Introduction

The Columbia River Basin Fish and Wildlife Program 1

The 2000 Fish and Wildlife Program and the Mainstem Plan 1

Expectations for the elements of the Mainstem Plan 1

A different Mainstem Plan for a different context 2

Vision of the Mainstem Plan 5

Biological Objectives

Overarching objectives and priorities for the mainstem 7

Specifi c objectives and performance standards for habitat characteristics and for 7

 population performance

Mainstem habitat conditions 7

Migration/passage conditions for anadromous fi sh 9

Resident fi sh/wildlife 9

Strategies

Overarching strategies 11

Strategies in specifi c areas 13

Mainstem habitat 13

Juvenile and adult passage, in general 14

Juvenile fi sh transportation 14

Spill 15

Juvenile bypass systems 16

Adult passage 17

Water management 17

Monitoring and evaluation 23

Research 25

Annual and in-season decisionmaking 25

Mid-Columbia Hydroelectric Projects 26

Revised Transition Provisions

Appendix A: Analysis of the Adequacy, Efficiency, Economy and Reliability of the Power 

System 

Appendix B: Findings on the Recommendations for Mainstem Plan Amendments to the 

2000 Columbia River Basin Fish and Wildlife Program

Table of Contents

2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 1

The Columbia River Basin 

Fish and Wildlife Program

The states of the Columbia River 

Basin, Idaho, Montana, Oregon and 

Washington, formed the Northwest 

Power Planning Council, an interstate 

compact agency, under the authority 

of the Pacifi c Northwest Electric 

Power Planning and Conservation 

Act of 1980. The Power Act directs 

the Council to develop a program to 

protect, mitigate and enhance fi sh 

and wildlife of the Columbia River 

Basin affected by the development 

and operation of the basin’s 

hydroelectric facilities, while also 

assuring the Pacifi c Northwest an 

adequate, effi cient, economical and 

reliable power supply. The Act also 

directs the Council to inform the 

public about fi sh, wildlife and energy 

issues and to involve the public in its 

decisionmaking.

The Council’s Columbia River 

Basin Fish and Wildlife Program, 

fi rst adopted in 1982 and periodically 

revised, is the nation’s largest 

regional effort to recover, rebuild, and 

mitigate impacts on fi sh and wildlife. 

As a planning, policy-making and 

reviewing body, the Council develops 

and then monitors implementation 

of the fi sh 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 fi sh and 

wildlife program to begin a complete 

revision of the program. In the fi rst 

phase of the amendment process, 

the Council reorganized the program 

around a comprehensive framework 

of scientifi c 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 fi sh and 

wildlife and other desired benefi ts 

from the river; basinwide biological 

performance objectives, which 

describe in general the fi sh 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 

scientifi c 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 

fi sh 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 specifi c 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 scientifi c foundation. 

The Council intends to incorporate 

the specifi c 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 fi sh 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 with the 

recommendations, and comments 

received on the recommendations. 

The Council conducted an extensive 

public comment period on the draft 

mainstem plan before fi nalizing 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 specifi c 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 fi sh and 

wildlife affected by the development 

and operation of hydroelectric facilities 

Introduction
2 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

while assuring the region an adequate, 

effi cient, 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 fi sh;

• system water management;

• passage spill at mainstem dams;

• adult and juvenile passage 

modifi cations at mainstem dams;

• juvenile fi sh transportation;

• adult survival during upstream 

migration through the mainstem;

• reservoir elevations and operational 

requirements to protect resident 

fi sh and wildlife;

• water quality conditions; and

• research, monitoring and evaluation.

The Council evaluated the mainstem 

plan recommendations and these 

program amendments for consistency 

with the program framework elements 

adopted in 2000, including the vision, 

biological objectives, habitat and 

hydrosystem strategies, and underlying 

scientifi c principles.

A Different Mainstem Plan for 

a Different Context

In the past, the Council’s fi sh and 

wildlife program included detailed 

hydrosystem operations for fi sh 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 benefi t 

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 confi guration, 

river fl ows, 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 suffi cient fl ow, spill 

and passage operations to benefi t 

listed fi sh, and so the Council 

should adopt additional measures 

to that end;

• recommendations that concluded 

the biological opinions exceeded 

what was necessary to benefi t listed 

fi sh, 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 

fl ow and spill operations that are, 

in the view of those making the 

recommendations, more biologically 

and economically effi cient in how 

the limited resources of the region 

are applied; and

• recommendations that concluded 

the operations specifi ed in the 

biological opinions are not suffi cient 

to protect, enhance or mitigate 

for the adverse effects of the 

hydrosystem on fi sh and wildlife 

not listed for protection under the 

Endangered Species Act, and may 

be especially adverse to resident 

fi sh (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 confl ict 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 fi sh 

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 fl exibility or changes in the 

implementation of the biological 

opinions, as described below.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 3

• Scientifi c and policy uncertainty 

continues to plague a number 

of mainstem actions intended to 

benefi t anadromous fi sh, leading 

to an inability to measure the 

extent of the benefi ts 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 fi sh and high costs to the 

power system. The mainstem 

plan includes provisions for how 

to improve the way the region 

engages in fi sh 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 specifi c 

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 fi sh and wildlife agencies 

for more biologically effective 

spill, fl ow and other mainstem 

operations and actions at the 

minimum economic cost. The 

Council understands the biological 

opinions have suffi cient fl exibility 

in implementation to accommodate 

recommendations of this type; that 

is, the biological opinions were 

adopted with the recognition that 

as new scientifi c 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 fi sh 

and wildlife program that not only 

protects, mitigates and enhances fi sh 

and wildlife but also assures that 

the region will continue to enjoy an 

adequate, effi cient, 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 fi sh 

and wildlife requirements of the Power 

Act and are consistent with its power 

supply obligations. The Council 

also reviewed the latest scientifi c 

information and comments on the 

effectiveness of fi sh and wildlife 

strategies to increase survival of 

specifi c populations. 

Energy systems, markets and 

policy have changed radically since 

the last revision of the fi sh 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 half-decade 

— 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 defi cit 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 benefi t fi sh and wildlife in order to 

maintain the reliability of the region’s 

power system. Even with signifi cant 

changes to the hydropower operations 

specifi ed for fi sh, 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, effi ciency, 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 supplies, reductions 

in demand, and loss of loads that 

have occurred since early 2001. The 

objectives and measures to protect, 

mitigate and enhance fi sh 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 
4 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

certain fashion. The analysis suggests 

possible actions by the federal 

agencies and others in the region to 

ensure that the federal system provides 

the specifi ed operations for fi sh 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 5

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 

fi sh and wildlife, mitigating across the 

basin for the adverse effects to fi sh and 

wildlife caused by the development 

and operation of the hydrosystem 

and providing the benefi ts from fi sh 

and wildlife valued by the people of 

the region. This ecosystem provides 

abundant opportunities for tribal and 

treaty-right harvest and for non-tribal 

harvest of fi sh and wildlife, and for the 

recovery of fi sh 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 fi sh 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 cost-effective and 

not put at risk the region’s adequate, 

effi cient, economical and reliable 

power supply.

The vision for the mainstem plan 

is consistent with the broader program 

vision set out above. Hydrosystem 

operations, fi sh 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 fi sh populations. This will 

allow for abundant, productive and 

diverse fi sh and wildlife populations. 

The vision includes providing 

conditions within the hydrosystem 

for adult and juvenile fi sh 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 fi sh 

population recovery in the subbasins; 

and 4) ensure that water management 

operations are optimized to meet the 

needs of anadromous and resident fi sh 

species, including those in upstream 

storage reservoirs, with the least 

cost so that actions taken maximize 

benefi ts to all species while ensuring 

an adequate, effi cient, economical and 

reliable power supply. Any system 

changes needed to achieve these goals 

must be implemented in such a way 

and over a suffi cient time period to 

allow the region to make whatever 

power system adaptations are needed, 

if any, to maintain an adequate, 

effi cient, 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.
6 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 7

Overarching Objectives 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 fi sh, 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 fi sh and 

wildlife populations to assure that fi sh 

and wildlife benefi ts are achieved at 

the least cost to the region’s fi nancial 

and water resources.

One of the overarching biological 

objectives for the program is the 

recovery of ESA-listed anadromous 

and resident fi sh affected by 

development and operation of the 

hydrosystem. Federal hydrosystem 

operations to benefi t fi sh 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 obligation 

to protect, mitigate and enhance all the

fi sh 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 fi sh and wildlife populations 

that support the recovery of listed 

species and abundant opportunities for abundant opportunities for

tribal trust and treaty-right harvest and 

non-tribal harvest.

In addition, the science relating to 

the rebuilding of Pacifi c 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 fi sh 

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 

fl ows. 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 

Biological Objectives
8 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

populations, so as to restore more 

natural population structures.

• 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, fl oodplains and uplands in 

the mainstem.

− Enhance the connections 

between the mainstem sections 

of the Columbia and Snake 

rivers and their fl oodplains, side 

channels and riparian zones.

− Manage mainstem riparian areas 

to protect aquatic conditions 

and form a transition to 

fl oodplain 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 fi sh 

passage at mainstem dams, fi sh 

transportation and harvest, to 

minimize artifi cial 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 fl uvial spawning habitat for 

mid-Columbia fall chinook core 

populations, derived at least in part 

from the Independent Scientifi c 

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 

fi sh and wildlife agencies, tribes, 

federal operating agencies, the 

Independent Scientifi c Advisory 

Board and the Independent 

Economic Advisory Board to 

evaluate the scientifi c 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 

fl ow more closely approximate 

natural hydrographic patterns. 

Ensure that any changes in water 

management are premised upon, 

and proportionate to, scientifi cally 

demonstrated fi sh and wildlife 

benefi ts. Examples of management 

actions or limitations consistent 

with this objective include:

− Attempt to provide natural 

spring freshets below the 

storage projects, within fl ood 

control constraints.

− Minimize fl uctuations in fl ows 

out of the storage reservoirs 

over an extended period of 

the summer and fall. To the 

extent this confl icts with use 

of the hydrosystem for load 

following, system operators 

should balance equitably 

the biological requirements 

of fi sh 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 refi ll are based substantially 

on local infl ows, and so that 

the reservoirs, in concert, can 

shape water releases to benefi t 

fi sh in and immediately below 

reservoirs and then, as the water 

travels downstream, benefi t 

anadromous fi sh.

− Operations based solely on 

efforts to achieve biological 

opinion fl ow targets in the 

lower Columbia river will 

adversely affect resident 

fi sh and may fail to benefi t 

anadromous fi sh if they do not 

take into account reasonable 

storage project operations.

− Operations should attempt to 

meet the requirements of both 

resident and anadromous fi sh.

− The amount of fl ow 

augmentation and the release 

schedule from storage reservoirs 

should be based on the best 

available science for each target 

species (resident or anadromous) 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 9

and weighted for the greatest 

benefi t 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 Columbia River mainstem. 

Evaluate fl ow regulation and 

changes to estuary-area habitat 

and biological diversity to better 

understand the relationship 

between estuary ecology and nearshore plume characteristics and 

the productivity, abundance, and 

diversity of salmon and steelhead 

populations.

• Where feasible, pursue restoration 

of anadromous fi sh 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 decisionmaking 

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 

fulfi lling this legal obligation, 

FERC decides not to require 

reintroduction of anadromous fi sh 

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 anadromous fi sh

• 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 fi sh and 

wildlife agencies and tribes, the 

Independent Scientifi c Advisory 

Board, and federal operating 

agencies to determine the 

possibility of adopting hydrosystem 

survival performance standards 

for non-listed populations of 

anadromous fi sh.

• 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 effi ciency and the 

effi ciency and probabilities of 

other passage routes in order to 

determine the passage methods, 

including spill volumes, that 

maximize survival of fi sh passing 

the dam and minimize fall-back 

and other effects on adult salmon.

• Improve adult fi sh 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 

fi sh and wildlife agencies and 

tribes, the Independent Scientifi c 

Advisory Board, and federal 

operating agencies to evaluate 

the scientifi c soundness and 

achievability of, and impact of 

ocean conditions on, these smoltto-adult survival rate objectives. 

Then, in a public review process, 

the Council either will confi rm 

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 smoltto-adult survival rate objectives for 

other populations.

Resident fi sh/wildlife

• Provide conditions that support 

the needs of resident fi sh species 

in upstream reservoirs and river 

reaches, as well as the needs of 

anadromous and resident species in 

the lower parts of the mainstem.

3 Under current system operations for migrating anadromous fi sh, 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 specifi c 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.
10 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

• In accordance with Section 

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

Act, and the Council’s primary 

strategy for hydrosystem fi sh 

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 non-federal 

hydroelectric facility for purpose 

of fl ow 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 fi sh and wildlife agencies and 

appropriate Indian tribes, that fl ow 

and spill operations are optimized 

to produce the greatest biological 

benefi ts with the least adverse 

effects on resident fi sh.

• 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 specifi c objectives for 

that species, incorporated here. 

The water management strategies 

in this mainstem plan (below) 

include a sturgeon operation 

strategy that is a refi nement of 

the fl ow 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 fi sh 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 inchannel habitat structure, function 

and complexity; 3); restore riparian 

and wetland habitats and fl oodplain 

function; and 4) maintain water 

temperatures within the tolerance 

range of native fi sh species.

• Contribute to providing the 

conditions necessary to protect 

spawning and rearing habitat 

for fi sh in, and adjacent to, Lake 

Roosevelt to build fi sh 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 11

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 

benefi t, fi sh 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 

refl ect, 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 fi sh. Enhance and 

restore habitats and ecological 

functions that connect to the 

protected areas.

− Protect biological diversity by 

benefi ting the range of species, 

stocks, and life-history types in 

the river.

− Provide conditions that best 

fi t 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 signifi cant 

contribution to the rebuilding of 

naturally spawning populations 

in areas of program habitat 

investments, or that provide the 

most signifi cant contributions 

to harvest while ensuring the 

least detrimental impacts on the 

survival of native fi sh species.

− Optimize actions to produce 

the greatest biological 

benefi ts for targeted species 

with the least cost, and the 

least adverse effects on other 

species, while ensuring an 

adequate, effi cient, 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 benefi t 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 

fi sh and wildlife agencies with 

jurisdiction over the operational 

needs of these listed species. The 

Council accepts these measures 

as part of the fi sh and wildlife 

program for the near term. 

Strategies

However, many of the biological 

opinion measures must be subject 

to systematic and rigorous 

monitoring and evaluation, as 

described below and in the more 

specifi c strategies, to determine if 

the measures have the biological 

benefi ts expected and represent 

the most cost-effective actions 

to achieve these benefi ts. Based 

on these evaluations, the Council 

may recommend to the federal 

operating and fi sh and wildlife 

agencies operations that differ 

from those in the biological 

opinions if the Council concludes 

the different operations provide 

the same or greater benefi ts to 

listed fi sh and wildlife than current 

operations at a lower cost. The 

Council is confi dent that changes 

in operations of this nature can be 

made consistent with the fl exibility 

built into the biological opinions.

• The 2000 NMFS and USFWS 

biological opinion operations may 

not be optimal when the needs of 

fi sh 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 specifi c strategies 

to benefi t all fi sh and wildlife 

affected by the hydrosystem, not 

just listed species. Where the 

strategies intended to benefi t nonlisted species appear to confl ict 

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 
12 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

Council intends instead that the 

federal operating agencies make 

every effort practicable to use 

the operational fl exibility 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 scientifi c testing 

of a particular operation in the 

biological opinions. The Council 

is confi dent these changes also 

can be made consistent with the 

fl exibility 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 fi sh and wildlife in the 

Columbia Basin. The Council calls 

on the federal operating agencies 

and fi sh and wildlife agencies 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, fl ow 

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 benefi ts from 

biological opinion operations 

require additional understanding 

or verifi cation, or where benefi ts 

to non-listed species from varied 

operations may be signifi cant 

without adverse impacts on listed 

species, or both. This approach 

is consistent with the biological 

opinions, which allow considerable 

fl exibility to conduct necessary 

tests. In the strategies, the Council 

specifi es 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 fi sh 

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 fi sh survival through 

the turbines.

4) Evaluate the benefi ts of 

incremental fl ow augmentation 

and determine the mechanisms 

for fl ow/survival relationships 

on the Columbia and Snake 

rivers.

5) Measure the effects of steady 

June through September 

outfl ows from Libby and Hungry 

Horse dams in Montana.

6) Identify the effects of shifting 

summer fl ows later in the 

summer.

7) Evaluate and document the 

impact of predation in the 

mainstem in terms of numbers 

of listed fi sh taken, and 

estimated impact on smolt-toadult return ratios.

8) Evaluate and document the 

impact of harvest operations in 

terms of numbers of ESA-listed 

fi sh taken and estimated impact 

on smolt-to-adult return ratios.

9) Test other uncertainties 

proposed by independent 

science panels and fi sh 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 benefi ts for 

enhancing listed and non-listed fi sh 

populations over the long term. 

In many cases, if it were better 

understood why certain operations 

were benefi cial to fi sh it would be 

possible to adjust the operations 

to provide better survival. For 

example, the benefi ts of fl ow 

augmentation in the Snake River 

may be related to travel time, 

turbidity, temperature or reservoir 

fl uctuations. 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 benefi ts of 

the operations so that choices can 

be made to assure that the same 

survival benefi ts are achieved 

through the lowest-cost 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 benefi ts 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 benefi ts need to be 

more clearly demonstrated. Only 

through controlled experiments 

can we reach a conclusion as to 

the merits of continuing these 

operations. Recent scientifi c 

reports call into question several of 

these operations, especially active 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 13

management of the storage projects 

to provide fl ow augmentation.

It should be emphasized that this 

approach represents more than 

passive observation. It includes 

the option of implementing largescale fi eld 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 fi sh species. 

In implementing large-scale fi eld 

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 fi sh 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 and Wildlife Service to 

exercise the fl exibility within the 

biological opinions to implement 

these tests. We also encourage 

NOAA Fisheries and USFWS to 

make changes in the biological 

opinions when these scientifi c 

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 fl ows 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 fi sh 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 confl ict with operations 

intended to benefi t juvenile or 

adult salmon migration, the system 

operators and the fi sh and wildlife 

agencies and tribes should identify 

potential confl icts, priorities, tradeoffs, and opportunities and consult 

with the Council, affected entities, 

and the public on how best to 

resolve confl icting 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 fi sh 

into blocked areas, including 

above Chief Joseph and Grand 

Coulee dams.
14 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

• Identify the importance of 

protecting or improving mainstem 

habitat for recovering bull trout 

populations. The Council calls on 

the relevant state and federal fi sh 

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 

fi sh structures along the shores 

of Lake Roosevelt to diversify 

food available to fi sh 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 

fi sh passage through mainstem 

dams should emphasize adult 

survivals as a high priority. In 

addition, strategies should protect 

biological diversity by benefi ting 

the broad range of species, 

stocks, and life-history types in 

the river, not just listed species, 

and should favor solutions that 

best fi t 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 fi sh 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 

Scientifi c Review Panel will 

apply these strategies during the 

panel’s review of the reimbursable 

portion of the Bonneville fi sh and 

wildlife budget, which includes 

the Corps’ passage program; 2) 

will itself apply these standards 

in its review of any Independent 

Scientifi c 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 fi rms independent of the 

Corps of Engineers.

• For the purpose of planning for 

this fi sh 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 fi sh and wildlife 

program every fi ve years, at a 

minimum. If, within that fi ve-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 fi sh 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 

benefi ts from transportation 

of migrating juvenile salmon. 

Therefore, the Council 1) 

continues to accept juvenile fi sh 

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 

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 fi sheries stated in the relevant 

subbasin plans.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 15

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 benefi ts of maximizing 

or minimizing transportation, 

the federal operating agencies 

must recognize that signifi cant 

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 fi sh is 

either the only passage alternative 

available or the most signifi cant 

passage alternative.

• The three highest priorities for 

juvenile transportation studies 

should be to:

1) evaluate whether the survival 

benefi ts of transport from 

McNary Dam are suffi ciently 

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 Scientifi c 

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 

benefi ts for populations that 

are important to the biological 

objectives of this program, and 

that cannot be transported, or are 

ineffectively transported. 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 fl ow levels and 

for the range of fi sh populations 

that pass the project. The federal 

action agencies and NOAA 

Fisheries, in consultation with the 

other federal and state fi sh 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 fi sh 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 fi sh 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 fi sh and wildlife 

agencies, in consultation with the 

state fi sh and wildlife agencies 

and tribes and the Independent 

Scientifi c 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, 
16 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

levels of survival and biological 

benefi t to migrating fi sh 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-specifi c estimates of 

smolt passage survival by 

species through spillways. 

Spill effi ciency information 

should be updated and applied 

in future spill decisions and 

passage modeling analyses. 

The Council recognizes the 

diffi culty in obtaining reliable 

empirical survival estimates 

linked specifi cally 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 

benefi ts of the current summer spill 

program for outmigrating juvenile 

fall chinook, and to determine 

whether the biological benefi ts 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 fi sh during the 

months of July and August averages 

one-third of the total cost impact of 

all mainstem operations designed 

for fi sh and wildlife protection. 

While the summer spill program 

provides survival advantages to 

in-river outmigrants, the Council 

recommends an evaluation of the 

effi cacy 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 benefi ts 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 

benefi t to fi sh 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 effi cient 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 

fi nancial resources that result to 

implement additional prioritized 

measures in the Council’s fi sh and 

wildlife program.

• The Council intends to recommend 

specifi c spill strategies at specifi c 

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 longterm impact to the benefi cial use for 

which the deviation was authorized.

Juvenile bypass systems

• To provide passage for juvenile 

fi sh that most closely approximates 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 17

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 fi sh 

injury and mortality;

3) modify turbines to improve 

juvenile survival; and

4) conduct research on fi sh diseases 

at fi sh passage facilities.

Adult passage

• The U.S. Army Corps of Engineers 

should improve the overall 

effectiveness of the adult fi sh 

passage program. This includes 

expediting schedules to design 

and install improvements to fi sh 

passage facilities. The ultimate 

survival and successful spawning 

of adult fi sh are a high Council 

priority because returning adults 

determine the size and health of 

future fi sh populations. Where it 

is benefi cial, 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 fi sh counts; expansion of fi sh 

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 

fi sh passage; and the connection 

between fi sh passage design and 

fi sh behavior. In particular:

1) as a priority for the Corps of 

Engineers’ capital construction 

program, correct adult fi sh 

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 fi sh counting 

accuracy; and 

4) conduct research on fi sh diseases 

at fi sh passage facilities.

Water management

• Manage water through the 

hydrosystem so that patterns of 

fl ow 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 fi sh 

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, fi sh and wildlife benefi ts, 

while assuring the region an 

adequate, effi cient, 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 fl uctuations 

in fl ow, including fl oods. 

Reduce large and rapid shortterm fl uctuations. Reduce or 

eliminate stranding and other 

problems associated with 

fl uctuation 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 benefi ts 

from releases can be shown to 

provide improved fi sh 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 fl ow 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 nearshore plume characteristics and 

the productivity, abundance, 

and diversity of salmon and 

steelhead populations.

• Systemwide water management, 

including fl ow augmentation 

from storage reservoirs, should 

attempt to meet the needs of 

anadromous and resident fi sh 

species in the river and upstream 

storage reservoirs, so that actions 

taken to benefi t one species do 

not unnecessarily come at the 

expense of other species. Flow 

augmentation is defi ned as the 

intentional release or drafting 

of water from storage reservoirs 

for the purpose of increasing 

fl ows to enhance migratory 
18 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

conditions for juvenile and 

adult life-stages 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 confl icts and 

seek recommendations from 

the Council, fi sh and wildlife 

agencies, tribes, and other affected 

entities on how best to balance 

the different needs prior to the 

implementation of fl ow actions.

• The Council recognizes the 

continuing controversies over 

a) the nature, extent of, and 

reasons for the fl ow-survival 

relationship for migrating salmon 

and steelhead; b) the consistency 

between the fl ow targets and 

the fl ow measures; and c) fl ow 

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 scientifi c research for review 

by the Independent Scientifi c 

Advisory Board that documents 

the fl ow augmentation actions 

taken, the benefi ts of fl ow 

augmentation for fi sh survival 

and the precise attributes of fl ow 

that may make it benefi cial.

2) The Council will consult with 

these and other entities to 

determine whether and how 

to conduct a comprehensive 

evaluation of survival, fl ow 

targets, and fl ow augmentation 

to determine the relationship 

between specifi c management 

actions and changes in lifecycle and lifetime survival. 

This evaluation will, among 

other things:

– evaluate the scientifi c 

validity of the fl ow targets 

and fl ow augmentation 

actions in the 2000 

Biological Opinion;

– evaluate how often, and for 

what duration, river fl ows, 

whether augmented or not 

from storage releases, meet 

the spring and summer fl ow 

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;

– quantify the volume and 

shape of water that has been, 

and is being, provided as 

fl ow augmentation;

– translate to the extent 

possible the incremental 

increase in fl ows from fl ow 

augmentation to changes 

in water velocity and 

temperature;

– evaluate and predict to the 

extent possible how changes 

in adult survival relate to 

changes in fl ow; and

– evaluate hydrosystem 

operations and establish 

the relative benefi ts and 

costs of those operations to 

native fi sh 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 

fl ow 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 

fi sh throughout the mainstem 

Columbia and Snake rivers.. 

The Council understands 

these objectives to be fl exible 

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 benefi t 

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 benefi t 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 fi sh listed 

under the Endangered Species 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 19

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 fi sh 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 confl ict 

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 fl exibility 

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 

scientifi c testing of a particular 

operation in the biological opinion. 

The Council calls on the federal 

operating agencies and fi sh 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 fl ows, while maintaining 

consistency with this mainstem 

plan’s fl ow 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 fl ows 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 fl ows required by 

the Vernita Bar agreement and 

by subsequent agreements to 

extend stable fl ows 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 operators of the 

mid-Columbia projects to take the 

steps necessary, separately and 

together, to further reduce fl ow 

fl uctuations through the Reach that 

affect spawning and rearing.

Spring reservoir/fl ow operations 

in general

• Refi ll 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 refi ll should be late 

July for Libby and the end of June 

for the other projects, the system 

operators should work to adjust the 

actual refi ll date based on reservoir 

conditions and infl ow 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 fl ood control rule curve 

by April 10 and to refi ll by June 

30 (late July for Libby), otherwise 

passing the spring runoff through 

the storage reservoirs. The NOAA 

Fisheries biological opinion retains 

the fl exibility to allow active fl ow 

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 fl exibility to allow for fl ow 

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 fl ood control operations 

and Integrated Rule Curve 

operations. At Hungry Horse and 

Libby dams, continue to implement 

the VARQ fl ood 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 

benefi t of native resident fi sh in 

those reservoirs. Operations should 

reduce the frequency of refi ll 

failure (to within fi ve feet of full 

pool) at Hungry Horse and Libby 

reservoirs as compared to historic 

operation. Implement seasonal 

fl ow windows and fl ow ramping 

rates in the Flathead and Kootenai 

rivers downstream of the storage 

reservoirs, and maintain minimum 

fl ows in the Flathead and Kootenai 
20 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

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 slidingscale fl ow strategy for bull trout 

specifi ed 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 fl ood 

control operations called for in

the NOAA Fisheries 2000 

Biological Opinion.

• Operations at Libby Dam to 

benefi t 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 

specifi es a “tiered” strategy for fl ow 

augmentation from Libby Dam to 

simulate a natural spring freshet, 

controlled within fl ood constraints. 

Volumes are determined by 

forecasted water availability so 

that higher fl ows are released 

when ample water is available 

and minimal fl ow augmentation 

occurs during drought. The 

Council recommends that the 

average fl ow augmentation volumes 

outlined in Figure 1 be used as a 

guide for sturgeon operations at 

Libby Dam. These augmentation 

volumes are not specifi ed volumes 

and should represent targets 

for planning purposes. Actual 

augmentation volumes in any given 

year will depend on fl ood control 

constraints, reservoir refi ll targets, 

water availability, and benefi ts 

to the Kootenai white sturgeon 

population. This strategy represents 

a refi nement to volumes specifi ed 

in the 2000 Biological Opinion.7 

7 The sturgeon tiered fl ow strategy is a fi sh recovery action that is separate and distinct but compatible with the VARQ fl ood control operation. 

The tiered fl ow 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 fl ows. Release volumes are still based on water 

availability, but the volumes to be released are calculated over the entire range of possible infl ows (dashed line) rather than grouped into the 

original six tiers.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 21

The Council also recognizes that 

additional work is required to 

further refi ne appropriate sturgeon 

operations at Libby Dam, and 

recommends that regional entities 

continue to work to increase the 

biological benefi ts provided by the 

fl ow augmentation volumes.

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 fi sheries 

evaluation information indicates 

a change in Figure 2.

2) March-to-May elevations are 

recommended minimums, with 

the understanding that fl ood 

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 refi ll by the end 

of June.

4) As much as possible, manage 

the reservoir and dam 

discharges to produce steady 

fl ows across each season and 

each day to minimize reservoir 

fl uctuations 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:

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 

fl ow 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 fl ows 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 fl ow targets 

do not account for differences 

in characteristics between 

fl ow augmentation sources, 

or the biologically signifi cant 

components of those sources. 

Given that existing fl ow 

targets are often unattainable, 

simply striving to meet fl ow 

targets regardless of the 

degree of biological benefi t 

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 fl ow 

objectives at Lower Granite 

Figure 2: Grand Coulee

Period Minimum Elevation Minimum Mean 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 fi ll to 1290 40-60 days or maximum 

historically achievalbe for 

the month

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 confl ict 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 Power Act, §10(i), 94 Stat. 2735.
22 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

Dam. Given the competing 

issues of fl ow augmentation 

and available water resources, 

the Council requests 

Bonneville, in coordination 

with NOAA Fisheries, U.S. 

Fish and Wildlife Service, state 

fi sh and wildlife managers and 

tribes to: a) defi ne Endangered 

Species Act harvest and 

recovery objectives for 

anadromous fi sh in specifi c 

mainstem sections and in 

tributaries of the mainstem; 

and b) develop alternative 

strategies to fl ow 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 refi ll 

failure (to within fi ve feet 

of full pool) as compared to 

historic operations; implement 

seasonal fl ow windows and fl ow 

ramping rates in the Flathead 

and Kootenai rivers downstream 

of the storage reservoirs and 

maintain minimum fl ows 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 

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 fi sheries 

resources in the reservoirs 

and rivers downstream, 

while providing additional 

fl ow augmentation for fi sh 

immediately below the 

project(s) and in the lower 

Columbia River.

− Draft each storage reservoir 

according to elevation 

limitations that, when 

combined with projected 

infl ows, result in stable and 

“fl at” or very gradually 

declining weekly average 

outfl ows 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 

signifi cant fl exibility within 

the biological opinions to 

implement this operation 

as an experiment. If there 

is disagreement on this, 

the Council calls on the 

federal operating agencies 

and federal fi sh 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 fl ows, 

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 fl ow, 

fl ow 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 fl ow-survival 

relationship through the 

lower Columbia system, if 

any exists; b) determining 

whether fl ow augmentation 

from the upper Columbia 

storage projects has any 

effect on levels of survival; 

and c) determining the 

benefi ts to resident fi sh from 

this operation. The Corps of 

Engineers and the Bureau of 

Reclamation should consult 

with a team formed from the 

Council, the Independent 

Scientifi c Advisory Board, 

the Montana Department 

of Fish, Wildlife and Parks, 

the Confederated SalishKootenai Tribes, NOAA 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 23

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 

signifi cantly benefi t listed 

and non-listed resident 

fi sh in the reservoirs and 

in the portions of the 

rivers below the reservoirs 

without discernible effects 

on the survival of juvenile 

and adult anadromous fi sh 

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 fi sheries 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 fi sheries 

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 fl uctuations and 

ramping rates and produce 

steady fl ows across each season 

and each day to minimize 

reservoir fl uctuations 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, fi sh and wildlife 

managers, and others should 

consult with the Council to 

determine how to provide 

the biological benefi ts of a 

1283 operation while meeting 

biological opinion requirements, 

including chum fl ows and 

operating to protect fl ows 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 refi ll 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 fi sh 

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 fi sh and 

wildlife and the adverse impacts 

on the Clearwater County 

regional economy because of 

impacts to resident fi sh and 

wildlife. The Council will 

review the ISAB and IEAB 

reports, consult with the relevant 

fi sh and wildlife managers, 

and make recommendations to 

Bonneville on any additional 

fi sh 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 
24 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

management activities that are 

aimed at improving habitat 

conditions for fi sh 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 confi rm 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. The primary 

purpose of the Center is to 

provide technical assistance and 

information to fi sh 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 fi sh and wildlife program. 

In performing this function, the Fish 

Passage 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 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 fl ow 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 satisfi ed; 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 

confl icts between anadromous 

and resident fi sh.

The Council has established 

an oversight board for the 

Fish Passage Center, with 

representation from NOAA 

Fisheries, state fi sh and wildlife 

agencies, tribes, the Council, and 

others to provide policy guidance 

for the Fish Passage 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 Fish Passage Center and 

developing a goal-oriented 

plan for next year’s operation. 

The Fish Passage 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 Fish Passage 

Center shall include funds for a 

manager and for technical and 

clerical support in order to perform 

its stated functions. The fi sh 

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 fi sh and 

wildlife, as well as the ability 

to communicate and work with 

fi sh and wildlife agencies, tribes, 

the Council, project operators, 

regulators, and other interested 

parties, including members of 

the public. The fi sh passage 

manager will be selected by, and 

be subordinate to, the Executive 

Director of the Columbia Basin 

Fish and Wildlife Authority, in 

consultation with the oversight 

board. The Executive Director 

of the Columbia Basin Fish 

and Wildlife 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 fi sh passage information for 

use by the region, not just by 

fi sh and wildlife managers. No 

information collected by the Fish 

Passage Center, and no analyses 

by the Fish Passage Center, shall 

be considered proprietary. The 

oversight board and the fi sh and 

wildlife managers will ensure 

that the database conforms to 
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 25

appropriate standards for data 

management, including review 

of the database by an appropriate 

scientifi c or data review group. 

The fi sh and wildlife managers 

will provide a liaison position 

at the Columbia Basin Fish and 

Wildlife Authority between the 

public and the Fish Passage 

Center to ensure that all parties 

have timely and thorough access 

to the database. The Council 

may revise the functions of the 

Fish Passage 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 fi sh and wildlife mangers, will 

propose to the oversight board 

candidates for a technical advisory 

committee, whose purpose will 

be to establish technical protocols 

and scientifi c requirements for the 

Fish Passage Center and to review 

the scientifi c and technical aspects 

of the performance of the Fish 

Passage 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 

identifi es 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.

• Research aimed at optimizing 

fi sh and wildlife benefi ts and 

energy production. Actions 

taken to benefi t fi sh 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 fi sh and 

wildlife and energy benefi ts, or at 

least to increase one set of benefi ts 

without degrading the other. As 

an example, spill is an operation 

for fi sh 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 fi sh 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 benefi ts to 

fi sh and wildlife

2) widespread scientifi c 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 

fi sh 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 scientifi c panels. 

People at the policymaking level 

should be more involved in the 

fi nal 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 
26 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program

operation plans for fi sh and 

wildlife, in-season management 

of hydrosystem operations for fi sh 

and wildlife and recommendations 

to Congress for funding for 

passage improvements. At 

present, this decision structure 

is insuffi cient to integrate fi sh 

and power considerations in a 

timely, objective and effective 

way, and it focuses on listed 

fi sh with little consideration for 

unlisted anadromous and resident 

fi sh 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 

signifi cant role in this.

3) Have the technical capability to 

analyze differing hydrosystem 

operation proposals relative to 

impacts on salmon, steelhead, 

sturgeon and resident fi sh 

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 defi ned set of 

decisionmaking criteria and hold 

participants accountable for the 

decisions they make, according 

to the established criteria.

Mid-Columbia Hydroelectric 

Projects

• The Council will review and, as 

appropriate, include in the program 

settlement agreements for the midColumbia hydroelectric projects.
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 27

In 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 specifi cally 

repealed in a subsequent 

rulemaking; or

3) Three years have elapsed following 

the fi nal approval of this program, 

whichever occurs fi rst.

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 fi sh 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 fl ows, 

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 specifi c measures in the 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 mainstem 

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 specifi cally repealed in a 

subsequent program amendment 

process. This includes any 

resident fi sh 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 specifi c 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 fi nal approval of 

the amendments.

Revised Transition Provisions
28 2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program
2003 Mainstem Amendments to the Columbia River Basin Fish and Wildlife Program 29

Analysis of the Adequacy, Efficiency, Economy 

and Reliability of the Power System

[fi nal paper to be approved and attached at the time the Council also approves fi ndings on recommendations]

Appendix A
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

Findings on the Recommendations for Mainstem Plan Amendments to the 2000 Columbia 

River Basin Fish and Wildlife Program

[fi ndings to be approved by the Council in the month following April 2003]

Appendix B