Council Document 2003-11

TABLE OF CONTENTS

Introduction

The Columbia River Basin Fish and Wildlife Program 5

The 2000 Fish and Wildlife Program and the Mainstem Plan 5

Expectations for the elements of the Mainstem Plan 6

A different Mainstem Plan for a different context 6

Vision of the Mainstem Plan 9

Biological Objectives

Overarching objectives and priorities for the mainstem 11

Specific objectives and performance standards for habitat characteristics and for 11

 population performance

Mainstem habitat conditions 11

Migration/passage conditions for anadromous fish 13

Resident fish/wildlife 13

Strategies

Overarching strategies 15

Strategies in specific areas 17

Mainstem habitat 17

Juvenile and adult passage, in general 17

Juvenile fish transportation 18

Spill 18

Juvenile bypass systems 20

Adult passage 20

Water management 21

Monitoring and evaluation 27

Research 28

Annual and in-season decisionmaking 29

Mid-Columbia Hydroelectric Projects 29

Revised Transition Provisions 31

Appendix A: Analysis of the Adequacy, Efficiency, 33

Economy and Reliability of the Power System 

Appendix B: Findings on the Recommendations for 55

Mainstem Plan Amendments to the 2000 Columbia River 

Basin Fish and Wildlife Program
4 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 5

The Columbia River 

Basin Fish and Wild- life Program

The states of the Columbia River Basin, Idaho, Montana, Oregon 

and Washington, formed the Northwest Power and Conservation Council, an interstate compact agency, 

under the authority of the Pacific 

Northwest Electric Power Planning 

and Conservation Act of 1980. The 

Power Act directs the Council to 

develop a program to protect, mitigate and enhance fish and wildlife of 

the Columbia River Basin affected by 

the development and operation of the 

basin’s hydroelectric facilities, while 

also assuring the Pacific Northwest 

an adequate, efficient, economical 

and reliable power supply. The Act 

also directs the Council to inform the 

public about fish, wildlife and energy 

issues and to involve the public in its 

decision-making.

The Council’s Columbia River 

Basin Fish and Wildlife Program, 

first adopted in 1982 and periodically revised, is the nation’s largest 

regional effort to recover, rebuild, 

and mitigate impacts on fish and 

wildlife. As a planning, policymaking and reviewing body, the 

Council develops and then monitors implementation of the fish and 

wildlife program, which is implemented by the federal agencies 

that manage, operate and regulate 

the basin’s hydroelectric facilities. 

These include the Bonneville Power 

Administration, the U.S. Army Corps 

of Engineers, the Bureau of Reclamation and the Federal Energy Regulatory Commission and its licensees.

The 2000 Fish 

and Wildlife 

Program and the 

Mainstem Plan

In 2000, the Council adopted a 

set of amendments to the fish and 

wildlife program to begin a complete revision of the program. In 

the first phase of the amendment 

process, the Council reorganized the 

program around a comprehensive 

framework of scientific and policy 

principles. The fundamental elements of the revised program are 

the vision, which describes what 

the program is trying to accomplish 

with regard to fish and wildlife and 

other desired benefits from the river; 

basinwide biological performance 

objectives, which describe in general the fish and wildlife population 

characteristics needed to achieve 

the vision; implementation strategies, which will guide or describe 

the actions needed to achieve the 

desired ecological conditions; and 

a scientific foundation, which links 

these elements and explains why 

the Council believes certain kinds 

of actions should result in desired 

habitat conditions and why these 

conditions should improve fish and 

wildlife populations in the desired 

way.

The program amendments in 

2000 set the stage for subsequent 

phases of the program revision 

process, in which the Council is to 

adopt specific objectives and action 

measures for the river’s mainstem 

and tributary subbasins, consistent 

with the basinwide vision, objectives and strategies in the program 

and its underlying scientific foundation. The Council intends to 

incorporate the specific objectives 

and measures for tributaries into the 

program in locally developed subbasin plans for the more than sixty 

subbasins of the Columbia River.

This document comprises a 

coordinated plan of operations for 

the mainstem Columbia and Snake 

rivers. The Council adopted the 

mainstem plan in April 2003.

In preparing the mainstem plan, 

the Council solicited recommendations from the region’s state and federal fish and wildlife agencies, Indian 

tribes and others, as required by the 

Northwest Power Act. Various agencies and tribes responded, and the 

Council also received recommendations from other interested parties. 

The Council prepared a draft after 

reviewing the recommendations, 

supporting information submitted 

Introduction
6 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

these program amendments for consistency with the program framework 

elements adopted in 2000, including 

the vision, biological objectives, habitat and hydrosystem strategies, and 

underlying scientific principles.

A Different Mainstem 

Plan for a Different 

Context

In the past, the Council’s fish and 

wildlife program included detailed 

hydrosystem operations for fish and 

wildlife. In December 2000, NOAA 

Fisheries (formerly the National 

Marine Fisheries Service) and the 

U.S. Fish and Wildlife Service 

issued biological opinions for the 

operation of the Federal Columbia River Power System to benefit 

populations of salmon, steelhead, 

bull trout and white sturgeon listed 

as threatened or endangered under 

the federal Endangered Species Act 

(ESA). The hydrosystem measures 

in these opinions run to hundreds 

of pages of detail and hundreds of 

measures on system configuration, 

river flows, reservoir management, 

passage improvements, spill, juvenile transportation, predator management and more. These measures 

are built on foundations developed 

in the Council’s program over the 

last 20 years.

In developing this mainstem plan, 

the Council asked for recommendations addressing, in part, how the 

plan should relate to the biological 

opinions on hydrosystem operations. The relevant recommendations 

received can be loosely grouped into 

four categories:

• recommendations that the Council 

adopt a mainstem plan consistent 

with the objectives and measures 

in the biological opinions;

• recommendations that concluded 

the biological opinions do not 

prescribe sufficient flow, spill 

and passage operations to benefit 

listed fish, and so the Council 

should adopt additional measures 

to that end;

with the recommendations, and comments received on the recommendations. The Council conducted an 

extensive public comment period on 

the draft mainstem plan before finalizing these program amendments.

Expectations for 

the Elements of the 

Mainstem Plan

The role of the mainstem plan 

and the Council’s expectations for it 

were described in the 2000 Fish and 

Wildlife Program in the section on 

Basinwide Hydrosystem Strategies 

and in the section entitled Schedule for Further Rulemakings. The 

mainstem plan is to contain specific 

objectives and action measures for 

the federal operating agencies and 

others to implement in the mainstem Columbia and Snake rivers to 

protect, mitigate and enhance fish 

and wildlife affected by the development and operation of hydroelectric facilities while assuring 

the region an adequate, efficient, 

economical and reliable power 

supply. The mainstem plan includes 

objectives and measures relating to, 

among other matters:

• the protection and enhancement 

of mainstem habitat, including 

spawning, rearing, resting and 

migration areas for salmon and 

steelhead and resident salmonids 

and other fish;

• system water management;

• passage spill at mainstem dams;

• adult and juvenile passage modifications at mainstem dams;

• juvenile fish transportation;

• adult survival during upstream 

migration through the mainstem;

• reservoir elevations and operational requirements to protect 

resident fish and wildlife;

• water quality conditions; and

• research, monitoring and 

evaluation.

The Council evaluated the mainstem plan recommendations and 

• recommendations that concluded 

the biological opinions exceeded 

what was necessary to benefit 

listed fish, to the detriment of 

the power supply and other uses 

of the river, and so the Council 

should adopt a mainstem plan 

with scaled back flow and spill 

operations that are, in the view 

of those making the recommendations, more biologically and 

economically efficient in how the 

limited resources of the region are 

applied; and

• recommendations that concluded 

the operations specified in the 

biological opinions are not sufficient to protect, enhance or mitigate for the adverse effects of the 

hydrosystem on fish and wildlife 

not listed for protection under 

the Endangered Species Act, and 

may be especially adverse to resident fish (listed and non-listed), 

and so the Council should adopt 

objectives and measures for that 

purpose that would be either supplemental to, or in some cases in 

conflict with, current implementation approaches to biological 

opinion operations.

The Council considered and drew 

from recommendations in all four 

categories in developing this mainstem plan. In general, however, two 

overriding concerns motivated the 

Council in deciding what objectives 

and measures to include in the plan:

• The mainstem plan includes a set 

of habitat considerations, objectives, principles and measures 

intended to protect, mitigate and 

enhance all the fish and wildlife 

of the Columbia River Basin 

affected by the development, 

operation and management of the 

hydrosystem, whether listed or 

not, as required of the Council 

by the Power Act. Objectives, 

actions and operations intended 

to protect, enhance and mitigate 

for the effects of the hydrosystem 

on species other than those listed 

as threatened or endangered may 

require federal agency flexibility 

or changes in the implementa-
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 7

tion of the biological opinions, as 

described below.

• Scientific and policy uncertainty 

continues to plague a number 

of mainstem actions intended to 

benefit anadromous fish, leading to an inability to measure 

the extent of the benefits gained, 

and to great differences of opinion as to the value of continuing 

these actions. Moreover, some 

of these actions have adverse 

impacts on resident fish and high 

costs to the power system. The 

mainstem plan includes provisions for how to improve the way 

the region engages in fish and 

wildlife research, power system 

operations, monitoring and 

evaluation for the mainstem, and 

how and what decisions are made 

on the basis of that information. 

This includes: 1) describing an 

approach and a set of factors for 

prioritizing research; 2) recommending specific priorities for 

mainstem research; and 3) suggesting how to better integrate 

research, monitoring and evaluation results into decisions about 

mainstem actions and power 

system operations in the context of the Columbia basin as a 

whole. The Council’s goal is to 

provide recommendations to the 

federal hydrosystem operating 

agencies and fish and wildlife 

agencies for more biologically 

effective spill, flow and other 

mainstem operations and actions 

at the minimum economic cost. 

The Council understands the biological opinions have sufficient 

flexibility in implementation to 

accommodate recommendations 

of this type; that is, the biological 

opinions were adopted with the 

recognition that as new scientific 

information is developed, actions 

called for in the opinions could 

and, where found appropriate, 

would be changed.

The Council reviewed comments 

on the proposed vision, objectives, 

and strategies in the draft mainstem 

plan and then decided, consistent 

with the review procedures and standards in the Power Act, on the most 

appropriate mainstem vision, objectives, and strategies for both listed 

and non-listed species.

Another difference between this 

and past Council mainstem programs concerns the region’s power 

supply requirements. The Power 

Act requires the Council to adopt 

a fish and wildlife program that 

not only protects, mitigates and 

enhances fish and wildlife but also 

assures that the region will continue 

to enjoy an adequate, efficient, economical and reliable power supply. 

The Council evaluated: 1) current 

hydrosystem operations; 2) the 

recommendations for mainstem 

amendments; and 3) the October 

2002 draft mainstem amendments 

to ensure that the adopted objectives and measures for mainstem 

hydrosystem operations meet the 

fish and wildlife requirements of the 

Power Act and are consistent with 

its power supply obligations. The 

Council also reviewed the latest scientific information and comments on 

the effectiveness of fish and wildlife 

strategies to increase survival of 

specific populations. 

Energy systems, markets and 

policy have changed radically since 

the last revision of the fish and 

wildlife program in the mid-1990s. 

Federal hydrosystem operations in 

2001 brought a concrete example 

of a problem that the Council had 

seen developing over the last halfdecade — the electricity demands 

placed on the federal hydrosystem 

were increasingly greater than what 

the federal system could produce 

in a year of historically low runoff 

and river levels. Yet the dynamics 

of regional and west coast energy 

developments prevented the Bonneville Power Administration from 

acquiring new, long-term resources 

that could have closed the gap. 

Problems with West Coast power 

markets in 2000 and 2001 prevented 

Bonneville from being able to make 

up the energy deficit in those markets, leading to a situation in 2001 

in which the federal agencies were 

forced to curtail regional load and 

reduce system operations intended 

to benefit fish and wildlife in order 

to maintain the reliability of the 

region’s power system. Even with 

significant changes to the hydropower operations specified for fish, 

the system still produced inadequate 

energy to meet the demands of the 

region. This forced many of the 

region’s utilities to curtail loads 

while also spending large sums to 

purchase power.

For these reasons, the analysis of 

the adequacy, efficiency, economics 

and reliability of the region’s power 

supply that accompanies this mainstem plan includes consideration 

of the current status of the region’s 

power system. The Council’s conclusion is that the region’s power 

system should be adequate and 

reliable for the next few years, due 

to the development of new power 

“The Council’s goal 

is...more biologicially 

effective spill, flow and 

other mainstem operations 

and actions at the minimum economic cost.”

The Federal Columbia River 

Power System includes 31 

dams. The total capacity is 

22,512 megawatts, or 44.8 

percent of the region’s total 

generating capacity.
8 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

supplies, reductions in demand, 

and loss of loads that have occurred 

since early 2001. The objectives and 

measures to protect, mitigate and 

enhance fish and wildlife included 

in this mainstem plan do not affect 

that conclusion. The analysis also 

concludes, however, that the region 

faces the possibility in later years of 

spiraling back into the power supply 

problems seen in 2001 unless measures are taken to ensure that new 

resources are added to the regional 

power supply in a more certain fashion. The analysis suggests possible 

actions by the federal agencies and 

others in the region to ensure that the 

federal system provides the specified operations for fish and wildlife 

and meets the electricity demands in 

most, if not all, low-water years. The 

Council is reviewing and revising 

its 20-year power plan as called for 

by the Northwest Power Act. The 

power plan will address the region’s 

power supply and reliability issues in 

more detail.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 9

The long-term vision of the 

Council’s 2000 Fish and 

Wildlife Program is of a 

Columbia River Basin ecosystem 

that sustains abundant, productive 

and diverse communities of fish and 

wildlife, mitigating across the basin 

for the adverse effects to fish and 

wildlife caused by the development 

and operation of the hydrosystem 

and providing the benefits from fish 

and wildlife valued by the people of 

the region. This ecosystem provides 

abundant opportunities for tribal 

and treaty-right harvest and for nontribal harvest of fish and wildlife, 

and for the recovery of fish and 

wildlife affected by the operation 

of the hydrosystem. This program 

is to be “habitat-based.” Wherever 

feasible, the program vision is to 

be accomplished by protecting and 

restoring the natural ecological 

functions, habitats and biological 

diversity of the Columbia River 

Basin.1 Where this is not feasible, 

other methods that are compatible 

with naturally reproducing fish and 

wildlife populations will be used. 

Where impacts have irrevocably 

changed the ecosystem, the program 

will protect and enhance the habitat 

and species assemblages compatible 

with the altered ecosystem. Actions 

taken under the program will also 

provide conditions that meet water 

quality standards under the Clean 

Water Act. They must also be costeffective and not put at risk the 

region’s adequate, efficient, economical and reliable power supply.

The vision for the mainstem 

plan is consistent with the broader 

program vision set out above. 

Hydrosystem operations, fish passage efforts, habitat improvement 

investments and other actions in the 

mainstem should be directed toward 

protecting, enhancing, restoring and 

connecting2 natural river processes 

and habitats, especially spawning, 

rearing, resting and migration habitats for salmon, steelhead, sturgeon 

and important resident fish populations. This will allow for abundant, 

productive and diverse fish and wildlife populations. The vision includes 

providing conditions within the 

hydrosystem for adult and juvenile 

fish that: 1) most closely approximate natural physical and biological 

conditions; 2) support the expression 

of life history diversity; 3) allow for 

adequate levels of mainstem survival 

to support fish population recovery in the subbasins; and 4) ensure 

that water management operations 

are optimized to meet the needs of 

anadromous and resident fish species, including those in upstream 

storage reservoirs, with the least 

cost so that actions taken maximize 

benefits to all species while ensuring an adequate, efficient, economical and reliable power supply. Any 

system changes needed to achieve 

these goals must be implemented in 

such a way and over a sufficient time 

period to allow the region to make 

whatever power system adaptations 

are needed, if any, to maintain an 

adequate, efficient, economical and 

reliable power supply.

Vision of the Mainstem Plan

1 Throughout the provisions of these mainstem amendments, the Council’s position is consistent with the position of NOAA Fisheries’ 2000 

Biological Opinion with reference to breaching lower Snake River dams.

2

 “Restore” as used in the mainstem plan means to take an action in a particular area that currently has no habitat value for spawning or rearing 

or other desired population condition (because, for example, the area has been blocked inundated or dewatered at an inopportune time), so 

that the area will have value for that purpose. It does not mean to re-establish the conditions that existed at any particular point in time, 

including the time before non-Indian settlement and development of the Columbia basin.

“Enhance,” by contrast, when referring to habitat conditions, means to take an action in an area that currently has some value for spawning 

or rearing or other desired condition so as to increase that value.

“Connecting” habitat becomes important when a migrating population has areas of productive habitat that it cannot use to full advantage (or 

use at all) because the habitat is inaccessible to the population or because the areas in between productive habitat are not productive without 

improvements. It also does not mean or imply a Council position in support of the breaching of dams in the mainstem.
10 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 11

Overarching Objec- tives and Priorities 

for the Mainstem

The biological objectives stated here for the mainstem plan are 

intended to be based on, and consistent with, the biological objectives 

stated in the 2000 Fish and Wildlife 

Program.

These biological objectives and 

accompanying operational strategies are designed to improve the 

life-cycle survival of important 

populations of listed and unlisted 

salmon, steelhead, resident fish, 

and wildlife. The Council’s goal 

is to apply the available resources 

in the most effective way possible 

to achieve protection, mitigation, 

recovery and delisting of threatened 

and endangered species in the shortest possible time. This demands 

that the Council set clear priorities 

for resource expenditures to protect, 

mitigate, and enhance fish and wildlife populations to assure that fish 

and wildlife benefits are achieved at 

the least cost to the region’s financial and water resources.

One of the overarching biological objectives for the program is the 

recovery of ESA-listed anadromous 

and resident fish affected by development and operation of the hydrosystem. Federal hydrosystem operations to benefit fish now are focused 

on listed populations through the 

2000 Biological Opinions on the 

Operation of the Federal Columbia 

River Power System from NOAA 

Fisheries for salmon and steelhead 

and the U.S. Fish and Wildlife Service for Kootenai white sturgeon 

and bull trout. Achieving these biological performance standards for 

listed species as stated in the biological opinions is a key biological 

objective of the Council’s program 

and this mainstem plan.

Under the Northwest Power Act, 

however, the Council has an obligaBiological Objectives

tion to protect, mitigate and enhance 

all the fish and wildlife of the Columbia Basin affected by the development, operation and management of 

the hydrosystem. Concern over the 

listed populations is only one part 

of the Council’s broader mandate. 

And so a goal of the program, as also 

stated in the overarching objectives 

of the program framework, is to provide habitat conditions that sustain 

abundant, productive, and diverse 

fish and wildlife populations that 

support the recovery of listed species 

and abundant opportunities for tribal 

trust and treaty-right harvest and 

non-tribal harvest.

In addition, the science relating to 

the rebuilding of Pacific salmon, as 

incorporated into the objectives and 

habitat strategies in the 2000 Fish 

and Wildlife Program, indicates that 

success in protecting and enhancing abundant and diverse naturally 

spawning populations of salmon 

and steelhead and other native fish 

requires an emphasis on protecting, 

enhancing, connecting, and restoring habitats and populations that 

are relatively productive. This is a 

priority for actions that should be 

equal to protecting migration and 

spawning conditions for ESA-listed 

populations. This priority includes, 

for example, protecting and improving mainstem migration conditions 

for important non-listed tributary 

populations in the middle part of the 

river. These include, for example, 

spring chinook in the John Day and 

Deschutes rivers. Also, historically 

the most productive populations in 

the Columbia system were those 

that spawned in the mainstem or 

the lower parts of the tributaries, as 

described in the habitat strategies in 

the 2000 Fish and Wildlife Program, 

and that have been either extirpated 

(e.g., those that spawned in the mainstem above Chief Joseph Dam or in 

the area now inundated by John Day 

Dam) or remain relatively productive 

(e.g., Hanford Reach fall chinook). 

Accordingly, this plan emphasizes 

protecting and restoring mainstem 

spawning and rearing habitats and 

populations. These general objectives for the mainstem are consistent 

with, and incorporate, the basinwide 

vision, biological objectives, and the 

habitat and hydrosystem strategies in 

the 2000 Fish and Wildlife Program.

Specific Objectives 

and Performance 

Standards for Habitat Characteristics 

and for Population 

Performance

Mainstem habitat conditions

• Identify and protect habitat areas 

and ecological functions that are 

relatively productive for spawning, resting, rearing, and migrating salmon and steelhead in the 

mainstem. This includes, among 

other things, protecting the Hanford Reach fall chinook habitat 

by determining and providing 

appropriate spawning and rearing 

flows. In addition, where feasible, restore and enhance habitats 

and ecological functions that connect to the protected productive 

areas to support the expansion 

of productive populations and 

to connect weaker and stronger 

populations, so as to restore more 

natural population structures.

Five species of Pacific 

salmon—pink, chum, sockeye, coho and chinook; and 

two anadromous trout—

steelhead and sea-run cutthroat—are found in the 

Columbia River Basin.
12

2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

• Protect, enhance, restore and 

connect freshwater habitat in 

the mainstem for the life history stages of naturally spawning 

anadromous and resident salmonids. Protect and enhance ecological connectivity between aquatic 

areas, riparian zones, floodplains 

and uplands in the mainstem.

− Enhance the connections 

between the mainstem 

sections of the Columbia 

and Snake rivers and their 

floodplains, side channels and 

riparian zones.

− Manage mainstem riparian 

areas to protect aquatic 

conditions and form a 

transition to floodplain 

terrestrial areas and side 

channels.

− Identify, protect, enhance and 

restore the functions of alluvial 

river reaches in the mainstem.

− Where feasible, reconnect 

protected and enhanced 

tributary habitats to protected 

and enhanced mainstem 

habitats, especially in the 

area of productive mainstem 

populations.

• Allow for biological diversity to 

increase among and within populations and species to increase 

ecological resilience to environmental variability.

− Expand the complexity and 

range of mainstem habitats to 

allow for greater life history 

and species diversity.

− Manage human activities 

in the mainstem, such as 

fish passage at mainstem 

dams, fish transportation and 

harvest, to minimize artificial 

selection or limitation of life 

history traits.

• Increase the amount of spawning habitat for fall chinook core 

populations in the lower and 

mid-Columbia area and in the 

lower Snake area. The Council 

acknowledges the recommendation from the four tribes of the 

Columbia River Inter-Tribal Fish 

Commission that the federal 

agencies act to provide 9,000 

additional acres of spawning habitat for Snake River fall chinook 

and 40 additional miles of fluvial 

spawning habitat for mid-Columbia fall chinook core populations, 

derived at least in part from the 

Independent Scientific Group’s 

Return to the River report (1996 

and 2000). However, the Council 

does not adopt at this time these 

or any other numerical targets for 

increased fall chinook spawning 

habitat. Instead, the Council will 

consult with the state and federal 

fish and wildlife agencies, tribes, 

federal operating agencies, the 

Independent Scientific Advisory Board and the Independent 

Economic Advisory Board to 

evaluate the scientific soundness, 

achievability, and implications 

of the tribes’ recommended targets, as well as other reasonable 

alternatives, and then in a public 

review process will consider 

adoption of a set of numerical 

objectives for additional mainstem spawning habitat.

• Where feasible, manage the 

hydrosystem so that patterns of 

flow more closely approximate 

natural hydrographic patterns. 

Ensure that any changes in water 

management are premised upon, 

and proportionate to, scientifically 

demonstrated fish and wildlife 

benefits. Examples of management actions or limitations consistent with this objective include:

− Attempt to provide natural 

spring freshets below the 

storage projects, within flood 

control constraints.

− Minimize fluctuations in flows 

out of the storage reservoirs 

over an extended period of 

the summer and fall. To the 

extent this conflicts with use 

of the hydrosystem for load 

following, system operators 

should balance equitably 

the biological requirements 

of fish with power supply 

requirements of the region.

− Apply rules of operation for 

all the storage projects, such 

as the Integrated Rule Curves 

developed by the Montana 

Department of Fish, Wildlife 

and Parks for Libby and 

Hungry Horse dams, so that 

drawdown and refill are based 

substantially on local inflows, 

and so that the reservoirs, 

in concert, can shape water 

releases to benefit fish in and 

immediately below reservoirs 

and then, as the water 

travels downstream, benefit 

anadromous fish.

− Operations based solely on 

efforts to achieve biological 

opinion flow targets in the 

lower Columbia river will 

adversely affect resident 

fish and may fail to benefit 

anadromous fish if they do not 

take into account reasonable 

storage project operations.

− Operations should attempt to 

meet the requirements of both 

resident and anadromous fish.

− The amount of flow 

augmentation and the release 

schedule from storage 

reservoirs should be based on 

the best available science for 

each target species (resident 

or anadromous) and weighted 

for the greatest benefit to all 

species.

• Identify, protect, enhance, restore, 

and connect ecosystem functions 

in the Columbia River estuary and 

nearshore ocean discharge plume 

as affected by actions within the 

 “Where feasible, manage 

the hydrosystem so that 

patterns of flow more 

closely approximate natural hydrolgraphic patterns.”
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 13

Columbia River mainstem. Evaluate flow regulation and changes 

to estuary-area habitat and biological diversity to better understand 

the relationship between estuary 

ecology and near-shore plume 

characteristics and the productivity, abundance, and diversity of 

salmon and steelhead populations.

• Where feasible, pursue restoration of anadromous fish in mainstem areas blocked by dams. 

Where this is not feasible, other 

measures will be used to protect, 

mitigate, and enhance related 

habitat and species assemblages. 

Under Section 4(h)(11)(A)(ii) 

of the Northwest Power Act, 

the Federal Energy Regulatory 

Commission has an obligation 

to take the Council’s program, 

including this provision, into 

account at each relevant stage 

of decision-making to the fullest 

extent practicable as it exercises 

its responsibilities. This includes 

decisions on whether to license 

or re-license a non-federal hydroproject on the Columbia and 

Snake mainstem. If, after fulfilling this legal obligation, FERC 

decides not to require reintroduction of anadromous fish into 

an area blocked by a particular 

hydroproject, actions to enhance 

habitat and species assemblages 

that exist above the blockages 

should be used in mitigation.

Migration/passage 

conditions for anad- romous fish

• The NOAA Fisheries 2000 Biological Opinion includes hydrosystem survival performance 

rates for inriver passage of 

affected life stages of ESA-listed 

salmon and steelhead through the 

eight federal dams in the lower 

Columbia and lower Snake rivers 

(Table 9.2-3). The program 

adopts these objectives. Achieve 

these objectives at the minimum 

economic cost.

• The Council will consult with 

state and federal fish and wildlife 

agencies and tribes, the Independent Scientific Advisory Board, 

and federal operating agencies to 

determine the possibility of adopting hydrosystem survival performance standards for non-listed 

populations of anadromous fish.

• Maximize spillway survival by 

selecting the most biologically 

effective level of spillway discharge at each project while not 

exceeding interim gas supersaturation standards.3

 Balance spillway survival probabilities against 

spillway passage efficiency and 

the efficiency and probabilities 

of other passage routes in order 

to determine the passage methods, including spill volumes, that 

maximize survival of fish passing 

the dam and minimize fall-back 

and other effects on adult salmon.

• Improve adult fish migration survival through the system.

• Meet state and federal water 

quality standards under the Clean 

Water Act.

• As an interim objective, contribute to achieving smolt-to-adult 

survival rates (SARs) in the 2-6 

percent range (minimum 2 percent; average 4 percent) for listed 

Snake River and upper Columbia 

salmon and steelhead. The Council will consult with state and 

federal fish and wildlife agencies 

and tribes, the Independent Scientific Advisory Board, and federal 

operating agencies to evaluate the 

scientific soundness and achievability of, and impact of ocean 

conditions on, these smolt-toadult survival rate objectives. 

Then, in a public review process, 

the Council either will confirm 

these smolt-to-adult survival rates 

as program objectives or revise to 

different objectives. At the same 

time, the Council will investigate the possibility of developing 

smolt-to-adult survival rate objectives for other populations.

Resident fish/

wildlife

• Provide conditions that support 

the needs of resident fish species 

in upstream reservoirs and river 

reaches, as well as the needs of 

anadromous and resident species 

in the lower parts of the mainstem.

• In accordance with Section 

4(h)(11)(A) of the 1980 Power 

Act, and the Council’s primary 

strategy for hydrosystem fish 

passage and operations under the 

2000 Fish and Wildlife Program, 

the Administrator of the Bonneville Power Administration, and 

other federal agencies responsible for managing, operating or 

regulating any federal or nonfederal hydroelectric facility for 

purpose of flow or spill advantages to ESA-listed species shall 

assure, in consultation with the 

Secretary of the Interior and the 

Administrator of NOAA Fisheries, together with state fish and 

3 Under current system operations for migrating anadromous fish, including under 2000 Biological Opinion operations, the federal operating 

agencies must secure waivers to the existing water quality standards to allow for spill operations that will result in total dissolved gas 

supersaturation levels of up to 120 percent. The Council considers current operations as well as any other specific spill operations included 

in these amendments to be “interim” while the Council works with the region to determine the most biologically effective level of spillway 

discharge at each project and for the system as a whole.
14 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

wildlife agencies and appropriate 

Indian tribes, that flow and spill 

operations are optimized to produce the greatest biological benefits with the least adverse effects 

on resident fish.

• Enhance the abundance and productivity of white sturgeon in the 

mainstem in order to rebuild and 

sustain naturally produced populations of sturgeon and sustain 

an annual harvest of sturgeon. 

Operate the hydropower system 

to maximize spawning and rearing success of white sturgeon 

in reservoirs, while operating in 

concert with the needs of salmonids. The U.S. Fish and Wildlife Service’s 2000 Biological 

Opinion concerning hydrosystem operations that affect listed 

Kootenai River white sturgeon 

includes specific objectives for 

that species, incorporated here. 

The water management strategies 

in this mainstem plan (below) 

include a sturgeon operation 

strategy that is a refinement of 

the flow strategy in the Fish and 

Wildlife Service’s Biological 

Opinion. The Council’s strategy 

is intended to be a more effective operation for achieving the 

objectives in the opinion and in 

this program.

• Provide mainstem conditions 

that help to protect and enhance 

bull trout habitat and thus help 

to enhance the abundance and 

productivity of bull trout populations. The U.S. Fish and Wildlife Service’s 2000 Biological 

Opinion concerning hydrosystem 

operations that affect listed bull 

trout populations includes objectives for that species, which are 

adopted here.

• Contribute to providing the conditions necessary to restore populations of native fish and wildlife 

in the areas above and below 

Hungry Horse and Libby dams 

to self-sustaining levels capable 

of supporting harvest. This 

includes protecting, restoring, 

and enhancing reservoir, riparian, 

and wetland habitats above and 

below Hungry Horse and Libby 

dams to meet the goals set forth 

in the management and mitigation 

plans and the recommendations 

of the Montana Department of 

Fish, Wildlife and Parks and the 

Confederated Salish and Kootenai 

Tribes.4 As part of this objective, 

1) improve the seasonal pattern 

and stability of river discharges 

and reservoir conditions; 2) 

restore in-channel habitat structure, function and complexity; 

3); restore riparian and wetland 

habitats and floodplain function; 

and 4) maintain water temperatures within the tolerance range of 

native fish species.

• Contribute to providing the 

conditions necessary to protect 

spawning and rearing habitat 

for fish in, and adjacent to, Lake 

Roosevelt to build fish populations to levels capable of supporting harvest consistent with 

the goals set forth in the management and mitigation plans and 

the recommendations of the Spokane and Colville Tribes.5

• As part of implementing the 

wildlife strategies and achieving the wildlife objectives of the 

2000 Program, improve survival 

and production of wildlife species in the mainstem affected by 

the development, operation, and 

management of the hydrosystem by reducing limiting factors 

to wildlife in the mainstem and 

improving riverine and riparian 

mainstem habitat conditions for 

these species.

4 When the Council adopts subbasin plans into the program, which will supersede existing management and mitigation plans, the objective will be 

to implement the strategies and achieve the objectives in the relevant subbasin plans.

5 When the Council adopts subbasin plans into the program, which will supersede existing management and mitigation plans, the objective will be 

to implement the strategies and achieve the objectives in the relevant subbasin plans.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 15

Overarching 

Strategies

• The strategies stated here for 

the mainstem plan are based on, 

and consistent with, the general 

basinwide objectives and habitat 

and hydrosystem strategies stated 

in the 2000 Fish and Wildlife 

Program.

• All of the strategies in this mainstem plan will cease to have effect 

seven years after the effective date 

of these program amendments.

• All decisions on actions that

affect, or are intended to 

benefit, fish and wildlife in the 

mainstem Columbia and Snake 

Rivers — whether embedded in 

long-range plans, annual plans, 

or in-season management, and 

whether concerning water management or passage or reservoir 

operations — should reflect, or 

be based on, the following general strategies:

− Protect the habitat areas 

and ecological functions 

that are at present relatively 

productive for the life stages 

of the species important to 

the biological objectives of 

this program, including for 

spawning, resting, rearing, 

and migration of salmon and 

steelhead and resident fish. 

Enhance and restore habitats 

and ecological functions that 

connect to the protected areas.

− Protect biological diversity by 

benefiting the range of species, 

stocks, and life-history types 

in the river.

− Provide conditions that best 

fit those natural behavior 

patterns and river processes 

that most closely approximate 

the physical and biological 

conditions needed by the 

relevant species.

− With regard to hatchery 

populations of salmon and 

steelhead, prioritize mainstem 

protection and support to those 

hatchery populations that 

provide the most significant 

contribution to the rebuilding of 

naturally spawning populations 

in areas of program habitat 

investments, or that provide the 

most significant contributions 

to harvest while ensuring the 

least detrimental impacts on the 

survival of native fish species.

− Optimize actions to produce 

the greatest biological 

benefits for targeted species 

with the least cost, and the 

least adverse effects on other 

species, while ensuring 

an adequate, efficient, 

economical and reliable 

power supply.

• In December 2000, NOAA Fisheries and the U.S. Fish and Wildlife Service adopted biological 

opinions for the operation of the 

Federal Columbia River Power 

System for the benefit of populations of salmon, steelhead, bull 

trout and Kootenai white sturgeon 

listed as threatened or endangered 

under the Endangered Species Act. 

The measures in these opinions 

represent the recommendations 

of the federal fish and wildlife 

agencies with jurisdiction over the 

operational needs of these listed 

species. The Council accepts 

these measures as part of the fish 

and wildlife program for the near 

term. However, many of the biological opinion measures must be 

subject to systematic and rigorous monitoring and evaluation, as 

described below and in the more 

specific strategies, to determine if 

the measures have the biological 

benefits expected and represent 

the most cost-effective actions to 

achieve these benefits. Based on 

these evaluations, the Council may 

recommend to the federal operating and fish and wildlife agencies 

operations that differ from those 

in the biological opinions if the 

Council concludes the different 

operations provide the same or 

greater benefits to listed fish and 

wildlife than current operations at 

a lower cost. The Council is confident that changes in operations of 

this nature can be made consistent 

with the flexibility built into the 

biological opinions.

• The 2000 NMFS and USFWS biological opinion operations may not 

be optimal when the needs of fish 

and wildlife other than listed species are taken into account. Based 

on the vision, the biological objectives, and the overarching strategies stated earlier, the Council is 

adopting water management and 

other specific strategies to benefit 

all fish and wildlife affected by 

the hydrosystem, not just listed 

species. Where the strategies 

intended to benefit non-listed species appear to conflict with the biological opinions, the Council does 

not mean that the federal operating 

agencies should act contrary to 

the biological opinions in order to 

implement strategies in this program. The Council intends instead 

that the federal operating agencies 

make every effort practicable to 

use the operational flexibility in 

the biological opinions to meet the 

biological opinion requirements 

and implement the other strategies 

in the Council’s program. The 

exception is where the Council 

calls for explicit scientific testing 

of a particular operation in the 

biological opinions. The Council 

is confident these changes also 

can be made consistent with the 

flexibility built into the biological 

opinions without adverse effects 

on listed species and will lead to 

a more broad-based, sustainable, 

and cost-effective protection and 

recovery of fish and wildlife in 

the Columbia Basin. The Council 

calls on the federal operating agencies and fish and wildlife agencies 

Strategies
16 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

to consult with the Council, states, 

and tribes on the implementation 

of these strategies.

• The Council recognizes the need 

to test certain assumptions and 

uncertainties in the biological 

opinions as they relate to spill, 

flow augmentation, reservoir drafting, predator control, and harvest. 

The Council supports the development of tests and experiments for 

the hydrosystem even where some 

may require temporary departures 

from current biological opinion 

operations. These experiments 

will focus on areas where the 

quantitative benefits from biological opinion operations require 

additional understanding or verification, or where benefits to nonlisted species from varied operations may be significant without 

adverse impacts on listed species, 

or both. This approach is consistent with the biological opinions, 

which allow considerable flexibility to conduct necessary tests. In 

the strategies, the Council specifies 

what tests need to occur and why. 

In particular, the Council emphasizes the need for the following 

types of testing:

1) Determine more precisely 

the relationship between fish 

survival and various levels of 

spill at the individual dams 

and for the system.

2) Implement and test new 

spill technologies such as 

removable spillway weirs.

3) Evaluate turbine operations 

at the different dams to 

determine optimum fish 

survival through the turbines.

4) Evaluate the benefits 

of incremental flow 

augmentation 

and determine 

the mechanisms for flow/

survival relationships on the 

Columbia and Snake rivers.

5) Measure the effects of steady 

June through September 

outflows from Libby and 

Hungry Horse dams in 

Montana.

6) Identify the effects of shifting 

summer flows later in the 

summer.

7) Evaluate and document the 

impact of predation in the 

mainstem in terms of numbers 

of listed fish taken, and 

estimated impact on smolt-toadult return ratios.

8) Evaluate and document the 

impact of harvest operations 

in terms of numbers of ESAlisted fish taken and estimated 

impact on smolt-to-adult 

return ratios.

9) Test other uncertainties 

proposed by independent 

science panels and fish and 

wildlife managers summarized 

in this program and in the 

basinwide research plan.

There are several purposes for 

these tests. First and foremost is to 

determine the type of operation that 

provides the best benefits for enhancing listed and non-listed fish populations over the long term. In many 

cases, if it were better understood why 

certain operations were beneficial to 

fish it would be possible to adjust the 

operations to provide better survival. 

For example, the benefits of flow 

augmentation in the Snake River may 

be related to travel time, turbidity, 

temperature or reservoir fluctuations. 

Whatever the reason, operations could 

be made more effective if these mechanisms were better understood.

Another purpose of these tests is 

to better quantify the benefits of the 

operations so that choices 

can be made to assure 

that the same survival 

benefits are achieved 

through the lowestcost operation. This 

is largely the purpose behind many 

of the spill tests and tests involving 

removable spillway weirs. Early 

results appear to show that removable spillway weirs can provide the 

same benefits as baseline spill but use 

one-tenth of the water. This constitutes a considerable savings in terms 

of hydropower generation.

Finally, there are some operations 

where the benefits need to be more 

clearly demonstrated. Only through 

controlled experiments can we reach a 

conclusion as to the merits of continuing these operations. Recent scientific 

reports call into question several of 

these operations, especially active 

management of the storage projects to 

provide flow augmentation.

It should be emphasized that this 

approach represents more than passive 

observation. It includes the option of 

implementing large-scale field tests 

of hypotheses that will sometimes 

require changes in hydrosystem operations. In some cases, there may be 

risks associated with conducting the 

experiment, but these risks must be 

weighed against the risks of continuing operations without accurate information and against the potential risks 

to other fish species. In implementing 

large-scale field tests, or any other 

hydrosystem tests, the Council recognizes that water used from Columbia 

River and Snake River storage reservoirs, or from tributary streams within 

the Columbia River Basin, will be 

obtained through federal water rights 

where they exist, or through the individual states where such water may 

be made available in accordance with 

state water law.

The Council is prepared to take 

steps necessary to properly design 

experiments and ensure that they are 

implemented. In some cases this 

may require the Council to work 

with fish and wildlife agencies and 

tribes to establish project teams that 

can develop and oversee appropriate 

tests while assuring opportunities for 

public input.

The Council calls on NOAA 

Fisheries and the United States Fish 
17

2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

and Wildlife Service to exercise the 

flexibility within the biological opinions to implement these tests. We 

also encourage NOAA Fisheries and 

USFWS to make changes in the biological opinions when these scientific 

reviews and tests are completed and 

the results provide compelling reasons for change.

Strategies in 

Specific Areas

Mainstem habitat

• Through system operations and 

investments in mainstem habitat improvements, increase the 

extent, diversity, complexity, and 

productivity of mainstem habitat 

by protecting, enhancing, and 

connecting mainstem spawning, rearing, and resting areas. 

Actions to consider include, but 

are not limited to:

− providing appropriate 

spawning, rearing, and resting 

flows in the mainstem

− excavating backwater sloughs, 

alcoves, and side channels

− reconnecting alcoves, sloughs 

and side channels to the main 

channel

− dredging/excavation of lateral 

channels that have silted in

− enhancement of wetlands

− creating islands and shallowwater areas

− adding large woody debris to 

these systems

− stabilizing the water levels of 

the rivers and reservoirs to the 

extent practicable

− planting riparian and aquatic 

plants at appropriate locations

− acquiring and protecting lands 

adjacent to the mainstem

• Federal and state fish and wildlife 

agencies should analyze each proposed action to increase mainstem 

spawning and rearing habitat to 

ensure that the proposal may be 

implemented without adversely 

affecting the migration of listed 

populations through the mainstem.

• In instances where proposed operations to protect or enhance mainstem spawning and rearing habitat 

may conflict with operations 

intended to benefit juvenile or 

adult salmon migration, the system 

operators and the fish and wildlife 

agencies and tribes should identify 

potential conflicts, priorities, tradeoffs, and opportunities and consult 

with the Council, affected entities, and the public on how best to 

resolve conflicting needs.

• NOAA Fisheries’ 2000 Biological Opinion calls on the federal 

operating agencies, in conjunction 

with the Environmental Protection 

Agency and the U.S. Geological 

Survey, to develop a program to 

1) identify mainstem habitat sampling reaches, survey conditions, 

describe cause-and-effect relationships and identify research needs; 

2) develop improvement plans 

for all mainstem reaches; and 3) 

initiate improvements in three 

mainstem reaches. The Council adopts a similar measure as 

well, provided that this mainstem 

habitat initiative does not focus 

wholly, or even predominantly, 

on the mainstem habitat needs of 

the populations currently listed. 

Salmon mitigation, enhancement, 

and rebuilding opportunities in 

the mainstem may have greater 

relation to non-listed populations 

than to listed populations.

• Evaluate the feasibility of reintroducing anadromous fish into 

blocked areas, including above 

Chief Joseph and Grand Coulee 

dams.

• Identify the importance of protecting or improving mainstem 

habitat for recovering bull trout 

populations. The Council calls on 

the relevant state and federal fish 

and wildlife agencies to conduct 

the necessary research and report 

the analysis to the Council at the 

earliest possible date.

• Develop and implement actions 

that create littoral habitat and fish 

structures along the shores of 

Lake Roosevelt to diversify food 

available to fish and provide additional rearing habitat.

• Implement actions to stabilize and 

improve Columbia River white 

sturgeon and to recover listed Kootenai River white sturgeon.

• Implement actions to stabilize and 

improve burbot populations in the 

upper Columbia.6

• In the long-term, implement 

actions to reduce toxic contaminants in the water to meet state 

and federal standards.

Juvenile and adult passage, 

in general

• Consistent with the biological 

objectives and overarching strategies, all actions to provide or 

improve juvenile and adult fish 

passage through mainstem dams 

should emphasize adult survivals 

as a high priority. In addition, 

strategies should protect biological diversity by benefiting the 

broad range of species, stocks, 

6 When the Council adopts subbasin plans into the program, which will supersede existing management and mitigation plans, the objective will 

be to implement the strategies and achieve the objectives relating to white sturgeon, burbot and Lake Roosevelt fisheries stated in the relevant 

subbasin plans.

“All actions to provide 

or improve juvenile and 

adult fish passage through 

mainstem dams should 

emphasize adult survivals 

as a high priority.”
18 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

and life-history types in the river, 

not just listed species, and should 

favor solutions that best fit natural 

behavior patterns and river processes. To meet the diverse needs 

of multiple species and allow for 

uncertainty, multiple juvenile passage methods may be necessary at 

individual projects.

• The U.S. Army Corps of Engineers, working within the 

regional fish and wildlife project 

selection process, should report 

to the Council annually on how 

decisions on passage improvements take into account the 

strategies in the Council’s program. In addition, the Council: 

1) expects that the Independent 

Scientific Review Panel will 

apply these strategies during the 

panel’s review of the reimbursable portion of the Bonneville 

fish and wildlife budget, which 

includes the Corps’ passage program; 2) will itself apply these 

standards in its review of any 

Independent Scientific Review 

Panel report and resulting recommendations to Congress on these 

passage budget items; and 3) 

will recommend to Congress, in 

its reimbursable budget recommendations, that budget requests 

from the Corps of Engineers be 

evaluated for consistency with 

these principles.

• The Corps of Engineers should 

apply Value Engineering to all 

projects that exceed $10 million, 

using firms independent of the 

Corps of Engineers.

• For the purpose of planning for 

this fish and wildlife program, 

and particularly the hydrosystem portion of the program, the 

Council assumes that, in the near 

term, the breaching of any dams 

in the mainstem will not occur. 

The Council revises its fish and 

wildlife program every five 

years, at a minimum. If, within 

that five-year period, the status 

of the lower Snake River dams 

or any other major component of 

the Columbia River hydrosystem 

has changed, the Council can 

take that into account as part of 

the review process.

Juvenile fish 

transportation

• Because the existence of the 

dams and reservoirs creates 

conditions that are not natural, 

the Council, while seeking to 

improve inriver conditions, recognizes that there are survival 

benefits from transportation 

of migrating juvenile salmon. 

Therefore, the Council 1) continues to accept juvenile fish 

transportation as a transitional 

strategy; 2) will give priority to 

the funding of research that more 

accurately measures the effect of 

improved inriver migration compared to transportation and the 

comparative rate of adult returns 

to the spawning grounds of 

transported and inriver migrants; 

3) will recommend increasing 

inriver migration when research 

demonstrates that salmon survival would be improved as a 

result of such migration, and vice 

versa; and 4) endorses the strategy of “spread the risk” until it 

is determined whether migration 

inriver or transportation provides the best levels of survival.

• NOAA Fisheries’ 2000 Biological Opinion includes a series of 

measures concerning the transportation of ESA-listed juvenile 

salmon and steelhead. These are 

part of the biological opinion 

measures that the Council 

incorporates into its 

mainstem plan.

• In analyzing in any year the 

potential benefits of maximizing or minimizing transportation, 

the federal operating agencies 

must recognize that significant 

populations of salmon and steelhead important to the biological 

objectives of this program enter 

the mainstem hydrosystem either 

below the transport projects altogether or above McNary Dam but 

are not effectively transported at 

McNary. Inriver passage of these 

fish is either the only passage 

alternative available or the most 

significant passage alternative.

• The three highest priorities for 

juvenile transportation studies 

should be to:

1) evaluate whether the survival 

benefits of transport from 

McNary Dam are sufficiently 

greater, at least under certain 

circumstances, than inriver 

passage to justify continuing 

(or increasing) the transport 

effort from that dam;

2) conduct a transportation study 

that targets Snake River fall 

chinook; and

3) more clearly determine what 

delayed survival effects, if 

any, occur due to transport, 

such as adverse effects on 

homing behavior.

• NOAA Fisheries should conduct 

annual evaluations of the effectiveness of transportation and 

report the results to the Council 

and the Independent Scientific 

Advisory Board.

Spill

• When making long-term, annual, 

and in-season decisions for 

when, and to what extent, to 

spill water for passage, priority 

should be given to 1) minimizing 

impacts on returning adults and 

2) optimizing passage survival 

benefits for populations that 

are important to the biological 

objectives of this program, and 

that cannot be transported, or 

are ineffectively transported. 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 19

This includes spring chinook 

from the John Day River; wild, 

naturally spawning, and key 

hatchery populations of spring 

chinook from other tributaries 

above Bonneville Dam but below 

the transport projects (or where 

only a small proportion are collected at McNary), such as from 

the Deschutes, Hood, Umatilla, 

Wind, Klickitat, Umatilla and 

Yakima rivers; the listed Middle 

Columbia steelhead; Hanford 

Reach fall chinook; and Snake 

River chinook, to the extent 

transportation should be determined to be ineffective. These 

spill objectives will require a 

better understanding of the spill 

levels that optimize passage survival at each dam and how these 

change at various flow levels and 

for the range of fish populations 

that pass the project. The federal action agencies and NOAA 

Fisheries, in consultation with 

the other federal and state fish 

and wildlife agencies and tribes, 

should determine an optimal passage strategy at each dam and for 

each passage route. The Council 

seeks to maximize improvements in life-cycle survival. This 

requires determining the cumulative effects on fish survival of 

passing multiple dams and taking 

that information into account.

 • Spill should be managed according to the most biologically 

effective level at each project. 

Spillways continue to be an 

effective inriver passage route, 

more benign in general than 

juvenile bypass systems or turbine passage. On the other hand, 

1) spilling to the maximum gas 

supersaturation levels of 120 

percent may be increasing 

mortality at some dams when 

compared to what would occur 

at lesser volumes of spill; 2) 

spillway passage can also be 

the passage method most costly 

to the regional power system, 

especially in years of low water 

or high market prices for energy; 

3) the difference in survival 

between spillway passage and 

other passage methods may in 

some, but not all, instances be 

minimal; 4) the maximum level 

of fish survival at each project 

may be different from, and not 

necessarily correlated with, the 

most spill; and 5) spill may have 

negative effects on returning 

adults. For these reasons, the 

Council will work with the federal operating and fish and wildlife agencies, in consultation with 

the state fish and wildlife agencies and tribes and the Independent Scientific Advisory Board 

in a rigorous evaluation of the 

biological effectiveness and costs 

of spillway passage at each project and bring that information to 

bear in a systematic way in decisions on when, and how much, 

to spill. The goal of this evaluation should be to determine if it 

is possible to achieve the same, 

or greater, levels of survival and 

biological benefit to migrating 

fish as currently achieved while 

reducing the amount of water 

spilled, thus decreasing the 

adverse impact on the region’s 

power supply. At the conclusion 

of this evaluation, the Council 

will conduct a public review process with the goal of providing 

recommendations to the federal 

agencies for the most biologically effective spill actions at the 

lowest cost possible.

• This evaluation should include, 

or set in motion, at least the following:

1) Dam-specific estimates of 

smolt passage survival by 

species through spillways. 

Spill efficiency information 

should be updated and applied 

in future spill decisions and 

passage modeling analyses. 

The Council recognizes the 

difficulty in obtaining reliable 

empirical survival estimates 

linked specifically to spill 

conditions, but the power 

system impacts of spill require 

an improvement in the quality 

of this information.

2) Additional research on the 

biological consequences 

of various spill strategies 

is needed to determine the 

long-term effects of extended 

exposure to high levels of gas 

supersaturation on life-cycle 

survivals.

3) The interaction between 

spill, dissolved gas levels, 

adult passage, and survival 

needs additional research to 

better determine if, and how, 

spill strategies affect adult 

migration and survival, and 

what can be done to minimize 

those effects.

• As a particular focus, the Council calls for NOAA Fisheries, the 

federal operating agencies, and 

salmon managers to immediately 

implement tests to examine the 

benefits of the current summer 

spill program for outmigrating 

juvenile fall chinook, and to 

determine whether the biological benefits can be achieved in 

a more effective and less costly 

manner. Summer spill costs are 

high. Using a 50-year historical 

water record, the Council staff 

estimated that the cost of bypass 

spill for fish during the months 

of July and August averages onethird of the total cost impact of 

all mainstem operations designed 

for fish and wildlife protection. 
20

2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

While the summer spill program 

provides survival advantages to 

in-river outmigrants, the Council 

recommends an evaluation of the 

efficacy and cost of all actions 

available to improve juvenile 

and adult survival. These tests 

should be designed to encompass the full life cycle of fall 

chinook and evaluate all sources 

of mortality. This provision is 

not intended to dispute that spill 

is generally considered to be the 

safest passage route for in—river 

juvenile migrants, but rather to 

pursue more rigorous analysis 

and assessment of alternatives 

that may provide similar, or more 

effective, biological benefits at 

reduced cost.

• The U.S. Army Corps of Engineers, in consultation with these 

other entities, should place a priority on designing, testing, and 

evaluating methods and devices 

that could produce the same or 

greater benefit to fish while spilling less water, especially what 

are known as removable spillway weirs. If these methods and 

devices produce positive results, 

they should be implemented as 

soon as it is practical to do so.

• If efficient and effective use of 

spill, including the substantive 

spill experiments called for earlier, results in increased volumes 

of water passing through active 

turbines for power generation, 

apply an equitable part of the 

additional financial resources that 

result to implement additional prioritized measures in the Council’s 

fish and wildlife program.

• The Council intends to recommend specific spill strategies at 

specific projects after comprehensive spill survival studies 

have concluded. The Council 

intends these studies to begin 

immediately. The federal agencies’ 2003 plans for system operations to accelerate spill testing 

at John Day and Ice Harbor dams 

are examples of the types of tests 

that should be conducted.

• Until the cumulative effects of 

high levels of spill are better 

understood, the Council recommends that the region continue 

to monitor and evaluate spill 

strategies. The Council recommends that more strenuous efforts 

be undertaken to avoid exceeding total dissolved gas saturation limits of 120 percent, over a 

time period of the twelve highest hourly measurements at all 

Federal Columbia River Power 

System projects engaged in spill 

operations. State authority to 

grant a variance from the Federal 

Clean Water Act standard of 110 

percent total dissolved gas supersaturation requires a determination by the state that the variance 

creates no long-term impact to 

the beneficial use for which the 

deviation was authorized.

Juvenile bypass systems

• To provide passage for juvenile 

fish that most closely approximates natural physical and biological conditions, and to increase 

the energy produced by the hydrosystem, the U.S. Army Corps of 

Engineers should:

1) continue testing and 

developing surface bypass 

systems, taking into account 

the widest range of biological 

diversity as described in 

the biological objectives 

and overarching strategies, 

utilizing an expedited 

approach to prototype 

development, and ensuring 

full evaluation for the 

developmental phase;

2) relocate bypass outfalls in 

those circumstances where 

there are problems with 

predation and juvenile fish 

injury and mortality;

3) modify turbines to improve 

juvenile survival; and

4) conduct research on fish 

diseases at fish passage 

facilities.

Adult passage

• The U.S. Army Corps of Engineers should improve the overall 

effectiveness of the adult fish 

passage program. This includes 

expediting schedules to design 

and install improvements to fish 

passage facilities. The ultimate 

survival and successful spawning 

of adult fish are a high Council 

priority because returning adults 

determine the size and health of 

future fish populations. Where it 

is beneficial, cool water releases 

from reservoirs should continue to 

be used to facilitate adult migration. More emphasis should be 

placed on research; monitoring 

and evaluation; increased accuracy of fish counts; expansion 

of fish counting to all species of 

interest; installation of PIT-tag 

and radio-tag detectors; evaluation of escapement numbers to 

spawning grounds and hatcheries; 

research into water temperature 

and spill effects on fish passage; 

and the connection between fish 

passage design and fish behavior. 

In particular:

1) as a priority for the Corps 

of Engineers’ capital 

construction program, correct 

adult fish passage problems 

and report annually to the 

Council on progress;

2) install adult PIT-tag detectors 

at projects that do not have 

them;

3) improve fish counting 

accuracy; and 

“The Council recommends that more strenuous efforts be undertaken 

to avoid exceeding total 

dissolved gas saturation 

limits of 120 percent.”
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 21

Of the original salmon and 

steelhead habitat available 

in the Columbia River Basin, 

55 percent of the area, and 

31 percent of the stream 

miles, have been blocked by 

dam construction.

4) conduct research on fish 

diseases at fish passage 

facilities.

Water management

• Manage water through the hydrosystem so that patterns of flow 

more closely approximate the 

natural hydrographic patterns 

and are directed at re-establishing natural river processes where 

feasible, and produce the highest possible survival rates for 

a broad range of affected fish 

within the physical limitations 

of the multiple purposes of the 

region’s storage reservoirs and 

hydrosystem. Assure that any 

changes in water management 

are premised upon, and proportionate to, fish and wildlife benefits, while assuring the region an 

adequate, efficient, economical, 

and reliable power supply. Elements of this general strategy for 

water management include:

1) Frame habitat restoration in 

the context of measured trends 

in water quantity and quality.

2) Allow for seasonal 

fluctuations in flow, including 

floods. Reduce large and 

rapid short-term fluctuations. 

Reduce or eliminate stranding 

and other problems associated 

with fluctuation of the 

hydroelectric system.

3) Increase the correspondence 

between water temperatures 

and the naturally occurring 

regimes of temperatures 

throughout the basin. To the 

extent possible, use stored 

water to manage water 

temperatures below the storage 

reservoirs where temperature 

benefits from releases can be 

shown to provide improved 

fish survival.

4) Identify, protect, and restore 

ecosystem functions in the 

Columbia River estuary and 

nearshore ocean discharge 

plume as affected by actions 

within the Columbia River 

hydrosystem. This includes 

evaluating flow effects, river 

operations, and estuary-area 

habitat changes, as well as 

local effects from activities 

such as dredging and 

pollution from urban areas, to 

better understand and improve 

the relationship between 

estuary and near-shore 

plume characteristics and 

the productivity, abundance, 

and diversity of salmon and 

steelhead populations.

• Systemwide water management, 

including flow augmentation 

from storage reservoirs, should 

attempt to meet the needs of 

anadromous and resident fish 

species in the river and upstream 

storage reservoirs, so that actions 

taken to benefit one species do 

not unnecessarily come at the 

expense of other species. Flow 

augmentation is defined as the 

intentional release or drafting of 

water from storage reservoirs for 

the purpose of increasing flows 

to enhance migratory conditions for juvenile and adult lifestages of salmon and steelhead 

through the reach of the lower 

river hydroelectric dams. The 

federal system operators, NOAA 

Fisheries and the U.S. Fish and 

Wildlife Service should identify 

potential conflicts and seek recommendations from the Council, 

fish and wildlife agencies, tribes, 

and other affected entities on 

how best to balance the different 

needs prior to the implementation of flow actions.

• The Council recognizes the continuing controversies over: a) the 

nature, extent of, and reasons for 

the flow-survival relationship for 

migrating salmon and steelhead; 

b) the consistency between the 

flow targets and the flow measures; and c) flow augmentation in 

general, with these implications:

1) The Council continues to call 

on Bonneville, in consultation 

with NOAA Fisheries and the 

U.S. Fish and Wildlife Service, 

to prepare an annual report 

based on scientific research 

for review by the Independent 

Scientific Advisory Board 

that documents the flow 

augmentation actions taken, the 

benefits of flow augmentation 

for fish survival and the precise 

attributes of flow that may 

make it beneficial.

2) The Council will consult with 

these and other entities to 

determine whether and how 

to conduct a comprehensive 

evaluation of survival, flow 

targets, and flow augmentation 

to determine the relationship 

between specific management 

actions and changes in lifecycle and lifetime survival. 

This evaluation will, among 

other things:

– evaluate the scientific validity 

of the flow targets and flow 

augmentation actions in the 

2000 Biological Opinion;

– evaluate how often, and for 

what duration, river flows, 

whether augmented or not 

from storage releases, meet 

the spring and summer flow 

targets in the 2000 Biological 

Opinion, and what additional 

amounts of water from what 

sources would be required 

to meet the targets on a 

sustained basis;
22 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

– quantify the volume and shape 

of water that has been, and 

is being, provided as flow 

augmentation;

– translate to the extent possible 

the incremental increase in 

flows from flow augmentation 

to changes in water velocity 

and temperature;

– evaluate and predict to the 

extent possible how changes in 

adult survival relate to changes 

in flow; and

– evaluate hydrosystem 

operations and establish the 

relative benefits and costs 

of those operations to native 

fish throughout the Columbia 

watershed.

At the conclusion of such an evaluation, the Council will conduct 

a public review process with the 

goal of determining whether to 

provide revised recommendations 

to the federal agencies for continuing or modifying the current 

water management program for 

migrating salmon and steelhead. 

The Council may also decide at 

that time, if necessary, to initiate 

a process to further amend the 

mainstem portion of the Council’s 

program to address system management matters.

3) The spring and summer 

flow objectives in NOAA 

Fisheries 2000 Biological 

Opinion are guidelines for 

understanding and evaluating 

water management actions 

in the Columbia Basin 

intended to establish and 

support habitat conditions for 

many life stages of multiple 

species of fish throughout 

the mainstem Columbia and 

Snake rivers. The Council 

understands these objectives to 

be flexible guidelines that do 

not determine or override the 

multiple set of objectives and 

strategies in the two biological 

opinions and in this program.

Operations of the Federal Columbia River Power System established 

in the 2000 Biological Opinions as 

a baseline for the water management strategies of this Program

• NOAA Fisheries’ 2000 Biological Opinion includes a series of 

measures concerning water management for the benefit of listed 

juvenile salmon and steelhead, 

while the U.S. Fish and Wildlife 

Service’s 2000 Biological Opinion includes a set of measures 

concerning water management for 

the benefit of listed bull trout and 

Kootenai River white sturgeon. 

The water management measures 

in these biological opinions are 

part of this program, and the 

Council concurs that these are 

appropriate operations to protect, 

mitigate, and enhance those anadromous and resident fish listed 

under the Endangered Species 

Act and affected by the Columbia 

hydrosystem. The measures and 

objectives in these two biological 

opinions need to be reconciled 

if there are inconsistencies, and 

some of the water management 

strategies in the Council’s program are intended, at least in part, 

for that purpose.

• The Council is adopting additional water management strategies to protect, mitigate, and 

enhance all fish and wildlife 

affected by the hydrosystem and 

meet the biological objectives 

and vision of its program. To the 

extent these water management strategies appear 

to conflict with the biological opinions, the 

Council does not mean 

that the federal operating agencies should act 

contrary to the biological opinions in order to implement the 

strategies in this program. The 

Council intends instead that the 

federal operating agencies make 

every effort practicable to use the 

operational flexibility in the biological opinions to meet the biological opinion requirements and 

implement the water management 

strategies in this program. The 

exception is where the Council 

calls for explicit scientific testing 

of a particular operation in the 

biological opinion. The Council 

calls on the federal operating 

agencies and fish and wildlife agencies to implement the 

Council’s recommendations in 

consultation with the Council, the 

states, and the tribes.

Hanford Reach/mainstem and 

estuary spawning, rearing, and 

resting habitat

• Manage flows, while maintaining 

consistency with this mainstem 

plan’s flow and reservoir operations, to protect, improve, and 

expand spawning, rearing, and 

resting habitat in the mainstem 

and estuary. In particular, the 

federal and non-federal project 

operators should provide suitable and stable flows to establish 

and protect the habitat conditions 

necessary for spawning and rearing in the Hanford Reach on an 

equal basis as managing water 

to support the migration of listed 

species. This includes providing 

the flows required by the Vernita 

Bar agreement and by subsequent 

agreements to extend stable flows 

to reduce or prevent stranding 

problems in the Reach. It also 

includes the need for the Bureau 

of Reclamation, as the operator of 

Grand Coulee Dam, and the oper-
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 23

ators of the mid-Columbia projects to take the steps necessary, 

separately and together, to further 

reduce flow fluctuations through 

the Reach that affect spawning 

and rearing.

Spring reservoir/flow operations 

in general

• Refill should be a high priority 

for spring operations at Hungry 

Horse, Libby, Grand Coulee, 

and Dworshak dams so that the 

reservoirs have the maximum 

amount of water available during 

the summer. While on average 

the target date for refill should be 

late July for Libby and the end 

of June for the other projects, the 

system operators should work 

to adjust the actual refill date 

based on reservoir conditions and 

inflow forecasts.

• Incorporating the 2000 Biological Opinions of NOAA Fisheries 

and the U.S. Fish and Wildlife Service into this program 

includes the opinions’ approach 

to spring water management 

in general, which the Council 

understands as operating the 

storage reservoirs to ensure a 

high probability of water surface 

elevations within one-half foot of 

the upper flood control rule curve 

by April 10 and to refill by June 

30 (late July for Libby), otherwise passing the spring runoff 

through the storage reservoirs. 

The NOAA Fisheries biological opinion retains the flexibility 

to allow active flow augmentation to occur in the spring under 

certain circumstances at the call 

of the Technical Management 

Team. The Council calls on the 

federal agencies not to exercise 

this flexibility to allow for flow 

augmentation or additional reservoir drafting in the spring except 

under extraordinary circumstances and only after consultation with the Council.

Spring operations at Hungry Horse 

and Libby dams

• VARQ flood control operations 

and Integrated Rule Curve 

operations. At Hungry Horse 

and Libby dams, continue to 

implement the VARQ flood control operation called for in the 

biological opinions and implement the Integrated Rule Curve 

operations as recommended by 

the Montana Department of Fish, 

Wildlife and Parks for the benefit 

of native resident fish in those 

reservoirs. Operations should 

reduce the frequency of refill 

failure (to within five feet of full 

pool) at Hungry Horse and Libby 

reservoirs as compared to historic 

operation. Implement seasonal 

flow windows and flow ramping 

rates in the Flathead and Kootenai rivers downstream of the 

storage reservoirs, and maintain 

minimum flows in the Flathead 

and Kootenai rivers as described 

by the U.S. Fish and Wildlife Service 2000 Biological Opinion and 

the Montana Department of Fish, 

Wildlife and Parks, including the 

sliding-scale flow strategy for 

bull trout specified by the biological opinion. Implement VARQ 

operations in an attempt to avoid 

the more extreme adverse effects 

at Grand Coulee that occur in a 

small percentage of years. The 

Corps of Engineers should consult with the Council to identify 

those occurrences and effects and 

to determine what might be done 

to minimize or avoid them, and 

report annually to the Council on 

VARQ implementation to show 

that these extreme adverse effects 

are not occurring. The Corps of 

Engineers should also place a 

priority on conducting the further 

comprehensive review of flood 

control operations called for in 

the NOAA Fisheries 2000 Biological Opinion.

• Operations at Libby Dam to 

benefit Kootenai River white 

sturgeon. The U.S. Fish and 

Wildlife Service’s 2000 Biological Opinion concerning hydrosystem operations that affect 

ESA-listed Kootenai River white 

sturgeon specifies a “tiered” strategy for flow augmentation from 

Libby Dam to simulate a natural 

spring freshet, controlled within 

flood constraints. Volumes are 

determined by forecasted water 

availability so that higher flows 

are released when ample water is 

available and minimal flow augmentation occurs during drought. 

The Council recommends that the 

average flow augmentation volumes outlined in Figure 1 be used 

as a guide for sturgeon operations 

at Libby Dam. These augmentation volumes are not specified 

volumes and should represent 

targets for planning purposes. 

Actual augmentation volumes in 

any given year will depend on 

flood control constraints, reservoir 

refill targets, water availability, 

and benefits to the Kootenai 

white sturgeon population. This 

strategy represents a refinement 

to volumes specified in the 2000 

Biological Opinion.7 

The Council also recognizes that 

additional work is required to 

further refine appropriate sturgeon operations at Libby Dam, 

and recommends that regional 

entities continue to work to 

increase the biological benefits 

provided by the flow augmentation volumes.

7 The sturgeon tiered flow strategy is a fish recovery action that is separate and distinct but compatible with the VARQ flood control operation. 

The tiered flow strategy in the U.S. Fish and Wildlife Service’s 2000 Biological Opinion differs from the original plan that was adopted 

by the international White Sturgeon Recovery Team. During a March 25-26, 2002, meeting with the U.S. Army Corps of Engineers, the 

Recovery Team determined that some problems could be corrected by establishing a new calculation for sturgeon flows. Release volumes 

are still based on water availability, but the volumes to be released are calculated over the entire range of possible inflows (dashed line) 

rather than grouped into the original six tiers.
24 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

Spring operations at Grand 

Coulee Dam

• Operate Grand Coulee Dam in 

the winter and spring (from January through June) consistent with 

biological opinion operations and 

ordinary hydrosystem operations, 

with the following considerations:

1) Attempt to meet the following 

minimum monthly elevation 

targets in Lake Roosevelt 

while trying to achieve the 

minimum monthly mean 

retention times as follows, 

until fisheries evaluation 

information indicates a change 

in Figure 2.

2) March-to-May elevations are 

recommended minimums, 

with the understanding that 

flood control operations will 

determine the actual upper 

elevation.

3) Two high priorities for Grand 

Coulee through the year 

should be to contribute to the 

establishment and protection 

of the necessary conditions in 

the Hanford Reach described 

earlier and to refill by the end 

of June.

4) As much as possible, manage 

the reservoir and dam 

discharges to produce steady 

flows across each season and 

each day to minimize reservoir 

fluctuations and ramping rates.

Spring and summer water management in the Snake River

• Spring and summer water management in the Snake River 

should be consistent with NOAA 

Fisheries’ 2000 Biological Opinion, with the following additional 

observations:

Figure 2: Grand Coulee

 Minimum Mean 

Period Minimum Elevation Water Retention Time

January 1270 ft above sea level 45 days

February 1260 40 days

March-April 15 1250 30 days

April 16 1255 30 days

May 1265 35 days

June fill to 1290 historically 40-60 days or maximum 

 achievalbe for the month
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 25

1) Providing water from the 

Bureau of Reclamation’s upper 

Snake River Basin projects 

and Idaho Power Company’s 

Hells Canyon projects to assist 

in achieving Snake River 

flow objectives at Lower 

Granite Dam is not part of the 

2000 Biological Opinion and 

will largely be addressed in 

separate, ongoing ESA Section 

7 consultations. Flows or 

volumes of water will be made 

available from upper Snake 

River storage by the Bureau 

of Reclamation or any other 

entity only if consistent with 

applicable state and federal 

law, including but not limited 

to, Idaho Code §42-1763B.8

2) The Council encourages 

the Bonneville Power 

Administration, Idaho Power 

Company, and the Bureau 

of Reclamation to execute a 

shaping agreement to ensure 

that flows from Brownlee 

Reservoir will occur to assist 

juvenile and adult migration 

when most needed, at the call 

of the Technical Management 

Team (TMT).

3) Lower Granite flow targets 

do not account for differences 

in characteristics between 

flow augmentation sources, 

or the biologically significant 

components of those sources. 

Given that existing flow 

targets are often unattainable, 

simply striving to meet flow 

targets regardless of the 

degree of biological benefit 

obtained is an ineffective and 

uneconomical strategy for 

salmon recovery.

4) Cost-effective analysis 

for the “same biological 

objectives(s)” is an action 

commensurate with statutory 

provisions of the 1980 Power 

Act when reviewing issues 

surrounding flow objectives 

at Lower Granite Dam. 

Given the competing issues 

of flow augmentation and 

available water resources, 

the Council requests 

Bonneville, in coordination 

with NOAA Fisheries, U.S. 

Fish and Wildlife Service, 

state fish and wildlife 

managers and tribes to: a) 

define Endangered Species 

Act harvest and recovery 

objectives for anadromous 

fish in specific mainstem 

sections and in tributaries of 

the mainstem; and b) develop 

alternative strategies to 

flow augmentation that will 

achieve “the same biological 

objectives.” Factors 

related to this analysis are 

expected to include hatchery 

objectives, ocean effects, 

dissolved gas trauma losses 

from spill and spill effects 

on migrating juveniles and 

returning adults.

Summer reservoir operations at 

Hungry Horse and Libby, Grand 

Coulee and Dworshak Dams

• Hungry Horse and Libby 

Dams:

1) Reduce the frequency of refill 

failure (to within five feet 

of full pool) as compared to 

historic operations; implement 

seasonal flow windows and 

flow ramping rates in the 

Flathead and Kootenai rivers 

downstream of the storage 

reservoirs and maintain 

minimum flows in the 

Flathead and Kootenai rivers 

as described by the U.S. Fish 

and Wildlife Service 2000 

Biological Opinion and the 

Montana Department of Fish, 

Wildlife and Parks.

2) As an experiment, implement 

and evaluate an interim 

summer operation as follows:

− Summer reservoir drafting 

limits at Hungry Horse and 

8 No provision of this amendment may, by recommendation of the Council, propose to “(1) affect the rights or jurisdictions of the United 

States, the States, Indian tribes, or other entities over waters of any river or stream or over any groundwater resource, (2) alter, amend, 

repeal, interpret modify or be in conflict with any interstate compact made by the States, or (3) otherwise be construed to alter, or establish 

the respective rights of States, the United States, Indian tribes, or any person with respect to any water or water related right.” Northwest 
26

2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

Libby should be 10 feet 

from full pool by the end of 

September (elevations 3550 

and 2449, respectively) in 

all years except the lowest 

20th percentile water supply 

(drought years) when the 

draft could be increased to 20 

feet from full pool by the end 

of September. This would 

protect fisheries resources 

in the reservoirs and rivers 

downstream, while providing 

additional flow augmentation 

for fish immediately below 

the project(s) and in the lower 

Columbia River.

− Draft each storage reservoir 

according to elevation 

limitations that, when 

combined with projected 

inflows, result in stable and 

“flat” or very gradually 

declining weekly average 

outflows from July through 

September. The Council 

understands that the effect of 

these operations and summer 

drafting limits would be to 

reduce the drafting of these 

two reservoirs in summer 

compared to what they would 

be under ordinary biological 

opinion operations. The 

Council believes there is 

significant flexibility within 

the biological opinions to 

implement the summer 

reservoir operations as an 

experiment. If there is 

disagreement on this, the 

Council calls on the federal 

operating agencies and 

federal fish and wildlife 

agencies to consult on the 

operation of these two 

projects in an effort to reach 

agreement that will allow this 

operation as an experiment. 

The agencies should also 

continue to investigate 

creative water management 

actions for summer flows, 

including what are known 

as the “Libby-Arrow” and 

“Libby-Duncan” swaps, 

although implementation 

of the summer operations 

experiment at Hungry 

Horse and Libby is not to be 

dependent on these actions.

− Little information exists 

about the relationship, if 

any, between levels of flow, 

flow augmentation and 

juvenile and adult salmon 

survival through the lower 

Columbia hydrosystem 

reach. Therefore, the focus 

of the experiment and 

evaluation to accompany 

the implementation of 

these summer operations at 

Hungry Horse and Libby 

should be on: a) ascertaining 

the nature, extent of and 

reasons for a flow-survival 

relationship through the 

lower Columbia system, if 

any exists; b) determining 

whether flow augmentation 

from the upper Columbia 

storage projects has any effect 

on levels of survival; and 

c) determining the benefits 

to resident fish from this 

operation. The Corps of 

Engineers and the Bureau of 

Reclamation should consult 

with a team formed from the 

Council, the Independent 

Scientific Advisory Board, 

the Montana Department of 

Fish, Wildlife and Parks, the 

Confederated Salish-Kootenai 

Tribes, NOAA Fisheries and 

the U.S. Fish and Wildlife 

Service to design a proper 

experiment and evaluation 

of this nature to take place 

during the implementation 

of these operations. The 

Council’s hypothesis is that 

the proposed operations 

will significantly benefit 

listed and non-listed resident 

fish in the reservoirs and 

in the portions of the 

rivers below the reservoirs 

without discernible effects 

on the survival of juvenile 

and adult anadromous fish 

when compared to ordinary 

operations under the 

biological opinions.

− As the federal operating 

agencies implement this 

operation, they should ensure 

there is no adverse biological 

impact on Lake Roosevelt 

fisheries due to changes 

in reservoir elevations or 

water retention times. The 

operating agencies should 

report annually to the Council 

on the nature and extent of 

impacts to Lake Roosevelt 

from this summer operation 

at Hungry Horse and Libby. 

The Council will analyze 

this information, and if the 

Council decides the impacts 

to Lake Roosevelt fisheries 

are unacceptably adverse, 

the Council will make 

additional recommendations 

on operations to the federal 

operating agencies.

• Operate Grand Coulee Dam

from July through December consistent with the biological opinion 

operations and with ordinary 

hydrosystem operations, with the 

following considerations:

1) Draft evenly from Lake 

Roosevelt to the target 

elevation by the end of 

August. As much as possible, 

manage the reservoir and 

dam discharges to minimize 

fluctuations and ramping rates 

and produce steady flows 

across each season and each 

day to minimize reservoir 

“The Council believes 

there is significant flexibility within the biological 

opinions to implement the 

summer reservoir operations as an experiment.”
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 27

fluctuations and ramping 

rates. Attempt to draft no 

lower than 1283 feet by the 

end of August.

2) From September through 

December, attempt to 

maintain a minimum 

elevation of 1283 feet to 

maximize water retention 

times and protect kokanee 

access and spawning. Federal 

operators, fish and wildlife 

managers, and others should 

consult with the Council to 

determine how to provide 

the biological benefits of 

a 1283 operation while 

meeting biological opinion 

requirements, including chum 

flows and operating to protect 

flows for the Hanford Reach.

3) Attempt to maximize water 

retention times from June to 

December of 40 to 60 days, 

or the maximum historically 

achievable for each month.

4) Two high priorities for Grand 

Coulee through the year 

should be to contribute to the 

establishment and protection 

of the necessary conditions in 

the Hanford Reach described 

above and to refill by the 

end of June. Summer and 

fall operations should be 

consistent with these priorities.

• Dworshak Dam

1) Operate Dworshak Dam 

consistent with the provisions 

of the 2000 Biological 

Opinion as implemented 

through the Corps of 

Engineers acting as a member 

of, and in coordination 

with, the regional Technical 

Management Team, and 

do so in a manner that a) 

recognizes the concerns and 

interests of the Nez Perce 

Tribe, the Idaho Department 

of Fish and Game, the 

Idaho Department of Water 

Resources, and the Idaho 

Legislature, as expressed in 

the jointly approved Idaho 

Dworshak Operations Plan, 

adopted December 21, 2000; 

and b) that accommodates the 

salmonid and resident fish 

objectives of the Council’s 

program and the 1980 

Northwest Power Act.

2) The Independent Science 

Advisory Board and the 

Independent Economic 

Analysis Board shall review 

the operation of Dworshak 

Dam to assess the adverse 

impacts of those operations 

on resident fish and wildlife 

and the adverse impacts on the 

Clearwater County regional 

economy because of impacts 

to resident fish and wildlife. 

The Council will review the 

ISAB and IEAB reports, 

consult with the relevant fish 

and wildlife managers, and 

make recommendations to 

Bonneville on any additional 

fish and wildlife mitigation 

responsibilities deemed 

appropriate under the 

Power Act.

Monitoring and 

evaluation

• The 2000 Fish and Wildlife Program describes a general strategy 

for monitoring and evaluation. 

The emphasis is on developing 

and implementing standards and 

procedures for monitoring and 

evaluating management activities 

that are aimed at improving habitat conditions for fish and wildlife. The goals are to determine 

whether the biological objectives 

of the program are being achieved 

at the basinwide level and at 

lower levels, and to make sure 

that the evaluation information 

is used to adapt or change management strategies that are not 

achieving the biological objectives. The monitoring and evaluation elements stated earlier in the 

various mainstem strategies, and 

the general provisions in this section, are intended to be consistent 

with this general strategy.

• The Council may assist the federal agencies in reviewing the 

results of research, monitoring 

and evaluation efforts to identify whether actions taken are 

achieving the performance standards and objectives in the 2000 

Biological Opinions, and also 

whether the research and evaluation results confirm or call into 

question the soundness of the 

standards themselves.

• Fish Passage Center. The mainstem plan calls for the continued 

operation of the Fish Passage 

Center (Center). The primary 

purpose of the Center is to provide technical assistance and 

information to fish and wildlife 

agencies and tribes in particular, and the public in general, 

on matters related to juvenile 

and adult salmon and steelhead 

passage through the mainstem 

hydrosystem. This information 

relates to the implementation of 

the water management measures 

in the Council’s fish and wildlife 

program. In performing this 

function, the Center shall:

1) Plan and implement the annual 

smolt monitoring program;

2) Gather, organize, analyze, 

house, and make widely 

available monitoring and 

research information related 

Historic annual runs of 

salmon and steelhead were 

believed to have measured 

between 11 and 16 million 

fish, but declined to about 

one million by the 1990s.
28 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 

to juvenile and adult passage, 

and to the implementation of 

the water management and 

passage measures that are part 

of the Council’s program;

3) Provide technical information 

necessary to assist the agencies 

and tribes in formulating inseason flow and spill requests 

that implement the water 

management measures in the 

Council’s program, while 

also assisting the agencies 

and tribes in making sure that 

operating criteria for storage 

reservoirs are satisfied; and 

4) In general, provide the 

technical assistance 

necessary to coordinate 

recommendations for storage 

reservoir and river operations 

that, to the extent possible, 

avoid potential conflicts 

between anadromous and 

resident fish.

The Council has established an 

oversight board for the Center, with 

representation from NOAA Fisheries, state fish and wildlife agencies, 

tribes, the Council, and others to 

provide policy guidance for the 

Center and to ensure that the Center 

carries out its functions in a way 

that assures regional accountability 

and compatibility with the regional 

data management system. The 

oversight board’s responsibilities 

will include conducting an annual 

review of the performance of the 

Center and developing a goal-oriented plan for next year’s operation. 

The Center shall prepare an annual 

report to the oversight board and the 

Council, summarizing its activities 

and accomplishments. There will be 

no other oversight board or board of 

directors for the Center.

Operation of the Center shall 

include funds for a manager and 

for technical and clerical support in 

order to perform its stated functions. 

The fish passage manager will be 

selected based on his or her knowledge of the multiple purposes of the 

regional hydropower system, and of 

the water needs of fish and wildlife, 

as well as the ability to communicate and work with fish and wildlife agencies, tribes, the Council, 

project operators, regulators, and 

other interested parties, including 

members of the public. The fish 

passage manager will be selected by, 

and be subordinate to, the Executive 

Director of the Columbia Basin Fish 

and Wildlife Authority (Authority), 

in consultation with the oversight 

board. The Executive Director of 

the Authority and the Chair of the 

Council (or the Chair’s designee) 

will conduct an annual review of the 

manager’s performance.

The Center shall continue to provide an empirical database of fish 

passage information for use by the 

region, not just by fish and wildlife 

managers. No information collected 

by the Center, and no analyses by 

the Center, shall be considered proprietary. The oversight board and 

the fish and wildlife managers will 

ensure that the database conforms to 

appropriate standards for data management, including review of the 

database by an appropriate scientific or data review group. The fish 

and wildlife managers will provide 

a liaison position at the Authority 

between the public and the Center 

to ensure that all parties have timely 

and thorough access to the database. 

The Council may revise the functions of the Center as the region 

develops a comprehensive data management system.

To assist the oversight board, the 

Executive Director of the Columbia 

Basin Fish and Wildlife Authority, in 

consultation with the fish and wildlife 

mangers, will propose to the oversight 

board candidates for a technical advisory committee, whose purpose will 

be to establish technical protocols and 

scientific requirements for the Center 

and to review the scientific and technical aspects of the performance of 

the Center. The oversight board will 

select the technical advisory committee from the names submitted by the 

Executive Director of the Authority. 

The technical advisory committee will 

report to the oversight board.

Research

• 2000 Fish and Wildlife Program. The 2000 Fish and Wildlife Program describes a general 

approach regarding research 

related to the Program, including 

the development by the Council 

of a basinwide research plan that 

identifies key uncertainties for 

the program and its biological 

objectives, and the steps needed 

to resolve these uncertainties, 

coordination of this overall plan 

with particular research elements, 

including ocean research, and a 

call to make research results and 

other information important to the 

program more readily available. 

The research elements stated earlier in the various mainstem strategies, and the general provisions 

in this section, are intended to be 

based on, and consistent with, this 

general strategy.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 29

• Research aimed at optimizing 

fish and wildlife benefits and 

energy production. Actions 

taken to benefit fish and wildlife 

should also consider and minimize 

impacts to the Columbia basin 

hydropower system if at all possible. The goal should be to try to 

optimize both values to the greatest degree possible. Thus, a high 

priority for mainstem research in 

general should be to try to determine what actions can be taken to 

provide both high fish and wildlife 

and energy benefits, or at least to 

increase one set of benefits without 

degrading the other. As an example, spill is an operation for fish 

with a serious energy impact for 

the power system. As described 

above in the strategy on spill, this 

operation should be examined 

to determine whether spill can 

be more effectively utilized to 

help fish and lessen its impacts to 

energy production.

• Approach to prioritizing 

research ideas and proposals. In 

deciding what mainstem research 

to fund or implement, the assigning of priorities should take into 

account a wide array of factors, 

such as:

1) potential biological benefits to 

fish and wildlife

2) widespread scientific value — 

can what is learned be applied 

to other situations?

3) management application

4) degree of uncertainty of the 

question asked

5) cost of the research

6) cost of the proposal on power 

system.

7) potential cost to implement the 

results of research

8) level of completion/

duplication

9) legal relevance — does the 

research activity respond to the 

biological opinion and/or to 

the fish and wildlife program, 

or to other legal requirements?

10) “doability” in the technical 

 sense — is the proposal a

 reasonable way to complete 

 this activity?

11) “doability” in the legal/ 

 institutional sense

Research proposals should be 

evaluated against each of these 

important elements, with the results 

combined in a variety of ways 

to expose the weight of different 

variables. A broad representation 

of people and interests should be 

involved in prioritizing proposals, 

including the independent scientific 

panels. People at the policymaking 

level should be more involved in 

the final decisions on long-term and 

annual research plans.

Annual and In-season 

Decisionmaking

• Through the biological opinions, 

the federal agencies have established an implementation structure 

for deciding on annual operation 

plans for fish and wildlife, inseason management of hydrosystem operations for fish and wildlife 

and recommendations to Congress 

for funding for passage improvements. At present, this decision 

structure is insufficient to integrate 

fish and power considerations 

in a timely, objective and effective way, and it focuses on listed 

fish with little consideration for 

unlisted anadromous and resident 

fish species and wildlife. The 

Council continues to recommend 

to the federal agencies that this 

implementation structure, which 

includes the Technical Management Team and the Implementation Team, be jointly sponsored 

by the Council and the federal 

agencies. The implementation 

structure should allow for effective participation in these considerations by the relevant federal agencies, the Council and states, the 

tribes of the Columbia River Basin 

and other affected entities in a 

highly public forum. Discussions 

to this end began in 2001, but then 

were overcome by events. The 

Council will re-initiate the discussions to jointly sponsor these coordination teams.

The Council recommends that the 

forum then broaden its focus to 

improve in-season hydrosystem 

operations decisionmaking, in the 

following ways:

1) Include expertise in both 

biological and power system 

issues.

2) Have the technical capability 

to analyze and present power 

supply forecasts, hydrosystem 

operational alternatives, and 

other power related issues. 

The Council should play a 

significant role in this.

3) Have the technical capability 

to analyze differing 

hydrosystem operation 

proposals relative to impacts 

on salmon, steelhead, sturgeon 

and resident fish migration, 

survival, spawning, and 

rearing, and relative to impacts 

on wildlife.

4) Regularly schedule meetings, 

as often as required, to deal 

with short-term, real-time 

decisions (e.g. weekly inmigration season), as well 

as middle and long-term 

issues (e.g. addressing longer 

term reliability issues in a 

way that removes risk to 

providing operations to meet 

requirements of salmon).

5) Operate with a defined set of 

decisionmaking criteria and 

hold participants accountable 

for the decisions they make, 

according to the established 

criteria.

Mid-Columbia Hydro- electric Projects

• The Council will review and, as 

appropriate, include in the program settlement agreements for 

the mid-Columbia hydroelectric 

projects.
30 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 31

I

n the 2000 Fish and Wildlife 

Program amendments, the Council provided that all measures in 

the program that were “not directly 

superseded” by the adoption of the 

basinwide provisions in the amendments would “continue to have force 

and effect until”:

1) A subbasin plan has been 

adopted by the Council for the 

subbasin in which the project 

[or measure] is located (or, 

for research and mainstem 

measures, a research or 

mainstem plan);

2) The measure has been 

specifically repealed in a 

subsequent rulemaking; or

3) Three years have elapsed 

following the final approval 

of this program, whichever 

occurs first.

The Council is both applying and 

revising these transition provisions at 

this time, in this way:

• Final adoption of the mainstem 

plan amendments to the fish and 

wildlife program will supersede 

all provisions, objectives, and 

measures in the Council’s 1994-

95 Columbia River Basin Fish 

and Wildlife Program that relate 

to systemwide hydrosystem 

operations, systemwide water 

management, mainstem flows, 

mainstem and storage reservoir 

operations, spill, bypass systems, 

smolt monitoring, mainstem 

operations research and evaluation, and other matters related 

to juvenile and adult salmon 

migration through the mainstem, 

including all of Sections 5 and 6 

of the 1994-95 program.

• All other specific measures in the 

1994-95 program that have not 

been directly superseded by the 

adoption of the 2000 Fish and 

Wildlife Program amendments 

or by the adoption of the mainRevised Transition Provisions

stem plan amendments remain in 

effect until 1) a subbasin plan has 

been adopted by the Council for 

the area in which the measures 

is located; or 2) the measure has 

been specifically repealed in a 

subsequent program amendment 

process. This includes any resident fish substitution or mitigation measures, such as the Lake 

Roosevelt monitoring or production programs, that occur in the 

mainstem but that are not directly 

related to systemwide operations 

or salmon migration.

• With adoption of the mainstem 

plan amendments, the Council 

deletes the three-year sunset 

clause from the Transition Provisions in the 2000 Fish and 

Wildlife Program amendments. 

No specific measure in the Fish 

and Wildlife Program prior to the 

adoption of the 2000 Program 

amendments will expire simply 

because three years have elapsed 

from the final approval of the 

amendments.