the outfalls at Bonneville Dam per 

se, it highlights the need for setting long-term goals in evaluating fish passage. The existing 

intake screens alone will not achieve the 80% or 95% short-term goals. Spill or other measures 

would be required to achieve the short-term goals. Obviously, an increase in FGE with improved 

screens would actually be harmful if the diverted fish are released from the bypass into an area 

where they would experience a rate of mortality that might be higher than they would experience 

passing the dam by other routes. In this case attainment of short-term goals would actually be 

injurious to salmon recovery. 

At Bonneville Dam the effectiveness of bypass will have to be evaluated after the outfall 

relocation is complete. Because spill is now required to achieve the FPE goal, there is a need to 

know the species composition of fish in spill and the relative efficacy of spill and other measures 

for passage of juvenile emigrants.

c. Does the proposed implementation of bypass relocation at Bonneville dam have a high 

probability of achieving the expected biological benefit (salmon survival improvement) without 

undue risk to other anadromous and/or resident fish populations? 

The relocation of the bypass outfall has no known expected benefits or risks for species 

other than salmon and steelhead as averages over the season. The bypass outfall relocation is 

likely to reduce rates of predation at the outfalls for all species and stocks that are diverted by the 

intake screens to a degree that depends on the size of the emigrant and the season of emigration. 

Rigorous evaluation and appropriate modification (i.e., adaptive management) will be required to 

assess the results of the outfall relocation.
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 21

d. Does the proposed implementation of bypass relocation at Bonneville dams provide 

potentially interim (within the next 10 years) biological benefits, or is it consistent with 

longer-term increasingly normative system configuration strategies? 

There are both interim and long-term benefits of relocation, although the long-term 

benefits are less certain than the short-term. In the interim, the relocation will solve the 

predation problems of the existing bypass systems. On the basis of currently available 

information, intake screens and the associated bypass systems are expected to be a part of future, 

long-term salmon recovery programs where hydroelectric dams are operated to produce power at 

times when juvenile emigrants are present. Increasing normative strategies such as those that 

rely on surface bypass and higher spill amounts may render the bypass outfall location relatively 

less important to recovery than it would otherwise be, but the feasibility of these remains to be 

demonstrated. Benefits of relocation of the outfall may decrease with time if predator 

populations expand, adapt and diversify in response to the change in habitat in order to take 

advantage of a concentration of prey.

The outfall is part of the turbine intake bypass system that includes screens known to 

operate selectively on different species and life history types, as we have pointed out in several 

places, including our response to the questions on John Day Dam in this report. The search for 

more effective means of improving survival of the full diversity of salmon and steelhead 

populations needs to be expanded. Until such means are developed, the decision to relocate the 

outfalls at Bonneville Dam must be made in consideration of alleviating the presently high 

mortalities of subyearling chinook through the existing bypass system. These mortality rates are 

extreme enough that the question of selectivity of the system over time is secondary to the 

question of immediate survival. 

Bonneville Outfall Relocation Discussion

More individual fish and more stocks pass Bonneville Dam, the lowermost project on the 

Columbia River, than at any other project on the river. Because of this, fish passage 

improvements at Bonneville Dam are the "keystone" for realizing the benefits of restoration 

efforts upstream (FWP: NWPPC, 1987). Ideally, Bonneville Dam ought to possess a project 

survival superior to any other on the river, yet its bypass system is the poorest in terms of FGE 

and survival of fish exiting the bypass (Whitney et al., 1997). Given the lack of success of past 

mitigation attempts at Bonneville Dam, what sort of measures should be tried next?

The relative importance of bypass outfall relocation, as well as the desirability of 

improving FGE at Bonneville Dam, is a function of the success of alternative measures for 

improving survival of juvenile salmon at the project such as improved spill effectiveness, surface 

bypass and gas (supersaturation) abatement. The availability of surface bypass and the 

feasibility of gas abatement will influence the policy decisions on what proportion of the juvenile 

salmon and steelhead would be passed via spill. Policy makers need to recognize that decisions 

for expenditures on FGE improvements, and expenditures for outfall relocation ought to be 

balanced against the probability that other means may be developed for elevating the fish 

passage efficiency and the project survival at Bonneville Dam.

From our long-term perspective, measures designed to improve survival of juvenile 

salmon may be viewed as being intended to lead to increases in abundance of adults, though the 

effects may be smaller than can be measured with present methods. The inability to date to relate 

improvements in survival of juveniles to improvements in adult returns may be due to numerous 

factors, including inadequacies in the data or in the approaches used. Nevertheless, we advise 
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 22

that in making decisions on measures for salmon protection and enhancement, there be a 

continued focus on long-term rather than short-term goals. This will call attention to the fact, as 

experience tells us, that large improvements in salmon survival are going to be required, if we 

expect to be able to detect them.

The fact that few of the measures undertaken in the past on behalf of salmon can be 

demonstrated to have led to increases in adult populations (restriction of fishing, enforcement, 

hatcheries and transportation) leads us to the conclusion that new approaches must be developed 

and tested. Innovative and creative approaches need to be fostered, yet examined and tested 

rigorously, so that the effective actions can be quickly recognized and modified further as 

needed.

Bonneville Recommendation

The high mortality inflicted upon juvenile salmon by predators at the present bypass 

outfall locations justifies relocation of the outfalls to locations and habitats where predation rates 

are expected to be significantly reduced. In addition to relocation of the outfall for the juvenile 

bypass system, we encourage integrated, long-term planning and study of other planned 

alterations. Other planned alterations to the juvenile fish passage facilities scheduled at 

Bonneville Dam, include increasing FGE of intake screens at both powerhouses, replacing the 

existing bypass conduits at the powerhouses, joining the two conduits to a common outfall, 

investigating surface bypass, and implementing gas abatement measures (COE briefing to the 

ISAB). The ISAB recommendation for bypass outfall relocation does not constitute a blanket 

endorsement of additional changes to the rest of the bypass system at Bonneville Dam. The 

concerns expressed over the future of mechanical bypass in the portion of this report dealing 

with John Day extended length screens also apply to Bonneville.
ISAB - Letter / Memorandum 9 June 1998

ISAB 98-4: First Report on the COE Capital Construction Project Review 23

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Robins, C. R., R. M. Bailey, C. E. Bond, J. R. Brooker, E. A. Lachner, R. N. Lea, and W. B. 

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