Mainstem Passage Strategies In the Columbia River System:

Transportation, Spill, and Flow Augmentation

Prepared by:

Albert Giorgi

Mark Miller

John Stevenson

Prepared for:

Northwest Power Planning Council

851 SW 6th Ave., Suite 1100

Portland, OR 97204

January 31, 2002
Transportation, Spill, and Flow Augmentation Page ii Northwest Power Planning Council

BioAnalysts, Inc. January 2002

Table of Contents

LIST OF TABLES .........................................................................................................................................................................iii

LIST OF FIGURES ........................................................................................................................................................................iv

LIST OF ABBREVIATIONS ...................................................................................................................................................... vi

EXECUTIVE SUMMARY ......................................................................................................................................................... vii

INTRODUCTION............................................................................................................................................................................1

1.0 TRANSPORTATION......................................................................................................................................................1

1.1 Survival Evaluation..................................................................................................................................................4

1.2 Recent Estimates.......................................................................................................................................................7

1.2.1 Transport Inriver Ratio (TIR).........................................................................................................................9

1.2.2 Smolt-to-Adult Return Rate (SAR).............................................................................................................14

1.2.3 TIRs and Flow.................................................................................................................................................16

1.2.4 Differential Delayed Effects (D-Estimates)...............................................................................................17

1.2.5 Statistical Inferences......................................................................................................................................20

1.2.6 Mechanisms Contributing to Delayed Differential Effects For Transport ...........................................21

1.3 Summary ..................................................................................................................................................................24

1.4 Critical Uncertainties and Research Opportunities...........................................................................................26

1.5 Literature Cited.......................................................................................................................................................28

2.0 SPILL ...............................................................................................................................................................................30

2.1 Spill-Related Smolt Survival................................................................................................................................31

2.1.1 Smolt Survival Through Spillways.............................................................................................................31

2.1.2 Estimating Survival of the Smolt Population as Related to Spill Conditions:.....................................33

2.1.3 Spillway Passage Efficiency.........................................................................................................................34

2.2 Spillway Survival Estimates.................................................................................................................................35

2.3 Population Level Responses to Spill Conditions..............................................................................................40

2.3.1 Empirical Based Observations.....................................................................................................................40

2.3.2 Model Analyses ..............................................................................................................................................47

2.4 Incidental Effects of Spill......................................................................................................................................49

2.4.1 Total Dissolved Gas.......................................................................................................................................49

2.4.2 Adult Passage Impacts...................................................................................................................................52

2.5 Summary ..................................................................................................................................................................53

2.6 Critical Uncertainties and Research Opportunities...........................................................................................55

2.7 Literature Cited.......................................................................................................................................................56

3.0 FLOW AUGMENTATION..........................................................................................................................................60

3.1 Premise 1–Increasing water velocity in reservoirs increases smolt migration speed, which results in 

improved survival. ...............................................................................................................................................................60

3.1.1 Flow and Migration Speed............................................................................................................................62

3.1.2 Flow and Smolt Survival...............................................................................................................................65

3.1.3 Recent Estimates of Smolt Survival............................................................................................................67

3.2 Premise 2–Lowering water temperature in the summer improves migratory and rearing conditions for 

juvenile and adult salmonids, ultimately improving survival. .....................................................................................71

3.3 Flow Augmentation Evaluations..........................................................................................................................72

3.5 Summary ..................................................................................................................................................................79

3.6 Critical Uncertainties and Research Opportunities...........................................................................................81

3.7 Literature Cited.......................................................................................................................................................83

4.0 APPENDICES ................................................................................................................................................................87
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LIST OF TABLES

Table 1.1Proportion of juvenile Snake River spring/summer and fall chinook salmon and 

steelhead outmigrants collected from LGR, LGO, and LMO transported below BON during 

the period 1994-1999 (Data from 2000 NMFS BO). ..............................................................4

Table 1.2Percent smolt-to-adult returns (SAR) for transported (TR) and inriver (IR) migrant 

wild and hatchery chinook salmon and steelhead smolts PIT tagged and released at or 

upstream from Lower Granite Dam (LGR) and detected at LGR as adult (from Sandford 

and Smith, In press). Non-detected PIT tagged inriver fish are those smolts that were not 

detected at any collection facility downstream from LGR. We apply the term TIR to the 

ratios reported by the authors. Confidence intervals (95% CI) are for TIR estimates. 

Numbers of returning adults (n) for SAR estimates are in parenthesis. ..................................9

Table 1.3Smolt-to-adult returns (SAR) (LGR-LGR) estimates for PIT tagged hatchery and 

wild spring/summer chinook salmon transported and in-river migrants from the Snake River 

(from Bouwes et. al 2001). Hatchery fish were PIT tagged and released at spring/summer 

fish hatcheries upstream from Lower Granite Dam (LGR). The full complement of adult 

returns has not been realized for the 1999 SAR estimates. Tlgr =smolts transported at LGR, 

To=smolts transported from all Snake River dams upon first detection, Co=smolts never 

detected, C1=smolts detected at one or more dams. Numbers of returning adults (n) for 

SAR estimates are in parenthesis...........................................................................................12

Table 1.4D estimates for wild Snake River spring/summer chinook salmon and steelhead as 

reported in the 2000 BO by NMFS (2000a). SART is the estimated SAR for transported 

fish. SARI is the estimated SAR for inriver (control) fish. Total adult returns are provided 

in parenthesis for all estimated SARs. Survival is the estimated survival from Lower 

Granite Dam to Bonneville Dam for inriver fish (per-project and per-kilometer 

extrapolation). D is estimated for each year (along with 95% confidence intervals), and 

geometric mean of the yearly D is provided. (1997 adult returns incomplete at time of 

calculation). ...........................................................................................................................18

Table 1.5The ratios of SARs for different transport and in-river hatchery groups. Tlgr refers to 

the fish transported from LGR, To refers to smolts transported at all projects upon first 

detection (weighted by the proportion actually transported), Co refers to smolts that 

migrated in-river and never detected above MCN dam. All SARs are the LGR-LGR SARs 

except for the D-value. The D-value is the ratio of the transport BON-LGR SAR to the 

control (in-river) BON-LGR SAR (from Bouwes et al. 2001)..............................................19

Table 2.1Survival rates of juvenile salmonids at low, medium, and high spill rates. Estimates 

of survival for Wanapum, Rock Island and Little Goose dams represent direct effects. 

Survival estimates at The Dalles represent total effects. .......................................................40

Table 2.2 Spill analysis with associated survival estimates and standard errors (in parentheses) 

provided by spill blocks pre-spill, spill, and post-spill (from Zabel et al. in press). .............44

Table 2.3 Survival Estimates and collection efficiency estimates (parentheses) at the John Day 

project (FPC 2001). ...............................................................................................................45
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LIST OF FIGURES

Figure 1.1Location of collection-transport facilities (T), screened-bypass systems (B), and 

surface flow bypass systems (SB) on the Columbia and Snake rivers. Transport-collection 

facilities can be operated in bypass mode. Transport facilities can also be operated in a 

bypass mode. Surface bypass systems are to be installed at Rocky Reach1 and Bonneville2

dams in 2002 and functional in 2003.......................................................................................2

Figure 1.2Transport inriver ratio (TIR) for hatchery and wild chinook salmon smolts PIT 

tagged and released at or above Lower Granite Dam. Only TIR estimates with bounded 

confidence intervals are plotted. ............................................................................................10

Figure 1.3Transport inriver ratios (TIR’s) for chinook smolts transported from Lower Granite 

Dam (Tlgr/Co) and chinook transported at all projects upon first detection (To/Co). The 

geometric mean (GM) for the three years is indicated. .........................................................11

Figure 1.4Transport inriver ratio (TIR) for hatchery and wild steelhead smolts PIT tagged and 

released at or above Lower Granite Dam. .............................................................................13

Figure 1.5Comparison of wild chinook salmon SARs for transported and inriver controls 

before 1997 and after 1997. ...................................................................................................15

Figure 1.6LGR-LGR SARs for different transport and inriver groups. Tlgr refers to the fish 

transported from LGR, To refers to smolts transported at all projects upon first detection, 

and Co refers to smolts that migrated inriver and were never detected upstream from 

McNary Dam (MCN). Geometric mean (GM) calculated for the three years......................15

Figure 2.1. Spill survival estimates reflecting total effects, using PIT tags in a paired-release 

design. Survival estimates represent the average across years and species for a given spill 

condition (i.e., deflector vs. unmodified spillbays and varying levels of spill). Averages 

were calculated using estimates reported in Muir et al. (2001a) and Ploskey et al. (2001). .37

Figure 2.2 Mean survival (across years and species) that reflects only direct effects (balloon 

tag-based estimates) through spillbays with and without flow deflectors at Bonneville, Little 

Goose, and Wanapum dams. .................................................................................................38

Figure 2.3 Survival rates of juvenile salmonids at low, medium, and high spill rates. Estimates 

of survival for Wanapum, Rock Island and Little Goose dams represent direct effects as 

estimated using balloon tags (Appendix B). Survival estimates at The Dalles Dam represent 

total effects obtained with PIT tags (from Ploskey et al. (2001); Appendix B). ...................39

Figure 2.4Estimated survival by stock for the pre-spill, spill and post-spill periods for fish 

migrating through McNary Dam and John Day reach. The line of above each bar represents 

one standard error (from Zabel et al. in press).......................................................................43

Figure 2.5 Total dissolved gas levels in the tailrace of Priest Rapids, Wanapum, Rock Island, 

Rocky Reach and Wells dams, April 1 – September 30, 1999. The solid horizontal line 

represents NMFS 2000 BO TDG tailrace standard. ..............................................................50
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Figure 2.6 Total dissolved gas levels in the tailrace of Priest Rapids, Wanapum, Rock Island, 

Rocky Reach and Wells dams, April 1 – September 30, 2000. The solid horizontal line 

represents NMFS 2000 BO TDG tailrace standard. ..............................................................51

Figure 3.1Flow augmentation provided to the Columbia Basin from the Upper Columbia and 

Snake River areas. .................................................................................................................61

Figure 3.2 Survival estimates for juvenile spring and summer chinook salmon, Oncorhynchus 

tshawytscha, migration through the upper dam (Little Goose Dam, 1973-74; Lower Granite 

Dam, 1975-79) on the lower Snake River to either John Day Dam (1976-79) or The Dalles 

Dam (1973-75) compared with the average river flow at Ice Harbor Dam during the period

(± 7 days) of peak migration for the years 1973 through 1979 (from Williams and Matthews 

1995)......................................................................................................................................66

Figure 3.3Per-project survival versus river flow for Snake River spring-summer chinook 

salmon (from Zabel et al. In press)........................................................................................68

Figure 3.4 Relationship among median travel time (days) and estimated survival from Lower 

Granite Dam to McNary Dam, and flow exposure index (kcfs measured at Lower 

Monumental Dam, yearling chinook salmon, 1995-1998 (from NMFS 2000b)...................69

Figure 3.5Relationship among median travel time (days) and estimated survival from Lower 

Granite Dam to McNary Dam, and flow exposure index (kcfs) measured at Lower 

Monumental Dam, steelhead, 1995-1998. (from NMFS 2000b)...........................................69

Figure 3.6 Estimated per-project survival (i.e., per dam/reservoir combination) with standard 

errors for yearling chinook salmon and steelhead from 1993 through 2000. Number above 

bar is the number of projects over which survival was estimated (from Zabel et al. In press).

...............................................................................................................................................70

Figure 3.7  Estimated increase in water velocity (as a percentage of total velocity) that is 

attributable to flow augmentation volumes as estimated by HDR during the springs (10 

April – 20 June) and summers (21 June – 31 August) 1991-1995 (from Giorgi and Schlecte 

1997)......................................................................................................................................76

Figure 3.8  Percent decrease (i.e., benefit attributable to flow augmentation) in estimated smolt 

travel times (average of the median travel times for each of the three release dates) for 

yearling chinook using base flows calculated by HDR. The asterisk in 1993 indicates that 

the CRiSP model predicted no change in travel time associated with flow augmentation 

(from Giorgi and Schlecte 1997). ..........................................................................................76

Figure 3.9 Average increase in survival attributable to flow augmentation for yearling 

chinook, steelhead, and sub-yearling chinook from release point at the head of Lower 

Granite Pool (a) through Lower Granite Dam and (b) to Ice Harbor Dam. Survival 

estimates were derived using the CRiSP model under three release scenarios (i.e., Early, 

Mid and Late) (from Giorgi and Schlecte 1997). ..................................................................77
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LIST OF ABBREVIATIONS

BO Biological Opinion

BON Bonneville Dam

BPA Bonneville Power Administration

CBFWA Columbia Basin Fish and Wildlife Authority

COE Army Corps of Engineers

COLTEMP COE temperature model

CRiSP Columbia River Smolt Passage Model

CWT Coded wire tag

D Differential Delayed Effects associated with transporting smolts

ESA Endangered Species Act

ESU Evolutionary Significant Unit

F Fahrenheit

FA Flow Augmentation

FCRPS Federal Columbia River Power System

FGE Fish Guidance Efficiency

FPC Fish Passage Center

GBT Gas Bubble Trauma

HEC-2 Hydraulic Model

IH Ice Harbor Dam

ISG Independent Science Group

JD John Day Dam

kcfs Kilo-cubic feet per second

LGO Little Goose Dam

LGR Lower Granite Dam

LMO Lower Monumental Dam

Maf Million acre feet

MCN McNary Dam

NMFS National Marine Fisheries Service

NPPC Northwest Power Planning Council

PATH Plan for Analyzing and Testing Hypotheses

PIT tag Passive Integrated Transponder Tag

PRD Priest Rapids Dam

RIS Rock Island Dam

RRH Rocky Reach Dam

SAR Smolt-to-Adult Return Rate (%)

SIMPAS NMFS Simulated Passage Model

SOR System Operation Review

TDA The Dalles Dam

TDG Total Dissolved Gas

TIR Transport Inriver Ratio

Vc Inriver Migrant Survival

WAN Wanapum Dam

WE Wells Dam
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EXECUTIVE SUMMARY

The National Marine Fisheries Service 2000 Biological Opinion (BO) for the Federal Columbia 

River Power System (FCRPS) prescribes guidelines for smolt transportation, spill and flow 

augmentation to improve survival of salmonid stocks listed under the ESA (Appendix A). With 

respect to these strategies the NPPC is concerned about the following issues:

1. What does the scientific literature inform us regarding the benefits, shortcomings, or risks 

associated with each passage strategy, and as compared to other passage options?

2. Which aspects of the scientific information are in dispute?

3. What are the critical uncertainties attending each strategy?

4. What is being, or could be done to reduce uncertainty and disputes?

In terms of scope, the NPPC seeks information for both ESA-listed and unlisted salmonid 

populations across a range of water years. The Council seeks clear, concise and succinct 

treatment of these issues. Our approach is to review key research and analyses that have 

appeared in the literature, then distill out the key findings and synthesize the results. The focus 

is on evaluations conducted under contemporary river operations, which were initiated in the 

early 1990s and formalized as guidelines in the 1995 and 2000 Federal Columbia River Power 

System Biological Opinions. Additionally, we identify key uncertainties and gaps in the 

information base, and identify research that is in place or planned to fill those gaps.

Smolt Transportation

Using general, annual indices of performance, both NMFS and CBFWA analyses showed that 

the majority of the time, fish transported from Lower Granite and Little Goose dams produced 

TIRs higher than or equal to corresponding inriver control groups. Bouwes et al. (2001) 

concluded modest transportation benefits were evident for hatchery chinook, and slight to 

negligible benefits for wild fish. Sandford and Smith (in press) state that, “once a juvenile fish is 

entrained in a bypass system at a “collector dam”, transporting the fish maximizes the probability 

of its eventual return as an adult.” Based on assessments by those two investigations, it appears 

that there is a survival advantage associated with transporting Snake River hatchery 

spring/summer chinook and steelhead, particularly from the upper two dams, Lower Granite and 

Little Goose dams. However, the rationale for transporting smolts from Lower Monumental and 

McNary dams is less clear. The benefits of transporting Snake River hatchery fish from those 

dams are equivocal.

In some years, small sample sizes have resulted in poor or undefined precision for key estimates. 

This can limit the ability to make statistically defensible conclusions. Authors examining recent 

estimates do not confidently state that transported fish survive at significantly higher rates than 

inriver counterparts. Neither Sandford and Smith (in press), nor Bouwes et al. (2001) explicitly 

tested key hypotheses such as; D > Vc, or TIR > 1.0. Presumably future analyses by these two 

research groups will do so. In recent times the resurgence in adult returns offers improved 

precision and opportunities for meaningful statistical tests
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Whether or not wild fish respond favorably to transportation is difficult to ascertain at this 

juncture. Even though the limited numbers` of evaluations indicate higher return rates for 

transported smolts, the estimates are based on such small sample sizes that the precision for wild 

fish is particularly poor. Thus, reliance on the point estimate as a representative value is 

questionable.

Survival from smolt to returning adult (SAR) for hatchery and wild spring summer chinook has 

increased substantially since 1993, and has been increasing steadily from 1997-1999, reaching 

SAR levels in 1999 that approach and in some cases exceed the 2% minimum recovery threshold 

for wild stocks as identified in PATH (Figures 1.5 and 1.6). This suggests that neither transport 

nor inriver migration conditions may be a bottleneck to recovery, when marine-based survival is 

at some adequate level.

No mass transportation study has been conducted that targets Snake River fall chinook. Such 

evaluations are warranted, and planned for initiation in 2002

There is evidence to suggest that homing fidelity may be impaired for some species of 

transported fish, including fall chinook, sockeye, and steelhead. Studies that target 

spring/summer chinook and steelhead require emphasis. Straying may in part contribute to 

delayed effects associated with transporting smolts. It may be advantageous to ascertain the 

extent of straying associated with transport of all species to address certain ESA concerns. 

Excessive straying may result in increased hatchery fish intermingling among wild adults on the 

spawning grounds. This may not be desirable. Ongoing telemetry/PIT tag-based studies of adult 

passage should offer additional insight on this matter.

Delayed differential effects relative to inriver migrants are consistently evident for transported 

fish. However, by-and-large adult return rates to Lower Granite Dam exceed those of inriver 

migrants designated as controls. In such cases, there would still be a survival advantage to 

transport Snake River fish from Lower Granite and likely Little Goose dams.

Spill

Apart from the Snake River stocks, which can largely be transported, the majority of smolts 

emanating from the rest of the basin continue to migrate in-river to below Bonneville Dam. 

Optimizing smolt survival during downstream migration has been a longstanding goal of 

fisheries managers.

We focus on contemporary passage survival estimates and estimation techniques (balloon-, 

radio-, and PIT-tag methods) developed during the 1990’s that continue to be applied this 

decade.

The collective information indicates that spillways appear to be the safest passage routes 

available at dams, even more benign than many smolt bypass systems, particularly those 

involving the screening of turbine intakes. The magnitude of smolt survival through spillways 

varies across dams and species. This is particularly evident when total effects are reflected in the 
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empirically obtained estimates. This suggests that species- and dam-specific estimates should be 

updated for each dam and applied in any future passage modeling analyses.

Spillway flow deflectors (gas abatement devices) appear to increase smolt mortality relative to a 

standard spillbay, by 1-3 percentage points. Even so, survival will typically still exceed the 

turbine route at most dams. The potential for increased smolt losses at the concrete needs to be 

balanced against gains associated with gas abatement. It is not clear that passage models 

currently provide an accurate assessment of this tradeoff.

Studies assessing the direct and total effects associated with spillway passage indicate that 

survival is related to discharge at some sites, with mortality increasing at excessive discharge 

volumes. The difference in survival across discharges can range from negligible to nearly 7 

percentage points, depending on the dam and species.

In passage modeling analyses, values for model parameters should be periodically updated for 

each dam and species. The set of empirical estimates that characterize smolt passage survival 

through spillways, as well as spill efficiency, are being continually expanded. However, that 

collective information is not being systematically compiled and synthesized on a regular basis 

for the hydrosystem at large. Notable exceptions include papers by Muir et al. (2001a), Ploskey 

et al. (2001) and Anglea et al. (2001) for selected sites.

Passage modeling may afford the only practical means to evaluate the relative benefits of various 

spill scenarios, at the level of the overall smolt population. The other approach requires 

obtaining reliable empirical survival estimates linked specifically to spill conditions. This 

requires a well-designed experimental protocol that will likely be very difficult to implement in 

this complex system of competing uses

The NMFS Total Dissolved Gas standard of a maximum 120% saturation in the tailrace of 

Columbia River dams is generally achievable by following the dam-specific gas caps identified 

in the Biological Opinion, and implementing the spill program currently in place in the MidColumbia. The exception occurs in higher flow years when spill volumes cannot be effectively 

controlled due to flows exceeding the hydraulic capacities at the various dams. The standard 

appears satisfactory for protecting salmonid species within the hydro-system, but it exceeds 

water quality guidelines established by the Environmental Protection Agency.

The full biological impacts of a spill program have not been evaluated in their entirety. Smolt 

survival receives emphasis. Model analyses try to predict changes in smolt survival to below 

Bonneville Dam. Quantitative system analyses have not formally addressed the potential for 

impacts on adult mortality. Empirical evaluations conducted in situ, have limitations as well. 

For example those recently conducted by Zabel et al. (in press) and FPC (2001) observed 

changes over small segments (projects), thus cumulative effects through the system are not 

evident. Furthermore, results from empirical evaluations are equivocal, because spill effects 

have not been clearly isolated from other factors. 

The effects of spill operations and levels on adult passage behavior as linked to long-term 

survival are not well understood. Some of the recent adult passage research suggests that higher 

spill volumes may exacerbate migration delay and fallback. But, convincing quantitative 
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relationships have not been developed. Adult passage studies are continuing and may provide 

insight on these matters.

Flow Augmentation

Flow augmentation (FA) is the intentional release of water from storage reservoirs for the 

purpose of increasing flows to enhance migratory conditions for juvenile and adult life stages of 

salmonids in the Snake and Columbia rivers. Flow augmentation provided to the upper 

Columbia River (downstream from Chief Joseph Dam) comes from large storage reservoirs such 

as Grand Coulee Dam and a complex of storage reservoirs that drain into it from Canada and 

Montana. In the Snake River flow augmentation is provided from Dworshak Dam and through 

the Hells Canyon Complex in Idaho (Figure 3.1). The foundation for prescribing such actions is 

based on two premises:

1. Increased water velocity ‡ increases migration speed of smolts ‡ increases survival.

2. Lowering water temperature (summer) ‡ improves migratory and rearing conditions for 

both juvenile and adult salmonids ‡ results in improved survival.

Information obtained or reported since the early 1990’s is the focus of this report, but a brief 

historical backdrop is provided where needed. Both river operations and the mark-recapture 

tools and associated analytical procedures have changed markedly from previous decades. Thus, 

the contemporary information is most applicable today.

Flow effects on smolt migration speed: For most spring-migrating species the evidence indicates 

that increased flow (water velocity) contributes to swifter migration speed. Information 

regarding fall chinook is equivocal.

• River discharge appears to be the most influential variable affecting migration speed of 

steelhead and sockeye salmon in the Snake and mid-Columbia rivers.

• Two factors, flow and the degree of smolt physiological development, explain the 

observed variation in the migration rate of yearling chinook salmon (except in the midColumbia where only smolt development has been identified as a predictor variable).

• At least four variables have been implicated as influencing the migration speed of subyearling (fall or summer/fall) chinook; flow, water temperature, turbidity and fish size. 

However, strong correlations among these predictor variables confound the ability to 

identify causative agents.

Flow effects on smolt survival: PIT tag based smolt survival estimates acquired since 1993 

provide the most relevant data set for characterizing smolt survival dynamics through the 

impounded mainstem Snake and Columbia rivers.

• Based on recent PIT tagged based estimates there is little evidence supporting a flow 

survival relationship across the water years experienced from 1993-2000, for yearling 

chinook or steelhead. 

• However, in 2001 under the extreme low flow conditions, steelhead survival decreased 

dramatically to about 63% per project (typically it is near 90%). Slow migration speed 
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and rapidly increasing water temperatures are implicated as causative factors affecting 

residualization and mortality.

• A complex of factors is implicated as influencing Snake River fall chinook survival 

including, flow, water temperature and turbidity. These environmental variables are 

strongly correlated during the summer migration, confounding the ability to identify the 

most influential one. Knowing if water velocity or temperature is the most influential 

could be important when the decision is to use Dworshak or Hell’s Canyon for flow 

augmentation, since the temperature of those water sources differs greatly.

The premise for reducing summer water temperature, particularly in the Snake River, to improve 

rearing and migratory conditions for juvenile fall chinook and adult salmonids appears sound.

• The literature indicates that maintaining river temperatures at or below 20°C is 

advantageous to both life stages of fall chinook, and adult steelhead, all of which are in 

the river in August and early September.

However, it is not clear that releasing cool water from Dworshak effectively alters the thermal 

structure of most of the Lower Snake River. The major effect is localized at two upper reservoirs 

(LGR, LGO) according to results reported by Bennett et al. (1997).

• When cool water enters the reservoirs it sinks to the bottom. This can provide cool 

refugia in deeper waters, but not uniform cooling of reservoirs.

• The greatest change in temperature attributable to FA releases from Dworshak are 

evident at LGR, where water temperatures under FA are predicted to be as much as 4-8 

°F below base conditions at certain times. At Ice Harbor the difference is on the order of 

1-2 °F.

Flow Augmentation Evaluations are generally lacking. Only a handful of studies have attempted 

to:

• Quantify the volume and shape of water provided specifically as FA.

• Translate that incremental increase in flows to changes in water velocity and 

temperature.

• Predict the change in smolt travel time and survival attributable to those increases

• Identify whether populations of interest (e.g. ESA stocks) have encountered FA events.

The last such evaluation treated information through the 1995 water year, and only for the Snake 

River. Given the community’s sensitivity to this controversial management action, a holistic 

comprehensive updated evalua tion seems prudent, and long overdue. The scope of future 

evaluations need to more fully address the balance of benefits and risks between anadromous and 

resident fish resources.
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INTRODUCTION

This issue paper was prepared at the request of the Northwest Power Planning Council (NPPC). 

It is meant to assist their understanding the state of the scientific information pertaining to three 

smolt passage strategies employed in the mainstem Columbia River System. Those strategies of 

particular interest to the NPPC include the use of transportation, spill, and flow augmentation as 

means to improve smolt survival. We have organized this paper to treat each strategy separately. 

The National Marine Fisheries Service 2000 Biological Opinion (BO) for the Federal Columbia 

River Power System (FCRPS) prescribes guidelines for using each of these strategies (Appendix 

A). With respect to these strategies the NPPC wants the following issues addressed:

1. What does the scientific literature inform us regarding the benefits, shortcomings, or 

risks associated with each passage strategy, and as compared to other passage options?

2. Which aspects of the scientific information are in dispute?

3. What are the critical uncertainties attending each strategy?

4. What is being, or could be done to reduce uncertainty and disputes?

In terms of scope, the NPPC seeks information for both ESA-listed and unlisted salmonid 

populations across a range of water years. The Council seeks clear, concise and succinct 

treatment of these issues. Our approach is to review key research and analyses that have 

appeared in the literature, then distill out the key findings and synthesize the results. The focus 

is on evaluations conducted under contemporary river operations, which were initiated in the 

early 1990s and formalized as guidelines in the 1995 and 2000 Federal Columbia River Power 

System Biological Opinions. Additionally, we identify key uncertainties and gaps in the 

information base, and identify research that is in place or planned to fill those gaps.

1.0 TRANSPORTATION

Three dams in the lower Snake River, Lower Granite (LGR), Little Goose (LGO), and Lower 

Monumental (LMO), and McNary (MCN) on the Columbia River are equipped with screened 

bypass systems that permit the interception, collection and transport of migrating smolts (Figure 

1.1).
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Figure 1.1Location of collection-transport facilities (T), screened-bypass systems (B), and 

surface flow bypass systems (SB) on the Columbia and Snake rivers. Transport-collection 

facilities can be operated in bypass mode. Transport facilities can also be operated in a 

bypass mode. Surface bypass systems are to be installed at Rocky Reach1 and Bonneville2

dams in 2002 and functional in 2003.

These dams have facilities for holding, and loading large numbers of smolts (up to several 

hundred thousand per day) onto barges or trucks. Transported smolts are then taken to release 

sites downstream from Bonneville Dam (BON), where they are liberated. Barging is the 

preferred conveyance, and is typically employed. Trucks are rarely used, typically only when 

fish numbers are so few that barging becomes impractical. By virtue of the location of these 

facilities Snake River salmonid stocks are the principal populations subject to transport. Upper 

Columbia River stocks encounter only one collector dam, McNary Dam, which under current 

management operations, de-emphasizes transport in favor of spill as a passage option. Specifics 

regarding operations and time frames for transport, spill and flow management can be viewed in 

the Annual Fish Passage Plan compiled by the COE, and in the 2000 NMFS BO (NMFS 2000a, 
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see excerpts Appendix A in this report). Most transport evaluations that involve survival 

estimation have focused on Snake River stocks, since transport targets them.

Even before all the dams were completed on the lower Snake River, the collection and 

transportation of smolts was being considered as a passage strategy to maximize smolt survival. 

Studies were first initiated in the late 1960s and were staged at Ice Harbor, Little Goose and 

Lower Granite dams as they were constructed (Park 1993). With the development of screened 

diversion systems that diverted smolts from turbines, a dilemma arose regarding their fate. 

Should they be collected and transported around all dams to below Bonneville Dam, or should 

they be bypassed and returned to the tailrace to continue migration downstream? The primary 

goal of transportation research was to assess whether the collection and transport of smolts from 

Snake River dams yielded higher survival to returning adult than permitting smolts to migrate 

inriver.

After three decades of transportation evaluations, disputes regarding the efficacy of 

transportation persisted among fisherie s managers. The proponents of transportation argued that 

in the majority of years the survival through to returning adults was higher for transported smolts 

than for fish migrating inriver. The critics of transportation argued that the estimates were not

robust and may be biased, and that the absolute survival rates were far too low to consider 

transport an appropriate passage strategy. That dispute continued in the 1990s, when armed with 

a new tool (PIT tag), a new era of evaluation emerged. That new era is the focus of this paper.

The transportation debate has focused on Snake River populations, because they encounter a 

series of collector dams that can accommodate transportation. Nevertheless, a limited number of 

studies have been conducted at McNary Dam in the 1980s (Park 1993), and at Priest Rapids Dam 

from 1984-1988 using sockeye salmon (Chapman et al. 1997).

In the 2000 BO, NMFS provided estimates of the percentage of the Snake River populations that 

were transported during the years 1994-1999 (Table 1.1). The estimates are for the populationat-large, a mixture of hatchery and wild fish. Assuming that fish guidance efficiency (FGE) is 

relatively stable among years, fluctuations in annual percentages are attributable to variation in 
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spill provided annually at the collector dams. High spill levels shunt more fish away from the 

powerhouse, where the screened collection/bypass system is situated. Averaged over six years, 

72-77% of the Snake River spring/summer chinook salmon and steelhead in the Snake River 

were collected and transported to below Bonneville Dam (Table 1.1). Over a 5-year period, 

approximately 48% of the juvenile fall chinook salmon were collected and transported to below 

Bonneville Dam.

Table 1.1Proportion of juvenile Snake River spring/summer and fall chinook salmon and steelhead outmigrants 

collected from LGR, LGO, and LMO transported below BON during the period 1994-1999 (Data from 2000 NMFS 

BO).

Proportion ESU Transported

Chinook Salmon

Year Spring/Summer Fall Chinook Steelhead

1994 89.2 --- 89.0

1995 64.0 59.6 71.4

1996 70.9 42.4 74.8

1997 65.5 26.5 78.5

1998 72.0 48.1 75.0

1999 72.2 61.8 73.1

5-Year Average --- 47.7 ---

6-Year Average 72.3 --- 77.0

1.1 Survival Evaluation

The most direct means to determine if transporting smolts improves survival over inriver 

migration is to compare the survival rates of fish subjected to each passage option. NMFS has 

been conducting such evaluations since the 1970s. Reviews of historical estimates are provided 

in the NMFS White Paper that treats smolt transportation (NMFS 2000b). Herein, we do not 

revisit the dated historical evaluations, but concentrate on investigations and analyses conducted 

during the most recent decade. These evaluations are most instructive because they reflect smolt 

exposure to contemporary operating conditions, and include upgraded state-of the-art collection 

facilities, and the use of PIT tags to provide survival estimates.

Over the last decade the PIT tag has emerged as the preferred marking tool for use in 

transportation evaluations. Juveniles are implanted with the tag, which they retain through 

adulthood. In the Snake and Columbia rivers, Lower Granite Dam is currently the only site 

where returning adult salmonids can be interrogated for the presence of PIT tags, and as such is 
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the only terminal sampling facility. The development of the contemporary PIT tag detection and 

diversion systems have enabled new and improved analytical capabilities.

Prior to 1993, inriver reference (control) groups did not reflect the actual known fate of marked 

control groups that were released to continue their migration inriver. The contemporary PIT 

system changed that and produced more complete capture history information for downstream 

migrants. As a consequence, a variety of reference (control) groups can be constructed from the 

population of inriver migrants. This capability rectifies a long-standing concern that controls 

designated in previous evaluations were not entirely satisfactory, in that their actual capture 

history subsequent to leaving Lower Granite tailrace was unknown (Mundy et al. 1994, Ward et 

al. 1997). A chief concern was that some unknown fraction of the freeze-branded fish released 

to the river was subsequently transported at downstream sites.

In recent years, two research groups have been estimating smolt-to-adult return rates (SARs) and 

conducting smolt transportation evaluations. Investigators with NMFS (Harmon et al. 2000; 

Marsh et al. 1997, 2000; NMFS 2000b; Sandford and Smith in press), and investigators affiliated 

with the Columbia Basin Fish and Wildlife Authority (CBFWA) have conducted the majority of 

this research (Bouwes et al. 2001). Collectively, these investigations represent the best current 

evaluation of actual contemporary mass transport operations, since the experimental fish are 

commingled with the general population in production barges, in accordance with normally 

scheduled operations. Furthermore, the transport period for experimental groups spans the 

natural migration period when the bulk of downstream migrants are transported.

It is commonly held that implementing the river operations (spill, flow augmentation, etc.) 

specified in the BO, in conjunction with the predatory fish removal program, should substantially 

improve smolt survival through the impounded mainstem river. This in turn ensures that inriver 

migrants used in contemporary transport studies represent the best inriver survival that can be 

realized. Thus, a representative control (reference) group can be used for comparison with 

transported fish. There was concern in the previous era that this was not always the case (Mundy 

et al. 1994, Ward et al. 1997). Below we define four central estimates that emerge in most 

transport evaluations.
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Smolt-to-Adult Return Rates (SAR)--In transportation studies, the foundation estimate is the 

smolt-to-adult return rate (expressed as a %). Its calculation requires counting or estimating the 

number of smolts comprising an experimental group of interest at a specific reference location. 

Today these fish are typically PIT tagged. The next step is to count or estimate the number of 

adults returning to an established sampling or reference location, from that same group. For any 

experimental group (e.g. transported or migrating inriver) the SAR is calculated as the proportion 

(%) of the number of smolts to the number that return as adults for any tagged group:

SAR = (number of returning adults)/ (number of smolts)

Transport to Inriver Ratio, (TIR)--For transport evaluations, SARs for a group transported as 

smolts are compared to a reference, or control group that migrated inriver downstream through 

the hydrosystem. The comparison is usually expressed as a ratio that is referred to by various 

synonymous terms including, transport/control ratio (T/C), transport benefit ratio (TBR), or 

transport to inriver ratio (TIR, or T/I). The magnitude of TIR is an index of the effectiveness of 

transporting fish as follows:

• TIR > 1.0-- Indicates that transported fish survive to returning adult at rates exceeding 

inriver controls.

• TIR < 1.0--Indicates that inriver fish survive to returning adult at higher rates than those 

transported.

For any experimental group (e.g., transported at LGR, or all transported fish) the TIR is 

calculated as the ratio of SAR of transported smolts to the SAR of the control group:

TIR = (SAR of transported fish)/ (SAR of inriver migrants)

Inriver Migrant Survival, (Vc)--Vc is defined as the estimated survival rate of smolts migrating 

inriver from point of release of controls to just downstream of Bonneville Dam. The magnitude 

for Vc has been estimated by using either passage models (e.g., SIMPAS), or extrapolating 

empirical reach-specific survival estimates.
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Delayed Differential Effects, (D)--The parameter referred to as “D” represents the delayed 

differential effects associated with transporting smolts. It surfaced as part of the salmon 

modeling efforts conducted during the Plan for Analyzing and Testing Hypotheses (PATH). It is 

a means to express and quantify any delayed effects (usually presumed to be mortality) that 

accompany transported smolts relative to counterparts migrating inriver. The magnitude of D 

provides information that can be considered when selecting between transport or inriver 

migration as the preferred management strategy, but it is most useful for application in lifecycle 

model analyses.

• D >1.0--No differential delayed effects are indicated for transported fish, the survival to 

returning adult for transported fish exceeds that of inriver migrants.

• 1.0> D >Vc--Delayed effects relative to inriver migrants are indicated and attributable to 

transport, but the survival of transported fish (through return as adults) still exceeds that 

of inriver migrants.

• D < Vc--Delayed effects associated with transport are severe and inriver migrants survive 

at overall higher rates than transported fish.

D can be calculated using empirical TIR estimates and independent estimates of smolt survival 

inriver (Vc), as described by Peters et al. (1999):

D = (TIR) (Vc)

1.2 Recent Estimates

Typically, NMFS has estimated SARs for two different classes of tagged fish; those intercepted 

and tagged at dams, and those that were tagged prior to migration. The standard NMFS 

experimental protocol involved intercepting and PIT tagging smolts guided into the bypass 

system at Lower Granite Dam. One experimental group is then transported via barge from that 

site, while a corresponding reference group is released into the tailrace to migrate downstream. 

This process is repeated throughout the smolt migration period. At subsequent 

collector/transport dams some fraction of the reference group is removed and transported. PIT 

detectors document these removals. Some fraction of the tagged inriver reference group 

continues the migration downstream past Bonneville Dam. During their journey, fish can pass 

through turbines, spillways, sluiceways, screened bypass systems, or be diverted back to the river 
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from collection systems at collector dams. These fish are the basis for designating various 

reference (control) groups of interest.

NMFS has also estimated SARs using fish tagged and released upstream from Lower Granite 

Dam (Sandford and Smith in press). Those authors recently updated and compiled SAR lgr-lgr 

(smolts at Lower Granite and adults back to Lower Granite Dam) estimates for the years 1993 

through 1997 (the last year for which they had complete adult return data) for both fish tagged 

upstream from and at Lower Granite Dam. These estimates are considered the most reliable and 

should supersede any previously published estimates for those years (Gene Matthews, personal 

communication). SARs were estimated for several groupings of transported and inriver fish, as 

were ratios of the SARs (i.e. TIR, although the authors do not use the term). In this report we 

present their estimates for the group of fish transported from Lower Granite and Little Goose 

dams combined, because those dams extract the vast majority of the smolts for transport. 

Control fish presented herein as designated by Sandford and Smith (in press) are those that were 

never detected at any collector dam (including McNary Dam) below the site of release. The 

undetected control groups have gained favor as the most representative of the general untagged 

population of smolts (Sandford and Smith in press, Bouwes et al. 2001). They reported estimates 

for both the composite hatchery and wild populations.

Sandford and Smith (in press) reported transport control ratios, but did not refer to them 

specifically as such. In conversations, the authors noted that their paper did not mean to, nor did 

it, constitute a comprehensive transport analysis, but such an effort is forthcoming. This may 

explain why no statistical comparisons or hypotheses have been formally treated as yet. Herein 

we refer to their calculated ratios as TIRs, because they are equivalent.

The CBFWA investigators (Bouwes et al. 2001) relied solely on fish tagged upstream from 

Lower Granite Dam for their analyses. In fact, since 1997 they have intentionally PIT tagged 

and released several hundred thousand spring and summer chinook at hatcheries upstream from 

Lower Granite Dam in an attempt to ensure ample sample sizes. Under this protocol the history 

of fish tagged at each hatchery is tracked as they migrate seaward. Their transport and inriver 

fates are documented as they move downstream through the complex of PIT detectors. Bouwes 

et al. (2001) also tracked the passage history for wild spring and summer chinook tagged 
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BioAnalysts, Inc. January 2002

upstream from Lower Granite Dam. They produced SAR estimates for the different passage 

fates, which were used to calculate TIR. We focus on the group they documented as transported 

from Lower Granite Dam, and their designated undetected controls. These estimates are most 

similar to those reported in Sandford and Smith (in press) and provide a common currency for 

making comparisons between the studies. For the same reason we present their SAR lgr-lgr 

estimates, but not their SAR bon-lgr estimates.

Table 1.2Percent smolt-to-adult returns (SAR) for transported (TR) and inriver (IR) migrant wild and hatchery 

chinook salmon and steelhead smolts PIT tagged and released at or upstream from Lower Granite Dam (LGR) and 

detected at LGR as adult (from Sandford and Smith, In press). Non-detected PIT tagged inriver fish are those smolts 

that were not detected at any collection facility downstream from LGR. We apply the term TIR to the ratios 

reported by the authors. Confidence intervals (95% CI) are for TIR estimates. Numbers of returning adults (n) for 

SAR estimates are in parenthesis.

Chinook Steelhead

Migration SAR (%) 95 %CI SAR (%) 95% CI 

Year TR (n) IR (n) TIR Lower Upper TR (n) IR (n) TIR Lower Upper

Wild

1993 0.10 (3) 0.00 (0) NA NA NA 0.18 (2) 0.00 (0) NA NA NA

1994 0.68 (13) 0.26 (6) 2.58 1.38 7.18 1.09 (9) 1.05 (6) 1.04 0.39 4.19

1995 0.37 (9) 0.47 (9) 0.79 0.44 1.50 0.00 (0) 0.00 (0) NA NA NA

 1995* 0.38 (100) 0.22 (34) 1.72 1.05 2.85 - - - - -

1996 0.48 (2) 0.20 (4) 2.43 0.00 13.91 1.23 (2) 0.35 (2) 3.51 0.00 Inf

 1996* 0.11 (9) 0.08 (3) 1.42 0.47 5.56 - - - - -

1997 1.61 (4) 1.63 (14) 0.98 0.15 2.50 0.98 (3) 0.43 (2) 2.27 0.00 Inf

Hatchery

1993 0.07 (4) 0.06 (2) 1.08 0.42 Inf 0.11 (3) 0.35 (2) 0.30 0.04 Inf

1994 0.09 (3) 0.09 (7) 1.00 0.31 2.54 0.54 (22) 0.10 (7) 5.40 3.26 12.12

1995 0.77 (26) 0.45 (27) 1.73 1.14 2.85 0.75 (22) 0.90 (11) 0.83 0.48 1.76

 1995* 0.53 (466) 0.38 (178) 1.40 1.17 1.68 - - - - -

1996 0.22 (6) 0.17 (29) 1.28 0.73 1.91 0.38 (7) 0.36 (14) 1.05 0.55 1.88

 1996* 0.13 (47) 0.12 (21) 1.07 0.68 1.77 - - - - -

1997 0.88 (232) 0.67 (162) 1.32 1.17 1.51 0.51 (10) 0.17 (7) 2.98 0.88 7.53

* Released at LGR. There were no “Non-detected” fish. Therefore, fish “Bypassed Once” were used as the divisor in the ratio.

1.2.1 Transport Inriver Ratio (TIR)

Sandford and Smith (in press) reported annual estimates of TIR and associated SARs for both 

hatchery and wild chinook for the years 1993-1999. Several of the TIR estimates were based on 

such low numbers of returning adults that 95% confidence intervals could not be reliably 

estimated with ranges from (0 to infinity) in some cases (Table 1.2). We considered only those 
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TIR estimates that had bounded confidence limits (not extending to either 0 or infinity) as being 

useful indices of performance, and use those to construct graphs herein. Bouwes et al. (2001) 

also calculated TIRs for chinook tagged above Lower Granite Dam, but over the years 1997-

1999 (the authors note only partial returns for 1999). The calculations based on fish transported 

from Lower Granite Dam (Tlgr) and controls never detected inriver (Co) generally comport with 

those presented by Sandford and Smith (In press).

Chinook Salmon--For hatchery fish tagged upstream from Lower Granite Dam and subsequently 

transported from Lower Granite and Little Goose dams, all four useable annual estimates were 

equal to or greater than 1.0 (Sandford and Smith, in press). As noted above, a TIR>1 indicates 

that transported fish survive at rates exceeding inriver controls. For wild chinook, two estimates 

were greater than 1.0, and two were less than 1.0 (Table 1.2, Figure 1.2). In general the 95% CI 

are broader for the wild fish due to smaller sample sizes. For wild and hatchery chinook smolts 

intercepted and tagged at Lower Granite Dam in 1994 and 1996, all four TIR estimates were 

greater than or equal to 1.0 (Table 1.2, Figure 1.2). In these cases too, wild fish had the largest 

confidence intervals (CI).

2.58

1.00 0.98

1.73

1.28 1.32

0.79

2.43

0.00

0.50

1.00

1.50

2.00

2.50

3.00

1994 1995 1996 1997

Year

Transport Inriver Ratio (TIR)

Wild Chinook (TIR)

Hatchery Chinook (TIR)

*Data from Sandford and Smith (In press)

Figure 1.2Transport inriver ratio (TIR) for hatchery and wild chinook salmon smolts PIT 

tagged and released at or above Lower Granite Dam. Only TIR estimates with bounded 

confidence intervals are plotted.
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In Bouwes et al. (2001), TIRs for all three years of hatchery fish transported from Lower Granite 

Dam exceeded 1.0, as did the TIR estimates for fish transported from all dams (To) (Table 1.3, 

Figure 1.3). They did not report CI or measures of precision for these TIR estimates. However, 

the adult returns, and associated SARs (Table 1.3), are considerably higher than those witnessed 

from 1993-1996 (Table 1.2). This suggests precision should be improved over CI estimates 

reported by Sandford and Smith (in press). The findings of the two studies are consistent. In 

every year that has been studied, hatchery chinook salmon transported from Lower Granite and 

Little Goose dams have yielded annual TIR estimates greater than or equal to1.0, indicating a 

survival advantage to transporting them from those sites.

1.40

1.70

1.56 1.57

1.18

1.29

1.19

1.26

0.00

0.50

1.00

1.50

2.00

1997 1998 1999 GM

Year

Transport Inriver Ratio (TIR)

LGR Transported (Tlgr/Co)

All Transported (To/Co)

*Data from Bouwes et al. (2001)

Figure 1.3Transport inriver ratios (TIR’s) for chinook smolts transported from Lower 

Granite Dam (Tlgr/Co) and chinook transported at all projects upon first detection (To/Co). 

The geometric mean (GM) for the three years is indicated.
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Table 1.3Smolt-to-adult returns (SAR) (LGR-LGR) estimates for PIT tagged hatchery and wild spring/summer 

chinook salmon transported and in-river migrants from the Snake River (from Bouwes et. al 2001). Hatchery fish 

were PIT tagged and released at spring/summer fish hatcheries upstream from Lower Granite Dam (LGR). The full 

complement of adult returns has not been realized for the 1999 SAR estimates. Tlgr =smolts transported at LGR, 

To=smolts transported from all Snake River dams upon first detection, Co=smolts never detected, C1=smolts 

detected at one or more dams. Numbers of returning adults (n) for SAR estimates are in parenthesis.

Migration SAR TIR

Year Tlgr (n) To (n) Co (n) C1 (n) Tlgr/Co To/Co

Hatchery

1997 0.85 (205) 0.77 (211) 0.60 (171) 0.51 (225) 1.40 1.18

1998 1.47 (697) 1.21 (757) 1.07 (263) 0.54 (341) 1.70 1.29

1999 2.37 (575) 1.76 (973) 1.40 (495) 1.17 (740) 1.56 1.19

1997-1999

(Geometric Mean)

1.27 1.05 0.60 0.80 1.57 1.26

Wild

1994 - 0.49 (11) 0.15 (6) - - -

1995 - 0.30 (8) 0.35 (10) - - -

1996 - 0.40 (2) 0.27 (6) - - -

1997 - 1.71 (4) 1.76 (16) - - -

1998 - 1.12 (15) 1.29 (42) - - -

1999 - 1.88 (39) 1.93 (78) - - -

1994-1999

(Geometric Mean) - 0.77 0.63 - - -

1995-1999

(Geometric Mean) - 0.85 0.84 - - -

Steelhead--For steelhead tagged above Lower Granite Dam and transported from Lower Granite 

and Little Goose dams, 3 of 4 annual TIR estimates for hatchery fish were greater than 1.0 

(Figure 1.4, Table 1.2). Only one of the wild steelhead estimates had definable confidence 

intervals, and that estimate was near 1.0. Sound inferences are not possible at this time using 

wild fish tagged upstream from Lower Granite Dam. Moreover, no steelhead smolts were 

intercepted and tagged at Snake River dams in 1993-1997. In general, the results across years 

are more variable and thus equivocal than is the case for chinook salmon. It is difficult to 

conclude that transport or inriver passage is generally more favorable for this species.
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BioAnalysts, Inc. January 2002

1.04

5.40

0.83

1.05

2.98

0.00

1.00

2.00

3.00

4.00

5.00

6.00

1994 1995 1996 1997

Year

Transport Inriver Ratio (TIR)

Wild Steelhead (TIR)

Hatchery Steelhead (TIR)

*Data from Sandford and Smith (In press)

Figure 1.4Transport inriver ratio (TIR) for hatchery and wild steelhead smolts PIT tagged 

and released at or above Lower Granite Dam.

Transport at LGR/LGO vs. LMO/MCN--The Bouwes et al. (2001) showed that Snake River 

chinook transported from Lower Monumental and McNary dams yield lower TIRs than fish 

transported from Lower Granite and Little Goose dams. To indicate this difference, we 

compared TIRs for fish transported from the upper two dams to fish collected and transported 

from all dams (Figure 1.3). Sandford and Smith (in press) also observed this pattern, where they 

compared transport control ratios for the combined smolts transported from Lower Granite and 

Little Goose dams to fish transported from all sites. Those authors concluded:

“...fish transported from Lower Granite or Little Goose dams and nondetected 

fish generally had higher SARs (sometimes significantly) than fish transported 

from Lower Monumental or McNary dams and bypassed.”

Based on this assessment the survival advantage for transporting spring/summer chinook or 

steelhead from Lower Monumental Dam or McNary Dam is doubtful, or at best unclear.

Hatchery vs. Wild--Comparing TIR estimates for wild and hatchery fish revealed an inconsistent 

pattern. Only Sandford and Smith (in press) calculated transport to control ratios for both wild 

chinook salmon and steelhead. Across the years for which comparisons could be made (1994-

1997), the TIR pattern for chinook salmon was evenly split. In two years (1994, 1996), wild fish 
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BioAnalysts, Inc. January 2002

exhibited higher TIRs, whereas in 1995 and 1996, hatchery chinook salmon TIR estimates were 

higher than wild fish (Figure 1.2). The pattern is inconclusive. It is not clear whether inriver 

migration or transport should be the preferred passage strategy for wild chinook salmon. In the 

single year when a valid steelhead comparison could be made, the TIR for wild steelhead (1.04) 

was far less than that for the hatchery fish (5.40) (Table 1.2, Figure 1.4). However, 95% CI were 

extremely broad compared to the annual estimates, diminishing the reliability of this comparison.

1.2.2 Smolt-to-Adult Return Rate (SAR)

The magnitude of the SAR estimates used to calculate the TIRs varied dramatically across years 

(Tables 1.2 and 1.3, Figures 1.5 and 1.6). Since 1993, SARs have increased an order of 

magnitude for chinook salmon. SARs for transported chinook salmon tagged upstream from 

Lower Granite Dam ranged from a low of 0.07% in 1993 (Table 1.2) to a high of 2.37% for the 

1999 out-migration (Table 1.3). Furthermore, the 1999 estimate did not include a full 

complement of adult returns (Bouwes et al. 2001). The low SARs evident prior to 1997 are 

indicative of poor overall survival, as realized in very low numbers of returning adults. Small 

sample sizes result in broad and in some cases undefined (0 to infinity) confidence intervals 

associated with the TIRs prior to 1997 (Table 1.2). In general, poor precision limits the ability to 

conduct meaningful statistical tests or make strong inferences. Indeed neither group of 

investigators made statements regarding the statistical significance associated with their findings. 

Their interpretations and conclusions rely on patterns of point estimates (annual) as observed 

across a number of years.

However, the Columbia Basin is now realizing a dramatic increase in adult returns for all 

salmonid species. This is reflected in the dramatic increase in chinook SARs as estimated since 

1997 (Table 1.3, Figure 1.5 and 1.6). If increased adult returns continue at these levels for a few 

more years, new opportunities for more statistically robust analyses may arise. Interestingly, 

some of the annual SAR estimates for transported fish from the 1997-1999 migration years are 

approaching 2%. This is the base threshold level that PATH identified as necessary to ensure a 

high probability of recovery for Snake River spring/summer chinook.
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0.49

0.30

0.40

1.71

1.12

1.88

0.15

0.35

0.27

1.76

1.29

1.93

0.00

0.50

1.00

1.50

2.00

2.50

1994 1995 1996 1997 1998 1999

Year

Percent SAR

All Transports (To)

Never Detected Inriver (Co)

*Data from Bouwes et al. (2001)

Figure 1.5Comparison of wild chinook salmon SARs for transported and inriver controls 

before 1997 and after 1997.

1.47

2.37

1.27

0.77

1.21

1.76

1.05

0.60

1.07

1.40

0.85 0.60

0.00

0.50

1.00

1.50

2.00

2.50

1997 1998 1999 GM

Year

Percent SAR

LGR Transported (Tlgr)

All Transports (To)

Never Detected Inriver (Co)

*Data from Bouwes et al. (2001)

Figure 1.6LGR-LGR SARs for different transport and inriver groups. Tlgr refers to the 

fish transported from LGR, To refers to smolts transported at all projects upon first detection, 

and Co refers to smolts that migrated inriver and were never detected upstream from McNary 

Dam (MCN). Geometric mean (GM) calculated for the three years.

Intra-annual changes in SAR--Some investigators have reported that SAR estimates for 

transported fish appear to increase over the smolt migration period. Using PIT tagged yearling 

chinook salmon released in 1995, Marsh et al. (2000) observed a seasonal trend in SARs, when 

they tracked the performance of replicate groups released throughout the spring migration 
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season. Fish transported after the first week of May exhibited a 250% (hatchery) and 700% 

(wild) increase in SAR, compared to replicates released prior to that date. By comparison, 

control fish exhibited consistently low SARs that were of the same general magnitude as the 

early transport group. The precision of individual replicates is poorer than that previously noted 

for the annual estimates, so statistical significance could not be demonstrated. However, a 

similar seasonal increase in SARs for transported fish was observed in 1990 (Harmon et al. 

1993). They reported that fish transported after mid-May produced SARs 400-600% higher than 

fish transported prior to that period. Marsh et al. (2000) suggest the pattern might be attributable 

to differential survival driven by estuarine/marine conditions that varied over the spring. During 

the spring there is a transition period by which marine processes shift influencing primary and 

secondary productivity. They reason that since transported fish make the journey to the estuary 

in about 3 days, while corresponding controls require 2-3 weeks, they may encounter different 

marine conditions. They imply that the early transported group got to the estuary too early, when 

conditions were not favorable to survival.

For chinook salmon, SARs for transport and control groups typically rise and fall in unison 

(Table 1.3, Figures 1.5 and 1.6). This suggests some factor(s) common to all passage groups 

influence absolute survival through to returning adult. This pattern seems less evident prior to 

1997 when there were fewer returning adults (Table 1.2, Figure 1.2). Recent literature suggests 

climatological, marine-based processes are plausible mechanisms (Hare et al. 1999).

1.2.3 TIRs and Flow

Marsh et al. (2000) examined the relationship between transportation indices and river flow 

(kcfs) in 1995. The working hypothesis was that inriver survival should increase with flow, 

which in turn could depress the TIR estimate. Unexpectedly, they observed a significant positive 

correlation between the TIR estimates for replicate groups and flows ranging from 60 to about 

120 kcfs. The authors theorized the counter-intuitive relationship had more to do with an 

increase in the survival of transported fish throughout the season as associated with timing of 

ocean entry. Whether or not the hypothetical, estuarine/marine mechanisms might be flow 

related has been an unresolved point of discussion. The inriver SARs showed no relationship to 

flow.
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In 1998, NMFS investigators analyzed similar data but focused on inriver and transport SARs for 

individual replicates as the response variable (Marsh et al. 2001). They observed no relationship 

between control SAR and flow at Lower Granite Dam, ranging from 60 to 130 kcfs. They did 

observe a significant (P=0.02), but weak (R-squared = 0.09) positive relationship between 

transport SARs and flow at Bonneville Dam. We conclude that there is no evidence here of a 

meaningful relationship.

1.2.4 Differential Delayed Effects (D-Estimates)

Both NMFS (2000a) and Bouwes et al. (2001) have derived estimates of D from the recent PIT 

tag era datasets. The NMFS reported estimates in the BO that were calculated for wild chinook 

and steelhead stocks from the Snake River for the smolt years 1994-1997. Those authors note 

the estimates should be viewed with caution, since few adult returns were realized (Table 1.4), 

which translated to poor precision. They emphasize that much more data will be required before 

reliable D estimates can be derived. With those caveats, we are reluctant to infer much regarding 

insight associated with the reported estimates. The calculated geometric means for wild chinook 

ranged from 0.63 to 0.73, and 0.52 to 0.58 for wild steelhead for the years 1994-1997.

The range in reported geometric means is directly attributable to the manner in which Vc was 

estimated. NMFS used two different expansions of empirical reach-specific smolt survival 

estimates, one based on per project expansion and the other on a per kilometer expansion. This 

illustrates an important point in the interpretation and relevance of D estimates. Any given set of 

empirical SAR estimates or TIR estimates can generate different absolute D values, depending 

on how Vc is estimated. Given this sensitivity, reporting absolute D values alone (particularly 

when they are < 1.0) offers little insight. The key issue is whether D differs significantly from 

Vc. Its real value is as a performance measure relative to the inriver survival actually realized by 

smolts.
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Table 1.4D estimates for wild Snake River spring/summer chinook salmon and steelhead as reported in the 2000 

BO by NMFS (2000a). SART is the estimated SAR for transported fish. SARI is the estimated SAR for inriver 

(control) fish. Total adult returns are provided in parenthesis for all estimated SARs. Survival is the estimated 

survival from Lower Granite Dam to Bonneville Dam for inriver fish (per-project and per-kilometer extrapolation). 

D is estimated for each year (along with 95% confidence intervals), and geometric mean of the yearly D is provided. 

(1997 adult returns incomplete at time of calculation).

Wild Chinook Salmon Wild Steelhead

InriverSurvivalInriverSurvival

Year SART SARI (Vc) D 95% CI SART SARI (Vc) D 95% CI

Per-project Extrapolation

1994 0.52 (13) 0.25 (6) 0.335 0.85 0.01 1.69 1.29 (8) 1.16 (6) 0.416 0.51 -0.04 1.06

1995 0.30 (8) 0.33 (10) 0.557 0.55 0.03 1.06 0.40 (1) 0.00 (0) 0.583 NA

1996 0.52 (2) 0.24 (5) 0.469 1.02 -0.69 2.72 0.59 (1) 0.58 (4) 0.531 0.54 -0.68 1.76

1997 2.46 (4) 2.05 (17) 0.474 0.61 -0.08 1.29 0.82 (3) 0.57 (3) 0.474 0.71 -0.45 1.87

Geometric 

Mean

1994-1997 0.73 94, 95, 97 0.58

Per-kilometer Extrapolation

1994 0.52 (13) 0.25 (6) 0.260 0.66 0.01 1.31 1.29 (8) 1.16 (6) 0.336 0.41 -0.04 0.86

1995 0.30 (8) 0.33 (10) 0.501 0.49 0.02 0.96 0.40 (1) 0.00 (0) 0.528 NA

1996 0.52 (2) 0.24 (5) 0.412 0.89 -0.60 2.39 0.59 (1) 0.58 (4) 0.476 0.49 -0.61 1.58

1997 2.46 (4) 2.05 (17) 0.417 0.54 -0.07 1.14 0.82 (3) 0.57 (3) 0.474 0.71 -0.45 1.87

Geometric 

Mean

1994-1997 0.63 94, 95, 97 0.52

Bouwes et al. (2001) derived D estimates for the smolt years 1997-1999, recognizing that adults 

for the last year are still at large (Table 1.5). The D estimates reported by Bouwes et al. (2001) 

were produced somewhat differently than the NMFS estimates. They employed different SAR 

reference locations (BON-LGR), and included all fish transported from any collector dam for 

wild and hatchery fish. Then they produced another estimate for hatchery fish based on Lower 

Granite Dam transported fish only. Estimates of Vc were based on per kilometer expansions, 

similar to one of the NMFS protocols.

For wild chinook the geometric means were 0.568 and 0.511, for the years 1994-1999 and 1995-

1999, respectively. Hatchery estimates based on To/Co and Tlgr/Co, were 0.62 and 0.77, 

respectively. Hatchery fish appear to respond more favorably to transport, but no statistical tests 

were performed.
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Table 1.5The ratios of SARs for different transport and in-river hatchery groups. Tlgr refers to the fish transported 

from LGR, To refe rs to smolts transported at all projects upon first detection (weighted by the proportion actually 

transported), Co refers to smolts that migrated in-river and never detected above MCN dam. All SARs are the LGRLGR SARs except for the D-value. The D-value is the ratio of the transport BON-LGR SAR to the control (in -river) 

BON-LGR SAR (from Bouwes et al. 2001).

SAR D-Value

Year Tlgr/Co To/Co D(Tlgr) D(To)

Hatchery

1997 1.401 1.183 0.532 0.450

1998 1.698 1.290 0.880 0.663

1999 1.558 1.190 1.024 0.775

1997-1999

Geometric Mean 1.5 1.262 0.769 0.621

Wild

1994 - 3.189 - 0.958

1995 - 0.867 - 0.403

1996 - 1.489 - 0.526

1997 - 0.975 - 0.480

1998 - 0.868 - 0.538

1999 - 0.974 - 0.637

1994-1999

Geometric mean - 1.226 - 0.568

1995-1999

Geometric Mean - 1.012 - 0.511

The difficulty in resolving differences between estimates reported by different research groups is 

that no single methodology is being used. D can be estimated by a number of similar methods 

that may yield different values. Furthermore, given the poor precision associated with D, the 

opportunity for sound statistically based inferences is absent. As a consequence, some may view 

D to be a confusing and rather abstract parameter that has little intuitive relevance. Furthermore, 

it appears that except for some modeling applications, D provides little more information to the 

fisheries manager than prevailing TIR estimates used to derive D. Obviously you can place no 

more statistical confidence in D estimates than the SAR and TIR estimates from which they are 

derived.

Collectively, the D estimates suggest that differential delayed effects are nearly always indicated 

for transported fish of either species, as indicated by the dominance of values < 1.0. However, 
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BioAnalysts, Inc. January 2002

that is not necessarily bad, if D > Vc. But given the poor precision attending estimates, this 

cannot be adequately tested.

The opportunity for deriving useful D estimates for Snake River fall chinook is even more 

questionable, because the foundation data are lacking. Basic inriver survival and SAR estimates 

for fall chinook smolts do not exist. Furthermore, no satisfactory fall chinook passage survival 

model has been developed to produce reliable alternative estimates of inriver survival (Vc). This 

means that useful estimates of D will likely not be available for this species in the foreseeable 

future. Nevertheless, it may be possible to obtain useful TIR estimates, if adequate numbers of 

juveniles can be PIT tagged.

1.2.5 Statistical Inferences

Some of the estimates reported herein have a weak statistical foundation. Rarely have the 

authors specified levels of statistical significance between or among estimates, or have formal 

hypothesis tests been explicitly conducted. Although, we expect NMFS will evaluate 

transportation in this manner, generally, investigators rely on interpreting patterns of annual 

estimates observed across years. Many of the annual SAR, TIR, and D estimates have such poor 

precision that their usefulness even as general indices may be questionable.

The only way to advance toward more quantitatively robust analyses is to increase the sample 

size of returning adults from experimental lots. This can be accomplished by increasing the 

numbers of juveniles PIT tagged. However, substantially increasing that effort by any 

substantial amount (2-10 fold) seems impractical. Alternatively, investigators can rely on the 

natural cycles, outside the hydrosystem, to improve survival during marine residence, and then 

take analytical advantage of the increase in adult returns. The latter appears more likely, and 

evidence for such is already apparent with the recent increases in adult abundance basin wide. 

The conventional position is that marine conditions have entered a phase conducive to fostering 

survival of northwest salmonid stocks (Hare et al. 1999).
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1.2.6 Mechanisms Contributing to Delayed Differential Effects For Transport

Stress and Fish Condition--One mechanism potentially contributing to delayed transport effects 

could be stress incurred during the transportation process. Over the last two decades, researchers 

have investigated the potential for such effects (Matthews et al 1986, Maule et al. 1988). Byand-large those studies documented changes in certain physiological indices that were 

attributable to the collection and transport of smolts. The observed changes were typically of 

short durations, and depending on the index, levels returned to base conditions within 24-72 

hours. For example, Maule et al. (1988) studied fall and spring chinook at McNary Dam. They 

used a variety of physiological measures (plasma cortisol and glucose, and white blood cell 

counts, as well as physical tests including, salt water challenge, secondary stress and swimming 

performance). They found that the most stressful event was loading fish into the barge. But fish 

started to recover during transport, and those in barges (16-h recovery), were more fully 

recovered than the shorter duration (3-h) truck transport.

Most investigations have used hatchery fish, and relevance to wild counterparts has regularly 

been questioned. However, Congleton et al. (2000) investigated transport effects on both wild 

and hatchery chinook and steelhead. For certain physiological indices, they observed differences 

between species and origin. They concluded that the collective results indicated chinook salmon 

were more stressed by barge transport than steelhead. They made no definitive conclusion as to 

whether overall wild and hatchery fish are differentially affected by barge transport, but note 

difference in many physiological indices. A key finding was that cortisol levels in chinook were 

positively and significantly correlated with the density of steelhead in the barge. They postulate 

that this may be a response to the aggressive behavior of steelhead. They go on to note that 

steelhead did not appear to be stressed by transportation. Importantly, they note that it is not 

known if the observed elevated stress indices are linked with reduced survival following 

liberation from barges.

Congleton et al. (2001) have addressed this last point by analyzing steelhead-loading densities, 

physiological indices of chinook and ensuing chinook SARs for fish transported from Lower 

Granite Dam in 1995, 1998 and 1999. Preliminary findings have not identified any obvious 

relationships between SARs estimates for wild or hatchery chinook and the density of steelhead 
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BioAnalysts, Inc. January 2002

in barges at the time of transport. They caution that any conclusion would be tentative, since the 

power of the test may have been insufficient to detect an effect, or an effect may not occur in all 

years.

Based on the collective information it is difficult to determine whether or not stress associated 

with the collection and transport of smolts contributes to delayed differential mortality. The 

thought has been if stress was an important factor, there may be some ways to minimize it and 

improve the long-term survival of transported fish.

Homing Fidelity-- SAR estimates for transported fish may reflect processes other than mortality. 

Impaired homing could be considered a delayed effect associated with transport, and may be 

reflected in D values as calculated by different groups. If adults en route to Lower Granite Dam 

that were transported as smolts stray at higher rates than inriver counterparts, then the SAR 

estimates for transported fish will be depressed, since they have no opportunity to be detected at 

Lower Granite Dam. Lower Granite Dam is currently the only fishway fitted with PIT tag 

detectors capable of interrogating returning adults. At this point we examine information that 

describes the potential for homing impairment as attributable to transportation.

There have been studies that indicate transport can impair homing. Bugert et al. 1997 conducted 

an investigation using coded wire tagged (CWT) fall chinook salmon (both sub-yearling and 

yearling aged) from Lyons Ferry Hatchery on the Snake River. The transport protocol for this 

study differed from that employed in general mass transportation operations, in that the 

transported fish were barged around only two dams, Lower Monumental and Ice Harbor, and 

were released in the Snake River rather than downstream from Bonneville Dam. Even with this 

short transport (<34h) and the constant replenishment of ambient water to provide homing cue, 

homing was affected. They found that transported fish strayed to freshwater areas outside the 

Snake River basin at a rate significantly higher than those released directly from the hatchery, at 

5.9 and 0.3%, respectively.

Other investigators have also observed evidence of homing effects for transported sockeye 

salmon. Chapman et al. (1997) analyzed adult return data for sockeye salmon collected at Priest 

Rapids and Wanapum dams. In that study, one experimental group was released below Priest 
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BioAnalysts, Inc. January 2002

Rapids Dam, whereas the transported group was released from the shoreline below Bonneville 

Dam. Those authors concluded that the truck transport impaired homing of adult sockeye 

between Bonneville and Priest Rapids Dam.

These studies suggest that a more systematic and comprehensive evaluation of homing as 

influenced by mass transportation of smolts is warranted, particularly as it is implemented in the 

Snake River. But as yet homing studies targeting the mass transport of Snake River populations 

have not received emphasis. Parties have recognized the need, but logistical and sampling 

constraints associated with a variety of marking tools have limited the opportunity.

A long-standing criticism of past transportation studies was that they failed to assess the potential 

effects on homing ability back to natal tributaries (Mundy et al. 1994). However, the recent 

Bouwes et al. (2001) experimental protocol could provide some insight on this issue, at least for 

stream-type hatchery chinook. The evaluation would require that the hatcheries above Lower 

Granite Dam interrogate returning fish for PIT tags to establish inter-hatchery stray rates. This 

information can be useful and may be available, but has not yet been analyzed. However, such 

estimates would still be limited, because they could not reflect straying that may occur prior to 

arrival at Lower Granite Dam.

Documenting straying rates en route to Lower Granite Dam would require the emplacement of 

adult PIT detectors at fishways at other dams on the river. Coverage would need to extend from 

Bonneville and include strategic sites throughout the mainstem river. Also, studies directed at 

wild stocks have been lacking, owing to sampling difficulties associated with detecting PIT 

tagged fish in streams. But a new detector plate suitable for deployment in streams may be 

available in the next few years and this could offer new sampling capabilities.

Just recently, an alternative approach has been developed that provides new capabilities 

including estimates of straying from Bonneville Dam upstream. Bjornn and Keefer (2001 

abstract) reported preliminary results from research conducted in 2001. They intercepted spring 

migrating chinook and steelhead at Bonneville Dam and implanted radio tags into adults that had 

been PIT tagged as smolts. Therefore they could determine where the fish emanated (PIT 
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information) and their migration fates as smolts, then as adults track their routes upstream with 

the radio tags. This is precisely the type of information that is required to assess the effects of 

transport on homing.

The data have not been completely analyzed as yet, but they made some preliminary 

observations thus far. They found that, in general, straying between the upper Columbia to the 

Snake (as far as LGR) was minimal. However, with respect to the effect of barging, they 

observed that transported steelhead had returned to Lower Granite Dam at rates lower than those 

that migrated inriver as smolts. The ultimate fate of the missing fish has not been indicated. 

However, the results are preliminary and they refrained from making firm conclusions until 

analyses are complete. Nevertheless, this observation does implicate homing impairment as a 

contributing mechanism to D. Further evaluations of this type will be most instructive.

The protocol of Bjornn and Keefer (2001) currently provides the best information for describing 

straying patterns and frequency between Bonneville Dam and the location where smolts were 

first PIT tagged. However, this protocol does not capture homing effects that may have been 

manifested prior to arrival at Bonneville Dam. Evaluation of homing effects that are expressed 

in that zone will no doubt prove to be much more challenging. We are not aware of any research 

that is being proposed to address that issue.

1.3 Summary

In some years, small sample sizes have resulted in poor or undefined precision for SAR, TIR and 

D estimates. This can limit the ability to make statistically defensible conclusions. Authors 

examining recent estimates do not confidently state that transported fish survive at significantly 

higher rates than inriver counterparts. Neither Sandford and Smith (in press), nor Bouwes et al. 

(2001) explicitly tested key hypotheses such as, D > Vc, TIR > 1.0. Presumably future analyses 

by these two research groups will do so. We say this because recent increases in observed SARs 

indicate that in the next few years, PIT tagged fish may be returning in numbers that sufficiently 

improve samples sizes, potentially resulting in improved precision and permitting stronger 

statistically supportable inferences. This increasing trend in adult returns has been apparent 

since the 1997 smolt migration year.
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Using general, annual indices of performance, both NMFS and CBFWA analyses showed that 

the majority of the time, fish transported from Lower Granite and Little Goose dams produced 

TIRs higher than or equal to corresponding inriver control groups. Bouwes et al. (2001) 

concluded modest transportation benefits were evident for hatchery chinook, and slight to 

negligible benefits for wild fish. Sandford and Smith (in press) state that, “once a juvenile fish is 

entrained in a bypass system at a “collector dam”, transporting the fish maximizes the probability 

of its eventual return as an adult.” Based on assessments by those two investigations, it appears 

that there is a survival advantage associated with transporting Snake River hatchery 

spring/summer chinook and steelhead, particularly from the upper two dams, Lower Granite and 

Little Goose dams. However, the rationale for transporting smolts from Lower Monumental and 

McNary dams is less clear. The benefits of transporting Snake River hatchery fish from those 

dams are equivocal.

Whether or not wild fish respond favorably to transportation is difficult to ascertain at this 

juncture. Even though the limited numbers` of TIR estimates are generally >1.0, the estimates 

are based on so few adult returns that the precision for this class of fish is particularly poor 

(Table 1.2). Thus, reliance on the point estimate as a representative value is questionable in our 

opinion.

Survival from smolt to returning adult (SAR) for hatchery and wild spring summer chinook has 

increased substantially since 1993, and has been increasing steadily from 1997-1999, reaching 

SAR levels in 1999 that approach and in some cases exceed the 2% minimum recovery threshold 

for wild stocks as identified in PATH (Figures 1.5 and 1.6). This suggests that neither transport 

nor inriver migration conditions may be a bottleneck to recovery, when marine-based survival is 

at some adequate level.

No mass transportation study has been conducted that targets Snake River fall chinook. Such 

evaluations are warranted.

There is evidence to suggest that homing fidelity may be impaired for some species of 

transported fish, including fall chinook, sockeye, and steelhead. Studies that target 
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BioAnalysts, Inc. January 2002

spring/summer chinook and steelhead require emphasis. Straying may in apart contribute to D. 

It may be advantageous to ascertain the extent of straying associate with transport of all species 

to address certain ESA concerns. Excessive straying may result in increased hatchery fish 

intermingling among wild adults on the spawning grounds. This may not be desirable.

Delayed differential effects relative to inriver migrants are consistently evident for transported 

fish. However, the magnitude of the D regularly exceeds survival of the smolt stage through the 

hydrosystem (Vc), so the survival of transported fish (through return as adults) still exceeds that 

of inriver migrants. In such cases, there would still be a survival advantage to transport Snake 

River fish from Lower Granite and Little Goose dams.

1.4 Critical Uncertainties and Research Opportunities

Species Coverage-- Not all species have been adequately evaluated with respect to survival 

associated with transportation. By and large much of the useful data has been obtained using 

hatchery fish or run-of-river populations dominated by such. There is concern that wild stocks 

may react differently to transport. But it has been difficult to obtain robust SAR estimates for 

wild fish since their abundance has been low, and they need to be collected and tagged in their 

natal streams. The recent resurgence in returning adults should boost wild juvenile abundance, 

and provide new opportunity to increase the number of PIT tagged individuals for use in 

transport survival evaluations.

An evaluation of transporting Snake River fall chinook is warranted. NMFS with Army Corps of 

Engineers funding will conduct such an eva luation starting in 2002, using Lyons Ferry Hatchery 

stock.

MCN Evaluations--There have been no TIR studies conducted for stocks passing at McNary 

Dam since the 1980s. Evaluations under contemporary operating conditions using PIT tags are 

warranted. Such evaluations were planned by NMFS for 2001 but did not materialize. However, 

2002 study designs are being formulated and the research is expected to go forward next year.

These evaluations are critical in deciding the preferred management strategy for mid-Columbia 

stocks passing McNary Dam
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Homing Fidelity--Quantifying the extent of straying attributable to smolt transportation may be 

useful in assessing hatchery stock introgression into wild spawning areas. Also, it may explain 

to what extent straying may be contributing to the composite delayed effects now reflected in the 

generic index, D. Analyses like those currently underway at the University of Idaho are most 

instructive and should continue. It is our understanding this line of research will continue. PIT 

and radio tag technologies offer improved capabilities to better document straying within the 

mainstem Columbia and Snake rivers. The emplacement of PIT tag detectors capable of 

interrogating adults at strategic dam sites in the Snake and Columbia rivers would provide new 

analytical capabilities.

Direct Mortality--Many may consider this a minor issue, but to date there are no reliable 

empirical estimates of the smolt mortality incurred from the time of collection through to release 

from either a barge or truck. The convention is to presume survival to be 98% (NMFS 2000a, 

2000b). This value is based on general observations during barging. If the actual direct 

mortality is substantively higher than presumed, it may explain some of the effects currently 

packaged within the parameter D.

Statistically Defensible Inferences--Many of the SAR, TIR, and D estimates obtained early in 

the 1990s have such poor precision that there usefulness even as general indices are 

questionable. Only since the 1997-outmigration have adult returns increased to the degree that 

precision has greatly improved. It would be advisable to continue and expand transport 

evaluations, during this period when we are witnessing robust adult returns. This in turn should 

continue to realize increased sample sizes and improve precision of key estimates. It is our 

understanding that indeed transport studies will continue for spring chinook and steelhead, and 

be expanded to include Snake River fall chinook, as well as evaluations directed at upper 

Columbia River stocks transported from McNary Dam.
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1.5 Literature Cited

Bjornn and Keefer. 2001 (abstract). Homing and survival of adult salmon and steelhead PIT 

tagged as smolts as related to seaward migration history and other factors. Abstract, 

AFEP Annual Review, USACOE, Walla Walla, WA.

Bouwes, N., Petrosky, C., Schaller, H., Wilson, P., Weber, E., Scott, S., Boyce, R., DeHart, M., 

2001. Comparative survival study (CSS) of PIT tagged spring/summer chinook. Status 

report for migration years 1997-2000 mark/recapture activities. BPA contract #8712702, 

34 p. plus appendices

Bugert, R.M., Mendel, G.W., Seidel, P.R., 1997. Adult returns of subyearling and yearling fall 

chinook salmon released from a Snake River hatchery or transported downstream. North 

American Journal of Fisheries Management 17, 638-651.

Chapman, D.W., Carlson, C., Weitkamp, D.E., Matthews, G.M., Stevenson, J.R., Miller, M., 

1997. Homing in sockeye and chinook salmon transported around part of their smolt 

migration route in the Columbia River. North American Journal of Fisheries 

Management 17, 101-113.

Congleton, J.L., LaVoie, W.J., Schreck, C.B., Davis, L.E., 2000. Stress Indices in Migrating 

Juvenile Chinook Salmon and Steelhead of Wild and hatchery Origin before and after 

Barge Transportation. Transactions of the American Fisheries Society 129, 946-961.

Congleton, J., T. Wagner, J. Evavold, D. Fryer, B. Sun. 2001. (Abstract) Evaluation of 

physiological changes in transported chinook salmon and effects on performance and 

survival. AFEP presentation 2001.

Hare, S.R., N.J. Mantua, R.C. Francis, 1999. Inverse production regimes: Alaska and West 

Coast Pacific Salmon. Fisheries. American Fisheries Society 24: 6-14.

Harmon, J., B. Sanford, K. Thomas, N. Paasch, K. McIntrye, and G. Matthew. 1993. Research 

related to transportation of juvenile salmonids on the Columbia and Snake Rivers, 1992. 

NMFS, Northwest Fisheries Science Center, Seattle, Washington. Report to U.S. Army 

Corps of Engineers, Walla Walla District, Walla Walla, WA. Contract DACW68-84-

H0034. 37 P. +Appendix.

Harmon, J., Marsh, D.M., Paasch, N.N., Thomas, K.L., McIntyre, K.W., Sandford, B.P., 

Matthews, G.M., 2000. Research related to transportation of juvenile salmonids on the 

Columbia and Snake Rivers, 1998. NMFS, NFSC, Seattle, WA.

Marsh, D., J. Harmon, N. Paasch, K. Thomas, K. McIntyre, B. Sandford, and G. Matthews. 

1997. Research related to transportation of juvenile salmonids on the Columbia and 

Snake Rivers, 1996. NMFS, Northwest Fisheries Science Center, Seattle, Washington. 

Report to U.S. Army Corps of Engineers, Walla Walla District, Walla Walla, WA. 

Contract E86960099. 26 p. +Appendices.
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Marsh, D.M., Harmon, J.R., Paasch, N.N., Thomas, K.L., McIntyre, K.W., Sandford, B.P., 

Matthews, G.M., 2000. Research related to transportation of juvenile salmonids on the 

Columbia and Snake Rivers, 1999. NMFS, NFSC, Seattle, WA.

Marsh, D.M., Harmon, J.R., Paasch, N.N., Thomas, K.L., McIntyre, K.W., Sandford, B.P., 

Matthews, G.M., 2001. Research related to transportation of juvenile salmonids on the 

Columbia and Snake Rivers, 2000. NMFS, NFSC, Seattle, WA.

Matthews, G.M., Park, D.L., Achord, S., Ruehle, T.E., 1986. Static seawater challenge test to 

measure relative stress levels in spring chinook salmon smolts. Transactions of the 

American Fisheries Society 115, 236-244.

Maule, A.G., Schreck, C.B., Bradford, C.S., Barton, B.A., 1988. Physiological effects of 

collecting and transporting emigrating juvenile chinook salmon past dams on the 

Columbia River. Transactions of the American Fisheries Society 117, 245-261.

Mundy, P.R., Neeley, D., Steward, C.R., Quinn, T.P., Barton, B.A., Williams, R.N., Goodman, 

D., Whithey, R.R., Erho, M.W., Botsford, L.W., 1994. Transportation of juvenile 

salmonids from hydroelectric projects in the Columbia River Basin; An independent peer 

review, Final Report. Phil Mundy, Fisheries and Aquatic Sciences, Report for U. S. Fish 

and Wildlife Service, Portland, OR.

National Marine Fisheries Service (NMFS). 2000a. Biological Opinion: Reinitiation of 

consultation on operation of the Federal Columbia River Power System, including the 

juvenile fish transportation program, and 19 Bureau of Reclamation Projects in the 

Columbia Basin. National Marine Fisheries Service, Seattle, WA.

National Marine Fisheries Service (NMFS). 2000b. Summary of Research Related to 

Transportation of Juvenile Anadromous Salmonids around Snake and Columbia River 

Dams - White Paper. Northwest Fisheries Science Center, National Marine Fisheries 

Service, Seattle, WA.

Park, D. 1993. Transportation as a means of increasing wild salmon survival. Prepared for 

BPA. 35 p.

Peters, C., Marmorek, D., Parnell, I. (eds.) 1999. Decision analysis report for Snake River fall 

chinook. Prepared by ESSA Technologies, Ltd. Vancouver, BC, 332p.

Sandford, B., and Smith, S. (in press). Estimation of smolt-to-adult return percentages for Snake 

River Basin anadromous salmonids, 1990-1997. Journal of Agricultural, Biological and 

Environmental Statistics, 7(1): 79-100.

Ward, D.L., Boyce, R.R., Young, F.R., Olney, F.E., 1997. Review and assessment of 

transportation studies for juvenile chinook salmon in the Snake River. North American 

Journal of Fisheries Management 17: 652-662.
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2.0 SPILL

The 2000 Biological Opinion NMFS (2000a) specifies spill operations for the FCRPS during the 

smolt migration periods in the spring and summer (Appendix A). Apart from the Snake River 

stocks, which can largely be transported, the majority of smolts emanating from the rest of the 

basin continue to migrate in-river to below Bonneville Dam. Optimizing smolt survival during 

downstream migration has been a longstanding goal of fisheries managers. As early as the 

1970’s investigators identified a positive relationship between smolt survival and spill volumes 

discharged at Snake River dams (Sims and Ossiander 1981). Whitney et al. (1997) reviewed 

passage route survival studies that indicated smolt survival was generally higher through 

spillways than through turbines. Is the information acquired prior to the 1990’s particularly 

relevant today? We suggest not. The spill operations in place today (as prescribed in the MidColumbia spill agreement and 2000 NMFS Biological Opinion), as well as the structural 

configurations of many spillways (e.g., flow deflector presence), differ substantially from those 

of the earlier era. Herein we focus on contemporary passage survival estimates and estimation 

techniques (balloon-, radio-, and PIT-tag methods) developed during the 1990’s that continue to 

be applied this decade.

Recently, analyses conducted by Muir et al. (2001a) indicate that spillway survival of smolts 

exceeds that incurred through both turbines and collector/bypass systems at dams on the Snake 

River. For these reasons, routing smolts through spillways is generally considered to be the 

safest passage strategy at Columbia-Snake River dams. However, there are risks associated with 

spilling water for smolt passage. Two of the more prominent risks involve spill contributing to 

total dissolved gas super-saturation and also alteration of migratory behavior of adult salmon.

Total Dissolved Gas--Generally, total dissolved gas (TDG) increases with increased spill 

volumes. When TDG levels become excessive, it can create hazardous conditions for all life 

stages of salmonids, as well as other aquatic organisms. One means to control TDG is to impose 

caps on spillway discharge as prescribed in the NMFS Biological Opinion. Those caps can be 

effective until total river flow exceeds both powerhouse capacity and the dam-specific spill cap. 

One means to abate TDG concentrations is to minimize the depth to which water plunges into the 

stilling basin. To accomplish this, spillway flow deflectors have been designed and installed at a 
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number of dams throughout the system. The flow deflectors are horizontal structures applied to 

the downstream face of each spillbay. These devices re-direct falling water horizontally, thus 

minimizing plunge depth and associated pressure that compresses gas in solution.

Adult Fallback--Large volumes of spill can delay adult migration by occluding or masking 

fishway entrances located in spillway tailraces (NMFS 2000b). Adult fallback can be 

exacerbated at some dams when spill occurs. Fallback is the process whereby adult salmonids 

pass upstream via the fishway, but fallback downstream through some portal (spillway, 

powerhouse or bypass system). Fallback can put adults at increased risk as associated with 

trauma, or migrational delay. Later in this report we describe a situation at Bonneville Dam that 

forms a sort of case study on this topic.

2.1 Spill-Related Smolt Survival 

2.1.1 Smolt Survival Through Spillways

There are two types of survival estimates that can be used to characterize smolt survival through 

a spillway (or for that matter any dam passage route). One type reflects only direct effects, and 

the other is a broader measure that reflects both direct and indirect effects (total effects). The 

objectives for obtaining these types of spillway survival estimates are to:

• Identify the safest routes of passage at a dam.

• Determine the configuration of the spillway that maximizes survival (e.g. flow deflectors 

present/absent, or alternative design).

• Determine if the survival of spilled smolts is sensitive to spill discharge volumes or 

percent water spilled.

Mortality Associated with Direct Effects--The most fundamental level of smolt survival 

estimates are those that reflect only direct effects associated with passage through a route. At a 

spillway, that is from the time smolts enter the intake until they egress from the stilling basin. 

Mortality incurred during this phase is due to physical trauma experienced during spill passage. 
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The magnitude of direct mortality can be estimated for any passage route (spillway, turbine, or 

bypass).

Currently, the preferred method for estimating this type of survival involves a mark-recapture 

protocol using balloon tags (Normandeau et al. 1996a). Briefly, a group of smolts are fitted with 

a deflated tag, and individually injected into the entrance of the passage portal via a hose. 

Within a few minutes after arrival in the stilling basin, the tag inflates and buoys the smolt to the 

surface in the tailrace, where it is retrieved. Fish are netted from the tailrace from a vessel, and 

held for a 48-hour observation period. A corresponding control group is released in the tailrace 

close to the dam, and similarly recaptured and held for observation. The treatment and control 

groups are used to estimate survival through the spillway (Normandeau et al. 1996b). Since fish 

are removed from the tailrace within a brief period (minutes), the resultant spill survival 

estimates reflect only direct acute effects that are expressed in 48 hours.

Mortality Reflecting both Direct and Indirect Effects (Total Effects)--At some dams, and under 

some conditions, smolts passing through a spillway (or some other passage route) may be 

predisposed to encounter some additional hazard in the tailrace (e.g. a concentration of predatory 

fish staging downstream from the spillway tailrace). Survival estimates based on balloon tags 

will not reflect those additional indirect effects. A different experimental approach must be 

employed to reflect the total effects smolts incur when passing through a spillway. The typical 

procedure requires bracketing the zone of concern by releasing a tagged group at the spillway 

entrance (treatment), and another experimental group a few kilometers downstream (the control). 

PIT-tags have been used extensively in such studies (Muir et al. 2001a), particularly in the Snake 

River where an extensive complex of PIT detection systems are in place. However, in river 

reaches where PIT detection capabilities are limited, alternative procedures using radio tags have 

been developed (Skalski et al. 2001).
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2.1.2 Estimating Survival of the Smolt Population as Related to Spill Conditions 

Empirically Based Estimates--Neither of the types (direct and total effects) of empirically based 

survival estimates described thus far, in and of themselves, can be used to estimate the degree to 

which the population-at-large benefits from a spill program. To empirically establish this 

requires a different study design. One approach that has been used by fisheries agencies involves 

estimating the survival of the general population as it passes one or more projects (pool and dam) 

under different spill regimes (Zabel et al. in press). Such composite, project-wide, survival 

estimates reflect survival probabilities through the various routes and the percentage of the 

population using those routes. Obviously, the survival estimate through an entire project can 

reflect other processes in addition to spill effects. This can complicate isolating effects only 

attributable to the spill treatment, as we will observe later in recent case studies.

Model Analyses--An alternative approach for assessing the effects of a spill program on the 

smolt population is to conduct a computer-facilitated model analysis. This involves assembling 

an assortment of independent passage-related estimates and incorporating them into a smolt 

passage model such as SIMPAS or CRiSP. The model can then be configured to represent 

different river, dam, and spill conditions. The output from a smolt passage model would 

typically be the predicted overall smolt survival through the hydro-system under the different 

spill scenarios. The recent 2001 spill analysis conducted by NPPC staff is an example of such an 

application (NPPC 2001). Compiling the fish-related input for the model requires the acquisition 

of independent estimates of survival probabilities through each route at each dam, for each 

species, including indirect and reservoir effects. Also required are corresponding estimates of 

smolt passage proportions through the various routes, preferably across a range of operating 

conditions. Acquiring this set of data for each dam has proven to be difficult to accomplish. 

Typically, it has been necessary to adopt a consensus-selected set of site-specific values, or 

global default values that are applied in model analyses. The reader is referred to the NMFS 

FCRPS Biological Opinion and PATH analyses for a description of such components and values 

adopted in those forums.
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2.1.3 Spillway Passage Efficiency

Spillway passage efficiency (SPE) is defined as the proportion of the smolt population passing a 

dam via the spillway (Anglea et al. 2001). This parameter in combination with the spillway 

survival probability, in large part, dictates the change in survival a smolt population experiences 

under different spill operations. Steig (1994) and Whitney et al. (1997) surveyed SPE estimates 

available at the time of their review. Investigators in PATH also recognized the importance of 

this parameter, and provided an initial review of SPE estimates available in 1996 for use in that 

modeling forum (Marmorek and Peters 1998). At that time, the estimates were incomplete and 

imprecise. As a consequence, PATH investigators concluded that a range of SPE values from 

1.0 to 2.0 should be used in a sensitivity analysis to demonstrate the importance of this 

parameter. Subsequent to that survey, the regional effort to estimate SPE at dams throughout the 

hydro-system has expanded with the intention of improving the quality of estimates. NMFS 

(2000b) updated estimates reported up to that point. More recently, Anglea et al. (2001) and 

Ploskey et al. (2001) compiled and synthesized SPE data sets from two dams, John Day and The 

Dalles. The reader is referred to those documents for details regarding specific estimates.

There are two primary methods for estimating SPE, hydroacoustic monitoring and radio 

telemetry. Hydroacoustic monitoring involves the deployment of fixed beam transducers at 

passage routes, and monitoring targets passing through those beams. Alternatively, the passage 

routes can be fitted with telemetry equipment and the passage fate of radio-tagged smolts 

recorded. If sampling coverage is sufficient, estimates of SPE can be obtained. Spillway 

Passage Efficiency estimates based on Hydroacoustic sampling can be used to make inferences 

about the general mixed population of fish, whereas telemetry-based estimates are speciesspecific. The review and synthesis reports prepared by Anglea et al. (2001) and Ploskey et al. 

(2001) reveal several important considerations regarding SPE estimates. Spillway Passage 

Efficiency can:

• Vary by species.

• Display diel patterns at some dams.

• Vary depending on the tool employed.

• Vary with the percent of water discharged through the spillway.
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These sources of variability make it very difficult to prescribe a single value that can be used to 

accurately represent SPE at a dam. It is likely the collective estimates available at a dam will 

need to be intensely inspected with the hope of identifying an algorithm suitable for predicting 

SPE.

2.2 Spillway Survival Estimates

Are Spillways The Safest Passage Routes?--To address this issue, we rely on survival estimates 

using PIT-tagged smolts where the control groups are released approximately 1-2 km 

downstream from a dam. This protocol captures both direct and indirect tailrace effects. In our 

opinion, these types of estimates are the most instructive in characterizing total effects associated 

with passage through a spillway, or other dam passage routes. This is critical to get a useful and 

representative comparison among routes. Estimates of this type have only been obtained at dams 

in the Snake and Lower Columbia rivers. Similar types of passage route- specific survival 

estimates have been obtained using radio tags, but typically controls have been released much 

closer to the dam (Lady et al. 2000; and Skalski et al. 2001), and thus may not fully capture the 

indirect effects incurred throughout the extended tailrace. We discuss those here, but do not 

emphasize them.

Muir et al. (2001b) compiled route-specific survival estimates for PIT-tagged steelhead and 

yearling chinook at Snake River dams (Appendix B). Across dams and species, the estimated 

relative survival was highest through spillbays (without flow deflectors), and ranged between 

98.4-100%. The range of relative survival estimates through bypass systems and turbines was 

95.3-99.4% and 86.5-93.4%, respectively.

The only other site where such PIT-tag investigations have been conducted is The Dalles Dam 

on the Lower-Columbia River. Ploskey et al. (2001) compiled route-specific survival estimates 

for that site, which were originally generated by NMFS investigators (Appendix B). The 

estimated relative survival of spring migrants (coho or yearling chinook) was 96%, 92%, and 81-

86% for spillbays, sluiceways, and turbines, respectively (Ploskey et al. 2001). The authors 
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further concluded that these estimates were all lower than estimates for other projects in the 

Columbia River Basin. For summer-migrating sub-yearling chinook, the respective relative 

survival estimates for spillbays, sluiceways, and turbines were 92%, 93%, and 84%.

There is additional supporting evidence in the Mid-Columbia River. Route-specific survival 

estimates obtained using radio tags at both Rock Island and Rocky Reach dams indicate that the 

highest relative survival is generally estimated for smolts passing through the spillway 

(Appendix B). This pattern was observed in four out of five assessments conducted in 1999-

2000 (Lady et al. 2000; and Skalski et al. 2001). In the fifth assessment, yearling chinook at 

Rock Island dam survived at equivalent rates through the spillway and Powerhouse 2. In some 

cases, significant differences among passage route survival estimates could not be demonstrated 

due to the level of precision accompanying the point estimates. Nevertheless, precision always 

appeared reasonable. Furthermore, the ranking was consistent across dams and species with 

spillway survival being the highest of the passage routes. Based on these data, we conclude that 

spillways are the safest passage routes at dams where these types of evaluations have been 

conducted.

Do Flow Deflectors affect Smolt Survival?--We consider both PIT-tag and balloon tag estimates 

as being instructive for examining this issue. In general, the presence of spillbay flow deflectors 

decreases survival relative to the non-deflector condition. In the Snake and Lower Columbia 

rivers, PIT-tag based estimates comparing those conditions at Little Goose and Lower 

Monumental dams can be viewed in Figure 2.1. For those dams, Muir et al. (2001a) reported 

that the relative survival through spillways was highest with deflectors absent (98.4-100%) 

compared to deflectors present (92.7-100%). They also noted that although the point estimates 

were lower for the deflector present condition, statistically significant differences could not be 

demonstrated.
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101.0% 100.4% 99.7% 98.4%

95.3% 93.5% 92.7%

88.9%

0.0%

10.0%

20.0%

30.0%

40.0%

50.0%

60.0%

70.0%

80.0%

90.0%

100.0%

110.0%

120.0%

LGR - UnmodifiedLGO - Unmodified

LGO - Deflector

LMO - Unmodified

TDA - 30% SpillTDA - 40% Spill

LMO - Deflector

TDA - 64% Spill

Dam and Spill Condition

Survival 

Figure 2.1. Spill survival estimates reflecting total effects, using PIT tags in a pairedrelease design. Survival estimates represent the average across years and species for a given 

spill condition (i.e., deflector vs. unmodified spillbays and varying levels of spill). Averages 

were calculated using estimates reported in Muir et al. (2001a) and Ploskey et al. (2001).

A number of balloon tag studies have been conducted at Wanapum, Little Goose, and Bonneville 

dams, which are useful for comparing smolt survival through spillbays with and without flow 

deflectors. In those studies, 13 separate comparisons between spillbays with and without 

deflectors were made at varying spill levels. In 85% of the comparisons (11 of 13), survival of 

fish passing the project via a spillbay without a deflector was equal to or greater than spillbays 

with deflectors. Those data are summarized in Figure 2.2.
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100.0% 100.0% 99.7% 99.2% 98.6% 97.0%

0.0%

20.0%

40.0%

60.0%

80.0%

100.0%

120.0%

Bonneville Little Goose Wanapum

Dam

Survival

Unmodified Deflector

Figure 2.2 Mean survival (across years and species) that reflects only direct effects 

(balloon tag-based estimates) through spillbays with and without flow deflectors at 

Bonneville, Little Goose, and Wanapum dams.

Although differences in survival rates associated with the two spillway conditions have rarely 

been found to be significant, a consistent pattern is evident. Smolts passing spillways with flow 

deflectors consistently exhibit survival rates lower than spillways absent of deflectors. The 

reduction in survival equates to 1-3% depending on the dam and species, as well as the tool 

employed. It appears that flow deflectors depress survival, but survival still exceeds that evident 

in turbine passage (Muir et al. 2001a).

Whitney et al. (1997) reported that flow deflectors could reduce TDG by 10 to 20% at a 

particular spill discharge. This benefit must be weighed against the potential for increased smolt 

mortality that appears to be generally associated with the presence of flow deflectors. We have 

not encountered an analysis of this tradeoff in the general literature on this topic.

Is Smolt Survival Sensitive to the Volume of Water Spilled?--Survival estimates reflecting 

either direct or total effects can be instructive in addressing this issue. The effect of spill volume 

on smolt survival has been investigated at Wanapum, Rock Island, Little Goose, and The Dalles 

dams. Figure 2.3 and Table 2.1 summarize the results from those studies:
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0.000

0.200

0.400

0.600

0.800

1.000

1.200

WAN/Yearlings/1998WAN/Yearlings/1999

RIS/Yearlings/1999

LGO/Steelhead/1997

TDA/Yearlings/'97-00

TDA/Subyearlings/'97-00

Project/Age Class/Year

Survival

Low

Medium

High

Figure 2.3 Survival rates of juvenile salmonids at low, medium, and high spill rates. 

Estimates of survival for Wanapum, Rock Island and Little Goose dams represent direct 

effects as estimated using balloon tags (Appendix B). Survival estimates at The Dalles Dam 

represent total effects obtained with PIT tags (from Ploskey et al. (2001); Appendix B).

Collectively, the survival estimates at varying spill levels indicate that some benefits may be 

associated with lower spill levels. However, the range in estimates spans from no effect to as 

much as nearly 7% difference in survival, depending on species. The most dramatic differences 

have been observed at the Dalles Dam, where spillway survival decreases steadily as spill 

fractions increase from 30% to 64% (Figure 2.3, Table 2.1). Clearly, there is a strong indication 

that spillway survival could be maximized by selecting the most benign level of spillway 

discharge at a specific site. Of course, these survival probabilities need to be balanced against 

spillway passage efficiency and other passage route usage, in order to determine the spill volume 

(or percent) that maximizes the survival of the smolt population passing the entire dam. That 

exercise involves a modeling analysis. We have not encountered any study that has 

systematically evaluated such across the various dams.
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Table 2.1Survival rates of juvenile salmonids at low, medium, and high spill rates. Estimates of survival for 

Wanapum, Rock Island and Little Goose dams represent direct effects. Survival estimates at The Dalles represent 

total effects.

Year Project Species Survival Condition

1998 WAN Hatchery Yearling Chinook 1.000 2,000 cfs

0.993 5,000 cfs

0.945 10,000 cfs

1999 WAN Hatchery Yearling Chinook 0.994 2,800 cfs

0.976 6,000 cfs

0.995 7,500 cfs

1999 RIS Hatchery Yearling Chinook 0.995 2,500 cfs

0.995 10,000 cfs

1997 LGO Hatchery Steelhead 1.000 1,800 cfs

1.000 5,600 cfs

1.000 9,500 cfs

1997-2000 TDA Coho and Chinook Yearlings 0.960 30% spill

0.950 40% spill

0.900 64% spill

1997-2000 TDA Subyearling Chinook 0.945 30% spill

0.920 40% spill

0.877 64% spill

2.3 Population Level Responses to Spill Conditions

2.3.1 Empirical Based Observations

Muir et al. (2001a) estimated the survival of yearling chinook salmon and steelhead migrating 

through the Lower Snake and Columbia rivers for the years 1993-1998. They reported that the 

mean smolt survival per-project through the Snake River ranged from 86 to 94% for yearling 

chinook and 88 to 92% for steelhead. Although they did not conduct a formal spill analysis, they 

noted that survival was highest in years (1995-1998) when spill levels were highest and of 

longest duration (in terms of days provided). However, in four of those years total river 

discharge was high and may have been a contributing factor. Their observations are not 
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definitive, but certainly suggest that spill was a likely agent contributing to the improved survival 

of smolts migrating in-river.

2001 Analyses--Recently, two different fisheries agencies (FPC and NMFS) have analyzed the 

effects of spill on smolt survival in 2001, one of the lowest water years on record. Both groups 

relied on project-specific (pool and dam combined) smolt survival estimates generated from PITtag data as the foundation for their analyses. Each, in their own manner, blocked the migration 

period into spill and non-spill periods, and then compared survival estimates during each 

treatment period. To our knowledge, these two analyses represent the only examples of 

empirically based spill evaluations of this sort.

NMFS Analysis-- In 2001, NMFS analyzed the effects of spill on survival of smolts passing 

several projects in the lower Columbia including McNary, John Day, and the reach encompassed 

by The Dalles and Bonneville dams (Zabel et al. in press). The response variable being smolt 

survival through one or more projects blocked by weekly release groups. Several stocks of PITtagged fish were monitored as they migrated downstream through the hydro-system, including: 

Snake River spring/summer chinook and steelhead, Upper Columbia spring chinook, Yakima 

spring chinook, and upper Columbia summer/fall chinook. During the 2001 smolt migration 

period, spill was limited to a single discrete temporal block extending from the latter part of May 

to the first part of June. Zabel et al. (in press) estimated survival during pre-spill, spill, and postspill periods (treatment blocks). They tested whether survival was higher during the spill period.

As smolts migrated through the John Day project (McNary tailrace to John Day tailrace) Zabel et 

al. (in press) estimated the highest survival occurred during the spill period (Figure 2.4). This 

was the case for each of the five stocks they monitored, with only one (steelhead) failing to 

exhibit a significant difference in survival. Yet they did not conclude that the observed survival 

patterns were clearly attributable to the spill event. This is because they had additional 

information as a backdrop. That data indicated that survival of Snake River spring/summer 

chinook displayed a temporal trend of increasing survival during May, independent of spill 

conditions. The pattern was observed in 2001, as well as in three previous years (1998-2000) 

when spill occurred throughout the month of May (USACE 1998; 1999; 2000). They suggest 
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that the spill event in 2001 appears to have occurred coincidentally with the period they 

historically observed peak survival. They suspect that a regular natural temporal rhythm of 

survival is occurring and confounds any a posteriori inferences regarding 2001 spill effects. 

Also, they noted that the pronounced decrease in survival during the post-spill period suggests 

other mechanisms affecting survival may be at play. Although Lower Columbia flows were 

relatively stable over the study period, water temperature increased from 9 to 18 degrees 

Centigrade over the study period. Temperature-mediated predator-related smolt mortality 

relationships are well accepted (Vigg and Burley 1991), and may explain the post-spill drop-off 

in survival. If, as Zabel et al. (in press) suggests, the inherent annual peak in survival coincided 

with the spill in 2001, then this may obfuscate the true extent of effects attributable to spill alone. 

For this reason NMFS felt the analysis was inconclusive.
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Figure 2.4Estimated survival by stock for the pre-spill, spill and post-spill periods for fish 

migrating through McNary Dam and John Day reach. The line of above each bar represents 

one standard error (from Zabel et al. in press).

Zabel et al. (in press) observed that fish passing through other projects did not exhibit such 

consistent positive responses to the presence of spill, as was indicated at the John Day project. 

In assessing the effects of providing spill at McNary Dam, they observed that smolt survival was 

higher during the pre-spill period, for both stocks they analyzed (Table 2.2). There may be 

complicating factors here, in that the response variable in this case is survival from Lower 

Monumental tailrace through both the Ice Harbor and McNary projects. No spill occurred at Ice 

Harbor, and conditions encountered there may have influenced survival over this extended reach. 

Thus, we view this result with some caution.
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Table 2.2 Spill analysis with associated survival estimates and standard errors (in parentheses) provided by spill 

blocks pre-spill, spill, and post-spill (from Zabel et al. in press).

Survival Estimates (Standard Error) P-values

Stock Reach Pre-Spill Spill Post-Spill H1 H2 Conclusion

Snake River Chinook MCN-JDA 0.712 (0.018) 0.805 (0.018) 0.514 (0.045) <0.001 0.001 All different

U. Columbia Spring Chinook MCN-JDA 0.726 (0.064) 0.868 (0.048) 0.390 (0.107) 0.047 0.080 Spill different

U. Columbia Sum/Fall Chinook MCN-JDA 0.845 (0.020) 0.904 (0.020) 0.680 (0.041) 0.004 0.001 All different

Yakima River Chinook MCN-JDA 0.716 (0.025) 0.817 (0.037) 0.593 (0.110) 0.014 0.213 Spill different

Snake River Steelhead MCN-JDA 0.312 (0.023) 0.371 (0.055) 0.130 (0.060) 0.253 No spill effect

Snake River Chinook LMO-MCN 0.732 (0.004) 0.625 (0.007) 0.166 (0.023) <0.001 <0.001 All different

Snake River Steelhead LMO-MCN 0.311 (0.008) 0.218 (0.014) NA <0.001 <0.001 All different

U. Columbia Sum/Fall Chinook JDA-BON 0.304 (0.152) 0.817 (0.095) NA 0.017 NA Spill different

Yakima River Chinook JDA-BON 0.549 (0.272) 0.592 (0.088) NA 0.310 NA No spill effect

As smolts migrated from John Day tailrace to Bonneville tailrace, they passed two projects (The 

Dalles and Bonneville) where only a pre-spill and spill treatment period was encountered. Two 

stocks were analyzed. The survival of upper Columbia summer/fall chinook was dramatically 

and significantly higher during the spill period (0.817), compared to the pre-spill period (0.304). 

However, through the same reach over the same general timeframe, the survival of Yakima 

spring chinook was nearly the same during the pre-spill and spill period, at 0.549 and 0.592, 

respectively.

FPC Analysis--Analysts at the Fish Passage Center also conducted a preliminary analysis of spill 

effects on smolt survival at John Day Dam in 2001, and released the information in the form of a 

technical memorandum (FPC 2001). They too relied on project survival estimates derived from 

PIT tag data. In contrast to Zabel et al. (in press), they blocked the study into only two time 

periods, 1-21 May (no spill) and 22 May - 9 June (spill occurred at John Day). Additionally, the 

experimental population as designated was an admixture of PIT-tagged Upper Columbia and 

Snake River populations passing McNary Dam, not individual populations as treated by Zabel et 

al. (in press).
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They observed that a significant increase in survival of both yearling chinook and steelhead 

occurred after 21 May (Table 2.3), coincident with spill. They also observed a decrease in 

collection efficiency between the two periods suggesting a pronounced shift of the smolt 

population toward and through the spillway, when spill was provided. The implication being 

that the pronounced increase in survival could be attributable to a substantial proportion of the 

smolt population using the spillway.

Table 2.3 Survival Estimates and collection efficiency estimates (parentheses) at the John Day project (FPC 

2001).

Dates Yearling Chinook Steelhead

5/1-5/21 0.788 (0.369) 0.314 (0.400)

5/22-6/9 0.897 (0.204) 0.381 (0.096)

Based on their analyses, they advised that it would be prudent to provide spill even in low flow 

years like 2001.

The observed change in collection efficiency reflects both spillway usage and perhaps changes in

fish guidance efficiency at screens in the powerhouse. Independent estimates of these 

parameters could be instructive when interpreting mechanisms that influence spillway passage 

and survival. In 2001, such estimates could be forthcoming from radio telemetry studies 

conducted by Counihan and Petersen (2001 abstract). But analysis of those data has not yet been 

completed.

Conclusions--For the spill assessment at John Day Dam, Zabel et al. (in press) make a 

compelling argument as to why the observed changes in survival may not actually reflect spill 

effects. We acknowledge the potential for confounding, associated with the observed temporal 

trend in smolt survival, is plausible and of concern. On the other hand, all five stocks they 

monitored exhibited the highest survival during the period spill was provided. Clearly, the 

experimental design will not permit resolution of this matter. These same concerns should apply 
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in the FPC analyses as well. But they did not treat temporal trends to the extent tha t NMFS did. 

The apparent high passage rates of smolt through the spillway, as inferred from shifts in 

collection efficiency, certainly indicate a plausible mechanism that could magnify survival 

during the spill period.

The fact of the matter is, there is no clear hypothesis test that can be performed here. The 

analyses could not clearly isolate spill as a discrete treatment. Thus, it is not possible to estimate 

the change in survival attributable to spill alone. Nevertheless, the high spillway passage rates 

observed at John Day Dam, even under modest spill levels (FPC estimated near 13% of total 

discharge), suggest that providing spill contributed to the improved smolt survival. Perhaps 

pending radio telemetry estimates can provide more insight on this matter.

The FPC and NMFS analyses reinforce the consideration that it is very difficult in a system as 

complex as the FCRPS to isolate a single variable (in this case, spill) and its effect on survival. 

The 2001 conditions with spill off/on/off is probably the clearest delineation we have 

experienced over many years of survival studies, with respect to spill treatment. Since this 

fortuitous situation was not satisfactory for drawing sound conclusions, then only a more 

sophisticated and complex treatment design can resolve the matter. It is certainly possible to 

design such a treatment protocol. The difficulty will be implementing it in a normal, or above 

normal, water-year, when involuntary spill occurs naturally and unexpectedly. The lower wateryears, or perhaps summer periods, offer the best opportunity to implement a more satisfactory 

planned experimental treatment schedule.

At projects other than John Day, results from Zabel et al. (in press) were even less clear. The 

McNary analysis involved a potentially complicating condition. The response variable was 

survival from the Lower Monumental tailrace through both the Ice Harbor and McNary projects. 

No spill occurred at Ice Harbor Dam, and conditions encountered there may have influenced 

survival over this extended reach. Thus, it is difficult to conclude anything related to McNary 

spill from that dataset.
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At the lower Columbia dams (The Dalles and Bonneville), the two populations displayed 

dramatically different responses during the only two treatment periods available (pre-spill and 

spill) (Zabel et al. in press). Given this information, it is difficult to conclude that the 

pronounced increase in survival witnessed for the summer/fall chinook was strictly spill induced. 

The change in survival was so large (from 0.304 to 0.817) that it is difficult to postulate the spillrelated mechanisms that would elicit a nearly three-fold increase in survival during the spill 

period.

2.3.2 Model Analyses

Computer-based smolt passage models (e.g., CRiSP or SIMPAS) can be employed to estimate 

the total mortality experienced by a smolt population encountering a particular spill scenario at 

either a single dam, or through a series of dams. A recent analysis by NPPC staff illustrates such 

an application (NPPC 2001). Within a passage model, the amount of water spilled can be 

prescribed at each dam, as can total river flow and temperature profiles. Using these 

environmental and operational conditions to characterize the system, the fate of smolts is traced 

through the hydro-system. The output of the models is smolt survival through some specified 

reach of river. Rules embedded in the model dictate what proportion of the smolt population 

passes through the different routes (spill, turbine and bypass), and what mortality rate is 

associated with each of those routes. Reservoir mortality can be reflected in different ways, 

depending on the construct of the model. Of course, the accuracy of the model-predicted smolt 

survival relies heavily on the quality of the estimates for route-specific survival, the fraction of 

the population using the route, reservoir mortality, and in this specific case - any indirect effects 

that are spill-related.

Our objective here is to highlight key issues pertaining to the application of passage models in 

spill analyses. We do not intend to contrast and compare various models and underlying 

assumptions. Several previous analytical forums have invested years and produced voluminous 

reports doing so (System Operation Review, and the Plan for Analyzing and Testing 

Hypotheses).
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Passage models use various empirical estimates of smolt survival, passage route efficiencies, and 

behavioral characteristics as either input, or rules, to construct and drive the model. Where 

estimates are lacking or unsatisfactory, values are often assumed or generalized estimates 

applied. Considerable research has been directed at improving smolt passage-related estimates 

in recent years. Research on these topics has intensified under the auspices of the USACE 

Anadromous Fish Evaluation Program, particularly over the last three to five years. It stands to 

reason that the most useful model predictions are those based on the most current information. 

The information is becoming voluminous, thus compiling and selecting the most appropriate and 

representative sets of estimates can be a formidable task. Of particular concern are the criteria 

adopted for selecting the best estimate from a pool of competing candidate values or algorithms. 

In our opinion, it would be folly for one individual, or even a single fishery agency to establish 

the criteria and then select the “best” estimates. There will surely be factions that take exception 

to the resultant set of estimates. It seems more appropriate for diverse technical groups to 

develop and apply criteria for assembling the most representative set that could be adopted as a 

standard.

Most of the parameter values internal to SIMPAS were adopted from datasets assembled during 

PATH. Many of those values are due for updating. Therefore, analyses conducted with the 

model may not reflect the most current understanding of certain passage conditions. 

Furthermore, the SIMPAS model became available after PATH had terminated. As a 

consequence, it was not subjected to the model assessments, comparisons, and parameter 

sensitivity tests that prevailed during that forum. Since the SIMPAS model is becoming more 

commonly applied in regional assessments, it may be advisable that this model and the standard 

data sets used for input and calibration be reviewed and updated.

Recently, the NPPC staff used the SIMPAS model to evaluate relative changes in smolt survival 

under four spill scenarios (NPPC 2001). They found that the greatest change in survival across 

spill scenarios was evident for stocks emanating from the Lower Columbia River, followed by 

Mid-Columbia, then Snake River stocks. The difference among smolt sources was primarily 

attributable to their exposure to transportation. The analysis was sound, but did the tool they 
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employ accurately represent spill-related survival, particularly under the extreme low flow 

conditions witnessed in 2001? Given our impression of the status of the model, that is not clear. 

2.4 Incidental Effects of Spill

2.4.1 Total Dissolved Gas

The NMFS 2000 Biological Opinion specified that Total Dissolved Gas (TDG) levels were to be 

limited to 115 and 120 percent in the forebays and tailraces of hydroelectric facilities in the 

Federal Columbia River Power System (FCRPS), respectively. To ensure these constraints were 

implemented, the Biological Opinion specified that real time physical measurements of TDG 

were to be taken throughout the FCRSP.

According to an assessment in the recent Mainstem Provincial Review for the five years of 

physical monitoring, where spill volumes were dictated primarily by the BO regulated spill 

program, TDG levels have been successfully restricted to the desired levels. The biological 

monitoring program has demonstrated that compliance with the TDG limits outlined in the 1995 

Biological Opinion typically results in less than 1% of the juvenile migrants sampled exhibiting 

signs of gas bubble trauma (GBT). In contrast, conditions producing involuntary spill (i.e., when 

river flow exceeds powerhouse capacity and spill caps) have resulted in TDG levels of 130 to 

140 percent for a number of consecutive days, resulting in 3.2 to 3.3 percent of the migrants 

exhibiting signs of GBT. It should be noted however, that research correlating mortality 

associated with the exhibited level of GBT symptoms has not been conducted. Regardless, 

exhibited signs of GBT are low when TDG levels are managed as specified in the NMFS 2000 

Biological Opinion.

Hydroelectric projects not part of the FCRPS, and therefore not regulated by the NMFS 2000 

Biological Opinion, include Priest Rapids, Wanapum, Rock Island, Rocky Reach, and Wells 

dams. Review of gas data in the Mid-Columbia reveals that the FERC projects are essentially 

operating within the NMFS Biological Opinion guidelines for TDG levels in the tailrace of the 
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dams. That is, TDG levels for the most part do not exceed the 120 percent tailrace limit. To 

illustrate this, we present data from two recent years, 1999 and 2000 (Figures 2.5 and 2.6).

100

105

110

115

120

125

130

135

140

145

150

1-Apr 15-Apr 29-Apr 13-May 27-May 10-Jun 24-Jun 8-Jul 22-Jul 5-Aug 19-Aug 2-Sep 16-Sep 30-Sep

Date

TDG (Percent Saturation)

PRD

WAN

RIS

RRH

WEL

Figure 2.5 Total dissolved gas levels in the tailrace of Priest Rapids, Wanapum, Rock 

Island, Rocky Reach and Wells dams, April 1 – September 30, 1999. The solid horizontal 

line represents NMFS 2000 BO TDG tailrace standard.
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100

105

110

115

120

125

130

135

140

145

150

1-Apr 15-Apr 29-Apr 13-May 27-May 10-Jun 24-Jun 8-Jul 22-Jul 5-Aug 19-Aug 2-Sep 16-Sep 30-Sep

Date

TDG (Percent Saturation)

PRD

WAN

RIS

RRH

WEL

Figure 2.6 Total dissolved gas levels in the tailrace of Priest Rapids, Wanapum, Rock 

Island, Rocky Reach and Wells dams, April 1 – September 30, 2000. The solid horizontal 

line represents NMFS 2000 BO TDG tailrace standard.

In 1999, the total dissolved gas levels within the tailraces of most of the Mid-Columbia projects 

were well below the 120% NMFS standard. The exception was Priest Rapids Dam, where TDG 

levels in the tailrace exceeded 120% on 36 occasions between April 23 and June 15. However, 

TDG levels were seldom greater than 122%, and therefore, sustained TDG levels of this nature 

likely had minimal effects on salmonids. On August 4, TDG levels within the Rock Island 

tailrace reached 134.4%. However, this value appears suspect since gas levels at Rock Island 

prior to and after the event were low. Also, gas levels downstream of Rock Island did not exhibit 

similar trends on the same date.

Similar trends appear in the data from 2000 for the Mid-Columbia, where TDG levels were 

typically below the 120% tailrace threshold. Only TDG levels within the Priest Rapids tailrace 

approached or exceeded the 120 percent limit. However, the 120% threshold was exceeded 

infrequently, and at low levels. The 150.3% value for Rock Island on April 23 appears to be 

erroneous for the same reasons as explained above for the apparent outlier in 1999.
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2.4.2 Adult Passage Impacts

Spilling water does not offer any direct benefit to migrating adults. However, there can be risks 

associated with spilling water. We previously discussed potential risks associated with total 

dissolved gas saturation, and concluded that the NMFS Biological Opinion spill program does 

not endanger salmonids. The spill discharge caps specified in the 2000 FCRPS Biological 

Opinion appear effective in this regard. This interpretation appears consistent with the 

characterization presented in NMFS assessment of adult passage with respect to the managed 

spill program (NMFS 2000b).

Apart from concerns regarding direct mortality, spilling water can also alter migratory patterns, 

and in some cases result in protracted migration of adults, particularly when flows and spill 

levels are high (NMFS 2000b). These river conditions can occlude fishway entrances and may 

increase fallback. Fallback is the behavior whereby adult fish move downstream past dams they 

have already ascended. It is disadvantageous because it can cause injury, mortality or 

migrational delay. Bjornn and Peery (1992) examined radio telemetry data for a relationship 

between fallback frequency and prevailing flow and spill levels at several Columbia River dams, 

and identified positive significant correlations at some of the dams. However, in 1996 Bjornn et 

al. (2000) examined the same type of data for chinook salmon. They reported that fallback 

appeared to increase with increasing spill and flow, but the correlations were very weak as 

evidenced by r-squared values that were all less than 0.17 at each of the 4 dams (Bonneville, The 

Dalles, John Day, and McNary) for both predictor variables. We would conclude that no 

meaningful relationship was demonstrated. These results contrast with their previous 1993 

analysis. They also presented evidence indicating that increased fallback at dams may depress 

survival through to spawning. Approximately 71.4% of the chinook salmon that fell back at 

Bonneville Dam survived and were detected either entering major tributaries, or at least passing 

Priest Rapids Dam. In contrast, 77.7% of fish that did not fallback at Bonneville Dam survived 

to, and were detected at, those same locations. The implication is that fallback may induce 

trauma, or protract migration, which contributes to reduced survival.
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English et al. (1998) compared migration rates and fallback rates for three species of salmon at 

Rocky Reach and Rock Island Dams. They observed increased travel times and fallback rates in 

1997 compared to 1993. They noted that spill discharge was substantially higher in 1997, and 

implied that increased spill was a likely agent. However, they did not conduct a formal analysis 

of spill and other potential factors on fallback.

It is not clear if spilling water as prescribed in the NMFS Biological Opinion exacerbates 

fallback, and thus increases risk to adults. Results from the evaluations presented here are not 

consistent. The relationship between fallback and spill discharge appears to be dependent on the 

year and/or dams investigated. We have not encountered an analysis that specifically and 

explicitly evaluates the effects of existing spill programs on adult passage. In our view, this is a 

deficiency, and an analytical effort involving a meta-analysis of data across dams, years, and 

species may be warranted.

2.5 Summary

Spillways generally appear to be the safest passage routes available at a dam, even more benign 

than many smolt bypass systems, particularly those involving the screening of turbine intakes. 

The magnitude of smolt survival through spillways varies by dam and species. This is 

particularly evident when total effects are reflected in the empirically obtained estimates. A 

number of studies have indicated that survival is related to spillway discharge levels at some 

sites, with mortality increasing at excessive discharge volumes. The difference in survival across 

discharge levels can range from negligible to nearly 7 percentage points, depending on dam and 

species. 

In passage modeling analyses, values for model parameters should be periodically updated for 

each dam and species. The set of empirical estimates that characterize smolt passage survival 

through spillways (and other routes) and spill efficiency are being continually expanded. 

However, that collective information is not typically being systematically compiled and 

synthesized on a regular basis. Notable exceptions include papers by Muir et al. (2001a), 

Ploskey et al. (2001) and Anglea et al. (2001) for selected site.
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Passage modeling may afford the only practical means to evaluate the relative effectiveness of 

various spill scenarios. Obtaining reliable empirical survival estimates linked specifically to spill 

conditions will be extremely difficult.

Spillway flow deflectors appear to increase smolt mortality relative to a standard spillbay, by 1-3 

percentage points. The potential for increased smolt losses at the concrete need to be balanced 

against gains associated with gas abatement. It is not clear that passage models currently provide 

an accurate assessment of this tradeoff. The Total Dissolved Gas standard of a maximum 120% 

saturation in the tailrace of Columbia River dams is generally achievable by following the damspecific gas caps identified in the NMFS Biological Opinion and implementing the spill program 

currently in place in the Mid-Columbia. The exception occurs in higher flow years when spill 

volumes cannot be effectively controlled due to flows exceeding the hydraulic capacities at the 

various dams. During these periods, spill discharge naturally exceeds the caps prescribed in the 

Biological Opinion (Appendix A). The standard appears satisfactory for protecting salmonid 

species within the hydro-system.

The effects of spill operations and levels on adult passage behavior as linked to long-term 

survival are not well understood. Some of the research suggests that higher spill volumes may 

exacerbate migration delay and fallback. But convincing quantitative relationships have not 

been developed.

The full biological impacts of a spill program have not been evaluated in their entirety. Smolt 

survival receives emphasis. Model analyses try to predict changes in smolt survival to below 

Bonneville Dam. Empirical analyses such as those conducted by Zabel et al. (in press) and FPC 

(2001) observe changes over small segments (projects), thus cumulative effects through the 

system are not evident. Results from empirical evaluations are equivocal; spill effects are not 

clearly isolated from other factors. Quantitative system analyses have not formally included the 

potential for impacts on adult mortality.
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2.6 Critical Uncertainties and Research Opportunities

Evaluating Spill Effects at the Population Level-- The only analysis that has attempted to assess 

the change in survival for the smolt population subjected to different spill scenarios is the 2001 

model analysis conducted by NPPC staff. That analysis may not be entirely satisfactory because 

the SIMPAS model used in the analysis likely requires updating. An expanded and hopefully 

improved set of passage related estimates are available since it was constructed. We suggest this 

and other models be examined as candidates for similar applications. In our opinion passage 

models may offer the most tractable means to estimate the relative benefits associated with 

various spill strategies. We think it will be very difficult and likely impractical to conduct welldesigned manipulative experiments that can isolate spill effects, in this complex, and often times 

uncontrollable, river system.

Spill Effects on Adult Passage and Long-term Survival-- The effects of spill levels on adult 

passage behavior and ultimately survival to spawning remain unclear. Some of the research 

suggests that higher spill volumes may exacerbate migration delay and fallback. But convincing 

quantitative relationships have not been developed. Telemetry-based passage monitoring is 

planned for 2002 in the FCRPS. We suggest that this be established as a long-term monitoring 

effort, with broad species coverage. The type of information being collected by University of 

Idaho investigators and the Mid-Columbia PUDs should provide a foundation for exploring these 

relationships.
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2.7 Literature Cited

Anglea, S., T. Poe, A. Giorgi. 2001. Synthesis of radio telemetry, hydroacoustic, and survival 

studies of juvenile salmon at John Day Dam (1980-2000). Prepared by Battelle for the 

U.S. Army Corps of Engineers, Portland, Oregon.

Bjornn, T. C., and C. A. Peery. 1992. A review of literature related to movements of adult 

salmon and steelhead past dams and through reservoirs in the Lower Snake River. U. S. 

Army Corps of Engineers, Walla Walla District. 79 p.

Bjornn, T. C., M. L. Keefer, C. A. Peery, K. R. Tolotti, R. R. Ringe, P. J. Keniry, L. C. 

Stuehrenberg. 2000. Migration of adult spring and summer chinook salmon past 

Columbia and Snake river dams, through reservoirs and distribution into tributaries, 1996. 

A report for Project MPE-P-95-1. Technical Report 2000-5. U.S. Army Corps of 

Engineers and Bonneville Power Administration, Portland, OR.

Counihan, T. D., and J. H. Petersen. 2001 Abstract. Estimate the survival of migrant juvenile 

salmonids in the Columbia River from John Day Dam through Bonneville Dam using 

radio-telemetry. Abstract from the U.S. Army Corps of Engineers’ Anadromous Fish 

Evaluation Program 2001 Annual Research Review.

English, K.K., T.C. Nelson, C. Sliwinski, and J.R. Stevenson.1998. Assessment of passage 

facilities for adult sockeye, chinook, and steelhead at Rock Island and Rocky Reach Dams 

on the mid-Columbia river in 1997. Wenatchee, WA., Chelan county PUD.

Fish Passage Center (FPC). 2001. Technical memorandum, 22 October 2001. Fish Passage 

Center, Portland, Oregon.

Lady, J., J.R. Stevenson, J.R. Skalski, and A.E. Giorgi. 2000. A pilot study to estimate routespecific survival and passage probabilities of steelhead smolts at Rocky Reach and Rock 

Island Dams, 1999. Wenatchee, WA: Chelan PUD.

Marmorek, D.R. and C.N. Peters, editors. 1998. PATH weight of evidence report. Vancouver, 

B.C., Canada. ESSA Technologies. 

Muir, W.D., R.N. Iwamoto, C.R. Pasley, B.P. Sandford, P.A. Ocker, and T.E. Ruehle. 1995. 

Relative survival of juvenile chinook salmon after passage through spillbays and the 

tailrace at Lower Monumental Dam, 1994. Seattle, WA: CZES, funded by USACE, 

contract #E86940101.

Muir, W. D., S. G. Smith, J. G. Williams, and B. P. Sanford. 2001a. Survival of juvenile 

salmonids passing through bypass systems, turbines, and spillways with and without flow 

deflectors at Snake River dams. North American Journal of Fisheries Management 

21:135-146.
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Muir, W. D., S. G. Smith, J. G. Williams, and E. E. Hockersmith. 2001b. Survival estimates for 

migrant yearling chinook salmon and steelhead tagged with Passive Integrated 

Transponders in the Lower Snake and Lower Columbia rivers, 1993-1998. North 

American Journal of Fisheries Management 21:269-282.

National Marine Fisheries Service (NMFS). 2000a. Biological Opinion: Reinitiation of 

consultation on operation of the Federal Columbia River Power System, including the 

juvenile fish transportation program, and 19 Bureau of Reclamation Projects in the 

Columbia Basin. National Marine Fisheries Service, Seattle, WA.

National Marine Fisheries Service (NMFS). 2000b. Passage of juvenile and adult salmonids 

past Columbia and Snake river dams - White Paper. Northwest Fisheries Science Center, 

National Marine Fisheries Service, Seattle, WA.

Normandeau Associates, Inc., and J. R. Skalski. 1998. Chinook salmon smolt passage survival 

through modified and unmodified spillbays at Rock Island Dam, Columbia River, 

Washington. Report prepared for Public Utility District No. 1 of Chelan County, 

Wenatchee, WA.

Normandeau Associates, Inc. and J.R. Skalski. 1999. Evaluation of mortality and injury 

associated with smolt passage through spillbays with a sloped flow deflector and no flow 

deflector at the Wanapum Dam. Drumore, PA: Normandeau Associates, Inc. 

Normandeau Associates, Inc. and J.R. Skalski .2000a. Evaluation of prototype shallow flat flow 

deflector at Wanapum Dam spillbay 5 relative to chinook salmon smolt passage survival, 

1999. Drumore, PA: Normandeau Associates, Inc. 

Normandeau Associates, Inc. and J. Skalski.1999. Spillway passage survival investigation of 

juvenile chinook salmon at Rock Island dam, Washington. Wenatchee, WA. Chelan PUD. 

Normandeau Associates, Inc., and J. R. Skalski. 2001. Juvenile chinook salmon survival and 

condition after passage through a slotted spillbay with a submerged spill pool flow 

deflector at Rock Island, Columbia River. Report prepared for Public Utility District No. 

1 of Chelan County, Wenatchee, WA. 

Normandeau Associates, Inc., J.R. Skalski, and Mid Columbia Consulting.1996a. Fish survival 

investigation relative to turbine rehabilitation at Wanapum Dam, Columbia River, 

Washington. Drumore, PA: Normandeau Associates, Inc., and Mid Columbia Consulting 

for Grant County PUD #2.

Normandeau Associates, Inc., J.R. Skalski, and Mid Columbia Consulting.1996b. Fish survival 

in passage through the spillbay and sluiceway at Wanapum Dam on the Columbia River, 

Washington. Drumore, PA: Normandeau Associates, Inc., UW, Mid Columbia Consulting. 

Normandeau Associates, Inc., J.R. Skalski, and Mid Columbia Consulting.1996c. Potential 

effects of spillway flow deflectors on fish condition and survival at the Bonneville Dam, 

Columbia River. Portland, OR: U.S. Army Corps of Engineers, Portland District. 
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Normandeau Associates, Inc., J. R. Skalski, and Mid Columbia Consulting, Inc. 1996d. 

Evaluation of chinook salmon smolt (Oncorhynchus tshawytscha) survival and condition 

associated with passage through the surface bypass collector at Lower Granite Dam, Snake 

River, Washington. Report prepared for U. S. Army Corps of Engineers, Walla Walla, 

WA.

Normandeau Associates, Inc., J. R. Skalski, and Mid Columbia Consulting, Inc. 1997. Juvenile 

steelhead passage survival through a flow deflector spillbay versus a non-flow deflector 

spillbay at Little Goose Dam, Snake River, Washington. Report prepared for Department 

of the Army, Walla Walls District COE, Walla Walla, WA.

Normandeau Associates, Inc., J. R. Skalski, and Mid Columbia Consulting, Inc. 2000. Passage 

survival and fish condition at the surface bypass/collector at Lower Granite Dam, 2000. 

Report prepared for Department of the Army, Corps of Engineers, Walla Walla District, 

Walla Walla, WA.

Ploskey, G., T. Poe, A.E. Giorgi, and G. Johnson.2001. Synthesis of radio telemetry, 

hydroacoustic, and survival studies of juvenile salmon at the Dalles Dam (1982-2000). 

Battelle.

Sims, C.W., and F.J. Ossiander. 1981. Migrations of juvenile chinook salmon and steelhead in 

the Snake River, from 1973 to 1979, a research summary. National Marine Fisheries 

Service, Northwest and Alaska Fisheries Center, and Coastal Zone and Estuarine Studies 

Division, Montlake, U.S. Army Corps of Engineers, Contract #DACW68-78-C-0038, 

Seattle, WA.

Skalski, J.R. and A.E. Giorgi.1999. Summary of smolt survival studies, 1980-1999 at Rocky 

Reach and Rock Island Dams. Wenatchee, WA: Chelan PUD. 

Skalski, J.R., R.L. Townsend, A.E. Giorgi, and J.R. Stevenson.1998. Recommendations on the 

design and analysis of radiotelemetry studies of salmonid smolts to estimate survival and 

passage efficiencies. Volume XI in the BPA Technical Report Series, The design and 

analysis of salmonid tagging studies in the Columbia basin. BPA (DOE/BP-02341-9), 

Portland, OR.

Skalski, J.R., J.R. Stevenson, J. Lady, R. Townsend, A.E. Giorgi, M. Miller, and K. 

English.2000a. An Assessment of project, pool, and dam survival for chinook and 

steelhead smolts at Rocky Reach and Rock Island dams using radiotelemetry and PIT-tag 

techniques, 2000. Che lan County PUD, Wenatchee, WA.

Skalski, J.R. and J.A. Perez-Comas.2000b. The design and analysis of salmonid tagging studies 

in the Columbia basin, Volume 16. Alternative designs for future adult PIT-tag detection 

studies. University of Washington, School of Fisheries, Columbia Basin Research, Seattle, 

WA.
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Skalski et al. (2001) Skalski, J.R., J. Lady, R. Townsend, A.E. Giorgi, J.R. Stevenson, C.M. 

Peven and R.D. McDonald. 2001. Estimating in-river survival of migrating salmonid 

smolts using radiotelemetry. Canadian Journal of Fisheries and Aquatic Sciences 

58(10):1987-1997.

Skalski, J. R., R. Townsend, J. Lady, A. E. Giorgi, and R. D. McDonald. In press. Estimating 

route-specific passage and survival probabilities at a hydroelectric project from smolt 

radiotelemetry studies. Canadian Journal of Fisheries and Aquatic Sciences.

Steig, T. W. 1994. Review of spring and summer spill effectiveness for juvenile salmon and 

steelhead at various Columbia and Snake river dams, 1983-1992. Lake and Reservoir 

Management, 9(1):154-162.

Stevenson, J.R., J.R. Skalski, J. Lady, R. Townsend, A.E. Giorgi, and R. McDonald. 2000. A 

pilot study assessing the feasibility of using radio telemetry and PIT-tag techniques to 

estimate project, pool, and dam survival of steelhead smolts at Rocky Reach and Rock 

Island Dams. Wenatchee, WA: Chelan County PUD. 

USACE (US Army Corps of Engineers). 1998. Annual Fish Passage Report.

USACE (US Army Corps of Engineers). 1999. Annual Fish Passage Report.

USACE (US Army Corps of Engineers). 2000. Annual Fish Passage Report.

Vigg, S., and C. C. Burley. 1991. Temperature-dependent maximum daily consumption of 

juvenile salmonids by northern squawfish (Ptychocheilus oregonensis) from the Columbia 

River. Canadian Journal of Fisheries and Aquatic Sciences, 48:2491-2498.

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. Prepared for the Northwest Power Planning Council, Portland, Oregon, 

Report 97-15, 101 p.

Zabel, R.W., S.G. Smith, W.D. Muir, D.M. Marsh, J.G. Williams and J.R. Skalski.2001. In 

Press. Survival estimates for the passage of spring-migrating juvenile salmonids through 

Snake and Columbia River dams and reservoirs, 2001- draft. Prepared for U.S. Department 

of Energy, Bonneville Power Administration (DE-AI79-93BP10891).
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3.0 FLOW AUGMENTATION

Flow augmentation (FA) is the intentional release of water from storage reservoirs for the 

purpose of increasing flows to enhance migratory conditions for juvenile and adult life stages of 

salmonids in the Snake and Columbia rivers. Flow augmentation provided to the upper 

Columbia River (downstream from Chief Joseph Dam) comes from large storage reservoirs such 

as Grand Coulee Dam and a complex of storage reservoir that drain into it from Canada and 

Montana. In the Snake River flow augmentation is provided from Dworshak Dam and through 

the Hells Canyon Complex in Idaho (Figure 3.1). The foundation for prescribing such actions is 

based on two premises:

5. Increased water velocity ‡ increases migration speed of smolts ‡ increases survival.

6. Lowering water temperature (summer) ‡ improves migratory and rearing conditions for 

both juvenile and adult salmonids ‡ results in improved survival.

We focus on information obtained or reported since the early 1990’s, but a brief historical 

backdrop is provided where needed. Our rationale for emphasizing contemporary conditions is 

consistent with what we expressed earlier. Both river operations and the mark-recapture tools 

and associated analytical procedures have changed markedly from previous decades. Thus, the 

contemporary information is most applicable today. In some cases we present a brief historical 

background. However, the historical material is more fully reviewed in the NMFS white paper 

regarding salmonid travel time and survival (NMFS 2000), in Giorgi (1993), and Cada et al. 

(1997).

3.1 Premise 1–Increasing water velocity in reservoirs increases smolt migration speed, 

which results in improved survival.

Reservoir Effects-- This premise has been examined and analyzed for over three decades since 

as early as the late 1970’s (Raymond 1979, 1988; Sims and Ossiander 1981). According to the 

premise, as river discharge volumes increase (flow), the water velocity in the reservoirs 

increases. In response, the migration speed of salmonid smolts increases (or travel time 

decreases). The shorter smolt travel time, the shorter the exposure to predatory fish or birds, or 
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seasonally increasing water temperature. All are potential agents causing smolt mortality in the 

reservoirs. Thus, it is reasoned that swifter migration should result in higher survival of smolts 

through the reservoirs.

Figure 3.1Flow augmentation provided to the Columbia Basin from the Upper Columbia 

and Snake River areas.

Biological Window--There is another aspect to the premise that has been argued as well. Apart 

from mortality incurred during passage through the hydrosystem, it has been suggested that 

migration delay may impair survival of smolts at seawater entry. The conceptual model holds 

that smolts are swept seaward by river currents, and historically the timing of seawater entry was 

dictated by the shape and intensity of the hydrograph, and this in turn was synchronized with a 

“biological window”. And thus, slower migration associated with impoundments has disrupted 

the natural timing of ocean-entry, potentially placing smolts at a disadvantage. This theoretical 

window has two aspects; the ecological/environmental condition of estuarine and marine waters, 

and the physiological preparedness for smolts to adapt to seawater. As yet there has been no 
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definitive convincing research conducted on this topic. However, the community is now 

embarking on a new era of estuarine/marine research that may offer insight on these matters. In 

particular, research target processes influencing Extra Mortality as identified in PATH may be 

most instructive. That body of research is still being formulated as part of the Research 

Monitoring and Evaluation Plan, developed by the Action agencies, in response to the FCRPS 

BO.

3.1.1 Flow and Migration Speed

Early investigations described the migratory characteristics of spring/summer yearling chinook 

and steelhead through the Snake and Columbia rivers (Ebel and Raymond 1976, Bentley and 

Raymond 1976). Typically, travel time and/or survival estimates for the composite wild and 

hatchery populations were presented, often in the form regression analyses that included 

estimates from a number of years (Sims and Ossiander 1981).

Impoundment of the Snake and Columbia Rivers has decreased the migration speed of yearling 

chinook salmon and steelhead. Ebel and Raymond (1976) estimated that in 1973, yearling 

chinook salmon and steelhead took about 65 days to reach the Dalles Dam from trap sites on the 

Salmon River in Idaho. They suggested this was approximately twice the time required before 

dam construction. Bentley and Raymond (1976) also presented data that indicated migration of 

smolts was slower after impoundment. Following the construction of Lower Monumental and 

Little Goose dams on the Snake River, yearling chinook smolts took about twice as long to 

traverse the distance from release sites on the Salmon River to Ice Harbor Dam.

NMFS investigators first provided evidence that prevailing river discharge volumes influenced 

the rate of migration through certain segments of the Snake and Columbia rivers. Sims et al. 

(1978) observed that during the dramatically low flows in 1977, yearling chinook traversed the 

reach from those same Salmon River traps to the Dalles Dam in 57 days; whereas, in 1975 and 

1976 Sims et al. (1976 and 1977) indexed travel time at 21 and 27 days, respectively, about half 

that observed in 1977 with the same numbers of dams in place. In 1976 and 1977, the flow 

index for the Snake River ranged from 110-140 kcfs, whereas in 1977 it was 40 kcfs as reported 
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by Giorgi (1993). These data sets provided the first quantitative treatment of the relationship of 

flow on smolt migration speed through the hydroelectric system.

Sims and Ossiander (1981) expanded the data set and presented a synthesis of flow/travel time 

estimates for the yearling chinook and steelhead for the years 1973-1979. They correlated 

annual indices of travel time with the flow at Ice Harbor Dam during the migration peak. The 

correlation indicated that in years when flows were high, fish moved faster from the upper dam, 

either Little Goose of Lower Granite, to the Dalles Dam.

The Fish Passage Center has continued to add to this smolt travel time data set since 1984. In 

1993, Berggren and Filardo (1993) synthesized information available through 1990, and 

analyzed smolt travel time as associated with a number of predictor variables including flow, 

water temperature, and release date (a surrogate for the level of smolt physiological 

development). They found that combinations of these variables provided the best explanation of 

the observed variability in smolt travel time. However, they reported that average river flow 

explained most of the variability observed in smolt travel time multiple-regression models for 

most stocks. They reported flow-travel time algorithms for Snake River yearling chinook and 

steelhead, and steelhead from the mid-Columbia, as well as sub-yearling chinook migrating 

through John Day Pool. No model could be developed that was satisfactory for explaining the 

observed travel time of yearling chinook in the mid-Columbia, from RIS to MCN Dam.

How much change in smolt travel time do these models predict per unit flow? To depict this we 

offer one example. Using the Berggren and Filardo (1993) bivariate flow-based model for Snake 

River yearling chinook, Giorgi (1993) predicted the change in travel time attributable to 

incremental increases in river discharge. He demonstrated that when base flows were low, the 

proportionate change in travel time was highest. For example, as Snake River flow increased 

from 40 to 50 kcfs, the average travel time per project decreased from 5.0 to 4.2 days, whereas 

when flows increased from 100 to 110 kcfs, travel time decreased by only 1/10 of a day, from 

2.7 to 2.6. Clearly the most dramatic responses would be expected in low flow years.

Giorgi et al. (1994) examined a data set for freeze-branded sub-yearling chinook migrating 

through the John Day Pool. Using data from 1981-1983, they failed to find a consistent 
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relationship between smolt travel time and any of the three-predictor variables (flow, water 

temperature or release date). They characterized the migratory patterns as a complicated mix of 

rearing and migratory behavior, often punctuated by extensive upstream excursions of several 

kilometers. They also noted that strong correlations among the predictor variables limited 

analytical opportunities for confidently identifying causative agents affecting travel time. Their 

findings differed from those of Berggren and Filardo (1993).

Recent Investigations--In the 1990’s research focused on identifying a more complete suite of 

factors that influenced migration speed through the hydro-system. The collective research 

indicated that the species responded differently to various factors. Yearling chinook migration 

speed was linked to both flow (water velocity) and/or the level of smolt development (Beeman et 

al. 1991; Muir et al. 1994; Giorgi et al. 1997). Whereas, river discharge (flow) was the dominant 

factor that explained the majority of variability in steelhead migration speed (Giorgi et al. 1997; 

Buettner and Brimmer 2000), and sockeye salmon (Giorgi et al. 1997).

Fall chinook revealed a more complex situation. In the Snake River, flow, water temperature, 

and turbidity have been correlated with migration speed (Muir et al. 1999). Furthermore, the 

predictor variables were correlated among themselves. Over the course of the summer migration 

period, river discharge decreases, temperature increases, and turbidity decreases. In this 

situation, it is very difficult to analytically demonstrate effects attributable to a single predictor 

variable. In the mid-Columbia system Giorgi et al. (1997) found that the size of sub-yearling 

chinook was the best predictor of migration speed between Rock Island and McNary Dams. In 

their multiple regression analysis using four years (1992-1995) of PIT-tag data, no 

environmental variable was identified as being influential.

Evolution of Information--The Fish Passage Center (FPC) has been estimating the travel time of 

smolts for the impounded lower Snake and Columbia rivers since the 1980’s. Over the last 

decade they have adopted the PIT-tag as the preferred tool for documenting migration. 

However, not since the work of Berggren and Filardo (1993) has there been a comprehensive 

multi-year analysis of factors affecting smolt travel time reported by the FPC.
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Similarly, the NMFS has been calculating and reporting smolt travel time estimates on an annual 

basis since 1993. They, too, have not yet formally analyzed the data to assess the factors 

affecting smolt travel time. But it is our understanding such an analysis is underway. According 

to Smith et al. (2000), with regard to exploring relationships among smolt survival, smolt travel 

time, smolt quality, system operations, and environmental conditions, such analyses are 

forthcoming, “Such investigations are ongoing, and results will be published primarily in peerreviewed scientific journals, as they become available.”

Synthesis--Until NMFS and the FPC provide comprehensive analyses from 1993 through 2001, 

the community must rely on previous investigations to characterize smolt behavioral responses to 

water velocity. In summary;

• River discharge appears to be the most influential variable affecting migration speed of 

steelhead and sockeye salmon.

• Both flow and the level of smolt development explain variation in the migration rate of 

yearling chinook salmon (except in the mid-Columbia where only smolt development has 

been identified as a predictor variable).

• At least four variables have been implicated as influencing the migration speed of subyearling (fall or summer/fall) chinook; flow, water temperature, turbidity and fish size. 

Strong correlations among these predictor variables confound the ability to identify 

causative agents.

3.1.2 Flow and Smolt Survival

Translating river flow, or smolt migration rate, into smolt survival is the critical issue 

underpinning the rationale for providing flow augmentation. Its foundation extends back to the 

initial analyses of Sims and Ossiander (1981), who described a positive relationship between 

increased river discharge and the survival of smolts (yearling chinook and steelhead) migrating 

through the Snake River and portions of the Lower Columbia River. That relationship drove the 

adoption of the original “Water Budget” in the 1980s and ultimately flow augmentation, as we 

know it today. However, some investigators have identified limitations associated with those 

early estimates. According to Williams and Matthews (1995), the 1970s data (Figure 3.2) 
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reflected conditions that no longer exist in the contemporary hydro-system. They suggest that 

the high smolt mortality witnessed in low flow years was in part associated with slow migration, 

but was exacerbated by sub-optimal turbine and powerhouse operations. Such operations are not 

in place today. For this reason they concluded that the Sims and Ossiander flow-survival 

relationship will probably not accurately predict the survival of yearling chinook under present 

hydrosystem conditions. They did not dispute the existence of a flow-survival relationship, just 

that the historical one had little application and new data were required. Their paper was a 

prelude to a new era of smolt survival analysis in the Columbia and Snake rivers. It set the stage 

for acquiring representative smolt survival estimates under contemporary conditions.

Figure 3.2 Survival estimates for juvenile spring and summer chinook salmon, 

Oncorhynchus tshawytscha, migration through the upper dam (Little Goose Dam, 1973-74; 

Lower Granite Dam, 1975-79) on the lower Snake River to either John Day Dam (1976-79) 

or The Dalles Dam (1973-75) compared with the average river flow at Ice Harbor Dam 

during the period (± 7 days) of peak migration for the years 1973 through 1979 (from 

Williams and Matthews 1995).

Cada et al. (1997), reviewed literature from within and outside of the Columbia River Basin 

relating to the influence of water velocity on the survival of juvenile salmon and steelhead. Most 

of the studies they reviewed identified a positive relationship between outmigration flows and 

survival, but they noted there was substantial uncertainty regarding many of the estimates. For 

example, early survival estimates made in the basin did not estimate variances or identify 

potential biases or errors. In many cases the relationships described did not investigate 
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interactions with factors other than water velocity. Other influential factors that were examined 

in the review included predation, water quality, and physiological state of the smolts at the time 

of migration. Despite the limitation of existing data, Cada et al. (1997) felt the general 

relationship of increasing smolt survival with increasing flow in the Columbia River Basin still 

appeared to be reasonable.

3.1.3 Recent Estimates of Smolt Survival

Yearling Chinook Salmon and Steelhead--In the NMFS (2000) White Paper on smolt survival 

and flow, the authors summarized two decades of yearling chinook survival estimates and flow 

indices. Using annual survival and flow indices, they failed to identify a relationship between 

the two variables. Even more recently, Zabel et al. (in press) updated the multi-year flowsurvival plot for yearling chinook salmon, including estimates from 2001-drought year (Figure 

3.3). On an average per-project basis, 2001 inriver survival was certainly one of the lowest 

observed since 1993, but it was similar to estimates obtained in 1993 and 1984, and did not 

approach the depressed levels estimated in 1973 and 1977. Using their survival index as a 

performance measure, a pronounced flow effect is not readily apparent for yearling chinook. In 

contrast, on the same graph they depict data from the 1970’s when a flow-survival relationship 

was evident.
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Figure 3.3Per-project survival versus river flow for Snake River spring-summer chinook 

salmon (from Zabel et al. In press).

NMFS (2000b) also examined the PIT-tag data (1995-1998) in greater detail and plotted the 

survival of individual release groups against corresponding flow indices for both yearling 

chinook and steelhead (Figures 3.4 and 3.5). No relationship was apparent. They plotted the 

same survival estimates against the median travel time of each group and found no relationship 

with migration rate. They did, however, identify a strong consistent inverse relationship between 

travel time and flow for yearling chinook salmon. They suggest that in the absence of a flow or 

migration rate-survival relationship, some other benefits may be provided by the swifter 

migration as mediated by increased flow levels. They speculate that higher flows may improve 

estuary and Columbia River plume conditions and associated survival through those zones, but 

offered no empirical evidence for such. Interestingly, NMFS research efforts are now staged in 

an attempt to investigate such mechanisms in 2002 and beyond.
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Figure 3.4 Relationship among median travel time (days) and estimated survival from 

Lower Granite Dam to McNary Dam, and flow exposure index (kcfs measured at Lower 

Monumental Dam, yearling chinook salmon, 1995-1998 (from NMFS 2000b).

Figure 3.5Relationship among median travel time (days) and estimated survival from 

Lower Granite Dam to McNary Dam, and flow exposure index (kcfs) measured at Lower 

Monumental Dam, steelhead, 1995-1998. (from NMFS 2000b).

In contrast to yearling chinook, estimates that Zabel et al. (in press) presented for steelhead 

indicate a dramatic decrease in survival during 2001 as compared to other years over the last 

decade (Figure 3.6). Two factors are implicated as causing this dramatic increase in inriver 

mortality of Snake River steelhead. First, of all the salmon species, steelhead migration speed 

appears to be the most sensitive to flow and associated water velocity. This position is based on 

relatively strong correlations reported by Berggren and Filardo (1993) and Giorgi et al. (1997). 

Secondly, water temperatures got hotter sooner, in 2001 than they had in the preceding three 

years (see DART web page for inspection of these data). This pattern was evident in both the 

lower Snake and Columbia Rivers. More importantly, water temperatures exceeded 12°C early 

in the steelhead migration. This, coupled with slow migration speed, can compromise the 

migratory process in steelhead. Increasing water temperature can disrupt the migratory behavior 
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of steelhead. Steelhead smolts commonly remain in the system, and there is laboratory evidence 

that suggest temperatures in excess of 12°C may cause reversion from smolt to parr (Zaugg and 

Wagner 1973). It is plausible that if migration is slow as witnessed in 2001 (Zabel et al. in 

press), then steelhead smolts could be exposed to seasonally increasing water temperatures, and 

increased risk of residualization.

Figure 3.6 Estimated per-project survival (i.e., per dam/reservoir combination) with 

standard errors for yearling chinook salmon and steelhead from 1993 through 2000. Number 

above bar is the number of projects over which survival was estimated (from Zabel et al. In 

press).

Snake River Fall Chinook Salmon--For fall chinook salmon, the best information has been 

reported by Muir et al. (1999). Using PIT-tagged juveniles from Lyons Ferry Hatchery, they 

estimated survival in the lower Snake River. From release sites upstream from Lower Granite 

Dam to that site they found significant correlations between survival and all three environmental 

variables they examined (flow, water temperature and turbidity). Over the course of the summer, 

survival decreased when flows and turbidity decreased and water temperature increased. 

Predictor variables were highly correlated, confounding the ability to identify the causative 

agents.

As fish migrated from Lower Granite Dam to Lower Monumental Dam, the range of 

environmental conditions encountered by juvenile fall chinook in 1995 and 1996 appeared to be 
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narrow and may have obfuscated any relationships with survival. But in 1997, significant 

correlations between smolt survival and each of the three predictor variables were apparent, with 

temperature, then flow and turbidity showing the greatest r-squared values, respectively (Muir et 

al. 1999).

3.2 Premise 2–Lowering water temperature in the summer improves migratory and 

rearing conditions for juvenile and adult salmonids, ultimately improving survival.

Within the impounded lower Snake River, summer water temperatures can reach levels that 

impose risks to juvenile and adult salmonids. During the summer, juvenile fall chinook rear and 

migrate through that river segment, and adult steelhead and fall chinook migrate upstream. River 

temperatures can often exceed 20°C (Giorgi and Schlecte 1997). Temperature tolerance for 

juvenile fall chinook has been reported to range from 5.5 to 20°C (Groves 1993). This suggests 

that juvenile fall chinook can be at risk associated with inhospitable thermal conditions in the 

Snake River. If there were a means to reduce water temperature, particularly to below 20°C, this 

would minimize such risk.

Water temperature is also an important factor affecting predation-related mortality incurred by 

juvenile salmon. Reducing water temperatures below 20°C can be beneficial in decreasing the 

consumption rates of northern pikeminnow, (Ptychocheilus oregonensis), a primary predator of 

salmon smolts. Vigg and Burley (1991) developed a model that predicts that decreasing water 

temperature from 21.5 to 17°C could reduce the number of prey consumed by pikeminnow from 

7.01 to 4.25 per day. This suggests that water temperature regulation in the Snake River could 

indirectly provide survival benefits to juvenile fall chinook.

Lower water temperatures in the summer can also be advantageous for adult salmonids as they 

migrate upstream. Both fall chinook and steelhead are migrating upstream in the late summer 

when temperatures are highest. Bjornn and Peery (1992) reviewed literature regarding adult 

passage in the lower Snake River. They reported that steelhead appear to delay migration when 

water temperatures exceed 21-22°C (although they did caveat that data were limited).
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Overall, it appears that if water temperatures in the Snake River could be maintained below 

20°C, this would minimize risk to adult and juvenile life stages. However, we have not 

encountered any analyses that would permit one to predict survival changes as related to water 

temperature.

3.3 Flow Augmentation Evaluations

None of the information presented thus far constitute analyses of the effectiveness of flow 

augmentation. Establishing general relationships between flow and either migration speed or 

survival certainly provides a rationale for entertaining flow augmentation as a strategy to 

improve survival. However, an evaluation of the biological benefits of providing additional 

water in any particular year has many facets and requires a more focused analysis. In 1996, BPA 

funded a flow augmentation evaluation study (Giorgi and Schlecte 1997) and directed the 

investigators to address four key objectives:

1. Determine the volume and timing of water that was drafted from storage reservoirs 

and provided above base flows, which could be identified as flow augmentation for 

anadromous fish.

2. Estimate the extent to which flow augmentation increased water velocity or 

decreased water temperature as compared to base conditions.

3. Predict the magnitude of fish responses in terms of smolt migration speed or 

survival, as attributable to that incremental change in environmental conditions (flow, 

temperature).

4. Identify the degree to which populations of interest (ESA-listed stocks) were exposed 

to FA events.

BPA felt these were fundamental issues that required resolution in the context of a 

comprehensive evaluation of flow augmentation effectiveness. Most of these objectives first 

emerged and were analytically treated in a comprehensive System Operation Review that was 

conducted by the Action Agencies and completed in 1994. Surprisingly, few, if any, 

comprehensive evaluations of flow augmentation have been published, which address all or even 
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most of the issues identified above. Typically, the annual reports published by the FPC address 

objectives 1 and 4. Objectives 2 and 3 are not explicitly analyzed, except in terms of reporting 

general smolt travel time or survival estimates on an annual basis. The NMFS BO is deficient in 

this regard as well. BO specifies volumetric (in Maf) standards for flow augmentation, and 

prescribes seasonal flow (kcfs) targets. However, no quantitative analysis describing the change 

in water velocity, smolt speed or survival benefits is offered that can be attributed to providing 

the additional water through flow augmentation. Furthermore, the smolt passage model 

(SIMPAS) used in the BO lacks an explicit flow-survival function or any flow-related 

mechanisms to affect survival through reservoirs. As a consequence, that model, as currently 

configured, is incapable of predicting the change in survival attributable to flow augmentation. 

Dreher (1998) provided a very general assessment of the effectiveness of flow augmentation in 

changing water velocity and meeting the flow targets specified in the BO. He concluded that the 

volumes of water in storage reservoirs currently earmarked for flow augmentation in the Snake 

River: 1) provide only small incremental increases in average water velocity through the 

hydrosystem, and 2) is insufficient to meet flow targets in all years. However, his analysis 

offered no insight with respect to the fish responses. Clearly it was quite limited in scope and 

thus offers little utility in terms of assessing benefits of flow augmentation. In fact, the author 

did not purport his analysis to be an evaluation of flow augmentation, but rather a treatment of 

some rather specific water issues.

Connor et al. (1998) conducted a study that had implications to summer flow augmentation in the 

Snake River. Using PIT-tagged juvenile fall chinook that reared upstream from Lower Granite 

Dam, they regressed tag detection rates at the dam (survival index), against flow and temperature 

separately. They found that over four years, the detection rate was positively correlated to mean 

summer flow (r-squared = 0.993, P = 0.003) and negatively correlated with maximum water 

temperature (r-squared = 0.984, P = 0.008). They acknowledged that the predictor variables 

were highly correlated, limiting specific inferences regarding the effects of the individual 

variables. They also graphically depicted the temperature changes coincidental with flow 

augmentation from Dworshak Dam and the Hell’s Canyon Complex in 1993 and 1994. Water 

temperatures at Lower Granite Dam dropped approximately 5-6°C during the period of flow 
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augmentation. They concluded that summer flow augmentation especially cooler water released 

from Dworshak Reservoir could improve survival of juvenile fall chinook, at least to arrival at 

Lower Granite Dam. This evaluation was one of the more well-rounded appearing in the 

literature. However, it would be advantageous if the geographic impact zone could be expanded 

beyond the single dam (LGR). Also, some indication of the change in water velocity attributable 

to the flow augmentation would be instructive. Nevertheless, their approach offers a model for 

future assessments, particularly if true survival estimates, rather than detection rates, can be used 

as the response variable.

In 1997, Giorgi and Schlecte (1997) conducted an evaluation of the effectiveness of flow 

augmentation in the Snake River for the years 1991-1995. The purpose of that BPA-funded 

study was to estimate the volumes and shape of flow augmentation water delivered to the Snake 

River, and to assess the biological consequences to ESA-listed stocks. There were four steps to 

the study:

1. Provide an independent estimate of the volume and shape of water drafted from 

storage reservoirs that could be classified as flow augmentation.

2. Estimate the incremental change in water velocity and temperature that was 

attributable to the water delivered as flow augmentation.

a. Two physical models were used to estimate the changes in water velocity –

HEC-2 and CRiSP

b. Changes in water temperature attributable to flow augmentation were 

estimated with time series analysis.

3. Estimate the incremental change in smolt migration speed and survival (where 

possible) for yearling chinook, steelhead and fall chinook salmon associated with 

providing the flow augmentation water.

a. Models included CRiSP, Berggren and Filardo (1993), and a fall chinook 

migration model by Connor et al. (1994).

4. Estimate to what extent ESA-listed salmonid populations encountered flow 

augmentation events.
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They found that for the years 1991-1995, the Snake River flow augmentation volume ranged 

from an annual low of 1.35 to 2.56 Maf. Those volumes were insufficient to sustain the flow 

targets established by NMFS for the duration of the smolt migration period. However, over the 

five years, flow augmentation increased water velocity through Lower Granite Pool an average 

of 3-13% (Figure 3.7). During the summer, the increase was more pronounced with an increase 

of 5-38% change in water velocity attributable to providing flow augmentation water.

Correspondingly, the change in smolt travel time predicted by the different passage models 

varied considerably (Figure 3.8). For example, the decreases in travel time for yearling chinook 

ranged from 5-16% over five years, whereas CRiSP predicted a 0-5% decrease. Only the CRiSP 

model was readily available for application in predicting survival through Lower Granite Dam 

and through to Ice Harbor Dam. Those results are depicted in Figure 3.9.
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Figure 3.7  Estimated increase in water velocity (as a percentage of total velocity) that is 

attributable to flow augmentation volumes as estimated by HDR during the springs (10 April 

– 20 June) and summers (21 June – 31 August) 1991-1995 (from Giorgi and Schlecte 1997).

Figure 3.8  Percent decrease (i.e., benefit attributable to flow augmentation) in estimated 

smolt travel times (average of the median travel times for each of the three release dates) for 

yearling chinook using base flows calculated by HDR. The asterisk in 1993 indicates that 

the CRiSP model predicted no change in travel time associated with flow augmentation 

(from Giorgi and Schlecte 1997).
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Figure 3.9 Average increase in survival attributable to flow augmentation for yearling 

chinook, steelhead, and sub-yearling chinook from release point at the head of Lower Granite 

Pool (a) through Lower Granite Dam and (b) to Ice Harbor Dam. Survival estimates were 

derived using the CRiSP model under three release scenarios (i.e., Early, Mid and Late) 

(from Giorgi and Schlecte 1997).

Since Giorgi and Schlecte (1997) conducted their analyses, the models have been updated. 

Furthermore, over the last five years, a variety of empirical passage-related estimates have been 

acquired and need to be incorporated into the passage models. No doubt some of their results 

would change to some extent if the same years were analyzed today with updated information. 

That is not important in the context of future assessments. We do, however, suggest that the 

approach used by these investigators, and that of Connor et al. (1998) offer tractable models for 

future flow augmentation evaluations.
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Temperature Control Studies--Several investigations evaluated the effectiveness of Snake River 

FA in reducing summer water temperature in the Lower Snake River. Specifically, the use of 

Dworshak Reservoir as a coldwater source for decreasing water temperature in August and early 

September has been the focus of investigators (Karr et al.1992; Karr et al. 1998; Bennett et al. 

1997). Karr et al. (1992) first provided results that indicated that strategic releases of outflow 

from Dworshak Reservoir could reduce water temperature in the Snake, at least to the vicinity of 

LGR Dam. Bennett et al. (1997) conducted a more comprehensive study involving water 

temperature model analysis and field monitoring for the years 1991-1993. They established that 

the Army Corps of Engineers model (COLTEMP) provided reliable predictions of changes in 

water temperature associated with flow augmentation releases upstream. The reduction in Snake 

River water temperature associated with coldwater releases from Dworshak Reservoir was 

greatest at LGR and diminished as water moved downstream to IH. Depending on the year and 

base flow characteristics, the change in temperature at LGR typically ranged from 1-4 °F. 

However, the model predicted differences as great as 6-8 °F, which extended for a period of 

several weeks. Here again, the prediction depended on base flows and the volume released for 

flow augmentation. At Ice Harbor Dam the decrease in temperature was typically small, on the 

order of 1-2 °F. They also reported that the cold water released upstream tended to sink toward 

the bottom of the reservoirs, and mixed at the dams. This suggests that deep cool water may be 

available as refugia, but cooling throughout the water column cannot be realized. Also the 

degree of cooling decreases in the lower reaches of the river. As yet, biological information has 

not been integrated with this or similar evaluations. The authors recommended that this is a 

necessary next step.

Benefits and Risks to other species--Drafting flow augmentation water from storage reservoirs 

alters conditions within the storage reservoirs and in the tributaries connecting with the 

Columbia and Snake rivers. These processes in turn have effects on resident fish inhabiting 

those waters. This introduces a broad and complex facet attending the implementation of flow 

augmentation. It is beyond the scope of this paper to treat this topic in detail, but we identify key 

issues. Risks associated with flow augmentation were broached by the Independent Scientific 

Group’s publication “Return to the River”. Therein they expressed uncertainty regarding the 
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magnitude of a flow-survival, and the strategy to use non-seasonal flow augmentation in an 

attempt to force subyearling chinook from the mainstem (ISG 1996). In their words,

“Underscoring these substantial uncertainties in flow augmentation rationale is 

the fact that summer drawdowns in upstream storage reservoirs, for example 

Hungry Horse Reservoir in Montana, to accomplish summer smolt flushing in the 

lower Columbia river has direct and potentially negative implications for nutrient 

mass balance and food web productivity in Flathead Lake, located downstream 

from Hungry Horse. “

The issue they raise involves balancing expected benefits to anadromous fish against ecosystem 

function and potential risk to other native species. The Kootenai River white sturgeon inhabit 

waters downstream from Libby Dam, and are listed under the ESA. Paragamian and Kruse 

(2001) found that river temperature and river stage (sensitive to flow) were the best predictors of 

female sturgeon migrating to spawning areas in the Kootenai River. Part of the recovery effort 

for this species involves drafting water from Libby reservoir at strategic times during the spring. 

Depending on the magnitude and timing of the water releases, these actions could compete 

against or enhance flow augmentation that targets anadromous salmonids in the Columbia River.

Clearly a complex array of water management activities has evolved in the Columbia Basin. The 

net balance among competing and complementary strategies is uncertain. Apart from the System 

Operation Review conducted in the early 1990s, we have not encountered a comprehensive 

multidisciplinary evaluation of flow augmentation, which attempts to assess and quantify the full 

suite of benefits and risks to anadromous and resident fish species and their habitat. The 

tendency has been for groups to focus on the species under their jurisdiction, or within their 

geographic zone.

3.5 Summary

Flow effects on smolt migration speed: For most species the evidence indicates that increased 

flow (water velocity) contributes to swifter migration speed. Information regarding fall chinook 

is equivocal. River discharge appears to be the most influential variable affecting migration 

speed of steelhead and sockeye salmon in the Snake and Mid-Columbia rivers. For yearling 

chinook salmon, flow, and the degree of smolt physiological development, explain the observed 
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variation in the migration rate (except in the mid-Columbia where only smolt development has 

been identified as a predictor variable). At least four variables have been implicated as 

influencing the migration speed of sub-yearling (fall or summer/fall) chinook; flow, water 

temperature, turbidity, and fish size. However, strong correlations among these predictor 

variables confound the ability to identify causative agents.

Flow effects on smolt survival based on PIT-tag estimates acquired since 1993 provide the most 

relevant data set for characterizing smolt survival dynamics through the impounded mainstem 

Snake and Columbia rivers. Based on recent estimates there is little evidence supporting a flowsurvival relationship across the water years experienced from 1993-2000, for yearling chinook or 

steelhead. However, in 2001 under the extreme low flow conditions, steelhead survival 

decreased dramatically to about 63% per project (typically it is near 90%). Slow migration speed 

and rapidly increasing water temperatures are implicated as causative factors affecting 

residualization and mortality. A complex of factors are implicated as influencing Snake River 

fall chinook survival, including flow, water temperature and turbidity. These environmental 

variables are strongly correlated during the summer migration, confounding the ability to 

identify the most influential one. Knowing if water velocity or temperature is the most 

influential could be important when the decision is to use Dworshak or Hell’s Canyon for flow 

augmentation, since the temperature of those water sources differs greatly.

The premise for reducing summer water temperature, particularly in the Snake, to improve 

rearing and migratory conditions for juvenile fall chinook and adult salmonids appears sound. 

The literature indicates that maintaining river temperatures at or below 20°C is advantageous to 

both life stages of fall chinook, and adult steelhead, which are in the river in August and early 

September.

However, it is not clear that releasing cool water from Dworshak effectively alters the thermal 

structure of most of the Lower Snake River. The major effect is localized at two upper reservoirs 

(LGR, LGO). Based on results reported by Bennett et al. (1997), when cool water enters the 

reservoirs it sinks to the bottom. This can provide cool refugia in deeper waters, but not uniform 

cooling of reservoirs. The greatest change in temperature attributable to FA releases from 
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BioAnalysts, Inc. January 2002

Dworshak are evident at LGR, where water temperatures with FA are predicted to be as much as 

4-8° F lower than base conditions at certain times. At Ice Harbor the difference is on the order of 

1-2° F.

Comprehensive flow augmentation evaluations are generally lacking. Only a handful of studies 

have attempted to quantify the volume and shape of water provided specifically as FA, and 

translate that incremental increase in flows to changes in water velocity and temperature. 

Certainly there is a need for a prediction of the change in smolt travel time and survival 

attributable to those increases and to identify whether populations of interest (e.g. ESA stocks) 

have sufficiently encountered flow augmentation events. The last such evaluation treated 

information through the 1995 water year, and only for the Snake River. Given the community’s 

sensitivity to this controversial management action, a holistic comprehensive updated evaluation 

seems prudent, and long overdue. The scope of future evaluations need to more fully address the 

balance of benefits and risks between anadromous and resident fish resources.

3.6 Critical Uncertainties and Research Opportunities

Flow-survival relationships for spring-migrating species--In the Snake River, the NMFS PITtag-based smolt survival estimates acquired since 1993 form a strong foundation for examining 

and defining such relationships. It is our understanding those efforts will, and in our view 

should, continue to be expanded geographically to the lower and upper Columbia River, when 

and where possible. Radio telemetry, or some other device, may need to be employed in the 

upper Columbia because PIT detector installations are lacking and the opportunities to install 

them are not readily apparent.

Factors influencing fall chinook survival--Disentangling the complex of factors that are 

implicated as influencing Snake River fall chinook salmon survival is an important goal, because 

it may guide decisions regarding the most suitable water source for use in FA. To accomplish 

this may require well-designed experimental manipulation of Dworshak and Hell’s Canyon 

dams. Established management practices and political considerations may limit opportunities in 
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BioAnalysts, Inc. January 2002

this regard. Absent a well-designed experiment, we will likely be left with the equivocal results 

we now have.

Holistic evaluations of FA effectiveness--A multi-faceted, comprehensive evaluation of the 

biological benefits and risks associated with flow augmentation is advisable. Wherever possible, 

quantitative analyses should be undertaken. The effort will require physical and smolt passage 

modeling. Updating certain tools will be required, given the abundance of passage and survival 

information collected since the models used in PATH were constructed and validated. To fully 

address concerns regarding anadromous fish and resident fish will require a significant effort. 

But without such an effort it is not clear how the region can determine if the status quo as 

prescribed in the FCRPS is an effective water management strategy for measurably improving 

salmon survival.
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3.7 Literature Cited

Beeman, J., D. Rondorf, J. Faler, P. Haner, S. Sauter, and D. Venditti. 1991. Assessment of 

smolt condition for travel time analysis. 1990 Ann. Rep. To BPA, DOE/BP-35245-4, 71 

p.

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. 

Bentley, W. B., H. L. Raymond. 1976. Delayed migrations of yearling chinook salmon since 

completion of Lower Monumental and Little Goose Dams on the Snake River. TAFS, 

105:422-424.

Berggren, T. J., and M. J. Filardo. 1993. An analysis of variables influencing the migration of 

juvenile salmonids in the Columbia River basin. NAJFM. 13(1):48-63.

Bjornn, T. C., and C. A. Peery. 1992. A review of literature related to movements of adult 

salmon and steelhead past dams and through reservoirs in the Lower Snake River. U. S. 

Army Corps of Engineers, Walla Walla District. 79 p.

Buettner, E. W., and A. F. Brimmer. 2000. Smolt monitoring at the head of Lower Granite 

reservoir and Lower Granite Dam. Ann. Report 1998 Operations. DOE/BPA, Contract 

No. DE-B179-83BP11631 

Cada, G. F., M. D. Deacon, S. V. Mitz, and M. S. Bevelhimer. 1997. Effects of water velocity 

on the survival of downstream-migrating juvenile salmon and steelhead: a review with 

emphasis on the Columbia River. Rev. Fish. Sci. 5(2):131-183.

Connor, W. P., H. L. Burge, and W. H. Miller. 1994. Rearing and emigration of naturally 

produced Snake River fall chinook salmon juvenile. In Identification of the spawning, 

rearing and migratory requirements of fall chinook salmon in the Columbia River Basin. 

Ed. D. W. Rondorf and W. H. Miller. Annual Progress Report of 1992 by the United 

States Fish and Wildlife Service, Contract DE-AI79-91BP21708, to Bonneville Power 

Administration, Portland, OR. pp 92-38

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. 

NAJFM. 18:530-536.

Dreher K. J. 1998. Competing for the Mighty Columbia River- Past, Present and Future: The 

Role of Interstate Allocation. A view on Idaho’s experience with flow augmentation. 
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BioAnalysts, Inc. January 2002

Presented to: American Bar Association section of natural resources, energy and 

environmental law. April 30-May 1, 1998. Boise, Idaho. 16 p.

Ebel, W., and H. Raymond. 1976. Effects of atmosphere gas saturation on salmon and steelhead 

trout of the Snake and Columbia rivers. NMFS, Marine Fisheries Review, 38(7):1-14.

Giorgi, A. E. 1993. Flow augmentation and reservoir drawdown: strategies for recovery of 

threatened and endangered stocks of salmon in the Snake River Basin. Recovery issues 

for threatened and endangered Snake River salmon: Technical Report 2 of 11. 

DOE/BPA, Project No. 93-013, Contract No. DE-AM79-93BP99654. 50 p.

Giorgi, A. E., D. R., Miller, and B. P. Sanford. 1994. Migratory characteristics of juvenile 

ocean-type chinook, Oncorhynchus tshawytscha, in John Day Reservoir on the Columbia 

River. Fish. Bull., U.S. 92:872-879.

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.

Giorgi, A. E., and J. W. Schlecte. 1997. Evaluation of the effectiveness of flow augmentation in 

the Snake River 1991-1995. Bonneville Power Administration, DOE/BP-24576-1, 

Portland, OR.

Groves, P. A. 1993. Habitat available for, and used by, fall chinook salmon within the Hell’s 

Canyon Reach of the Snake River. 1992 Annual Progress Report, Environmental Affairs 

Department, Idaho Power Company, Boise, ID.

Independent Scientific Group (ISG). 1996. Return to the River: restoration of salmonid fishes in 

the Columbia River ecosystem. Prepublication copy, September 10, 1996, available 

from: Northwest Power Planning Council, Portland, Oregon. 584 p.

Karr, M., B. Tanovan, R. Turner, D. Bennett. 1992. Water temperature control project, Snake 

River, interim report: Model studies and 1991 operations. Columbia River Inter-Tribal 

Fish Commission, U.S. Army Corps of Engineers, Univ. of Idaho.

Karr, M. H., J. K. Fryer, 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. Fisheries and Aquatic Sciences, Lake Oswego, OR. 

Muir, W. D., W. S. Zaugg, A. E. Giorgi, and S. McCutcheon. 1994. Accelerating smolt 

development and downstream movement in yearling Chinook salmon with advanced 

photoperiod and increased temperature. Aquaculture, 123:387-399.

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) 
Flow Augmentation Page 85 Northwest Power Planning Council

BioAnalysts, Inc. January 2002

to Bonneville Power Administration, Portland, OR. Contracts DE-A179-93BP10891 and 

DE-A179-91BP21708, projects 93-029-00 and 91-029-00, 71 p. BPA report DOE/BP10891-8.

National Marine Fisheries Service (NMFS). 2000. White Paper: Salmonid travel time and 

survival related to flow in the Columbia River Basin. Seattle, WA. 68 p.

Paragamian, V., and G. Kruse. 2001. Kootenai River White Sturgeon spawning migration 

behavior and a predictive model. NAJFM 21:10-21.

Raymond, H. L. 1979. Effects of dams and impoundments on migrations of juvenile chinook 

salmon and steelhead from the Snake River, 1966-1975. Transactions of the American 

Fisheries Society, 108:505-529.

Raymond, H. L. 1988. Effects of hydroelectric development and fisheries enhancement on 

spring and summer chinook salmon and steelhead in the Columbia River basin. North 

American Journal of Fish Management, 8:1-24.

Sims, C.W., W. W. Bentley, R.C. Johnsen. 1977. Effects of power peaking operations on 

juvenile salmon and steelhead trout migrations – progress 1976. NOAA-NMFS-CZES, 

NW/Alaska Fisheries Center;U.S. Army Corps of Engineers. Contract No. DACW68-77-

C-0025, Seattle WA. 

Sims, C.W., W. W. Bentley, R.C. Johnsen. 1978. Effects of power peaking operations on 

juvenile salmon and steelhead trout migrations – progress 1977. NOAA-NMFS-CZES, 

NW/Alaska Fisheries Center;U.S. Army Corps of Engineers. Contract No. DACW68-77-

C-0025, Seattle WA. 

Sims, C.W., R.C. Johnsen, W. W. Bentley. 1976. Effects of power peaking operations on 

juvenile salmon and steelhead trout migrations 1975. NMFS, Northwest Fisheries 

Center, Seattle, WA.

Sims, C. W., and F. Ossiander. 1981. Migrations of juvenile chinook salmon and steelhead in 

the Snake River, from 1973 to 1979, a research summary. Report to U. S. Army Corps of 

Engineers, Portland, OR. Prepared by National Marine Fisheries Service, Contract No. 

DACW68-78-C-0038. 

Smith, S. G., W. D. Muir, G. A. Axel, R. W. Zabel, J. G. Williams, and J. R. Skalski. 2000. 

Survival estimates for the passage of juvenile salmonids through Snake and Columbia 

River dams and reservoirs, 1999. Report to DOE/BPA, Contract No. 199A117679, 

Project No. 1993-029-00.

Vigg, S., and C. C. Burley. 1991. Temperature-dependent maximum daily consumption of 

juvenile salmonids by northern squawfish (Ptychocheilus oregonensis) from the 

Columbia River. Canadian Journal of Fisheries and Aquatic Sciences. 48:2491-2498.
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Williams, J. G. and G. M. Mathews. 1995. A review of flow and survival relationships for 

spring and summer chinook salmon, Oncorhynchus tshawytscha, from the Snake River 

Basin. Fisheries Bulletin 93:732-740.

Zabel, R.W., S.G. Smith, W.D. Muir, D.M. Marsh, J.G. Williams, J. R. Skalski. 2001. Survival 

estimates for the passage of spring-migrating juvenile salmonids through Snake and 

Columbia river dams and reservoirs, 2001. Prepared for DOE/BPA, Contract No.DEAI79-93BP10891, Project No. 93-29.

Zaugg, W. S., and H. Wagner. 1973. Gill ATPase activity related to parr-smolt transformation 

and migration in steelhead trout (Salmo gairdneri): influence of photoperiod and 

temperature. Comp. Biochem. Physiol. 45:955-965.
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4.0 APPENDICES
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Appendix A-1. Seasonal flow objectives prescribed for spring and summer on the Snake River at Lower 

Granite Dam and on the Columbia River at Priest Rapids, McNary, and Bonneville dams (NMFS 2000).

Spring Summer

Location Dates Flow (kcfs) Dates Flow (kcfs)

Snake River at Lower Granite Dam 4/03-6/20 85-100 6/21-8/31 50-55

Columbia River at Priest Rapids 

Dam

4/10-6/30 135 NA NA

Columbia River at McNary Dam 4/10-6/30 220-260 7/01-8/31 200

Columbia River at Bonneville Dam 11/1 -

Emergence

125-160 NA NA
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Appendix A-2. Seasonal flow objectives at Lower Granite, Priest Rapids, and McNary dams 

based on different forecasts of runoff volumes (NMFS 2000). 

Flow Determination

Location Season Forecast

Volume Forecast

(Maf)

Flow Objective 

(kcfs)

< 16 85

> 16 and ≤ 20 85-100

Lower Granite 

Dam

Spring Based on the April final runoff 

volume forecast at Lower

Granite Dam for April to July.

> 20 100

< 80 220

> 80 and ≤ 92 220-260

 Lower Granite 

Dam

Summer Based on the June final runoff 

volume forecast at Lower

Granite Dam for April to July.

> 28 55

Priest Rapids Dam Spring NA NA 135

< 80 220

> 80 and ≤ 92 220-260

McNary Dam Spring Based on the April final runoff 

volume forecast at the Dalles

dam for April to August

> 92 260

McNary Dam Summer NA NA 200
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Appendix A-3. Estimated spill levels and gas caps for FCRPS projects during spring (all) and 

summer (non-transport projects) (NMFS 2000).

Estimated Spill Level2 Hours

Project1(kcfs) (military) Limiting Factor

Snake River

Lower Granite Dam 60 1800-0600 Gas cap

Little Goose Dam 45 1800-0600 Gas cap

Lower Monumental Dam 40 24 hours Gas cap

Ice Harbor Dam 100 (night) 24 hours Nighttime -gas cap

45 (day) Daytime-gas cap

Columbia River

McNary Dam 12-150 1800-0600 Gas cap

John Day Dam 85-160 /60%3 (night) 1800-06004 Gas cap/percentage

The Dalles Dam 40% of instant flow 24 hours Tailrace flow pattern and 

survival concerns (ongoing 

studies)

Bonneville Dam 90-150 (night) 24 hours Nighttime -gas cap

75 (day) Daytime-adult fallback

1

 Summer spill is curtailed beginning on or about June 20 at the four transport projects (Lower Granite, Little Goose, Lower Monumental, and 

McNary dams) due to concerns about low inriver survival rates.

2

 Estimated spill levels shown in the table will increase for some projects as spillway deflectors optimization measures are implemented. 

3

 The TDG cap at John Day Dam is estimated at 85 to 160 kcfs, and the spill cap for tailrace hydraulics is 60%. At project flows up to 300 kcfs, 

spill discharges will be 60% of instantaneous project flow. Above 300 kcfs project flow, spill discharges will be at the gas cap (up to the 

hydraulic limit of the powerhouse).

4

 Spill at John Day Dam will be 7:00 p.m. to 6:00 a.m. (night and 6:00 a.m. to 7:00 p.m. (day) between May 15 and July 31.
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Appendix B. Estimates for survival for various passage routes at Bonneville, The Dalles, Lower Monumental, Lower Granite, 

Wanapum, Rock Island, and Rocky Reach dams on the Columbia and Snake rivers. References to footnotes appear on the last page.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

Bonneville Dam

1995 Hatchery Chinook Spill 1.0 0.991-1.0 BT Normandeau et al. (1996c) Spillbay with flow deflector (Spillbay 4); 12,000 cfs; 90% C.I.

1995 Hatchery Chinook Spill 1.0 0.977-1.0 BT Normandeau et al. (1996c) Spillbay without flow deflector (Spillbay 2); 12,000 cfs; 90% C.I.

The Dalles Dam

1995 Hatchery Chinook Spill 0.955 0.927-0.982 BT Ploskey et al. (2001)1 Unmodified spillbay (Bay 3); 10,500 cfs; 90% C.I.

1995 Hatchery Chinook Spill 0.993 0.972-1.02 BT Ploskey et al. (2001)1Spillbay 4; surface flow bypass vertical I-slot; 10,500 cfs; 90% C.I.

1995 Hatchery Chinook Spill 0.990 0.951-1.00 BT Ploskey et al. (2001)1Spillbay 6; surface flow bypass overflow weir, 4,500 cfs; 90% C.I.

1997 coho Spill 0.871 0.804-0.939 PT Ploskey et al. (2001)264% spill, 95% C.I.

1997 subyearling chinook Spill 0.921 0.855-0.987 PT Ploskey et al. (2001)264% spill, 95% C.I.

1998 coho Sluiceway 0.96 0.87-1.05 PT Ploskey et al. (2001)330% spill, 95% C.I.

1998 subyearling chinook Sluiceway 0.89 0.81-0.98 PT Ploskey et al. (2001)330% spill, 95% C.I.

1998 coho Spill 0.89 0.82-0.96 PT Ploskey et al. (2001)364% spill, 95% C.I.

1998 subyearling chinook Spill 0.75 0.68-0.83 PT Ploskey et al. (2001)364% spill, 95% C.I.

1998 coho Spill 0.97 0.88-1.07 PT Ploskey et al. (2001)330% spill, 95% C.I.

1998 subyearling chinook Spill 0.89 0.80-0.99 PT Ploskey et al. (2001)330% spill, 95% C.I.

1999 Coho and chinook 

yearlings Spill 0.94 0.90-0.97 PT Ploskey et al. (2001)4

64% spill, 95% C.I.

1999 subyearling chinook Spill 0.96 0.92-1.00 PT Ploskey et al. (2001)464% spill, 95% C.I.
Transportation, Spill and Flow Augmentation Northwest Power Planning Council

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Appendix B. Continued.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

The Dalles Dam 

1999 Coho and chinook 

yearlings Spill 0.95 091-0.98 PT Ploskey et al. (2001)4

30% spill, 95% C.I.

1999 subyearling chinook Spill 1.00 0.96-1.04 PT Ploskey et al. (2001)430% spill, 95% C.I.

2000 Coho and chinook 

yearlings Sluiceway 0.95 0.92-0.98 PT Ploskey et al. (2001)5

40% spill, 95% C.I.

2000 subyearling chinook Sluiceway 0.96 0.88-1.04 PT Ploskey et al. (2001)540% spill, 95% C.I.

2000 Coho and chinook 

yearlings Sluiceway 0.976 NA RT Ploskey et al. (2001)6

Spill levels unknown

2000 Coho and chinook 

yearlings Spill 0.95 0.92-0.99 PT Ploskey et al. (2001)5

40% spill, 95% C.I.

2000 subyearling chinook Spill 0.92 0.83-1.01 PT Ploskey et al. (2001)540% spill, 95% C.I.

2000 Coho and chinook 

yearlings Spill 0.929 NA RT Ploskey et al. (2001)6

Spill levels unknown

2000 Coho and chinook 

yearlings Turbine 0.81 0.78-0.84 PT Ploskey et al. (2001)5

40% spill, 95% C.I.

2000 subyearling chinook Turbine 0.84 0.76-0.92 PT Ploskey et al. (2001)540% spill, 95% C.I.

2000 Coho and chinook 

yearlings Turbine 0.856 NA RT Ploskey et al. (2001)6

Spill levels unknown

Lower Monumental Dam

1994 Yearling Chinook Spill 0.984 0.033 PT Muir et al. (2001)7Spillbay 8 without deflector; Relative Recovery method (RR); 125-136 m3/s

1994 Yearling Chinook Spill 0.927 0.023 PT Muir et al. (2001)9Spillbay 7 with deflector; Relative Recovery method (RR); 125-136 m3/s

1994 Yearling Chinook Turbine 0.865 0.018 PT Muir et al. (2001)8 Relative Recovery method (RR); Unit 6B, 135 MW

1995 Yearling Chinook Bypass 0.954 0.034 PT Muir et al. (2001)9 Relative Recovery method (RR); Unit 6C, collection channel

1995 Steelhead Bypass 0.929 0.060 PT Muir et al. (2001)9 Relative Recovery method (RR); Unit 6C, collection channel
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Appendix B. Continued.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

Lower Granite Dam

1993 Yearling Chinook Spill 1.021 0.026 PT Muir et al. (2001)10 Spillway with deflector using relative recovery method (RR); Bay 3, 108 m3/s

1993 Yearling Chinook Turbine 0.920 0.025 PT Muir et al. (2001)10 Estimates derived using relative recovery method (RR); Unit 6B, 135 MW

1994 Yearling Chinook Bypass 0.994 0.023 PT Muir et al. (2001)8 Estimates derived using relative survival method (RS); Unit 6C, collection channel

1995 Steelhead Bypass 0.979 0.031 PT Muir et al. (2001)9 Estimates derived using the relative survival method (RS); Unit 6C, collection channel

1997 Steelhead Bypass 0.953 0.016 PT Muir et al. (2001)11 Estimates derived using relative recovery method (RR); Unit 6B, trashrack

1997 Hatchery Steelhead Spill 1.000 0.010 BT Normandeau et al. (1997) Spillbay 1 without deflector; 1,800 cfs

1997 Hatchery Steelhead Spill 1.000 NA BT Normandeau et al. (1997) Spillbay 1 without deflector; 5,600 cfs

1997 Hatchery Steelhead Spill 1.000 NA BT Normandeau et al. (1997) Spillbay 1 without deflector; 9,500 cfs

1997 Hatchery Steelhead Spill 1.000 NA BT Normandeau et al. (1997) Spillbay 1 without deflector; 5,600 cfs; released into vortice upstream of tainter gate

1997 Hatchery Steelhead Spill 0.983 0.012 BT Normandeau et al. (1997) Spillbay 1 without deflector; 9,500 cfs; released into vortice upstream of tainter gate

1997 Hatchery Steelhead Spill 0.990 0.017 BT Normandeau et al. (1997) Spillbay 3 with deflector; 1,800 cfs

1997 Hatchery Steelhead Spill 0.980 0.011 BT Normandeau et al. (1997) Spillbay 3 with deflector; 5,600 cfs

1997 Hatchery Steelhead Spill 1.000 NA BT Normandeau et al. (1997) Spillbay 3 with deflector; 9,500 cfs

1997 Hatchery Steelhead Spill 1.000 NA BT Normandeau et al. (1997) Spillbay 3with deflector; 5,600 cfs; released into vortice upstream of tainter gate

1997 Hatchery Steelhead Spill 0.992 0.008 BT Normandeau et al. (1997) Spillbay 3 with deflector; 9,500 cfs; released into vortice upstream of tainter gate

1997 Steelhead Spill 1.004 0.015 PT Muir et al. (2001)11 Spillbay 1 without deflector using relative recovery method (RR); 139-283 m3/s

1997 Steelhead Spill 0.972 0.015 PT Muir et al. (2001)11 Spillway with deflector using relative recovery method (RR); Bay 3, 139-283 m3/s

1997 Steelhead Turbine 0.934 0.016 PT Muir et al. (2001)11 Estimates derived using the relative recovery method (RR); Unit 6B, 135 MW

1993 Yearling Chinook Spill 1.021 0.026 PT Muir et al. (2001)10 Spillway with deflector using relative recovery method (RR); Bay 3, 108 m3/s
Transportation, Spill and Flow Augmentation Northwest Power Planning Council

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Appendix B. Continued.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

Lower Granite Dam

1994 Yearling Chinook Bypass 0.994 0.030 PT Muir et al. (2001)8 Relative survival method (RS); Unit 6A, collection channel

1995 Yearling Chinook Bypass 0.976 0.036 PT Muir et al. (2001)9 Relative survival method (RS); Unit 6A, collection channel

1995 Steelhead Bypass 0.983 0.019 PT Muir et al. (2001)9 Relative Survival method (RS); Unit 6A, collection channel

1995 Yearling Chinook Turbine 0.927 0.027 PT Muir et al. (2001)9 Relative Survival method (RS); Unit 4B, 135 MW

1996 Hatchery Chinook SBC 0.958 0.928-0.988 BT Normandeau et al. (1996d) Surface Bypass Collector (SBC); 90% C.I.

1996 Hatchery Chinook Spill 0.975 0.952-0.988 BT Normandeau et al. (1996d) Spillbay 2; 90% C.I.

1996 Steelhead Spill 1.010 0.019 PT Muir et al. (2001)12 Spillbay 1 without deflector;Relative Survival method (RS); 110 m3/s

2000 Hatchery Chinook SBC 0.970 0.945-0.994 BT Normandeau et al. (2000) Surface Bypass Collector (SBC); 90% C.I.

2000 Hatchery Chinook Spill 0.976 0.954-0.999 BT Normandeau et al. (2000) Spillbay 2; 90% C.I.

Wanapum Dam 

1996 Hatchery Yearling 

Chinook

Overflow 

Weir 0.920 0.023 BT Normandeau et al. (1996b) Overflow weir; 2,000 cfs

1996 Hatchery Yearling 

Chinook

Overflow 

Weir 0.969 0.023 BT Normandeau et al. (1996b) Overflow weir; 4,000 cfs

1996 Hatchery Yearling 

Chinook Sluiceway 0.974 0.014 BT Normandeau et al. (1996b) Sluiceway; 2,000 cfs

1996 Hatchery Yearling 

Chinook Spill 0.957 0.014 BT Normandeau et al. (1996b) Spillbay with deflector (Spillbay 2); 4,300 cfs

1996 Hatchery Yearling 

Chinook Spill 0.996 0.004 BT Normandeau et al. (1996b) Spillbay without deflector (Spillbay 3); 4,300 cfs

1996 Hatchery Yearling Coho Turbine 0.897 0.027 BT Normandeau et al. (1996a)13 Induction of fish 10' below turbine intake ceiling; 9,000 cfs

1996 Hatchery Yearling Coho Turbine 0.924 0.023 BT Normandeau et al. (1996a)13 Induction of fish 10' below turbine intake ceiling; 11,000 cfs

1996 Hatchery Yearling Coho Turbine 0.948 0.022 BT Normandeau et al. (1996a)13 Induct ion of fish 10' below turbine intake ceiling; 15,000 cfs

1996 Hatchery Yearling Coho Turbine 0.885 0.026 BT Normandeau et al. (1996a)13 Induction of fish 10' below turbine intake ceiling; 17,000 cfs
Transportation, Spill and Flow Augmentation Northwest Power Planning Council

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Appendix B. Continued.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

Wanapum Dam

1996 Hatchery Yearling Coho Turbine 0.949 0.020 BT Normandeau et al. (1996a)13 Induction of fish 30' below turbine intake ceiling; 9,000 cfs

1996 Hatchery Yearling Coho Turbine 0.968 0.017 BT Normandeau et al. (1996a)13 Induction of fish 30' below turbine intake ceiling; 11,000 cfs

1996 Hatchery Yearling Coho Turbine 1.000 0.013 BT Normandeau et al. (1996a)13 Induction of fish 30' below turbine intake ceiling; 15,000 cfs

1996 Hatchery Yearling Coho Turbine 0.968 0.014 BT Normandeau et al. (1996a)13 Induction of fish 30' below turbine intake ceiling; 17,000 cfs

1998 Hatchery Yearling 

Chinook Spill 1.000 ± 0.026 BT Normandeau and Skalski (1999) Unmodified spillbay (Spillbay 3); 2,000 cfs; 90% C.I.

1998 Hatchery Yearling 

Chinook Spill 0.993 ± 0.031 BT Normandeau and Skalski (1999) Unmodified spillbay (Spillbay 3); 5,000 cfs; 90% C.I.

1998 Hatchery Yearling 

Chinook Spill 0.945 ± 0.061 BT Normandeau and Skalski (1999) Unmodified spillbay (Spillbay 3); 10,000 cfs; 90% C.I.

1998 Hatchery Yearling 

Chinook Spill 0.990 ± 0.022 BT Normandeau and Skalski (1999) Spillbay 4; 14° sloped flow deflector; 2,000 cfs; 90% C.I.

1998 Hatchery Yearling 

Chinook Spill 0.976 ± 0.041 BT Normandeau and Skalski (1999) Spillbay 4;14° sloped flow deflector; 5,000 cfs; 90% C.I.

1998 Hatchery Yearling 

Chinook Spill 0.928 ± 0.063 BT Normandeau and Skalski (1999) Spillbay 4; 14 °sloped flow deflector; 10,000 cfs; 90% C.I.

1999 Hatchery Yearling 

Chinook Spill 0.994 0.985-1.004 BT Normandeau and Skalski (2000a) Unmodified spillbay (Spillbay 3); 2,800 cfs; 90% C.I.

1999 Hatchery Yearling 

Chinook Spill 0.976 0.957-0.996 BT Normandeau and Skalski (2000a) Unmodified spillbay (Spillbay 3); 6,000 cfs; 90% C.I.

1999 Hatchery Yearling 

Chinook Spill 0.995 0.991-1.019 BT Normandeau and Skalski (2000a) Unmodified spillbay (Spillbay 3); 7,500 cfs; 90% C.I.

1999 Hatchery Yearling 

Chinook Spill 0.983 0.968-0.999 BT Normandeau and Skalski (2000a) Spillbay 5; shallow-flat flow deflector; 2,800 cfs; 90% C.I.

1999 Hatchery Yearling 

Chinook Spill 0.982 0.966-0.999 BT Normandeau and Skalski (2000a) Spillbay 5; shallow-flat flow deflector; 6,000 cfs; 90% C.I.

1999 Hatchery Yearling 

Chinook Spill 0.976 0.965-1.007 BT Normandeau and Skalski (2000a) Spillbay 5; shallow-flat flow deflector; 7,500 cfs; 90% C.I.
Transportation, Spill and Flow Augmentation Northwest Power Planning Council

BioAnalysts, Inc. January 2002

Appendix B. Continued.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

Rock Island Dam

1997 ROR Yearling Chinook Pool 0.949 0.303 RT Skalski and Giorgi (1999)

1997 ROR Steelhead Pool 0.9897 0.055 RT Skalski and Giorgi (1999)

1997 Hatchery Yearling Chinook Spill 0.951 0.920-0.979 BT Normandeau and Skalski (1998) Spillbay 21; slotted, 1,850 cfs; 90% C.I.

1999 ROR Steelhead Project 0.9863 0.0474 RT Lady et al. (2000) Estimate from Route-Specific Survival Model (RSSM)

1999 ROR Steelhead Project 0.9983 0.0467 RT Stevenson et al. (2000) Estimate from Paired-Release Recapture Model (PRRM)

1999 Hatchery Yearling Chinook Spill 0.995 0.981-1.0 BT Normandeau and Skalski 

(2000b) Spillbay 31; 2,500 cfs; 90% C.I.

1999 Hatchery Yearling Chinook Spill 0.995 0.997-1.0 BT Normandeau and Skalski 

(2000b) Spillbay 31; 10,000 cfs; 90% C.I.

1999 ROR Steelhead Spill 1.0939 0.0654 RT Lady et al. (2000)

1999 ROR Steelhead Turbine P.H. 1 0.7488 0.1816 RT Lady et al. (2000)

1999 ROR Steelhead Turbine P.H. 2 1.0135 0.0547 RT Lady et al. (2000)

2000 ROR Steelhead Project 0.9258 0.0183 RT Skalski et al. (2000a) Estimate from Route-Specific Survival Model (RSSM)

2000 ROR Steelhead Project 0.9196 0.017 RT Skalski et al. (2000b) Estimate from Paired-Release Recapture Model (PRRM)

2000 Hatchery Yearling Chinook Project 0.9476 0.0186 RT Skalski et al. (In Press.) Estimate from Route-Specific Survival Model (RSSM)

2000 Hatchery Yearling Chinook Project 0.9475 0.0192 RT Skalski et al. (In Press.) Estimate from Paired-Release Recapture Model (PRRM)

2000 ROR Yearling Chinook Project 0.9445 0.0190 RT Skalski et al. (In Press.) Estimate from Route-Specific Survival Model (RSSM)

2000 ROR Yearling Chinook Project 0.9391 0.0156 RT Skalski et al. (In Press.) Estimate from Paired-Release Recapture Model (PRRM)

2000 Hatchery Yearling Chinook Spill 1.000 1.00-1.00 BT Normandeau and Skalski (2001) Spillbay 29; notched with middle release; 2,500 cfs; 90% C.I.

2000 Hatchery Yearling Chinook Spill 0.990 0.978-1.00 BT Normandeau and Skalski (2001) Spillbay 29; notched with periphrial release; 2,500 cfs; 90% C.I.

2000 ROR Steelhead Spill 0.9668 0.0239 RT Skalski et al. (2000a)

2000 Hatchery Yearling Chinook Spill 1.0150 0.0217 RT Skalski et al. (In Press.)

2000 ROR Yearling Chinook Spill 0.9863 0.0305 RT Skalski et al. (In Press.)

2000 ROR Steelhead Turbine P.H. 1 1.0000 0.0493 RT Skalski et al. (2000a)

2000 Hatchery Yearling Chinook Turbine P.H. 1 0.9115 0.0711 RT Skalski et al. (In Press.)

2000 ROR Yearling Chinook Turbine P.H. 1 0.9702 0.0520 RT Skalski et al. (In Press.)

2000 ROR Steelhead Turbine P.H. 2 0.9420 0.0227 RT Skalski et al. (2000a)

2000 Hatchery Yearling Chinook Turbine P.H. 2 0.9722 0.0237 RT Skalski et al. (In Press.)

2000 ROR Yearling Chinook Turbine P.H. 2 0.9959 0.0212 RT Skalski et al. (In Press.)
Transportation, Spill and Flow Augmentation Northwest Power Planning Council

BioAnalysts, Inc. January 2002

Appendix B. Continued.

Passage

Year Species Route Survival S.E. C.I. Method Source Comment

Rocky Reach Dam

1997 ROR Yearling Chinook Bypass 0.9772 0.274 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Steelhead Bypass 0.7756 0.138 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Yearling Chinook Dam 0.926 0.283 RT Skalski and Giorgi (1999)

1997 ROR Steelhead Dam 0.919 0.05 RT Skalski and Giorgi (1999)

1997 ROR Yearling Chinook Pool 0.9474 0.022 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Yearling Chinook Pool 0.934 0.025 RT Skalski et al. (1998) Estimate from Single Release-Recapture Model (SRM)

1997 ROR Steelhead Pool 0.9562 0.017 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Steelhead Pool 0.959 0.018 RT Skalski et al. (1998) Estimate from Single Release-Recapture Model (SRM)

1997 ROR Yearling Chinook Spill 0.9408 0.3060 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Steelhead Spill 0.8893 0.0860 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Yearling Chinook Surface Coll. 1 0.8885 NA RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Steelhead Surface Coll. 1 0.9932 0.051 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Yearling Chinook Turbine 0.9175 0.297 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1997 ROR Steelhead Turbine 0.9078 0.074 RT Skalski et al. (1998) Estimate from Route-Specific Survival Model (RSSM)

1999 ROR Steelhead Project 0.9612 0.0376 RT Lady et al. (2000) Estimate from Route-Specific Survival Model (RSSM)

1999 ROR Steelhead Project 0.9658 0.0375 RT Stevenson et al. (2000) Estimate from Paired-Release Recapture Model (PRRM)

1999 ROR Steelhead Spill 1.0622 0.0759 RT Lady et al. (2000)

1999 ROR Steelhead Surface Coll. 1 1.0926 0.0429 RT Lady et al. (2000)

1999 ROR Steelhead Surface Coll. 2 1.0036 0.0596 RT Lady et al. (2000)

1999 ROR Steelhead Turbine 0.8972 0.0675 RT Lady et al. (2000)
Transportation, Spill and Flow Augmentation Northwest Power Planning Council

BioAnalysts, Inc. January 2002

Appendix B. Concluded.

1 Original work by Normandeau et al. (1996), and reported in Ploskey et al. (2001).

2 Original work by Dawley et al. (1998), and reported in Ploskey et al. (2001).

3 Original work by Dawley et al. (2000a), and reported in Ploskey et al. (2001).

4 Original work by Dawley et al. (2000b), and reported in Ploskey et al. (2001).

5 Original work by Dawley and Absolon (2000 Preliminary), and reported in Ploskey et al. (2001).

6 Original work by Counihan et al. (In Prep.), and reported in Ploskey et al. (2001).

7 Original work by Muir et al. (1995a), and reported in Muir et al. (2001).

8 Original work by Muir et al. (1995b), and reported in Muir et al. (2001).

9 Original work by Muir et al. (1996), and reported in Muir et al. (2001).

10 Original work by Iwamoto et al. (1994), and reported in Muir et al. (2001).

11 Original work by Muir et al. (1998), and reported in Muir et al. (2001).

12 Original work by Smith et al. (1998), and reported in Muir et al. (2001).

13 The work by Normandeau et al. (1996a) was a separate evaluation of turbine survival from other work conducted at Wanapum Dam in 1996, where spill 

survival was evaluated with yearling chinook.

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