Columbia River Basin Research Plan 

By the 

Northwest Power and Conservation Council 

February 2006 

Council document 2006-3

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TABLE OF CONTENTS

I. Introduction ................................................................................................................................. 3 

Vision Statement ......................................................................................................................... 3 

Scope and Audience of the Columbia River Basin Research Plan ............................................. 3 

II. Objectives................................................................................................................................... 5 

Scientific Principles..................................................................................................................... 5 

III. Implementing the Research Plan .............................................................................................. 7 

Fish and Wildlife Program Project Selection Process................................................................. 7 

Interaction with Other Research Plans in the Pacific Northwest................................................. 8 

Regional Research Partnership: A Forum for Collaboration....................................................... 8 

Monitoring and Data Management in Support of Research........................................................ 9 

Relationship to Subbasin Plans ................................................................................................. 10 

IV. Focal Research Themes and Critical Uncertainties................................................................ 11 

(1) Hatcheries/Artificial Production .......................................................................................... 11 

(2) Hydrosystem ........................................................................................................................ 13 

(3) Tributary and Mainstem Habitat.......................................................................................... 14 

(4) The Estuary .......................................................................................................................... 15 

(5) The Ocean ............................................................................................................................ 16 

(6) Harvest................................................................................................................................. 17 

(7) Population Structure and Diversity...................................................................................... 18 

(8) Effects of Climate Change on Fish and Wildlife ................................................................. 19 

(9) Toxics................................................................................................................................... 19 

(10) Invasive Species................................................................................................................. 20 

(11) Human Development ......................................................................................................... 21 

(12) Monitoring and Evaluation ................................................................................................ 22 

V. Appendixes............................................................................................................................... 24 

Appendix A. Context for the Research Plan.............................................................................. 24 

Appendix B. Implementing the Research Plan in Fiscal Years 2007-2009 .............................. 26 

Appendix C. Developing New Institutional Arrangements ...................................................... 41 

Appendix D. Monitoring and Evaluation .................................................................................. 46 

Appendix E. Data Management ................................................................................................ 52 

Appendix F. Integrating Research Results into Council Policy and Decision-making............. 54 

Appendix G. Critical Uncertainties........................................................................................... 56

VI. References............................................................................................................................... 60 

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I. INTRODUCTION

For 25 years, the Northwest Power and Conservation Council (Council) has supported a 

diverse range of research to pursue the biological objectives of the Columbia River Basin Fish 

and Wildlife Program (program). Research is necessary to provide scientifically credible answers 

to questions addressing uncertainties pertinent to management. The term “research” is defined 

broadly to include parameter estimation, pattern recognition, observation, categorization, data 

collection to quantify important relationships and processes, tests of hypotheses, and 

improvements in statistical methods. 

Research projects implemented under the program and others in the Columbia River 

Basin have advanced scientific understanding of fish and wildlife and their restoration. Despite 

this concerted effort, critical uncertainties remain and research lacks focus. Consequently, the 

Council requested development of a Columbia River Basin Research Plan (research plan) in the 

2000 Program to guide the development of its research program and to foster collaboration with 

the research programs of the other resource management entities within the region. (For 

additional explanation of the context for the research plan, see Appendix A.). 

Vision Statement 

The research plan will inform decision-making and management actions to conserve and 

recover fish and wildlife addressed in the Council’s Fish and Wildlife Program by 

identifying and helping to resolve critical uncertainties. 

The research plan identifies major research themes and critical uncertainties for research 

funding. In so doing, the research plan provides guidance for addressing key uncertainties that 

affect anadromous fish, resident fish, wildlife, and the ecosystems that support them. The 

research plan will help the Council manage the program by informing decision-making, 

facilitating scientific review, focusing project selection, providing a basis for redirecting future 

research, and making the program more effective. 

Scope and Audience of the Columbia River Basin Research Plan 

The geographic scope of the research plan is limited to the Columbia River Basin. The

primary audience for the research plan is policy- and decision-makers responsible for natural 

resource management within the Columbia River Basin, such as the Council members and 

regional executives. The research plan also will provide guidance useful to researchers, project 

sponsors, and planners. The research plan provides a programmatic framework for research 

under the program and associates the research needed for recovery planning under the 

Endangered Species Act (ESA) with the broader responsibilities of the program.

In addition to improving implementation of the program, the research plan forges links to 

the research activity of the many parties that share responsibility for fish and wildlife 

management in the Columbia River Basin. For example, Bonneville Power Administration 

(Bonneville) and its funding of the Council program supports the work of the U.S. Army Corps 

of Engineers, Bureau of Reclamation, NOAA Fisheries, Environmental Protection Agency, and 

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land management agencies such as the U.S. Forest Service, and the U.S. Bureau of Land 

Management. The Columbia Basin tribes, in their role as co-managers, make significant 

contributions in the areas of harvest management, hatchery production, monitoring, and habitat 

restoration. The state fish and wildlife agencies also play key roles in implementation of the 

program. The Columbia Basin Fish and Wildlife Authority (CBFWA) represents state and 

federal fish and wildlife managers and tribes in the Council’s program. 

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II. OBJECTIVES

The objectives of the research plan are to: 

• Improve monitoring, evaluation, and the application of results 

• Address critical uncertainties identified in subbasin plans 

• Increase accountability for the annual expenditures of research funds 

• Improve input from independent scientists, fish and wildlife agencies and tribes, and 

other interested parties in the region

• Improve coordination among mainstem research programs 

• Improve access to the information generated by the research and restoration projects of 

the program 

The research plan is intended to improve communication among scientists, cooperation 

among institutions, and better coordination of long-term biological monitoring. A key dialogue 

that the research plan can facilitate regards the role and use of biological and ecological research 

to inform decision-making on major conflicts in the basin that have profound socio-political 

implications, such as the persistent disagreements about the relationship of flow and survival of 

fish or the influence of hatchery fish on wild stocks. For example, fundamental issues of fish 

migration and of the interaction of hatchery and wild fish remain poorly understood, yet the 

consequences are substantial both for listed species and for the economy of the region. In fact, 

the President’s Committee on the Environment and Natural Resources stated: “Basic scientific 

information is lacking for many of the remedial actions that must be taken over a longer term.” 

(CENR 2000). 

Despite a large body of knowledge about the needs of fish and wildlife, instances remain 

in which the region lacks information to understand fully which mitigation or restoration actions

will be most effective. The intent of the research plan is to facilitate prioritization and

implementation of research that addresses those uncertainties as they affect anadromous fish, 

resident fish, and wildlife and the ecosystems that support them. Over time, research completed 

under the research plan will reduce critical uncertainties by increasing scientifically based 

knowledge. In sum, the research plan will help the Council manage the program by informing 

decision-making, facilitating scientific review, focusing project selection, providing a basis for 

redirecting future research, and most importantly, making restoration projects more effective. 

Scientific Principles

In 1998 the Council introduced a set of broad scientific principles and applied these 

principles to a description of the Columbia River as an ecosystem in the publication 

Development of a Regional Framework (NPCC 1998, Document 98-16). Subsequently, the 

Council continued to develop an explicit scientific foundation by articulating a set of eight 

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scientific principles and discussing their implications for salmon restoration (see, 2000 

Columbia River Basin Fish and Wildlife Program, NPCC Document 2000-19, page 15). These 

principles were derived from a number of reviews and recovery strategies for Columbia River 

salmon including Return to the River (Williams 2005) that developed a conceptual foundation 

for restoration of salmonid fish in the Columbia River Basin. The scientific principles are 

grounded in established scientific literature to provide a stable foundation for the Council’s 

program (see Columbia River Basin Fish and Wildlife Program, 2000, Section B2 (Basinwide 

Provisions). The Council intends that all actions taken to implement this program be consistent 

with these principles: 

Principle 1. The abundance, productivity and diversity of organisms are integrally linked 

to the characteristics of their ecosystems. 

Principle 2. Ecosystems are dynamic, resilient and develop over time 

Principle 3. Biological systems operate on various spatial and time scales that can be 

organized hierarchically

Principle 4. Habitats develop, and are maintained, by physical and biological processes 

Principle 5. Species play key roles in developing and maintaining ecological conditions 

Principle 6. Biological diversity allows ecosystems to persist in the face of environmental 

variation 

Principle 7. Ecological management is adaptive and experimental 

Principle 8. Ecosystem function, habitat structure and biological performance are affected 

by human actions

Other science review groups (National Research Council 1996; CENR 2000) also have 

emphasized the need for an ecosystem perspective as a basis for designing a recovery program

for salmon in the Pacific Northwest. Consequently, the scientific foundation developed by the 

Council represents an important step in the development of restoration and recovery programs 

grounded on ecological principles. 

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III. IMPLEMENTING THE RESEARCH PLAN

Research will be implemented by two different but complementary approaches, the 

Project Selection Process for fiscal years 2007-2009 and a Regional Research Partnership 

(research partnership). While the research plan is intended to guide funding of research under the 

Council’s fish and wildlife program, it also can help initiate a regional dialogue and guide 

research policy through the research partnership. The research plan could help launch the 

research partnership by bringing focus to initial discussions of how best to address research 

topics that are shared by the Council and other entities. The advantage of this dual approach is 

that it encompasses the range of research relevant to the Council’s program, specifically: 

• Research appropriate for the Council to fund 

• Research that is funded in part by the Council, is broader in scope than the fish and 

wildlife program, but ultimately is necessary to reduce the scientific uncertainties 

affecting the program

• Research that is inappropriate for the Council to fund but needs to be synthesized to 

update and inform the conceptual foundation and strategies used in the Council’s 

program 

Fish and Wildlife Program Project Selection Process 

The research plan identifies general research themes rather than specific issues in order to 

provide guidance that will be durable. These themes will be revisited during the next three 

funding cycles of the program. Thus, the life of the research plan will be nine years, with 

sequential three-year research, monitoring, and evaluation implementation plans to be developed 

by a work group comprising staff from the Council, Bonneville, and CBFWA. The work group 

would develop a draft implementation plan by following the guidance of the research plan and 

by drawing from the pool of project proposals approved for funding by the Independent 

Scientific Review Panel (ISRP). Consequently, peer review of a draft implementation plan would 

not be a prerequisite for Council approval but could be sought if the plan identified gaps that 

required request for proposals. The work group will meet initially to draft an implementation 

plan in support of the program for fiscal years 2007-2009. The implementation plan will 

facilitate implementation of the research plan by: 

 

• Identifying priority uncertainties within the research plan for implementation in the 

pending funding cycle 

• Identifying projects that address these uncertainties 

• Being responsive to advancements in science and technology 

• Ensuring continuity in data collection 

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Thus, the critical uncertainties identified in the research plan can serve to inform and 

shape the research agenda for the region with details to be developed as the research plan is 

implemented. For these reasons the research plan is structured as a framework guidance 

document for decision-makers and executives. The 2007-2009 project selection process will be 

used to address priority uncertainties set forth in the research plan, restoration priorities set forth 

in subbasin plans, and some of the monitoring priorities identified by the Pacific Northwest 

Aquatic Monitoring Partnership, or PNAMP (PNAMP, 2002). (For additional explanation of 

implementation in the project selection process see Appendix B.) 

Interaction with Other Research Plans in the Pacific Northwest 

The Council recognizes that the status quo for research within the region consists of 

multiple, separate research plans. These plans refer to the “need to coordinate” with other similar 

efforts, but rarely set forth explicit steps to implement such coordination. Consequently, the 

Council developed the research plan, in part, to enhance current coordination and facilitate future 

collaboration. This research plan recognizes other research plans as important components of a 

potentially integrated regional research program and provides a framework for establishing 

linkages between existing research programs and initiatives. Many of the critical uncertainties 

identified in other research plans in the region have been incorporated into this research plan. 

Thus, this research plan identifies research that can be funded directly through the program as 

well as recommendations for research that will require collaborative, multi-party funding 

commitments by the Council and other entities with similar research mandates. 

The Council does not intend to subsume other research programs into the fish and 

wildlife program and then direct their funding. To the contrary, the Council intends to use 

program resources to catalyze research requiring long-term commitments such as research 

supporting the development of a regional approach to monitoring. To the extent possible, the 

research plan will facilitate the coordination of processes already in place. For example, other 

plans include the Federal Research, Monitoring, and Evaluation Plan, Anadromous Fish 

Evaluation Program, Washington State Salmon Recovery Plan, and the PNAMP Aquatic 

Monitoring Strategy. These plans are not detailed in this research plan. Facilitation will include 

the convocation of a Regional Research Partnership. 

Regional Research Partnership: A Forum for Collaboration 

Many other resource management entities share responsibility for research in support of 

fish and wildlife stewardship within the Columbia River Basin. Challenges to addressing critical 

uncertainties include how to manage shared responsibility for funding under overlapping 

mandates and how to sustain long-term funding commitments to support research. Operating 

individually, resource management agencies have been unable to secure funding commitments 

necessary to mount and sustain long-term or large-scale field experiments — at the scale of river 

subbasins or basins. These challenges could be met, however, through a research partnership. 

The partnership would facilitate coordination of research within the Columbia River 

Basin and also research outside the basin that is highly relevant to program management. The 

research partnership would provide a forum for Council involvement in discussion of how best to 

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coordinate research conducted by others, such as federal programs that are implemented in states 

represented on the Council. To ensure the research partnership is a manageable size, membership 

would comprise entities that conduct a research program or fund research within the region and 

would exclude the multiple parties that receive research funds from those same entities. The 

research partnership would facilitate coordination of research within the Columbia River Basin 

by: 

• Eliminating redundancies 

• Facilitating collaborative projects 

• Redirecting savings to new research priorities 

• Improving communication among scientists, cooperation among institutions, and 

coordination of long-term biological monitoring 

The Council is well positioned to co-sponsor a collaborative regional research program 

that encompasses the entities involved in fish, wildlife, and hydrosystem mitigation in the 

Columbia Basin. In particular, the Council’s membership, structure, and open public meetings 

and hearings provide opportunities to facilitate coordination among the parties funding research 

programs. The effort to inaugurate the research partnership could be staffed by the Council until 

such time that the partnership becomes sufficiently organized for its members to provide support 

on a rotating basis. CBFWA, Bonneville, NOAA, and the U.S. Geologic Survey all have offered 

to work with Council staff to help sponsor the research partnership. Initial expectations for the 

research partnership should be modest, but as its members develop mutual trust over time the 

partnership could become a useful vehicle for negotiating and advancing on a regional research 

agenda. (Further explanation of the research partnership is provided in Appendix C.) 

Monitoring and Data Management in Support of Research 

Implementation of the research plan will require administrative support in two key areas: 

monitoring and evaluation, and data management. Support for monitoring will come from

PNAMP, a partnership that coordinates existing monitoring programs into a regional approach 

that can provide a basis for evaluation at the programmatic scale (see Appendix D). Support for 

data management will come from the Northwest Environmental Data Network (NED) and 

StreamNet, which are working with others to develop a regional data-standards program to 

support regional data-networking — a concept the Council supports (see Appendix E). 

The efforts of PNAMP, NED, StreamNet and others already benefit the region 

significantly. The Regional Research Partnership offers the opportunity to increase the regional 

benefit by improving the coordination of research, monitoring, evaluation, and data management

and, as a result, potentially redirecting the Council’s program based on project results. 

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Specifically: 

• The research partnership would improve the ability of the region to reduce scientific 

uncertainty 

• The monitoring partnership would support the programmatic evaluation of the program

• The data partnership could develop a data repository for analytical manipulation of data 

at the programmatic scale 

To succeed, the research program must institutionalize accountability at the 

programmatic scale and therefore must be closely coordinated with PNAMP and NED. It will be

essential to make the results of these initiatives available to the region. This could be 

accomplished by the publication of a “Columbia River Basin Journal,” which could provide a 

vehicle for disseminating results of program actions and a forum for advancing regional 

knowledge (see Appendix F). 

Relationship to Subbasin Plans 

In 2000 the Council initiated subbasin planning to help local entities develop fish and 

wildlife restoration plans. In 2004 and 2005, 57 subbasin plans that identified needs and 

opportunities for restoration became part of the fish and wildlife program. The cooperative and 

inclusive participation of federal, state, tribal, and local stakeholders in subbasin planning 

created the opportunity for stakeholders to address collectively the critical uncertainties within a 

subbasin. A staff review found that a minority of the subbasin plans explicitly identified critical 

uncertainties. Those uncertainties will support the implementation plan for Fiscal Years 2007-

2009. 

Yet many subbasin plans did not include research or monitoring strategies, and few 

addressed larger-scale conservation and restoration efforts at the provincial or basin scale, 

indicating the need for coordinated planning to ensure that research addresses uncertainties 

relevant to a majority of subbasins. The results of proposed research projects should have broad 

application to other provinces or to the basin as a whole, irrespective of where they are located. 

Consequently, research projects that address the critical uncertainties identified in the research 

plan and that potentially will help multiple subbasins will be given preference in the projectselection process. 

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IV. FOCAL RESEARCH THEMES AND CRITICAL UNCERTAINTIES

The research plan divides important scientific critical uncertainties into 12 focal research 

themes. The list of critical uncertainties is accepted in the region; the research plan does not 

include extensive background beyond that necessary to establish the significance of each topic of 

uncertainty. The critical uncertainties are described at a high level so that the research plan can 

provide long-range guidance while preserving flexibility of implementation in the near-term. As 

well, the critical uncertainties are presented this way in order to elicit the development of specific 

research hypotheses and project proposals without constraining innovative approaches. The 

critical uncertainties were synthesized from the fish and wildlife program, reports of the 

Independent Scientific Advisory Board (ISAB) and the ISRP, regional fish and wildlife 

managers, subbasin plans, national science groups, biological opinions, and other research plans 

within the region (see Appendix G). 

(1) Hatcheries/Artificial Production

It is estimated that more than 83 million fish were released from hatcheries in the 

Columbia River Basin in 2004 (FPC 2004). There are many hatcheries in the basin, and they 

have diverse purposes including, for example, the culture and release of salmonids, white 

sturgeon, and largemouth bass. Hatchery uncertainties are therefore partitioned by purpose as 

defined in the Artificial Production Review (NPCC 1999, Council Document 99-15). These 

include uncertainties of supplementation and captive rearing for conservation and preservation 

and uncertainties of conventional production for harvest and reintroduction. The proportion of 

hatchery fish harvested in the various fisheries has not been determined. 

Artificial production is authorized under many mandates in federal and state law, and the 

Council funds only a modest portion of total hatchery production. The purposes of artificial 

production include conventional production to mitigate for hydrosystem construction and 

operation by providing harvest for commercial, sport, and tribal fisheries; conservation of 

depleted (often ESA-listed) populations using supplementation, captive rearing, and captive 

broodstocks; and reintroductions of species such as coho and fall Chinook salmon into subbasins 

where they have been extirpated. 

Using artificial production to provide a harvest opportunity carries with it a cost of 

increasing the risk of extinction or extirpation of naturally spawning independent populations. 

The Council's 1999 Artificial Production Review defined principles for using artificial 

production in the basin, beginning with determining the purpose of each hatchery program

through the Artificial Production Review Evaluation (NPCC 2004, Document 2004-17). An 

urgent need remains for fundamental information on the interactions of hatchery-produced fish 

with wild fish populations (Williams 2005; CENR 2000; NPPC 1999, Document 99-15; NPPC 

1999, Document 99-4; NPCC 2000, 2000 Columbia River Basin Fish and Wildlife Program; 

ISAB 2003, Document 2003-3). 

The essential issue for hatcheries now is to determine the balance between their 

effectiveness and their hazards. Specifically, how detrimental are the releases from “segregated” 

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mitigation and harvest-augmentation programs to wild fish owing to ecological interactions and 

interbreeding, and how detrimental are the supplementation programs to target and non-target 

natural populations from ecological interactions and interbreeding? The question of hatchery 

impacts on natural production extends from local and stock-specific interactions to interactions 

within large-scale mixed-stock fisheries over very large spatial and temporal scales. Moreover, 

there needs to be a better understanding of integrating the hatchery approach, which has expected 

limitations, with other approaches. The Council’s 2000 Program recommends that 

supplementation and habitat restoration be linked with the goal of reestablishing self-sustaining 

natural salmon populations. The program explicitly directs an experimental approach to all 

hatchery projects (2000 Fish and Wildlife Program, page 29). 

Critical Uncertainties:

Conventional Hatchery Production — 

1. What is the cost to natural populations from competition, predation (direct and 

indirect), and disease caused by interactions with hatchery-origin juveniles and from harvest in 

fisheries targeting hatchery-origin adults? 

2. To what extent can interactions between production-hatchery fish and naturally 

produced wild fish be reduced — for example with the goal of achieving sustainable long-term

productivity and resilience of the wild component of the population by spatial or temporal 

partitioning of natural and artificial production at the subbasin, province, basin, and regional 

scale? 

Supplementation — 

3. What is the magnitude of any demographic benefit to the production of natural-origin 

juveniles and adults from the natural spawning of hatchery-origin supplementation adults?

4. What are the range, magnitude, and rates of change of natural spawning fitness of 

integrated (supplemented) populations, and how are these related to management rules, including 

the proportion of hatchery fish permitted on the spawning grounds, the broodstock mining rate, 

and the proportion of natural origin adults in the hatchery broodstock?

5. Can the carrying capacity of freshwater habitat be accurately determined and, if so, 

how should this information be used to establish the goals and limitations of supplementation 

programs within subbasins? 

All Hatcheries — 

6. What is the relationship between basinwide hatchery production and the survival and 

growth of naturally produced fish in freshwater, estuarine, and ocean habitats? 

7. What effect do hatchery fish have on other species in the freshwater and estuarine 

habitats where they are released? 

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(2) Hydrosystem 

Construction and operation of the hydrosystem caused extensive changes in the Columbia 

River Basin including major alteration of the riverine environment. Evidence of this alteration 

includes slow-moving water in reservoirs, habitat degradation in the mainstems of rivers, powerpeaking fluctuations in flow, elevated water temperatures, and barriers to fish migration. 

Therefore the fish and wildlife program emphasizes research of mainstem river operations, 

including spill, flow augmentation, and fish transportation. Fish-passage standards, objectives, 

designs, and evaluations must be related to increases in adult fish returning to spawning grounds 

(juvenile-to-adult survival rates), not just the incremental survival of juvenile fish or adult fish 

through the Columbia River Basin hydropower system. 

Technologies that most closely approximate the natural physical and biological 

conditions of migration most likely would accommodate diverse species life histories, and 

multiple passage systems likely are needed to fully protect all species. For example, surface 

bypass systems take advantage of the tendency of yearling smolts to pass dams near the surface 

of the river. Fish that migrate lower in the water column can be diverted into other bypass 

systems or passed through the turbines. 

River operations significantly different than the status quo need to be tested to provide 

information for resolving key uncertainties about the hydrosystem impacts on fish. There is 

considerable uncertainty about the effects of changes in river flows, spill, and water quality on 

the migratory behavior of juvenile and adult fish. Experimental studies of all aspects of 

mainstem flow manipulation, including load following, are needed to determine the effects on 

fish survival (ISAB Document 2003-1). For instance, determining the effects on migration of 

stage waves and turbulent bursts or pulsing flows may provide information that supports 

opportunities for water management that could be 1) more effective in moving fish and 2) 

provide greater opportunity for power generation than current procedures. The secondary effects 

of flow differences on near-shore habitat conditions in reservoirs (temperature, flow, and food 

production) and effects of shoreline modifications along reservoirs (rip-rap, erosion, and 

permanent sloughs) also need to be evaluated. Additionally, recent studies on out-migrating 

juvenile fall Chinook indicate that they have a more complex migratory life history than 

previously thought, calling into question the estimated juvenile survival through the hydrosystem

and the current use of transportation, spill, and flow augmentation to protect fall Chinook (ISAB

Document 2004-2). 

Previous large-scale analytical assessments (Peters and Marmorek 2001; Karieva et al. 

2000; Wilson 2003) evaluated management options for halting the decline of the Snake River 

stream-type Chinook populations. These results depended on whether the source of mortality in 

the estuary and early in the ocean residence of fish is related to earlier hydrosystem experience 

(delayed mortality) during downstream migration. Substantial evidence suggests that Snake 

River Chinook salmon experience delayed mortality as the result of their passage through the 

hydrosystem (Budy et al. 2002). 

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Critical Uncertainties: 

1. What is the relationship between levels of flow and survival of juvenile and adult fish 

through the Columbia Basin hydrosystem? Do changes in spill and other flow manipulations 

significantly affect water quality, smolt travel rate, and survival during migration? How do 

effects vary among species, life-history stages, and migration timings? What is the role of 

hydrodynamic features other than mid-channel velocity in fish migration? What is the 

relationship between ratios of transport, inriver return rates, and measurements of juvenile 

survival (D values)? 

2. Under what conditions is delayed mortality related to downstream migration through 

the hydrosystem, and what is the magnitude of that delayed mortality? 

3. What are the effects of multiple dam passages, transportation, and spill operations on

adult fish migration behavior, straying, and pre-spawn mortality, and juvenile-to-adult survival 

rates?

4. What is the effect of hydrosystem flow stabilization, flow characteristics, and channel 

features on anadromous and resident fish species and stocks? What are the ecological effects of 

hydrosystem operations on downstream mainstem, estuarine, and plume habitats and on 

populations of fish and wildlife?

5. What are the optimal temperature and water quality regimes for fish survival in 

tributary and mainstem reaches affected by dams, and are there options for hydrosystem

operations that would enable these optimal water quality characteristics to be achieved? What 

would be the effects of such changes in operations and environment on fish, shoreline and 

riparian habitat, and wildlife?

(3) Tributary and Mainstem Habitat 

Degradation, loss, and fragmentation of habitat have contributed substantially to the 

depletion of fish and wildlife populations in the Columbia River Basin. Fish and wildlife habitat 

has been severely degraded by dams and diversions, sedimentation from forestry and agriculture, 

and the introduction of nonnative species. Native fish and wildlife are sustained by complex and 

interconnected habitats, which are created, altered, and maintained by natural physical processes. 

Restoration efforts must focus on restoring habitats and habitat connectivity and on developing 

ecosystem conditions and functions that will support diverse species. 

The 2000 Fish and Wildlife Program places importance on improved natural habitat for 

fish spawning and rearing throughout their life cycle, including tributary, estuary, and marine 

stages. The critical ecosystem features for the full life cycle of salmonid species and stocks must 

be defined (CENR, 2000), and the dynamic relationships between habitat and fish and wildlife 

productivity must be better understood to conserve and restore fish and wildlife populations. A 

comprehensive life-cycle approach that addresses both natural variability in environmental 

conditions and human impacts on physical, chemical, and biological processes affecting fish and 

wildlife populations must be defined (ISAB, 2003-2). 

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Several critical knowledge gaps must be addressed. The Interior Columbia Basin 

Ecosystem Management Project was largely limited to federally managed lands, and the Council 

should support a similar initiative to assess the status of habitat throughout the Columbia River 

Basin, as this information is essential in developing a sound, basinwide restoration strategy. The 

rate of habitat loss should be quantified, and locations of habitat loss and restoration should be 

inventoried and evaluated to assess how well the current and projected habitat template supports 

the life history needs of fish and wildlife. The effectiveness of present best management 

practices and restoration techniques must be resolved by scientific evaluation at both site-specific 

and watershed scales. Finally, little is known about the food webs in the Columbia Basin, 

especially in the tributaries (e.g., how have they been altered by land and water use, by the 

introduction of toxics and of non-native plants and animals, by harvesting, and by climate 

change). Scientific understanding of the role of nutrients in the growth of juvenile salmon in 

freshwater and estuarine conditions is also incomplete, but fewer adult salmon returning to 

spawn in many streams has resulted in decreased import and transport of nutrients such as 

nitrogen and phosphorus. 

Critical Uncertainties:

1. To what extent do tributary habitat restoration actions affect the survival, productivity, 

distribution, and abundance of native fish populations? 

2. Are the current procedures being used to identify limiting habitat factors accurate? 

3. What are the impacts of hydrosystem operations on mainstem habitats, including the 

freshwater tidal realm from Bonneville Dam to the salt wedge? How might hydrosystem

operations be altered to recover mainstem habitats? 

4. What pattern and amount of habitat protection and restoration is needed to ensure longterm viability of fish and wildlife populations in the face of natural environmental variation as 

well as likely human impacts on habitat in the future? 

(4) The Estuary 

The Columbia River estuary constitutes the physical and biological interface for fish as 

they move between their freshwater and ocean life stages. Juvenile anadromous fish rear and 

undergo adaptation to marine conditions in the estuary, and rearing locations, seasonal timing, 

residence timing, and migration pathways differ between species and stocks. Wetlands and tidal 

channels are important rearing habitats for some fish. The Columbia River estuary also provides 

important rearing habitat for other marine animals and year-round habitat for estuarine species. 

The estuary has been impacted by habitat development and management locally, and 

upriver. Changes in biological processes range from alteration in the food web to the exclusion 

of fish from large portions of the tidal marshes. Changes in seasonal flows following the 

development of the hydrosystem have resulted in changes to estuarine circulation, sedimentation, 

and biological processes. Although all of the anadromous fish flow through this unique 

environment, the effects of restoration projects in the estuary have not been evaluated and many 

basic biological functions of the estuary in the life cycle of fish remain poorly understood. 

15
Monitoring of the physical environment, such as that currently under way by the Oregon 

Graduate Institute, and evaluation of large-scale manipulations of estuarine habitats can be 

combined to better understand the role of the estuarine environment and its degradation or 

restoration in the success or failure of salmonid populations (ISRP, 2003-13). 

Critical Uncertainties:

1. What is the significance to fish survival, production, and life-history diversities of 

habitat degradation or restoration in the estuary as compared with impacts to other habitats in the 

basin? How does this partitioning of effects vary among species and life-history types? 

2. What are the highest priority estuarine habitat types and ecological functions for 

protection and restoration (e.g., what are most important habitats in the estuary for restoring and 

maintaining life-history diversities of subyearling Chinook and chum salmon, and how effective 

were past projects in restoring nursery/feeding areas)?

3. What specific factors affect survival and migration of species and life-history types of 

fish through the estuary, and how is the timing of ocean entry related to subsequent survival?

(5) The Ocean 

Recent research has established that global- and regional-scale processes in the ocean and 

atmosphere can influence the production of anadromous species such as salmon, lamprey, and 

cutthroat trout, as well as the structure and dynamics of marine ecosystems. Natural variation in 

these processes must be understood to correctly interpret the response of fish to management 

actions in the Columbia Basin. 

The marine survival of juvenile fish, and their growth rates and age and size structures, 

are linked to local and regional processes in the North Pacific Ocean. Salmon abundances in the 

California Current region (off Washington, Oregon, and California) and in the Gulf of Alaska 

(Alaska Current) may respond in opposite ways to shifts in climatic regime. For example, during 

periods of a strong low pressure in atmospheric circulation over the North Pacific Ocean in 

winter (Aleutian Low), zooplankton production and early marine survival of juvenile salmonids 

generally increase in the Alaska Current and decrease in the California Current. Climatic phase 

shifts characteristic of the strong Aleutian Low regime occurred from about 1925 to 1946 and 

after 1976/77; both periods were marked by precipitous declines in the coho salmon fishery off 

Oregon. Opposing cycles of salmon abundance between the Alaska Current and the California 

Current regions underscore the importance of stock-specific regulation of ocean fisheries. In 

1999, a phase shift in the Victoria climate pattern and sea surface temperature seems to have 

influenced productivity of the California Current more than the Alaska Current. As a result of 

favorable marine conditions in both the California and Alaska currents, the total production of 

salmon in the eastern North Pacific and Gulf of Alaska reached an all-time high in the early 

2000s. 

While the marine production of salmon can be tied to major oceanic and atmospheric 

circulation, salmon life cycles are shorter than the inter-decadal periods of large-scale climatic 

change, and short-term climate change phenomena such as the El Nino-Southern Oscillation also 

16
can have a strong influence on freshwater and marine survival of salmonids. Thus, the ability to 

predict adult salmon returns in the face of both short-term and long-term climate change is 

critical to harvest management and recovery of depressed stocks of Columbia River salmonids. 

While the abundance of salmonids is known to track large- and small-scale shifts in climate, the 

specific mechanisms of biological response are poorly understood. Decadal and interannual 

cycles of ocean productivity have the potential to mask changes in the survival of salmon during 

freshwater phases of their life cycle, confounding interpretation of the performance of restoration 

efforts and increasing losses of some stocks. There is also increasing evidence that ocean 

fisheries on groundfish (Pacific whiting, walleye, pollock, halibut, etc.) and coastal pelagic 

species (squid, sardines, anchovies, etc.) may affect salmonids through food web interactions. 

Stocks with different life history traits and ocean migration patterns may be favored under 

different combinations of climate and more local conditions, and such differences may afford 

stability to salmon species in the face of environmental variability. Conservative standards for 

harvest, hatchery practices, and freshwater habitat protection may be necessary even during 

periods of high ocean productivity to maintain the genetic diversity needed to withstand 

subsequent troughs in productivity. 

Critical Uncertainties:

1. Can stock-specific data on ocean abundance, distribution, density-dependent growth 

and survival, and migration of salmonids, both hatchery and wild, be used to evaluate and adjust 

marine fishery interceptions1

, harvest, and hatchery production in order to optimize harvests and 

ecological benefits within the Columbia River Basin? 

2. Can monitoring of ocean conditions and abundance of salmon and steelhead during 

their first weeks or months at sea improve our ability to predict interannual fluctuations in the 

production of Columbia Basin Evolutionarily Significant Units (ESUs) or populations to enable 

appropriate changes to harvest levels? 

3. How can interannual and interdecadal changes in ocean conditions be incorporated into 

management decisions relating to hydrosystem operations, the numbers and timing of hatchery 

releases, and harvest levels to enhance survival rates, diversity, and viability of ESA-listed 

salmonids?

4. What are the effects of commercial and sport fishing on ocean food webs?

(6) Harvest 

Harvest management for many fish populations in the Columbia River Basin has 

substantially changed due to state and federal listings. Harvest for listed populations is managed 

under biological opinions that attempt to ensure fisheries do not pose jeopardy to listed fish 

species. Most current harvest management targets fish from mitigation hatcheries; productivity to

support harvest has been largely divorced from production in natural habitat. 

 

1

 Interceptions are catches of juvenile, immature, or maturing fish by non-target fisheries. 

17
The ISAB Harvest Management Review (ISAB, 2005-4) addressed the question: what 

constitutes a sound scientific basis for the management of Pacific salmonids in the Columbia 

River Basin? The report also noted critical uncertainties as to the effect of harvest on the 

conservation of naturally produced salmonids, including the fundamental need to better monitor 

and understand mixed-stock fisheries. Three fundamental components of harvest management 

were identified as causes of concern: a paucity of quantitative data for analyses by population 

units; limited identification and assessment of the catches of hatchery and wild stocks to identify 

trends in their status and provide a biological basis for production goals; and limited evidence of 

accounting for uncertainty in management plans. 

Critical Uncertainties:

1. What are the effects of fishery interceptions and harvest in mixed-stock areas, such as 

the ocean and mainstem Columbia, on the abundance, productivity, and viability of ESUs or 

populations, and how can fishery interceptions and harvests of ESUs or populations, both 

hatchery and wild, best be managed to minimize the effects of harvest on the abundance, 

productivity, and viability of those ESUs and populations? 

2. What new harvest and escapement strategies can be employed to improve harvest 

opportunities and ecological benefits within the Columbia Basin while minimizing negative 

effects on ESUs or populations of concern? Can genetic techniques be used to quantify impacts 

on wild or ESA-listed stocks in ocean fisheries? 

3. How can the multiple ecological benefits that salmon provide to the watersheds where 

they spawn (e.g., provision of a food resource for wildlife and a nutrient source for streams and 

riparian areas) be incorporated effectively into procedures for establishing escapement goals? 

(7) Population Structure and Diversity 

Fish and wildlife populations are characterized by life history, ecological, behavioral, 

phenotypic, and genetic diversity, which buffer populations against short- and long-term

environmental variation. For anadromous salmonids, stock diversity has been reduced by the 

extinction of many local populations, as well as a reduction in population size of most remaining 

populations. Moreover, losses of genetic diversity within populations may have decreased fitness 

and therefore decreased the probability of long-term persistence for many stocks. A better 

understanding is needed of the dominant processes influencing the distribution, interconnection, 

and dynamics of populations through time and space. 

Additionally, populations are a fundamental unit of viability analysis, and effectively 

evaluating the status of a species may depend on correctly understanding its population structure. 

Identification of strong, weak, and at-risk native populations is a critical step in determining what 

actions can be taken to preserve and protect populations (see ISAB, 2001-7). Several species 

(e.g., resident and anadromous rainbow, ocean and reservoir type fall Chinook) have cooccurring life-history types that are poorly understood and pose critical problems for 

management. 

18
Critical Uncertainties:

1. What approaches to population recovery and habitat restoration are most effective in 

regaining meta-population structure and diversity that will increase viability of fish and wildlife 

in the Columbia River Basin? 

2. How do artificial production and supplementation impact the maintenance or 

restoration of an ecologically functional metapopulation structure? 

3. What is the relationship between genetic diversity and ecological and evolutionary 

performance, and to what extent does the loss of stock diversity reduce the fitness, and hence 

survival rate and resilience, of remaining populations? 

4. What are the differential effects of flow augmentation, transportation, and summer 

spill on “ocean type vs. reservoir type” fall Chinook? 

(8) Effects of Climate Change on Fish and Wildlife 

Variation in climate and ocean conditions are now recognized as major contributors to 

fluctuations and trends in fish and wildlife abundance. Global climate change may interact with 

shorter-term climate patterns to accentuate these effects on fish and wildlife. In the Pacific 

Northwest, reduced ocean survival of salmon and stressful freshwater conditions, due to low 

precipitation, low stream flow, and high stream temperatures, tend to be concurrent. The changes 

in regional snowpack and stream flows in the Columbia Basin that are projected by many climate 

models could have a profound impact on the success of restoration efforts and the status of fish 

and wildlife populations. Nevertheless, climate change is rarely incorporated into natural 

resource planning. Additionally, the cumulative effects of human development of the Basin may 

become apparent only when climatic conditions trigger a dramatic response. 

Critical Uncertainties:

1. Can integrated ecological monitoring be used to determine how climate change 

simultaneously affects fish and wildlife and the freshwater, estuarine, ocean, and terrestrial 

habitats and ecosystems that sustain them? 

2. Can indices of climate change be used to better understand and predict interannual and 

interdecadal changes in production, abundance, diversity, and distribution of Columbia Basin 

fish and wildlife? 

3. What long-term changes are predicted in the Columbia River Basin and the northeast 

Pacific Ocean, how will they affect the fish and wildlife in the region, and what actions can 

ameliorate increased water temperatures, decreased summer river flows, and other ecosystem

changes?

(9) Toxics 

Toxic contaminants need to be evaluated by the fish and wildlife program, as toxics could 

negate much of the good work being accomplished in the basin. Toxics have been recognized as 

19
a problem since bald eagles and osprey, which eat fish from the river that contain various 

contaminants, were almost eliminated from the Columbia Basin by the mid-1970s. Reproduction 

continues to be adversely affected by DDE in a portion of the Columbia River osprey population. 

Many of the legacy contaminants (e.g., DDE, PCBs) have been declining for years, but new 

emerging contaminants are taking their place as contaminants of concern. Flame-retardants 

polybrominated diphenyl ethers (PBDEs) are one group of special concern in the Columbia 

River. Based upon data from the upper Columbia River, PBDE concentrations in fish are 

doubling every 1.6 years, and PBDEs have been found in bald eagle eggs from the lower 

Columbia River and in all 15-osprey eggs sampled from Puget Sound in 2003. Many other 

emerging contaminants, including modern pesticides and pharmaceuticals, need to be 

investigated. An adequate toxics monitoring and research program needs to be developed as a 

coordinated effort of various agencies and groups, including the Council. 

Critical Uncertainties: 

1. What is the distribution and concentration of toxics, including emerging contaminants, 

in the Columbia River Basin, and what are/have been their trends over time? 

2. How do toxic substances, alone and in combination, affect fish and wildlife 

distribution and abundance, survival, and productivity? 

(10) Invasive Species 

Invasive species2

 comprise one of the most significant alterations of native ecosystems 

and are rapidly becoming a dominant component of ecosystems within the Columbia River Basin 

(Office of Technology Assessment, 1993). For instance, a recent survey found 81 nonnative 

aquatic species below Bonneville Dam3

 and, although the impacts of non-native fish stocked for 

recreation are widely recognized, many other non-native plants and animals also could have a 

large impact on aquatic habitat and productivity (e.g., Eurasian milfoil, New Zealand mud snail, 

zebra mussel, Japanese knotweed, Himalayan blackberry, giant reed, and riparian-associated 

animals such as livestock). Non-native species affect native fish and wildlife both directly (e.g., 

as predators or competitors, or indirectly, by altering food webs, water chemistry, physical 

habitat attributes). Some of the most challenging long-term management problems involve 

nonnative, invasive species, such as the widespread rainbow and brook trout, which were 

introduced to provide angling opportunities. Intentional introductions of taxa have proven just as 

likely to cause harm as unintentional introductions (Office of Technology Assessment, 1993). 

Additionally, there is conflict between the value of fish passage restoration for native 

species and the chance that such passage may allow non-native species, such as New Zealand 

 

2

 For the purpose of this plan, invasive and native species are defined as, as follows: “invasive 

species” means an alien species whose introduction does or is likely to cause economic or 

environmental harm or harm to human health, and “native species” means a species that 

historically occurred or currently occurs in an ecosystem, without being the result of an 

introduction. (Section 1 of Presidential Executive Order 13112 Invasive Species). 

3 www.clr.pdx.edu/projects/cr_survey

20
mudsnails, crayfish, other nonnative fish (e.g., Atlantic salmon), and new diseases, to spread. 

Thus, there is a need for better assessments of the biological and economic consequences of 

invasions, including research to identify patterns and consequences of invasions on species and 

ecosystems. Initial baseline information and monitoring are necessary to detect trends in 

abundance of non-native and invasive species, and targeted research on invasives is required to 

better understand the structural and functional changes in ecosystems, habitats, and food webs 

that they cause. 

There have been relatively few examples of success in eradicating well-established 

invasive species at an ecosystem level. Prevention of introduction and detection of new 

introductions are therefore essential. A proactive approach to anticipating invasions and 

identifying areas at-risk could potentially save many millions of dollars in future efforts to 

control species once they become established and threaten native flora and fauna. Research is 

needed to identify pathways of introduction and related preventive actions that can reduce the 

risks of introduction and spread of non-native species. 

Critical Uncertainties:

1. What is the current distribution and abundance of invasive and deliberately introduced 

nonnative species (e.g., the baseline condition), and how is this distribution related to existing 

habitat conditions (e.g., flow and temperature regimes, human development, restoration actions)? 

2. To what extent do (or will) invasive and nonnative species significantly affect the 

potential recovery of native fish and wildlife species in the Columbia River Basin? 

3. What are the primary pathways of introduction of invasive and nonnative species, and 

what methods could limit new introductions or mitigate the effects of currently established 

invasives? 

(11) Human Development 

 

Like climate change, the impact of human population growth in the Columbia Basin is 

widely recognized, but is rarely incorporated into fish and wildlife planning. The human 

population of the Columbia Basin is increasing rapidly, a trend that is expected to continue. This 

increase is largely concentrated in and around urban areas, but affects non-urban areas as well, 

through recreation, housing, and changing land uses. At the same time, the economy of the 

region is shifting, with the potential for both positive and negative impacts on fish and wildlife 

and their habitats. The Council’s program and the NOAA Fisheries restoration plans do not 

include consideration of human population trends. The fish and wildlife program mitigates 

human impacts on fish, wildlife, and their habitats, and it is important to consider demographic 

and economic trends and their potential impacts on efforts to restore and recover fish and 

wildlife resources. 

Critical Uncertainties:

1. What changes in human population density, distribution, and economic activity are 

expected over the next 20 years? 50 years? 

21
2. How might the projected changes under different development scenarios affect land 

use patterns, protection and restoration efforts, habitats, and fish and wildlife populations? 

(12) Monitoring and Evaluation 

Adaptive management, using scientifically well-informed management actions and 

information drawn from their implementation, is recognized as essential to effective 

implementation of the fish and wildlife program. Adaptive management requires monitoring and 

evaluation, including status and trend monitoring of fish, wildlife, habitats, and ecosystems, and 

action effectiveness research, to provide information with which to evaluate project outcomes 

relative to project objectives and programmatic standards. Monitoring contributes needed 

information to address whether biological and programmatic performance objectives established 

within the fish and wildlife program (e.g., subbasin plans and mainstem amendments; FCRPS 

BiOp; and ESA Recovery Plans) are being met; how current management should be changed to 

better meet those objectives; what factors are limiting ability to achieve performance standards 

or objectives; and what mitigation actions are most effective at addressing the limiting factors. 

This research plan identifies four critical monitoring and evaluation needs, listed below, in 

addition to the need to support additional monitoring priorities and programs as a collaborative 

partner in a Regional Research Partnership. 

Some priority research topics require a monitoring program for answers. For example, 

supplementation has significant critical uncertainties that require extensive and coordinated 

monitoring to resolve (ISRP and ISAB, 2005-15). This can be addressed by coordination of 

supplementation projects across the Columbia River Basin so that, in aggregate, they constitute a 

basinwide adaptive management experiment that includes un-supplemented reference streams. 

Thus, an initial monitoring and evaluation priority will be to address the following four critical 

uncertainties: 

Critical Uncertainties:

1. Can a common probabilistic (statistical) site selection procedure for population and 

habitat status and trend monitoring be developed cooperatively?

2. Can a scientifically credible trend monitoring procedure based on remote sensing, 

photography, and data layers in a GIS format be developed?

3. Can empirical (e.g., regression) models for prediction of current abundance or 

presence-absence of focal species concurrent with the collection of data on status and trends of 

wildlife and fish populations and habitat be developed?

4. Make best professional judgment, based on available data, as to whether any new 

research in the spirit of the Intensive Watershed Monitoring approach should be instigated 

immediately. Most new intensive research should arise as a result of the interaction of existing 

inventory data with new data arising in population and habitat status and trend monitoring. 

The last three uncertainties were identified as key steps for building a foundation to 

address critical monitoring needs of the fish and wildlife program, as well as to support the 

22
coordinated monitoring and evaluation needs of other regional research and management 

programs, see ISRP Retrospective Report (ISRP, 2005-14). 

There are a number of existing efforts in the region to coordinate and collaborate around 

monitoring and evaluation, but until recently there has been a lack of an organizing principle or

central forum to facilitate these efforts. In 2005, the Pacific Northwest Aquatic Monitoring 

Partnership (PNAMP) was chartered to provide such a forum. As members of PNAMP, the 

Council, Bonneville, and the fish and wildlife managers are working to implement the fish and 

wildlife program within the context of a regional network of monitoring effort so that the shared 

monitoring needs and objectives of the program can be achieved. The Council has directly 

supported this work through the Collaborative Systemwide Monitoring and Evaluation Project 

(CSMEP) to assure and facilitate implementation within the Columbia Basin. In close 

coordination with PNAMP, the CSMEP has been working since October 2003 to develop 

rigorous approaches to monitoring and evaluation that directly serve the needs of specific 

decisions, and build on the strengths of existing monitoring infrastructure. PNAMP and CSMEP 

have been, and will continue, working closely together. 

23
V. APPENDIXES

Appendix A. Context for the Research Plan 

Objectives of the Council’s Fish and Wildlife Program 

This appendix provides additional explanation of the rationale for the research plan. In 

1980, Congress passed the Pacific Northwest Electric Power Planning and Conservation Act4

that authorized the states of Idaho, Montana, Oregon, and Washington to create the Northwest 

Power and Conservation Council. The Act directs the Council to develop a program to: 

“...protect, mitigate and enhance fish and wildlife, including related spawning grounds 

and habitat, on the Columbia River and its tributaries ... affected by the development, 

operation and management of [hydroelectric projects] while assuring the Pacific 

Northwest an adequate, efficient, economical and reliable power supply.” 

The Council’s Columbia River Basin Fish and Wildlife Program is one of the largest 

regional efforts in the nation to recover, rebuild, and mitigate impacts of hydropower dams on 

fish and wildlife. As a planning, policy-making, and reviewing body, the Council develops and 

monitors the program, which is funded by the Bonneville Power Administration and 

implemented by tribal, state, and federal fish and wildlife managers and others. The Council 

adopted the first fish and wildlife program in November 1982. The latest revision of the 

program, in 2000, marked a significant departure from past versions, which consisted primarily 

of a collection of measures directing specific activities. In contrast, the 2000 Program establishes 

a basinwide vision for fish and wildlife along with four overarching biological objectives: 

• A Columbia River ecosystem that sustains an abundant, productive, and diverse 

community of fish and wildlife 

• Mitigation across the basin for the adverse effects to fish and wildlife caused by the 

development and operation of the hydrosystem

• Sufficient populations of fish and wildlife providing abundant opportunities for tribal 

trust and treaty right harvest and for non-tribal harvest 

• Recovery of the fish and wildlife affected by the development and operation of the 

hydrosystem that are listed under the Endangered Species Act 

 

4

 Pacific Northwest Electric Power Planning and Conservation Act of 1980 (Public Law 96-501, 

94 Stat. 2697 (December 5, 1980), codified with amendments in U.S Code Annotated 16, 

section 839 (2000)). Relevant to this research plan, Section 839b(h)(6)(B) directs the 

Council to include in the fish and wildlife program measures the Council determines are 

based on, and supported by, the best available scientific knowledge. 

24
Mandate for the Research Plan 

Critical uncertainties have persisted for years because the relevant research questions are 

difficult to answer due to: environmental variability; the complexity of the Columbia River Basin 

environment; and the inherent difficulty in agreeing on specific problem definitions. In addition, 

over the course of the development of the program, the Council adopted specific measures for 

research without a research plan to provide clear prioritization of the remaining critical 

uncertainties. Without a research plan it was difficult to focus on those uncertainties, and so in 

the 2000 Program the Council called for development of a Columbia River Basin Research Plan. 

The plan will guide the development of a research program and foster collaboration with the 

research programs of other resource management entities within the region. Specifically, the 

Basinwide Provisions (D.9) state that: 

“The Council will establish a basinwide research plan, similar to the subbasin plans, 

which identifies key uncertainties for this program and its biological objectives and the 

steps needed to resolve them. The plan will identify major research topics, including 

ocean research, and establish priorities for research funding.”

25
Appendix B. Implementing the Research Plan in Fiscal Years 2007-2009 

This appendix explains the methods by which research project proposals were solicited; 

reviewed by the Independent Scientific Review Panel, and evaluated against decision criteria for 

identifying priorities. The appendix includes a table depicting the conceptual framework for a 

regional approach to research, monitoring, and evaluation and describes how the research plan 

will be implemented in Fiscal Years 2007-2009. 

Project Selection Process for Fiscal Years 2007-2009 

The project selection process for fiscal years 2007-2009 provides a vehicle for 

implementing research that is central to the program, research that supports the mitigation and 

restoration of wildlife, resident fish, unlisted anadromous fish, and listed anadromous fish. In 

contrast to the fiscal years 2004-2006 funding cycle, the fiscal years 2007-2009 process will 

benefit from the priorities established in the research plan, in subbasin plans, in the PNAMP 

Aquatic Monitoring Strategy, and in NOAA recovery planning documents. Furthermore, the 

authors of these planning documents collaboratively developed a framework for implementing a 

regional approach to research, monitoring, and evaluation. This is depicted in Table 1 at the end 

of this appendix. These sets of priorities, and the framework, have provided targets for project 

proposals and guidance for the review and evaluation of ongoing and proposed research. 

The Fiscal Years 2007-2009 project selection process provides an immediate opportunity 

to begin work on these critical uncertainties. The competing demands on program funding 

underscore the need for an assessment of proposed research activity in relation to on-going 

research. Many restoration projects contribute to resolving critical uncertainties because they 

have a research component, but research is a component and not the primary focus. Therefore, 

the implementation of new research may require a reallocation of research dollars during Fiscal 

Years 2007-2009 and subsequent funding cycles. In many cases, existing projects may provide a 

strong start for a new research focus. For example, ongoing projects with strong links to regional 

research priorities will be considered as vehicles for addressing those priorities. 

The fact that there may be multiple ongoing projects addressing a research topic does not 

preclude an enterprising sponsor from proposing a new or novel approach to the same problem. 

In the past, the Council has received project proposals submitted in response to solicitations that 

were geographic in scope; the Council did not actively seek proposals to address specific critical 

uncertainties. The prior open approach to solicitations proved costly in terms of failing to address 

the knowledge gaps, frustrating project sponsors, and expending ISRP review time on proposals 

that neither the Council nor Bonneville would consider funding. In the past the ISAB and ISRP 

have suggested directing the available research and monitoring resources to a smaller number of 

projects that are well-designed and have the intellectual and financial resources to generate 

useful information. 

Methods of Project Solicitation 

The Northwest Power Act affords the Council broad discretion to develop the procedures 

for conducting project review and selection. 

26
Rolling Provincial Reviews 

For planning purposes within the Columbia River Basin, the Council has delineated 11 

ecological provinces comprising groups of adjoining subbasins that have similar ecological 

attributes. These provinces constitute the geographic scale at which the recent project selection 

process was implemented on a three-year cycle. 

Each province has its own uncertainties concerning environmental issues and fish and 

wildlife populations, some of which might be resolved by research projects. Subbasin plans have 

helped identify the most appropriate geographic locations for siting research projects. In cases 

where multiple provinces share similar uncertainties, solutions in one province may inform

efforts in others. Project sponsors were free to propose research projects unique to their 

geographic location but were encouraged to propose research that provides a basis for 

extrapolation outside of the subbasin in which the project is located. Research projects with 

basinwide implications should compete with each other in the mainstem/systemwide project 

review, not in multiple provincial reviews. 

Requests for Proposals 

In the past, the Council identified questions of particular importance and initiated 

requests for proposals in coordination with Bonneville as needed. Future project solicitations that 

occur after completion of the research plan may attract research proposals consistent with 

recommendations in the plan. However, for research recommendations for which no proposals 

are forthcoming, and/or for recommendations the Council decides to implement in the interim,

requests for proposals could be initiated. Requests for proposals should be used independent of, 

or in concert with, broader solicitations to ensure the efficient effort of project sponsors, the 

ISRP, the managers, and the Council. 

Review of Project Proposals by the ISRP 

The Northwest Power Act also requires all project proposals to undergo an independent 

scientific review of specific project proposals by the ISRP to ascertain their scientific and 

technical merits. The 1996 amendment to the Northwest Power Act requires the ISRP to 

determine whether projects proposed for funding: 

• Are based on sound science principles 

• Benefit fish and wildlife 

• Have clearly defined objectives and outcomes 

• Have provisions for monitoring and evaluation of results 

• Are consistent with the program

Thus, current decision criteria for ranking projects as “fundable or not fundable” are 

based primarily on technical merit and do not include specific reference to research priorities. 

27
Consequently, this research plan should enable the ISRP to better compare and evaluate projects 

for relevance to critical uncertainties. 

In addition to the ISRP’s scientific review, proposals are evaluated within a policy 

context to determine their potential contribution to management decision-making. The regional 

fish and wildlife managers provide recommendations to the Council on these matters, and it is 

essential that they continue their key role in determining which projects are most likely to benefit 

fish and wildlife, including research projects that may provide the basis for eventual management

actions. In summary, the Council’s recommendations for Bonneville funding rest on a mix of 

priorities, legal considerations, technical adequacy, management urgency, regional opportunities, 

and available funding. 

Identifying Projects that Address Research Priorities 

The research plan addresses overarching research questions. However, from time to time 

rapidly emerging management uncertainties may arise that warrant updating the research plan 

with additional research priorities. The ISRP and ISAB recommend developing implementation 

plans that prioritize research for each three-year project funding cycle. This would include 

determining the relative importance of projects to research priorities. The following criteria are 

proposed to identify priority research in the Fiscal Years 2007-2009 project selection process. 

Critical Uncertainties - Projects that address critical uncertainties identified in this 

research plan will be considered priority projects. The results of such work must have broad 

application. For example, they must provide a basis for extrapolation across ecologically similar 

subbasins, or provinces. 

Time Required, Statistical Power - If the activity is likely to produce useful results within 

the five- to 10-year timeframe for the biological opinion, it will be ranked higher than one that 

requires more time to yield information relevant to management decisions. Activities that yield 

statistically reliable results given the design of the experiment (duration, type, and intensity of 

monitoring) will be ranked higher than those that do not. If survival rates are being monitored, 

the change should be large enough to be important in reducing extinction risks or increasing the 

likelihood of recovery. 

ESU Significance - Monitoring directed at ESA-listed ESUs will be ranked higher than 

activities directed at other stocks. For those directed elsewhere, there should be another 

justification for conducting the activity (for example, determining smolt-to-adult returns for 

Middle Columbia Chinook in order to compare the Snake and Upper Columbia stocks). 

Populations with higher extinction risk or greater necessary increases in survival rates generally 

will receive higher priorities for both management and research actions. 

Cost Feasibility - In prioritizing competing research activities intended to produce 

roughly the same information, cost of the different activities will be one criterion in selecting 

projects for funding. Feasibility also will be important. For example, a project may be powerful 

and well designed but also impractical due to logistical constraints — for example, take permits 

cannot be issued quickly or customized equipment may take too long to build. 

28
Relationship to Other Research - To what extent does the proposed activity depend on 

other projects, and to what degree does it build on ongoing, related work? Some projects may 

conflict with other research. For example, a “control” stock for habitat enhancement cannot 

simultaneously be a “treatment” stock for nutrient supplementation. These conflicts require 

resolution before research activities are undertaken. 

Innovation - Innovation is a critical element of any large management or research 

program and should be encouraged. The Innovative Project category was suggested by the ISRP 

in past annual program reviews and was designed to improve knowledge, encourage creative 

thinking, and provide an opportunity for project sponsors to test new methods and technologies. 

Innovative projects were funded in Fiscal Years 1998, 2000, 2001, and 2002. Although 

innovative project solicitations were not pursued in Fiscal Years 2003-2005, Council members 

have expressed continued support for an innovative-project category. Although the innovative 

category is not being used in the Fiscal Years 2007-2009 funding cycle, the cycle still provides 

an immediate opportunity to fund innovative projects. Given the intractability of some research 

challenges it is important to keep the spark of innovation alive. 

29
RM&E Management Questions, Information Needs, and Cost-Sharing Agencies (BPA 11/14/05) 

RM&E Regional Information Needs Framework Component 

Management Questions 

SubordinateQuestions 

Metrics Data Required Survey or 

ExperimentalDesign 

Spatial Scale 

Tributary Habitat Status and Trend Monitoring

Are Columbia Basin fish populations meeting population level objectives (abundance, productivity, and diversity)?

What is size of adult 

salmonid and resident fish populations?

Numbers of adult fish Numbers of 

adults, spawners, or redds 

Census or spatiallybalanced survey6

Columbia BasinESU, Population, CorArea, or Subpopulation 

What is the 

distribution of salmonid and resident fish populations??

Presence/absence of adult fish 

Presence ofadults, spawners, or redds 

Census Columbia Basin

ESU, Population, CorArea, or Subpopulation 

What is the growth rate

of adult salmonid and resident fish populations??

Returns/Spawner, Lambda, Temporal Trends 

Numbers of adults, spawners, or redds 

Census or spatiallybalanced survey

Columbia BasinESU, Population, CorArea, or Subpopulation 

What is the freshwater 

productivity of these populations?

Smolts, fry or parr produced per adult, spawner, or redd

Number of smolts, fry or parr 

Census or spatiallybalanced survey

Columbia BasinESU, Population, CorArea, or Subpopulation 

What is the age

structure of these populations?

Age of returning adults or spawners 

Otolith, scale, orlength of adults or spawners 

Census or spatiallybalanced survey

Columbia BasinESU, Population, CorArea, or Subpopulation 

What fraction of the

spawners of these 

Ratio of hatchery to total fish abundances 

Number of hatchery

Census or spatiallybalanced survey Columbia Basin

ESU, 

5 FR= Fish Regulatory Agencies (NOAA and/or USFWS); AA= FCRPS Action Agencies (BPA, COE, BOR); LU= Land Managem

EPA= Environmental Protection Agency; S = State Agency; T= Tribe 

6 Spatially-Balanced Survey Design (e.g., EMAP-GRTS design; see Stevens and Olsen 2004)
populations is of

hatchery origin? 

produced adults or spawners 

Population, CorArea, or Subpopulation 

Are aquatic, riparian,and upland ecosystems of the Columbia Basin being degraded, restored or maintained relative to desired conditions or objectives?

What is the biological 

condition of spawning and rearing habitat forColumbia Basin fish populations?

Macro-invertebrate andfish assemblages

Spatially-Balanced

survey

Stream, watershed, subbasin 

What is the physical

condition of spawning and rearing habitat forColumbia Basin fish populations?

Valley characteristics (valley bottom types,valley widths and gradients, valleycontainment, road density, land ownership, land use); Channel characteristics (bedform types, channel types, gradient, width/depth ratio, stability); Riparian vegetation (structure,disturbance, canopycover); Habitat access (dams and diversions); Stream flows; Habitat quality (substrate, embeddedness, large woody debris, pools, off-channel habitat, fishcover) 

Spatially-balanced

survey 1

Stream, watershed, subbasin 

What is the water 

quality in spawning and rearing habitats for Columbia Basin fish populations?

Temperature, Turbidity,Conductivity, pH, Dissolved Oxygen,Nutrients, Toxic Pollutants and Heavy Metals 

Spatially-balanced

survey

Stream, watershed, subbasin 

Tributary What actions are most
Habitat Action 

EffectivenessResearch

effective at addressing the limiting factors preventing achievement of habitat, fish or wildlife performance objectives?

Did all tributary 

habitat actions in aggregate for a subpopulation increase juvenile survival or adult abundance, compared to a similar sub-population with few or no habitat actions?

Type, location, timing and intensity of habitat actions, and juvenile survival or adult abundances 

Depends on management actions 

Large-scale BeforeAfter (BA) Studies7 Watershed, Subbasin 

What contribution did 

all tributary habitatactions for an ESU make towardincreasing the ESUlevel populationgrowth rate?

Type, location, timing and intensity of habitat actions, and ESU population growth rates 

Depends on management actions 

Large-scale BeforeAfter (BA) Studies ESU scale 

Did a single tributary 

habitat action increase local fish abundance or distribution, orimprove local environmental conditions, compared to a similar control or reference site?

Type, location, timing and intensity of habitat action, local fishabundance ordistribution, and/or habitat conditions 

Depends on management actions 

Project-scaleBefore-AfterStudies8

Stream, Watershed 

Did some classes of 

actions (e.g., riparianrestoration actions) perform better than other classes (e.g.,passage improvement actions) in improving localized conditions or sub-populationjuvenile survival rates?

Type, location, timing and intensity of habitat actions, and local habitat conditions and/orjuvenile fish survivals 

Depends on management actions 

Project-scaleBefore-AfterStudies 

Stream, Watershed 

7 Intensive BA, BACI, or Staircase designs; see Roni et al. 20058 Intensive BA, Extensive BA, or replicated BACI; see Roni et al. 2005
Tributary 

Habitat Uncertainty Research

What are the limiting factors or threats preventing the achievement of desired habitat, fish or wildlife performance objectives?

What is the 

relationship of habitat processes and functions of upslope, riparian, and aquatic systems to biological and environmental habitat attributes?

Watershed condition metrics identified above. 

Watershed condition dataidentified above.

Depends on correlation or experimental approach 

Stream, watershed, subbasin 

What is the 

relationship of habitat attributes, processes, and/or functions to fish and wildlifeabundance, productivity, and diversity?

Watershed condition and fish population metrics identified above. 

Watershed condition and fish population data identified above. 

Depends on correlation or experimental approach 

Stream, watershed, subbasin 

Hydro Status and Trend Monitoring

Are salmon andsteelhead meeting juvenile and adult hydro passage objectives?

Are smolts achieving survival standards prescribed in theNOAA BOs?

Smolt survival estimates through impounded reaches of the Snake and lower ColumbiaSystem survival estimates reflecting delayed effects oftransported smolts 

PIT tag detection histories throughthe FCRPS Tagging ample #of fish at hatcheries assurrogates for wild ones. Annual estimates of D 

Cormack-JollySeber single release model 

LGR to BON tailrace, when possible 

Are adults achieving survival standards prescribed in theNOAA BOs?

Survival indices of adult salmon and steelhead through the FCRPS. NOTE- AFEP funds some, but not all, dataelements required under this objective. Close coordination with AFEP required 

PIT detection histories at ladder-based detectors, for known source fish. Estimates of stray rates Estimates of

Accounting of fates for returning PIT tagged fish. 

BON to uppermost dam as applicable toan ESU 
harvest removals

of PIT tagged fishin the Mainstem.Estimates ofincidental harvestmortality, e.g.,net drop out rates, catch and release related mortality,etc.

Hydro Action EffectivenessResearch

NOTE- AFEP funds elements required under this objective. Close coordination with AFEP is required.

HydroUncertainty Research

What is the magnitudeof delayed effectsassociated withtransporting smolts?

Under what conditions does inriver passage yield higher SARs than transport?

Estimates of D for wild and hatchery fish

PIT tag detections juveniles andreturning adults SAR for transport and inrivergroups, i.e. TIRestimatesInriver survival estimatesDirect transport survival estimates

Empirical estimates& model derived estimates forpopulations of some inriver migrants 

Individual transport sites todesignated return site. 

Is transport appropriate for some locations and not others?

TIR estimates for wild and hatchery fish

Do smolts migrating through the FCRPS incur delayed effects?

What is the magnitudeof such effects?

SARs linked to differentsmolt passage fates or experiences 

PIT tag detections as juveniles to describe migratoryexperience PIT detections ofreturning adults 

Compare SAR among treatment groups 

Variable 

What are the causesand can they be rectified?

Localized smolt survival rates (Identify zones of particularly intense mortality that could depress SAR) 

Variety, e.g. PIT,acoustic tag orradio telemetrydata from smolts. 

Compare survival with reference areas. 

Geographicallylocalized, e.g.bird predationcentered atislands 
Estuary

Habitat Environ

mental 

Status and Trend Monitoring

Are aquatic, riparian,and upland ecosystems of the estuary (from Bonneville Dam to the mouth of the Col. R.) being degraded, restored or maintained relative to desired conditions or objectives?

Using a hierarchicalhabitat classification system based on existing hydrogeomorphology, to what quantitative extent are we avoiding further loss to existing shallow water wetland habitat and restoring degraded habitats, in particular for listed salmonids?

Characterization of Vegetation cover, Geology/ soils, Floodplain topography, Bathymetry

Habitat classification 

Census (mensurative) orspatially balancedsurvey

BON to mouth 

What is the amount of habitat in absolute acreage, by habitat type, that was restored annually and byproportion of the total lost historically for each habitat type for each reach of theCRE?

Measurements of Areaaffected 

Habitat classification Habitat condition 

Census (mensurative) or spatiallybalanced survey

BON to mouth 

What is the index of habitat connectivity byreach and itsstatus/trend?

Connectivity — Inventory of Passage barriers and Total edge, density and sinuosity of floodplain and tidal channels. 

Habitat connectivity

Census (mensurative) or spatiallybalanced survey

BON to mouth 

What are the status/trends in attributes of the CRE, plume, and ocean ecosystems?

What are estuary habitat physical properties?

Habitat —Characterization of Vegetation cover, Geology/ soils, Floodplain topography, Measurements ofBathymetry

Habitat condition and classification 

Statistical(mensurative) orSpatially balanced survey

BON to mouth 

What are estuary fishpopulation properties, especially withrespect-listedsalmonids?

Fish – Estimates of Species composition,Age/size-structure, Stock identity, Temporal distribution, Spatial distribution, Migration pathways, Growth rate, Residence time, Prey availability,Foraging success, Survival rate, Predation index 

Life historydiversity, spatial distribution,growth, survival 

Statistical(mensurative) or spatiallybalanced survey

BON to mouth 
What are estuary 

hydrograph and water quality properties?

Water — Measurementsof Hydrograph, Temperature, Salinity,Dissolved oxygen, pH, Turbidity, Nutrients, Toxics 

River discharge, water quality

Statistical(mensurative) or spatiallybalanced survey

BON to mouth 

What are invasivespecies properties?

Invasives — Invasive species list, Invasive spatial distribution, Invasive abundance 

Invasive species assessment 

Statistical(mensurative) or spatiallybalanced survey

BON to mouth 

What are the environmental conditions and salmon ecology in the Col. R.plume and oceanrelative to salmon production andsurvival?

Plume and Ocean — Estimates of Juvenile salmon usage, Growth, Survival, Zooplankton prey base, and Anchovy/herring index in the plume andMeasurements of Sea surface temperature, Northern oscillation index, Upwelling index,chlorophyll 

Ocean and plume conditions, Growth,residence time, survival,

Statistical(mensurative) or spatiallybalanced survey

Plume and N. Pacific Ocean 

EstuaryAction EffectivenessResearch

What actions are mosteffective at addressing the limiting factors preventing achievement of habitat, fish or wildlife performance objectives?

What is the cumulative effect of multiplehabitat restoration projects on the C

RE 

ecosystem?

See “

Connectivity”, 

“Habitat” and “

Fish” 

above 

Habitat cond’s,habitat connectivity, fauna, life historydiversity, spatial dist., growth, survival, predation, waterquality physical cond., 

Effectiveness (mensurative) orLarge-scale BeforeAfter (BA) Studies 

BON to mouth 

What are the effects ofhydrologic reconnection projects (e.g., dike breaches, new tide gates and culverts) andrevegetation projects?

See “

Connectivity”, 

“Habitat”, “

Fish” and

“Invasives” above 

Habitat connectivity, life history diversity,spatial dist.,growth, survival, invasive species

Effectiveness (mensurative) orProject-scaleBefore-AfterStudies 

BON to mouth 

What possible changes to FCRPS operations might improve habitat conditions in the CRE for Columbia basin salmonids?

Ibid. Ibid. Effectiveness 

(mensurative) orLarge-scale BeforeAfter (BA) Studies 

BON to plume 

Estuary

What are the limiting 

What is the ecological See “Connectivity”, Habitat cond’s, Effectiveness BON to plume 
Uncertainties

Research

factors or threats in theestuary preventing theachievement of desired habitat, fish or wildlife performance objectivesin the Col. Basin?

importance of the Columbia River estuary and oceanic plume to the viability and recovery of salmonid populations in the ColumbiaBasin?

“Habitat”, “Fish”, “Invasives” and “Plume and Ocean” above 

habitat connectivity, fauna, life historydiversity, spatial dist., growth, survival, predation, waterquality physical cond., river discharge, plume conditions 

(mensurative) orLarge-scale BeforeAfter (BA) Studies 

What are the effects oftoxics on salmonids?

See “Fish” above, plus estimates ofconcentrations and distributions of Toxics 

Water quality, life historydiversity, spatial distribution,growth 

Depends on correlation or experimental approach 

BON to mouth 

What are the causal mechanisms affectingsurvival of juvenilesalmon during their first months in the ocean?

See “Fish” and “Plumeand Ocean” above 

life historydiversity, spatial dist., growth, survival, predation plume conditions

Depends on correlation or experimental approach 

BON to plume 

What is the survival rate by species ofjuvenile salmonids migrating downstream from Bonneville Dam to the mouth of the Columbia River?

Estimates of smolt survival rates, predation indices 

Survival Cormack-JollySeber single release 

model 

BON to mouth 

HatcheryStatus and Trend Monitoring

What is the relative proportion of hatcheryspawning salmon and steelhead compared towild fish populations?

Ratio of hatchery fish to total fish abundance 

Numbers of hatchery-originand natural-origin fish on spawninggrounds 

Develop requisite marking guidelines and proceed with the marking of remaining groups of unmarked fish released from hatcheries to facilitatemonitoring of hatchery-origin fish in natural spawning areas

Census or spatiallybalanced survey

HatcheryAction Effectiveness

Can hatchery reforms reduce the deleterious effects of artificial 

Returns/spawner,lambda, temporal trends, or other metrics as 

Numbers of adults, spawners, or redds, or other 

Studies of modifiied hatchery

As required byexperimental design 
Research production on listed 

populations, therebycontributing to a reduction in extinctionrisk for affectednatural populations?

determined byexperimental design 

data as determined byexperimental design 

practices(“reforms”) that involve controlled experiments designed and replicated sufficiently to provide statisticallyand biologicallymeaningful results pertinent to multiple programs. 

Can properly designed intervention programsusing artificial production make a net positive contribution torecovery of listed populations?

Returns/spawner,lambda, temporal trends 

Numbers of adults, spawners, or redds 

Treatment and control studies using existing safety-net programs intended to reduce extinction risk oftargeted populations. 

Selectedpopulations 

HatcheryUncertaintiesResearch

What is the reproductive success of hatchery fish spawning in the wild relative tothe reproductive success of wild fish?

Number of offsping 

produced by hatchery xhatchery, hatchery x wild, and wild x wild matings in natural spawning areas and subsequent adult returns from each type of cross

DNA pedigree analysis

Hatchery/wildreproductive success studies

Selectedpopulations 

Harvest Statusand Trend Monitoring

What are the boundaries ofuncertainty around harvest point estimates?

What are the harvest rates on listed wild fish?

Numbers of adult fish harvested and numbersof adult fish escaping 

Dam Counts; harvest estimates; PIT tag detections at dams

Census at Dams; sub-sample in fisheries 

Columbia BasinESU 

Harvest Action EffectivenessResearch

Are new selective gear types effective atharvesting?

Catch Per Unit of Effort; Catch related to capitaland operating expense 

Standardized measures of catch and effort 

Columbia BasinESU 

Harvest Action EffectivenessResearch

What is the postrelease survival of salmon caught in a mark-selective fishery compared to fish thatwere not harvested?

 Survival rates Tagging for fish 

that are caught compared tothose not caught 

Treatment/control Columbia Basin

ESU 

Predator Status and 

What is the impact ofpredators on juvenile 
Trend 

Monitoring

salmonids within theColumbia River Basin?

What are the nesting distribution, colonysize, and colonyproductivity for the major avian predatorswithin the Columbia River Basin?

Presence/absence of avian predator colonies,colony size, number ofnesting pairs, reproductive chronology,reproductive success rates 

Colony location,colony size, number of nesting pairs, timing ofreproductive events,reproductive success 

Census; statistical sample

Columbia Basinor colony

What are the juvenilesalmonid consumption rates of major avian predators within the Columbia River Basin?

Diet composition, consumption rates 

On-colony PIT tag depositionrates and detectionefficiency, dietsamples, bill load observation 

Statistical sampling of targeted populations 

Columbia Basinor colony

What are the consumption rates of major pisciverous predators in theColumbia River Basin?

Abundance, distribution,diet composition,fecundity consumption rates 

Abundance, distribution, diet composition, consumption rates 

Statistical sampling of targeted populations 

Columbia Basin 

What is the impact ofpredators on adult salmonids within theColumbia River Basin?

What are the consumption rates of mammalian predators (marine) in the Columbia River Basin?

Abundance, distribution,consumption rates, diet composition 

Abundance, distribution,consumption rates, diet composition 

Census or statistical sampling 

Columbia Basin(BON to estuary) 

Predator Action EffectivenessResearch

What are the mosteffective management alternatives/actionsthat could be used to reduce the impact ofpredators?

What is the effect of alternativemanagement alternatives/actionsused to reduce the impact of avian

% Change in Juvenile Salmonid Survival, % Change in AvianPredation Rate

Colony location,colony size, number of nesting pairs, timing ofreproductive events,

Large-scale BeforeAfter (BA) Studies9 Columbia River

alternate habitatlocation, or colony

9 Intensive BA, BACI, or Staircase designs; see Roni et al. 2005
predators? reproductive

success, Oncolony PIT tag deposition rates and detectionefficiency, dietsamples, bill load observation 

What is the effect of management alternatives/actionsused to reduce the impact of pisciverous predators?

% Change in Juvenile Salmonid Survival, % Change in pisciverous Predation Rate

Abundance, distribution, diet composition, fecundityconsumption rates 

Large-scale BeforeAfter (BA) Studies Systemwide Columbia Basin 

Predator Uncertainty ResearchWildlife Status and Trend MonitoringWildlifeAction EffectivenessResearch

What are the speciesresponse to the various protection/restorationefforts?

How has the mitigationtarget species responded to fee title versus conservation easements?

Target species abundance for pre/post protection measure 

Numbers of adults by targetspecies

Large-scale BeforeAfter (BA) Studies10or 

Project-scaleBefore-AfterStudies11

Columbia basin 

How has the mitigationtarget species responded to various habitat enhancement efforts?

Target species abundance for pre/post enhancement measure 

Numbers of adults by targetspecies

Large-scale BeforeAfter (BA) Studies or Project-scaleBefore-AfterStudies 

Columbia basin 

WildlifeAction EffectivenessResearch10 Intensive BA, BACI, or Staircase designs; see Roni et al. 200511 Intensive BA, Extensive BA, or replicated BACI; see Roni et al. 2005
Appendix C. Developing New Institutional Arrangements 

Historically, science has played two different roles in salmon management. The first, a 

technical leadership role, has involved establishing the fundamental relationship between 

salmon and their environment that collectively forms the basis for management decisions. 

The second, a “sustaining,” has involved selectively seeking data and analyses to support 

regulatory actions or policy decisions by agencies, tribes, or other organizations. Ideally, 

science focuses on the more objective first role, but in fact, salmon management has been 

dominated by the second. 

— Committee on the Environment and Natural Resources, 2000 

The “sustaining” role of science dominates restoration and recovery efforts in the 

Columbia River Basin today. This does not impugn the quality of the science, but it does help 

explain why some work of apparently low relevance continues while results of higher relevance 

from other work are not applied. It also helps explain disparities in the availability of data to 

support various management alternatives, particularly alternatives that are politically 

controversial. In selecting new research projects agencies understandably tend to avoid those that 

seem to offer limited support for, or might contradict, current management practices. Thus, the 

scientific basis for management decisions is skewed by the almost indefinite institutional funding 

of non-controversial research. This results in repetitive research that generates data of 

diminishing value. 

The National Research Council (NRC) stated that current institutional arrangements in 

the Pacific Northwest have contributed to the salmon problem and probably will need

modification if an understanding of how to include “good science” as part of the institutional 

arrangement is important (National Research Council 1996). The NRC recommended that the 

adoption of a coordinated, interagency approach to new scientific efforts could help reduce the 

tendency to fund research in areas of past agency investment. 

Further, the NRC found that cooperative management implies an institutional change or 

shift in the structure of decision-making that acknowledges the role of various interests, such as 

consumers, representatives of different industries, and environmentalists in the areas of policy, 

planning, implementation, and evaluation. Although the Northwest Power Act process falls short 

of the ideal of “power-sharing in the exercise of resource management” (Pinkerton, 1992), it 

does merge the inherent conflicts of fish and wildlife mitigation and hydropower production in a 

way that forces conflicts into the open and fosters joint action.

A great deal is known about the requirements of salmon, yet much remains unknown, and 

some gaps in knowledge are crucial to a long-term, stable solution to the salmon 

problem. Enough is known in the short term to improve the prospects of salmon if 

knowledge is applied wisely and quickly, but not enough information is known to warrant 

confidence in a long-term regional plan for salmon....the components of the salmon 

problem are so diverse that no one person can know all that needs to be known for a 

comprehensive solution. Thus, the salmon problem is in a sense a cognitive problem 

whose solution will depend on close cooperation and collaboration of people with many 

kinds of experience and expertise. (Emphasis added.) 

41
— National Research Council, 1996 

Regional Research Partnership: A Forum for Collaboration 

The Columbia River Basin research plan could provide a starting point for the 

development of a regional research agenda by providing a rough framework on which discussion 

of coordination among potential partners could focus. While the research plan does not constitute 

a complete research agenda for the region, it does provide a framework for developing one 

through the identification of potential partners, programs, and funding sources for working on 

research questions in which all have interests. The disagreement that exists over priorities for 

research stems from the various different, yet sometimes overlapping, management authorities 

within the Columbia River Basin and the broad geographic scope of the region. The research 

plan can help diminish this disagreement by: 

• Fostering agreement on a manageable number of well-chosen priorities 

• Stating the priorities in ways that promote effective research solutions

• Providing a means for resolving disagreements on priorities 

• Taking advantage of unforeseen research opportunities that arise from advancements in 

technology and scientific knowledge or are simply facilitated by immediate 

environmental or social opportunities

• Fostering collaborative research with other entities

The 2000 Fish and Wildlife Program states that a meeting of fish and wildlife agencies, 

tribes and hydrosystem operating agencies should be convened regularly to identify key 

uncertainties about the operation of the hydrosystem and associated mainstem mitigation 

activities. Executives of the agencies and tribes have tried in the past to coordinate decisionmaking on various aspects of resource management across the Columbia River Basin. Yet no 

similar effort has been mandated to coordinate the research agendas of the various management 

entities. Therefore, this research plan proposes the convocation of a Regional Research 

Partnership as a vehicle for meeting the directives set forth above and making a major step 

toward implementing the recommendation of the NRC. 

Implementing Regional Research Priorities 

The role of the Regional Research Partnership would be to update and prioritize currently 

identified research needs and facilitate coordination of the research efforts of the various state, 

federal, and tribal agencies to ensure that limited funds are allocated for the most important 

critical uncertainties. The Council is strongly positioned to convene the Regional Research 

Partnership as the framework established by the Northwest Power Act has been characterized as 

the largest attempt to cooperatively manage power and fish and wildlife (Lee et al. 1980). A 

Regional Research Partnership could help the region move beyond the institutional impediments 

to coordinating research and providing a forum where researchers could transcend disciplinary 

and institutional boundaries, cross-pollinate ideas, and find peer support for potentially 

controversial recommendations. The partnership could foster integration of the currently 

compartmentalized research agendas and budgets of entities that share common objectives. The 

fish and wildlife scientists and managers in the region could accomplish this by cooperatively 

42
developing the forum and a process for identifying research priorities that address shared critical 

uncertainties. 

A major challenge for the research partnership would be to develop a programmatic 

approach for managing research within the region and, as a result, move beyond the piecemeal 

solutions that have undercut the success of past restoration efforts. For example, the partnership 

could develop a comprehensive effort to reduce sources of mortality across the life cycle of the 

salmon. 

The research partnership could be an appropriate forum for organizing the type of 

multiparty experiments that often have been proposed in ISAB and ISRP reports, or by the 

Council itself, such as studies of the flow/survival relationship for juvenile salmonids. 

Uncertainties related to supplementation, tributary restoration actions, mainstem passage and 

survival, and other issues have been discussed in many ISAB and ISRP reports. These reports 

provide suggestions as to how these uncertainties might be addressed. In most cases, it is 

suggested that answers can best be obtained by coordinated experiments such as the loadfollowing experiment suggested by the ISAB. In sum, the research partnership could provide a 

venue to support coordinated experiments by identifying ways to share resources, experience, 

and expertise; fostering teamwork; and leveraging investments from multiple sources. 

Identifying Regional Research Priorities 

There always will be more research questions to answer than there are resources to 

provide answers. Therefore, research should be focused first on those questions that have the 

greatest relevance to the region. For example, does a critical management uncertainty apply to 

single or multiple subbasins, a single population or multiple populations? 

Scientists who work with “systems theory” often warn that trying to optimize one 

component of a complex system like the Columbia River Basin, such as the mainstem, may not 

necessarily increase the system’s overall performance. Furthermore, the current emphasis on 

mainstem research may not provide the certainty that is sought in relation to the recovery of 

ESA-listed salmonids. In order to achieve an ecological approach it will be important to maintain 

a diversity of research activities across the basin that supports anadromous fish, resident fish, and 

wildlife. The critical uncertainties set forth in the research plan should guide the selection of 

projects so that the funded projects move the program forward in a defined and consistent way 

that provides synergy across the projects. 

The federal, state, and tribal members of the research partnership should work together to 

identify shared critical uncertainties. The diverse membership of the research partnership should 

provide an opportunity for open debate among peers and a sense of equity in the outcomes. An 

initial task will be to develop a set of decision criteria to guide the identification of research 

priorities. It is anticipated that these decision criteria will be drawn from the prior experience 

with the internal prioritization processes of the respective members. Four key questions need to 

be addressed by the research partnership: 

• Who should decide the priority of the research agenda? 

43
• How should collaborative experiments be designed and implemented (e.g., cost sharing 

and other means)? 

• Why and how should data be collected, stored, and analyzed? 

• Who should be responsible for synthesis and dissemination of the results and for 

identifying management implications?

The research partnership should meet as necessary to identify priorities and develop 

funding estimates that the members can use to inform their respective budget requests. 

Facilitating Programmatic Coordination 

Currently, a myriad of entities such as universities, private consultants, tribes, state and 

federal agencies conduct research within the region, yet the lack of a forum for coordination 

often results in poor communication between project sponsors. This increases the risks of: 

duplication of effort and inefficient use of funds; conflict among research project objectives; 

damage to long-term monitoring sites; and increased intrusive sampling of ESA-listed and 

sensitive native species. The research partnership could facilitate communication between all 

researchers working within a specific watershed so that they are aware of and coordinate with 

each other’s plans and projects in advance. The research partnership also could facilitate 

communication between individuals conducting similar research in different locales. It could also 

help identify research projects that complement one another, such as multiple treatments of the 

same question in different locations to increase sample size. Additionally, multiple studies of

different issues within a single watershed could share monitoring to provide a more holistic view 

of the outcomes. Restoration activities could be coordinated so as not to interfere with ongoing 

research. Finally, the research partnership could coordinate the compilation of technical 

information on the best tools for research and monitoring and its dissemination to the region. 

Collaborative Funding 

In 2000, the Council shifted from an annual project funding cycle to a three-year cycle. 

Because state and federal agencies remain on an annual funding cycle, it is difficult for them to 

make long-term funding agreements. Consequently, formal arrangements such as memoranda of 

agreement (MOAs) may be necessary to secure long-term funding commitments for selected 

large-scale field experiments. Bonneville and the U.S. Forest Service have such an agreement, 

for example. In regard to the program, it is important to acknowledge the difficulty inherent in 

reprogramming existing funds to support additional research initiatives within the available 

direct-program budget. 

Yet the important question is not how much investment in additional research the 

program might afford, but rather how to develop a comprehensive regional research agenda that 

can be funded from multiple sources, sustained, and managed mutually. A more systematic and 

strategic approach to leveraging investment by many parties is warranted. The research plan 

44
identifies critical uncertainties that need to be addressed by multi-agency initiatives, cooperative 

funding agreements, and shared responsibility for implementation. 

New large-scale field experiments should be conducted collaboratively via shared 

funding arrangements with other entities. It might be argued that there are already de-facto largescale field experiments underway, but they were not designed to resolve specific uncertainties or 

establish cause-and-effect relationships. It may be possible to link project-scale efforts in order to 

achieve large-scale field experiments, such as by sharing controls for hatchery and habitat 

projects. However, the current funding structure does not facilitate development of controls; for 

example, much of the research on hatchery effectiveness has been done without paired study of 

natural production. Similarly, much of the research on habitat treatments has been conducted 

without paired control sites. For these reasons current research activity that resembles large-scale 

field experiments does so by default, not by design. 

Some identified research and monitoring needs are currently, or should be more 

appropriately, the requirement or shared responsibility of federal or state agencies other than 

Bonneville under mandates other than the Northwest Power Act. This point is particularly 

relevant to ESA recovery planning and implementation research needs that are proposed for the 

Columbia River Basin but have application coast-wide. Discrete elements of the identified 

research and monitoring present differing degrees of opportunities for regional coordination and 

shared funding. To succeed it is incumbent upon the research partnership to develop and 

implement incentive strategies. Incentives may include funding, regulatory flexibility, or 

recognition, all of which can work in combination. Thus, there is a need to work cooperatively 

with entities that represent alternative funding sources, such as the Trust for Public Land, and 

others, and have responsibilities that overlap those of the Council. The regional entities should 

recognize that all programs are limited by what they can afford to sustain but that by working 

together all could benefit from focused, coordinated expenditures. 

45
Appendix D. Monitoring and Evaluation

In the 2000 Fish and Wildlife Program Basinwide Provision D.9 states: 

“The Council will initiate a process involving all interested parties in the region to 

establish guidelines appropriate for the collection and reporting of data in the Columbia 

River Basin.” 

Consequently an important objective of the research plan is to encourage development of 

an effective and economical approach to long-term monitoring that provides a basis for future 

programmatic-scale evaluations. Some components of a regional monitoring program, such as 

counts of returning anadromous adult fish at dams, estimates of the number of out-migrating 

juvenile fish, harvest estimates, hatchery production, and so on, already have been developed in 

the Columbia Basin. Yet the program needs to facilitate the development of additional 

components that are important, including long-term PIT-tagging of important populations of 

anadromous fish, coordinated estimates of spawners or escapement into tributaries by 

standardized sampling and estimation methods, and standardized habitat and water quality 

sampling and estimation methods. 

In order to effectively implement subbasin, recovery, and conservation plans, it is 

necessary to follow a logical process and paradigm of Assess, Design, Implement, Monitor, 

Evaluate and Adaptively Adjust plans and their implementation processes (Figure 1.). 

Assess

Adjust

Evaluate

Design

Implement

Monitor

Figure 1. A framework for adaptive management (Nyberg, 1999). 

The axiom that “all plans fail at implementation” can be avoided by following the steps 

toward adaptive management set forth in Figure 1. 

• Assessing limiting factors and critical uncertainties 

• Designing projects, programs and monitoring to maximize both on-the-ground 

effectiveness and learning

• Coordinated and documented implementation of projects 

• Consistent monitoring through standardized methods, protocols, and training 

• Timely and thorough evaluation of effectiveness 

46
• Overall guidance to the region to adjust plans and programs at the province and subbasin 

levels 

Monitoring and evaluation are at the heart of adaptive management because they provide 

the information, data, and analysis that decision-makers and resource managers need to track the 

progress, or lack of progress, of plans and populations. The success of current plans and 

programs depends on the consistent application of well-designed research, monitoring, and 

evaluation at multiple scales. These scales range across tributaries with major projects, 

populations, major population groups, subbasins, ESUs or Distinct Population Segments, and the 

entire Columbia Basin. To be useful to decision-makers, a regional approach to monitoring must 

identify the information required for different types of decisions at each scale, such as 

management of harvests, the hydrosystem, and hatcheries; and decisions on the protection and 

restoration of habitat).

Evaluating the occurrence and magnitude of trends over time requires a commitment to 

long-term monitoring (multiple years), and consistent data collection through networks of sites 

that represent the target population(s) of interest. Substantial research has been conducted on 

trend detection — discussion of form of trend, best tools to detect trend — (see Esterby 1993). 

Yet there has been little discussion in the ecological literature of what constitutes a ‘‘policyrelevant’’ trend and how well we can measure or detect it (Urquhart, Paulsen and Larsen 1998). 

Current Monitoring Activity 

Monitoring under the program primarily has been conducted to evaluate work across all 

subject areas, but at the project scale. This approach has generated information from monitoring 

individual or opportunistic protection and restoration efforts and the effects of isolated or tactical 

actions and activities. To advance, the limited resources available for monitoring must be 

focused on a more programmatic approach that is designed to identify the need for and detect the 

sum total effect of actions at the population, subbasin, and/or province scale. This can support 

future analyses of more strategic actions and plans and allow decisions to be made at a higher 

scale that is population- and ecosystem-based. Finally, performance metrics and high-level 

indicators can support a programmatic approach to evaluation that can be reported to Congress, 

the Council and to state, federal, and tribal resource managers (see Figure 2.) 

While work at the project scale has intrinsic value and should be continued in many 

cases, it cannot substitute for the lack of a monitoring program of sufficient scope to provide a 

basis upon which the program as a whole can be evaluated and re-directed. Monitoring is 

required at a number of different scales to assess the performance of the program relative to 

biological and programmatic objectives, to identify where and why there are performance 

problems, and to identify the most effective actions needed to correct problems so that program

objectives can be achieved. This type of monitoring and evaluation across multiple geographic 

and temporal scales requires standardized approaches and programmatic, long-term

commitments and interconnections for effectively combining information and answering 

program management questions. The absence of a regionally coordinated approach to monitoring 

and evaluation in the Columbia River Basin has constrained restoration and planning efforts for 

decades. 

47
For this reason, it is important that a more hierarchical approach be utilized with 

increased emphasis on achieving useful outcomes from monitoring. Specifically, methods need 

to be developed and implemented so that monitoring results can be “rolled up” to provide 

scientifically defensible evaluations of whether the ecological condition of a subbasin, an ESU, 

or the Columbia River Basin as a whole is improving or declining over time. 

This capability would be very useful to policy and decision-makers as they deliberate on 

future actions that affect the long-term, ecological health of the basin. 

A

B Annual reports,

planning documents

C

D

E

High-level indicators for press

releases, presentations, publications

Graphics, maps,

indicators

Statistical summaries

and graphs

Watershed and

project raw data

and data sets

OMB, Congress, Legislature,

Governor, public

Researchers, managers,

public

Technical staff,

public

Modelers,

researchers

Scientists

Figure 2. In the monitoring information pyramid, examples of types of information are on the left 

and related users or generators of that information are represented on the right.

Moving monitoring from the project scale to larger spatial scales has both benefits and 

challenges. One benefit of focusing on the population scale is that it has direct relevance to fish 

managers, who want to know whether actions upstream of the monitoring location actually 

improved a fish population’s production in addition to improving habitat conditions in the 

restored reaches. For example, did actions lead to an increase in the number of smolts per 

spawner? The population scale is also of great interest to agencies like NOAA Fisheries, which 

is charged with evaluating the status of listed populations. 

There are also some significant challenges at larger spatial scales. Reliably attributing 

observed changes in fish survival or production to particular sets of management actions requires 

careful monitoring design. Otherwise one might erroneously infer that observed changes were 

48
due to management actions when in fact they were the result of natural variation in freshwater 

climate or ocean conditions. Ideally, one would monitor both ‘treated’ areas (those with habitat 

restoration actions) and nearby ‘reference’ areas (those without restoration actions) for several 

generations of fish populations both before and after implementation of actions while 

simultaneously measuring other explanatory variables. One significant challenge in shifting 

monitoring to larger spatial scales — populations, subbasins, and provinces — is that at larger 

scales it becomes increasingly difficult to establish the strong contrasts required to evaluate 

effectiveness. That is, it is increasingly difficult to compare and contrast specific areas and times 

with and without certain classes of restoration actions. For example, adjacent subbasins could 

have a variety of implemented restoration actions. Comparing fish production among these 

subbasins over time would not lead to any clear inferences about which actions (if any) were 

responsible for the observed differences in trends. Therefore, it still would be necessary to 

conduct effectiveness evaluations at finer spatial scales (project to population) for a carefully 

selected subset of restoration actions and locations in order to generate information of value to 

the program. 

Provincial-scale Objectives and the Need for High-Level Indicators 

It will be important for the provincial-scale objectives required by the program to 

encompass a set of core objectives common to the four states while respecting additional 

reporting needs of each state. The process of developing, negotiating, and gaining regional 

acceptance of province-level objectives will be highly analogous to the ongoing efforts of 

Washington and Oregon. These efforts have been driven either by statutory requirements or by 

pressure from Congress and legislatures for accountability. Once established, province-scale 

objectives will provide focus for efforts to develop a regional approach to monitoring that can 

support evaluation of the overall effectiveness of the program. Figure 2. above shows the 

relationship between types of information and how each supports decision-making. For example, 

the status of high-level indicators compels the activities at the bottom of the pyramid — on-theground methods, protocols, and logistical implementation requirements. High-level indicators 

also can help direct decisions and recommendations about the analytical processes and statistical 

designs in the middle of the pyramid. 

In order to implement adaptive management, resource management agencies need highlevel indicators that are easy to understand in terms of every-day definitions and experiences and 

yet flow explicitly from on-the-ground monitoring programs providing information on progress 

toward biological objectives. A subcommittee of PNAMP currently is working to develop a pool 

of high-level indicators that can be used as the basis for developing province-scale objectives 

that the agencies and tribes of the Pacific Northwest can endorse and implement. Through the 

coordinated use of high-level indicators, a uniform message about watershed health can be 

developed with all participating agencies using the same terms and coming to similar 

conclusions. 

49
Components of a Regional Framework For Research, Monitoring and Evaluation 

Through this research plan, the program will contribute to the design and implementation 

of a coordinated and integrated regional approach to monitoring. Existing regional programs (see 

Figure 3) are being networked based on a monitoring framework comprising: 

• Common management questions and information needs supporting the management 

questions 

• Common research, monitoring, and evaluation categories, monitoring designs and 

protocols that allow the communication and networking of regional programs

• Common understanding of responsibilities and cost sharing of the monitoring needs 

The management questions and project category components of this framework are well 

developed through ongoing regional coordination efforts as set forth in Table 1. It is clear that 

many of the objectives and management questions of the fish and wildlife program overlap with 

those of other regional entities and local, state, federal, and tribal governments. The costs of the 

monitoring and research needed to adequately address these common management questions are 

more than one program can adequately support or fund. Only through the combined efforts of 

multiple entities can a sufficient level of information be developed to guide these regionally 

shared resource management decisions through coordinated, standardized, and programmatic 

approaches to monitoring. 

The components of the research plan that provide support for the development of a 

regional monitoring framework are its long-term vision and its organization around biological 

concepts and management questions. Several other large-scale planning documents support this 

approach by identifying similar objectives and priorities. Source documents that have contributed 

to the conceptual foundation of the regional approach include: 

• Monitoring Section of ISRP’s Retrospective Report (NPCC 2005) 

• Research Plan for the Columbia River Basin (NPCC 2006)

• Strategy for Coordinating Monitoring of Aquatic Environments in the Pacific Northwest 

(PNAMP 2005)

• Considerations for Monitoring in Subbasin Plans 2004 (PNAMP 2004) 

• Conservation of Columbia Basin Fish; Final Basinwide Salmon Recovery Strategy 

(Federal Caucus 2000) 

• Research, Monitoring, and Evaluation (RME) Plan for the NOAA Fisheries 2000 Federal 

Columbia River Power System (FCRPS) Biological Opinion (Action Agencies and 

NOAA 2003) 

• ISAB and ISRP Review of the Action Agencies and NOAA Fisheries’ Draft Research, 

Monitoring & Evaluation Plan for the NOAA-Fisheries 2000 Federal Columbia River 

Power System Biological Opinion (RME Plan) (ISAB and ISRP, 2004-1) 

• Updated Proposed Action for the FCRPS Biological Opinion Remand (Action Agencies 

2004) 

• Proposed Design and Evaluation of Preliminary Design Templates (CSMEP 2004) 

50
• Data Quality Objectives for Decisions Relating to Status and Trend of Fish Populations, 

as well as Action Effectiveness of Habitat, Hatchery, Harvest and Hydrosystem Actions 

(CSMEP 2005) 

• Scope of Work for Implementation of the Northwest Environmental Data Network 

Project (Northwest Environmental Data Network 2005).

Figure 3. Regional Partnership of Monitoring Efforts.

PNAMP 

Pacific NW 

Aquatic Monitoring 

Partnership

Federal Caucus 

RME Program 

Washington Salmon Recovery

Fund Monitoring Program 

Oregon Water Enhancement 

Board Monitoring Program 

NPCC and BPA 

Columbia Basin

F&W Program NOAA Pacific Coast Salmon 

Recovery Fund Program 

EPA National and State 

Level Monitoring Programs

USFS and BLM 

Monitoring Programs 

CSMEP Collaborative 

Systemwide Monitoring

and Evaluation Project 

California NW Forest Plan

Monitoring Program 

Tribal Monitoring

Programs 

BOR Habitat 

Monitoring Program

UC, JD, Salmon River, and

Columbia Estuary Pilot

Projects Intensively 

Monitored Watersheds 

Lower Columbia River

Estuary Program

Watershed Condition and 

Fish Monitoring Protocols 

Test Projects 

USFWS Bull Trout 

RME Program 

51
Appendix E. Data Management 

A regional approach to monitoring cannot be achieved without the support of a data 

management system that can serve as a repository for the data and provide public access on a 

timely basis for analytical manipulation. To be successful a data management system must be 

able to assist scientists in the identification and development of data standards as they relate to 

the monitoring of wildlife, resident, and anadromous fish and their habitats. This objective helps 

to identify solutions that improve access, sharing, and coordination among different collectors 

and users of this monitoring data. It also provides a data reporting foundation that could support 

coordinated agency reporting, uniform monitoring protocols, and improved data quality and 

quantity. Objectives include: 

• Develop a consistent data management methodology within and across each of the types 

of monitoring 

• Establish a close working relationship for data consistency across the data sources 

• Identify and document the specific data needs of the region for watershed condition 

monitoring, fish population monitoring, and effectiveness monitoring 

• Develop and recommend data collection standards and information to be shared across 

the various monitoring programs 

• Share requirements and results with regional data networking entities to ensure sharing of 

monitoring data 

• Test the collection protocols, sampling methods, and data-sharing mechanisms

• Implement coordinated solutions within regional programs 

• Incorporate common analytical capabilities and reporting capacity

• Provide public access sections or linked Web sites for informational and collaborative 

processes

There are many different interests and initiatives concerned with improving data 

collection or management in the Columbia Basin and the Pacific Northwest. These efforts 

involve many different constituencies, mandates, and obligations. At present there is no common 

regional data management network that links these interests and initiatives. To address this 

situation the Council initiated a process to identify data needs in the basin by surveying available 

data and filling any data gaps. The Council, NOAA Fisheries, and other regional entities 

supporting this effort consider it imperative to develop a regional data network. This network 

would utilize existing data bases, facilitate data management and sharing, help subbasin 

planners, and underpin salmonid recovery efforts under the FCRPS Biological Opinion. This 

initiative is being led by the Northwest Environmental Data Network (NED). 

A memorandum of agreement between the Council and NOAA Fisheries guides this 

initiative, which currently is developing an administrative arrangement, a cost sharing 

agreement, and a draft memorandum of understanding for potential partners in regional 

information system development. This initiative has been supported within the region by the 

ISRP (Council Document ISRP 2000-3), from independent analysis by Science Applications 

International Corporation (SAIC 2003), and in comments received from the public. The data 

management strategy also is intended to increase the public accountability of this program by 

making the results accessible not only to specialists but also to the public. The Council is 

52
collaborating on a process for establishing an Internet-based system for the efficient 

dissemination of data for the Columbia Basin. This system will be based on a network of data 

sites, such as StreamNet, Northwest Habitat Institute, Fish Passage Center, Columbia River Data 

Access in Real Time (DART), and others, linked by Internet technology. 

The methods and protocols used in data collection must be consistent with guidelines 

approved by the Council and adopted by the region. It is important to note that while the ISRP 

checks these criteria, it is Bonneville that enforces the guidelines. Guidelines appropriate for the 

collection and reporting of data at the project scale include: 

• The project must have measurable, quantitative biological objectives 

• The project must either collect or identify data that are appropriate for measuring the 

biological outcomes identified in the objectives 

• Projects that collect their own data for evaluation must make this data and accompanying 

metadata available to the region in electronic form

• Data and reports developed with Bonneville funds should be considered to be in the 

public domain 

• Data and metadata must be submitted within six months of their collection 

It is important that all projects reach completion in a timely manner. At the present time 

many researchers do not end their projects at the completion of the performance period but add 

new objectives that extend the performance period. This gives rise to projects with multiple and

sometimes unrelated objectives that more closely resemble small programs than discrete projects. 

(“Infrastructure” projects may warrant an exception to the requirement for an end date.)

In order to satisfy their contractual obligation, sponsors should be required to submit to 

Bonneville a final report at the conclusion of every research project. Specific ending dates should 

be required for project objectives and tasks to help sponsors meet their intended deadlines. 

Bonneville should enforce its contracts to withhold payment for projects that have not completed 

the reporting requirement. The final report should be in a form that facilitates review of the 

results.

53
Appendix F. Integrating Research Results into Council Policy and Decision-making 

Research results must be reviewed and evaluated in order to direct new research and 

inform ongoing work to protect and restore fish and wildlife. The effectiveness of new actions 

and the results of research into those actions must be evaluated objectively before the results are 

widely applied in order to avoid misinterpretation. For example, for a time logjams were 

considered impediments to salmon passage and were removed from streams. This is what 

research appeared to support. But further objective evaluation revealed that logjams have value 

in moderating stream flows, reducing sediment transport, and creating pools where smolts rest 

and rear. So rather than remove logjams, fisheries scientists began placing logs and logjams in 

streams. 

The review of research results must be conducted across projects and subject areas to 

determine the contribution of particular results to overall improvements in management. Some

tools and metrics for evaluating research contributions across the “H” topic areas — hydropower, 

harvest, hatcheries, and habitat — and across all life stages of a species were developed and used 

during subbasin planning. Others currently are being developed under the auspices of PNAMP 

and through various ESA-related processes. Additional tools and metrics may need to be 

developed.

Annual workshops sponsored by the Regional Research Partnership could provide a 

forum for evaluating and disseminating the results of research. The results of individual research 

projects can provide a basis for larger-scale reviews of the effectiveness of the research program

and discussion of additional complementary approaches, including: 

• Broader-scale analysis that applies information from several projects to address a 

particular question 

• Synthesis reports of work completed in a particular area, such as the Giorgi report, 

“Mainstem Passage Strategies in the Columbia River System: Transportation, Spill, and 

Flow Augmentation” (Council Document 2002-3) 

• Expanded provincial review presentations 

• Workshops structured around single topics driven by specific questions, such as 

transportation effects, and projects synthesized to address that topic 

• Workshops and symposia on emerging topics, such as toxics 

These workshops could help assess future research priorities through oral presentations, 

reporting of results of relevant studies, and the development of scenarios for applying research 

results in support of management actions. The workshops could promote the exchange of 

scientific results and provide the Council with information to better inform future funding 

decisions. 

54
Dissemination of Research Results 

The Council will work with the other members of the Regional Research Partnership to

develop a strategy for the transfer of research results to other researchers and interested parties. 

The public nature of Bonneville funding implies that research results are the property of the 

general public. Bonneville should post all final research reports on its Web site to facilitate 

access. Research reports and data should be made available to scientific collaborators, 

administrators, and the public for additional analyses. The final reports, and any other products 

derived from them, should be submitted to the StreamNet Library. This library includes materials 

relating to the natural resources of the Pacific Northwest and maintains a regional depository of 

all research projects funded under the fish and wildlife program. The StreamNet Library provides 

regional services that include reference, referral, data base searching, inter-library lending, and 

document delivery. 

The ISRP has recommended that all project proposals reference past achievements and 

that annual and final reports be issued on time and made available to the region. The ISRP also 

recommended that “...CBFWA ... include in its Annual Implementation Plan a report of past 

accomplishments at the watershed and subregional/subbasin levels or topical level....” Further, 

the ISRP has supported publication of evaluations of work conducted under the fish and wildlife 

program in a “Columbia River Basin Journal,” as a way to disseminate results and provide a 

forum for advancing regional knowledge on program actions (see Fiscal Year 2000 Annual 

Implementation Work Plan, Vol. I., p. 21). Such a journal could: 

• Provide short turn-around on the presentation of program results to a regional audience 

that includes managers 

• Provide a common information base to support decision-making by the middlemanagement groups 

• Help focus discussion on future directions 

55
Appendix G. Critical Uncertainties 

Critical Uncertainties Defined 

Critical uncertainties arise from the most important policy issues facing the region. In 

1993 the Scientific Review Group (SRG) defined critical uncertainties: 

“...as questions concerning the validity of key assumptions implied or stated in the Fish 

and Wildlife Program. Critical uncertainties identify important gaps in our knowledge 

about the resources and functional relationships that determine fish and wildlife 

productivity. Resolution of uncertainties will greatly improve chances of attaining 

recovery goals in the Fish and Wildlife Program.”

The research plan divides complex scientifically important issues into critical

uncertainties. The research plan provides a rationale for why the critical uncertainties are 

important, but does not include extensive background beyond that necessary to establish 

significance of the issue. Full syntheses of current knowledge on each research topic are not 

provided because doing so would require a much longer research plan. The critical uncertainties 

are described at a high level to preserve flexibility of implementation and to prevent the research 

plan from quickly becoming dated. The critical uncertainties were compiled from the fish and 

wildlife program, various reports of the ISAB and the ISRP, regional fish and wildlife managers, 

subbasin plans, recommendations from national science groups, biological opinions, and other 

research plans within the region. Chapter IV introduces long-standing and contemporary focal 

research themes and critical uncertainties important to the program and to the region. 

By articulating and organizing these uncertainties the research plan will help the region

agree upon research priorities, address knowledge gaps, and avoid duplication of effort. The 

research plan describes the critical uncertainties in terms that are intended to elicit the 

development of specific research hypothesis and project proposals. Therefore each research 

theme profiles the topic and why it is important. This approach highlights the central issues while 

preserving the challenge for investigators to develop more innovative or integrative approaches. 

The ISAB and ISRP recommend against an overly detailed rendition of research needs, 

pointing out that this inadvertently might diminish innovative responses; preclude flexibility to 

incorporate new information and techniques; and result in early obsolescence of the research 

plan. Further, the ISAB and ISRP cautioned that too many research recommendations could 

precipitate difficulty in reaching consensus on priorities. Consequently inventories of all the 

potential research topics identified during the public review of the research plan do not appear in 

the plan but will be considered during the development of the implementation plan. Taken 

together the critical uncertainties set forth in Chapter IV and the inventories supporting the 

implementation plan will provide a framework for guiding more detailed discussions of the 

allocation of research funding. 

56
Sources of Critical Uncertainties 

Independent Science Groups

The Council has relied on committees of scientists for their expert advice on fish and 

wildlife issues ever since the Council was formed. In the early 1990s, the Council asked its 

Scientific Review Group to identify critical scientific uncertainties for the purpose of focusing 

implementation of the fish and wildlife program. In January 1993 the SRG issued its report, 

entitled Critical Uncertainties in the Fish and Wildlife Program (SRG 1993-2). 

The SRG concluded that a major shortcoming of the fish and wildlife program was that it 

lacked an explicit conceptual foundation “that couples life histories and production with 

appropriate ecosystem components.” The SRG identified six “ecological uncertainties that 

encompass the fish and wildlife program as a whole, as opposed to a long list of uncertainties 

associated with each of the program elements.” The six uncertainties were programmatic in 

scale, and are included here in their original form, but phrased as questions: 

 

• What are the key assumptions in the fish and wildlife program, and are they scientifically 

valid? 

• Can salmonid populations in the Columbia River be increased and sustained over the 

long-term, given the multitude of biological, physical, and cultural constraints?

• Can the diversity of anadromous salmonid stocks be sustained over the long-term?

• What are the relative contributions of habitat loss, harvest, predation, and mainstem

passage to reduced riverine survival and production of anadromous salmonids and other 

fish targeted in the program? 

• To what extent are hatchery production and supplementation programs detrimental to 

wild salmonid productivity and stock diversity?

• To what extent are assumptions in the wildlife part of the fish and wildlife program

ecologically sound?

Subsequently, the Council revised the fish and wildlife program and included actions to 

address the uncertainties, including creation of the Independent Scientific Group to provide an 

ongoing evaluation of the program on its scientific merits. Importantly, the Council made clear 

that uncertainties should be used to guide the prioritization and funding of research efforts 

conducted under the program. The Council created the ISRP for the purpose of reviewing 

projects proposed for funding under the program, and in this role the ISRP provides guidance on 

prioritizing research. The Council and NOAA Fisheries also jointly created the ISAB to provide 

advice to both agencies, and now also to the Columbia River Indian Tribes. Further background 

on the science review groups can be found at www.nwcouncil.org/fw/science.htm. 

57
Fish and Wildlife Managers

Many valuable recommendations were received from the fish and wildlife managers and 

other resource management entities and incorporated in the research plan. The fish and wildlife 

managers are uniquely qualified to help identify research priorities and determine when and 

where to implement projects. This is an important part of coordinating large-scale planning. The 

types of comments received ranged from very general points regarding the organization of the 

document to very specific comments on a particular research topic. 

National Scientific Reviews

The Committee on Protection and Management of Pacific Northwest Anadromous 

Salmon was formed in 1992 under the auspices of the National Research Council’s Board on 

Environmental Studies and Toxicology. The Committee was charged with assessing the state of 

the stocks, analyzing the causes of decline, and analyzing options for management, taking into 

consideration socioeconomic costs and benefits. The NRC Committee’s efforts culminated in the

1996 publication of Upstream: Salmon and Society in the Pacific Northwest. Although this 

initiative did not focus on research needs per se, it addressed gaps in knowledge, information 

needs, and scientific uncertainty. Key points from these topics as well as insights on institutional 

arrangements have been included in the research plan. 

In November 2000, the National Science and Technology Council Committee on 

Environment and Natural Resources released From the Edge: Science to Support Restoration of 

Pacific Salmon (CENR 2000). The report was prepared to support President Clinton’s Pacific 

Coastal Salmon Recovery Initiative, initiated in 1999 to help reverse the decline of Pacific 

salmon. It is important to note that key authors of this report included members of the ISAB. A 

major element of the initiative was to accelerate the use of federal science and technology to 

assist in the conservation of Pacific salmon. The CENR was requested to develop an assessment 

that identified knowledge gaps and research priorities based on the considerable amount of 

scientific information already in existence. The report discusses the science needs for 

remediation, reviews the findings of several management-oriented science summaries for the 

Columbia River Basin, discusses the role of science in a restoration program, and underscores 

the importance of monitoring the status of salmon stocks and the magnitude of risk factors. The 

report also identified six broad categories of relevant and important research that have been 

underemphasized in the past, including: 

• Definition of critical ecosystem features for the full life cycle of salmonid species and 

stocks 

• Quantitative definition and assessment of risks (natural and human caused) during 

upstream, downstream, and estuary/ocean life stages 

• Clarification of fundamentals of biological diversity in salmon species, races, and stocks 

• Development of remedial technologies that work with nature rather than replacing it 

• Clarification of the regional variation in the physical, biological, social, cultural, and 

economic environments of salmon 

58
• Development of quantitative indicators and analytical methods to assess the status of 

salmon, characterize risk factors, and evaluate outcomes of remediation efforts to 

improve environmental conditions or reduce risks 

Public Review of the Columbia River Basin Research Plan 

The Council accepted public comments on the draft Columbia River Basin Research 

Plan from October 1 to November 30, 2004. A total of 28 comments were received from the 

tribes (three), state agencies (eight), federal agencies (eight), local government (one), academic 

institutions (two), consulting firms (four), and private individuals (two). A list of all the entities 

that provided comments follows. 

Alaska Resource and Economic Development, Inc. (consulting firm, Wrangell, Alaska) 

Columbia Basin Fish and Wildlife Authority 

Columbia River Inter-Tribal Fish Commission 

Confederated Tribes of the Umatilla Indian Reservation 

Oregon State University, Institute for Natural Resources 

Economic Development Council, Clatsop County 

ESSA Technologies Limited (consulting firm Vancouver, British Columbia, Canada) 

Federal Caucus 

Lathim, Mr. Del (citizen, Pasco Washington) 

Lower Columbia River Estuary Partnership 

Montana Department of Fish, Wildlife, and Parks 

Natural Solutions (consulting firm, Helena MT.) 

Northwest Fisheries Science Center, NOAA 

Oregon Department of Environmental Quality 

Oregon Department of Fish and Wildlife 

Pacific States Marine Fisheries Commission 

Taylor, Mr. Bernie (citizen, Newberg, Oregon) 

Tinsley, Mr. Thomas (citizen, Springfield, Oregon) 

University of Notre Dame, Department of Biological Sciences 

US Bureau of Reclamation 

US Department of Energy, Bonneville Power Administration 

US Fish and Wildlife Service 

US Forest Service 

US Environmental Protection Agency 

US Geological Survey 

Washington Department of Fish and Wildlife 

Washington Department of Ecology 

Wyoming Game and Fish Department 

59
VI. REFERENCES

Annual Implementation Work Plan, Fiscal Year 2000. Columbia Basin Fish and Wildlife 

Authority. Vol. I., p. 21 

Budy, P., G.P. Thiede, N. Bouwes, C.E. Petrosky, and H. Schaller. 2002. Evidence linking 

delayed mortality of Snake River salmon to their earlier hydrosystem experience. North 

American Journal of Fisheries Management 22:35-51. 

Committee on the Environment and Natural Resources (CENR), 2000. From the Edge: Science 

to Support Restoration of Pacific Salmon. National Science and Technology Council. 

Esterby, S.R. 1993. Trend analysis methods for environmental data. Environmetrics 4:459-481. 

FPC, 2004. 2004 Annual Report of the Fish Passage Center, p. 118. Table 41. Fish Passage 

Center, Portland, OR. 

Karieva, P., M. Marvier, and M. McClure. 2000. Recovery and management options for 

spring/summer Chinook in the Columbia River Basin. Science 290:977-979. 

ISAB, 2001-7. Independent Scientific Advisory Board, Review of Salmon Recovery Strategies 

for the Columbia River Basin. Northwest Power Planning Council. Portland, Oregon. 

ISAB, 2003-1. Independent Scientific Advisory Board, Review of flow augmentation: update 

and clarification. Northwest Power Planning Council. Portland, Oregon. 

ISAB, 2003-2. Independent Scientific Advisory Board, Review of Strategies for Recovering 

Tributary Habitat. Northwest Power Planning Council. Portland, Oregon. 

ISAB, 2003-3. Independent Scientific Advisory Board, Review of Salmon and Steelhead 

Supplementation. Northwest Power Planning Council. Portland, Oregon. 

ISAB, 2004-2. Independent Scientific Advisory Board, ISAB Findings from the Reservoir 

Operations/Flow Survival Symposium. Northwest Power Planning Council. Portland, 

Oregon. 

ISAB, 2005-4. Independent Scientific Advisory Board, Report on Harvest Management of 

Columbia River Salmon and Steelhead. Northwest Power Planning Council. Portland, 

Oregon. 

ISRP and ISAB, 2004-1. Review of Draft Action Agency and NOAA Fisheries RME Plan. 

Northwest Power Planning Council. Portland, Oregon. 

ISRP and ISAB, 2005-15. Monitoring and Evaluation of Supplementation Reports. Northwest 

Power Planning Council. Portland, Oregon. 

ISRP, 2000-3. Review of Databases Funded through the Columbia Basin Fish and Wildlife 

Program. Northwest Power Planning Council. Portland, Oregon. 

ISRP, 2003-13. Independent Scientific Review Panel, Review of the Action Agencies' Draft 

Estuary Plan. Northwest Power Planning Council. Portland, Oregon. 

60
ISRP, 2005-14. Retrospective Report 1997-2005. Northwest Power Planning Council. Portland, 

Oregon. 

Lee, K.N. and D.L. Klemka, with M.E. Marts. 1980. Electric Power and the Future of the Pacific 

Northwest. University of Washington Press, Seattle, WA. 

National Research Council, 1996. Upstream: Salmon and Society in the Pacific Northwest. 

National Academy Press. 

NPCC, Council Document 99-4. Review of Artificial Production of Anadromous and Resident 

Fish. Northwest Power and Conservation Council. Portland OR. 

NPCC, Council Document 99-15. Artificial Production Report. Northwest Power and 

Conservation Council. Portland OR. 

NPCC, Council Document 98-16. Development of Regional Framework. 

NPCC, 2000-19. 2000 Columbia River Basin Fish and Wildlife Program. Northwest Power and 

Conservation Council. Portland OR. 

NPCC, Council Document 2002-3. Mainstem Passage Strategies in the Columbia River System: 

Transportation, Spill, and Flow Augmentation, aka "Giorgi Report". Northwest Power 

and Conservation Council. Portland OR. 

NPCC, Council Document 2004-17. Artificial Production Review Evaluation. Northwest Power 

and Conservation Council. Portland OR. 

Nyberg, B. 1999. Implementing Adaptive Management of British Columbia’s Forests – Where 

Have We Gone Wrong and Right? In: McDonald, G.B., J. Fraser and P. Gray (eds.). 

Adaptive Management Forum: Linking Management and Science to Achieve Ecological 

Sustainability. Ontario Ministry of Natural Resources, Peterborough, Ontario, Canada, 

pp. 17-20. 

Office of Technology Assessment (U.S. Congress). 1993. Harmful non-indigenous species in the 

United States. OTA-F-565 (Washington, DC: U.S. Government Printing Office) – also 

available online at: www.wws.princeton.edu/~ota/disk1/1993/9325 n.html

Peters, C.N. and D.R. Marmorek. 2001. Application of decision analysis to evaluate recovery 

actions for threatened Snake River spring and summer Chinook salmon (Oncorhynchus 

tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 58:2431-2446. 

Pinkerton, E.W. 1992. Translating Legal Rights into Management Practice: Overcoming Barriers 

to the Exercise of Co-Management. Human Organization 51:330-41. 

PNAMP, 2005. PNAMP Strategy for Coordinating Monitoring of Aquatic Environments

(Northern California, Oregon, Idaho, Washington). 

Roni, P., editor. 2005. Monitoring stream and watershed restoration. American Fisheries Society, 

Bethesda, Maryland. 350 pp. 

61
Scientific Applications International Corporation, 2003. Recommendations for a Comprehensive 

and Cooperative Columbia River Information Management System. Report to the 

NWPC, April 30, 2003. 

Scientific Review Group, 1993-2. Critical Uncertainties in the Fish and Wildlife Program

Northwest Power Planning Council. Portland, Oregon. 

Urquhart, Paulsen and Larsen, 1998. Monitoring for Policy-Relevant Regional Trends Over 

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