Independent Scientific Advisory Board

for the Northwest Power Planning Council,

the National Marine Fisheries Service,

and the Columbia River Basin Indian Tribes

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

Review of Flow Augmentation: 

Update and Clarification

Robert Bilby

Peter A. Bisson

Charles C. Coutant 

Daniel Goodman

Robert Gramling 

Susan Hanna

Eric Loudenslager

Lyman McDonald

David Philipp

Brian Riddell

Richard Whitney, Ad Hoc 

Member

February 10, 2003

ISAB 2003-1
Review of Flow Augmentation: Update and Clarification

Contents

Executive Summary............................................................................................1

I. Assignment, Background, and Procedure..........................................................8

II. Current Status of Scientific Knowledge .........................................................12

Snake River............................................................................................................................... 12

Mid Columbia and Lower Columbia Reaches.......................................................................... 17

Lower Columbia Reach ............................................................................................................ 17

Effects of Flow on Operation of the Hydrosystem................................................................... 18

IV. Answers to Questions..................................................................................26

Council Questions..................................................................................................................... 26

CRITFC Questions.................................................................................................................... 29

Additional General Questions from the Council ...................................................................... 30

Implications for Council’s Proposed Mainstem Amendments................................................. 31

Appendices

Appendix 1. Review of Fish Passage Center Findings on Flow Effects ...........33

Appendix 2. Survival Estimates for Juvenile Salmonids................................41

Flow Augmentation per se .................................................................................................... 41

1. Snake River....................................................................................................................... 42

2. Mid-Columbia Reach........................................................................................................ 44

3. Mainstem Columbia River Below McNary Dam............................................................. 45

Appendix 3. Alternative Hypotheses.............................................................................. 46

Velocity Hypothesis:............................................................................................................. 46

Fluctuating Flow Hypotheses:............................................................................................... 48

Fish Orientation Hypothesis:................................................................................................. 53

Dam Obstacle Hypothesis:.................................................................................................... 57

Pulsed Flow Hypothesis:....................................................................................................... 57

Appendix 4. Notes on the Mathematics of Reach Survival and Flow................59

Consolidated References for Text and Appendices.............................................63
1

Review of Flow Augmentation: Update and 

Clarification

Executive Summary

Background

At its November 14, 2002 meeting, the Northwest Power Planning Council asked the 

ISAB to update and clarify its review of flow augmentation by the end of January 2003. 

The Council and the Columbia River Inter-Tribal Fish Commission (CRITFC) submitted 

questions on the subject to the ISAB. The issue is timely for the Council as it proposes 

amendments to the mainstem portion of the Fish and Wildlife Program. The issue is 

important in a broader context, because flow commitments are part of the legal 

agreements under ESA for some listed stocks. The relationship between river flows and 

salmon production has been reviewed before by the ISAB, but many questions remain. 

Uncertainties about the relationship have been reiterated in presentations to Council by 

interested parties, in public comments on the Council’s proposed mainstem amendments, 

and in questions to the ISAB from Council members and the tribes. The issues are 

complex and have troubled the region for decades. Many specific questions arise from the 

broader issues. The ISAB considered the Council’s questions and deadline, and suggested 

(by memo of December 19) that it could make a short response to the questions within 

that timeframe, and, if requested, follow this response with more detailed information. 

This report contains our initial response. 

Stimulated by the specific questions posed by Council and others, the ISAB has taken a 

fresh look at the whole matter of river flow and fish survival with special emphasis on the 

Lower Snake River reaches. There have been improvements in study designs over the 

years, particularly in the PIT-tag and radiotelemetry studies. Also, the quantity and 

quality of accumulated data have improved, and the range of factors potentially related to 

survival of anadromous fish has been extended. This has allowed more patterns to be 

resolved in analyses. To focus only on the specifics of the questions posed to the ISAB 

would be to miss the point: the whole issue of flow and fish survival requires 

reevaluation. Management alternatives for improving survival of migrating juvenile 

anadromous fish include many dimensions beyond the current procedures for “flow 

augmentation.” The ISAB answered the specific questions in the text of this report, but 

considers them to be a subset of the broader issue. 

The executive summary provides our conclusions related to the needed reevaluation of 

flow issues, focusing on the Lower Snake River, and the text of the report contains the 

scientific justification for those conclusions and answers to the specific Council and 

CRITFC questions. The text provides, in sequence, a brief background for the flow 

augmentation issue, an overall conclusion of the ISAB regarding the present status of 

scientific knowledge bearing on flow augmentation, the specific questions asked of us 

and our answers, and a summary of the implications of our review for the Council’s draft 

mainstem amendments. A set of appendices provides more detailed evidence for our 
2

conclusions and answers, which we were not able to fully integrate with the text in the 

time available. The evidence is organized by specific findings about current scientific 

information. Hypotheses are presented that may explain the information and offer guides 

for managing the hydrosystem to benefit fish. As indicated, our report was prepared with 

limited time to refine the analysis in order to provide the Council with the thrust of our 

review by the stipulated deadline. The review could be further refined and enlarged with 

additional work. 

Development and operation of the hydroelectric system in the Columbia River Basin led 

to changes in the normal pattern of flow. Dams on U.S. and Canadian tributaries regulate 

flow in the mainstem. These reservoirs are lowered seasonally to allow storage capacity 

that will reduce the frequency and intensity of flooding, primarily during the spring 

freshet, and then refilled to provide sources of water for later power production and other 

uses. As a result, the magnitude and variability of the spring freshet through the lower 

Columbia River basin has been greatly reduced and the timing is partially controlled. 

These changes have many ecological consequences that might affect salmon production. 

In fact, flooding was almost certainly good for salmon production, but flooding is no 

longer considered a viable management option. Accordingly, attention has centered on 

less dramatic, incremental adjustments of the present flow regime, in the hope of 

identifying flow changes that confer benefit to salmon production.

There was early concern that juvenile salmonids migrating downstream at the time of the 

spring freshet might experience in-river mortalities that are higher than normal because of 

the diminished flows. Therefore, the Council’s first (1982) Fish and Wildlife Program 

specified a modest volume of water, identified as the “Water Budget,” relative to a base 

amount for hydropower and flood control, to be used in the spring months for the purpose 

of improving survival of migrating juvenile salmonids. Subsequently, specified flows 

have also been added to benefit summer migrants. “Flow augmentation,” as this 

programmed increment to some of the seasonally managed flows is called, does not in 

any way restore original natural flow. It has been a subject of contention from the time of 

its initiation, both because of competing uses and values for the stored water (e.g., 

hydropower, irrigation, recreation on fully filled reservoirs, and biological productivity in 

reservoirs or downstream rivers), and because the benefit to salmon of these incremental 

adjustments has not been well quantified. 

Review by the ISAB

In the time available, the ISAB gathered the latest scientific information on the 

relationships between smolt survival and flow, and the operational features of the 

hydrosystem that might affect them. We did this through briefings, review of the latest 

reports and publications, and independent data analyses. Because of interest in ESAlisted species, more information is available for the lower Snake River; little information 

was available for the mid-Columbia River.

A different perspective emerged from this latest review. We realize that the prevailing 

rationale for flow augmentation is inadequate. It is neither complete nor comprehensive. 
3

There is room for alternative explanations of available data that have both scientific 

justification and practical value for managing the hydrosystem for multiple uses 

including salmon recovery. 

The prevailing flow-augmentation paradigm, which asserts that in-river smolt survival 

will be proportionally enhanced by any amount of added water, is no longer supportable. 

It does not agree with information now available. 

First, for the lower Snake River studied between 1996 and 2001, there is a range of lower 

flows over which survival of PIT-tagged smolts increases with increasing flow and a 

range of high flows in which fish survival appears to be independent of incremental 

changes in flow. There is an apparent breakpoint in the relationship between survival and 

flow (i.e., a rather sharp change in the slope of models fitted to the data or a sharp corner 

on a “broken-stick” model) near 100 kcfs for yearling chinook salmon and steelhead and 

an appearance of a break near 50 kcfs for underyearling fall chinook salmon. The pattern 

is evident despite a large amount of scatter in the data. Whether these apparent 

breakpoints represent two distinctly different mechanisms at different flows or one 

continuous mechanism with a general curve is a subject we discuss. Survival data within 

years do not consistently show a pattern because the range of flows within a given year is 

relatively small.

Second, radiotelemetry of yearling chinook salmon and steelhead smolts in Lower 

Granite Reservoir (1996-2001) also showed an apparent breakpoint in the relationship of 

smolt behavior and flow near 100 kcfs. Above that level, smolts moved through the 

reservoir at decreasing velocities as flow decreased and the dam was approached, but 

passage was generally not hindered. At flows below 100 kcfs, smolt migrations were 

slowed markedly at the dam, often to zero, and they began extensive upstream 

movements. These upstream wanderings often exceeded the length of Lower Granite pool 

and took many days, potentially exposing smolts to more predators, excessive use of 

stored energy, or other factors affecting survival. Similar results were seen for 

underyearling fall chinook salmon in Little Goose Reservoir 1995-1997. 

Third, the current view of the effects of flow on smolts is also not consistent with a 

number of physical and biological mechanisms in reservoirs and at dams that clearly do 

not operate in a way that is strictly proportional to flow. The text and appendices describe 

some of these mechanisms. 

Superficially, the patterns for reach survival and telemetry suggest a survival benefit from 

increasing flow when flow is low, but no indications of added benefit at higher flows, 

within the range of flows that have occurred in the past few years. At a deeper level, 

however, many questions remain. These questions concern the possible mechanisms for 

the different effects at different flows (and whether they might be managed more 

effectively than flow alone). They also concern how travel time and survival of smolts in 

discrete river reaches relates to timing and success of passing down river, through the 

estuary, and into the ocean. This latter set of concerns is beyond the scope of this report, 

but is worthy of additional analysis. 
4

Snake River: A Different Rationale and Implications for Management

These results indicated to the ISAB that the prevailing rationale for decreased survival at 

lower flows (reduction in average river velocity, which slows migration and, for example, 

fosters predation) deserves reexamination. That is, why should there be a break in the 

flow-survival relationship? What causes it? Does the radiotelemetry study point to 

details of fish behavior that could provide some answers? Does reach survival change 

with flow simply as a result of changed exposure time to the same sources and rates of 

mortality? Is there an effect of flow on the mortality rate itself, such as smolts being 

exposed to a different suite of predators as they wander back upstream? Are the flow 

effects confined to the lower range of flow rates, or are we simply obscuring the effect at 

high flows by measuring reach survival over too short a distance? Would clarifying the 

causes for the observed data offer opportunities for hydrosystem management other than 

simply adding more water to the river? 

We identified several alternative explanations (hypotheses) for the correspondence of 

observed flow-survival data and radio-telemetry data, which are not necessarily mutually 

exclusive. These alternatives do, indeed, lead logically to management opportunities that 

extend beyond flow augmentation as presently defined. This report outlines several of 

them. We assembled enough information about them to suggest that they need serious 

further study and evaluation. 

Some of our explanations arose from asking, “What river operations, other than average 

flow rate, change in the vicinity of the breakpoints?” Such operations might be changed 

to benefit fish. 

One such operation is the fluctuation of dam discharges in ways that are more prominent 

at lower flows. We find that we have rediscovered a concern that was at the forefront of 

research in the Columbia River by NOAA Fisheries in the 1970s. We determined, 

through flow records obtained from DART and other databases, that discharges from the 

lower Snake River dams fluctuate hourly on a daily cycle (as is well known in the midColumbia). The cycle generally follows electricity demand—low at night and highest at 

the beginning and end of the workday. These fluctuating discharges produce pulses of 

flow in downstream reservoirs and dam forebays that are not described by the average 

annual, weekly, or daily flows that to-date have been used in fish-survival studies. Such 

fluctuations occur at flows that are less than the hydraulic capacities of the powerhouses 

in the Snake River and the fluctuations are much greater relative to the daily average flow 

the further these flows decline. The frequency and duration of fluctuations are greater at 

low flows than at higher flows. During flows typical when underyearling chinook 

migrate, in July and August the difference between daily maximum and minimum flow 

rates can exceed 150% of the daily average flow. At the lowest flows, typified by those in 

January 2003, we determined that the pulses of high and low discharge induce an 

oscillation (seiche) in the reservoirs, similar to water sloshing in a bath tub, that can 

induce reverse flow. There would be progressively greater disruptions of river-reservoir 

hydraulics as flows decline and fluctuations become more prominent. These altered 
5

hydraulic patterns likely affect fish orientation and migration, with increased exposure to 

predators and increased energy consumption at lower flows. This fits the previously 

observed flow/survival relationship, including the apparent breakpoints in the flowsurvival relationships, and it suggests a possible management solution. We believe 

stabilization of flows could be more effective in improving survival of juvenile salmonids 

than simply adding a volume of flow, as in flow augmentation, where water can be 

released intermittently. Instituting stable flows might be undertaken as an experiment. 

The effects on survival of juvenile salmonids should be measurable immediately. 

Other explanations for the correspondence of the apparent breakpoints and hydropower 

operations arose from considering the biological aspects of smolt migration in reservoirs 

that may be affected by differences in flow, either stable or fluctuating. Such aspects may 

be more difficult but not impossible to manage for the benefit of fish.

When smolts migrate downstream using various behavioral cues to distinguish direction, 

as is generally believed, the cues may diminish or disappear as flows are progressively 

more impounded near dams. The riverine turbulence and velocity cues may diminish to 

the point where the fish loses its orientation, stops migration, swims back upstream in an 

attempt to relocate the flow, or follows the reverse flow induced by a seiche. This is the 

migration pattern observed in telemetry studies of yearling chinook and steelhead and 

underyearling chinook, although the mechanism is not established. Further study of 

reservoir hydraulics at different flows and fish migration mechanisms are needed. 

Management approaches to providing more migration cues in reservoirs without 

augmenting flows might include artificial induction of turbulence and/or velocity and 

drawing reservoirs to lower levels to extend the riverine reaches closer to the dam. It is 

clear that different species and life stages of migrants behave somewhat differently and 

will require somewhat different solutions. Detailed travel time and survival relationships 

differed among yearling chinook salmon and steelhead, and underyearling chinook 

salmon. It is possible that the relationships also will be different for other stages of the 

life cycle and other anadromous species such as coho, sockeye, and lamprey. 

Some of the benefits of flow augmentation in the lower Snake River are actually intended 

for temperature control rather than to enhance the volume of water. The fact that summer 

temperatures are lowered by selective release of cold water from Dworshak Dam should 

be a stimulus to consider temperature management in its own right for summer and fall 

migrants, instead of as a component of aggregate flow changes. This consideration should 

include the time-dependent trade-off for using water sources differing in temperature 

(e.g., a warm Snake River from Hells Canyon Dam versus a cold Clearwater River 

entering Lower Granite pool) to produce combined effects on smolt physiology, 

migration, and survival. 

The effects of water clarity, gas supersaturation, and other factors in the lower Snake 

River may influence both migration and survival, as several studies have suggested. They 

probably contribute to the wide scatter among data points seen in flow-survival plots. 

These factors are often correlated with flow and temperature, and it is unlikely that their 
6

effects can be separated clearly by passive monitoring in the absence of deliberately 

designed experimental manipulations. In general, regression and correlation studies of the 

relationships of fish survival to flow, water clarity, temperature and other factors are 

consistent with our findings. However, we do not believe that further refinement of 

multiple regression estimates will by themselves resolve the relative influences of these 

factors. Controlled experiments are needed. The experiments are feasible, but may be 

regarded as excessively disruptive or have the potential to kill significant numbers of fish. 

The paradigm that faster movement of smolts to the estuary and ocean is always 

favorable for survival needs to be evaluated. Most of the reach survival studies we 

reviewed make this assumption. Increased migration rate and survival in the studied 

reaches (primarily the lower Snake River) does not ensure survival in lower reaches. The 

fish have to spend their time somewhere and could experience increased survival rates, 

the same survival rates, or decreased survival rates. We see a need for more specific 

analysis of the relationship between survival rates in the upper reaches of the rivers, 

survival rates in the lower reaches, date of arrival of smolts at the estuary, timing of 

ocean entry, and their subsequent ocean survival. We see the need for continuing 

analyses of the effect of annual flow during the outmigration period by separating 

measurement of in-river survival and ocean survival, with special attention to the more 

detailed mechanisms having to do with temperature, smolt condition, date of arrival in 

the estuary and ocean, and measures of ocean conditions. 

We recognize another factor that affects reach survival estimates and could produce 

curves resembling a “broken stick” model. The flow augmentation paradigm is 

ambiguous, because it fails to distinguish between effects of travel time in a reach and 

effects of the instantaneous mortality rate (from whatever cause) in that reach, and 

because it fails to place reach survival in the context of life cycle production. Total 

elapsed time affects the estimate of total mortality in a reach, due to expected effects of 

the life table for the fish. The analyses to date have not determined whether the pattern 

observed has a component due to changes in instantaneous mortality rate. Until that point 

has been resolved, we cannot know whether the observed pattern of better survival at 

higher flows is simply a result of shortening the exposure time in the measured reach, 

with no change in instantaneous mortality rate. Unfortunately practically nothing is 

known about favorable times for arrival to the estuary and ocean. The region is operating 

on the established fact that development and operation of the hydroelectric system has 

resulted in a shift in timing of outmigration of juvenile salmonids toward later times of 

arrival. On that basis, it has been reasonable to proceed with measures to speed their 

movement, regardless of whether instantaneous mortality is variable or constant. 

The Council’s proposed mainstem amendments, as interpreted to us by Council staff in 

terms of average flows, will likely not have major effects on the migration and reach 

survival of yearling chinook salmon and steelhead migrating in the river during peak 

flows of spring (generally over 100 kcfs in the lower Snake River). In contrast, the 

reduced flows in comparison to BiOp of July-August (near or below 50 kcfs) have the 

potential of significantly reducing the reach survival of underyearling chinook salmon. 

Transportation of smolts by barge or truck will lessen some of this effect, although our 
7

review has concentrated on in-river migrants. We encourage evaluation of factors other 

than just gross flow and flow augmentation as presently defined in the management plans 

(e.g., evaluation of the effects of fluctuating dam discharges and other mechanisms). 

Based on life cycle considerations, touched on only lightly here, we recommend that 

future analyses, wherever possible, consider survival to the estuary and survival from the 

estuary to adult return as important indicators of the effect of a flow regime.

Finally, the ISAB believes that, with improved knowledge and subsequent management 

actions, it may be possible to achieve improved survival of juvenile salmonids through 

the lower Snake River reaches and their dams, even at lower flows. With an expanded 

perspective, this might occur at lower costs for operation of the hydrosystem and more 

effective use of stored water for other purposes than is possible with the prevailing flowaugmentation paradigm. 

Mid-Columbia and Lower Columbia Reaches

Flow appears to be the most influential factor affecting migration speed of steelhead and 

sockeye; for yearling chinook no effect of flow on migration speed has been found (only 

level of smoltification affected migration speed); for subyearling chinook no 

environmental variable was found to affect migration speed in the mid-Columbia. Since 

1998, PIT tag and radiotelemetry studies have produced limited data on the survival of 

yearling chinook. Data on other species is even more limited. The studies-to-date do not 

indicate any statistically significant effect of flow on survival of juvenile salmonids in the 

mid-Columbia Reach, other than in the Hanford Reach, where stable flows are the issue.

Limited data are available for lower Columbia Reach. Low flows are likely to lead to 

residualization of steelhead. 

Life History Survival

Survival throughout the life history of the fish is the element of concern. Reduced or 

increased travel time may be disadvantageous if it results in arrival in the estuary and/or 

ocean at times when conditions are not favorable for survival. Further research is needed 

on relationships of travel time and survival and favorable times for arrival of fish in the 

estuary and ocean.

Resident Fishes

It is a well-established fact that storage reservoir drawdowns result in adverse effects on 

resident fish populations and their associated fisheries. In earlier reports we 

recommended that an effort be made to balance the needs of resident fishes upstream 

against those of juvenile salmon downstream. We identified the Rule Curves developed 

in Montana as being reasonable approaches to resolving difficult policy issues with 

biological implications. The subject of tradeoffs of benefits to salmon versus detriments 

to resident fishes is one of the subjects deserving high priority action by the Council.
8

Review of Flow Augmentation: Update and Clarification

I. Assignment, Background, and Procedure

Assignment:

At its November 14, 2002 meeting, the Council approved a request for the ISAB to 

update and clarify its review of flow augmentation, and submitted a list of questions to 

the ISAB. On December 12, 2002, CRITFC added a set of questions related to the 

Council’s request. We received additional questions from the Council, and were 

forwarded (for background) several questions posed in comments on the Council’s draft 

mainstem amendments. On December 19, 2002, the ISAB specified the questions that the 

ISAB felt it could address by January 31, 2003 and proposed a timeline to address 

questions it could not adequately address by January 31. The January 31 deadline was 

extended one week at the ISAB’s request. 

The Council asked the ISAB two different sets of questions related to the flow-fish 

survival relationship and of the role of flow augmentation from storage reservoirs. 

Because similar questions are raised by the Council’s draft mainstem amendments, the 

Council thought it would be useful to obtain an ISAB review in time to contribute to the 

Council’s final decisions on mainstem program amendments. 

This report answers Council and CRITFC questions that the ISAB could address by about 

the January 31 deadline. The report also provides a more general synthesis of new 

information and the ISAB’s views of flow augmentation. If requested, the ISAB can 

continue its review and provide more information on questions or issues it did not have 

adequate time to address. 

The questions arose, in part, from issues not resolved in the ISAB’s recent reviews of 

flow augmentation and flow-survival relationships (ISAB’s review of the Giorgi et al. 

2002 summary report [ISAB 2002-1] and ISAB’s Review of Lower Snake River Flow 

Augmentation Studies [ISAB 2001-5]). These questions concern the relevance of 

conclusions about year-to-year differences in survival at prevailing flows for determining 

the effects of within-year flow augmentation. Another set of questions concerns the 

proper statistical methods for evaluating information on flow/survival relationships. 

There was an expressed desire for scientific peer review of recent analyses by other 

regional groups related to flow and juvenile salmonid survival that were not examined in 

the previous ISAB reviews. These analyses include but are not limited to those of the 

Fish Passage Center (FPC), NMFS, USFWS, and the Idaho Department of Water 

Resources. 

We are pleased that during the hearing on December 11, 2001, Council and staff quoted 

several statements from previous ISAB reports. However, we stress that the report 

presented here represents results of our study of much information that was not 

previously available. Therefore, any conflict that might be discovered is to be resolved in 

favor of statements in the report presented here.
9

This report provides, in sequence, a brief background of the flow augmentation issue, an 

overall ISAB conclusion regarding the present status of scientific knowledge bearing on 

flow augmentation that is based on our review (regardless of the specific questions), the 

specific questions and our answers, an appendix that provides evidence supporting our 

conclusions and answers, an appendix that provides alternative hypotheses for the 

observed data, and an appendix that mathematically describes a null hypothesis for 

survival estimation. The evidence section is organized by specific points. Our report was 

prepared with limited time to refine the presentation in order to provide the Council with 

the thrust of our review in a timely manner, and could be further refined and enlarged 

with additional work. 

We acknowledge others who have contributed greatly to the evolution of thinking about 

flow and smolt survival. The region has a large contingent of capable experts in fishery 

biology and statistical analysis, and they have placed considerable emphasis on efforts to 

address this issue. We will not attempt to name them all because it is such a long list we 

are certain to inadvertently leave some out, but in preparing this report, we acknowledge 

especially the capable assistance of biologists and statisticians from NOAA Fisheries, the 

Fish Passage Center, the University of Washington, the U.S. Fish and Wildlife Service, 

and the Idaho Department of Fish and Game. The Fish Passage Center and the University 

of Washington, by means of DART, were particularly helpful in providing data and 

analyses at our request. We appreciate the review provided by Malcom W. Karr of our 

description of likely hydropower operations in the Snake River as affected by hydraulic 

capacities of the powerhouses. We take responsibility for any errors.

Our review has benefited by the fact that, at the request of the Council, the ISAB or its 

predecessor, the Independent Scientific Group (ISG), have participated in several related 

reviews in the past. These include review of the Hungry Horse/Libby situation (ISG 95-3; 

ISAB 97-3), a review of the Fish and Wildlife Program (ISG 1996; ISG 2000), review of 

the report by Dreher et al. (2000) (ISAB 2001-5) and review of Giorgi et al. (2001) 

(ISAB 2002-1).

Background:

Development and operation of the hydroelectric system in the Columbia River Basin led 

to changes in the normal pattern of flow (NWPPC 1982; NRC 1996; ISG 2000). In 

addition to storage dams on U.S. tributaries (e.g., Hungry Horse, Libby, Dworshak, and 

Brownlee) and dams on the mainstem, which for the most part were run-of-the-river 

projects with little storage capacity in their reservoirs, a 1961 treaty between the United 

States and Canada provided for construction of dams for substantial storage of water in 

the Canadian portion of the Columbia Basin, and of dams in the U.S. that would back 

water into Canada. In addition to the treaty, an agreement between BPA and B. C. Hydro, 

known as the “Non-Treaty Storage Agreement.” provides for additional storage behind 

Mica Dam in Canada (Resource Writers, Inc. 1991). These, and to some extent, Grand 

Coulee Dam, are the primary regulators of flow in the mainstem, as their reservoirs are 

lowered seasonally to allow for capacity that will alleviate flooding during the spring 

freshet, and refilled as sources of water to be stored for later power production and other 

uses. Similarly, Brownlee reservoir and other upstream reservoirs on the Snake River 
10

provide the storage capacity for flood control, irrigation and power production, and other 

uses on the Snake River. Dams below Brownlee on the Snake River are primarily run-ofthe-river projects with little storage capacity (Resource Writers, Inc., 1991). As a result, 

the magnitude of the spring freshet has been reduced1, and this reduction has many 

ecological consequences that might affect salmon production. One particular 

hypothesized relationship has attracted considerable attention, i.e., the concern that 

juvenile salmonids migrating downstream at the time of the spring freshet might 

experience in-river mortalities that are higher than normal because of the diminished 

flows. Therefore, the first Fish and Wildlife Program in 1982 specified a modest volume 

of water, identified as the “Water Budget” to be used in the spring months for the purpose 

of improving survival of juvenile salmonids as they make their way downstream 

(NWPPC, 1982; NRC, 1996; ISG, 1996, 2000)2. Subsequently, specified flows have been 

added to benefit summer migrants. Flow augmentation has been the subject of contention 

from the beginning.

Water volumes, identified in the NOAA Fisheries Biological Opinion and/or the 

Council’s Fish and Wildlife Program for flow augmentation, are released by the Corps of 

Engineers and BPA both from upriver Columbia River storage reservoirs and from upper 

Snake River reservoirs. In the Snake River, flow augmentation for the purpose of 

temperature reduction also takes place from the Corps’ Dworshak Dam on the Clearwater 

River, just above its confluence with the Snake River (Figure 1). 

 

1

 In addition to reducing the magnitude of the spring freshet, the effect of drawing upon water from the 

depths of Lake Roosevelt above Grand Coulee Dam has led to delay of the timing of peak summer water 

temperatures downstream since 1941, an effect that may reach as far downstream as Bonneville Dam (Ebel, 

et al., 1989). On the other hand, water at Brownlee Dam is drawn from the surface of the reservoir and is 

warmer than the incoming Snake River, and warmer than tributaries that enter below the dam, resulting in 

warmer temperatures in the river below (Anderson, Hinrichsen, and Van Holmes, 2000; Connor et al, in 

press). 

2

 The water budget and flow augmentation are specified in two parts, one as a volume of water to be 

provided from upper mainstem reservoirs, and the other from Snake River sources.
11

Figure 1. Columbia River basin showing storage reservoirs and run-of-the-river, 

non-storage reservoirs.

In the 1994 Fish and Wildlife Program, the Council proposed a specific hypothesis to be 

tested describing the relationship between flow, water velocity, and fish travel time and 

survival (NWPPC, 1994). The region’s scientific teams have concerned themselves with 

this issue since at least 1981 when Sims and Ossiander of NOAA Fisheries plotted the 

annual average survival estimates for yearling chinook salmon against average flows 

during the period of outmigration from 1973 through 1979 (Sims and Ossiander, 1981). 

That study formed the basis for the Council’s adoption of the water budget (McConnaha, 

1993). Analyses based largely on the Sims and Ossiander model have been updated and 
12

refined continually to the present, using an increasing accumulation of additional and 

more refined data on fish movements and survival. 

Procedure:

In developing the following response, the ISAB queried many scientists for their current 

research and analysis related to the debate concerning benefits of flow augmentation. One 

ISAB member attended the December 11, 2002 briefing of the Council where 

presentations were made by Karl Dreher of the Idaho Department of Water Resources, 

John Williams and Bill Muir of NOAA Fisheries, Chris Van Holmes of the University of 

Washington, and Bruce Suzumoto and John Fazio of Council staff. In addition, the ISAB 

arranged briefings on December 16, 2002 from Steve Smith of NOAA Fisheries, 

Margaret Filardo of the Fish Passage Center, Howard Schaller of the U.S. Fish and 

Wildlife Service, and Charles Petrosky of Idaho Fish and Game. Written reports were 

provided by these speakers, as well as by W.E. Connor of the U.S. Fish and Wildlife 

Service. Many other sources were consulted as shown in the references list at the end of 

this report, and in the acknowledgements. The Fish Passage Center, DART, and NOAA 

Fisheries responded to specific requests for additional data and analyses. In addition to 

reviewing the work of others, ISAB members conducted independent analyses of these 

and other data. The ISAB and its predecessor, the ISG, have been engaged in study of the 

issue in responding to previous requests from the Council or NOAA Fisheries. Reports 

resulting from these studies are cited in the text and the list of references.

II. Current Status of Scientific Knowledge 

Snake River

After careful study of currently available evidence, we have concluded that, for the Snake 

River, the analysis of effects of river flow on survival of juvenile salmon and steelhead 

conducted by NOAA Fisheries’ statistician, Steve Smith, is the most complete, up to 

date, and credible. That analysis includes a mathematical approach to describe a “broken 

stick model.”3 That study develops an estimate of a breakpoint in the data (i.e., a rather 

sharp change in the slope of curves fitted to the data) for yearling chinook and steelhead 

at average weekly Snake River flows of about 100 kcfs as measured at the lower Snake 

River projects, Figure 2. It is unclear if the breakpoint is related to a change in the 

instantaneous rate of mortality, to a change in the length of time spent in reaches of the 

river, or to a combination of factors. These relationships are discussed further throughout 

the text below, and Appendix 4 specifically discusses the effects of the instantaneous rate 

of mortality. 

While there are different ma thematical and statistical methods available for arriving at 

more precise estimates of the “breakpoint”, it is unlikely that there is a distinct best point 

 

3

 There are other terms used in the statistical literature to describe this phenomenon, but we choose to use 

the terminology first employed by Chapman et al., 1991 in the present context. There may be more precise 

methods of arriving at the point, but the method used by Smith is probably adequate for now.
13

under all conditions, and these NOAA Fisheries estimates should adequately serve for 

management purposes. The “broken stick” model reveals that there is a strong effect of 

flow on survival of yearling chinook and steelhead when average weekly flows in the 

Snake River are below the 100 kcfs breakpoint, and indicates no apparent relationship 

when flows are above that level. Under the current strategy of augmenting flows in order 

to correct the losses caused by development and operation of the hydrosystem, it would 

be necessary to provide sufficient average weekly flow of 100 kcfs during the period of 

outmigration of yearling chinook and steelhead, predominantly in late April, all of May, 

and early June each year. When natural flow is above that level in those months, no 

augmentation would be justified based on the current data, since no improvement in 

survival can be shown to occur. When flow is as low as in the years 1973 and 2001, it 

would undoubtedly tax the storage capacity of reservoirs in the Snake River to provide 

flows as high as 100 kcfs through the period of outmigration. 

According to the analysis by John Fazio, in low flow years, the Council’s proposed 

amendments would provide the same amount of flow as the BiOp during April and May 

at Lower Granite Dam, and somewhat less in June. By that time, the yearling chinook and 

steelhead outmigration is near its normal end, so the effect of reduced flows on their 

survival would probably not be substantial. We also conjecture that effects of reduced 

flows might be avoided with a different approach to management of the system.4 This 

possible alternative to the current “flow augmentation” will be discussed below.

The situation is different with fall chinook that migrate later in the year, travel through 

the system more slowly, and experience higher levels of mortality while migrating inriver than do yearling chinook and steelhead. Fall chinook migrate through the lower 

Snake River predominantly in July and August, when river flows typically will have 

declined below the apparent 100 kcfs breakpoint for the other fish. Plots of weekly 

survival of fall chinook versus average weekly flow during outmigration suggest a 

breakpoint somewhere between 40 kcfs and 50 kcfs (figure 3). During low flow years, the 

Council’s proposed amendments to the Fish and Wildlife Program would provide about 

the same flows in April and May at Lower Granite as the BiOp, but lower flows (by 

about 7.5 KCFS – a 17% reduction in expected flows as compared to the BiOp) than does 

the BiOp in July, a little less during the first two weeks of August (by 3.5%), but more 

during the last two weeks of August at Lower Granite Dam (by about 7.5 kcfs – roughly 

30%), Figure 4, and Table 1. The result is likely to be a larger negative effect on survival 

of fall chinook than on yearling chinook and steelhead, judging by flows in the 30% of 

driest years in the record.5 Again, we conjecture that there may be a way of ameliorating 

those effects on fall chinook, which may improve the survival of all three stocks 

 

4

Bruce Suzumoto used SIMPAS to estimate changes in survival that might result from the Council’s 

proposed modifications. But he says, “SIMPAS is not highly sensitive to changes in flows. Another 

regional model might be better to estimate the effect of flow changes on total system survival”. (Suzumoto, 

B. 2002. Mainstem juvenile survival: CRiSP modeling results. Memorandum of December 2, 2002 to 

Council members)

5

 The CRiSP analysis depends upon assumptions about spill amounts and spill effectiveness that may or 

may not be met, and it depends upon a specified effect of flow on survival, which we believe is improved 

upon by the NOAA FISHERIES “broken stick” model. 
14

whenever weekly average flows decline to below 100 kcfs. To adequately explain this 

proposal, it is necessary to provide sufficient background, based on our interpretation of 

the current status of scientific information. We will then answer the Council’s questions. 

In the process of doing so, the necessary foundation for our proposal will be established.

Figure 2. Plots of survival at various flow rates for yearling chinook and steelhead 

1995-2001 illustrating a broken stick model (from Steve Smith presentation to ISAB, 

December 16, 2002).
15

Figure 3. Relationship of Survival with Flow for Fall Chinook in the Snake River 

1999 and 2000 (from Berggren attachment to Fish Passage Center Memo of 

10/27/2000).

Subyearling chinook survival from sites above pool to Lower Granite Dam tailrace,

 1999 and 2000

0

0.1

0.2

0.3

0.4

0.5

0.6

0 10 20 30 40 50 60 70 80 90

LGR avg flow during period of middle 60% passage of each release

Survival Estimate

survival

pred

Inverse relationship 

Survival = 0.609 - 14.194 / 

Flow

R2 = 0.74
16

Figure 4 and Table 1. Fish and Wildlife Program Draft Mainstem Amendment 

compared to BiOp: Flows at Lower Granite (averaged over the driest 30%). (From 

John Fazio presentation to the ISAB, December 16, 2002).

Table 1. Changes to Summer Flows at Lower Granite Dam (average of driest 30%) 

July August 1-15 August 16-31 September

Percent Change - 17% - 3.5% 30% 20%

BiOp Flow 

(kcfs)

43 32 23 19

Council Flow 

(kcfs)

36 31 31 23

age over Driest 30%) (Average over 

Driest 30%)16-30 May June
17

Mid Columbia and Lower Columbia Reaches6

In the early 1980s the mid-Columbia PUDs sponsored juvenile salmonid survival studies 

that extended throughout the reach from above Wells Dam to below Priest Rapids Dam. 

(Chapman and McKenzie, 1980; McKenzie et al., 1982; 1983) These were intended to 

provide base line information on per project mortality rates, and were not designed to 

extract information on effects of factors like flow, temperature, or other variables. Since 

that time, the Fish Passage Center has conducted studies to measure smolt travel time and 

survival through the mid-Columbia Reach to McNary Dam. We depend upon the 

summary provided by Giorgi et al. (2000) for the following information on effects of 

flow on travel time in the mid-Columbia Reach: Flow appears to be the most influential 

factor affecting migration speed of steelhead and sockeye; for yearling chinook no effect 

of flow on migration speed has been found (only level of smoltification affected 

migration speed); for subyearling chinook no environmental variable was found to affect 

migration speed in the mid-Columbia. 

The mid-Columbia PUDs have conducted travel time and survival studies of yearling 

chinook, and steelhead since 1998 using PIT tag and radiotracking technologies. Rocky 

Reach Dam is equipped with a PIT tag detector. Survival estimates are available for 

hatchery chinook and steelhead for the reach of river from upriver hatcheries to Rocky 

Reach Dam. McNary Dam is the next project that can detect PIT tags. Survival estimates 

are available for the reach from Rocky Reach to McNary Dam that were conducted by 

the Fish Passage Center. These limited data do not show a relationship of travel times of 

yearling chinook and steelhead with flow, though it appears there may be a threshold of 

flow at about 70 kcfs below which movement may be slowed. However, earlier studies 

with more data have shown clear effects of flow on travel time of steelhead and sockeye 

in the mid-Columbia Reach (Giorgi et al., 1993; Berggren and Filardo, 1997). Calendar 

date is the most important determinant of migration speed.

The studies to date do not indicate any statistically significant effect of flow on survival 

of juvenile salmonids in the mid-Columbia Reach, other than in the Hanford Reach, 

where it has been clearly established that stable flows are required during spawning of 

fall chinook, incubation of eggs, emergence of fry, and now emigration of fry from the 

Reach (e.g. Tiffan et al., 2002). More information on this subject is provided under the 

heading of Effects of Flow on Survival in the text below and in the Appendix.

Lower Columbia Reach

Recoveries of PIT tagged fish from the mid-Columbia suggest that date of arrival at 

Bonneville Dam is key to their successful movement out of the river. Current evidence 

indicates that steelhead are likely to residualize between McNary and The Dalles if they 

are late, and yearling chinook are likely to die in place. Chinook are quite dependent 

upon flow for determining their movements in the Lower Columbia Reach. 

 

6

 We thank Shane Bickford of Douglas County PUD for the following information on studies of travel time 

and survival of juvenile salmonids in the mid-Columbia Reach (personal communication). 
18

PIT tagged fish from the Snake River are also recovered in the Lower Columbia Reach, 

providing information on travel time and survival (Bill Muir briefing). PIT tag detectors 

are now present at all of the lower river dams except The Dalles Dam. A major finding 

has been that there appears to be no benefit to transporting subyearling chinook from 

McNary Dam. These would primarily be fish from the mid-Columbia Reach, because 

Snake River fish are collected upstream for transportation. Survival of fish migrating inriver from McNary to below Bonneville Dam in these studies is higher than transported 

fish. Water temperature strongly affects survival of fish, but so do several other 

environmental variables. An experiment would be needed to separate the effects.

Findings and Synthesis: What Mechanisms Operate on Survival of Juvenile 

Salmonids When Flow is Reduced?

The following sections of the report develop a different viewpoint on the relationship of 

river flow and survival of outmigrating juvenile salmonids. We use the word “different”, 

but we note that it is not a new viewpoint. Researchers of NOAA Fisheries were working 

30 years ago under a project entitled “Effects of Power Peaking Operations on Juvenile 

Salmon and Steelhead Trout Migrations (Sims, Bentley, and Johnsen, 1977, 1978). They 

were clearly ahead of their time. Study techniques available at that time were not 

adequate for the task of documenting the effects they sought. That situation has changed 

recently with the development of the PIT tag for estimating mortality over short reaches 

and time intervals, and small radio tags that permit following immediate reactions of 

salmonid smolts to river conditions. We believe that viewpoint on power peaking sheds 

light on the mechanism that leads to the relationship. It does not negate previous studies 

that have demonstrated relationships of survival, flow, and other factors. But the 

mechanism that is suggested leads to a recommendation for a strategy other than simple 

flow augmentation. We believe the new strategy might reduce mortalities of juvenile 

salmonids induced by development and operation of the hydroelectric system in a way 

that could prove to be an additional or alternative for the flow augmentation strategy.

Effects of Flow on Operation of the Hydrosystem. Analysis of the Broken Stick 

Model: What are the mechanisms that could explain the broken stick model?

The hydroelectric system is cooperatively managed according to the “Pacific Northwest 

Coordination Agreement” (PNCA), an agreement among the various owners and 

operators of the major hydroelectric facilities in the Northwest (Logie, 1993). In the 

Columbia Basin, because the volume of water reaching lower river (run-of-the-river) 

projects is dependent upon releases from upstream, coordination is essential in order to 

optimize power production from the system as a whole, and to make it possible for lower 

river projects to maintain their reservoir elevations within allowable limits (Specified by 

the Federal Energy Regulatory Commission (FERC) or the BiOp). Water releases are 

coordinated on an hourly basis in the mainstem Columbia and Snake rivers. A summary 

of the Coordination Agreement was provided in ISG (2000-12). More details are 

provided in Logie (1993). The Agreement went into effect in 1965, and its term extends 

until June 30, 2003. The Council has long expressed a particular interest in protection of 
19

fall chinook in the Hanford Reach, having received and acted upon recommendations 

from the ISAB on several occasions. The Coordination Agreement is a key piece in the 

ability to accomplish the Council’s measures for protection of fall chinook in the Hanford 

Reach, one of the few healthy populations of salmon in the Columbia Basin.

Hydraulic capacity7 of the run-of-the-river projects is a factor that affects the volume of 

water released from upstream storage reservoirs, after the requirements for flood control 

are met. In the mid-Columbia Reach the hydraulic capacity of each project is about 200 

kcfs. In the four lower Snake River projects, hydraulic capacity is about 130 kcfs at each 

powerhouse, except Ice Harbor where it is 110 kcfs (DART web site). There is an 

additional factor in the Snake River because the hydraulic capacity of the projects 

upstream of the lower Snake River projects is less, about 30 kcfs at Hells Canyon, 

Oxbow, and Brownlee dams, and 10 kcfs at Dworshak Dam. The generating capacity per 

unit volume of water is greater at Hells Canyon, Oxbow, Brownlee and Dworshak than 

the four lower Snake River projects due to their higher head and turbines installed to 

accommodate the head. Therefore, when Snake River flows decline to the neighborhood 

of 40 to 50 kcfs, it seems likely that these four powerhouses become the focus of 

optimization for power production out of the Snake River portion of the system.8 The 

result is likely to be that, as long as upper Snake River flows are above about 30 kcfs, 

there must be spill at the three Hells Canyon complex projects unless they can store the 

water for slow release later. Brownlee reservoir has some storage capacity that can be 

used for this purpose. Oxbow and Hells Canyon dams are run-of-the river projects, as are 

the four lower Snake River projects. Thus emerges a picture of “power peaking” 

operations in the lower Snake River.

In summary, as long as inflow is higher than about 100 kcfs, all of the powerhouses can 

operate at full hydraulic capacity. Spill will be required at the dams in the Hells Canyon 

complex when flow exceeds their hydraulic capacity at about 30 kcfs. When upstream 

inflow declines to the neighborhood of 100 kcfs and below, flows are likely regulated 

first to optimize production out of the four lower river projects, and intermittent releases 

from the Hells Canyon complex are likely to be the result. These intermittent flows likely 

increase in frequency, duration, and magnitude as the inflow declines further. When a 

breakpoint of near 30 kcfs inflow into Brownlee reservoir is reached, the focus on power 

operations will likely shift to the Hells Canyon complex, Hells Canyon, Oxbow and 

Brownlee, because those projects, having higher head, can produce more power per unit 

of water9. Thus, at flows of about 30 kcfs and below, intermittent flows out of Brownlee, 

and thus Oxbow and Hells Canyon dams likely will become more frequent, of longer 

 

7

 Hydraulic capacity is the volume of water that can be passed through the turbines at the particular 

powerhouse.

8

 1255 MW total for the Hells Canyon complex (1715.4MW including Dworshak) to provide 40 kcfs at 

Lower Granite, compared to 1098.5 MW for the four lower Snake R. powerhouses at 40 kcfs

9

 Another factor that enters the picture at Brownlee Dam and other Snake River storage reservoirs is that 

the state of Idaho does not allow water to be spilled at any upstream project for flow augmentation for fish. 

However, spill can take place when necessary to accommodate high inflow, and presumably to enhance 

power operations. Still another factor is that Idaho Power is not a party to the Pacific Northwest 

Coordination Agreement, so is likely to shift as early as feasible to maximize power production out of the 

Hells Canyon complex of dams. 
20

duration, and of greater magnitude as inflow decreases. Side flows from Dworshak Dam 

(10 kcfs) and the tributaries above Lower Granite will contribute additional flow, perhaps 

an additional 10 to 20 kcfs. As measured at Lower Granite Dam another break in 

operations will thus likely be exhibited in the neighborhood of 40 to 50 kcfs (30 + 10 + 

10).

The lower the flow, the greater the frequency, duration and magnitude of episodes 

of hourly flow fluctuations through the hydrosystem, Table 2.

Table 2 is a compilation of episodes of flow fluctuations during the same period in the 

years 1999 and 2000 for which Berggren, 2000 estimated weekly survival rates for fall 

chinook migrating out of the Snake River. Figure 5 illustrates an example of hourly 

fluctuations that were observed during one time period in July 1999. We used COE 

hourly flow records out of Lower Granite Dam, which is the same location used for the 

average weekly flow measurements used by Berggren. At flows less than 50 kcfs 

reductions in flow occurred an average of once a day, and amounted to a 23 % reduction 

in flow, for an average of 5 to 6 hours before flow was restored to a level that existed 

prior to the reduction. At higher flows, such as in the range of 100 to 150 kcfs, such 

episodes of flow reduction occurred less frequently, an average of one every two days, 

were of smaller magnitude, about 14% of flow and were of about the same duration. Such 

episodes of hourly fluctuation at lower Granite Dam must be considered in the context of 

the implications throughout the Snake River hydropower system. Thus, while Table 2 

depicts the flows out of Lower Granite Dam, those hourly flows represent flows arriving 

at Lower Granite Dam from upstream, (because there is little or no storage capacity in 

Lower Granite reservoir) i.e. releases from Hells Canyon Dam, Dworshak Dam, and side 

flow from tributaries, and they are flows that will be passed on to the three lower Snake 

River projects below Lower Granite Dam. 

Figure 5. Example of Hourly Flow Fluctuations in the Snake River 1999
21

__________________________________________________________________

Table 2. RAPID FLUCTUATIONS IN FLOW (HOURLY)

LOWER GRANITE DAM JUNE AND JULY 1999 AND 2000

I. FREQUENCY OF FLOW FLUCTUATIONS

FLOW #EPISODES #DAYS RATIO E/D

(KCFS)

<50 44 44 1.00

50-100 35 49 0.71

100-150 11 19 0.57

150+ 1 5 0.2

II. EXTENT OF FLUCTUATION 

FLOW NUMBER OF EPISODES AT PERCENT FLUCTUATION

(kcfs) 10% 15% 20% 25% 30% 35% 40% 45% AV.%

<50 8 8 5 7 7 7 2 1 23.4

50-100 9 11 12 1 1 1 - - - 16.3

100-150 7 2 - - - - - - 14.1

150+ 1 - - - - - - - 15.0

AVERAGE 18 PERCENT10

III. TIME OF DAY 58 NIGHT (2400h – 0600)

34 OTHER

IV. DURATION OF FLUCTUATION (HOURS)

AVERAGE 5-6 RANGE 1-8 HOURS

_______________________________________________________________________

We demonstrated, by independent analysis of flow data for Lower Monumental Dam 

from 1995-2002, that there are flow fluctuations at all times of year, but that the 

fluctuations are a greater percentage of the daily average flow at times when average 

flows are low. These relationships are shown in Figure 6.

 

10 An “episode” is apparent from an examination of hourly flow records. It appears as a sudden, sharp 

reduction in flow, followed by some fluctuations to a minimum, followed in turn by a return to flow that 

was present before the reduction. The ISAB included only reductions that exceeded 10%, assuming that 

smaller reductions may not be important.
Figure 6. Daily Flow Fluctuations at Lower Monumental Dam, April 1 - September 30 (1998, 2000, 2001, and 2002)

22

________________________________________

w:\em\ww\isab\projects\flowaug\lower monumental flow fluc.doc

0

50

100

150

200

250

300

91 105 119 133 147 161 175 189 203 217 231 245 259 273

April 1 - September 30, 1998

Total Flow KCFS

0

0.5

1

1.5

2

2.5

3

(Max-Min)/Avg

Average flow

Minimum flow

Maximum flow

(Max-min)/avg

0

50

100

150

200

250

300

91 105 119 133 147 161 175 189 203 217 231 245 259 273

April 1 - September 30, 2001

Total Flow KCFS

0

0.5

1

1.5

2

2.5

3

(Max-Min)/Avg

Average flow

Minimum flow

Maximum flow

(Max-min)/avg

0

50

100

150

200

250

300

91 105 119 133 147 161 175 189 203 217 231 245 259 273

April 1 - September 30, 2000

Total Flow KCFS

0

0.5

1

1.5

2

2.5

3

(Max-Min)/Avg

Average flow

Minimum flow

Maximum flow

(Max-min)/avg

0

50

100

150

200

250

300

91 105 119 133 147 161 175 189 203 217 231 245 259 273

April 1 - September 30, 2002

Total Flow KCFS

0

0.5

1

1.5

2

2.5

3

(Max-Min)/Avg

Average flow

Minimum flow

Maximum flow

(Max-min)/avg
23

Effects on Fish: Review of Premises that Would Explain Effects of Flow on Survival

Giorgi et al. (2002) identified the premises that have governed the mainstem measures 

adopted to improve survival of migrating juvenile salmonids. With respect to flow 

augmentation the operating premise has been:

Premise 1. Increasing water velocity in reservoirs increases smolt migration speed, which 

results in improved survival. The mechanism has been thought to operate through 

reducing the time of exposure to predatory fish or birds, or exposure to warming waters. 

The ISAB (ISAB 2002-1) suggested two possible additional mechanisms: reductions in 

flow below dams leads to reduced primary and secondary production in tailwaters, which 

lessens the food supply, particularly for fall chinook that feed as they migrate (ISG, 2000-

12). Interruptions of flow due to power operations becomes more frequent, is of longer 

duration, and is of greater magnitude as flows decrease, Table 2. These flow interruptions 

exacerbate all of the factors that enter into survival of migrating juvenile salmonids, 

including the potential for smolts to travel upstream and to be stranded (Tiffan et al. 

2002).

Premise 2. Lowering water temperature in the summer improves migratory and rearing 

conditions for juvenile and adult salmonids, ultimately improving survival. This premise 

is being addressed through releases of cold water from the depths of Dworshak reservoir. 

Unlike the flow augmentation from upper Columbia River and upper Snake River 

projects, which we believe is impossible to identify as discrete bodies of water, releases 

from Dworshak are identifiable (through model analysis) by their cooler temperature, at 

least as far downstream as the tailrace of lower Granite Dam (Dreher et al., 2001), or 

possibly to Ice Harbor (1 –2 degrees Bennett et al., 1997). It is of utmost importance to 

note that the effectiveness of Dworshak releases for this purpose are strongly affected by 

the relative volume of flow from the Hells Canyon complex. In fact, if not closely 

coordinated for the benefit of fish, the resulting sharp fluctuations of temperature and 

drying of the shore zone in the mainstem Snake River might do more harm than the good 

intended. The CRiSP model can be used to illustrate and evaluate this issue (Andersen, 

Hinrichsen and Van Holmes, 2000). 

While the mechanisms hypothesized to operate to reduce or increase survival when flow 

is low are all reasonable, none of them has actually been shown to cause a reduction or 

increase in survival. Results to date have been from observational studies where 

conclusions and predictions are based on correlations of survival with various factors. In 

other words, no study has shown that predation increases because flow decreases in the 

Columbia or Snake rivers, that the cold water releases from Dworshak reservoir actually 

cause improved survival of salmonids, or that turbid water causes a decrease in predation. 

The one exception appears to be with fall chinook in the Hanford Reach, where it has 

been demonstrated that fluctuations in flow have led to stranding and direct mortality of 

these juveniles (e.g. Wagner et al., 1999; Tiffan et al., 2002). Actually, we believe all of 

these factors may be acting together to reduce the survival of juvenile salmonids 
24

migrating out of the Snake River. However, we have some new conjectures about the 

mechanisms that may be involved in causing the effects. We discuss these further below.

As previously mentioned, Steve Smith of NOAA Fisheries conducted a mathematical 

analysis to identify the point of intersection of the two segments of the broken stick 

model identified for yearling chinook and steelhead in the Snake River. His estimate is 

96.4 kcfs for yearling chinook and about 101 kcfs for steelhead, which means that at 

flows below about 96.4 kcfs there is a significant positive effect of flow on average 

annual survival of yearling chinook, while at flows above that level there is no effect 

discernable with these data, Figures 2 and 3. Note also that our Table 2 shows that the 

frequency, duration, and magnitude of flow fluctuations become increasingly apparent 

the further flow declines below 150 kcfs. This is not surprising, considering that the 

hydraulic capacity of the four lower Snake River projects is 110 to 130 kcfs. Wha t we 

observe from this overview is that as river flow declines from spring to summer and 

reaches about 130 kcfs, flows are likely to become more intermittent, due to interruption 

of flow in the effort to optimize returns from power production. The estimate for the 

point of intersection of the two segments of the broken stick coincides with this change in 

hydropower operations. The point of intersection must be viewed as just that – an 

estimate, which comes close to identifying the flow level at which flow more frequently 

becomes intermittent. We conclude that intermittent flow associated with Snake River 

flows less than 130 kcfs could explain the broken stick model. 

On its face, a breakpoint or zone in the flow-survival relationship would suggest a high 

value for flow augmentation at daily average flows below this level. With this logic, any 

incremental addition of daily average flow below the breakpoint would have a 

proportional increase in survival, on average. This thinking is similar to the present 

paradigm, except that it applies only to the lower average flows. However, if the 

mechanism(s) affecting survival differ above and below the flow breakpoint, then adding 

more water below that flow may not sufficiently raise survival without concurrent change 

in the true mechanisms. To be specific, since the further one looks below the breakpoint 

the greater the percentage of daily average flow that is fluctuated hourly in dam 

discharges, then supplying more stable discharges may be more effective in improving 

smolt survival than simply supplying more water. Conceivably, even the lowest survival 

estimates obtained at the lowest flows, near 10-20% could be raised to the level seen at 

100 kcfs (80%) if flows were stabilized (Figure 7). Clarifying the mechanisms affecting 

smolt survival should allow water managers to evaluate and contrast the alternative risks 

and benefits among relevant management options (hydro cycling, maintaining storage 

reservoir elevations, irrigation, etc.). 

Further discussion of these topics is included in Appendices.
Figure 7. Within year plots of survival versus flow for yearling chinook and steelhead 1995-2001 illustrating a broken stick 

model (from Steve Smith presentation to ISAB, December 16, 2002).

25
26

IV. Answers to Questions

Council Questions

1. What is the evidence and to what extent will flow augmentation from storage 

reservoirs result in the same environmental attributes as higher flow under natural 

conditions? In other words, how sound is the scientific approach of research that 

looks at correlations of fish movement and survival in relation to natural variations 

of environmental conditions such as flow, temperature, and turbidity, and then 

extrapolates to infer that man-made additions of flow will result in the same 

environmental attributes? Are there studies that more directly measure the effects of 

flow augmentation? If so what are the results of those studies? 

Answer:

Flow augmentation from storage reservoirs, as presently configured will not necessarily 

produce the same environmental attributes as higher flow under “natural” conditions 

because there is no requirement to provide the extra water in a “natural” way. The 

seasonal hydrograph in the Columbia Basin is so far from the hydrograph that prevailed 

before construction of the hydrosystem that the amount of flow that is at stake in the 

present discussions about flow augmentation is too small to restore “natural” conditions 

in that sense. Also, the observed correlation of annual aggregate smolt survival with gross 

measures of flow during the outmigration period remain unexplained; i.e., it is not known 

what specific attributes of the annual variation in conditions associated with gross 

measures of flow during the outmigration period are most important or causally 

responsible for the changes in smolt survival. For this reason we have no way of knowing 

whether the flow increments that are provided by the present flow augmentation policy 

will or will not induce conditions that enhance smolt survival. Finally, we can identify a 

number of respects in which even the short timeframe (hourly) variation in flow under 

present flow management is distinctly different from natural flows in several ways, and is 

likely to adversely affect smolt survival.

At flows below hydraulic capacity of powerhouses in the lower Snake River or midColumbia River, there are frequent hourly interruptions of flow, a characteristic of a 

regulated river as contrasted with an unregulated (or normative) river. The ISAB 

provided a review of literature on this subject as a set of appendices to their Hungry 

Horse/Libby review (ISAB 97-3). Higher flows without a requirement for stable releases 

at the proper temperatures are not guaranteed to have the beneficial result of a change in 

the direction of “normative.” Intermittent flows, on an hourly time scale, are not 

characteristic of the normative river and are most likely to be disruptive to downstream 

migration of juvenile salmonids, and to lead to decreased survival within the affected 

reaches. 

Because it is not possible to identify the portion of flow that consists of augmentation, it 

is not possible to conduct a more direct measurement of the effects of flow augmentation. 

The ISAB previously advised that to assess the effects directly, there would need to be a 
27

study specifically designed to isolate and measure the effects (ISG 1996, 2000), as have 

others (Skalski, Mundy and McConnaha 1989).

2. To what extent will incremental flow augmentation within a year have the same effect 

on survival as the year-to-year changes in flow that are also accompanied by year-toyear changes in climate and ocean conditions? 

A. Relevant to the draft mainstem amendments, to what extent will changes in 

reservoir release strategies that could result in decreases in spring and summer 

flows of approximately 10% or less have a statistically significant effect on 

juvenile salmon and steelhead survival? 

B. A linked question is what scientific evidence exists that decreased travel time 

as a result of flow augmentation will result in increased juvenile survival? 

Answer:

Based on a literal interpretation of studies reviewed, incremental flow augmentation of 

the magnitude presently mandated within a year is not likely to have a dramatic beneficial 

effect on in-river smolt survival of outmigrants. This conclusion holds most likely for 

yearling chinook and perhaps fall chinook, particularly if the water is provided by 

intermittent dam discharges, rather than provided as steady flow. Effects of the current 

amount and management of flow augmentation on subsequent estuary and ocean survival 

are unknown, but are important to investigate.

A. Decreases of 10% in spring and summer flows are not likely to have deleterious 

effects on reach survival in the lower Snake River, provided that the remaining flows are 

maintained at or above an approximate breakpoint of 100 kcfs for spring migrants. 

Below approximately 100 kcfs, steady levels of flow or other management alternatives 

may be needed to avoid deleterious effects. 

It is important, however, to distinguish between the reality of an effect and its 

detectability in the context of a particular monitoring program. We note that the wording 

of the question in terms of “statistical significance” of the effect is inappropriate. 

Statistical significance is a property of the inference from the data (e.g., the sample size); 

it is not a property of the effect itself. Any positive effect on smolt survival potentially 

benefit the salmon depending on downstream mortality rates, regardless of whether the 

effect is large enough to be recognizable from our measurements against the background 

of variation from other causes. Detectability is a function of the intensity and accuracy of 

our measurements, which may matter to us and to our decisions, but which is of no direct 

consequence to the salmon. Detectability will be a predictable problem for our ability to 

evaluate effects of a 10% change in flow. This problem arises because 10% is a small 

change in flow compared to natural variation in flow, and because the plausible changes 

in survival associated with this small intervention are likely to be small compared to 

variation in survival from other natural and unnatural causes. That is, a small signal is 

hard to detect in the presence of large noise.
28

We also need to be sensitive to the possible additive nature of “small effects.” In the 

context of a complicated recovery plan that is attempting to manage an entire ecosystem 

and attempting to achieve improvements in all stages of the salmon life cycle, neglect of 

too many small effects—even effects that are too small to measure by monitoring—may 

consign the salmon to death by a thousand cuts. Small effects could still matter.

B. Decreased travel time and survival through a particular reach are linked. Assuming a 

constant rate of instantaneous mortality, the more time spent in a reach, the higher the 

total mortality. The more critical questions are whether instantaneous mortality rates are 

increased in a given reach as a result of low flow (or other factors such as temperature, 

particle travel time, turbidity and calendar date), and whether decreased travel time 

through a reach results in decreased mortality rates measured downstream. Survival 

throughout the life history of a fish is the element of concern. Reduced or increased travel 

time may be disadvantageous, as John Williams pointed out, if it results in arrival in the 

estuary and ocean at times when conditions are not favorable for their survival (i.e., when 

the instantaneous rate of mortality experienced there may be larger). Unfortunately 

practically nothing is known about favorable times for arrival. The region is operating on 

the established fact that development and operation of the hydroelectric system has 

resulted in a shift in timing of outmigration of juvenile salmonids toward later times of 

arrival.

The paradigm that faster movement of smolts to the estuary and ocean is always 

favorable for ultimate survival needs to be evaluated (we did not include that as part of 

our scope of work). Most of the reach survival studies we reviewed make this 

assumption. Increased migration rate and survival in the studied reaches (primarily the 

lower Snake River) does not ensure survival in lower reaches. The fish have to spend 

their time somewhere and continue to be subject to: perhaps increased survival rate, 

perhaps the same survival rate, or perhaps a decreased survival rate. We see a need for 

more specific analysis of the relationship between survival rates in the upper reaches of 

the rivers, survival rates in the lower reaches, date of arrival of smolts at the estuary and 

their subsequent ocean survival. We see the need for continuing analyses of the effect of 

annual flow during the outmigration period by separating measurement of in-river 

survival and ocean survival, with special attention to the more detailed mechanisms 

having to do with temperature, smolt condition, date of arrival in the estuary, and 

measures of ocean state. 

3. Are the statistical methods used in recent flow-survival analyses rigorous and 

technically sound? Did the analyses properly incorporate and treat 2001 low-water-year 

data? 

Answer:

Yes, insofar as possible. As discussed further below (see Appendix 1), technical 

soundness does not necessarily mean that any given statistical method is the most 

appropriate approach. 
29

CRITFC Questions

1. To what extent do system flood control operations lead to conflicts, if any, between 

resident and anadromous fish? What modifications to system operations could help 

to accommodate the needs of both anadromous and resident fish? Would the actions 

in the Council’s draft amendment improve or lessen instream conditions for growth 

and survival of anadromous and native resident fish? The actions in CRITFC 

amendment? The ODFW amendment?

Answer: 

The ISAB draws upon some past reviews that touch on this subject, such as our 

review of Hungry Horse/Libby (ISAB 97-3). We called attention to the wellestablished fact that storage reservoir drawdowns result in adverse effects on resident 

fish populations and their associated fisheries. We recommended that an effort be 

made to balance the needs of resident fishes upstream against those of juvenile 

salmon downstream. We identified the Rule Curves developed by Brian Marotz in 

Montana as being reasonable approaches to resolving difficult policy issues with 

biological implications. And we pointed out, as did Al Wright, that the subject of 

tradeoffs of benefits to salmon versus detriments to resident fishes is one of the 

subjects deserving of high priority action by the Council. With additional time, the 

ISAB could review the recent literature and consider this question in more depth.

2. What studies linking fish populations and reservoir operations exist for the 

operations of these projects? What evidence indicates a relationship between 

primary and secondary productivity and the growth and survival of resident fish 

populations in these reservoirs? What is the evidence of the effect of water retention 

times on primary and secondary productivity and what is the relationship to agespecific resident fish growth and survival? Is there empirical evidence of reduction in 

the populations of resident fish in Libby, Hungry Horse, and Grand Coulee reservoirs 

due to reservoir elevations? What is the general health of resident fish populations in 

these reservoirs? Is there evidence suggesting any recruitment failures that these 

populations have experienced year-class failures in recent years (ten to twenty 

years)? Is this evidence linked to reservoir operations? Which operations? Other 

effects? Please coordinate with the CBFWA Resident Fish Committee in answering 

these questions.

Answer: 

See the ISAB 97-3 review of Hungry Horse/Libby, especially Appendix 5. There is a 

large body of scientific literature on the subject of operations of these projects and 

their links with fish populations. There are studies dealing specifically with local 

situations that are referenced in the ISAB report on Hungry Horse/Libby. In addition, 

there is an even larger body of relevant literature that has been produced nationally 

and internationally dealing with the same issue. The ISAB reviewed both, in the 

Appendix to the Hungry Horse/Libby review. It has been concluded, based on 

numerous examples, tha t drawdowns of reservoirs and rivers lead to reductions in 

basic productive capacity of those bodies of water, leading in turn to reductions in 
30

carrying capacity for fish. The larger and more frequent the drawdowns the more 

severe the negative effects become on the associated biota.

3. In terms of life cycle and ecological processes affecting overall population health, 

identify mechanisms that would be impacted by changes in flow? Given the various 

influences of flow over the life cycle of anadromous fish, what is the proper context of 

consideration of incremental benefits generated from reach survival estimates? What 

is the risk of judging benefits of flow management regimes solely on incremental 

survival changes estimated from short reach survival studies?

Answer:

The ISAB has begun to assemble a discussion of several hypotheses for how changes 

in flow probably affect smolts, using an ecological and life-cycle context. It is clear 

that there is more to the subject than changes in average daily flow, incremental inriver survival changes, and survival over short reaches. This review of hypotheses is 

incomplete at this time, but it is provided here in its present state as an indication. 

Also, see the answer to part B of the Council’s second question above.

4. What information would be necessary to eliminate or reduce flow targets considering 

the effects of flow over the life cycle and NWPPC program objectives? (The NWPPC 

program discusses SARs as a goal, the program flow changes will reduce the 

potential of achieving those SARS re: AT analysis).

Answer:

Each distinct hypothesis about life cycle effects of flow changes would require its 

own set of data for testing. In addition, to obtain data capable of resolving the signal 

from the noise, each might require a different deliberate experiment. As one example, 

our analysis of hourly flow fluctuations, which are more frequent, of longer duration 

and greater magnitude at low flows than at high flows, suggests that an increase in 

smolt survival in a given river reach might be achieved with no net increase in 

average flow, provided that the hydrosystem is required to maintain stable flows 

during the period of outmigration of juvenile salmonids. All of the data comport with 

this interpretation: simply adding a small amount of bulk flow to existing levels of 

flow without reducing the current level of hourly variation is probably not providing 

much improvement, if any, in reach survival.

Additional General Questions from the Council

1. Do the Council’s proposed departures from NOAA Fisheries BiOp with regard to 

spring and summer flows pose a risk to the survival of fish populations, including 

listed ESUs? If so what are the risks and how significant are they?

Answer:

It is not possible to carry out a formal risk analysis in the limited time and with the 

limited data available. However, our judgement is that substituting a requirement for 

stable flows during the period of outmigration of juvenile salmonids could lead to larger 

improvements in reach smolt survival than would be realized with a 10% increase in bulk 
31

flow with continued large hourly fluctuations. That prediction could lead to a number of 

specific recommendations, e.g., that hourly fluctuations in flow should be strictly limited 

to some specified small percentage of the predicted base flow for that month. 

We point out that decisions to implement actions that have any potential for adversely 

affecting an ESU that is listed under the ESA will be required to satisfy a burden of proof 

that no harm is likely to be done as a result of that action.

2. Will these proposed changes provide benefits for upriver fish populations, including 

listed ESUs? If so, what are the benefits and how significant are they?

Answer:

The Council’s proposed actions are likely to provide benefits for upriver populations, as 

the ISG previously pointed out. Depending upon how the water is managed, benefits 

could accrue to listed populations of Kootenai River sturgeon, and possibly to bull trout 

populations that inhabit reservoirs for which productivity should increase as drawdowns 

become less drastic. Furthermore, the fisheries in the affected reservoirs should benefit 

from the stabilized flows, as well as associated fisheries industries. With additional time, 

the ISAB could review the recent literature and consider this question in more depth.

Implications for Council’s Proposed Mainstem Amendments 

The ISAB’s flow augmentation review has implications for the Council’s proposed 

mainstem amendments. Council staff summarized the effects of the proposed 

amendments on Snake River flows compared to flows recommended by the 2000 

Biological Opinion (John Fazio presentation to ISAB; Figure 4, Table 1). Council staff 

anticipates some decrease in river discharges during the annual peak flows in late spring 

when yearling chinook salmon and steelhead migrate (amounting to less than 10% of 

generally high discharges). However, the greater impact would occur in the summer 

during declining flows when underyearling chinook salmon are migrating. 

The spring reductions in flow under the Council’s proposed plan would generally occur 

at levels higher than the postulated breakpoint in flow survival curves. Thus, no 

discernable effects on survival of spring migrants would be predicted under the brokenstick or similar model. 

In contrast, the proposed summer reductions in discharge would often occur below the 

postulated breakpoint. Thus, discernable reduction in survival of fall chinook 

underyearlings would be anticipated from the Council’s action. If diminished volume of

water in the river is truly the cause of decline in survival, then maintaining flows at the 

BiOp levels should have proportional benefits for survival. Preserving flows above the 

breakpoint for maximum survival is problematic, however, given the limited amount of 

stored water available. 
32

There are likely other mechanisms affecting survival below the flow breakpoint, 

however, as the ISAB review has identified. These mechanisms include the practice of 

fluctuating dam discharges within a day that is most prominent at lower flows, reduced 

attraction flows in dam forebays at lower flows, and diminished migration cues for fish in 

more slowly moving and/or hydraulically complex reservoirs. If such an operational 

feature occurs at the dams or in the reservoirs concurrent with lower flows, then 

maintaining daily average flows could be less essential than modifying operations. These 

mechanisms may be more amenable to management correction than the amount of water 

in the hydrosystem. 

The current practice of transporting smolts by barge or truck from the lower Snake River 

reduces the risk to migrants from factors affecting their survival in this reach and farther 

downstream. This will remain true if the Council’s proposed amendment is adopted. The 

ISAB and its predecessor advisory groups have previously acknowledged the benefits, 

especially at low flows, and risks of transportation. However, our present analysis has 

focused on the fate of smolts migrating in the river. Operational measures (such as 

stabilized flows) that improve in-river survival in the lower Snake River may relieve 

some of the need for transportation. 
33

Appendices

Appendix 1. Review of Fish Passage Center Findings on Flow Effects

The region has relied on analyses by the Fish Passage Center (FPC) for much of its 

understanding of the effects of flow (river discharge) on the migration rates and survival 

of downstream-migrating smolts. Although review of the FPC’s analyses was not 

explicitly included in the Council’s set of questions, it was necessary for understanding of 

the prevailing views of flow effects and the efficacy of flow augmentation. Such a review 

of the FPC’s analyses is important background for answering the questions asked of the 

ISAB by the Council. 

The work of the Fish Passage Center that relates smolt travel time and survival to water 

travel time and flow is of high technical quality, but its basic model and methods of 

presentation are now inadequate to make confident predictions for management, and 

other interpretations of the accumulated data are needed. Much of the FPC’s position in 

support of flow augmentation is based on several oft-repeated and recently updated 

analyses (FPC correspondence of October 14 and December 9). We comment on several 

of the technical details of these analyses below.

1. The relationship between water transit time and flow for Snake River hatchery 

chinook salmon and steelhead. The FPC notes that there is a close relationship between 

the water transit time and the corresponding flow between points on the Snake River. 

Figure 8 shows water transit time during the migration period of two migratory fish 

groups, steelhead and hatchery chinook, presumably calculated over slightly different 

migration dates. It is not surprising that FPC finds a close relationship between flow and 

water transit time, because water transit time is calculated from flow. As we understand 

it, the FPC first determined the dates during which specific groups of PIT-tagged fish 

were in the river. They then determined the average reservoir elevations on those 

inclusive dates and calculated the respective average reservoir volumes (there is some 

variation in volume of water in the river-reservoir system from one time to another, but it 

is not large). The average total discharge for those same dates was used to calculate a 

volume replacement time or water travel time (days) between Lower Granite Dam and 

Ice Harbor Dam. 
34

Figure 8. Water transit time from LGR to IHD vs. average discharge (Figure 1 of FPC 

October 14, 2002 memo).

The ISAB considers the method scientifically acceptable as an estimate of theoretical 

water particle travel time averaged over several days. It is not a direct measure of water 

travel time that would be influenced by reservoir hydraulics and short-term variations in 

flow. It is, at best, a rough approximation. 

The shape of the curve is informative. Assuming the accuracy of the highest water transit 

time plotted, the relationship appears to show increasingly longer water transit times as 

flow declines, especially noticeable below about 50-60 kcfs, although the relationship is a 

continuous curve. This accelerated increase in water transit times per unit of flow is 

important for evaluation of the next figures from the FPC and helps to explain the 

“broken stick” or similar models for the relationship between survival and flow.

2. The relationships between fish travel times and water transit time. The FPC 

compared median fish travel times to McNary Dam for each group of fish released at 

Lower Granite Dam with the respective water transit time calculated as above. They 

applied simple linear regression to the data, obtaining fairly poor fits for chinook (r2= 

0.5-0.6) but better fits for steelhead (r2=0.87), where 1.0 is a perfect fit. They 

acknowledged that alternative models might better fit the relationships.
35

Figure 9. Fish transit time vs. water transit time for wild yearling chinook, hatchery 

yearling chinook, and steelhead (Figures 2-4 of FPC October 14, 2002 memo).
36

Use of a theoretical, calculated water transit time that reflects highly averaged flow 

conditions to compare with measured fish travel times is legitimate scientifically, and is 

an effort to translate flow rates into something that is likely to have a direct influence on 

fish, but it seems to obscure the desired objective: to relate fish migration rates to flow 

rates. If nothing else, it interferes with effective communication of methods and results. 

Management options include altering flow rates and reservoir elevations, each of which 

must be entered into calculations to relate to the figures presented by the FPC. Thinking 

to future management, river managers should be capable of getting current data and 

computing water transit time on an instantaneous basis, managing flow and temperature, 

etc. Perhaps a surface plot showing the relationship of water transit time to flow and 

volume would relate the three. 

Taken at face value, however, the plots are informative. Chinook salmon travel time is 

poorly related to water transit time at flows below that corresponding to about 10-12 d 

water transit time. Above that flow level, the travel times for both hatchery and wild 

chinook salmon show high variation, with the fish travel times considerably longer than 

those for the 5-10 day water transit times. Steelhead show a fairly tight relationship of 

fish travel times to water transit times at flows above that corresponding to about 12 d 

water transit time; below that flow level the few data points also show more scatter. 

Using the FPC’s figure for the relationship between water transit time and flow (Figure 

8), the 10-12 d water transit time is equivalent to an average weekly Snake River 

discharge rate of about 50-60 kcfs. These figures suggest that different mechanisms 

probably affect smolt migration rates in the Lower Snake River above and below average 
37

flow rates of about 50-60 kcfs. The regression equations obtained by the FPC should be 

recomputed to allow for the different relationships across water transit times. 

3. Relationship of smolt survival to water transit time (as a surrogate for flow). The 

FPC plotted smolt survival against water transit time (as a surrogate for flow rate), using 

the same groups of PIT-tagged smolts followed from Lower Granite Dam to McNary 

Dam that were used in the fish and water travel time analyses. Survival showed an 

apparent downward trend at higher water transit times (lower flows) for wild and 

hatchery yearling chinook salmon and steelhead, and these trends were quantified with 

curvilinear regressions. The regressions had generally poor fits for chinook but better for 

steelhead (r2 values were approximately 0.3, 0.4, and 0.7, respectively). 

Figure 10. Survival vs. water transit time for wild yearling chinook, hatchery 

yearling chinook, and steelhead (Figures 7-9 of FPC October 14, 2003 memo).
38
39

There are two aspects to a low r2, and these have different implications for the predictive 

power of the regression and the adequacy of the model being used. Simple scatter, which 

can be the cause of a low r2 merely means that there is noise in the data or random noise 

in the underlying relationship. On the other hand, an appearance of a different underlying 

shape than the one that is being fit suggests that the model that is being “fit” could be the 

wrong model. The choice of model will limit the shapes that can be fit. Also, the range of 

shapes that a model is capable of assuming will greatly affect the distance over which 

data influence the resulting estimate. Generally, the greater the complexity of the model, 

the more the estimates in one portion of the range will be independent of the data from 

other portions of the range. For this reason, with limited quantities of noisy data, a more 

complex model may be a better fit to the data, but the confidence about the estimates in a 

restricted range will be weaker.

The shallow curve trends fit by the FPC’s regression analyses seem forced in comparison 

to a visual inspection of the pattern in the data. A visual inspection of the data suggests a 

better fit would be obtained from a model that was capable of turning a sharper corner, or 

that consisted of two straight line segments with two different slopes in the relationship in 

two different ranges of values for flow, i.e., a so-called “broken stick” model. Broken 

stick and more complex models are known as multiphase. There are known statistical 

methods to estimate objectively the location of the breakpoint (Seber and Wild 1989, 

Hastie and Tibshirani 1990). There are also a variety of statistical techniques, such as 

smoothing splines, for objectively fitting arbitrary curved shapes, and there are a variety 

of statistical techniques allowing for different degrees of tightness of curves.

If a broken-stick model were to be fitted to the FPC plots, there is apparent high in-river 

smolt survival at flows above that corresponding to about 10-12 d water transit time with 

essentially no detectable relationship to flow within this range for wild and hatchery 

chinook and only a slight relationship for steelhead. At lower flows, there is apparently a 

decline in survival with increasing water transit time, although the data show much 

scatter. Using FPC’s figure (Figure 8) again to convert water travel time to flow rates 

indicates that the change in survival occurs near 50-60 kcfs. In other words, in-river smolt 

survival appears from the FPC data as if it could be independent of flow above about 50-

60 kcfs up to about 180 kcfs, which is the limit in the data. 

For flow management purposes, a more quantitative definition of alternative models, 

including the broken-stick model, for survival vs. water transit time (flow) is desirable. 

These statistical methods rely on models that are “non-linear” in the coefficients to be 

estimated and require customized computing software not usually available in the 

commonly used statistical software packages. Flow-survival data that the ISAB reviewed 

from NOAA Fisheries suggests a breakpoint somewhat higher, near 100-100 kcfs (Steve 

Smith presentation, unpublished analysis). Dr. Smith’s pilot analysis was non-subjective, 

but involved an assumption to allow ordinary least squares theory to be used to fit the 

model, namely, that the line above the break-point had zero slope. The ISAB recognizes 

the value of fitting such models to these data. We recommend that the pilot analyses be 

expanded to take full advantage of the theory of fitting and comparing multiphase models 
40

with and without breakpoints. Also, see Appendix 4, where a model is developed on the 

assumption of a constant instantaneous rate of mortality.

Because both fish travel time and survival data from the FPC appear to exhibit similar 

broken stick patterns with breakpoints apparently near 50-60 kcfs, the ISAB believes that 

it would be fruitful to examine the physical and biological mechanisms in the riverreservoir system that might be causing such discontinuity in the relationship. Intermittent 

flows brought about by hydropower operations are a likely cause, as we discuss 

elsewhere. Deciphering the mechanisms behind the different fish travel times and 

survival rates is likely to lead to more mechanistic and technically supportable water 

management approaches than would sole reliance on simple regressions assuming a 

highly constrained shallow curvilinear relationship over the entire range. Knowledge of 

mechanisms will provide independent knowledge as to the range of plausible models that 

should be fit statistically, and will confer higher confidence in the resulting estimates.
41

Appendix 2. Survival Estimates for Juvenile Salmonids

In this appendix, we make several points about survival of different species and life 

stages, as developed from newly acquired data, and contrast the situation in the Snake 

and Columbia rivers. The appendix is a work in progress, as new information is received 

nearly daily. A later section explores several hypotheses, including the current one used 

by the FPC, to explain the travel time and survival data in ways that may point to new 

hydrosystem management approaches.

Because the circumstances differ for the Snake River, the upper mainstem Columbia (the 

mid-Columbia Reach), and the lower Mainstem Columbia River, we separate the list of 

findings below according to the respective reaches. We also separate the list of findings 

for yearling chinook, fall chinook, steelhead and sockeye. Coho are being reintroduced 

both in the mid-Columbia Reach and Snake River, but there are as yet insufficient data 

available on survival of their juveniles to make any conclusions with respect to their 

responses to flow. Data on survival of sockeye juveniles are also lacking.

The process of ISAB review involves evaluation of inputs of various types from 

numerous diverse sources. We felt it to be important in this case to document the findings 

we arrived at after careful review. These findings served as a basis for our answers and 

for our recommendations. 

Flow Augmentation per se

Finding: Direct effects of flow augmentation cannot be isolated for measurement, 

with the exception of releases from Dworshak, which are labeled by the temperature 

of water released.

In his presentation to the Council on December 11, 2002, Karl Dreher for the Idaho 

Department of Water Resources and at the December 16 ISAB briefing Margaret Filardo 

of the Fish Passage Center both said that the flows provided as augmentation, under 

present policy and management, are not identifiable. Former Council member Kai Lee 

reached the same conclusion in the chapter he wrote in NRC 1996. Since the 

augmentation flows, other than those from Dworshak, are not identifiable under present 

operations, their effects cannot be directly measured in the river as associated changes in 

measurements of survival of juvenile salmonids. The Fish Passage Center, beginning 

with their fist annual report (and restated in their December 10, 2002 letter to Council 

member Karier in answer to his question 3), reported they have been unable to identify in 

the river, the specific volume of water intended for the water budget or flow 

augmentation. The reason for the inability to identify the masses of water that constitute 

flow augmentation is that the volumes released by the COE and BPA simply supplement 

(augment) what would have been the normal release in the particular water year being 

experienced, i.e. the timing of release of that volume of water is shifted to conform to the 

BiOp’s requirements for passage of juvenile salmonids. Thus, the water is not treated 

differently than the other portion of the seasonal flow, as it is used for power production, 

and some may be spilled or used for other purposes. This is also true for releases from 
42

Dworshak Dam. Dworshak releases are a special case, which we will discuss further in a 

later section. 

It is important to observe at this point that flow augmentation does not necessarily lead to 

spill, but on the other hand that some of the augmented flow may be used to satisfy 

requirements in the FWP or BiOp to provide specified spill volumes at particular dams in 

order to achieve targets for total survival of juvenile salmonids passing the dam. In fact 

system operators normally take care to avoid spill that might result directly from 

augmentation, since that would be considered to be “involuntary” spill. “Involuntary” 

spill, as a rule, occurs only when high flows lead to exceeding the power system’s ability 

to divert flow through the powerhouses (i.e. exceeding the hydraulic capacity of the 

individual project). “Involuntary” spill then is a separate and distinguishable strategy 

from spill called for in the FWP and the BiOp for the purpose of improving the overall 

survival of juvenile salmonids as they pass a hydropower dam. (See Whitney et al, 1997.)

1. Snake River

Yearling chinook

Finding: By comparing a series of average annual survival estimates for yearling 

chinook and annual flows averaged during the period of outmigration for a series of 

years from 1973 to 2001, a positive relationship has been demonstrated, i.e. survival 

is higher in years of higher average flows in the Snake River. 

For yearling chinook in the Snake River, when annual average survival estimates are 

plotted against average river flow during the outmigration for the same year, NOAA 

Fisheries has demonstrated that there is higher average survival of migrating juveniles in 

years when average river flows are higher. 

Finding: The relationship demonstrated for yearling chinook is well described by a 

“broken stick” model, first suggested by Chapman et al. 1991. Examination of the 

plot of points for average survival of yearling chinook against average annual flow 

shows an increase in survival with flow up to a point beyond which increases in flow 

do not bring further increases in survival (Figure 2).

NOAA Fisheries estimates the point of intersection of the two lines occurs at a flow of 

96.4 kcfs for yearling chinook and 101 kcfs for steelhead. Beyond that point (about 100 

kcfs) no relationship of survival and flow can be demonstrated. 

Finding: Estimates of survival of yearling chinook within a year are best limited to 

the years 1995 to 2001, because those are the years when detections of PIT tagged 

juveniles were sufficient to arrive at usable estimates. Survival in the year 2001 was 

significantly related to flow. In the data provided by NOAA Fisheries it is apparent 

that the flows during that year were less than 100 kcfs during the migration, the 

only year for which the average flow was that low. In addition, date of release from 

the hatchery and degree of smoltification have been shown to affect travel time and 

survival of yearling chinook in the Snake River. For fall chinook, because 
43

environmental variables are highly correlated with one another (flow, temperature, 

and turbidity) it has not been possible to determine whether one factor is more 

important than another (Smith et al. in press). 

That there was only one year during which it was clear that there was a within-year 

relationship of flow and survival) is puzzling when taken together with the fact, stated 

previously, that a significant relationship has been found in analyses of annual average 

estimates of survival and flow. A close examination of the figures provided by NOAA 

Fisheries (S. Smith and J. Williams) shows that the data for none of the other years 

suggests a significant within-year trend of survival related to flow, Figure 7. However, it 

seems that survival was lowest in years when flows were low, below about100 kcfs for 

the duration of the outmigration, as in 2001 Continuing observations are necessary.

For now, we provide a conservative and literal conclusion that the volume of water 

available in a particular water year directly affects the average survival of juvenile 

yearling chinook migrating out of the Snake River. In terms of practical application of 

augmented flow within a particular year, an assumption might be made that the line that 

describes the relationship for multiple years might be used to predict the effects of 

increments of increased survival to be expected from increments of flow within a year. 

However, it ought to be possible to test this assumption by within-year analyses, and the 

analyses conducted have not succeeded in verifying the validity of such an assumption. 

Probably, the range of flows that have occurred within a given year during the period 

when yearling chinook are migrating downstream, generally is not broad enough, and the 

within-year variation with flow has not be sufficiently decoupled from variation in 

confounding factors such as temperature and date. The exception seems to be when 

average flow is less than 100 kcfs, under which condition the short-term flow survival 

relationship is strong enough, even for a restricted range of flow variation, to make it 

detectable relative to the variability in survival brought about by other factors. Note that 

we expect the broken stick model to apply here, so that in years of flow above hydraulic 

capacity of powerhouses there will be a weak or no relationship, whereas in low flow 

years, there very likely will be a stronger relationship. 

Fall Chinook

Finding: For fall chinook there is no lengthy series of annual measurements of 

average survival such as is available for yearling chinook. Short series (four years, 

each providing one point for analysis) produced what the authors felt (Connor et al. 

1998) demonstrated higher rates of PIT tag recovery at Lower Granite Dam of fall 

chinook tagged upstream in years having higher average flow during the annual 

outmigration. On the other hand, Andersen, Hinrichsen, and Van Holmes, in an 

analysis of average annual survival estimates for the years 1995 through 1998, found 

no significant effect of average annual flow on survival to Lower Granite Dam 

(Andersen et al., 2000, page 19). But the latter authors found that analyzing weekly 

PIT tag detections provided sufficient data to identify a significant relationship of 

flow and survival to Lower Granite Dam (page 11). A similar study (because it 

plotted weekly rate of survival against weekly average flow) by the FPC for the 
44

combined years 1999 and 2000, showed a strong relationship of survival with flow, 

higher flows during the two years being associated with higher survival (Figure 4). 

But pooling survival estimates from the two years was necessary to obtain a large 

enough sample size to yield a significant estimated relationship because the range of 

flows in the individual years was not sufficient. 

Within a year, a significant effect of flow on survival of fall chinook to Lower Granite 

Dam has been demonstrated (Andersen, Hinrichsen and Van Holmes, December, 2000 

submission to the Council, re. review of the Giorgi et al. report). However, those authors 

found no significant effect of average annual flow and average survival between years.

Steelhead

Finding: Survival of juvenile steelhead generally has followed the same pattern 

annually as yearling chinook, with the exception of 2001, when steelhead survival 

was much lower (Giorgi et al., 2002, referring to Zabel et al. in press). Giorgi et al. 

felt that the reason for low estimates of survival of steelhead in 2001, a year of unusually 

low flows and associated factors, was increased residualization of the smolts, rather than 

mortality per se. It is apparent that part of the “mortality” estimated for steelhead in 

2001was due to residualization, the failure of fish to continue their migrations out of the 

system (Bill Muir, John Williams personal communications). John Williams of NOAA 

Fisheries has described observing a “rainbow trout” fishery that developed above 

McNary Dam that was based upon steelhead smolts that had failed to emigrate. 

Incidentally, the same phenomenon has been observed in the mid-Columbia Reach 

(Shane Bickford, personal communication). 

2. Mid-Columbia Reach

In the text proper, we have summarized what information is available on survival 

estimates of juvenile salmon as they might be affected by flow in the mid-Columbia 

Reach, and we will not repeat it here. We do provide relevant information on the 

Hanford Reach fall chinook, which are adversely affected by unstable flows.

Fall Chinook

Finding: An estimated 2 million juvenile fall chinook were killed in the Hanford 

Reach during their outmigration in 2001. This compares with losses of 93,000 in 

1999, losses of 45,000 in 2000, and losses of 67,000 in 2002.11

It is well established that mortalities of juvenile fall chinook in the Hanford Reach are 

brought about by fluctuations in flow, which lead to their stranding and death as the water 

level recedes too rapidly for them to adjust. The volumes of flow are not the same in 

every year, as they are set according to criteria in the Vernita Bar Agreement with the 

objective of maintaining appropriate boundaries for spawning, rearing and incubation of

 

11 Information taken from Tiffan et al. unpublished proposal #35036 for FY2003; response to comments by 

the ISRP, and from Tiffan, Garland and Rondorf, 2002. In the proposal Tiffan cites Murray, 2002 as the 

source, but omitted that from his list of references. He also cites CRSS, 2000, with no listing in his 

references. In the joint publication they cite Hoffarth, Unpublished as the source of numbers.
45

fall chinook in the Hanford Reach. In 1999 an interagency agreement was reached that is 

intended to supplement the Vernita Bar Agreement for protection of fall chinook.12 The 

supplement is intended to provide stabilized flows to encompass the period after 

emergence of fry from the gravel when they are still in the shallows feeding and 

beginning to emigrate. That supplement spells out permissible magnitudes of flow 

fluctuations for five different levels of river flow. The permissible fluctuations range 

from about 25% to 43% of average river flow. For weekdays, average flow under the 

Agreement is to be calculated as a rolling 5-day average of the previous five weekdays, 

and for weekend days as the BPA Friday Priest Rapids Dam estimates for Saturday and 

Sunday. This provision introduces the potential for fluctuations of even larger magnitude 

between weekend days versus weekdays. In 2001, hourly regulation of flow at times 

brought about water level fluctuations of 6 to 9 vertical feet (Tiffan, unpublished proposal 

#35036 and MCRSS 2001). It is evident from the result in the year 2001 that provisions 

of the supplement are inadequate for protection of fall chinook fry in some years, such as 

2001, when flows were low and protection measures were relaxed. We note seve ral 

omissions in the supplement. The supplement includes no stipulation of limits to either 

duration or frequency of fluctuations. We observe that the permissible magnitudes of 

fluctuation are as large as those observed at Lower Granite Dam, where there is no effort 

being made to stabilize flows for salmonid fry. See Table 1 in the main body of the text. 

Tiffan et al. (2002) analyzed the situation in terms of available rearing area for fall 

chinook under various flow volumes. The model they developed can be used to estimate 

the area of near-shore habitat that likely will be exposed at a given flow, or that will 

result from reductions in flow that are permitted under the present agreement. They 

conclude that the provisions of the agreement are inadequate for the protection of 

juvenile fall chinook rearing in the Hanford Reach.

3. Mainstem Columbia River Below McNary Dam

Finding: Average annual survival of up-river, i.e. mid-Columbia fall chinook from 

McNary Dam to John Day Dam is higher in years of higher average flows (Muir). 

This observation is based on four data points (four years). A possible explanation for this 

is that the reservoir above John Day Dam is a primary location where significant 

predation by northern pikeminnow has been documented and predation is facilitated by 

lower flows. 

 

12 As a result of a previous review, the ISAB recommended to the Council that the existing Vernita Bar 

Agreement be supplemented to provide protection for emigrating fry of fall chinook (ISAB 99-5). The 

Vernita Bar Agreement is described in ISG, 2000, NWPPC Doc. 2000-12, pp. 451-2. The extension of the 

Agreement subsequently called for by the Council is developed on an interim basis annually. The 2002 

agreement may be viewed at 

www.nwd.wc.usace.army.mil/tmt/documents/fish/2003/hanford_fall_chinook.pdf
46

Appendix 3. Alternative Hypotheses 

for Explaining Current Data on Smolts and Flow

The sufficiency of flow (river discharge) as a predictor of survival for out-migrant 

salmon and steelhead smolt for purposes of flow management decisions has been 

questioned by the Idaho Water Users, the Idaho Council members, and others. The 

importance of river discharge is argued by the Fish Passage Center through graphs they 

have produced relating salmon/steelhead smolt survival to water travel time, which is a 

function of river flow (e.g., Figures 9 and 10). Similar graphs of survival versus water 

travel times or flow have been developed by NOAA Fisheries. When data are aggregated 

over sufficient years to attain a wide range of average river flows (including the low flow 

year of 2001), statistically significant linear relationships can be demonstrated using 

standard regression techniques. However, as more years and more survival estimates 

have been added over time, the purported linear relationship takes on a “broken stick” 

appearance (first suggested by Chapman et al. 1991). The broken stick model also agrees 

closely with the rather sharp changes in the slope at about the same “breakpoint” of other 

curves fitted to the data. In these models, the portion of the survival data at longer water 

travel times (lower river flows) shows a relationship with water travel time (flow) and 

another portion at shorter water travel times (higher flows) shows little relationship (FPC 

data discussed in Appendix 1; NOAA Fisheries analyses by Smith et al.). 

The broken stick model postulated to describe the relationship of average annual survival 

estimates for yearling chinook to average annual flows during outmigration, based on 

data obtained from 1973 to 1979, has been fitted by the NOAA Fisheries after 

accumulation of PIT tag data from 1995 to 2001. Under the broken-stick model, water 

might be managed for fish without much regard for water flow rates above about 100 

kcfs, for example, yet be intimately tied to flow for fish migrating at lower flow rates. 

However, hydrosystem management would be benefited by knowing what environmental 

changes occur in the vicinity of the breakpoint and below that affect fish survival. With 

such knowledge, there may be causative factors other than the quantity of water that 

could be managed to benefit fish. The mechanisms by which fish survival differs with 

flow are not clear. This section discusses several alternative hypotheses and the evidence 

that does or does not support each of them. 

Velocity Hypothesis:

The prevailing hypothesis has pointed to different river velocities at different flow rates 

as the primary influence on smolt survival (FPC 2002). Analysts have presumed that the 

river-reservoir system flows at a faster velocity when there is higher volume of discharge. 

It is also assumed that faster smolt migration means less time available for negative 

influences of predation, disease, high temperature, high dissolved gas, or other damaging 

factors, and thus higher survival at higher flows. In support of the velocity assumption, 

the FPC has calculated probable average water travel times through the Lower Snake 

River as a function of flow (average daily river discharge) and the volume of the riverreservoir system during times when migrating salmon and steelhead are present (Figure 
47

8). The volume differs somewhat from one migration period to another, depending on 

reservoir elevations during actual migrations. The pattern of water travel times results 

from the gross replacement of the available water volume in the river-reservoir reach by 

the amount of inflow. Similarly, the FPC has assumed that fish migrate essentially 

passively and that their travel times will be similar to the water travel times, or at least 

directly related to them. This assumption is tested by plots of fish travel times in relation 

to water travel times, which generally show a statistically significant relationship, with 

fish traveling faster at short water travel times (=higher water velocities)(Figures 9-10). 

The relevance of the velocity hypothesis for water management is the assumption that an 

increased river discharge through water management (e.g., flow augmentation) will cause 

water to travel faster through the hydrosystem (higher velocities) and thus fish will 

migrate faster. Thus, management for higher flows, through flow augmentation or other 

means, is expected to lead to higher smolt survival during the outmigration. If the 

velocity hypothesis is correct, the year-to-year data relating flow (water travel time) to 

survival are both relevant and predictive. 

We believe there is more to the relationship than is revealed by the type of analysis that 

has been used. The estimates of velocity can be faulted on several grounds. First, actual 

measured velocities in the reservoirs of the lower Snake River at different flow rates are 

few (but see Venditti et al. 2000), at least as could be determined by the ISAB in 

inquiries among regional researchers. Second, the gross water replacement formula for 

estimating velocities does not consider details of channel hydraulics or reservoir 

circulation, as has been pointed out by Dreher et al., 2000. Such details will influence 

how river discharge translates to water velocities seen by fish (and resulting fish 

movements). Flows (and therefore channel velocities and water travel times) also are not 

constant through daily cycles due to fluctuating flows at hydropower facilities. At the 

lowest flows, we determined that the pulses of high and low discharge induce an 

oscillation (seiche) in the reservoirs that can induce reverse flow. The broken-stick 

pattern between flow and survival suggests that there is more involved than simple 

average velocity relationships across the range of possible flows. In addition to 

recognition of a broken-stick type of relationship it is apparent that fish travel times tend 

to have a greater variability at longer water travel times (equivalent to lower river flow 

rates) than at shorter water travel times (higher flow rates) (See Appendix 1). As 

discussed earlier, this suggests some difference in mechanisms at different flows. 

Beyond flow (water travel time and velocity), there are other co-occurring factors that 

can affect smolt survival. NOAA Fisheries has identified especially temperature and 

turbidity. Flow augmentation from Dworshak Dam in late summer to bring Snake River 

temperatures closer to optimal for salmon (Karr et al. 1998) is an example of capitalizing 

on known temperature effects that go beyond just velocity. These factors need not be 

related to velocity, thus reducing the predictive power of flow. 
48

Fluctuating Flow Hypotheses:

As we have pointed out, one change in hydrosystem operations that occurs across a range 

of seasonal daily average flow rates is the amount of within-day fluctuation caused by 

variable hydropower generation. Each day has variable flow on an hourly basis (Figures 5 

and 6). The ranges between minimum and maximum flows do not differ greatly among 

different average flows, but the fluctuation range is a higher proportion of the daily 

average flow when the daily average flow is low (Figure 6). This means that the 

fractional within-day variation in flow (and probably river velocities and fish travel 

times) seen in a river or reservoir is greater at lower average flows than it is at higher 

average flows. For 1998, for example, the daily variation in flow from Lower 

Monumental Dam was a small percentage of the daily average flow (10-20%) during 

May and June. This contrasts with the fluctuations being a high percentage of daily 

average flow in July and August, the period of outmigration of fall chinook, often 

exceeding 100%. 

The mechanism by which this flow fluctuation might affect smolt survival is open to 

speculation, although circumstantial evidence points to some likely mechanisms. Also, 

the relationships of fluctuating flows to the breakpoints in flow-survival curves deserve 

some discussion in terms of mechanisms. We examined several alternatives, as follows.

Fish Stranding: 

We discuss this hypothesis because of the analogy with the Hanford Reach stranding 

issue rather than its likelihood of being a major mechanism in the Snake River. In the 

Hanford Reach, stranding of underyearling chinook salmon by fluctuating flows has been 

identified as an important factor causing mortalities (Wagner et al. 1999; Tiffan et al., 

2002). Research has identified that fry of fall chinook, in particular, use shoreline areas 

for feeding and rearing during the high flows of daytime, but are often left stranded in 

isolated pools or on large flats and gravel bars when the river flow rapidly decreases. 

Because of these mortalities, the Vernita Bar Agreement that regulated Priest Rapids 

Dam discharges during spawning of adults, and incubation of eggs was modified to 

provide more stable flows during the time when underyearlings are most abundant in the 

Hanford Reach. A similar problem but to a smaller degree might occur in the lower 

Snake River. It is likely smaller because the lower Snake River is nearly exclusively a 

simple channel that is filled by impoundments (having steep sides and few flat zones for 

stranding). Fluctuations in discharge may still affect survival but probably not to the 

same level as in the Hanford reach.

Unstable Reservoir Hydraulics Confusing to Fish: 

We hypothesized that rapid changes in river discharge at an upstream dam (both increase 

and decrease) would cause hydraulic instability in the downstream reservoir, potentially 

affecting local hydraulic patterns and thus migration rates of fish in these unstable flows 

(and susceptibility to many of the same survival-reducing factors identified by the FPC). 

Vendetti et al. (2000) observed wandering and upstream swimming by radio-tagged 
49

underyearling chinook salmon in Little Goose pool in July-August 1995-1997, as well as 

large differences in migration rates. Plumb et al. (2001) has observed similar behavior in 

the Lower Granite pool during the period 1996-2001. 

We initially tested this hypothesis by obtaining current (mid-January 2003) hourly data 

on discharges, forebay elevations, and tailwater elevations for the four lower Snake River 

dams at low flows from the Corps of Engineers web site. Mid-January typically has the 

lowest Snake River flows.

We discovered seiches (periodic oscillations of the water surface that involve water 

movements upstream and downstream; i.e., the “sloshing bathtub”) in the lowermost 

three reservoirs (Little Goose, Lower Monumental, and Ice Harbor) during weekdays but 

not in Lower Granite reservoir (Figures 11 and 12). The observed seiches, not heretofore 

reported for the lower Snake River reservoirs, are consistent with the oscillation being 

caused by pulsing outflows at the three upstream dams (Lower Granite, Little Goose, and 

Lower Monumental, respectively). Lower Granite reservoir has an undammed portion of 

river above the head of the reservoir and receives side flow from tributaries, both of 

which are factors that would damp the effects of oscillations. Dam outflows ranged from 

zero at night to 10-30 kcfs in daytime. Further support for the oscillations being forced by 

pulsed discharges came from observation that the oscillations dampened during a 

weekend of stable flows (about 13 kcfs), but were reinitiated when flows again fluctuated 

markedly in the following week. Oscillations in Little Goose and Lower Monumental 

pools had periods of somewhat over two hours, whereas Ice Harbor pool had a complex 

oscillation with many apparent harmonics or sub-oscillations (befitting the Ice Harbor 

pool with its more complex morphometry). The oscillations of Little Goose and Lower 

Monumental pools had single or odd-numbered nodes (centers of oscillation), because the 

upswings occurred in reverse sequence (mirror image) at forebays and tailwaters. Figure 

13 illustrates surface elevation changes and seiche-induced flows in a theoretical lake 

basin (Lemmin and Mortimer 1986). The tailwater oscillations had higher amplitudes, 

consistent with shallower water and narrower channels than the forebays. We calculated 

that seiche-induced flow at a single node in Little Goose Reservoir on one example day 

would amount to about 10 kcfs, reversing direction every 1.4 hours. During hours of zero 

discharge from Lower Granite Dam, this flow reversal would actually flow alternately 

upstream and downstream at 10 kcfs. When the dam discharged its peak of 20 kcfs for 

the day, the downstream flow at the node would be accelerated to about 30 kcfs and 

decelerated to about 10 kcfs downstream every 1.4 hours. These complex flows and 

potential seiches at low flows could be disruptive for downstream migrants and 

potentially cause the wandering and upstream swimming of radio-tagged smolts observed 

in Little Goose pool in 1995-1997 by Vendetti et al. (2000) and in Lower Granite pool in 

1996-2001 by Plumb et al. (2003). There is a large literature on seiches in lakes and 

coastal waters, much of it from European limnological research of the late 1800s and 

early 1900s (e.g., see Hutchinson 1957). 

Subsequent to making these analyses and discovering the winter seiches, we obtained

hourly records of flows and elevations of tailwaters and forebays for 1995-2002 from 

DART (courtesy of Chris Van Holmes, University of Washington DART). It appears that 
50

flows do not get as low as zero during the months of fish migrations, but that 

considerable pulsing still occurs at times when downstream migrants are present (e.g., 

Figure 6). We found that during 2001, the year of the study by Plumb et al. 2000, there 

were periodic episodes of flow reduction every day but two days of those included in 

their study. Most, 46 of 60, occurred in the hours from 0100 to 0400h, during which the 

minimum flow reached about 65% of flow in the preceding and following time intervals, 

and lasted an average of about 7 hours (some as long as 15 and 18 hours). No seiches 

were apparent in the records of water elevations during the weeks of fish migrations, 

although a thorough examination of the data set should be conducted. The documented, 

large variations in flow through a daily cycle undoubtedly create complex hydraulics that 

are disruptive to the downstream migration of fish. This alternative hypothesis for 

decreased survival at low flows should be investigated further.

Figure 11. Little Seiche. 
51

Figure 12. Prominent Seiche. 
52

Figure 13. Surface elevation changes and seiche-induced flows in a theoretical lake basin 

(Lemmin and Mortimer 1986).

Fluctuating Forebay Flows: 

The fluctuation of dam discharges within a day by power operations affects the dam’s 

forebay as well as its tailwater. As water in a Snake River reservoir nears an operating 

powerhouse, its velocity increases progressively within a zone extending about 300 ft 

upstream of the dam (Adams et al 1997). The velocities attained are proportional to the 

powerhouse discharge rate. Thus, downstream migrants are exposed to hourly changes in 

forebay velocities when dam discharges fluctuate. 

Fish behavior in the near forebay has been shown to strongly affect the time taken to pass 

a dam (Plumb et al. 2003). This behavior is related to the daily average river flow rate, 

with major changes occurring for spring chinook salmon and steelhead near 100 kcfs. 

Therefore, it is likely that short-term, within-day variations in forebay velocities could 

cause variations in behavior and affect dam passage times. The variable velocity 

environment could foster some of the behavioral anomalies seen by Plumb et al. in 2001, 

a drought year (e.g., upstream movement). These authors noted that powerhouse 

operations included daily shifts of load from turbines at one end of the powerhouse to the 

other end. These could also create conditions confusing to migrating fish.
53

Although the field observations of velocities and fish behavior were conducted at times 

when flows were at seasonal highs and yearling chinook salmon and steelhead were 

migrating, the relative intensity of flow fluctuations is greater at lower flows in summer 

when underyearlings are migrating. The flows experienced in spring 2001 were 

somewhat representative of flows typically seen later in the year when juvenile fall 

chinook are migrating. Thus, the strong behavioral responses seen for yearlings are 

probably magnified for underyearlings. 

Fish Orientation Hypothesis:

Fish behavior in different river conditions of velocity and turbulence has been proposed 

as a guidance mechanism for migration (Coutant 1998, 2000), and it may help explain the 

broken-stick response of fish survival to differences in water travel time and flow. 

Changes in behavior associated with fluctuating flows may explain the unusually high 

rate of residualization of steelhead smolts observed in the year 2001. Behavioral 

responses may provide opportunities for water management for benefit of fish that 

include factors other than increasing river flow rates through augmentation. 

For years, it has been believed that downstream-migrating salmon and steelhead make 

use of river currents to assist their downstream movement (Thorpe 1982). Thus, there is a 

strong demonstrated relationship between fish travel time and water travel time (e.g., 

Berggren and Filardo 1993). Yet, as shown in telemetry studies by Venditti et al. (2000) 

and Plumb et al. (2003), smolts lose their downstream orientation in reservoir forebays 

and show milling behavior and upstream forays extending several miles. While this 

observation does not negate the relationship found between fish travel time and water 

travel time, it adds a dimension that probably requires a different approach to 

amelioration of mortalities experienced in transit. It would appear that the smolts have 

lost their cues for “downstream” and are searching to relocate the downstream flow 

(Venditti et al. 2000). 

Salmon smolts exhibit several modes of migration. Often salmon smolts swim facing 

upstream near the surface of the main river channel or thalweg at a very slow velocity 

relative to the surrounding water (see references cited in Coutant and Whitney 2000). 

Despite a small component of forward swimming their net movement is downstream. 

Most smolts will, at times, leave this migration mode and move to shallower water, 

presumably to feed (underyearling chinook salmon, especially, demonstrate a daily cycle 

of daytime feeding along shorelines and nighttime movement to river channels where 

they are displaced downstream). Some, especially steelhead, will also actively swim

downstream at times, thus moving at a rate faster than the average water travel time 

(Muir et al. 1994; Peak and McKinley, 1998; Berggren and Filardo 1993). Nonetheless, 

downstream displacement is primarily a combination of riverine flow and the intentional 

positioning of a smolt to maintain its controlled orientation in it. 

The telemetry studies of wandering smolts in dam forebays and other locations with low 

river velocities suggest a disappearance of the attachment of smolts to river flows at some 
54

combination of river conditions. One possibility is that the river velocity may simply fall 

below the velocity that smolts swim to maintain their posture, resulting in a net upstream 

fish movement instead of downstream. However, riverine turbulence has been suggested 

as an important behavioral cue (Coutant 1998, 2000). It is hypothesized that smolts detect 

small pressure changes along their bodies (by the lateral line sensory system), which 

result from turbulence characteristic of a flowing river. So long as this turbulence is 

sensed, the fish “knows” that it is in a moving flow and it maintains its orientation in the 

water. When the appropriate level of turbulence is not sensed (a level yet to be 

determined experimentally or by field observation, which we can call the “critical 

turbulence”), then the fish leaves its flow-attachment mode and actively swims to 

relocate the zone of flow. As with other hypotheses, slowed migration presumably results 

in increased exposure to predators, disease, high temperatures, high dissolved gas, or 

other damaging factors that reduce survival. 

We hypothesize that a major factor determining smolt travel time through reservoirs such 

as those in the Snake River is the distance downstream that the critical turbulence level 

extends into the reservoir. Throughout a wide range of fairly high flows, the critical 

turbulence level is met or exceeded all the way to the dam (Figure 14a). In this case, fish 

travel time varies with the water travel time through the reservoir, and survival is high 

because the fish maintain rapid downstream displacement through the whole reservoir. 

There is no relationship of survival to flow at these high river discharge rates because 

speedy migration is maintained to and through the dam regardless of flow rate above a 

certain level. This conjecture conforms to the flat (no relationship) portion of the brokenstick model. However, at low flows the critical turbulence level is not maintained all the 

way to the dam (Figure 14b). In this situation, fish lose their orientation cue before 

reaching the dam and are left to wander through the downstream portion of the reservoir, 

slowing overall migration rate and exposing fish to factors that likely reduce survival. 

Also, more stored energy is used by the smolts as they must swim actively rather than be 

displaced passively, thus possibly reducing survival directly or indirectly. Fish travel time 

and survival are both related to flow at these lower flow rates because at higher flow rates 

the critical turbulence level will extend closer to the dam and the zone of fish wandering 

is smaller. This conforms to the portion of the broken-stick model wherein both fish 

travel time and survival are related to water travel time and flow. 

Fluctuating flows would be important in this hypothesis. Relationships between fish 

travel time and water travel time, as graphed by the FPC and others, are variable among 

individually PIT-tagged smolts, especially at longer water travel times (lower flows) 

(Figure 14c). This variability is hypothesized here to result from hourly fluctuating flows 

from dams throughout a day at lower daily average flows (Figure 6), which alter the rates 

of downstream displacement and the distance the critical turbulence level penetrates into 

a reservoir. Different smolts migrating at different times of day can be exposed to 

different rates of water movement and different locations along the length of reservoir 

where the critical turbulence level is no longer met. This would yield very different fish 

travel times for the same daily average flow and daily average water travel time, as has 

been demonstrated in the FPC analyses.
55

River modifications other than flow management have been suggested to assist smolts in 

their migration through reservoirs (Coutant 1998, 2001). These modifications generally 

consist of passive or active ways to increase turbulence and extend the distance that the 

critical turbulence level occurs in reservoirs like those on the Snake River. Structural 

features have been suggested to focus flows and generate riverine turbulence. Active 

approaches (pumps, propellers) may be useful in certain situations such as approaches to 

fish bypasses. These approaches for enhancing migration rates through reservoirs deserve 

more attention. We recognize that their application over the large reaches involved might 

pose significant engineering problems. Further hydrologic studies would be needed to 

identify places where they might be useful or necessary. Fish behavioral responses would 

need to be identified as well. When the alternative to such studies is flow augmentation 

from limited upstream sources, the additional attention may be justified.
56

Figure 14. Hypothesized effect of turbulence on smolt migration in reservoirs.
57

Dam Obstacle Hypothesis:

Migration rates of yearling steelhead and chinook salmon in spring declined to near zero 

within 400 ft of Lower Granite Dam when daily average flows were less than about 100 

kcfs (Plumb et al. 2003). This result emerged from radiotelemetry studies in 1996-2001 at 

annual average flows that ranged from above the average for recent years to a near record 

low. The 100 kcfs value is essentially the same as the apparent flow breakpoint seen in 

flow-survival curves for these species (e.g., FPC data and Smith 2002). This observation

suggests that the dam structure or some hydraulic features at the dam (e.g., lack of 

attraction flow, daily discharge cycle, lack of spill) act as a more prominent barrier at 

flows below 100 kcfs. These newly released data suggest value in examining dam 

structures or operations in more detail for potential management avenues below 100 kcfs 

to increase smolt survival, in lieu of reliance on augmented flow. Flow augmentation 

would appear to be valuable if it could bring flows above 100 kcfs in order to minimize 

stalled migration in the immediate dam forebay. That amount of water may not be 

available. More water alone, however, may not correct operational features that inhibit 

migration at and below this flow level. 

Pulsed Flow Hypothesis:

Pulses of flow have been hypothesized to aid fish migration through reservoirs. This 

would be generally contrary to hypothesized detrimental effects of flow fluctuations. The 

pulsed-flow hypothesis suggests that, during low-flow periods, pulses of high flow mixed 

with periods of little or no flow would stimulate smolts to migrate. The pulses would 

provide the favorable characteristics of high flows for short periods of time, allowing 

smolts to be “flushed out” within hours. The hypothesis has its origin in field 

observations that smolts often increase their passage rate when river discharges increase 

rapidly. 

In the lower Snake River, this hypothesis appears to run counter to the observed data, 

both for fall chinook salmon that migrate at low flows and at the lower flows in the 

generally higher flow range when yearling chinook and steelhead migrate. Travel times 

are longest and survival poorest during periods when flows are fluctuated the most. Thus, 

as a general rule, intentional pulsing would seem to be counterproductive here. 

However, the efficacy of pulsing may depend on the volumes of water involved and 

coordination of operations of dams to “keep the pulse going”, however. From the 

perspective of the fish orientation hypothesis (above), high flow rates in a pulse may be 

able to maintain smolt orientation all the way to the dam, but if the dam is not 

discharging at an appropriate rate to maintain the pulse, the benefit may be lost. In light 

of the radiotelemetry studies of yearlings, a pulse greater than 100 kcfs may be able to 

move smolts backed up at the dam during lower flows. In either case, passage rates and 

survival would be increased. Pulsing would require volumes of water greater than the 
58

apparent breakpoint in the flow-survival curves (near 100 kcfs) to be maximally 

effective. Pulses of lesser magnitude might aid migration rate and survival in proportion 

to their volume. 

The benefits of pulses may occur only during the pulses. Migration might be inhibited 

(and survival diminished) during the intervening periods of low flow, with no net gain. If 

seiches are produced, as we observed, the net effect could be counterproductive as an aid 

to fish migration. The low survival and decreased migration rates already demonstrated 

during periods of fluctuating flows might be taken as a failed test of the pulse hypothesis, 

at least in the range of flows experienced. Clearly, the efficacy of intentional pulses has 

yet to be demonstrated. 

This investigation leads to an unexpected recommendation of a measure to improve 

survival of juvenile salmonids, which we believe could be more effective than simply 

adding a volume of flow, as in flow augmentation. We believe that stabilization of flows 

could have a more beneficial effect on survival of juvenile salmonids than simply adding 

a volume of water, as at present in flow augmentation, where water can be released 

intermittently.
NOTES ON THE MATHEMATICS OF

REACH SURVIVAL AND FLOW

1 INTRODUCTION

The debate over a flow survival relationship has failed to distinguish between (1) the

possible role of flow in governing the speed of smolt outmigration, and (2) the possible

role of flow in affecting the mortality rate experienced by migrating smolts.

1.1 Speed

The speed of smolt migration determines the amount of time that the smolts will

spend in a given reach in the migration corridor. It is not an automatic conclusion

that a shorter time is necessarily good, from a life cycle persective. A shorter time in

a particular reach definitely lessens the time of exposure to mortality in that reach,

but after passing that reach, the smolts will still be exposed to mortality, wherever

they are. Thus, the reach survival benefit from reducing the time spent in a particular

reach will confer a net survival benefit only if that reach is a location of unusually

high instantaneous mortality compared to other locations during the outmigration.

Furthermore, smolts may be feeding and growing during the outmigration, so the

net benefit to production from the time spent in a particular reach will be the balance

between growth rate and mortality rate in that reach. The full cost benefit analysis

of hurrying the smolts through a particular reach will show a net benefit only if the

balance between growth and mortality in that reach is worse than in other reaches

where it will spend time during migration.

Finally, the speed of migration affects the date of arrival at the estuary. The

condition and physiological state of the smolt is crucial to its survival in the estuary.

Calendar date itself seems to play a large role, also, since it is now known from PIT

tag studies that the subsequent smolt to adult survival rate varies greatly with date

of arrival in the estuary. So, increasing the speed of migration through a reach can be

disadvantageous if it brings the smolt to the estuary at too early a calendar date, or in

the wrong physiological state. By the same token, decreasing the speed of migration

through a reach can also be disadvantageous if it brings the smolt to the estuary a

too late a calendar date, or in the wrong physiological state.

59
Note that measurements of reach survival in just one particular reach do not tell

us what the survival is elsewhere, or what the contribution is from time spent in that

reach for growth and condition. A comprehensive evaluation of the proper migration

speed for a reach will require analysis of measurements of the smolt to adult return

rate measured from the head of that reach.

1.2 Mortality Rate

An increase in the mortality rate is unambiguously bad. This is the rate of deaths

per unit time. For a given reach, an increase in the mortality rate would indicate that

conditions within that reach had become more hazardous.

Instantaneous mortality rate is not measured directly with available observations

from smolt monitoring. What is measured is reach survival and smolt to adult return

rate. Both of these measures are simple dimensionless fractions giving the number

alive at the end of an interval divided by the number alive at the begining. The

mortality rate is in units of reciprocal time.

For reach survival, the interval is a defined distance, not time. Thus the cumulated

mortality that is expressed in reach survival is a function of the time elapsed in

covering that distance, and the instantaneous mortality operating over that time,

and speed itself as that determines the time to cover the distance. An interpretation

of the patterns observed in the relation between reach survival and travel time or

flow requires an understanding of the relation between reach survival, instantaneous

mortality, migration speed, and flow.

2 A NULL MODEL FOR

REACH SURVIVAL PATTERNS

The starting point for an investigation of the factors influencing reach survival is a

null model which assumes that the instantaneous mortality is constant, and therefore

not affected by flow. Let the constant instantaneous mortality rate be μ. Let the

variable flow be f.

Let the distance spanned by a particular reach be a fixed value D. Let the variable

time elapsed to traverse the reach be t. Let the variable travel speed be v. The internal

relationship between travel time, speed, and distance, is the elementary

D = vt . (1)

The calculated speed for a water particle is, theoretically, approximately linearly

related to flow (as shown in the plots by the FPC). Empirically, smolt migration

speed, also appears to be, on average, linearly related to flow, as shown in the plots by

the FPC. But the resulting smolt migration speed does not necessarily duplicate the

theoretical water particle speed—which is to say, unsurprisingly, that smolt migration

is not a simple passive transport in the bulk fluid. Also, the empirical scatter plots

60
of smolt migration speed versus flow show a greatly increased random variation in

speed at the lower flows compared to higher flows.

For the moment, let us accept linearity of the migration speed with respect to

flow relationship, and treat the proportionality as an empirically determined value c.

Thus

t = cf . (2)

For a constant instantaneous mortality rate, the survival is a simple exponential

decay with time

s = e−μt . (3)

Taylor expanding the exponential function about zero t, a first order approximation

to the relationship between reach survival and travel time, under the null model, is

s ' 1 − μt , (4)

which is a straight line with a negative slope, where the negative of that slope is

simply the instantaneous mortality rate. This is consistent with the observed scatter

plots relating reach survival to travel time.

The linear flow speed relationship, in equation [2], and the elementary distance

speed relationship, in equation [1], when combined, can be solved for travel time as

proportional to the inverse of flow

t = D

cf . (5)

Substituting this time flow relationship to travel time, gives, for the exact exponential

reach survival equation [3], the reach survival flow relationship

s = e

−μD

cf . (6)

Making the same substitution into the Taylor approximation of equation [4] gives

s ' 1 − μD

cf , (7)

which corresponds to a hyperbola with an asymptote at s = 1 for large f, and

crossing the f axis at f = μD/c. This approximate appearance of a saturation curve

is consistent with the observed trend in the scatter plots of reach survival against

flow. But those empirical plots show much greater scatter in the end of the range

where reach survival and flow are both large.

So, based on visual inspection, the available data are suggestive of the null model,

with no relationship between flow and instantaneous mortality rate, and with a pattern between reach survival and flow that is based simply on the empirical relationship

between migration speed and and flow, and the mathematics of the relationship between travel time and speed. An analysis specifically to test for a relationship between

61
flow and instantaneous mortality will have to test for a systematic departure from

the pattern derived from the null model.

2.1 A Model of a Flow Survival Rate Relationship

A starting hypothesis for a relationship between flow and instantaneous mortality

rate might be the linear model

μ = μ0 − αf , (8)

where α is the steepness of the negative slope of the line, and μ0 is the base mortality

rate at zero flow. Note that this model is only reasonable for a modest slope over the

range of flows, to keep the mortality rate positive.

Substituting this in the exact exponential of equation [3] for reach survival gives

s = e

− (μ0−αf)D

cf

= (e

αD

c )e

− μ0D

cf , (9)

which recapitulates the basic shape of the relationship for a constant mortality rate

(with μ0 now playing that role) modified by a constant multiplicative factor, e

αD

c .

Since the effect on the reach survival flow relationship is multiplicative, it will be

strongest where the reach survival is largest, but this is also where the empirical

scatter plots show the greatest scatter, so detectability will be a delicate statistical

issue.

A test for an influence of flow on instantaneous mortality rate, with this model,

would hinge on discriminating α from zero.

3 CONCLUSION

The analyses that have been done to date have not separated an effect of flow on

mortality rate from the effect of flow on travel time. Both affect reach survival, but

reach survival is not an unambiguous objective from the perspective of the entire life

cycle. The benefit of increasing reach survival through reducing travel time depends

on a comparison of the growth survival balance within the reach in question and the

same balance further downstream, further modulated by the effect of travel time on

arrival date in the estuary, which can be too early or too late. Evaluation of the life

cycle benefit of the travel time effect, therefore, must rest on statistical analyses of

the effect on smolt to adult return rate, not on reach survival.

The benefit of increasing reach survival through reducing instantaneous mortality

rate would be unambiguous, but a new kind of statistical analysis would be required

to detect such an effect, from the present data collections.

62
63

Consolidated References for Text and Appendices

Adams, N. S., D. W. Rondorf, E. E. Kofoot, M. J. Banach, and M. A. Tuell. 1997. 

Migrational characteristics of juvenile spring chinook salmon and steelhead in the 

forebay of Lower Granite Dam relative to the 1996 surface bypass collector tests. 

1996 annual report to the U.S. Army Corps of Engineers, Contract E-86930151, 

Walla Walla, Washington. 

Andersen, J.J. 2000. Heat budget of water flowing through Hells Canyon and the effect of 

flow augmentation on Snake River water temperature. Report provided through the 

University of Washington, Columbia Basin Research, Seattle, WA. Available on the 

DART web site.16 pp. 

Andersen, J.J., R.A. Hinrichsen, and C. Van Holmes, 2000. Effects of flow augmentation 

on Snake River Fall Chinook. Unpublished report, December, 2000. 62 pp.

Bennett, D.H., M.A. Madsen, M.H. Karr. 1997. Water temperature characteristics of the 

Clearwater River, Idaho, and Lower Granite, Little Goose, Lower Monumental, and 

Ice Harbor Reservoirs, Lower Snake River, Washington, during 1991-1993, with 

emphasis on upstream water releases. Data volume II, project 14-16-0009-1579. 

Idaho Department of Fish and Game, Moscow ID.

Berggren, T.J. 2000. Subyearling chinook survival to Lower Granite Dam vs flow. 

Memorandum to FPAC of October 12, 2000, 2pp

Berrgren, T. J., and M. J. Filardo. 1993. An analysis of variables influencing the 

migration of juvenile salmonids in the Columbia River basin. North American Journal 

of Fisheries Management 13:48-63.

Chapman, D.A., A. Giorgi, M. Hill, A. Maule, S. McCutcheon, D. Park, W. Platts, K. 

Pratt, J. Seeb, L. Seeb, and F. Utter. 1991. Status of Snake River chinook salmon. 

Don Chapman, Consultants, Inc. Boise, Idaho, for the mid-Columbia P.U.Ds; Chelan, 

County P.U.D, Wenatchee, WA, Douglas County P.U.D., East Wenatchee, WA, and 

Grant County P.U.D., Ephrata, WA 520 pp.

Chapman, D. W., and D. McKenzie. 1980. Mid-Columbia River system mortality study. 

Report to mid-Columbia PUDs. Douglas County P.U.D No. 1, East Wenatchee, WA. 

23 pp.

Connor, W.P., H.L. Burge, and D.H. Bennett. 1998. Detection of PIT tagged subyearling 

chinook salmon at a Snake River dam: Implications for summer flow augmentation. 

North American Journal of Fisheries Management 18:530-536

Connor, W. P., R. K. Steinhorst, and H. L. Burge. In press. Migrational behavior and 

seaward movement of wild subyearling fall chinook salmon in the Snake River. North 

American Journal of Fisheries Management
64

Coutant, C. C. 1998. Turbulent attraction flows for juvenile salmonid passage at dams. 

Oak Ridge National Laboratory, Report ORNL/TM-13608, Oak Ridge, Tennessee. 

Coutant, C. C. 2001. Turbulent attraction flows for guiding salmonids at dams. American 

Fisheries Society Symposium 26:57-77.

Coutant, C. C., and R. R. Whitney. 2000. Fish behavior in relation to passage through 

hydropower turbines: a review. Transactions of the American Fisheries Society 

129:351-380. 

Dreher, K.J., C.R. Petrich, K.W. Neely, E.C. Bowles, and A. Byrne. 2000. Review of 

survival, flow, temperature, and migration data for hatchery raised, subyearling fall 

chinook salmon above Lower Granite Dam, 1995-1998. Idaho Department of Water 

Resources, Boise, ID 

Ebel, W.J., C.D. Becker, J.W. Mullan, and H.L. Raymond. 1989. The Columbia River: 

Toward a holistic understanding. Pages 205-219 in D.P. Dodge, ed. Proceedings of 

the International Large River Symposium (LARS). Special Publication of the 

Canadian Journal of Fisheries and Aquatic Sciences.

FPC (Fish Passage Center). 2002. Memorandum from Michelle DeHart to Members’ 

Management Ad Hoc Group entitled “Preliminary Update on Juvenile Migration 

Characteristics”. October 14, 2002. Portland, Oregon

Giorgi, A.E., T.W. Hillman, J.R. Stevenson, S.G. Hays, and C.M. Peven. 1997. Factors 

that influence the downstream migration rates of juvenile salmon and steelhead 

through the hydroelectric system in the mid-Columbia River Basin. North American 

Journal of Fisheries management 17:268-282

Giorgi, A., M. Miller, and J. Stevenson. 2002. Mainstem passage strategies in the 

Columbia River system: Transportation, spill, and flow augmentation. Unpublished 

report prepared for the Northwest Power Planning Council, Portland, OR. 98 pp.

Hastie, T.J., and R.J. Tibshirani. 1990. Generalized Additive Models. Monographs on 

Statistics and Applied Probability 43. Chapman and Hall, London.

Hutchinson, G. E. 1957. A treatise on limnology. Volume I. Geography, physics, and 

chemistry. John Wiley & Sons, New York. 

Independent Scientific Group (ISG). 2000. Return to the River: Restoration of Salmonid 

Fishes in the Columbia River Ecosystem. Report to the Northwest Power Planning 

Council. 538 pp. (Available on the Council’s web site.)

Independent Scientific Advisory Board (ISAB). Ecological impacts of the flow 

provisions of the Biological Opinion for endangered Snake River salmon on resident 

fishes in the Hungry Horse and Libby systems in Montana, Idaho, and British 
65

Columbia. (See especially Appendix 5 – Effects of drawdown on aquatic systems in 

reservoirs.) (ISAB 1997-3), NWPPC, Portland, OR, March 4, 1997. 

http:www.nwcouncil.org/library/isab/isab97-3.htm

Independent Scientific Advisory Board (ISAB). Review of Giorgi et al. report “Mainstem 

strategies in the Columbia River System: Transportation, spill and flow 

augmentation”. (ISAB 2002-1), Northwest Power Planning Council, Portland, OR. 

Independent Scientific Advisory Board (ISAB). Review of Lower Snake River flow 

augmentation studies. (ISAB 2001-5), Northwest Power Planning Council, Portland, 

OR

ISG 1995. ISG response to request for review of the Hungry Horse Mitigation 

Implementation Plan. ISG Report Number 1995-3, June 14, 1995. Available through 

the Northwest Power Planning Council.

ISG (Independent Scientific Group). 2000. Return to the River 2000. Restoration of 

salmonid fishes in the Columbia River ecosystem. Report 2000-12, Northwest Power 

Planning Council, Portland, Oregon. 

Karr, M. H., J. K. Fryer, and P. R. Mundy. 1998. Snake River water temperature control 

project. Phase II. Methods for managing and monitoring water temperatures in 

relation to salmon in the lower Snake River. Columbia River Intertribal Fish 

Commission and Fisheries and Aquatic Sciences, Portland, Oregon. 

Lemmin, U., and C. H. Mortimer. 1986. Tests of an extension to internal seiches of 

Defant’s procedure for determination of surface seiche characteristics in real lakes. 

Limnology and Oceanography 31:1207-1231. 

Logie 1993. Power System Coordination: A Guide to the Pacific Northwest Coordination 

Agreement. U.S. Department of Energy, Bonneville Power Administration, U.S. 

Department of the Army, Corps of Engineers, North Pacific Division, U.S. 

Department of the Interior, Bureau of Reclamation, Pacific Northwest Region. 

Portland, OR. 46 pp

McKenzie, D. D. Carlile and D. Weitkamp. 1983, 1983 System mortality study. Report to 

mid-Columbia PUDs. Douglas County PUD No. 1, East Wenatchee, WA 25 pp.

McKenzie, D., D. Weitkamp, T. Schadt, D. Carlile, and D. Chapman. 1982. 1982 System 

mortality study. Report to mid-Columbia PUDs. Douglas County PUD No.1, East 

Wenatchee, WA, 37 pp.

National Research Council (NRC) 1996. Upstream: Salmon and Society in the Pacific

Northwest. Report of the Committee on Protection and Management of Pacific 

Northwest Anadromous Salmonids for the National Research Council of the national 

Academy of Sciences. National Academy Press. Washington, D.C. 452 pp.
66

McConnaha, W.E. 1993. History of flow survival studies in the Columbia Basin. 

Northwest Power Planning Council. Memorandum to D. Bevan, Chairman, NOAA 

Fisheries Salmon Recovery Team, Portland, OR. 7 pp

Muir, W.D., A.E. Giorgi, and T.C. Coley. 1994. Behavioral and physiological changes in 

yearling chinook salmon during hatchery residence and downstream migration. 

Aquaculture 127:69-82. 

NWPPC (Northwest Power Planning Council). 1982. Columbia River Basin Fish and 

Wildlife Program Pursuant to Section 4(h) of the Pacific Northwest Electric Power 

Planning and Conservation Act of 1980 (P. L. 96-501). Adopted November 15, 1982, 

Portland, Oregon. 

NWPPC (Northwest Power Planning Council). 1994. Columbia River Basin Fish and 

Wildlife Program. Report 94-55, Portland, Oregon. 

Peak, S., and R.S. McKinley. 1998. A re-evaluation of swimming performance in 

juvenile salmonids relative to downstream migration. Can.j. Fish. Aquat. Sci. 

55:682.687.

Plumb, J. M., M. S. Novick, A. C. Braatz, J. N. Lucchesi, J. M. Sprando, N. S. Adams, 

and D. W. Rondorf. 2003. Behavior and migratory delay of radio-tagged juvenile 

spring chinook salmon and steelhead through Lower Granite Dam and reservoir 

during a drought year. USGS Columbia River Research Laboratory, Cook, 

Washington. Report for U.S. Army Corps of Engineers, Contract W68SBV00104592, 

Walla Walla District, Walla Walla, Washington. 

Resource Writers, Inc. 1991. The Columbia River System: The Inside Story. Bonneville 

Power Administration, U.S. Army Corps of Engineers, North Pacific Division, U.S. 

Department of Interior, Bureau of Reclamation, Pacific Northwest Region, Portland, 

OR. 82 pp

Seber, B.A.F., and C.J. Wild. 1989. Nonlinear Regression. John Wiley & Sons, New 

York.

Sims, C.W., W.W. Bentley, and R.C. Johnsen. 1977. Effects of power peaking operations 

on juvenile salmon and steelhead trout migrations – Progress 1976. Final Report of 

Research Financed by U.S. Army Corps of Engineers (Contract No. DACW68-77-C0025). 27 pp

Sims, C.W., W.W. Bentley, and R.S. Johnsen. 1978. Effects of power peaking operations 

on juvenile salmon and steelhead trout migrations – Progress 1977. Final Report of 

Research Financed by U.S. Army Corps of Engineers (Contract No. DACW68-77-C0025). 52 pp
67

Sims, C. W., and F. Ossiander. 1981. Migrations of juvenile chinook salmon and 

steelhead trout in the Snake River from 1973 to 1979. NMFS/NOAA Northwest and 

Alaska Fisheries Center, Seattle, Washington. Report to U. S. Army Corps of 

Engineers, Portland, Oregon. 

Skalski, Mundy, and McConnaha. 1989. Suggested work plan for flow/water budget 

smolt survival evaluation. Report to ad hoc Committee on Mainstem Research. 6p

Smith, S. S., W. D. Muir, and J. G. Williams. 2002. Factors associated with travel time 

and survival of migrant yearling chinook salmon and steelhead in the lower Snake 

River. North American Journal of Fisheries Management 22:385-405.

Suzumoto 2002. Memoranda of November 6, 2002 and December 2, 2002 to Council 

Members on the subjects of SIMPAS analysis of state proposals, and Mainstem 

juvenile survival: CRiSP modeling results, 6p and 4p

Thorpe, J. E. 1982. Downstream movements of juvenile salmonids: a forward speculative 

view. Pages 387-395 in J. D. McCleave, G. P. Arnold, J. J. Dodson, and W. H. Neill, 

editors. Mechanisms of migration in fishes. Plenum, New York. 

Tiffan, K.F., R.D. Garland, and D.W. Rondorf. 2002. Quantifying flow-dependent 

changes in subyearling fall chinook salmon rearing habitat using two-dimensional 

spatially explicit modeling. North American Journal of Fisheries Management 

22:713-726

University of Washington, Center for Quantitative Sciences. DART

Venditti, D. A., D. W. Rondorf, and J. M. Kraut. 2000. Migratory behavior and forebay 

delay of radio-tagged juvenile fall chinook salmon in a lower Snake River 

impoundment. North American Journal of fisheries Management 20: 41-52. 

Wagner, P.G., J. Nugent, W. Price, R. Tudor, and P. Hoforth. 1999. 1997-1999 

evaluation of juvenile fall chinook stranding on the Hanford Reach. Annual Report to 

Bonneville Power Administration. Contract 97B130417, Portland, OR

Whitney, R. R., L. D. Calvin, M. W. Erho, Jr., and C. C. Coutant. 1997. Downstream 

passage for salmon at hydroelectric projects in the Columbia River basin: 

development, installation, and evaluation. Report 97-15, Northwest Power Planning 

Council, Portland, Oregon.

Zabel, R.W., S.G. Smith, W.D. Muir, D.M. Marsh, J.G. Williams, and J.R. Skalski. 2002.

Survival estimates for the passage of spring-migrating juvenile salmonids through 

Snake and Columbia river dams and reservoirs. Annual report to Bonneville Power 

Administration, Portland, Contract DE-AI79-93BP10891. Available on the web at 

http://www.efw.bpa.gov/cgi-bin/FW/publications.cgi.