Independent Scientific Advisory Board

for the Northwest Power and Conservation Council,

Columbia River Basin Indian Tribes, 

and NOAA Fisheries

 851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

ISAB@nwcouncil.org

ISAB Findings from the 

Reservoir Operations / Flow 

Survival Symposium 

November 9 - 10, 2004 

Sponsored by the 

Northwest Power and Conservation Council 

and NOAA Fisheries

December 10, 2004 

ISAB 2004-2 
Review Subcommittee 

Peter A. Bisson, Ph.D., Senior Scientist at the Olympia (Washington) Forestry Sciences 

Laboratory of the U.S. Forest Service.

Charles C. Coutant, Ph.D., Distinguished Research Ecologist, Oak Ridge National Laboratory, 

Oak Ridge, Tennessee, Past President of the American Fisheries Society, with expertise in 

fish-habitat relationships. 

Daniel Goodman, Ph.D., Professor of statistics at Montana State University, an expert in 

ecological risk assessment. 

Eric J. Loudenslager, Ph.D., ISAB Chair, Hatchery Manager at Humboldt State University, 

California, an expert in genetics and fish culture. 

Lyman McDonald, Ph.D., Consulting Statistician at Western Ecosystems Tech., Inc., Cheyenne, 

Wyoming, formerly Professor at the University of Wyoming. 

Thomas P. Poe, M.S., Consulting Fisheries Scientist, an expert in behavioral ecology of fishes, 

formerly with the U.S. Geological Survey. (Ad Hoc Member) 

Richard R. Whitney, Ph.D., Consulting Fisheries Scientist, Leavenworth, Washington, formerly 

Professor in the School of Fisheries, University of Washington. (ISRP Member) 

Other Contributing ISAB Members

Robert Bilby, Ph.D., Ecologist at Weyerhaeuser Company an expert in riparian ecology.

Susan Hanna, Ph.D., Professor of resource economics at Oregon State University (also an IEAB 

member). 

Nancy Huntly, Ph.D., Professor of wildlife biology at Idaho State University. 

David P. Philipp, Ph.D., Principal Scientist at the Illinois Natural History Survey and Professor 

at University of Illinois, an expert in conservation genetics and reproductive ecology. 

Brian Riddell, Ph.D., Senior Scientist at the Pacific Biological Station, Department of Fisheries 

and Oceans Canada, Nanaimo, British Columbia, an expert in the biology of Pacific salmon 

and international fisheries management. 

Staff 

Erik Merrill, Project Coordinator for the ISRP and ISAB, Northwest Power and Conservation 

Council 
ISAB Findings from the Reservoir Operations / Flow Survival 

Symposium 

Contents 

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

II. Introduction .................................................................................................................... 3 

III. Responses to NOAA Fisheries’ Questions ................................................................... 5 

What is the “state of science”?........................................................................................ 5 

Refinement of the issue............................................................................................... 6 

Physical effects of water flow and velocity ................................................................ 6 

Relating flow to temperature ...................................................................................... 7 

Status and presence of affected anadromous stocks ................................................... 8 

Biological responses ................................................................................................... 9 

Which attributes are most critical? ............................................................................... 10 

Is there a practical and feasible experimental design to test the Council’s hypothesis?11 

What are the strengths and weaknesses of available models? ...................................... 13 

IV. Overall Council Hypothesis........................................................................................ 13

Literature Cited ................................................................................................................. 14 

Literature Used for this Review but not Cited in the Text................................................ 15 
1 

ISAB Findings from the Reservoir Operations / Flow Survival 

Symposium

I. Executive Summary 

On November 9th and 10th, 2004, the Northwest Power and Conservation Council and 

NOAA Fisheries sponsored a reservoir-operations/flow-survival symposium. The ISAB 

was asked to provide scientific feedback on the Council’s proposed operations of Hungry 

Horse and Libby hydroelectric projects, as described in the Council’s Mainstem 

Amendments, and NOAA Fisheries’ questions about Montana’s subsequent System 

Operations Request (SOR, referred to below as the Montana proposal). At issue is the 

potential trade-off between the probable detrimental biological effects on the resident 

fishes in reservoirs and rivers at Hungry Horse and Libby dams under flow management 

with existing BiOp operations and the unquantified potential detriment to anadromous 

fishes in the lower Columbia River under the Council’s 2003 Mainstem Amendment and 

Montana Systems Operations Request. There is also interest in determining the proper 

design of an experiment(s) to provide this quantification. The anadromous fish of most 

concern are ESA-listed Snake River fall Chinook salmon because they are believed to 

migrate during the August-September period when flows have been augmented by 

releases from Hungry Horse and Libby dams. 

The ISAB found the relevant science to be in flux, providing no unambiguous answers at 

this time. Flow-survival debates have been prominent in the region since the first Fish 

and Wildlife Program and its water budget (1982). The current amendment and 

Montana’s proposal have focused attention on one particular manifestation of the issue. 

Although the likely detrimental effects of current operations on the gross biological 

productivity (i.e., production through all levels of the ecosystem, including plants, 

invertebrates, and fish) of the Hungry Horse and Libby reservoirs and downstream rivers 

are easy to envision and are probably of a substantial magnitude, the way in which 

current operations will affect the species of greatest concern (sturgeon and bull trout) is 

actually unknown. The physical changes in flow in the Columbia River below Chief 

Joseph Dam (the uppermost limit of anadromous fish in the Columbia River) that would 

result from the Montana proposal are affected by so many factors that predictions remain 

too uncertain for fine-scaled biological analyses. Little attention has been paid to 

measuring the physical features of “flow” important to fish migration and survival, such 

as water velocity or within-day variations due to load following (power peaking). 

Reliance on broad averages and sweeping generalizations of flow-survival relationships 

are not adequate for resolving this specific issue. In addition, the effects of altered 

temperatures on salmon require reevaluation for their relationships to flow, in spite of 

new thermal modeling efforts. 

Although summer-migrating juvenile fall Chinook salmon from the Snake River have 

been the main concern for downstream effects of the Montana proposal, there is new 

information about this stock’s life history. Some juveniles are holding over their first 
2 

winter in fresh water and emigrating as yearlings in the spring (termed the “reservoir” life 

history, also referred to as the holdover life history). Importantly, a disproportionately 

large percentage of returning adults are originating from these holdovers. This new 

information leaves us with major unresolved implications for management because 

populations adopting the holdover life history will not respond to flow changes in the 

same way that the “ocean-type” summer-migrating fall Chinook normally do. Juvenile 

fall Chinook salmon have a complex life history, much more so than juvenile 

spring/summer Chinook salmon, with observations of juvenile fall Chinook salmon 

emigrating in the Snake and Columbia Rivers throughout most of the year. The intent of 

flow augmentation is to reduce mortality of smolts by speeding their migration to the 

ocean. With the recent findings of the large adult contribution from migrants exhibiting 

the reservoir life history, and also for PIT-tagged late fall migrants (NOAA Fisheries, 

unpublished data), the strategy of using flow augmentation to speed migration should be 

reassessed. 

In addition, estimates of survival of in-river migrants have included holdovers as an 

unknown part of the “mortality” experienced during emigration, i.e., a portion of those 

estimated to have died may actually have survived, but did not pass a tag detection 

facility downstream during their first year. Resolving the very large uncertainties about 

actual outmigration survival rates and the contributions of the two distinct life history 

patterns to the effective production of wild fall Chinook will require new data collected 

using a new study design. In particular, it will be important to obtain scales from 

returning adults as they pass Lower Granite Dam to secure a large enough statistical 

sample for determining frequencies of the two life history types at that stage. This task 

should be implemented in conjunction with continued studies of PIT-tagged smolts 

released above Lower Granite Dam, and the exploration of various options for radio 

tagging migrating smolts to determine their life history behavior, as well as the 

overwintering locations and mortality patterns for the reservoir type. The importance of 

these data collection issues for the Snake River fall Chinook goes far beyond the narrow 

questions concerning the Montana System Operations Request. For example, 

transporting Snake River fall Chinook salmon subyearling smolts to below Bonneville 

Dam likely affects the proportion of smolts utilizing the reservoir life history strategy, as 

well as their size and time of arrival to the ocean. This aspect of transportation needs 

evaluation. 

Traditional flow-survival analyses are currently benefiting from detailed statistical 

analyses, with the result that different functional mechanisms for fish survival appear to 

be operating at different flows. There is good physiological evidence supporting delayed 

effects of hydrosystem passage that are likely expressed in survival in the estuary and 

ocean. Because adults respond negatively to flow increases, the effects of these increases 

on them, not just on juveniles, need to be considered as well. No existing models seem 

adequate for evaluating the flow effects from the Montana proposal. 

All indications are that the down-river effects of the shifts in flow associated with the 

Council’s Mainstem Amendments of 2003 will be small. There is some uncertainty 

whether the effect is positive or negative because flows under the Montana proposal will 
3 

be slightly greater than BiOp flows at times and slightly less at other times. As a result, 

the Council’s hypothesis that the effects on survival of salmonids in the lower Columbia 

River will be indiscernible is probably reasonable. Nonetheless, there is reasonable 

concern for potential cumulative effects of even such small changes. 

No “passive” design for measuring downstream effects of the proposed change is likely 

to be effective in a reasonable period of time. Deliberate experimental flow 

manipulations of an amplitude considerably larger than flows that will result from the 

Amendments probably would allow empirical quantification of flow effects. Whether or 

not present institutional constraints would allow such manipulations, however, is an open 

question. An experimental trial of Montana’s proposed flow regime is unlikely to reveal 

incremental biological effects within a modest number of years because annual variability 

in flow and salmon survival due to other causes is much larger than the expected effect of 

the Montana proposal. 

II. Introduction 

On November 9th and 10th, 2004, the Northwest Power and Conservation Council and 

NOAA Fisheries jointly sponsored a reservoir operations / flow survival symposium. The 

ISAB was asked to participate in the symposium and provide scientific feedback on the 

Council’s Fish and Wildlife Program’s hypothesis for the proposed operations of Hungry 

Horse and Libby hydroelectric projects, as described in the Mainstem Amendments, and 

NOAA Fisheries’ questions related to those proposed operations. The ISAB was well 

prepared for the assignment, having reviewed and released numerous reports on the 

issues of flow augmentation and Montana operations over the past several years (ISAB 

1997, 2001, 2002, 2003; ISG 1995, 2000; ISRP 2004). The fact that in each of the ISAB, 

ISG, and ISRP reports new and important insights emerged and many previously 

identified issues lingered is a reflection of the state of uncertainty and science on this 

issue. The symposium continued this trend. 

 

The symposium was organized in response to the Council’s Mainstem Amendments of 

2003 that directed the region to test, implement, and evaluate an interim summer 

operation that employs new drafting limits at Hungry Horse and Libby dams. Summer 

drafting for flow augmentation in the lower river system would be limited to 10 feet from 

full pool by the end of September (elevations 3550 and 2449, respectively) in all years 

except the lowest 20th percentile water supply (drought years) when the draft could be 

increased to 20 feet from full pool by the end of September. Basically, the proposed 

Montana SOR operation would alter summer flow operations at storage reservoirs in 

Montana from the current strategy identified in NOAA Fisheries’ 2000 Biological 

Opinion to a strategy that would shift elevated August flows and water releases more into 

September. Details can be found in the Council’s Mainstem Amendments and in the 

System Operations Request filed by the State of Montana (2004-MT-2). 

This ISAB report responds to a Council request (November 5, 2004) to examine the 

Council’s hypothesis that the proposed Montana operations “will significantly benefit 
4 

listed and non-listed resident fish in the reservoirs and in the portions of the rivers below 

the reservoirs without discernible effects on the survival of juvenile and adult 

anadromous fish [in the Columbia River mainstem] when compared to ordinary 

operations under the biological opinions" (p.26, Council 2003). In addition, in a July 19, 

2004 letter from Bob Lohn, NOAA Fisheries Regional Administrator, to Judi Danielson, 

Council Chair, NOAA Fisheries posed four sets of questions that they felt were important 

in weighing the benefits and risks associated with the proposed action: 

1. What is the “state of the science”? What information is available and applicable to 

this question? On which points is there consensus, and on which is there 

widespread disagreement? 

2. Which of the attributes that are currently unknown or in general dispute are most 

important to decision making about hydro operations? What kinds of further 

research would be needed to resolve them? 

3. Is there an experimental design practical and feasible for implementation in the 

next water year that would allow meaningful testing of the Council’s hypothesis? 

If so, how would the experiment be structured? 

4. In modeling projected effects of flow on listed and non-listed fish -- especially in 

instances where empirical measurements are not available or not practical or 

feasible -- what are the relative strengths and weaknesses of the available models? 

Is there credible scientific information that certain models (and modeling 

assumptions) are likely to be more reliable than others? 

These NOAA questions pertain largely to potential changes in anadromous fish migration 

(especially ESA-listed Snake River stocks) in the Lower Columbia River from McNary 

Dam to downstream of Bonneville Dam that result from the modified drafting strategy at 

Libby and Hungry Horse Dams, two of the primary water storage facilities in the Federal 

Columbia River Power System. They also pertain to effects on anadromous fish 

migrations in the mid-Columbia River from Chief Joseph Dam, which blocks further 

anadromous fish migration, to McNary Dam. (Both Hungry Horse and Libby dams are on 

rivers that feed into the upper Columbia River in Canada and pass through intervening 

rivers, lakes and reservoirs in the U.S. and Canada.) 

Early in 2004 the ISRP, including several members of the ISAB subcommittee, reviewed 

Montana Fish Wildlife and Park’s Proposal to Evaluate the Biological Effects of the 

Northwest Power and Conservation Council’s Mainstem Amendments on the Fisheries 

Upstream and Downstream of Hungry Horse and Libby Dams, Montana (ISRP 2004). 

Although the ISRP found that the proposal would provide useful information on upriver 

physical and biological effects on resident fish in the reservoirs and downstream from the 

dams resulting from the Council’s proposed changes in dam operations, the ISRP added 

qualifications intended to improve the modeling effort and to focus the study on key 

indicators of trends in biological responses. The ISRP emphasized that the proposed 

study was but part of a broader question. The overarching issue is the tradeoff between 
5 

the costs and benefits to resident fish and fisheries in Montana/upper Idaho and the costs 

and benefits to anadromous fish in the lower Columbia River. Although brief 

presentations were provided on resident fish issues in Montana, the November 9-10, 2004 

symposium was focused on providing the most current information on the lower river 

part of the equation. Presentations were made by leading experts in the field, with 

facilitation by Dr. Willis McConnaha. 

Presentations covered the following topics: 

1) the Council’s proposed operation, including upriver biological effects; 

2) translating changes in flow to changes in velocity and temperature; 

3) the status and presence of affected anadromous stocks; 

4) biological responses to river conditions and flow augmentation, including reservoirtype chinook life histories, delayed effects, effects on adult passage, and modeling; and 

5) research needs and experimental feasibility, focused on anadromous fish in the lower 

river. 

The symposium and presentations were well organized, thought provoking, and provided 

sufficient background information for the ISAB to expeditiously generate some findings 

that we hope will move forward the regional understanding of the issue. The section 

below addresses the NOAA questions and concludes with observations on the Council’s 

hypothesis. 

III. Responses to NOAA Fisheries’ Questions 

What is the “state of science”? 

The state of relevant science is in flux. Scientific understanding of flow survival 

relationships for juvenile and adult salmonids has progressed over two decades from 

simplifying assumptions, regression analyses of broadly averaged variables, and 

sweeping generalizations of results toward a synthesis of issue-specific, detailed data. 

This shift does not denigrate previous work; it simply reflects a growing sophistication of 

our understanding of the consequences of hydrosystem operations on fish survival. Many 

questions remain unanswered. New technologies and the data they provide are showing 

that the earlier assumptions and generalizations are inadequate or inappropriate for 

current needs. Change is being forced by the analytical demands of important issues 

ranging from development of Biological Opinions on hydrosystem operation to specific 

issues like the present Mainstem Amendments and the Montana System Operation 

Request. 

This report is not the place for an in-depth scientific review. A few highlights from the 

informative symposium of November 9-10, however, will illustrate important points. The 

highlights are presented following the order of the agenda. 
6 

Refinement of the issue 

The current issue (i.e., the Montana proposal) has been refined. It has progressed from a 

general upriver-downriver competition for water and its timing to more specific, datadriven issues. The main issue is one of reconciling potentially competing protections for 

biological productivity of ESA-listed bull trout, Kootenai River white sturgeon, and other 

important species in the Hungry Horse and Libby environs in summer against the needs 

of lower river ESA-listed anadromous migrants and other stocks for water in August and 

September. The issues include balancing social/economic as well as biological changes. 

Because resource managers must make decisions about the Montana proposal, it is 

increasingly apparent that a clear focus for the issue is necessary for science to provide 

useful answers. Although the probable effects of the Montana proposal in Montana and 

Idaho are fairly apparent, there are questions about the data and models used there that 

can stand refinement, as the Montana biologists have proposed and Council has 

recommended for funding. The questions for science are not just about what changes in 

flows would do in a general sense, but more specifically concern justifying the existing 

BiOp flow patterns versus the specific proposed changes in flows in August and 

September, how these flows affect the Hungry Horse and Libby environs both upstream 

and downstream, how the flows are routed downstream as waves and water particles 

(which are different), and the specific biological effects anticipated from these flow 

changes in downstream reaches. More focused questions can yield more focused 

scientific study (even of existing data) and better answers. 

Physical effects of water flow and velocity 

The water routing models seem inadequate to the task at hand, which is predicting 

changed flows for fish in the mid-Columbia and lower Columbia in August and 

September, either in formulation or application. The Council has made general estimates 

of volumes and travel times in the lower river (some of which are based on simulated 50-

year averages that may inappropriately represent current variability or future conditions) 

that are informative but insufficient. The 14-step water model (monthly except twicemonthly for April and August) does not adequately depict the details of a water budget 

that can be translated to components of “flow” that are relevant to biological resources 

downstream of Chief Joseph Dam—quantity, velocity, timing, temperature, etc. Squarewave temporal targets, in which flow or other criteria change instantaneously with 

calendar date, are environmentally artificial no matter how convenient they are 

operationally. It was unclear to our team of mostly biologists whether the water models 

are technologically incapable of realistically determining downstream flow patterns from 

alternative Hungry Horse and Libby operations within a specific year (probably because 

of the effects of intervening facilities and their operations in the US and Canada) or if the 

calculations just included too many simplifying assumptions. If intelligent estimates of 

biological effects are desired, the hydrological aspects must be better developed and 

made more specific to the questions at hand. 

It is dismaying that so little attention has been placed on measuring river and reservoir 

water velocities when so much of the traditional lore of flow-survival relationships in the 

mainstem depends on calculated differences in these velocities (travel times). Velocity 

measurements have largely, but not exclusively, been restricted to dam forebays and 
7 

tailraces where other issues were addressed (e.g., bypass attraction and bypass outfall 

location). Hydrodynamic models have been developed and calibrated with cross-sectional 

velocity measurements for a number of forebays and tailraces in the mid-Columbia and 

lower Columbia and Snake River dams. These models are sensitive to changes in flow 

and may offer some means for detecting small changes in near-dam flow effects. This 

modeling approach needs to be extended to entire reaches and reservoirs. 

Pertinent details of factors that affect velocities experienced by juveniles and adults (as 

well as resident fish) in reservoirs—reservoir morphology, daily and hourly loadfollowing, potential seiches (reservoir “sloshing”)—are blurred by simple calculations 

based on average river discharge and average reservoir volumes. These details likely 

contribute strongly to the large scatter in estimates of both travel time and survival 

information now available. Without a grounding in actual measurements that involve 

these factors, it is difficult to see how operational changes at Hungry Horse and Libby in 

August and September can be translated into functionally significant changes in salmon 

migrations, especially fall Chinook salmon migrations in the lower river, or in any other 

downstream species. 

Relating flow to temperature 

The well-understood relationships of salmonids to temperature are often misperceived 

and misapplied in Columbia River Basin practice. First, temperatures of the discharges 

from Hungry Horse and Libby dams do not easily translate to downriver temperatures 

because of long intervening distances containing rivers and reservoirs. Water 

temperatures could change downstream mainly as a function of the water particle 

movement, not the downstream-moving flow pulse, which is actually a wave 

phenomenon. As the well-developed field of thermal modeling recognizes, it is the 

balance between local heat fluxes, temperatures of inflows, and the volumes of water in 

local reaches, as well as flow rates that determine reach temperatures. In contrast, the 

discharges from Dworshak Reservoir, especially in summer, are relevant, because the 

short travel distance in the Clearwater River retains the cold discharge temperatures well 

into the Snake River through the lower Snake River reservoirs. “Flow Augmentation” in 

the Snake River is often inappropriately equated largely with Dworshak flow. The 

temperature of these cold-water releases, as well as their volume, is most likely the 

dominant operational factor affecting salmon survival. The misunderstanding of this 

relationship has led to scientifically untenable suggestions to further augment the Snake 

River flows to benefit fish using flows from Brownlee Reservoir that are warmer (and so 

would negate some of the survival benefit from Dworshak releases). Ironically, the 

Action Agencies proposal to purchase extra Snake River flow in summer 2004 as an 

offset for reducing spill could have added to mortality, not survival (based on thermal 

requirements of the fish). 

Although temperature models are now being developed for the Columbia River that 

advance efforts started there in the 1960s, these efforts lag behind models in other river 

systems. The EPA model is one-dimensional, even though it would be more relevant for 

salmon survival to have multi-dimensional models that better reflect rearing and 

migration habitats, especially in the low flows and high ambient temperatures of 
8 

reservoirs in July, August, and September. It is encouraging that multi-dimensional 

modeling is being done in Lower Granite Reservoir, where the vertical and horizontal 

patterns of cold water from the Clearwater River (Dworshak Dam) can be related to 

salmon survival and life histories such as the newly recognized reservoir-type life history 

pattern for fall Chinook. 

Status and presence of affected anadromous stocks 

It was heartening to see the realistic portrayal of the status and presence of various stocks 

of salmon and lamprey in the reaches of the lower river potentially affected by 

operational changes in Hungry Horse and Libby flows. Years of monitoring are yielding 

tangible benefits for understanding the timing and abundances of relevant native stocks. 

It was clear, however, that lamprey carry out most of their migration in the pertinent time 

period, yet have received little attention for evaluating effects. It would have been helpful 

to have heard some comment as well on the potential effects of the Montana System 

Operations Request on the extensive community of resident and non-native fishes in the 

lower river. 

Prevailing views of the life history of Snake River fall Chinook salmon have been shaken 

by credible data demonstrating that a portion of the underyearlings halt their summer 

migration, overwinter in reservoirs, resume migration to the ocean in the spring, and 

return as adults – the so-called “reservoir” life history. Although other populations of fall 

Chinook salmon are known to include a significant component that remains in the river 

over the winter and migrates the following spring as yearlings (Wydoski and Whitney 

2003), data have only recently been accumulated that demonstrate it to be a significant 

element in the life history of the Snake River stock. Furthermore, these holdover fish 

have been shown to experience a higher per capita rate of return as adults than the 

subyearling emigrants. 

This scientific revelation raises questions about the estimates of smolt survival previously 

made for Snake River fall Chinook salmon; smolt mortality may have been overestimated 

and aggregate ocean mortality probably underestimated. Because the percentage of 

holdovers is not known, the magnitudes of the various misestimates also are not known. 

This lack of information adds considerable uncertainty when assessing the implications 

of the Montana proposal, the current BiOp flows from Hungry Horse and Libby that are 

intended to aid August-migrating underyearlings, and the current transportation program 

for fall Chinook. Given the apparent higher SAR of the reservoir life history, it becomes 

important to determine what conditions encourage smolts to select this life history option, 

and whether or not the Montana System Operations Request could bear on this selection 

process. If the original justification for an August flow augmentation from Hungry Horse 

and Libby is confounded by a change to a different migration strategy for fall Chinook 

originating in the Lower Snake River (and the survival deficit long believed to exist is, in 

part, actually retention of survivors), there is a new management reality to be faced. 

Clearly then, there is an urgent need to further understand and quantify the “reservoir” 

life history pattern of Snake River fall Chinook. 
9 

Biological responses 

Flow-survival analyses 

Our understanding of the complexity of relationships among flow, travel time, and 

survival is being aided by increasingly sophisticated statistical treatments, more data from 

additional years coupled with additional sampling within years, and increasing 

recognition of the factors that cause data scatter. These analyses cry out for fewer 

simplifying assumptions and more environment-specific information, as noted above. 

Flow thresholds for fish travel time and survival, seen as abrupt changes in slopes in 

many data sets, point to different functional mechanisms operating over different flow 

ranges. That is, different fish responses probably occur with different environmental 

conditions. The influence of load following that dominates discharge predominantly at 

low river flows is one example. These differences in functional mechanisms can be 

further explored and likely offer alternative ways to adjust hydrosystem operations to 

benefit fish. The ISAB has previously recommended such research. Whereas the 

incremental effect of flow changes from the Montana proposal on smolt survival as 

predicted from continuous models has been given most of the attention, a more pertinent 

question may be whether any of these functional thresholds for effects on survival will be 

crossed. 

 Delayed effects 

Physiological research is demonstrating the plausibility of delayed effects from 

hydrosystem passage. Whether the information is applied to issues of transportation, flow 

in general, or the specific Montana proposal, it is now clear that migrating juveniles go 

through physiological changes beyond just smoltification. Energy reserves stored in 

lipids and proteins change through migration. Different migration timing, temperatures, 

and the metabolic costs of feeding and predator avoidance affect these reserves and likely 

affect subsequent performance and survival in the river and estuary. Physiological 

indicators of nutrition and stress can help define energetically deficient or stressful 

reaches of the hydrosystem, leading to more specifically beneficial measures. For 

example, a correctable migration delay at one dam may cause greater physiological 

detriment than the incremental change in river travel times resulting from the Montana 

proposal. 

 Adults 

Recent telemetry data indicate that upstream-migrating adults respond differently to 

increased flow than juveniles in that adults’ migration is slower at higher river velocities, 

perhaps to their detriment. The Montana proposal might shift some flows to later in the 

season when more adult fall Chinook are in the river. New data show that warm 

temperature in summer is an important detriment for adult migrations, i.e., slower 

migration speeds at higher temperatures, delays while fish seek cool refuges, and the 

rapid use of energy reserves needed for the remainder of migration and the spawning 

process. Incremental benefits or costs to juveniles need to be evaluated in the context of 

generally opposite effects on adults, which are individually more valuable to the 

population than individual juveniles. The incremental effect on fall Chinook adults of the 

Montana proposal is unclear because of unknown details of the effect on temperatures. 
10 

 Models 

The degree to which science is in a state of flux was demonstrated by work with two 

models, CRiSP and SIMPAS, both of which have been, and might be used further in the 

future, in attempts to assess the downstream effects of the Montana proposal. CRiSP is 

being modified to include a novel, but unproven, predator-prey hypothesis that smolt 

survival depends on travel time and distance. The theoretical construct, however, requires 

testing and validation. CRiSP is also evolving in other ways (to accommodate new data) 

that warrant scrutiny before the model is applied uncritically. The model SIMPAS, which 

was used to formulate BiOp flow requirements and could be used to evaluate the 

Montana proposal, appears flawed because it subsumes effects of temperature (and all 

other variables) in ”flow.” When the effect of temperature goes from being a net benefit 

to being a detriment above about 20 C, it is scientifically untenable to assume that more 

warm flow is advantageous. SIMPAS may be inadequate not only for evaluating effects 

of the Montana proposal, but also for its fundamental use in determining BiOp flows. 

Climate change 

The regional fixation on flow-survival relationships generally ignores the broader issues 

of temperature and precipitation change from global warming and the effects of human 

population increase on water demand that could significantly impact water quality and 

quantity. These points were brought home by a National Research Council review of 

water withdrawals. 

Cumulative risks 

Notwithstanding those broad effects, the NRC Panel warned of the cumulative risks of 

many relatively minor changes with individually small effects. This is clearly the 

potential of the Montana proposal—small changes and small effects in the lower river 

that might accumulate with other influences (like more water withdrawals) to yield 

significant, long-term changes. The incremental effects of the Montana System 

Operations Request on the mid-Columbia and lower Columbia, however, are likely to be 

beneficial at certain times as well as detrimental at others because of the shifting of flows 

between months, rather than any consistently one-sided net change. 

 

Which attributes are most critical? 

Better definition of the physical changes in flow and its corollary attributes at various 

points in the hydrosystem from Hungry Horse and Libby to Chief Joseph Dam and from 

there to the estuary is essential to be able to make reasonable estimates of the likely 

biological effects of the Montana proposal. Stable operations through the Canadian 

portion of the system are apparently not guaranteed. Daily average flows are not adequate 

to describe flow changes throughout the hydropower system relevant for fish because of 

hourly load following, especially at low flows of August and September. Experience in 

the Hanford Reach has demonstrated detrimental effects on fall Chinook salmon from 

hourly fluctuations in flow. Gross approximations of flow changes provided by the water 

models cannot suffice when biologists are asked to estimate fine-scale effects. 
11 

Among the biological questions, the life-history status of the ESA-listed Snake River fall 

Chinook requires the highest priority attention. This is the stock of primary concern in 

passage through the lower Snake River and the lower Columbia River. Our current 

understanding is limited because of the newly discovered importance of holdover fish 

(the “reservoir” life history that migrates to sea in spring) and the high return rate of 

adults from these fish that do not emigrate in the relevant time frame of August and 

September. Where they are retained in the Snake and Columbia rivers in fall and winter is 

central to the issue. If they remain in the Snake through the normal August-September 

migration period, they are outside the influence of proposed flow changes from Hungry 

Horse and Libby; if they migrate into the lower Columbia in summer before holding, then 

they could be affected by the Montana proposal. A portion of the fish does remain in the 

Snake River to overwinter. Connor’s research includes samples of holdover juveniles 

caught in beach seines above Lower Granite Dam and others caught at the PIT tag 

detector at Little Goose Dam. Most likely, a variable portion of the fish remains behind in 

each reservoir on the way downstream. Speculations about retention location in the 

period when PIT-tag operations stop in the fall and resume in the spring need to be tested 

with more complete annual (winter) sampling. 

Using present estimates of both hydrology and biology, we conclude that the effects of 

the Mainstem Amendment and the Montana System Operations Request on salmonids 

downstream in the Columbia River are likely to be small. They may be significant only as 

they contribute in a small incremental way to accumulating effects of many other small 

changes, negative and positive, such as water withdrawals or other hydrosystem 

operational decisions. Science cannot currently define whether the incremental effect of 

the proposal is significant in this broader picture, but efforts in this direction seem 

warranted. 

Is there a practical and feasible experimental design to test the 

Council’s hypothesis? 

Although there is no experimental design that would immediately compensate for the 

lack of detailed flow information and our lack of understanding of the most important 

stock’s life history, some directed experiments could provide that information over time. 

There are improvements in the analysis of existing and accumulating data on flow and 

survival of many stocks that can perhaps be used to further identify small effects when 

they occur within the context of historical and existing flows. 

Finding a practical and feasible experimental design is difficult because the effects of the 

Montana proposal are likely to be small, both in terms of water amounts delivered and the 

resulting effects, if any, on survival. Considering the scientific uncertainties discussed 

above, any attempt to identify with precision what a “small” change in survival means is 

nearly futile. The range of estimates now available, however, suggests a numerically low 

change in overall salmon survival, with uncertainty over direction. 
12 

For example, in late 2002, the Council staff compared estimates of fish survival derived 

from SIMPAS (version 9) and CRiSP (Council memoranda dated November 6 and 

December 2 from Bruce Suzumoto to Council members). For SIMPAS, 11 populations of 

listed and unlisted stocks were examined; six for CRiSP; High, medium, and low flow 

regimes were evaluated. Using SIMPAS, the estimated percentage change in survival for 

Montana operations compared to the BiOp flows were 0, 0.3, 0.2 (high summer flow), 

-0.7, 0.5, 0 (medium summer flow), and 0, 0.2, and -0.5 (low summer flow) for Snake 

River fall Chinook, Lower Columbia Chinook, and Hanford Reach fall Chinook, 

respectively; all less than 1%. The most comparable results from CRiSP showed in-river 

survivals of 0.035 and 0.021 (high flow), -0.068 and -0.050 (medium flow), and -0.083 

and -0.049 (low flow) for Hanford Reach fall Chinook and Snake River subyearling 

Chinook, respectively; again, all estimates substantially less than 1%. Furthermore, 

“small” in this analysis ranges from an estimated loss of 7 fish in 1,000 to a gain of 5 fish 

in 1,000 using SIMPAS, whereas using CRiSP, there is an estimated loss of about 8 fish 

in 10,000 (less than 1 in 1,000) to a gain of 3.5 fish in 10,000 (less than 1 in 1,000). 

Although we are reluctant to place high confidence in either of these models, the 

estimated changes in survival are quantitatively low and of inconsistent sign. 

As another example, several graphs were shown at the workshop relating flow to salmon 

survival in the Columbia River, which can be used to estimate the anticipated survival 

change due to the Montana proposal. Council staff estimated the 50-year-average change 

in flow at McNary Dam to be diminished by 8.3 kcfs in July and 5.6 kcfs in August, but 

increased by 0.9 kcfs in September. The largest of these estimates (-8.3 kcfs) would yield 

an estimated change in survival from McNary to John Day of 0.01 percent (1 fish in 

10,000) using graphical analysis of the plot shown by Steve Smith of NOAA Fisheries. 

Using the regression equation of underyearling survival from Rock Island Dam to 

McNary provided by the Fish Passage Center (Berggren and Filardo), and the Council’s 

estimated July McNary flows, the change in survival for a decline of 8.3 kcfs would be 

0.0098 percent (less than 1 fish in 10,000). Use of these regressions assumes that factors 

operate similarly in all river reaches, which is probably not entirely valid. Again, the 

estimated change in survival is tiny and can be obscured by other factors. The clear 

caveat, however, is that the 50-year average flow changes due to the Montana proposal 

may not adequately reflect flow extremes caused by exceptionally wet or dry years, 

which could be important for population survival. 

It could be argued that the wide variability among data points used to develop the Smith 

and Fish Passage Center flow-survival curves indicates in each case that the percentage 

changes in survival from the Montana proposal would be statistically undetectable (i.e., 

the data would not meet the scientific standard for rejection of no effect). However, 

because the comparative analysis in each case uses the same data set with the same 

variability, the predicted effects can be quantified legitimately. We conclude that the 

effects would be small. 

It was pointed out in the symposium that experimental designs developed by federal 

researchers and others have been stymied by lack of cooperation by other agencies. 

Permission has not been granted for use of fish, taking of scales, tagging, and other data 
13 

collection. If lack of cooperation is indeed a factor, then the best experimental designs 

will require more effective interagency cooperation. 

The “easiest” experiment may already have been initiated (and is still underway), with 

detailed flow records and passage and survival data on juveniles and adults from PITtagged individuals awaiting collection and further analysis. This conclusion presumes the 

existence of appropriately detailed flow and other environmental records, including yeararound detection of smolts passing downstream. 

What are the strengths and weaknesses of available models? 

No present model is capable of an accurate, precise analysis of the effects of the Montana 

proposal. The two process models we examined, CRiSP and SIMPAS, contain unrealistic 

or untested assumptions. The models include an a priori effect of flow on survival based 

on simplified conditions, which to some extent predetermines the result. Nonetheless, 

both models suggest that the effect of the Montana System Operations Request will be 

small. The regression models we saw often contain so much data scatter that model 

fitting is itself uncertain. Because the regression models use the same data with the same 

scatter, however, comparisons can be made among flow conditions. The results to date 

from the Fish Passage Center and NOAA Fisheries regression models suggest the 

Montana System Operations Request would result only in small changes. 

IV. Overall Council Hypothesis 

The Council hypothesized in its Mainstem Amendments that certain modifications to 

current operations at Hungry Horse and Libby dams would significantly benefit resident 

fish without discernable adverse effects on the survival of juvenile and adult anadromous 

fish in the lower Columbia River. We conclude the following: 

1. Resident fish and fisheries influenced locally by the Hungry Horse and Libby 

water-release situations may receive important biological benefits from the flow 

modifications, assuming they are carried out as planned. It is almost certain that 

the general productivity in the Montana reservoirs and in the immediate 

downstream reaches will benefit considerably. What are uncertain are the effects 

on the species of greatest concern (sturgeon and bull trout) when the increased 

productivity propagates through the community of predators, prey, and 

competitors. If the effects on these species are very large, they may be detected 

by future monitoring, but attribution of cause may still be confounded unless the 

experimental design alternates to provide years when the Montana System 

Operations Request is implemented and years when it is not. 

2. Effects of the Council’s Mainstem Amendment and resulting Montana operations 

proposal on the survival of juvenile and adult anadromous fish in the Columbia 

River below Chief Joseph Dam will probably be very small. The available data 

and analytical tools do not allow us to say whether the net effect will be positive 
14 

or negative for fish present in the river in the August-September period. Other 

time periods were not addressed in the symposium. Based on the best information 

now available, the Council was likely justified in its hypothesis that the flow 

modifications at Hungry Horse and Libby dams outlined in its Mainstem 

Amendments would lead to effects on survival of juvenile salmonids in the 

mainstem Columbia River that will be too small to measure practically against 

both the measurement error itself and real background variation due to other 

causes. 

3. Recognition of the holdover or “reservoir” life history pattern of one of the 

foremost stocks of concern, the ESA-listed Snake River fall Chinook, complicates 

assessment of this stock in relation to the flow proposal. Because further research 

on this life history pattern is so critically needed, it is important to implement 

monitoring systems that will make it possible to quantify the magnitude of 

holdover behavior and how that affects estimates of smolt survival and SAR, as 

well as to reveal what factors affect holdover behavior and overwintering survival 

in freshwater. 

Literature Cited 

Independent Scientific Advisory Board (ISAB). 1997. 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 

Columbia. (See especially Appendix 5 – Effects of drawdown on aquatic systems in 

reservoirs.) (ISAB 1997-3), Northwest Power Planning Council, Portland, OR, March 

4, 1997. www.nwcouncil.org/library/isab/isab97-3.htm 

Independent Scientific Advisory Board (ISAB). 2001. Review of Lower Snake River 

flow augmentation studies. (ISAB 2001-5), Northwest Power Planning Council, 

Portland, OR. (Available on the Council’s website.) 

Independent Scientific Advisory Board (ISAB). 2002. 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. 

(Available on the Council’s website.) 

Independent Scientific Advisory Board (ISAB). 2003. Review of flow augmentation: 

update and clarification. (ISAB 2003-1), Northwest Power Planning Council, 

Portland, OR. (Available on the Council’s website.) 

Independent Scientific Group 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 and Conservation Council.) 
15 

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 website.) 

Independent Scientific Review Panel (ISRP). 2004. Memo: Second Review of Proposal 

to Evaluate the Biological Effects of the Northwest Power and Conservation 

Council’s Mainstem Amendments on the Fisheries Upstream and Downstream of 

Hungry Horse and Libby Dams, Montana (ISRP 2004-6 Final Review; see also ISRP 

2004-3 Preliminary Review). Northwest Power and Conservation Council. (Available 

on the Council’s website.) 

Northwest Power and Conservation Council. 2003 Mainstem Amendments to the 

Columbia River Basin Fish and Wildlife Program. April 2003. Council Document 

2003-11 (Available on the Council’s website.) 

Northwest Power and Conservation Council. 2004. Anadromous Fish Issues Regarding 

the Proposed Council Summer Flow Initiative: A Briefing Paper. October 21, 2004. 

(Available through the Council.) 

Wydoski, R. S., and R. R. Whitney. 2003. Inland Fishes of Washington. University of 

Washington Press and American Fisheries Society, Seattle, Washington and 

Bethesda, Maryland. 

Literature Used for this Review but not Cited in the Text 

Anderson, J., and C. Van Holmes. In review. Effects of flow and other covariates on 

juvenile salmon and steelhead survival through the Columbia and Snake rivers. 

CJFAS. 

Anderson, J., E Gurarie Richard W. Zabel (2005) Mean free-path length theory of 

predator-prey interactions: application to juvenile salmon migration. Ecological 

Modeling. 

Brown, R.S., D.R. Geist, and M.M. Mesa. 2002. The Use of Electromyogram (EMG) 

Telemetry to Assess Swimming Activity and Energy Use of Adult Spring Chinook 

Salmon Migrating through the Tailraces, Fishways, and Forebays of Bonneville Dam, 

2000 and 2001. PNNL 14080. Submitted to the US Army Corps of Engineers, 

Portland District. 

https://www.nwp.usace.army.mil/pm/e/reports/afep/bon/adult_studies/TheUseofElect

romyogram(EMG)TelemetrytoAssessSwimmingActivityandEnergyUseofAdultSpring

Chinook.pdf 

Brown, R.S., and D.R. Geist. 2002. Determination of Swimming Speeds and Energetic 

Demands of Upriver Migrating Fall Chinook Salmon (Oncorhynchus tshawytscha) in 

the Klickitat River, Washington. PNNL 13975. Submitted to Bonneville Power 
16 

Administration, Portland, Oregon. 

http://www.efw.bpa.gov/Environment/EW/EWP/DOCS/REPORTS/UPSTRM/U0000

0652-9.pdf 

 

Congleton, J., T. Wagner, J. Evavold, D. Fryer, and B. Sun. 2002. Evaluation of 

physiological changes in migrating juvenile salmonids and effects on performance 

and survival. Annual report to USACE. 

Connor, W., H. Burge, and D. Bennett. 1998. Detection of PIT-tagged subyearling 

chinook salmon at a Snake River dam: Implications for summer flow augmentation. 

NAJFM 18: 530-536. 

FPC. 2003. Fish Passage Center Annual Report for 2003. 456 pp. 

Geist, D.R., R.S. Brown, M.G. Mesa, S.P. VanderKooi, V. Cullinan, and C.A. 

McKinstry. 2003. The relationship of metabolic rate, electromyogram activity of red 

and white muscle, and swimming performance of adult spring chinook salmon from 

the Columbia River. Journal of Fish Biology 63:970-989. 

Geist, D.R., C.S. Abernethy, S.L. Blanton, and V. Cullinan. 2000. The use of 

electromyogram telemetry to estimate energy expenditure of adult fall chinook 

salmon. Transactions of the American Fisheries Society 129(1) 126-135. 

Giorgi, A., M. Miller, and J. Stevenson. 2002. Mainstem passage strategies, in the 

Columbia River System: Transportation, Spill, and Flow Augmentation. Prepared for 

the Northwest power Planning Council. Portland, OR. 

Giorgi, A. E., T. W. Hillman, J. R. Stevenson, S. G. Hays, and C. M. Peven. 1997. 

Factors that influence the downstream migration rate of juvenile salmon and 

steelhead through the hydroelectric system in the mid-Columbia River Basin. 

NAJFM. 17:268-282. 

Mesa, M.G., and C.D. Magie. 2004. Evaluation of energy expenditure in adult spring 

Chinook salmon migrating upstream in the Columbia River basin: an assessment 

based on sequential proximate analysis. 

https://www.nwp.usace.army.mil/pm/e/reports/afep/system/prox%20annual%20report

%20final%209-27-04.pdf 

Muir, W. D., S. G. Smith, E. E. Hockersmith, M. B. Eppard, W. P. Connor, T. Anderson, 

and B. D. Arnsberg. 1999. Fall chinook salmon survival and supplementation 

studies in the Snake River and lower Snake River reservoirs, 1997. Annual report 

(DOE/BP-10891-8) 

NRC. 2004. Managing the Columbia River, Instream Flows, Water Withdrawals, and 

Salmon Survival. National Research Council. The National Academies Press, 

Washington D.C. 246 pages. 
17 

SFTAFM. 2003. State, Federal, and Tribal Anadromous Fish Managers comments on the 

Northwest Power Planning Council Draft Mainstem Amendments as they Relate to 

Flow/Survival Relationships for Salmon and Steelhead. 

Williams, J., and eight other authors. 2004. Effects of the Federal Columbia River Power 

System on salmon populations. NOAA Technical Memorandum (October Draft). 

 

 

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