Draft Columbia River Basin 

Research Plan 

by the 

Northwest Power and Conservation Council 

October 2004 
Table of Contents 

I. Planning for the Future, Taking Stock of the Present 1 

Background 1 

A Research Plan for the Columbia River Basin 1 

Relationship to Other Research Plans in the Columbia River Basin 2 

Profile of Current Council Research Projects and Budget 2 

Critical Uncertainties and Research Recommendations for the Columbia River Basin 4 

Hatchery Effectiveness 4

Hydrosystem 7

Habitat 10 

Recovery Planning 13 

Monitoring and Evaluation 16 

Harvest Management 17 

Estuary 19 

Natural Variation and Ocean Productivity 21 

Emerging Issues 23 

Impacts of Climate Change on Fish and Wildlife Restoration 23 

Toxics 24 

Invasive Species 26 

Impact of Human Development Patterns on Fish/Wildlife Restoration 28 

 

II. Charting A Course for the Future: Identifying Research Priorities 29 

Allocation of Program Versus Research Expenditures 29 

Comparison of Current Council Research with Recommendations for Future Research 30 

Identifying Priorities for Future Research 31 

Balancing Curative and Preventative Approaches to Restoration 32 

Integrating Research Results into Council Policy and Decision-making 32 

Adaptive Management 33 

Evaluating the Council Research Program 34

III. Recommendations for Developing/Implementing Regional Research Agenda 36 

Institutional Arrangements 36 

Cooperative Research: Building a Regional Research Partnership 36 

Implementing Research Recommendations: Opportunities for Collaboration 38 

Hatchery Effectiveness 38 

Hydrosystem 39 

Anadromous Fish Evaluation Program 39 

Habitat 41 

Harvest Management 42 

Recovery Planning 43 

The NOAA/USFWS Biological Opinions: What Research and Why? 43 

Monitoring and Evaluation: How to Evaluate Research Projects? 43 

Pacific Northwest Aquatic Monitoring Partnership 44 

Federal Research, Monitoring, and Evaluation Plan 45 

Pacific Coastal Salmon Recovery Fund 45 

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Bonneville Environmental Foundation 46 

Estuary 46 

Natural Variation and Ocean Productivity 47 

Toxics 48 

Environmental Protection Agency 48 

Western Fisheries Research Center 49 

Invasive Species 49 

Subbasin Planning: When and Where to Implement Research Projects? 50 

State Research Initiatives 51 

Recovery Planning for Endangered Species: How Much Research Is Enough? 51 

NOAA Technical Recovery Team Products 51 

Long Term Commitment to Restoration and Recovery 52 

IV. References 53 

V. Appendixes 54 

Appendix A. Mandate for a Columbia River Basin Research Plan 54 

Northwest Power and Conservation Council 54 

Directives for a Columbia River Basin Research Plan 54 

Basinwide Provisions of the Fish and Wildlife Program 54 

Recommendations of the Four Governors 55 

The Objectives, Audience, and Scope of the Columbia River Basin Research Plan 55 

Proposed Schedule for Completing Research Plan 56 

Appendix B. Development of the Columbia River Basin Research Plan 57 

Past as Prologue 57 

Best Scientific Information 57 

Prior Efforts to Identify Research Priorities 58 

2002 Draft Columbia River Basin Research Plan 58 

Appendix C. Implementing the Columbia River Basin Research Plan 60

Project Selection Under the Fish and Wildlife Program 60 

Beyond Technical Merit: New Review Criteria for the ISRP? 61 

Project Selection Processes 62 

Project Selection Under the Corps’ Fish Program 64 

Meeting Fish and Wildlife Program Standards 64 

Evaluation and Reporting of Research Results 65 

Data Management 

Appendix D. Sources of Critical Uncertainties and Research Recommendations 

for the Columbia River Basin 67 

Research Recommendations from Council Independent Science Groups 67 

State of the Science Documents 68 

Research Recommendations From A National Perspective 69 

Appendix E. FY 04 Research Projects Profile 71

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I. Planning for the Future, Taking Stock of the Present 

Background 

For over 20 years the Northwest Power and Conservation Council (Council) has supported a 

diverse range of research efforts. Hundreds of excellent projects, including dedicated research 

projects and habitat restoration projects with research elements, have been completed since the 

inception of the program in 1982. Projects implemented under the Council’s fish and wildlife 

program and others in the Columbia River Basin have substantially advanced the state of 

scientific understanding of fish and wildlife restoration. Yet the continuing absence of a plan to 

coordinate research has contributed to a lack of focus on key research needs. (Appendix A. 

Mandate for a Columbia River Basin Research Plan). To complement its traditionally strong 

support for research, the Council has drafted this Columbia River Basin Research Plan for the 

primary purpose of guiding the development of a research program under its Columbia River 

Basin Fish and Wildlife Program (Appendix B. Development of the Columbia River Basin 

Research Plan). 

Many other resource management entities share responsibility with the Council for research in 

support of fish and wildlife stewardship within the Columbia River Basin. The Council 

recognized that the status quo for research within the region consists of multiple, separate 

research plans which make reference to the “need to coordinate” with other similar efforts but 

rarely set forth any explicit steps to implement such coordination (Appendix C. Implementing 

the Columbia River Basin Research Plan). The inherent difficulty in agreeing on specific 

problem definitions, shared funding responsibilities, and overlapping mandates, has resulted in a 

fragmentation of effort that explains why key research questions within the region persist. 

Consequently, a secondary purpose of this plan is to provide a programmatic framework upon 

which to coordinate research and facilitate the integration of disparate research efforts within the 

region. Now is the time to re-evaluate the Council’s approach to conducting research, to 

reinvigorate the fish and wildlife program’s research agenda for the future, and to provide 

guidance to regional research efforts. 

A Research Plan for the Columbia River Basin 

Research is necessary to provide scientifically credible answers to questions pertinent to 

management that are complicated by uncertainty (Appendix D. Sources of Critical Uncertainties 

and Research Recommendations for the Columbia River Basin). This plan identifies a range of 

short- and long-term research recommendations. For the purpose of this plan, the term 

“research” is used broadly and is intended to include more than just dedicated hypothesis testing. 

For example, “research” may include estimation, pattern recognition, observation, categorization, 

studies involving the collection of data to better quantify important known relationships, and 

improvements in statistical methods. 

Some research questions in the region have persisted for many years because resource 

management agencies have been unable to either secure or collaborate on funding commitments 

necessary to mount the necessary organized, large-scale field experiments. This research plan 

attempts to divide complex issues into treatable questions. By providing a vehicle for the 

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identification and organization of these questions, this plan can help the region identify gaps and 

avoid duplication. It can also help the region with a basis for establishing priorities for new 

investment and judging the relative priority of continued investment in ongoing research. In 

brief, the research plan is organized in the following manner: 

• First, the plan profiles a pool of critical uncertainties and research recommendations 

spanning all topic areas relevant to the program. These were identified by the Council’s 

independent scientific review groups, fish and wildlife managers, and other agencies and 

entities within the Columbia River Basin. 

• Second, research recommendations are compared to a summary of current research 

activity under the fish and wildlife program in order to identify knowledge gaps 

unaddressed by current research. 

• Third, short-term and long-term research priorities are recommended to address the gaps. 

Relationship to Existing Research Plans in the Columbia River Basin 

The Council developed the draft Columbia River Basin Research Plan to enhance current 

coordination and facilitate future collaboration. It 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. 

While developing the draft research plan, Council staff reviewed several research plans from

within the region and many of the research recommendations they contain have been 

incorporated into this plan. This plan recommends research to be funded through the fish and 

wildlife program, as well as recommendations for research that will require collaborative, multiparty funding commitments by the Council and other entities with similar research mandates. 

 

Profile of Current Council Research Projects and Budget

The research projects in the Council’s Fish and Wildlife Program address explicit and implicit 

research needs identified in regional planning documents legally mandated by either the 

Northwest Power Act or the Endangered Species Act, including: 

• The Council’s 2000 Columbia River Basin Fish and Wildlife Program, and the Council’s 

1994 Program as incorporated by reference in the 2000 version; 

• The National Marine Fisheries Service’s 2000 hydropower biological opinion; and, 

• The U.S. Fish and Wildlife Service’s 2000 resident fish biological opinion. 

The amounts of funding for research projects recommended under the Council’s fish and wildlife 

program for Fiscal Years 2004 and 2005 are presented in Table 1. These projects are categorized 

by the research topics presented in this chapter. Projects addressing multiple research topics are 

categorized according to a single primary topic. 

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Table 1 was generated from a search of project proposals that sorted the projects into research 

topics based on key words in the proposal titles and short descriptions. Many projects mingled 

research, restoration, and monitoring activities to a degree that defied easy definition. Therefore, 

for the purpose of this analysis, research was defined in a general way that could resolve such 

dilemmas. Specifically, research was defined as work that sought knowledge that would have 

future and broad benefit. Therefore, projects conducting monitoring for the purpose of current 

evaluation at the project scale were not deemed to be research. Another example is that work by 

the Army Corps of Engineers on improving fish passage was defined as research, whereas work 

under the Fish and Wildlife Program testing the effectiveness of passage strategies was 

considered monitoring. Consequently, this approach may have missed some research elements, 

especially those embedded within management, restoration, and monitoring and evaluation 

projects. A recent trend is that many restoration projects have added research and/or monitoring 

elements. The most important factor in this analysis was consistency, so all the Council’s 

projects were evaluated by one staff member. 

Table 1 also includes preliminary information for FY 05. It does not include relevant research 

studies pursued under other tribal, agency, university, and private programs, nor does it portray 

historical research efforts, such as completed or discontinued projects. (The summary 

information in Table 1 is derived from Appendix E. FY 04 Research Projects Profile, which 

provides the project proposal identification numbers, project titles and sponsors, and the FY 04 

funding levels.) 

 

Table 1. FY 04/05 Council Funding Recommendations by Research Topic 

Research Topic FY04 Percent FY05 Projects 

Hatchery Effectiveness 31,831,721 62.7% 32,085,271 51 

Hydropower 202,224 0.4% 175,487 1 

Habitat 13,669,649 26.9% 11,825,986 33 

Monitoring and Evaluation 327,026 0.6% 219,109 2 

Harvest Management 2,720,058 5.4% 1,703,086 2 

Natural Variation and Ocean Productivity 1,827,962 3.6% 1,890,113 1 

Predation 155,000 0.3% 155,000 1 

50,733,640 48,054,052 91 

This information raises two questions for the Fish and Wildlife Program. First is the total 

amount of spending on research appropriate? Clearly, the current research budget comprises a 

significant proportion of the overall program budget of $139 million dollars. Considering that 

some of the remaining budget is spent on management, administration, planning, overhead, and 

monitoring and evaluation, a relatively smaller share of the budget remains for restoration 

projects. 

The second question is whether the current allocation across the other categories is appropriate. 

Hydropower appears low given the importance of fish survival, but this is counterbalanced by 

the Corps’ research budget for FY04, including staff engineers, biologists etc., of approximately 

$40 million that primarily fits into this category (see Table 2). However, the hatchery research 

budget appears particularly high given the slow progress being made at hatchery reform. In light 

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of the recent evidence of significant predation on salmon smolts, the amount spent on predation 

appears especially small. It may benefit the Council to examine the benefits accruing to fish and 

wildlife from particular research topics with the intention of resetting the allocation of research 

dollars by topic. 

Table 2. Total FY 04 Corps of Engineers Funding Levels for anadromous fish research under the 

Anadromous Fish Evaluation Program. (Data source: the SCT Spreadsheet and the Fish and 

Wildlife Operations and Maintenance spreadsheet.)

Topic CRFM O&M Totals 

Adult Passage (Salmonids, Kelts, Lamprey, etc.) 2,871,000 1,146,000 4,017,000

Juvenile Passage (Spill, Turbines, etc.) 23,987,000 0 23,987,000

Transportation/Delayed Mortality (D) 2,624,000 2,216,000 4,840,000

Other 50,000 0 50,000

Estuary 4,100,000 0 4,100,000

Predation (Avian primarily) 1,717,000 282,000 1,999,000

35,349,000 3,644,000 38,993,000

Critical Uncertainties and Research Recommendations for the Columbia River Basin 

The next section of this chapter profiles long-standing and contemporary research topics 

addressing all facets of the fish and wildlife program. The profile for each topic comprises an 

overview; management needs; critical uncertainties; and the Council’s research 

recommendations. (Please note that not all profiles have all of these elements.) In 1993 the 

Scientific Review Group 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.”

This section was derived from the works of the independent science groups and the Fish and 

Wildlife Program. It also contains recommendations from the Army Corps of Engineers, 

Bonneville Power Administration, NOAA Fisheries, and the Lower Columbia River Estuary 

Partnership. It is anticipated that the final version of this plan will include additional 

recommendations from other resource management entities.

Hatchery Effectiveness

Overview: A critical issue facing the region is whether artificial production activities can play a 

role in providing significant harvest opportunities throughout the basin while also acting to 

protect and even rebuild naturally spawning populations. Several important research 

recommendations and critical uncertainties are central to addressing this issue. Columbia River 

Basin supplementation projects are considered to be experimental. Yet recent reviews have been 

critical and the science on this issue is far from settled. Two major reviews of hatchery-related 

issues were completed in 2003, the Artificial Production Review and Evaluation, and the ISAB 

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Review of Salmon and Steelhead Supplementation. One important criticism from the ISAB’s 

supplementation report is that inadequate replication and widespread failure to include unsupplemented reference streams, coupled with a lack of coordination among projects, make it 

unlikely that such projects, as currently conducted, will be able to provide convincing 

quantification of the benefits or harm attributable to supplementation. Some of the key findings 

include: 

1. Artificial production must be used in a manner consistent with ecologically based scientific 

 principles for fish recovery. 

2. Fish raised in hatcheries should have a minimal impact on fish that spawn 

 naturally. 

3. Fish reared in hatcheries or by other artificial means for the purpose of supplementing the 

 recovery of a wild population should clearly benefit that population. 

4. Improperly run, artificial production programs can damage wild fish runs. However, when 

 fish runs fall to extremely low levels, artificial production may be the only way to keep 

 enough of that population alive in the short-term to ensure a chance of recovering in the long 

 term. 

5. Hatcheries have been successful at preserving some of the genetic legacy, which would 

 otherwise have been lost, from salmon populations formerly occupying severely degraded 

 habitats. 

6. Existing hatchery populations should be protected and carefully evaluated to identify the 

 genetic legacy they contain and its potential role in rebuilding metapopulations. 

7. The decision about when and where to deploy supplementation programs should make use of 

 the metapopulation concept. 

What is not clear is the extent to which artificially produced fish can be mixed with a wild 

population in a way that would sustain and rebuild the wild population. The Council has 

weighed these uncertainties and recognized that inaction also holds a large risk. Hatchery 

operations including some instances of broodstock selection, inter-basin transfers, and release 

practices have contributed to the decline of natural production and loss of locally adapted stocks 

in the basin. Hatchery practices are one of the factors that have altered the genetic structure of 

stocks in the basin. 

Management Needs: This research plan provides a vehicle for addressing how hatchery 

operations can be integrated into the total production system and should assist in the recovery 

efforts in the subbasin. The objectives of each hatchery should; be established within the context 

of the subbasin where the hatchery operates, consider non-target species, and pay attention to the 

linkages between salmonids and their habitats, and the potential for metapopulation rebuilding. 

Research should be implemented to address the following management questions: 

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1. Can artificial production play a role in providing significant harvest opportunities while also 

protecting and possibly rebuilding naturally spawning populations? 

2. Under what conditions can conservation hatcheries be expected to provide a net long-term

 benefit to the viability of wild populations?

3. Do artificially propagated fish contribute to harvest and/or escapement of naturally 

 spawned fish and is the economic benefit of that contribution greater than its cost? 

4. Has the program achieved its objective; e.g., if it is a mitigation hatchery, has it replaced lost 

 natural production? 

5. How can hatcheries maintain genetic, behavioral, physiological, and ecological adaptations 

 similar to natural environments? 

6. What foods, rearing conditions, and hatchery management practices can favor the 

 establishment of self-sustaining wild runs? 

7. Should supplementation proceed independent of programs to restore habitat and improve the 

 productivity of the population in its natural environments?

Critical Uncertainties: Uncertainties exist regarding the potential for both benefits and harm to 

the naturally spawning populations. A major uncertainty is whether it is possible to integrate 

natural and artificial production systems in the same basin to achieve sustainable long-term

productivity. Some scientists and managers believe that it is likely that supplementation will 

produce an increased abundance of natural-origin salmon, and that reformed hatchery practices 

can reduce the risks from supplementation to acceptable levels. Other scientists and managers 

not only doubt that the expected increases in abundance will be realized, but also believe that 

there is a high probability that supplementation will cause significant harm, reducing the 

productivity and abundance of the natural-origin component of the integrated population. In 

addition, supplementation (with unmarked hatchery fish) can introduce uncertainty through 

masking the numbers of natural-origin fish, making a determination of reproductive success 

difficult (for both natural-origin and hatchery-origin fish). 

The immediate net demographic benefit or harm to population abundance from supplementation 

depends on three things: intrinsic biological parameters of the stock in its environment, policy 

constraints, and management control variables. The integration of these factors, much less their 

measurement, has not been adequately considered in supplementation evaluations to date. For 

hatchery programs where the hatchery and natural population are integrated, the empirical basis 

is inadequate for determining the cost to the natural population. The impacts of these hatchery 

programs on the extinction risk to, or recovery of, the remaining natural populations of salmon 

and steelhead have not been determined empirically and these knowledge gaps need to be filled. 

At present, little is known about the magnitude of any correlation between natural spawning 

fitness and hatchery spawning fitness in actual salmon populations. Nevertheless, modeling 

shows that this relationship has a large influence on the probability and magnitude of the 

depression in natural spawning fitness as a consequence of supplementation. How a decrease in 

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the fitness of natural-origin adults due to interbreeding with hatchery-origin adults translates into

a reduction in population abundance is unknown. 

A major uncertainty associated with the use of supplementation is the condition of the habitat 

that will receive the juvenile salmon. Is the habitat capable of supporting salmon at levels of 

survival that will bring about restoration? The ecological conditions required to expect to 

achieve benefits from supplementation have received little conceptual development or 

programmatic experimentation. 

The Council’s Research Recommendations: The genetic risks of supplementation as a means 

to increase natural spawners suggest that it would be prudent to continue to treat supplementation 

as experimental, that supplementation should only be deployed on a limited scale, and that better 

and more extensive monitoring of such experiments should be required to generate an empirical 

record capable of evaluating those experiments. 

1.1 Determine the effects of wild-hatchery fish interactions and the impacts of hatchery 

management programs on wild stocks. 

1.2 Test the assumptions about survival differences between hatchery and wild fish. 

1.3 Determine the origin and the temporal and spatial distribution of wild ocean-caught fish. 

1.4 Determine the long-term persistence of natural elemental signatures in fish scales. 

1.5 Improve the persistence of cold marks at the focus of otoliths in swim up fry to allow for 

subsequent detection. Although lethal otolith sampling is required to detect marks, this 

technique may still serve a useful purpose for certain research applications.

1.6 Assess the effectiveness of batch marking of fish scales using applied concentrations of

microelements. Micro-elemental marking of fish scales and otoliths may be an alternative to 

cold marking techniques in hatchery research. 

1.7 Determine the exact timing of imprinting in juvenile WCT and Bull trout. Assured 

imprinting on a specific water source will reduce the potential for straying when fish are 

planted to establish a new wild spawning run. 

Hydrosystem 

Overview: In April 2003, following a two-year public process, the Council adopted the 

mainstem amendments to its Columbia River Basin Fish and Wildlife Program that provide a 

broad range of recommended policies, operations and specific recommendations for future 

research. These amendments describe an experimental approach to many of the long-standing 

uncertainties regarding fish survival through different routes of passage and under different 

hydrosystem operational scenarios. To implement the amendments, a workplan has been 

developed that sets forth 45 different tasks, many of which address specific research issues such 

as tests of dam operations. An important task for the Council is to establish priorities for this 

Mainstem Amendment work plan (Task 43). An informal internal prioritization based on what 

needs the most attention from the Council has been conducted by staff, with the focus in being 

on summer spill and reservoir operations Council staff will carry these recommendations forward 

into the formal process for establishing priorities in the Regional Forum.

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There are more tasks envisioned in the mainstem amendments than the Council’s staff and 

budget resources can adequately cover. For this reason, staff will work with the Council to 

establish priorities for the tasks included in this work plan. This will help focus the Council’s 

resources and advise other agencies on those tasks that offer the most immediate benefits and are 

likely to be the most important to achieving the Council’s vision for the basin. 

The Council calls for specific changes in current operations in an experimental fashion that will 

help to shed more light on the biological needs of fish and wildlife. This section of the research 

plan is derived from the workplan for the mainstem amendments. (Some additional hydropower 

research recommendations appear in the monitoring and evaluation section of this chapter.) 

Management Needs:

1. Determine more precisely the relationship between fish survival and various levels of spill at 

 the individual dams and for the system. 

2. Implement and test new spill technologies such as removable spillway weirs. 

3. Evaluate turbine operations at the different dams to determine optimum fish survival through 

 the turbines and tailrace environment. 

4. Evaluate the benefits of incremental flow augmentation and determine the mechanisms for 

 flow/survival relationships on the Columbia and Snake rivers. 

5. Evaluate the biological effects of steady June through 

 September outflows from Libby and Hungry Horse dams in Montana. 

6. Evaluate and document the impact of predation in the mainstem in terms of numbers of ESA- 

 listed fish taken, and estimated impact on smolt-to-adult return ratios. 

7. Evaluate and document the impact of harvest operations in terms of numbers of ESA-listed 

 fish taken, and estimated impact on smolt-to-adult return ratios. 

8. Improve the effectiveness of the adult passage program. Evaluate the benefits of cool water 

 releases from reservoirs to facilitate adult migration. 

9. Monitor smolt to adult return ratios. Investigate the possibility of achieving the Council’s 

 interim objective of achieving smolt-to-adult survival rates in the 2-6 percent range for listed 

 Snake and Columbia river salmon and steelhead. 

10. Identify research that is needed to clarify habitat conditions in all of the mainstem reservoirs. 

11. Test other uncertainties proposed by the independent science panels and fish and wildlife 

 managers summarized in this research plan. 

Critical Uncertainties: The cumulative indirect effects of passing multiple dams during 

migration are uncertain. The cumulative effects of predation must be evaluated including marine 

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mammals, avian species (e.g. terns, cormorants, mergansers), as well as piscivorous fish (e.g., 

pike-minnow, walleye, and smallmouth bass). Further, the relationship between levels of flow 

and juvenile and adult salmon survival through the Columbia hydrosystem needs greater 

clarification. The present flow management strategy does not take into account the complex 

migratory behaviors of juvenile salmonids. For example, there is considerable uncertainty about 

the effects that changes in river flows designed to aid yearling migrants has had on subyearlings. 

Water budgets (basinwide, annual rule curves for water storage and release) need to be 

rigorously evaluated to determine what is actually being accomplished for survival of salmonid 

populations. The effects of augmented flows on rearing fall Chinook in unnaturally cold reaches 

of the Snake and Clearwater rivers must be determined. 

The role of hydrodynamic features other than mid-channel velocity in fish migration needs to be 

explored. A proven link to such features as stage waves and turbulent bursts, or pulsing flows 

may offer opportunities for water management that might be more effective in moving fish with 

less water than current procedures. The secondary effects of flow differences on nearshore 

habitat conditions of present-day reservoirs (temperature, flow, and food production) need to be 

measured and evaluated. The effects of shoreline modifications along reservoirs (rip-rap, 

erosion, and permanent sloughs) compared to the riverine condition need to be evaluated. 

Little is known about the cumulative effects on survival of both adults and juvenile salmon from

spilling water to gas supersaturation limits of 120 percent in the tailrace and 115 percent in the 

forebay at all mainstem projects. The relationship between inriver gas supersaturation levels and 

salmonid inriver survival is not well understood because (a) the supersaturation-exposure 

histories of inriver fish are not well understood, and these variable exposures are not easily 

related to laboratory dose-response experiments, and (b) injured fish can be lost through 

predation, disease, or other ecological factors that are not well quantified at the present time. 

The Council’s Research Recommendations: 

2.1 Design a comprehensive research program that will integrate specific passage research at 

each dam and through each passage route with overall system survival evaluations. 

2.2 Implement summer spill tests as soon as possible to examine the benefits of the current

summer spill program for outmigrating juvenile fall Chinook. 

2.3 Conduct research necessary to design, test, and implement new surface passage systems, 

e.g. removable spillway weirs. 

2.4 Continue to develop rigorous evaluations of spillway passage at each mainstem project. 

Determine an optimal passage strategy at each dam and for each passage route that 

maximizes improvements in life-cycle survival. 

2.5 Continue to evaluate biological effectiveness and costs of spill operations. Provide a 

systematic evaluation of the biological and cost effectiveness of using spills as a passage 

strategy. 

2.6 Implement an experimental operation at Libby that will limit the summer draft to 10 feet 

from full pool by the end of September. 

2.7 Implement an experimental operation at Hungry Horse that will limit the summer draft to 

10 feet from full pool by the end of September. 

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2.8 Determine the feasibility and implement research as necessary to evaluate the biological 

effects of flow augmentation from Libby and Hungry Horse on salmon survival in the 

Lower Columbia River. Design and implement new survival tests in the lower river to 

better understand the movement and survival of fall Chinook. 

2.9 Continue to evaluate turbine passage to determine the optimum fish survival through 

turbines. Continue the research and design work on improved turbines and the relationship 

between survivals and overall turbine operating efficiencies. 

2.10 Modify turbine designs to improve juvenile salmon passage survival. Evaluate alternative 

designs and implement as soon as possible in those dams where they would provide the 

greatest biological benefits. 

2.11 Continue to evaluate survival benefits of transport from McNary Dam to determine 

whether the survival benefits of transport from McNary are sufficiently greater, at least 

under certain circumstances, than inriver passage to justify continuing (or increasing) the 

transport effort from that dam.

2.12 Conduct a transportation study targeting Snake River fall Chinook. Evaluate relative 

success of transporting various groups of fish throughout the Snake River. 

2.13 Determine the differential delayed mortality “D” effects due to transport. 

2.14 Investigate and implement actions to reduce toxic contaminants from entering the Snake 

and Columbia rivers. 

2.15 Review operational procedures to identify efforts that could be taken to avoid exceeding 

total dissolved gas saturation limits of 120 percent, over a time period of the twelve 

highest hourly measurements at all Federal Columbia River Power System projects 

engaged in spill operations. 

2.16 Determine the feasibility and perform as necessary the research to determine the survival 

benefits of lowering total dissolved gas levels from the waiver amount of 120 percent to 

the Total Maximum Daily Load of 110 percent. 

2.17 Determine the effects of predation on salmonid recovery and how predation is affected by 

other environmental factors. 

2.18 Evaluate the impact of predation on fish survival and smolt-to-adult return rates. 

2.19 Determine the factors influencing predation rates on salmonid smolts in the Columbia

River estuary. 

2.20 Continue to improve estimates of the impacts of seabird predators on wild salmonids. 

2.21 Improve the estimates of the impact of pinniped predation on salmonid stocks and on the 

recovery of depressed stocks. 

Habitat 

Overview: Habitat required for salmonid migration, spawning, egg incubation and juvenile 

rearing has been severely degraded in the Columbia Basin by the cumulative effects of flow 

regulation by dams and diversions, sedimentation from forestry and agricultural activities, and 

massive introduction of non-native fish, invertebrates and riparian plants. Much of the alluvial 

floodplain and associated habitats that historically supported large, productive spawning 

populations and provided high-quality rearing habitats for maturing and migrating juveniles, has 

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been destroyed by reservoir inundation, degraded by altered flows from hydropower, flood 

control, and irrigation, or disconnected from the salmon ecosystem by dams that block migratory 

pathways. 

Sustained salmonid productivity requires a network of complex and interconnected habitats, 

which are created, altered, and maintained by natural physical processes in freshwater, the 

estuary, and the ocean. Ocean conditions, which can be variable, are important in determining 

the overall patterns of productivity of salmon populations. Restoration efforts must focus on 

restoring habitats and developing ecosystem conditions and functions that will allow for 

expanding and maintaining diversity within, and among, species in order to sustain a system of 

robust populations in the face of environmental variation. Incremental loss of incubation, rearing 

and spawning sites has reduced or eliminated production of salmonid stocks and disrupted 

natural metapopulation structure and dynamics. 

Life history diversity, genetic diversity, and metapopulation organization are ways salmonids 

adapt to their complex and connected habitats. These factors are the basis of salmonid 

productivity and contribute to the ability of salmonids to cope with environmental variation that 

is typical of freshwater and marine environments. Owing to the diverse climates and food web 

assemblages of the different eco-regions that comprise the Columbia River Basin, native 

salmonids displayed great diversity of life history types (stocks or populations) specifically 

adapted to the wide array of natural habitats. Thus, diversity has been substantially depleted by 

habitat loss, fragmentation and degradation. 

Management Needs: 

1. Quantify the benefit to aquatic species of on-the-ground habitat restoration and protection 

 measures. 

2. Determine the value of salmon pellets/carcasses to increase habitat productivity. 

3. Identify and protect habitat that supports existing populations that are relatively 

 healthy and productive. 

4. Identify and expand (reconnect) adjacent habitats that have been historically 

 productive or are likely to sustain healthy populations. 

5. Identify and rebuild healthy, naturally producing fish and wildlife populations. 

6. Protect and restore habitats and biological systems. 

7. Identify ecosystem conditions and functions that expand or maintain diversity within 

 and among species. 

8. Identify possible improvements to conditions in the estuary and plume?

9. Account for changes in fish survival with the variable nature of the ocean?

10. Identify current and critical habitat needs in the mainstem of the Columbia and Snake rivers 

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 and seek to increase the extent, diversity, complexity and productivity of mainstem habitat 

 by protecting, enhancing and/or connecting mainstem spawning, rearing and resting areas. 

Critical Uncertainties: In the face of uncertainty about the sufficiency of current land use 

practices, designation and protection of a well-distributed network of reserve areas and habitat 

patches from new land-disturbing activities is necessary to establish experimental natural 

baselines. Although "best management practices" (BMPs) may reduce impacts to habitat 

compared to unregulated land use, uncertainty about effectiveness of present BMPs must be 

resolved by scientific evaluation at both site-specific and watershed scales. The nutritional state 

of migrating salmonids requires research in relation to stability and productivity of food webs, 

including importance and effects of colonization of mainstem reservoirs by estuarine species and 

value of macrophytes for producing food for mid-Columbia salmonids. It is important to reestablish the seasonality of flow and temperature and to stabilize base flow and temperature 

fluctuations. The exact magnitude and timing of restored flows and temperature regimes need to 

be empirically determined for specific free-flowing segments and requires a broadly 

multidisciplinary approach. 

The relationship between habitat and salmonid productivity is dynamic. Understanding this 

relationship is critical to conserving and restoring habitat that will meet population-based 

salmonid restoration, recovery, and conservation. Therefore, a comprehensive life-cycle 

approach that addresses both natural variability in environmental conditions and human impacts 

on physical, chemical, and biological processes that affect salmonids needs to be defined. 

NOAA Fisheries’ 2000 Biological Opinion calls on the federal Action Agencies, in conjunction 

with the Environmental Protection Agency and the U.S. Geological Survey, to develop a 

program to 1) identify mainstem habitat sampling reaches, survey conditions, describe causeand-effect relationships and identify research needs; 2) develop improvement plans for all 

mainstem reaches; and 3) initiate improvements in three mainstem reaches. 

The Council’s Research Recommendations: 

3.1 Test the effectiveness of new timber harvest prescriptions, sustainable agriculture 

practices, and other land use practices for upland and riparian areas, in short- and longterm studies before considering them sufficient for conserving and enhancing water 

quality and salmonid habitats. 

3.2 Identify and protect a well-distributed network of reserve watersheds and riverine habitat 

patches to establish experimental natural baselines for evaluation of effectiveness of 

management practices. 

3.3 Conduct an integrated assessment of the role of food and feeding on the nutrition of 

downstream migrants leading to conclusions regarding action options for restoration of 

riverine food chains such as induced flooding, riparian habitat restoration) and promotion 

of estuarine food chains, for example species stocking. 

3.4 Test, through field studies, the nutritional state of migrating Snake River salmonids in 

relation to that of mid-Columbia stocks, to estimate the importance of food availability to 

salmon survival. 

3.5 Estimate, through field studies of insect colonization and growth during flooding and 

spatial analyses of floodplains, the quantity of salmonid food potentially produced by 

12
flooded riparian lands in the lower Columbia-Snake basins and lost by river regulation, 

and relate quantitatively to the food requirements of migrating juvenile salmon. 

3.6 Determine, through field studies, the current extent of the colonization of reservoirs by 

estuarine species and their role in reservoir food webs. 

3.7 Estimate, through field studies and laboratory feeding experiments, the importance of 

longitudinal continuity of food for relative survival of mid-Columbia (Hanford) and Snake 

River migrants 

3.8 Estimate, through field studies, the value of macrophytes for producing food for midColumbia salmonids 

3.9 Continue to evaluate the nutritional status of juvenile salmonids during transportation 

from upper river dams to below Bonneville Dam.

3.10 Evaluate nutrient cycling, carcass increases, and productivity of macro-invertebrates. 

3.11 Continue to provide storage reservoirs with selective withdrawal systems to more 

normalize or mitigate the annual temperature cycle in the river. 

3.12 Determine how temperatures in tributaries are part of the environmental change that has 

fragmented salmonid habitat, and develop programs to improve tributary temperatures for 

salmonids. 

3.13 Continue to evaluate the amount of spawning habitat for fall Chinook core populations in 

the lower and mid-Columbia area and in the lower Snake area. 

3.14 Enhance the abundance and productivity of white sturgeon in the mainstem. 

3.15 Conduct the necessary feasibility studies to restore, where feasible, anadromous fish to 

blocked areas. 

3.16 Determine the impacts of declining wild salmonid populations on ecosystem processes, 

such as the transport of marine derived nutrients from ocean to upland settings. 

3.17 Identify habitat elements necessary for bull trout and develop an inventory of streams that 

provide the cold-water habitat conditions necessary for bull trout. 

3.18 Determine the importance of protecting mainstem habitat for recovery of bull trout. 

3.19 Document the amount and timing of flows in subbasin plans, in order stabilize and 

improve burbot populations in the Kootenai River. 

3.20 Assess habitat carrying capacity needs, within the stream reaches and subbasins where 

supplementation is being conducted and throughout the required migration route. 

3.21 Determine how changes in plant communities, including riparian and upland vegetation, 

can affect salmonid habitat quality. 

3.22 Determine relationships between habitat quality and population trends of salmonids in 

estuaries, lowland streams, and urban/suburban and agricultural settings. 

3.23 Determine the effects of livestock browsing on aspen sprouts. 

Recovery Planning 

Overview: Different species and populations of salmonids in the Columbia River and elsewhere 

exhibit remarkable life history, ecological, behavioral, phenotypic, and genetic diversity. This 

diversity is a hallmark of salmonids in general and arose from differential or local adaptation to 

13
the varied and variable environments within the complex landscapes of the Pacific Northwest. 

Such diversity buffers salmonid populations against short- and long-term environmental 

variation and has become even more important today as human activities have increased the rate 

and amplitude of environmental fluctuations over those that occurred historically. 

The importance of local adaptation to salmonid populations has been underestimated. Generally 

there has been a lack of success in salmonid introductions and re-establishments within the basin. 

Diversity has been reduced by the extinction of many local populations, as well as a reduction in 

population size of most remaining populations. Losses of genetic diversity may have decreased 

the reproductive and ecological fitness, and therefore decreased the probability of long-term

persistence for many stocks. 

Under unconstrained conditions, metapopulation structure would act to stabilize losses of 

diversity and reproductive fitness within individual populations. Yet human-caused 

development has altered the organization of salmon populations and consequently probably 

altered metapopulation organization. This has very likely caused losses in adaptive capacity and 

resulted in a reduction in regional stability of production. Present restoration efforts have 

focused primarily on remaining satellite populations, which are smaller and less productive and 

may have higher probabilities of extinction than core populations. Human development and 

management actions have increased the potential for synchrony among geographically diverse 

local populations. This may have rendered present metapopulation organization more sensitive to 

the effects of regional variation by reducing metapopulation size, increasing local population 

extinction rates, and reducing dispersal between populations. Nevertheless, salmon populations 

in the Columbia River today can still form the base for rebuilding salmon abundance and 

diversity. 

After population identification, the next step in the technical recovery planning process is to 

develop biological criteria for population and ESU viability. In determining biological viability 

criteria, the NOAA Technical Recovery Teams, or TRTs, generally follow the guidelines 

discussed in the Viable Salmonid Populations and the Recovery of Evolutionarily Significant 

Units (NOAA Technical Memorandum NMFS-NFWSC-42, June 2000). The TRTs, are technical 

workgroups convened and chaired by NOAA Fisheries to determine the preliminary biological 

criteria necessary to ensure the viability of Evolutionarily Significant Units, or ESUs, listed 

under the ESA. 

Management Needs: 

1. Identify strong, weak, and at-risk native populations and determine what actions can be taken 

 to preserve and protect native populations. 

2. The importance of stock diversity must be explicitly recognized in all aspects of the 

 restoration effort. 

3. Ensure that monitoring and evaluation can verify whether or not certain life history 

 types are favored, or selected against, by the restoration action?

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Critical Uncertainties: Populations are often the fundamental unit of viability analysis, so 

effectively evaluating the status of a species may depend on correctly understanding its 

population structure (CENR, 2000). For restoration and recovery actions to succeed, there must 

be understanding of how these distinct populations individually respond to environmental 

variables that are likely controlled by very different limiting factors. Sub-watershed and sitespecific restoration and recovery actions must be tailored to specific populations and to their 

particular environmental and biological attributes (CENR, 2000). The first step is to identify the 

"independent populations" within an ESU, as these are the basic building blocks for the recovery 

of the ESU. 

The Council’s Research Recommendations: 

4.1 Determine whether fisheries management practices such as harvest, dam operations, 

hatchery operations, and transportation have reduced variation in salmonid stocks. 

4.2 Determine the extent that the use of hatchery stocks may have reduced the betweenpopulation component of genetic variation in some species, such as Lower Columbia 

River coho and Upper Columbia River Chinook. 

4.3 Determine whether re-establishment of metapopulation structure between Columbia Basin 

salmon populations would slow or stabilize the loss of diversity in isolated local 

populations? 

4.4 Identify and characterize interactions among basin populations, metapopulations, ocean 

survival rates, life history stage (survival) trends, and population viability.

4.5 Integrate analysis of habitat characteristics and spawner surveys with models to assess

trends in population dynamics and conduct sensitivity analysis of models and model 

parameters.

4.6 Determine distribution of spawner abundance relative to spawning habitat of differing 

quality. 

4.7 Determine the genetic basis of various life history strategies in salmonids.

4.8 Increase the number of genetic markers to enable researchers to determine the genetic 

integrity of individual fish to help select appropriate donor parents for replicating unique 

genetic strains of fish that are threatened by extirpation. 

4.9 Develop a set of precise quantitative definitions that link ESU, “independent population”, 

and “subpopulation”. 

4.10 Combine the definitions in 11.2 with a set of decision rules indicating how viability will 

be assessed for “independent populations,” how the viability of component independent 

populations,” within an ESU will determine ESA status for that ESU, and what burden of 

proof will apply to setting boundaries of “independent populations,” when the data are 

incomplete and the conclusions uncertain. 

4.11 Determine effectiveness and feasibility of using artificial propagation in bull trout 

recovery. 

4.12 Identify status, limiting factors, and management alternatives for lamprey. 

4.13 Determine capacity of each potential local bull trout population. 

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Monitoring and Evaluation 

Recognizing that research and monitoring are different types of activities, this section sets forth 

research needs within the field of monitoring and evaluation. The CENR (2000) report 

recommended that research efforts in the area of monitoring and evaluation would greatly 

enhance the scientific credibility of salmonid restoration and recovery plans by providing timely 

feedback to managers and policy makers. 

Overview: Understanding the effect of habitat conditions on anadromous and resident fish and 

wildlife population performance requires replicated observational studies or intensive research 

level experiments to be conducted at large spatial and long temporal scales. Few evaluations of 

tributary habitat in the Columbia Basin meet these criteria. The expense and effort needed to 

obtain the data necessary for evaluating the response of salmonids to habitat restoration is 

considerable. It is likely to require several generations of a population to get statistically 

supported answers to questions about the effectiveness of habitat restoration. This supports an 

approach of focusing intensive monitoring efforts on a relatively few locations and to involve 

multiple parties in a collaborative research effort. By implementing these evaluations with clear

objectives, careful employment of experimental and statistical design, disciplined adherence to 

the experimental constraints in treatment and reference sites, and patience, results can be 

obtained that will greatly improve the ability to ensure viable fish and wildlife populations.

For salmon and trout, the goal of most habitat restoration efforts is to improve survival through 

their entire period of freshwater residency. Individual restoration projects should collectively 

contribute to the attainment of this objective. To determine whether this is occurring, projects 

applied at the reach scale should be nested within, and clearly related to, the watershed-level 

objective for habitat condition and fish populations. Such a nested hierarchy creates an 

interconnectedness among projects that is critical to assessing the effectiveness of the restoration 

efforts through a monitoring and evaluation program. The Pacific Northwest Aquatic 

Monitoring Partnership has drafted a Regional Monitoring Coordination Plan in response to the 

request of the four Governors that provides a framework for coordinating current and future 

monitoring efforts of the states, tribes, and federal agencies and is complementary to this 

research plan. However, this plan does identify research in support of monitoring and 

evaluation. 

Management Needs: 

1. Monitor and evaluate the effectiveness of habitat improvement projects. 

2. Monitor and evaluate the habitat improvement projects making the most of scarce resources. 

The Council’s Research Recommendations: 

5.1 Develop a sound Tier I trend-monitoring procedure based on remotely sensed data 

obtained from sources such as aerial photography or satellite imagery. 

5.2 Develop and implement a long-term statistical monitoring program (Tier 2) to evaluate the 

status of fish and wildlife populations and habitat. This action would entail development 

of probabilistic (statistical) site selection procedures and establishment of common 

16
protocols for cost-effective “on the ground” or remotely sensed data collection of a limited 

number of indicator variables. 

5.3 Develop or improve existing empirical models for prediction of abundance or presenceabsence of focal species as data are obtained in a Tier 2 status-monitoring program. 

5.4 Implement a research monitoring (Tier 3) effort at selected locations in the Columbia 

Basin to establish the underlying causes for the changes in population and habitat status 

identified in Tiers 1 and 2 monitoring. 

5.5 Continue to determine the relative proportion and survival of migrating juvenile salmonids 

passing through the various passage routes, including spillways, located at the mainstem 

dams. 

5.6 Continue to determine the differences in migration timing and relative survival for 

transported and inriver juvenile salmon and steelhead. Determine the relationship 

between ratios of transport and inriver return rates and measurements of juvenile survival 

(D values). 

5.7 Continue to determine how specific flow and spill conditions affect passage success of

adult salmonids migrating past the mainstem dams. 

5.8 Continue to determine what the effects of multiple juvenile fish bypass are on juvenile 

salmonids migrating through the mainstem dams. 

5.9 Determine the biological and physiological effects on wild and hatchery juvenile 

salmonids that are exposed to stress from bypass, collection, and transportation at the 

mainstem dams. 

5.10 Continue to determine the effects of flow on survival, growth, migration timing, and smolt 

to adult return ratios of juvenile salmonids in the Columbia and Snake River basins. 

5.11 Continue to determine juvenile hydro survival (priority total system/secondary in-river) in 

relation to performance standards. 

5.12 Continue to determine the adult hydro survival in relation to performance standards. 

5.13 Continue to determine the effectiveness of transportation versus in-river migration. 

5.14 Continue to determine the reproductive success of hatchery fish spawning in the wild 

relative to wild fish. 

5.15 Determine the effects that hatchery reforms have in reducing extinction risk of listed 

species and contributing to recovery.

5.16 Determine the extent of harvest incidental mortality imparted on non-targeted, listed 

species. 

5.17 Determine the extent of harvest incidental mortality in terms of impact on pre-spawning 

survival and spawning success for listed species.

Harvest Management 

Overview: The exploitation incurred by fishing and other natural resource extraction activities 

on salmon reduced the production of salmon in the Columbia River Basin. Traditional harvest 

management, through imposition of limits on exploitation in directed salmon fisheries, has been 

insufficient to allow salmon populations of the Columbia River to persist at sustainable and 

harvestable levels. 

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Harvest management has failed to consider the relation of salmon abundance to other 

components of the ecosystem, which are connected by the life cycle of the salmon. Harvest 

regulation is a sufficient means of protecting and increasing salmon production only in the 

presence of reasonably pristine habitat. Estimates of salmon production from habitats that are 

constantly declining in productivity will always be too high. Harvest is a factor limiting their 

recovery, yet harvest restrictions in the absence of habitat restoration are not sufficient to permit 

recovery. Overfishing results when estimates of harvestable surplus are too high. A new harvest 

management paradigm is needed that will take habitat productivity into account. 

The ISAB is reviewing the scientific issues associated with harvest management, for example the 

establishment of biological management goals, the information needs for monitoring and 

evaluation, and relationship to recovery planning. The report will address the fundamental 

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

the Columbia River Basin. The ISAB is evaluating the ability to manage for smaller population 

groups given current methodologies, the concept of over-spawning, the role of salmon in the 

ecosystem, the treatment of uncertainty in stock assessments and management evaluation, and 

the assessment of harvest within a life cycle and recovery context. The harvest review will also 

include an examination of the effects of climate variability on the marine environment and the 

interplay of harvest, hatchery production, and varying ocean regimes. Harvest remains an 

important scientific issue and could become increasingly so in the immediate future if marine 

survival continues to improve resulting in large returns of some stocks. 

Management Needs: 

1. Identify and implement the equipment and marking techniques necessary to establish selective

 harvest techniques.

2. Develop an interim policy regarding the operation and harvest management of production 

 from each hatchery where monitoring has been inadequate to complete a comprehensive 

 evaluation. 

3. Determine the level of escapement at the watershed scale necessary to ensure that over- 

 harvest is not taking place?

4. Determine what evidence exists regarding stock-composition and stock-specific abundance, 

 escapement, catch, and age distribution. 

Critical Uncertainties: 

1. Directed and incidental harvest of Columbia River Basin salmon has occurred in the absence 

 of knowledge of harvest impacts on the abundances and viabilities of the majority of the 

 individual native spawning populations. 

2. Most Columbia Basin stocks are at low levels such that harvest in the ocean would have to be 

 very low or non-existent to allow the habitat restoration proposed in the fish and wildlife 

 program and the biological opinions to have a reasonable chance to succeed. 

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3. Uncertainties exist regarding stock-composition and stock-specific abundance, escapement, 

 catch, and age distribution. 

The Council’s Research Recommendations: 

6.1 Develop harvest levels that take into consideration the relation of salmon abundance to other 

components of the ecosystem that are connected by the life cycle of the salmon. 

6.2 Determine how to base sustained-yield management of a salmon population on numerical 

spawning escapement goals at the watershed level, which represent both the productive 

capacities of the habitats for the salmon population and all related salmon populations. 

6.3 Evaluate innovative techniques to improve access to harvestable stocks and reduce 

undesirable direct and indirect impacts to wild populations. 

6.4 Evaluate appropriateness of stocks used in weak stock management. 

This section will be updated based on the ISAB Harvest Management review scheduled for 

completion in January 2005. 

Estuary 

Overview: The Columbia River estuary is an important ecological feature of the Columbia 

River Basin, constituting the physical and biological interface for salmon and trout as they 

transition between their freshwater and ocean life stages. Juvenile salmon utilize various areas in 

the estuary to rear and undergo adaptation to marine conditions. Rearing locations, seasonal 

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

The Columbia River estuary also provides important rearing habitat for other animal species of 

marine origin, and year-round habitat for species that have evolved to live solely within an 

estuarine environment. 

The Columbia River estuary has undergone tremendous changes as a result of settlement and 

development, and these affected its physical character and biological resources. Physical 

characteristics such as depth, velocity, salinity, temperature, and turbidity vary dynamically 

within the Columbia River estuary, presenting a highly variable environment. The environmental 

changes that have occurred have substantially affected habitat availability, habitat quality, 

species composition, and other biological attributes of the estuarine ecosystem. The complexity 

of the physical and biological processes and interactions within the Columbia River estuary 

system contribute to the challenges and opportunities faced by aquatic organisms, including 

salmon and trout. While less is known about the potential for improvement in the estuary 

compared to other parts of the Columbia River Basin, there are indications that substantial 

improvements are possible, and that these improvements may benefit anadromous fish 

populations. 

Characterization of the estuary's physical and biological attributes that support salmon is 

underway, but is in its infancy. The draft NMFS report, Salmon at River's End: The Role of the 

Estuary in the Decline and Recovery of Columbia River Salmon, assessed the potential impact of 

flow regulation on juvenile salmon utilization of the estuary. The report found that hydrologic 

and climate factors likely have consequences for the estuarine physical environment. However 

19
with the existing data it is not possible to separate these effects from compounding factors or to 

rank these factors’ effects on salmon. Yet, it is clear that changes in the food web have occurred 

that affect the estuary's capacity to support juvenile salmon and that have reduced habitat 

complexity. 

The ISAB recommended an aggressive experimental program to reduce the likelihood of 

prolonged uncertainty about the impact of estuarine conditions. The ISAB also recommended 

incorporating monitoring of the physical environment, such as that currently under way by the 

Oregon Graduate Institute, with evaluation of large-scale manipulations of estuarine habitats. 

The intent of these restoration treatments would be to study changes presumed to have had 

negative impacts and to conduct these at a scale that can be measured within the natural 

environment. 

Management Needs: 

1. Determine what actions in the estuary are most beneficial to improving survival. 

2. Changes in the biological processes vary from a fundamental alteration in the basis of the 

 food web to the exclusion of sub-yearling Chinook and chum salmon from a large portion of 

 the tidal marshes. Determine how the effects of these specific changes can be partitioned 

 from the effects of numerous other impacts in the basin?

Critical Uncertainties: 

1. The impact of the significant loss of peripheral wetlands and tidal channels is uncertain. 

These habitats are important to the early rearing, survival and growth of chum salmon, subyearling Chinook, and smaller coho salmon in other West Coast estuaries. 

2. The effects of change in seasonal flows following the development of the hydrosystem are 

 uncertain. Those effects are closely associated with the impact of the development of the 

 navigation channel. In combination these developments have resulted in changes to estuarine 

 circulation, deposition of sediments, and biological processes. 

The Council’s Research Recommendations:

In 2003 the Lower Columbia River and Estuary Partnership (LCREP) and the Army Corps 

of Engineers sponsored a Lower Columbia River and Estuary Research Needs Identification 

Workshop. The following list of research recommendations is largely drawn from the 

proceedings of that workshop. The types of large-scale restoration programs to be evaluated 

include: 

7.1 Evaluate removal of dikes in the lower river and upper estuary to restore connections 

between peripheral floodplains and the river or fluvial zone of the estuary. 

7.2 Determine how to manage sources of salmonid predation in the estuary through 

restoration of natural habitats, removal of habitats artificially created due to channel 

construction and/or maintenance, or controlling predator populations. 

7.3 Determine an allocation of water within the annual water budget for the Basin, that would 

simulate peak seasonal discharge, increase the variability of flows during periods of

salmonid emigration, and restore tidal channel complexity in the estuary, aided by 

removing pile dykes where feasible. 

20
7.4 Implement selected restoration projects as experiments, with pre- and post-restoration 

project monitoring programs. 

7.5 Determine the effectiveness of ongoing PIT tagging and other tagging and marking studies 

and data to determine origin and estuarine habitat use patterns of different stocks. 

7.6 Determine additional shallow water bathymetry data needs for refining the hydrodynamic 

modeling, and identifying/evaluating potential opportunities for specific restoration 

projects. 

7.7 Identify priorities for off-site mitigation projects in Columbia River Estuary tributaries.

7.8 Conduct genetic research to identify genotypic variations in habitat use. 

7.9 Conduct research on food web dynamics. 

7.10 Conduct research on sediment transport and deposition processes in the estuary. 

7.11 Conduct research to understand juvenile and adult migration patterns. 

7.12 Conduct research on the linkages between physical and biological processes. 

7.13 Conduct research on the effect of toxic contaminants on salmonid fitness and survival in 

the Columbia River Estuary and ocean. 

7.14 Conduct research on the effects of invasive species and the feasibility to eradicate or 

control them. 

7.15 Conduct research on the role between micro- and macro-detrital inputs, transport, and endpoints. 

7.16 Evaluate flow effects, river operations, and estuary-area habitat changes on the 

relationship between estuary and near-shore plume characteristics and the productivity. 

Natural Variation and Ocean Productivity 

Overview: Global and regional-scale processes in the ocean and atmosphere can regulate the 

productivity of local marine, estuarine, and freshwater habitats for salmon. Although managers 

cannot control these processes, natural variability must be understood to correctly interpret the 

response of salmon to management actions in the Columbia Basin. 

Salmon abundances in the California Current region (off Washington, Oregon, and California) 

and in the Central North Pacific Ocean domain (off British Columbia and Alaska) respond in 

opposite ways to shifts in climatic regime. During periods of a strong Aleutian Low, 

zooplankton and salmon production generally increase in the Central North Pacific and decrease 

in the California Current, suggesting geographically distinct mechanisms of aquatic production. 

Climatic shifts characteristic of the strong Aleutian Low regime occurred twice this century: one 

from about 1925 to 1946 and another in 1976/77 to the present. Both periods were marked by 

precipitous declines in the coho salmon fishery off Oregon. Opposing cycles of salmon 

abundance between the Central North Pacific and the California Current regions underscore the 

importance of stock-specific regulation of ocean fisheries. Even during periods of high marine 

survival off Oregon, harvest limits must ensure that Columbia Basin stocks are not overexploited 

by northern fisheries trying to compensate for coincidental decreases in the production of stocks 

from Alaska and British Columbia. 

21
Salmon migrations are tied to major ocean circulation systems and yet salmon life cycles are 

shorter than the inter-decadal periods of large-scale climatic change. The abundance of salmon 

tracks large-scale shifts in climatic regime, yet the specific mechanisms of this tracking are 

poorly understood. Stocks with different life history traits and ocean migration patterns may be 

favored under different combinations of climatic regime and local habitat characteristics. Such 

differences afford stability to salmon species over multiple levels of environmental variability. 

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

salmon during freshwater phases of their life cycle, leading to erroneous interpretation of the 

performance of restoration efforts and increased losses of some stocks. The dynamics of salmon 

metapopulations will change under different climatic regimes if, for example, the dispersal of 

core populations or the rate of extinction of satellite populations is a function of fish density. 

Conservative standards of salmon protection may be necessary even during periods of high 

productivity to maintain the genetic slack needed to withstand subsequent productivity troughs. 

Habitat fragmentation and loss of local stocks will likely magnify the effects of productivity 

troughs by also increasing freshwater mortality, inhibiting recolonization of disturbed habitats, 

and slowing rates of population recovery. Thus, in concert with large-scale changes in climate, 

increases in the rates of local extinction and loss of stock diversity may lead to greater synchrony

in the dynamics of salmon populations. Regional patterns of salmon decline in the Columbia 

Basin and throughout much of the Pacific Northwest are generally consistent with this 

synchronization hypothesis. 

Management Needs: 

1. Determine the effects of ocean conditions on anadromous fish populations. 

2. Evaluate or adjust inland actions in response to ocean conditions. 

3. Determine if hatchery production should be scaled back during periods of low ocean 

 productivity in order to minimize competition in the estuary or marine environments? 

Critical Uncertainties: 

1. Lack of long-term monitoring of ocean conditions and the factors influencing survival of 

 salmon during their first weeks or months at sea severely limit understanding of the specific 

 causes of inter-decadal fluctuations in salmon production. 

2. Stock-specific distributions of Columbia Basin salmon in the ocean and the migratory patterns

 of hatchery versus wild salmon are poorly understood. It is important to know whether 

 hatchery practices affect the migratory patterns and potential marine survival of salmon. 

3. There is increasing evidence worldwide that ocean fisheries can have a destabilizing influence 

 on marine food chains. Harvest management programs based on stock recruitment 

 relationships and monitoring of individual species do not provide adequate indicators of the 

 effects of harvest activities on ocean food webs. 

The Council’s Research Recommendations: 

8.1 Determine how different species migrate and utilize the ocean environment. 

8.2 Determine the relative effects of the ocean on different fish stocks compared to the effects 

22
of inland actions. 

8.3 Integrate research on the effects of ocean conditions on productivity of salmon with 

estuarine and riverine research. 

Emerging Issues 

Impacts of Climate Change on Fish and Wildlife Restoration 

Overview: The potential impacts of global climate change are recognized at national and 

international levels. In addition, the impacts of short and longer-term climate variation and 

ocean conditions are now recognized as major contributors to fluctuations and trends in salmon 

abundance coast-wide. While a widely recognized phenomenon, the impacts of climate change 

are rarely incorporated into natural resource planning. The ISAB noted that the Council’s 

program and the NOAA Fisheries recovery strategies do not consider the impacts of climate 

change and implicitly assume a level base case. However, the changes in regional snowpack and 

stream flows in the Columbia Basin projected by many climate models could have a profound 

impact on the success of restoration efforts and the status of fish and wildlife populations. The 

cumulative effects of human disturbance may not become apparent until severe climatic stresses 

trigger a dramatic response. Such interactions may be particularly severe in the Pacific 

Northwest where periods of reduced ocean survival of salmon and periods of stressful freshwater 

conditions (due to reduced precipitation, low stream flow, and increased stream temperatures) 

tend to be concurrent. 

The Council has asked the ISAB to conduct a review of the potential impacts of climate change 

on the success and direction of the Council’s fish and wildlife program. The ISAB is to review 

projections of climate change and synthesize the current scientific understanding of climate 

trends in the Pacific Northwest and how these affect biologically important parameters such as 

marine conditions, stream flow, temperatures, and species ranges. The ISAB will focus on how 

these trends could impact the success of restoration efforts and suggest how consideration of 

these trends might impact the direction of the Council’s program and how the region should 

incorporate knowledge of climate trends in fish and wildlife planning and management. 

The Council requested that the climate change review address two distinct areas of concern, the 

ocean environment and the freshwater environment. The ISAB has proposed to bifurcate the 

review and first address the effect of climate variability on the ocean environment. As 

previously stated, the ISAB intends to complete this analysis as part of the harvest review. This 

approach should allow the ISAB to explore the relationship between varying ocean regimes, 

hatchery production, and harvest rates. In addition, the ISAB will address the Council’s question 

of how climate change may affect the frequency of short-term variation in oceanic conditions 

such as El Nino events as well as longer-term overall marine productivity. Short and medium

cyclic climate variations, as well as longer trends, are likely to impact choices for restoration and 

preservation of fish and wildlife habitats under the Council’s program. 

With regard to the freshwater environment, the ISAB’s Tributary Habitat Report (Council 

Document ISAB-2003-2) considered climate change, but did not explicitly address it. The ISAB 

believes a more complete review is warranted of the potential impact of climate change on the 

freshwater environment including changes to snowpack, stream flow, and species distribution. 

The ISAB intends to fully undertake the freshwater component of the review after completing 

23
the harvest review. The ISAB will focus on describing the potential scale of the impacts of

climate change on the success of restoration efforts and how the uncertainty of impacts could be 

incorporated into fish and wildlife planning and management. The review should be useful in 

informing future program amendments and recovery planning. 

Management Needs: 

1. Determine how climate trends in the Pacific Northwest affect biologically important 

 parameters such as marine conditions, stream flow, temperatures, and species ranges?

Critical Uncertainties: The risks of global warming are potentially great for Columbia Basin 

salmon due to the sensitivity of southern salmon stocks to climate-related shifts in the position of 

the sub-arctic boundary, the strength of the California Current, the intensity of coastal upwelling, 

and the frequency and intensity of El Niño events. While the potential effects of global warming 

on ocean circulation patterns are poorly understood, the implications for salmon restoration 

efforts throughout the Pacific Northwest are significant. 

The Council’s Research Recommendations: 

This section will be updated based on the ISAB Harvest Management review will be completed 

in January 2004.

Toxics 

Overview: Eco-toxicology is an emerging research area, as there is a lack of understanding 

about how contaminants may affect the survival and recovery of listed species, as well as people 

and the ecosystem. For example, in the 1950s the only acknowledged harmful impact of runoff 

from urban areas was flooding. The solution was to build conveyance systems to get water off 

the land. In the 1970s it was decided that the impact of runoff on channels warranted expensive 

channel armoring and detention ponds sized to reduce flow velocity in channels. In the 1980s it 

was learned that the sizes of ponds were still too small to prevent erosion. In the 1990s it was 

learned that dramatic declines in aquatic life and especially anadromous fish resulted from urban 

runoff. 

Today, a major issue is the lack of a "relative risk model" to extrapolate potential contaminant 

risk to salmon in the majority of areas where there are few or no data. (This topic will be 

discussed in a workshop sponsored by EPA and NOAA Fisheries and hosted by the Council in 

spring of 2004.) The inability make even a qualitative assessment of risk from contaminants 

basically anywhere in the Pacific Northwest is a major gap in our understanding that contributes 

to gaps in management. 

Environmental contaminants such as trace elements (including heavy metals), pesticides, 

petroleum, and related petrochemical compounds pose a substantial threat to some aquatic 

ecosystems. Fish are vulnerable in rivers and lakes draining watersheds that support irrigated 

agriculture, mining, fossil fuel power generation, large municipal/industrial complexes, and other 

concentrated sources of human-caused activities. Managers require contaminant surveys and biomonitoring to detect the occurrence and bioaccumulation of suspected contaminants. Studies are 

also needed in aquatic eco-toxicology to detect and quantify fate and effects in the environment. 

24
Endocrine disrupters are a particularly significant issue requiring basic research, currently 

undertaken by the Western Fisheries Research Center of the U.S. Geologic Survey. 

Chemical processes are critical determinants of habitat quality for salmonids, and they should be 

explicitly addressed at the outset of any restoration. In Seattle, adult coho salmon have perished 

when they came back to spawn in small urban streams. Many millions of dollars were spent to 

restore "habitat" in these systems, with a near-exclusive focus on physical processes. 

Longfellow Creek in West Seattle is a regional model for stream restoration, and yet almost 90-

percent adult pre-spawn mortality occurred in the 2002 coho run, apparently as a result of 

degraded water quality. 

It is important to integrate chemical processes into the "habitat" perspective, especially for 

agricultural and urban watersheds. Otherwise, restoration projects will continue to make the 

landscape appear restored, without addressing the health of the underlying ecosystem. The urban 

stream problem should be viewed as a case study in salmon habitat restoration. 

Management Needs: 

1. Determine the extent of toxic contaminants in fish in the Columbia River Basin. 

2. Determine how these contaminants affect fish survival and productivity.

3. Juvenile outmigrant Chinook salmon are accumulating appreciable levels of toxic 

 contaminants before they leave the Lower Columbia River estuary, and the levels are among 

 the highest seen in any populations examined to date by the U.S. Environmental Protection 

 Agency along the Oregon and Washington coasts. Part of this contamination comes from

 hatchery feeds and from bio-accumulative contaminants such as polychlorinated biphenyls and

 the DDT, but it also is known that salmon are exposed via contaminated prey items in the 

 Lower Columbia River. Other contaminants, though not bio-accumulative in fish, are still 

 toxic, and salmon collected at the confluence of the Willamette and Columbia rivers show 

 evidence such exposure as well. 

Critical Uncertainties: 

1. The sources and fluxes of contaminants in the Lower Columbia River estuary have not been 

 characterized. Little information exists as to how salmon and other species are being exposed, 

 such as the relative contributions from upstream sources versus lower river off-channel 

 sources versus hatchery feeds. 

2. Little information exists on contaminant body burdens in hatchery fish versus wild listed 

 stocks. Wild fish will not have the extra exposure from feed that is seen in hatchery fish, but 

 wild fish also may remain in the estuary longer and accordingly have more potential to take up 

 contaminants from the environment. It is known that off-channel habitats, where wild 

 juvenile salmon tend to be found, are the areas with comparatively higher levels of chemical 

 contaminants in sediment and presumably prey. 

3. The biological consequences of the current levels of exposure are unknown, but body burdens 

 of polychlorinated biphenyls are near levels of concern and fish are exposed to multiple 

25
 contaminants. 

4. Because of the critical nature of estuary use for several populations of Pacific salmon with 

 different life histories, toxic contaminant exposure poses a significant uncertainty in 

 considering recovery efforts for Columbia River stocks. 

The Council’s Research Recommendations: 

9.1 Determine how to develop a research, monitoring and evaluation program for chemical 

habitat. 

9.2 Determine how to identify and quantify sources of toxic contaminants in the Lower 

Columbia River. 

9.3 Determine the biological consequences of contaminant exposure in salmon, as well as 

consequences for other species, notably prey species and higher trophic levels, such as 

piscivorous birds. 

9.4 Determine the exposure patterns of wild versus hatchery fish, in populations with different 

life histories and patterns of estuary use, in various listed ESUs. 

9.5 Determine whether contaminant transport in suspended particulates contributes to 

contaminant uptake in fish. Contaminant monitoring and research should be conducted as 

part of overall investigations of chemical habitat quality, including studies of organic 

carbon transport and cycling. 

9.6 Determine the cause and effects of disease, tumors, and other abnormalities of fish on the 

population dynamics of the fish and the implications for ecosystem and human health. 

9.7 Determine potential nontarget impacts of management techniques, such as sub-lethal 

impacts of herbicides on salmonids. 

9.8 What alternative pesticides that can be used for the eradication of specific aquatic nuisance 

species? 

9.9 Evaluate bioaccumulation of toxins and heavy metals in native fishes. 

Invasive Species 

Overview: Invasive species comprise one of the most significant alterations of native 

ecosystems for fish and wildlife, and plants. Research is therefore needed regarding interactions

between native and invasive species, including predators, prey, food chain organisms, and those 

that alter habitat structure; how competitors respond to altered systems and to restoration and 

recovery actions; and how food supplies have been altered and how they can be restored (CENR, 

2000). 

It is important to note the distinction that exists between an invasive species and a non-native 

that is the result of a management decision. An example of a non-native fish species potentially 

impacting anadromous stocks is American shad. In addition to shad, there are a number of other 

introduced and exotic species present in the Columbia River Basin Ecosystem that we know very 

little about. Some of these species include: channel catfish, yellow perch, bluegill/other sunfish, 

crappies, Eurasian milfoil, Asiatic clams (Corbicula manilensis), and others. All of these species 

26
have an impact on juvenile salmonids, either directly (as predators) or indirectly (by altering the 

food base). As these species continue to become more dominant in the ecosystem they will have 

a greater impact on salmon populations. Once established, ANS can permanently alter habitat 

supporting native aquatic species. Research should be initiated as soon as possible to understand 

the significance of these impacts. Offsite projects, particularly lake rehabilitation, have been 

successful in removing hybridized fish populations, creating genetic reserves for native fish, 

drastically improving fisheries, and eliminating source populations for further illegal 

introductions. The Corps should be alert to regional decisions, including Council decisions, that 

might bear on passage or survival issues at the dams. 

Management Needs: 

1. Determine the extent that invasive species affect fish and wildlife in the Columbia River basin. 

2. Determine the extent that shad negatively impact anadromous fish. 

3. Determine the economic consequences of invasions, such as the effect of Hydrilla on native 

 species, recreation, lakefront property values, and power generation.

4. Determine what environmental manipulations can be accomplished in an environmentally 

 sensitive manner to reduce likelihood of establishment or inhibit growth and dispersal of 

 invasive populations? 

Critical Uncertainties: Habitat restoration may be ineffective at restoring native species where 

introduced non-native species are well established. Available science suggests that non-natives 

can be effectively suppressed where habitats are maintained by a natural range of flow and 

temperature variation. However, abrupt changes in reservoir management could temporarily 

drive existing populations of some non-native fishes into tributary habitats, increasing the risk of 

their colonization of tributaries. Conversely, reservoir changes also will likely create new 

mainstem habitat refugia for native fishes. The risk of dispersal and establishment of non-native 

fishes will be lowest where tributaries retain relatively natural streamflows, thermal regimes, 

habitat diversity, and intact native fish assemblages. 

The Council’s Research Recommendations: 

10.1 Determine the impact of non-indigenous (exotic) aquatic and terrestrial species on 

salmonid recovery. 

10.2 Determine the environmental constraints on abundance and distribution of currently 

established or eminently threatening species. 

10.3 Determine the ecological consequences of invasions (competition, predation, and 

cascading trophic effects on native species, nutrient cycling, effect of management 

activities). 

10.4 Determine how low-density populations of invasive species can be detected (new 

monitoring techniques and optimized search protocols). 

10.5 Develop rapid response methodologies to eliminate newly introduced species at the source 

of introduction before they spread and become unmanageable in the environment. 

10.6 Determine how presently accepted non-indigenous species (warm-water fish) can be 

27
managed to minimize ecological effects. 

10.7 Develop and research effective biological control agents to treat exotic invasive 

infestations.

 Impact of Human Development Patterns on Fish and Wildlife Restoration 

Overview: Like climate change, the impact of an increasing human population in the Columbia 

Basin is a widely recognized issue but one that is rarely incorporated into fish and wildlife 

planning. Human population of the Columbia Basin is increasing rapidly, a trend that is 

expected to continue. This increase is not occurring uniformly across the basin, but is largely 

concentrated in and around urban areas and contributes to specific impacts such as toxics. The 

increased population will potentially impact non-urban areas as well through increased recreation 

and housing in riparian and rural areas. At the same time, the economy of the region is shifting 

with the potential for both positive and negative impacts on fish and wildlife habitats. The ISAB 

has pointed out that the Council’s program and the NOAA Fisheries restoration plans do not 

include consideration of these trends but, as with climate change, assume a level base case. 

Because the Council’s fish and wildlife program mitigates human impacts on fish and wildlife 

habitats, it is important to consider human demographic trends and their potential impact on fish 

and wildlife habitats. In April 2002, the Council asked the ISAB to provide an analysis of the 

projected trends and patterns in human population growth patterns in the Columbia Basin and 

how these might affect the success and direction of the Council’s program.

Management Needs: The ISAB should review information on population projections and 

patterns of human population increases across the landscape. The review should discuss how 

these changes might affect fish and wildlife habitats and address how projected changes in 

economic patterns might moderate or exacerbate these impacts. Finally the ISAB should suggest 

how human demographic changes could be effectively incorporated into fish and wildlife 

planning. The ISAB should be clear that the Council is not asking for recommendations or 

conclusions on the need for changes in land use laws or other social aspects not associated with 

the development of subbasin plans and the Council’s program. The ISAB may conduct a review

of population growth at a future date. 

 

28
II. Charting A Course for the Future: Identifying Research Priorities 

This chapter summarizes current research projects under the fish and wildlife program, compares 

these projects with the recommendations for future research set forth in Chapter I, and identifies 

remaining gaps in knowledge. 

Allocation of Program Versus Research Expenditures 

The Northwest Power Act establishes Bonneville’s obligation to fully mitigate for fish and 

wildlife impacts from the development and operation of the hydropower system. The Council 

recognizes its obligation, in turn, to develop a program that guides Bonneville’s mitigation 

efforts and is staged to accommodate yearly budget limitations. The Council has adopted the 

following funding principles to prioritize among the many needs to address impacts to fish and 

wildlife throughout the basin: 

• The Bonneville Power Administration will fulfill its Fish and Wildlife Funding Principles 

(September 16, 1998) including the commitment to "meet all of its fish and wildlife 

obligations." 

• The determination of provincial budget levels should take into account the level of 

impact caused by the federally operated hydropower system. Other factors will also 

influence this determination including opportunities for off-site mitigation.

• Wildlife mitigation should emphasize addressing areas of the basin with the highest

proportion of unmitigated losses. 

Table 1 (page 3) portrays the current distribution of research funding in the fish and wildlife 

program under Bonneville’s “direct funded” category. All of the funding for a project is 

assigned to the primary topic, even for projects addressing multiple topics. A future phase of

analysis could achieve greater precision of funding by specifying amounts for each research 

objective within a project and more closely examining the connections between current projects 

and the research recommendations. Assessment of the relevance of on-going project objectives 

to the research recommendations identified in this plan should be made after this plan is 

finalized. 

The current allocation of funds targeting research indicates that two topics dominate 

expenditures under the research agenda, hatchery effectiveness at $30.1 million and habitat at 

$13.6 million. The Council is maintaining this allocation until a new budget allocation is 

adopted. Thus, the Fish and Wildlife Program includes a general allocation of expenditures to 

guide the overall program by resource category, but not a dedicated allocation to guide research. 

In addition the Council has not yet developed additional guidance on the allocation of funds by 

research topic, some of which are unique to a single resource category (topic of ocean 

productivity and category of anadromous fish), while others, such as monitoring and evaluation, 

are relevant to anadromous fish, resident fish, and wildlife. 

29
Comparison of Current Council Research with Recommendations for Future Research 

Chapter I identified specific recommendations by research topic. Tables 1 and 2 describe the 

number of projects and costs associated with on-going research by these topics under the direct 

funded and reimbursable programs, respectively. The relationship between research that is 

recommended and that which is on going is summarized in Table 3. Table 3 shows in a general 

way the extent to which research recommendations are being addressed by current projects and, 

thereby gaps in coverage. It natural for these gaps to exist considering that this is the first effort 

to compile a list of research recommendations for the region and that the current pool of research 

projects developed over a long period of time in response to: long-standing objectives of the 

Council’s Fish and Wildlife Program; Provincial Review project solicitations; and the 

requirements of the federal biological opinions and other planning documents. 

Table 3. Research Recommendations and Coverage of Recommendations by 

 Fish and wildlife Program and Army Corps of Engineers and Bonneville Projects

Research Topic 

and 

Number of 

Research 

Recommendations

in Parenthesis 

Number of 

Research 

Recommendations

Currently or

Previously

Implemented by 

the Council’s

Program 

Number of 

Research 

Recommendations

Partially

Implemented by 

the Council’s

Program 

Number of 

Research 

Recommendations

Currently or

Previously

Funded by the 

COE/BPA 

Number of 

Research 

Recommendations

Partially 

Implemented by 

the COE/BPA

Total Number of 

Research 

Recommendations 

Implemented in 

Whole or in Part 

Hatchery

Effectiveness (7) 

4 0 5 1 10

Hydropower (21) 1 0 12 3 16

Habitat (23) 8 2 1 0 11

Recovery

Planning (13) 

0 0 0 0 0

Monitoring/ 

Evaluation (17) 

7 7 10 0 24

Harvest 

Management (4) 

0 0 0 0 0

Estuary (16) 10 1 3 0 14

Natural Variation 

and Ocean 

Productivity (3) 

1 0 0 0 1

Toxics (9) 0 1 0 0 1

Invasive species 

(7) 

0 2 0 0 2

Total 120 31 13 31 4 Total 79

The results in Table 3 were derived from an evaluation of each research recommendation 

identified in Chapter I, as “covered, partially covered, or not covered” by the fish and wildlife 

program or the projects of the Army Corps of Engineers or Bonneville. Please note that neither 

the number of current projects, nor the amount allocated to a given topic in Tables 1 and 2, is 

indicative of whether research questions relevant to the recommendations set forth in Chapter I 

30
are being asked or answered. The purpose of Table 3 is simply to convey a sense of current fish 

and wildlife program coverage of the compiled research recommendations. The last column in 

Table 3 reports the total number of research recommendations fully or partially implemented by 

on-going or recent projects. For the topics of hatchery effectiveness, and for monitoring and 

evaluation, some recommendations are being implemented by more than one project. More 

importantly, please note that some research topics have no associated research activity, and 

therefore constitute “gaps.” Thus, Tables 1 and 2 portrayed current activity, while Table 3 

identifies gaps in knowledge that need to be addressed.

Yet Table 3 also indicates that many of the research recommendation set forth in Chapter I are 

already being addressed by current or recent projects. The fact that many of the research 

recommendations are already being addressed explains why the number and/or salience of those 

that remain may appear unexpectedly low for some research topics. Yet the apparently high 

degree of project coverage for some research topics by itself does not mean that the hard work 

has been completed. More realistically, it means the existing projects provide a strong start on a 

research program. Future analysis could more closely examine the connections between current

projects and research recommendations and identify opportunities for existing projects to address 

the remaining gaps. 

Identifying Priorities for Future Research 

Science is subject to the common tendency to add knowledge about already well-defined 

topics instead of seeking entirely new approaches and concepts. While incremental gains 

in understanding recognized problems are certainly necessary and it is appropriate to 

use science to support and refine existing management options, its value as a means to 

identify and test new options should not be overlooked. Research directed at further 

incremental gains in familiar subject areas must be balanced by research to close the 

many knowledge gaps. (Emphasis added.) 

-- Committee on the Environment and Natural Resources, 2000 

ISRP reviews have highlighted the need for a basinwide research plan that would help close 

these knowledge gaps by evaluating whether on-going research is salient, identifying needed 

shifts in emphasis, and identifying emerging research topics. The ISRP recommended that the 

research plan address overarching questions and assist in making decisions about the relative 

importance among projects by providing a prioritization for future research. Closing key gaps in 

knowledge was the priority for the research plan identified by the Council’s independent science 

groups at their workshop, and the Committee on the Environment and Natural Resources in their 

2000 report. 

To implement this recommendation, the draft research plan proposes to address knowledge gaps 

in the following way. A “gap in knowledge” is considered to exist whenever a research 

recommendation set forth in Chapter I is not being implemented or addressed by a research 

project under the Fish and Wildlife Program. The research recommendations that remain 

unaddressed are considered to be research priorities. This analysis was conducted by staff, and 

would be revised as part of the review of the research plan by the Council, ISAB and ISRP, fish 

31
and wildlife managers, and others. The significance of the remaining gaps is a management and 

policy issue. 

The research recommendation and critical uncertainties identified in the preceding section are 

sufficient to guide implementation of the research plan action at a programmatic scale, such as 

by informing the selection of specific research recommendations for requests for proposals. 

Implementation of the plan at the project scale will occur through ISRP review and the future 

project selection process. During this phase of implementation the technical feasibility and costeffectiveness of individual projects will be considered as factors in the review process. The 

Council, as necessary, may also respond to rapidly emerging management uncertainties by 

identifying additional research priorities. 

Balancing Curative and Preventative Approaches to Restoration 

Today the fish and wildlife program is in a transition period. After 20 years of implementing a 

broad-based program for restoring anadromous fish, resident fish, and wildlife, the Council is 

now reconfiguring the program to address new responsibilities under the Endangered Species 

Act (ESA). In order to successfully address these new and more specific responsibilities under 

the ESA, this draft research plan provides specific guidance for research.

The Council emphasizes a balanced approach to implementing the fish and wildlife program, 

despite strong external pressures to shift the entire program into an ESA implementation mode. 

Shifting program emphasis too far in the direction of the ESA could become self-defeating, as 

the curative approach embodied in the ESA is expensive and the outcomes are uncertain. In 

contrast, the fish and wildlife program embodies the preventative approach of protecting the 

viability of all affected species to preclude additional listings under the ESA. The preventative 

approach is less expensive and more likely to protect existing fish and wildlife. The Council 

must strike a balance between these two approaches, even while moving beyond the status quo. 

From a policy perspective, the Council has an interest in emphasizing research in the following 

areas: 

1. Mainstem operations including spill, flow augmentation and fish transportation. 

2. Rearing and spawning habitat, particularly quantification of benefits from riparian protection, 

 improved screening and increased seasonal water flows. 

3. Estuary and near shore ocean habitats. 

4. Evaluation of new approaches to harvest, such as selective harvest technology. 

Integrating Research Results into Council Policy and Decision-making 

The integration of scientific knowledge into management decision-making is a challenging task 

for public officials, planners, and environmental lawmakers. This integration is central to 

adaptive management, a concept that provides a framework for managers to launch the 

implementation of policies despite uncertainty, variability, and potential risks. At the core of this 

32
approach is a deliberate plan to learn from decisions and progressively fill knowledge gaps. This 

way, management actions, whether successful or not, provide valuable information to improve 

our understanding of program effectiveness and influence future management decisions in 

subsequent iterations of the research cycle. 

Adaptive Management 

In practice, adaptive management is a method for taking action in the absence of information, or 

when only limited information is available. This may occur when the information is so unique 

that it does not exist; there is no basis in prior experience from which to extrapolate; or, when 

prior experience occurred at such a different scale as to be irrelevant. Adaptive management 

provides a valuable tool for ensuring that timely feedback from such diverse activities informs 

the re-direction of future research to increase effectiveness. In their seminal work applying 

adaptive management in a hydropower context, Professor Kai Lee and the late Jody Lawrence 

wrote: 

Adaptive management is learning by doing... Adaptive management is both a conceptual 

approach and a strategy for implementation. As a conceptual approach, it sets a 

scientifically sound course that does not make action dependent on extensive studies. As

a strategy for implementation, adaptive management provides a framework within which 

measures can be evaluated systematically as they are carried out. Adaptive management 

encourages deliberate design of measures. This assures that both success and failures 

are detected early and interpreted properly as guidance for future action. Information 

from these evaluations should enable planners to estimate the effectiveness of protection 

and enhancement measures on a systemwide basis. Measures should be formulated as 

hypotheses. Measures should make an observable difference. Monitoring must be 

designed at the outset. Biological confirmation is the fundamental measure of 

effectiveness. (Emphasis added.) 

(From Adaptive Management: Learning from the Columbia River Basin Fish and Wildlife 

Program, Environmental Law Vol.16:431-460, 1986.) 

The National Research Council (NRC) related several lessons learned about the practicability of 

adaptive management and the institutional conditions that affect how experiments on the scale of 

an ecosystem can be conducted (NRC 1996). These lessons are: 

1. Learning takes from decades to as long as a century. Patience is both necessary and difficult, 

 particularly in institutional settings such as government that work in faster cycles. 

2. Systematic record keeping and monitoring are essential if learning is to be possible. But 

 collecting information is expensive and often hard to justify at the outset and during times of 

 budget stringency because the benefits of learning are hard to estimate quantitatively. 

3. Cooperative management in the design and execution of experiments is indispensable. 

 Experimentation within the context of resource use depends on the collaboration of resource 

 users. 

33
4. Adaptive management does not eliminate political conflict but can affect its character in 

 important, if indirect, ways. 

It is important to note that the NRC found that, paradoxically, each of these lessons runs counter 

to, or at cross-purposes with, the administrative framework of the ESA. This disconnection is 

the source of several factors confounding activity in the planning arena. One example is that the 

current approach to recovery planning for salmonids relies heavily on offsite habitat mitigation 

to generate increases in productivity. It may well be that habitat can meet this expectation, yet 

habitat restoration has historically been an underutilized “H,” and will require the longest 

timeline to quantify the benefits conferred by a projects in terms of increases in life stage 

productivity. 

 

Further, it remains to be seen whether experimental research on monitoring and evaluation will 

in fact generate a basis for quantitatively establishing causal linkage between benefits conferred 

at the project site yielding increases in life-stage productivity. The quest for biological 

confirmation, through the monitoring and detection of increases in life-stage productivity, is a 

central tenet of the 2000 FCRPS Biological Opinion. 

In sum, significant planning challenges arise from the disconnection between the quest for legal 

certainty and what are considered acceptable levels of scientific uncertainty. There is an 

expectation within legal proceedings that the certainty of science be absolute. Yet legal rules, 

such as the Federal Rules of Civil Procedure, have exceptions, and exceptions to the exceptions. 

In the legal arena, arguments are based on differing and competing applications of the rules to 

interpret facts. In the science arena, hypotheses are used to test what the facts are. Despite these 

difficulties, an important alignment of interest groups was achieved through the protracted 

negotiations that culminated in the Basinwide Recovery Plan (All-H Paper) and the derivative 

FCRPS Biological Opinion. Recognizing that it took five years to negotiate this approach to 

recovery, this plan acknowledges the importance of implementing the All-H approach long 

enough to constitute a fair test. 

Evaluating the Council’s Research Program 

An inaugural workshop of the Council’s three independent science groups was held in 2003 to 

consider progress on a regional research plan. The primary topics of discussion were critical 

uncertainties and research needs, and the findings of the workshop are reflected in Chapter I. 

This plan proposes that workshops of the independent science groups be held as needed, but in 

advance of future project selection processes. The evaluation of the research plan should be a 

standing agenda item. These workshops can provide an evaluation of progress, or lack of 

progress, on research issues significant to fish and wildlife in the Columbia River Basin. Science 

group workshops present an opportunity for: 

1. Discussion among the science groups of the ISRP’s Retrospective Review; 

2. Evaluation of progress toward answering the research questions in the plan; 

3. Highlighting research accomplishments; and, 

34
4. Updating the plan with new research questions and priorities. 

Workshops can provide a forum for moving forward, as well as looking back. In between the 

workshops, 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 critical questions, such as 

transportation effects, and projects synthesized to address that topic. 

• Workshops and symposia on emerging topics, such as toxics, are a good way to shift 

to a preventative mode of operation. 

Another mechanism for evaluating and re-directing the implementation of the research plan 

should be the convocation of ion Workshops to address emerging or previously unanticipated 

research issues as needed. These workshops will help assess future research topics through oral 

presentations by authorities on the topic, development of initial hypotheses by participants, 

reporting of results of relevant studies, evaluation of the potential contribution to the regional 

body of knowledge, and assessment of the ease or difficulty of implementing research results 

into management actions. The workshops will promote the free flow of scientific information 

and provide the Council with a credible basis for funding decisions. 

35
III. Developing and Implementing a Regional Research Agenda

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 

Acknowledgement of the dominance of the “sustaining” role of science in the Columbia River 

Basin is an essential element of any assessment of where restoration and recovery efforts stand 

today. This recognition does not impugn the quality of the science conducted in the basin, but it 

does help explain why in some cases work of apparently low relevance is continued, while in 

other cases the application of results of high relevance remains a promise unfulfilled. Further, it 

explains disparities in the availability of data to support various management alternatives. A 

common manifestation of this phenomenon is that insufficient information will be available on 

politically controversial management alternatives.

In the selection of new research projects, agencies understandably tend not to fund studies that 

seem to have limited usefulness for supporting current management practices, or that might 

produce results that actually contradict current practice. Thus, the scientific basis for making 

management decisions is skewed by the propensity of institutional funding sources to support 

non-controversial research on an almost indefinite basis, thus supporting repetitive research that 

generates diminishing data returns. Despite the systemic nature of some of these impediments, 

they can be overcome by a combination of conscious effort and alternative approaches. 

In 1996 the National Research Council stated that current institutional arrangements in the 

Pacific Northwest have contributed to the salmon problem and probably will need modification 

if the problem is to be solved and that an understanding of how to include “good science” as part 

of the institutional arrangement is important (NRC, 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. 

Cooperative Research: Building a Regional Research Partnership

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 

36
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.) 

-- National Research Council, 1996 

Although the Northwest Power Act process falls short of the ideal of “power-sharing in the 

exercise of resource management” (Pinkerton, 1992), it did merge the inherent conflicts of fish 

and wildlife mitigation and hydropower production in a way that forced conflicts into the open 

and fostered joint action. Further, 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). 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. 

The region lacks a regional decision making forum that can arbitrate between competing 

initiatives to implement the All-H approach. Therefore a forum should be convened where 

researchers can cross-disciplinary and institutional boundaries and find peer support for 

potentially controversial recommendations. A key challenge for such a research partnership is to 

move beyond the piece-meal solutions that may have undercut the overall success of past 

restoration efforts. The fish and wildlife scientists and managers in the region could accomplish 

this by cooperatively designing a research initiative to address the critical uncertainties regarding 

fish and wildlife restoration, for example mortality across the life cycle of the salmon. 

Recommendation: Policy makers such as the Council members and regional executives should 

foster cooperation of the currently compartmentalized research agendas and budgets of entities 

that share common objectives, by convening an informal forum to provide a point of interface for 

research program leads, such as a research consortium or partnership. 

In the past, attempts have been made to convene executive level multi-agency groups and fora 

for the purpose of coordinating resource management decision-making across the Columbia 

River Basin. These unsuccessful efforts indicate that it may not be possible to convene a single 

“super-group” that can address management decisions across all subject matter areas of resource 

management in the Columbia River Basin. This is in part due to significant differences between 

programs in their missions, structures, proposal development, and proposal review processes. 

Consequently, this plan simply recommends the convocation of a partnership to foster 

collaborative research. A research partnership could endeavor to transcend the institutional 

impediments described in the section on adaptive management. 

Recommendation: A research partnership should be convened to provide a forum for the 

identification of shared research priorities and development of collaborative implementation 

strategies. 

Many of the resource management entities contacted during the development of this research 

plan expressed support for this concept. The Council could convene and initially host a regional 

37
research partnership, as 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. 

Yet in order to succeed, a collaborative regional research initiative would require support in two 

key areas; monitoring and evaluation, and data management. The research partnership could 

draw support on monitoring issues from the Pacific Northwest Aquatic Monitoring Partnership 

(PNAMP), charted in 2004 to coordinate a regional approach to monitoring. The mission of 

PNAMP is to coordinate existing monitoring programs in an effort to develop the feedback 

mechanism that is missing at the programmatic scale. The Northwest Environmental Data 

Network is an initiative to deploy a regional data standards program to support regional data 

networking. The development of a regional data management partnership is a concept for which 

Council sponsored projects and support have already provided significant substance. 

If such a configuration of partnerships were to coordinate their respective efforts, the research 

partnership could increase the ability of the region to reduce scientific uncertainty; the 

monitoring partnership could support the evaluation that has long been missing from the 

Columbia River Basin; and the data partnership could support a data repository for analytical 

manipulation at different scales. Even if these partnerships are only semi-formal in an 

administrative sense, and only loosely coupled in a decision-making sense, the synergy that 

would result from linking research, monitoring and evaluation, and data management would 

significantly increase the ability of the region to re-direct its efforts based on the cumulative 

results of work at the project scale. 

Implementing Research Recommendations: Opportunities for Collaboration 

Basic scientific information is lacking for many of the remedial actions that must be taken 

over a longer term. 

-- Committee on the Environment and Natural Resources, 2000 

Hatchery Effectiveness

There is an urgent need for fundamental information on the interactions of hatchery-produced 

fish with wild populations (Return to the River, 1996; CENR, 2000). Effects of hatcheryproduced fish on wild stocks potentially include genetic alteration, competition, predation, and 

disease. The fish and wildlife program should include mechanisms to ensure that 

supplementation projects are collecting the data necessary to test their effectiveness. Project 

analysis and reporting should be required. 

Current monitoring and evaluation efforts are inadequate to estimate either benefit or harm from

ongoing supplementation projects. It is imperative that requisite reference populations be 

established and that adequate levels of monitoring and evaluation be included as part of the 

basinwide adaptive management experiment. Specifically, multiple supplementation projects 

should be coordinated across the Columbia River Basin so that in aggregate they constitute a 

38
basinwide adaptive management experiment, maximizing the information collected and 

attempting to reduce uncertainty. Future investment should be in establishing robust experiments 

with un-supplemented reference streams and rigorous monitoring. 

Sufficient attention must be given to evaluating ecological interactions, so that it will be possible 

to determine whether the intrinsic biological attributes of the species being supplemented, biotic 

interactions, or habitat limitations constrained the anticipated increases in natural-origin adult 

recruits. Many hypotheses and conjectures concerning supplementation are largely unevaluated. 

Recommendation: Determine the diversity of life history types and species that need to be 

maintained in order to sustain a system of populations in the face of environmental variation. 

Hydrosystem 

The Council has proposed increasing the priority of research on the migration corridor. If the 

Council plan for the mainstem is to provide the best benefit for fish migration, it must have better 

estimates of the magnitude of the benefits from spill, flow augmentation, and fish barging. The 

new research questions introduced for the mainstem should guide these additional expenditures.

Anadromous Fish Evaluation Program 

The U. S. Army Corps of Engineers, Northwestern Division, has sponsored biological studies 

continuously since 1952 in an integrated, applied research program to better understand and 

improve anadromous fish passage conditions at its multi-purpose projects on the Columbia and 

lower Snake Rivers, in Oregon and Washington. These research, monitoring, and evaluation 

studies are managed under the Anadromous Fish Evaluation Program (AFEP). The AFEP is the 

process that coordinates the Corps’ fish program with federal, state, and tribal fish and wildlife 

agencies that provide both technical and policy level input to the Corps on study objectives, 

experimental design, and methodologies. (A few AFEP studies are funded from project 

operations and maintenance accounts as well.) 

The main purpose of the AFEP is to produce scientific information to assist the Corps in making 

engineering, design, and operations decisions for the eight main-stem Columbia and Snake river 

projects to provide fish with safe, efficient passage through the mainstem migration corridor. 

Each project (dam) has multiple authorized purposes and uses, including migratory fish passage; 

and is affected by several environmental and project operating statutes. These include the ESA, 

Clean Water Act, National Environmental Policy Act, Northwest Power Act, and the Fish and 

Wildlife Coordination Act. At the current time, ESA guidelines for protection of listed salmon, 

steelhead, and white sturgeon species are contained in biological opinions prepared by NOAA 

Fisheries and U.S. Fish and Wildlife Service (USFWS), and strongly influence the Corps’ fish 

program, including the AFEP. These biological opinions include measures to evaluate and make 

decisions on new and existing passage technologies and system configurations. The resulting 

biological studies have a high priority in the AFEP program. Most are conducted to facilitate 

system configuration decisions by answering key questions about behavior, survival, and 

condition of fish as they migrate through the mainstem corridor. 

39
Most studies are integral components of elements of the Columbia River Fish Mitigation project, 

a large Corps construction account that funds numerous fish passage improvements at Columbia 

and Snake river mainstem dams. Research schedules are closely linked to those elements so that 

biological questions can be answered in a timely manner. Historically, Corps funded studies 

have focused primarily on project-specific adult and juvenile salmonid passage issues. However 

recently, estuarine, mechanism oriented, sturgeon and studies of juvenile and adult lamprey have 

been conducted as well. Most of the passage facilities and operations on the river have been 

developed and refined based on results of these studies. Passage issues include adult fish ladders 

and collection channels, juvenile bypasses with turbine intake screens, turbine passage, the 

juvenile fish transportation program, spill for juvenile fish passage, and a comprehensive set of

project/hydrosystem operating criteria. Consequently, research studies evaluate passage success,

survival, and fish condition for these technologies. Many research projects are related to new 

passage technologies, while some evaluate existing project features. 

Based in part on the recommendations by the ISRP, the Corps is also working to develop a longterm strategic plan for its fish research program. A long-term plan currently exists for Bonneville 

Dam and is being developed for John Day and The Dalles dams. A document is also being 

developed to examine the major system improvements at McNary and the Lower Snake River 

Dams. This plan will be incorporated or referenced in more detail in this plan at a later date. 

Short-Term Research Recommendations

1. Implement an experimental operation at Libby Dam that will limit the summer draft to 10 feet 

 from full pool by the end of September. (NOAA could not say what effect it would have on 

 outmigrating fish in the mainstem.) 

2. Implement an experimental operation at Hungry Horse Dam that will limit the summer draft 

 to 10 feet from full pool by the end of September. (NOAA could not say what effect it would 

 have on outmigrating fish in the mainstem.) 

3. If feasible, evaluate the biological effects on salmon survivals in the Lower Columbia River 

 of possible flow augmentation from Libby and Hungry Horse dams. Design and implement 

 new survival tests in the lower river to better understand the movement and survival of fall 

 Chinook. (Council is convening a Symposium on Reservoir Operation/Flow Survival to 

 address these first three issues.)

4. Studies directed at turbine improvements need to be undertaken in the context of other fish- 

 protection approaches available in the basin and prioritized for budgeting according to their 

 potential benefits to fish versus benefits to the power system.

Long-Term Research Recommendations

1. Continue the transportation study targeting Snake River fall Chinook. Evaluate relative 

 success of transporting various groups of fall Chinook throughout the Snake River. 

40
2. Implement actions to reduce the level of toxic contaminants in the Columbia and Snake 

 river released from Corps facilities. 

3. Determine habitat conditions in all of the mainstem reservoirs. 

4. The AFEP lacks, but would benefit from, a strategic, multi-year research plan or framework. 

 Strategic multi-year research plans with contingencies and alternative tests built in would 

 make the program stronger by reducing time and resources spent annually. (Initiated in 2004.) 

5. Strategic planning should be conducted by the Corps to identify where a more mechanism-

 oriented strategy (e.g. behavioral or mortality mechanisms) could yield benefits in research 

 productivity, efficiency and economy of time and funds (and thus faster implementation of 

 fish-protective features).

Habitat 

Major long-term interventions will be required to restore the spawning and rearing sites, 

migratory corridors, and the spatial and temporal diversity of these habitats and to reconnect 

habitat types important for the continuity in the life cycles of salmon (CENR, 2000). In response 

to the recommendation of the independent science groups, the 2000 Fish and Wildlife Program

places a greater importance on improved natural habitat for fish spawning and rearing throughout 

their life cycle, including estuary and marine stages. 

Through subbasin planning a greater emphasis can be placed on the protection and restoration of 

habitat. This will require additional research to verify and measure the benefits from a wide 

variety of coordinated actions. For example, it will be important to measure the benefits from

riparian protection, improved screening at water diversions, and increased seasonal flows. While 

we can assume such actions will be good for fish, there is little information about the magnitude 

of these benefits or how they may vary under different conditions. 

Restoration of fish and wildlife will require restoration of ecological functions and processes to 

reestablish healthy watersheds. For example, there is a need for scientific research to define what 

functions of a riverine ecosystem must be restored for salmon and how to accomplish this 

restoration while maintaining the societal benefits of electricity production, navigation, flood 

control, irrigation, and recreation provided by dams. 

Regarding mainstem habitat, an overview of current conditions needs to be developed and 

integrated into a coordinated plan for improving specific aspects of mainstem habitat. The 

mainstem habitat initiative is not focused on the mainstem habitat needs of the salmon and 

steelhead populations currently listed. Rather, it is a multispecies approach that recognizes that 

mitigation, enhancement, and rebuilding opportunities in the mainstem may have greater benefit 

for non-listed populations than to listed populations. 

Short-Term Research Recommendations

41
1. Determine the importance of protecting mainstem habitat for recovery of bull trout.

2. Determine how to stabilize and improve burbot populations. 

Long-Term Research Recommendations

1. Determine whether restoration of substantial mainstem habitat can be achieved by drawdown 

 of selected reservoirs to expose and restore alluvial reaches, for example in the upper ends of 

 John Day and McNary pools. 

 

2. Determine whether free-flowing reaches downstream of hydroelectric dams can be regulated 

 to achieve normative flow and temperature regimes thereby allowing the river to naturally 

 restore instream and floodplain habitats and food webs. 

3. Determine how to provide storage reservoirs with selective withdrawal systems to create a 

 more normal annual temperature cycle in the rivers. 

4. Conduct the necessary feasibility studies to restore anadromous fish to blocked areas. 

Harvest Management 

Harvest remains the primary reason for hatchery programs in the Columbia River Basin. This is 

especially true in the lower river, whereas the purpose of upper river programs appear more 

evenly divided between harvest and conservation. Yet the management of fisheries on mixed 

hatchery and wild stocks is believed to have contributed to the decline of natural production in 

the Columbia Basin. Because of declining natural production, those fisheries that still harvest 

Columbia River salmon are largely supported by hatcheries. 

Hatcheries intended solely to produce fish for harvest may be used to create a replacement for 

the lost or diminished stocks. Hatcheries must be located and operated in a manner that does not 

lead to adverse effects on other stocks through excessive straying or excessive take of weak 

stocks in a mixed-stock fishery. The risks of detrimental effects of straying are a de-facto 

supplementation to naturally spawning populations are real, and likely far more serious than the 

risks involved in a well-designed supplementation program. 

Short-Term Research Recommendations

1. Determine the relationship of salmon abundance to other components of the ecosystem that 

 are connected by the life cycle of the salmon. 

2. Ascertain whether sustained yield management of can be based on numerical 

 spawning escapement goals at the watershed level. 

42
Recovery Planning 

The NOAA/USFWS Biological Opinions: What Research and Why? 

On December 21, 2000, the federal government released the final version of a comprehensive, 

long-term strategy to restore threatened and endangered salmon and steelhead in the Columbia 

River Basin. This strategy outlined specific actions to be taken by the federal government and 

proposed additional actions for tribal, state and local governments, which together would prevent 

extinction of the 12 ESA-listed species and lead to their ultimate recovery. The biological goals 

were to halt the decline in salmon populations within five to ten years and establish increasing 

trends in abundance within 25 years. Details of the strategy reside in two documents: 

• A final biological opinion by NOAA Fisheries required under the ESA that will guide 

operations of the 29 federally owned dams in the Columbia Basin for salmon and 

steelhead recovery. 

• A final Basinwide Salmon Recovery Strategy (also referred to as the "All-H" Strategy) 

that incorporates requirements of the biological opinion with other measures to improve 

hatcheries, limit salmon harvest, and, most importantly, restore salmon habitat. 

Also on December 21, 2000, the USFWS released its final biological opinion on the effects of 

power system operations on the endangered Kootenai River white sturgeon and threatened bull 

trout. This strategy was based on the best available science, extensive public input, and broad 

discussions and consultations with tribal, state, and local authorities. It placed the highest priority 

on actions with the best chance of providing solid, predictable benefits for the broadest range of 

species. It also established mechanisms to gauge success, factor in new science as it became 

available, and adjust the recovery actions at major midterm reviews as needed. Federal agencies 

are using this strategy as a blueprint to guide their recovery efforts and interactions with state and

local governments and tribes. 

Monitoring and Evaluation: How to Evaluate Restoration Projects? 

A decade ago, the Scientific Review Group stated: 

We again call for immediate development and implementation of a system-wide 

 monitoring and evaluation program that is also responsive to critical uncertainties. 

-- Critical Uncertainties in the Fish and Wildlife Program (SRG 93-2) 

In essence, monitoring measures change while research identifies the causes of the change. The 

purpose of the monitoring and evaluation strategies of the fish and wildlife program is to assure 

that the effects of actions taken under the program are measured and analyzed to provide better 

knowledge of the results, and then use this knowledge to direct future actions. The absence of a 

monitoring and evaluation program for the Columbia River Basin has confounded restoration 

and planning efforts for decades. 

43
Rather than try to design a complete and comprehensive monitoring program, which it probably 

cannot afford, the region should identify and develop consensus about how much and what types 

of monitoring are needed, and can be afforded, for managing an effective fish and wildlife 

restoration program. All opportunities to conduct collaborative research on monitoring should 

be fully exercised. For example, the effectiveness research being conducted in pilot watersheds 

under the fish and wildlife program is highly analogous to work in Puget Sound under the aegis 

of the Pacific Coastal Salmon Recovery Fund. Further, the Bonneville Environmental 

Foundation has recently inaugurated similar work. These three corollary efforts, being conducted 

under separate mandates, point out the need for coordination at a broad scale. The issues of 

scientific leadership, institutional innovation, and governance are being addressed by the Pacific 

Northwest Aquatic Monitoring Partnership in regards to the prioritization, design, and 

coordination issues for large-scale monitoring linked to management experiments. 

Pacific Northwest Aquatic Monitoring Partnership 

A regional science based monitoring and evaluation program is necessary to assess the 

status of populations and habitat, as well as the adequacy of management and restoration 

actions in achieving restoration goals. Research needs include monitoring technologies, 

indicators of stock success and environmental health, databases for information storage 

and retrieval, straightforward evaluation procedures, and mechanisms to ensure 

communication to those who implement adaptive management. (Emphasis added.)

-- Committee on the Environment and Natural Resources, 2000

Several years ago, Federal Executives asked staff of the U.S. Forest Service’s Aquatic and 

Riparian Effectiveness Monitoring Program to develop a monitoring partnership with 

Washington, Oregon, and California agencies in support of the President’s Forest Plan. This 

resulted in an ad hoc group of state and federal natural resource and watershed specialists 

meeting since November 2001 to coordinate and integrate their different watershed condition 

monitoring efforts. This group is now operating as the Pacific Northwest Aquatic Monitoring 

Partnership or PNAMP. In recognition of the common objectives and overlap among 

participants in existing monitoring programs, the initial group decided to expand their 

partnership group to include the federal research, monitoring and evaluation planning and 

coordination effort, and to bolster the effort by inviting participation from tribal organizations. 

Participants to date have included a wide range of organizations – state, federal, and tribal. 

The PNAMP is developing a regional coordination plan for monitoring and evaluation, separate 

from this research plan. Nevertheless, many of the research needs essential for the development 

of the monitoring plan are identified in this research plan. The relationship between these two 

planning documents should be viewed as complementary. However, the scope of the PNAMP 

plan differs from that of the research plan in two ways. First, although the Partnership’s plan 

includes research efforts, it is focused on a single subject area, monitoring and evaluation. In 

contrast, the Council’s plan spans many topic areas, including monitoring and evaluation. 

Second, the Partnership’s plan encompasses the region within which the President’s Forest Plan 

is being implemented, from the Canadian border south to northern California, whereas the 

Council’s plan only encompasses the Columbia River Basin. 

44
Federal Research, Monitoring, and Evaluation Plan 

In NOAA’s 2000 biological opinion, monitoring and evaluation is a strong and central theme. 

Over a two year period, Bonneville, the Corps, and the Bureau of Reclamation work with NOAA 

Fisheries to develop a Research, Monitoring, and Evaluation (RME) Program for the NOAA 

Fisheries 2000 Federal Columbia River Power System (FCPRS) Biological Opinion and a 

Columbia River Federal Salmon Recovery Strategy MOU. Recommendations for research 

relevant to monitoring and evaluation and the hydrosystem identified in the RME plan are 

reported in this research plan. The ISRP reviewed the plan and issued Review of Draft Action 

Agency and NOAA Fisheries RME Plan (2004-1), which made several recommendations for 

revisions to the plan. Since then the Action Agencies have not responded to the ISRP or to 

Council staff as to the status of these recommendations. It is unclear whether the Action 

Agencies intend to go forward in reliance on their draft RME plan, or to instead use the RME 

section of the UPA to guidance RME activity in lieu of the original plan. 

The federal RME plan focused on stocks of anadromous fish listed under the ESA and called for 

programmatic monitoring and expanded coordination with other federal and state monitoring 

programs. In contrast, the monitoring coordination plan of the Pacific Northwest Aquatic 

Monitoring Partnership embraces monitoring for watershed conditions, status and trends, and 

project effectiveness. Although the federal monitoring plan addresses a narrower range of 

resources, it was developed over a two-year period and will make a significant contribution to 

the regional monitoring efforts. 

Pacific Coastal Salmon Recovery Fund 

The Pacific Coastal Salmon Recovery Fund (PCSRF) was established in fiscal year 2000 to 

provide grants to the states and tribes to assist state, tribal and local salmon conservation and 

recovery efforts. The goal of the PCSRF is to make significant contributions to the conservation, 

restoration, and sustainability of Pacific salmon and their habitat. The PCSRF was requested by 

the governors of the states of Washington, Oregon, California and Alaska in response to ESA 

listings of West Coast salmon and steelhead populations. The PCSRF supplements existing state, 

tribal and federal programs to foster development of federal-state-tribal-local partnerships in 

salmon recovery and conservation. It also promotes efficiencies and effectiveness in recovery 

efforts through the enhanced sharing and pooling of capabilities, expertise and information. 

The recovery of sustainable salmon populations will likely take decades, and require a 

substantial investment. Nonetheless, it is important to track the work accomplished by current 

investments and measure activities and changes on a regular basis. NOAA Fisheries has 

developed a comprehensive performance measurement system for the PCSRF in conjunction 

with the states and tribes in response to requests by Office of Management and Budget and 

Congress for program accountability. The MOUs between NOAA Fisheries and the states and 

tribes, which previously established criteria and goals for prioritizing PCSRF project funds have 

been amended to include these program-wide performance goals and reporting metrics. It is 

anticipated that the aggregation of these project level reporting metrics, combined with larger

45
scale watershed and subbasin assessments and results from monitoring and evaluation efforts, 

will allow, over the long term, an assessment of program effectiveness in terms of increased 

numbers of salmon. Bonneville is currently adopting these metrics into its project tracking 

system. 

 

Bonneville Environmental Foundation 

The Bonneville Environmental Foundation (BEF) initiated its Model Watershed Program in 

October 2003. BEF signed two 10-year agreements supporting long-term, monitoring-intensive 

watershed restoration efforts in Idaho's lower Kootenai River and the Chinook River in 

southwest Washington. In agreements with the Kootenai Tribe of Idaho and Sea Resources (a 

community-based watershed restoration organization located in Chinook, WA.), BEF has 

committed to provide scientific oversight, an independent peer review panel, and at least 

$500,000 in support of restoration and quantitative monitoring efforts over a 10-year period. 

With its model watershed approach, BEF is hoping that long-term investments in scientifically 

accountable restoration programs will prove more effective than short-term and piecemeal 

project grants scattered among Pacific Northwest watersheds. Over time, BEF plans to seek 

additional resources and apply its own funds to support 10 to 12 long-term Model Watershed 

programs across the Pacific Northwest. 

There is a clear opportunity to link the three sets of pilot intensively watersheds to increase the 

pool of experimental sites, which would save funds and time, specifically the BEF projects, the 

PSCRF projects, and the pilot watershed work under the FCRPS Biological Opinion. 

Short-Term Research Recommendations

1. Design and implement a research monitoring (Tier 3) effort at selected locations in the 

 Columbia Basin to establish the underlying causes for the changes in population and habitat 

 status identified in Tiers 1 and 2 monitoring. 

2. Determine juvenile hydro survival salmon and steelhead survival through the hydropower 

 system (priority total system/secondary in-river), in relation to performance standards. 

3. Determine the extent of harvest incidental mortality in terms of impact on pre-spawning 

 survival and spawning success for listed species.

Estuary 

The estuary is an important ecological feature that has been impacted by local habitat and upriver 

management actions. While less is known about the potential for improvement in the estuary 

than other parts of the Columbia River Basin, there are indications that substantial improvements 

are possible, and that these improvements may benefit most of the anadromous fish populations 

in the Columbia River Basin. Although all of the investment and effort in the Fish and Wildlife 

Program flow through this unique environment, the interaction of changes in the estuary with 

restoration projects has not been evaluated. A precautionary approach should be taken, given the 

current state of most salmonid populations in the Basin, the magnitude of change in the estuary, 

and the lack of prior research. 

46
Short-Term Research Recommendations

1. Collect additional shallow-water bathymetry data for refining the hydrodynamic 

 modeling and identifying/evaluating potential opportunities for specific restoration 

 projects. 

2. Increase understanding of juvenile and adult fish migration patterns. The Army Corps of 

 Engineers is funding juvenile fish research in the estuary, as research regarding adult fish was 

 not recommended in the regional forum (the forum is the means of collaborating the ESA- 

 related recovery work of federal agencies in the Columbia River Basin). 

3. Improve understanding of the effect of invasive species on restoration projects and salmon 

 and of the feasibility to eradicate or control the invasive species. 

4. Improve understanding of the biological meaning and significance of the estuarine turbidity 

 maximum relative to fish restoration actions. 

Long-Term Research Recommendations

1. Establish an allocation of water within the annual water budget for the basin that would 

 simulate peak seasonal discharge, increase the variability of flows during periods of salmonid 

 migration, and restore tidal channel complexity in the estuary, aided by removing pile dikes 

 where feasible. 

2. Increase genetic research to identify genotypic variations in habitat use. 

3. Increase understanding of sediment transport and deposition processes in the estuary.

Natural Variation and Ocean Productivity 

Shifts in oceanic regime involve substantial changes in the distribution of species, the structure 

of marine food chains, and the physical processes of biological production. Anticipating such 

change and understanding its effects on salmon production in the Columbia Basin will require 

evaluation of ecological indicators other than the abundance of salmon. Decadal cycles of ocean 

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

phases of their life cycle, leading to erroneous interpretation of the performance of restoration 

efforts and increased losses of some stocks (CENR, 2000). Therefore, remediation for poor 

ocean conditions should entail taking an ecosystem approach to salmon management in which 

variability and diversity on the freshwater side are considered normal attributes to be

safeguarded. 

 

Long-Term Research Recommendations

1. Determine the relative effects of the ocean on different fish stocks compared to the effects of 

47
 inland actions. 

2. Research on effects of ocean conditions on productivity of salmon must be integrated with 

 estuarine and riverine research. 

Toxics 

Environmental Protection Agency 

The Environmental Protection Agency’s (EPA) “Watershed Protection Approach” is a 

coordinating framework for environmental management that focuses public and private sector 

efforts to address the highest priority problems within hydrologically-defined geographic areas, 

taking into consideration both ground and surface water flow. Watersheds are the geographic 

unit below a subbasin, and are at the scale at which much of the restoration and planning work 

that will follow subbasin plans will occur. EPA provides many financial and technical resources 

to support local watershed protection efforts undertaken by state and tribal governments, public 

interest groups, industry, academic institutions, private landowners and concerned citizens. EPA 

has partnerships with the States and Tribes of Alaska, Idaho, Oregon, and Washington. 

EPA’s Watershed Protection Approach is a strategy for effectively protecting and restoring 

aquatic ecosystems and protecting human health. This strategy has as its premise that many 

water quality and ecosystem problems are best solved at the watershed level rather than at the 

individual water body or discharger level. Major features of the Watershed Protection Approach 

are: targeting priority problems, promoting a high level of stakeholder involvement, integrated 

solutions that make use of the expertise and authority of multiple agencies, and measuring 

success through monitoring and other data gathering. 

EPA also implements water quality standards that are the foundation of the water quality-based 

control program mandated by the Clean Water Act. Water Quality Standards define the goals for 

a water-body by designating its uses, setting criteria to protect those uses, and establishing 

provisions to protect water quality from pollutants. A Total Maximum Daily Load or TMDL, is a 

tool for implementing water quality standards and is based on the relationship between pollution 

sources and in-stream water quality conditions. The TMDL establishes the allowable loadings or 

other quantifiable parameters for a water-body and thereby provides the basis to establish water 

quality-based controls. These controls should provide the pollution reduction necessary for a 

water-body to meet water quality standards. 

The EPA Office of Water has various programs that store data in associated databases. These 

databases are separately managed with little coordination among them. Under Watershed 

Assessment, Tracking & Environmental Results (WATERS), an integrated information system

for the nation's surface waters, these program databases are being connected to a larger 

framework. This framework is a digital network of surface water features known as the National 

Hydrography Dataset which can link one program database to another, so that information can be 

shared across programs. 

48
Although the Office of Pesticide Programs has included endangered species considerations in its 

risk assessments for many years, the Endangered Species Protection Program (ESPP), was 

started in 1988. It is largely voluntary at the present time and relies on cooperation between the 

U.S. Fish and Wildlife Service, EPA regions, states, and pesticide users. 

Western Fisheries Research Center 

The Western Fisheries Research Center (WFRC) is part of the U.S. Geological Survey. 

WFRC conducts research on how ecosystem dynamics affect critical living aquatic resources in 

large river systems. WFRC is supporting the research needs of the U.S. Bureau of Reclamation, 

Army Corps of Engineers, and the Bonneville Power Administration. In terms of large 

ecosystems with multiple collaborators, the WFRC is working in the Columbia, Klamath, and 

Sacramento-Bay/Delta systems. Multiple collaborators and partners are also involved in WFRC 

contaminants projects, such as USFWS, U.S. Bureau of Reclamation, NOAA Fisheries, and the 

Water Resources Division of U.S. Geological Survey. Management of salmon by these entities 

and by NOAA Fisheries will also require increased research in estuaries. 

Short-Term Research Recommendations

1. Identify and quantify sources of toxic contaminants, which are contributing to the exposure of 

 salmon leaving the Lower Columbia River. 

2. Determination of the biological consequences of contaminant exposure in salmon, as well as 

 consequences for other species, notably prey species and higher trophic levels, such as 

 piscivorous birds. 

Long-Term Research Recommendations

1. Contaminant monitoring and research should be conducted as part of overall investigations of

 chemical habitat quality, including studies of organic carbon transport and cycling. 

2. Characterization of exposure patterns in wild versus hatchery fish, in populations with 

 different life histories and patterns of estuary use, in various listed ESUs. 

Invasive Species 

Mechanisms must be identified to reduce or eliminate the reproductive capacity or dispersal of 

non-native species in native salmonid habitats if riverine controls, for example by the restoration 

of flushing flows, prove ineffective in controlling non-native species. 

Short-Term Research Recommendations

1. Determine the ecological consequences of invasions, specifically, competition, predation, and 

49
 cascading trophic effects on native species, nutrient cycling, effect of management activities. 

2. Determine how to detect low-density populations of invasive species, develop new 

 monitoring techniques and optimized search protocols. 

 

3. Determine the feasibility of developing rapid response methodologies to eliminate newly 

 introduced species at the source of introduction before they spread. 

4. Determine the potential nontarget impacts of management techniques, specifically the sub- 

 lethal impacts of herbicides on salmonids. 

Long-Term Research Recommendations

1. Determine whether there are environmental constraint on the abundance and distribution of 

 currently established or eminently threatening species. 

2. Determine what factors limit invasive species in their native range, such as viruses, bacteria, 

 fungi, parasites, predators. 

3. Determine the ecological impacts of “naturalized” non-indigenous species. 

4. Determine whether regionally accepted non-indigenous species, such as warm-water fish, can 

be 

 managed to minimize ecological effects. 

5. Evaluate alternative pesticides for use in eradicating specific aquatic nuisance species. 

Subbasin Planning: Where and When to Implement Research Projects?

... to ensure that relevant scientific information, including socioeconomic information is 

available to decision makers in a useful format, a structured process is needed to involve 

community stakeholders and tribal governments and their issues, values, and priorities. 

-- Committee on the Environment and Natural Resources, 2000 

No one should expect science alone to resolve the challenges facing the region. Science has 

made, and will continue to make, a significant contribution to the regional dialogue on

restoration and recovery. Yet science remains but one of the streams of interdisciplinary 

information flowing to decision-makers who allocate common property resources. Social 

considerations and economic factors are also an important part of the mix of information before 

decision-makers, and at times these factors will be determinative. 

Sound science, thoughtful planning, and hard work on the ground are all important ingredients to 

the success of any restoration program. Yet without strong local support for restoration 

activities, the future of many Columbia River Basin species will remain in question. In 2000 the 

Council initiated subbasin planning in order to help local entities develop their own restoration 

50
plans. Subbasin planning has helped people define the future they seek for natural resource 

amenities in their subbasins, and thereby define their legacy to future generations. 

Subbasin planning have helped identify coordination needs and opportunities for fish and 

wildlife restoration by integrating strategies in the Council’s fish and wildlife program with other 

federal, state, tribal, Canadian, and volunteer fish and wildlife restoration programs. Subbasin 

plans have defined the goals, biological objectives, and strategies for individual subbasins. 

Through subbasin planning, inventories of regulatory requirements have been developed 

including ESA and Clean Water Act measures, water and land management objectives affecting 

fish and wildlife have been clarified, and program funding will be coordinated to maximize 

benefits to fish and wildlife. The cooperative and inclusive participation of federal, state, tribal, 

and local stakeholders in subbasin planning created the opportunity for subbasin plans to contain 

a collective expression of the critical uncertainties and research priorities within a subbasin. 

Both top-down, and bottom-up approaches are necessary to fully implement the research plan. 

Subbasin plans embody the bottom-up approach, as they will contain input from a wide range of 

stakeholders. The research plan provides regional-level guidance and a top-down approach to the 

identification of basinwide research needs that can be addressed in the next project selection 

process or by requests for proposals. Thus, implementation of research projects identified 

through subbasin planning (bottom-up) should be consistent with the overall research plan (topdown). 

The research plan will support research recommendations that have broad application to other 

provinces, or to the entire Columbia basin. Subbasin plans identify research needs either within 

a subbasin (geographically specific), or a prevalent need within the province or subbasin. 

Through provincial review and project selection, research projects that can have application 

beyond the subbasin will be reviewed more favorably than those with a smaller geographic 

scope. Research projects identified through subbasin plans can also be proposed for funding 

through any relevant RFPs. 

It will be important to understand the collective research needs within a province after subbasin 

plans are adopted. As part of the Council’s commitment to establishing provincial goals and 

objectives, assessing provincial research needs should be a part of that exercise. The Council 

will collating the research needs from each subbasin plan within a province, asses the major 

research needs, and compare them to the needs in other provinces for a basinwide perspective. 

As these uncertainties and research recommendations are identified, they will be incorporated in 

future iterations of this research plan. Naturally, there will be other research needs not identified 

through the subbasin planning process. The overall assessment of provincial or basinwide 

research needs therefore will not be limited to just those identified through subbasin planning. 

State Research Initiatives 

Research recommendations from Oregon and Montana are already incorporated throughout text. 

Recovery Planning for Endangered Species: How Much Research Is Enough? 

NOAA Technical Recovery Team Products 

51
The ESA requires that recovery plans contain objective, measurable goals for delisting; a 

comprehensive list of the actions necessary to achieve the delisting goals; and an estimate of the 

cost and time required to carry out those actions. In addition, NOAA Recovery Planning 

Guidelines suggest that recovery plans include an assessment of the factors that led to population 

declines or that are impeding recovery. Finally, it is important that the plans include a 

comprehensive monitoring and evaluation program for gauging the effectiveness of recovery 

measures and overall progress toward recovery. 

To implement these elements of recovery, NOAA Fisheries has formed geographically based 

Technical Recovery Teams (TRTs), in coordination with existing science teams and ongoing 

conservation planning efforts. NOAA Fisheries is also working with state, local, regional, tribal, 

and private entities to develop a collaborative recovery planning process for each planning area. 

The TRTs will provide technical support and analysis to these efforts and have been convened 

for the Puget Sound and Willamette/Lower Columbia/Southwest Washington regions, and the 

Interior Columbia River Basin. The TRTs will develop products that: 

1. Identify population and ESU de-listing goals; 

2. Characterize habitat/fish abundance relationships; 

3. Identify the factors for decline and limiting factors for each ESU; identify the early actions

 that are important for recovery;

4. Identify research, evaluation, and monitoring needs; and, 

5. Serve as science advisors to groups charged with developing measures to achieve recovery. 

The planning component of the ESA recovery planning process will focus on identifying the 

measures and actions necessary to achieve the recovery goals identified by the TRTs. According 

to NOAA Fisheries, recovery goals must, at a minimum, restore listed ESUs to levels at which 

they are no longer threatened and can therefore be de-listed under the ESA. NOAA Fisheries 

believes it is critically important to ground the recovery planning process in the many state, 

regional, tribal, local, and private conservation efforts already underway throughout the region, 

such as subbasin planning. 

Long Term Commitment to Restoration and Recovery 

Spirit of the Salmon (Wy-Kan-Ush-Mi Wa-Kish-Wit) is the title of the Columbia River 

Anadromous Fish Restoration Plan of the Nez Perce, Umatilla, Warm Springs and Yakama

Tribes. It provides a framework to restore the Columbia River salmon. A key theme of Spirit of 

the Salmon is that it makes a multiple generational commitment to salmon recovery. The first 

volume of the two-volume plan sets out 13 scientific hypotheses and the recommended actions 

associated with each, along with 10 institutional recommendations. Many of these 

recommendations comport with those of other large scale planning documents. The interests of 

the tribes touch all of the research topics in this plan, so they will be key partners in its 

implementation. 

52
IV. References 

CENR - Committee on the Environment and Natural Resources, 2000. From the Edge: Science 

to Support Restoration of Pacific Salmon. National Science and Technology Council, Committee 

on Environment and Natural Resources. 

Giorgi, A. 2003. Mainstem Passage Strategies in the Columbia River System: Transportation, 

Spill, and Flow Augmentation (Council Document 2002-3). 

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. 

Lee, K.N. and J. Lawrence, 1986. Adaptive Management: Learning from the Columbia River 

Basin Fish and Wildlife Program, Environmental Law Vol.16:431-460. 

National Research Council, 1996. Upstream: Salmon and Society in the Pacific Northwest. 

National Academy Press. 

NOAA, 2000. Viable Salmonid Populations and the Recovery of Evolutionarily Significant 

Units, Technical Memorandum NMFS-NFWSC-42, June 2000. 

NOAA, 2000. Viable Salmonid Populations and the Recovery of Evolutionarily Significant 

Units (NOAA Technical Memorandum NMFS-NFWSC-42, June 2000.) 

Northwest Power and Conservation Council. 2000 Columbia River Basin Fish and Wildlife 

Program. 

Northwest Power and Conservation Council. Development of a Regional Framework (Document 

98-16). 

Pinkerton, E.W. 1992. Translating Legal Rights into Management Practice: Overcoming Barriers 

to the Exercise of Co-Management. Human Organization 51:330-41. 

ISAB and ISRP Reports 

ISG Return to the River Report (NPCC 2000-12). 

Review of Strategies for Recovering Tributary Habitat (ISAB 2003-2). 

Review of Salmon and Steelhead Supplementation (ISAB 2003-3). 

Review of the Action Agencies' Draft Estuary Plan (ISRP 2003-13). 

 

Review of Salmon Recovery Strategies for the Columbia River Basin (ISAB 2001-7). 

Review of Draft Action Agency and NOAA Fisheries RME Plan (2004-1). 

53
IV. Appendixes

Appendix A. Mandate for a Columbia River Basin Research Plan

Northwest Power and Conservation Council 

In 1980, Congress passed the Pacific Northwest Electric Power Planning and Conservation Act1

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.” 

Directives for a Columbia River Basin Research Plan 

Basinwide Provisions of the Fish and Wildlife Program 

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 then 

monitors implementation of the program, which is funded by the Bonneville Power 

Administration (Bonneville) and implemented by tribal, state, and federal fish and wildlife 

managers and others. In its vision for the program, the Council states four overarching 

biological objectives: 

1. A Columbia River ecosystem that sustains an abundant, productive, and diverse community of 

 fish and wildlife. 

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

 development and operation of the hydrosystem. 

3. Sufficient populations of fish and wildlife for abundant opportunities for tribal trust and treaty 

 right harvest and for non-tribal harvest. 

4. Recovery of the fish and wildlife affected by the development and operation of the 

 hydrosystem that are listed under the Endangered Species Act. 

The Council adopted the first fish and wildlife program in November 1982. In that plan and in 

subsequent updates, the Council called for development of a research plan but also adopted 

specific measures for research without clear prioritization of remaining critical uncertainties. 

The 2000 Program, the latest revision of the program, marks a significant departure from past 

versions, which consisted primarily of a collection of measures directing specific activities. The 1

 Pacific Northwest Electric Power Planning and Conservation Act of 1980 (Public Law 96-501, 94 Stat. 2697

(December 5, 1980), codified with amendments at U.S Code Annotated 16, section 839 (2000)). See Section 

839b(h)(6)(B). 

54
2000 Program establishes a basinwide vision for fish and wildlife along with biological 

objectives, as noted above, and action strategies that are consistent with the vision. The purpose 

of the research strategy in program is to identify and resolve key scientific uncertainties. The 

program calls for the development of a basinwide research plan to address those uncertainties. 

The heart of the program is a set of immediate actions to improve conditions for fish and wildlife 

in the Columbia River Basin. Despite a large body of knowledge about the needs of fish and 

wildlife, there are still instances in which the region lacks the information to fully understand 

which actions will be most effective. The intention of the Council, and the Northwest Power Act, 

is for the region to make the best possible choice of actions based on the available information. 

Thus, lack of perfect information is not grounds for inaction. 

Although “Research, Monitoring, and Evaluation” appears as specific strategy in the program, 

that strategy also provides a broader vehicle for reducing uncertainties that undercut the effective 

implementation of the full suite of strategies in the program. Ultimately, the program will be 

implemented through 52 subbasin plans that have been developed locally in the Columbia River 

Basin. Some of the subbasin plans have identified research needs that can be efficiently 

addressed from a regional plan. 

Recommendations of the Four Governors 

Another directive to develop a regional research plan was included in the Recommendations of 

the Governors of Idaho, Montana, Oregon and Washington for Protecting and Restoring 

Columbia River Fish and Wildlife and Preserving the Benefits of the Columbia River Power 

System issued in June of 2003. In regard to research, the Four Governor’s Recommendation on 

Monitoring and Accountability stated: 

...the Council, working closely with the States, federal Agencies and Tribes should 

develop ... by year’s end, a draft systemwide research plan with budgets and priorities. 

The directive of the Four Governors was met by the submittal of a draft Columbia River Basin 

research plan to the Council on December 31, 2003. 

The Objectives, Audience, and Scope of the Columbia River Basin Research Plan

In order to further the objectives of the fish and wildlife program, this research plan will direct 

research activity in support of anadromous and resident fish and wildlife in the Columbia River 

Basin. The research plan will be an important tool for managing the fish and wildlife program

because it can inform Council decision-making, facilitate scientific review, focus project 

selection, and provide a basis for redirecting future research. The plan will reduce management 

uncertainty by increasing scientifically based knowledge. In brief, the objectives of the plan 

include identification of critical uncertainties, formulation of research recommendations, and 

identification of priorities for funding. Additional plan objectives include: 

1. Increased accountability for the annual expenditures of research funds. 

2. Improved input from independent scientific review, fish and wildlife agencies and tribes, 

 independent scientists and other interested parties in the region. 

55
3. Improved monitoring, evaluation, and the application of results. 

4. Improved coordination among mainstem research programs. 

5. Improved coordination with the research elements of subbasin plans. 

6. Improved accessibility of information from the fish and wildlife program. 

The primary audience for the plan is policy and decision makers responsible for natural resource 

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

executives. The plan also will provide useful guidance to planners, researchers, and project 

sponsors. The scope of issues in this draft plan does not include recounting the factors and 

events contributing to the decline of fish and wildlife species within the Columbia River Basin, 

as that history has been described by numerous other sources. The geographic scope of the plan 

is limited to the Columbia River Basin. In this draft form, the research plan addresses the fish 

and wildlife program and key pieces of research activity involving the Army Corps of Engineers, 

the U.S. Bureau of Reclamation, Bonneville, NOAA Fisheries, U.S. Fish and Wildlife Service 

and other entities. The next phase of development of the draft plan will include broadening the 

scope from an initial focus on the fish and wildlife program and implementation of the biological 

opinions to integration with other research programs, such as those of the U.S. Geologic Survey 

and the U.S. Environmental Protection Agency, and the Tribes. 

Proposed Schedule for Completing Research Plan 

Oct 1 Commence 30-day public review period 

Oct 30 Complete 30-day public review period 

Nov 22 Commence 30-day ISAB/ISRP review period 

Dec 7-9 ISAB/ISRP discuss research plan at Seattle meeting 

Dec 22 Complete 30-day ISAB/ISRP review period 

Jan 31 Complete revisions to plan based on ISAB/ISRP review 

Feb 15-17 Present final research plan to Council (contingent on potential schedule conflicts 

with adoption of subbasin plans and the power plan) 

March 15 Final Columbia Basin Research Plan completed 

56
Appendix B. The Development of a Columbia River Basin Research Plan 

Past as Prologue 

Best Scientific Information 

The Northwest Power Act instructs the Council to prepare a fish and wildlife recovery program

for the Columbia River Basin that includes measures “...based on, and supported by, the best 

available scientific knowledge.” The Council has sought “the best available scientific 

knowledge” in different ways as the fish and wildlife program evolved. The Power Act directs 

the Council to review the program at least every five years, and the Council has done so. With 

each revision, the Council paid attention to the mandate regarding best available scientific 

knowledge. In preparing the first version of the program, the Council formed the Scientific and 

Statistical Advisory Committee to assist in evaluating recommendations for measures to include 

in the program. In the 1984 Program, the Council created a Fish and Wildlife Committee 

comprising four Council members and gave the committee duties that included assessing past 

and present research projects. In the 1987 program revision, the Council created Technical 

Working Groups consisting of the representatives of agencies, tribes and some other parties. The 

Technical Working Groups were charged with summarizing existing information and identifying 

fish and wildlife program research needs in areas such as hatcheries, fish disease and habitat. 

The Independent Science Group (ISG) was created by the Council in the 1992 Program to 

provide advice and to conduct a review of the program, and that review became Return to the 

River (1996). The Scientific Review Group (SRG) and the ISG later evolved into the ISAB and 

the ISRP. 

The Council later addressed the need to satisfy the “best available scientific information” 

provisions of the Act through by utilizing the recommendations of the Basin’s fish and wildlife 

managers and incorporating independent scientific review into the decisionmaking process. 

In most years, the fish and wildlife managers, through the Columbia Basin Fish and Wildlife 

Authority (CBFWA), develop a draft annual program implementation work plan for the projects 

proposed for funding. This draft annual work plan is the culmination of a technical and 

management review of the feasibility of all proposed projects, and it establishes a proposed 

annual budget and project priorities. The ISRP and the Council review the projects proposed for 

funding in the context of the fish and wildlife managers’ draft work plan. The project reviews 

and advice of the fish and wildlife managers are valuable to the Council as it deliberates on its 

funding recommendations. In sum, the Council has an established process to satisfy program

measures on the best available scientific knowledge. 

The Council recognizes that the quality of the information collected through research is 

important to the credibility of its decision-making. Every year the Council implements its 

mandate to base program measures on the best available science by recommending the funding 

of numerous research projects to gather necessary scientific knowledge. 

57
Prior Efforts to Identify Research Priorities 

Since its inception, the Council has made significant efforts to identify research priorities 

including the following. Section 206 of the Council’s 1987 Fish and Wildlife Program contained 

what could be called a research plan for salmon and steelhead. Section 206 called on Bonneville 

to fund research in specified areas of emphasis over the ensuing five years. It also directed 

Bonneville to fund the Technical Working Groups whose responsibilities included developing 

five-year workplans in those areas of emphasis. The workplans were to be approved by the 

Council, thus becoming Council plans. Thus, section 206 provided the basis for the appointment 

of Technical Working Groups and their development of five-year research plans that included 

assessments of past research and identification of research needs. 

In Return to the River, the Independent Scientific Group (1996) developed a conceptual 

foundation for restoration of salmonid fishes in the Columbia River Basin. In 1998 the Council 

published the Development of a Regional Framework (Document 98-16) that introduced a set of 

broad scientific principles (Part I) and applied these principles to a description of the Columbia 

River as an ecosystem (Part II). This document also states that “A third part of the scientific 

foundation, a set of analytical tools based on Parts I and II, remain to be developed.” 

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

scientific principles and discussing their implications for salmon restoration (see page 15, 2000 

Fish and Wildlife Program, Council Document 2000-19). These principles were derived from a 

number of other reviews and recovery strategies for Columbia River salmon including Return to 

the River. Other science review groups (President’s Committee on the Environment and Natural 

Resources, 2000; and the National Research Council, 1996) have also emphasized the need for 

an ecosystem perspective as a basis for designing a recovery program for salmon in the Pacific 

Northwest. The science foundation developed by the Council represents an important step in the 

development of a recovery program founded on ecological principles. 

Thus, over the last decade these efforts have helped improve the ability to define uncertainties 

and develop research recommendations to address them. This should be viewed as an 

evolutionary progression, as it is now possible to separate some of the broader, vexing 

uncertainties into more discrete research questions or recommendations. While a derivative of 

these prior efforts, this draft research plan is also a continuance of them. It attempts to provide 

greater specificity in the application of scientific principles to critical uncertainties, rather than 

simply recommending a set of tools for addressing them. 

2002 Draft Columbia River Basin Research Plan

In January 2002, Council staff requested the ISRP to review an initial effort to complete a draft 

regional research plan. On April 15, 2002 the ISRP released its review (Council Document ISRP 

2002-4), which recommended a substantial reorganization of the staff’s draft plan. The ISRP 

found that the draft essentially defined existing research as the research program. The ISRP 

commented that the work underway at the project scale, or as elements within projects, did not 

constitute a program nor provide a sense of future direction. The draft plan also promoted a 

bottom-up approach to the identification of research priorities, tied to subbasin planning, that 

58
would result in repetition of research efforts. Rather than addressing policymakers, it tried to 

address multiple audiences, providing detailed guidance for those contemplating submission of a

research proposal, as opposed to those managing a program. It also provided a profile of ongoing research at that time and helpful information regarding the funding process

Consequently in 2003, despite a history of coordination and prioritization efforts, the Council 

still did not have a research plan that identified critical uncertainties and prioritized research 

recommendations. This is not to diminish the excellent research that has been completed in the 

past at the project scale. However, new research should not be undertaken without benefit of a 

programmatic framework. In order to succeed, the research program must institutionalize 

accountability. For that reason it will be developed in tandem with a regional monitoring 

coordination plan. 

59
Appendix C. Implementing the Columbia River Basin Research Plan

This plan identifies what types of research to fund. It also provides a rationale as to why to fund 

specific work and general recommendations as when to provide funding. Finally, it proposes a 

mechanism for how to fund much of the work necessary to the fish and wildlife program. 

However, this plan is not based on the assumption that the fish and wildlife program will fund all 

of the research needs of the region. 

This section explains how the short and long-term elements of the research agenda described in 

Chapter III will be implemented. Much of the short-term and some of the long-term research 

recommendations will be implemented under the fish and wildlife program. New large-scale 

field experiments should be conducted collaboratively via shared funding arrangements with 

other entities. Therefore, this implementation section applies to both the short and the long-term

elements of the research agenda, with the exception of multiple-sponsor projects. 

Some research questions will require large-scale field experiments, and these will require 

collaborative treatment and shared funding sources. It might be argued that there are already defacto large-scale field experiments underway, but they were not designed to resolve specific 

uncertainties or establish cause and affect relationships. It may be possible to link project-scale 

efforts together 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. As a result, 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. 

In 2000, the Council shifted from an annual funding cycle for projects to a three-year cycle. 

Because state and federal agencies remain on an annual funding cycle, it is difficult to make 

long-term funding agreements. Consequently, formal arrangements such as memoranda of 

agreements may be necessary to guarantee long-term funding commitments for selected largescale field experiments. The Council must design the project selection process that will follow 

the adoption of subbasin plans in 2004. 

Project Selection Under the Fish and Wildlife Program 

The Northwest Power Act affords the Council broad discretion to define the procedures for 

conducting project review and selection for many projects funded by Bonneville. In general, the 

Act requires all projects to undergo an independent scientific review by the ISRP to ascertain 

their scientific and technical merits. The ISRP consists of eleven members assisted by a number 

of Peer Review Group members. The ISRP was created by amendment to the Northwest Power 

Act in 1996 and charged with providing scientific review of projects funded by Bonneville under 

the Council’s program. Congressional report language subsequently expanded the role of the 

Panel to include scientific review of projects sponsored by the Corps and other federal agencies 

that are funded by Bonneville through reimbursement. The ISRP and the Council’s review 

process have served to appreciably increase the level of scientific rigor in Bonneville projects 

and hopefully have increased the effectiveness of projects to meet the Program’s vision. Unlike 

60
the ISRP, that is solely under the Council’s purview, the Independent Scientific Advisory Board 

(ISAB) is jointly sponsored by the Council, NOAA Fisheries, and the Columbia River Basin 

Indian Tribes. The ISAB provides general scientific advice on recovery efforts whereas the 

ISRP provides scientific review of specific project proposals. 

In addition, proposals are evaluated within a policy context to determine their potential 

contribution to management decision-making. Regional fish and wildlife managers often 

provide recommendations to the Council on these matters. In general, the Council’s 

recommendations for Bonneville funding rest on a mix of priorities, legal considerations, 

technical adequacy, management urgency, regional opportunities, and available funding. 

This section briefly describes the operational context of the fish and wildlife program, including 

a brief description of the project selection and funding process. The draft research plan does not 

provide detailed guidance for project performance and administration. Bonneville has the 

primary responsibility for the implementation and management of research contracts pertaining 

to activities under the fish and wildlife program, executed by Bonneville’s Contracting Officer 

Technical Representatives. 

Beyond Technical Merit: New Review Criteria for the ISRP? 

The ISRP and Scientific Peer Review Groups review projects proposed for funding to implement 

the Council’s program through Bonneville’s annual fish and wildlife budget. 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 any specific reference to research priorities. 

Therefore, this draft plan proposes four new approaches to the implementation of research: 

• First, ongoing projects containing objectives that approach, but do not squarely address a 

research recommendation set forth in Chapter I should be re-examined. 

• Second, all knowledge gaps should be initially considered as research needs for which 

projects will be sought based on a sequential priority, rather than implemented 

concurrently. 

• Third, new decision criteria for reviewing projects should be introduced for 

consideration by the ISRP. These criteria would provide additional guidance to 

61
implement the research priorities identified in this plan. Additional criteria the ISRP 

might consider in its review include: 

1. Does the proposed project address a discrete research priority or a discrete subissue of a complex research priority, which is defined in a request for proposals 

(RFP)?

2. Will resolution of the research question facilitate later treatment of related 

research questions?

3. Does the proposed mode of implementation require collaboration with other 

parties under a shared mandate?

• Fourth, RFPs should be used increasingly, in consultation with fish and wildlife 

managers, the ISAB and the ISRP to address specific research questions identified in this 

draft plan. Explicit review criteria for the particular research topic could be included in 

the RFP. 

The project review process currently benefits from CBFWA’s application of management 

criteria and from the ISRP’s requirement that projects “benefit fish and wildlife.” These criteria 

have been used to communicate the priority of projects. For example, a study may be technically 

sound but redundant with an ongoing project and thus not recommended for funding. With some

exceptions, the Council and Bonneville generally have not provided enough specific direction in 

solicitations regarding the research questions that need to be addressed. RFPs should include 

specific criteria that project proponents should address in proposals and that the ISRP, the 

Council, and CBFWA should consider in their reviews. 

By increasing specificity in research project solicitations, the fish and wildlife program can shift 

from a reactive mode to a proactive mode. The Council currently is on the receiving end of 

proposals submitted in response to solicitations that are geographic in scope. The Council does 

not actively seek proposals to address specific research questions. Because this draft research 

plan identifies ongoing research, research recommendations, and gaps, the opportunity exists to 

use RFPs, with designated budgets agreed to by Bonneville, to close the gaps. This approach 

would enable the ISRP review to remain primarily focused on the technical merit of proposed 

projects (the research, monitoring, and evaluation RFP effort for hatchery uncertainties is an 

example). The open solicitation approach has 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. 

Project Selection Processes 

This section describes how projects have been reviewed and selected in the past, and might be in 

the future. Please note that this prior experience will inform, but not dictate, the future project 

selection process, which is being developed for FY 06. 

62
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 and funding process was implemented on a three-year cycle. Provincial 

project solicitations were initiated at different times throughout the year and involved large-scale 

mailings of general announcements and calls for proposals to broad distribution lists that 

included federal, state, tribal, and local agencies, universities, private industry, and the general 

public. The announcements of proposal solicitations were also posted on the Council’s web site 

(www.nwcouncil.org), Bonneville’s web site (www.efw.bpa.gov), and CBFWA’s site 

(www.cbfwf.org). 

Following the completion of the first round of provincial reviews in 2003, the ISRP began to 

draft a Retrospective Review. The report focuses on programmatic issues and observations 

identified in ISRP reviews dating back to the panel’s first report in July 1997, and encompasses 

further review efforts related to the “measurable benefits” element of the retrospective task. The 

ISRP will complete this report in January 2005. 

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 should help 

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 would remain free to propose research projects unique to their 

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

extrapolation outside of the province in which the project is located. 

At this time, the future project selection process is under development. The sequence of when to 

solicit RFPs, in conjunction with solicitations to meet other needs identified in subbasin plans, 

will need to be resolved. An effort should be made to allow those research projects with 

basinwide implications to compete with each other in the same solicitation, instead of being 

proposed in multiple provincial reviews. 

Recommendation: Where feasible, research projects in one province should have broad 

application to other provinces, or to the basin as a whole. 

Innovative Project Reviews - 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, and the Council 

adjusted the selection process each year the process was used. Although Council staff supports 

the Innovative Project concept, staff did not recommend conducting an Innovative Project 

selection process for 2004, because funding the pending provincial review recommendations for 

2004 exhausted the available funds. Nevertheless, Council staff recognizes the value in funding 

innovative projects and believes that the fish and wildlife program’s research plan will provide 

greater focus to future funding of innovative projects. Given the intractability of some research 

challenges it is important to keep the spark of innovation alive. Innovation is a critical element 

63
of any large management program or research program and should be encouraged. Council 

members have expressed continued support for an innovative process. 

Requests for Proposals - In the past, the Council identified questions of particular importance 

and initiated requests for proposals in coordination with Bonneville as needed. 

Recommendation: Request 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.

The future form of the project selection process has yet to be determined. 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. 

Project Selection Under the Corps’ Fish Program 

In contrast to the Council’s program, the Corps funds research as prioritized by the regional 

forum and comprehensive plans such as the NOAA Biological Opinion and the Implementation 

plans of the hydro system Action Agencies. The Corps solicits pre proposals based on regionally 

ranked research needs. Research is approved following the iterative development of preproposals into final documents, whereby they are funded based on their quality and the regional 

ranking of the research need. At times, the Corps scheduling requirements necessitates some

proposals to be malleable to reflect newly acquired data and to adjust to changing runoff 

forecasts. A great deal of responsibility is thereby placed on researchers to deliver the final 

proposal through the iterative proposal review process. 

The Corps believes that it is important for their fish program to coordinate with the Council’s 

program. However, while similar, the programs exist on parallel paths due to their different 

overall purposes. The Corps program focuses primarily on project specific fish passage issues, 

usually at hydropower facilities, as opposed to the Council’s program taking a broader systemwide approach.

Meeting Fish and Wildlife Program Standards 

Evaluation and Reporting of Research Results 

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.)

Recommendation: Specific ending dates should be required for project objectives and tasks to 

help sponsors meet their intended deadlines. 

64
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. The final report should be 

in a form that facilitates review of the results. Research data should be made available to 

scientific collaborators, administrators, and the public for additional analyses. 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 website to facilitate access. The final 

reports, and any other products derived from them, should be submitted to the StreamNet 

Library. This library includes materials relating to the resources of the Pacific Northwest and 

maintains a regional depository of all research products funded under the fish and wildlife 

program. The StreamNet Library provides regional services that include reference, referral, 

database searching, inter-library lending, and document delivery. 

Data Management

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 has initiated a process for identifying data needs in the basin, 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 databases, facilitate data management and sharing, help subbasin planners, and underpin 

salmonid recovery efforts under the FCRPS Biological Opinion. 

A memorandum of agreement between the Council and NOAA Fisheries guides this initiative, 

which is currently 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 ISRP2

, from

independent analysis by Science Applications International Corporation (SAIC)3

, and in 

comments received from the public. The data management strategy is also intended to increase 

the public accountability of this program by making the results accessible not only to specialists, 

but also to the public at large. The Council is 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 who must enforce the guidelines. Guidelines appropriate for the 

collection and reporting of data at the project scale include: 

 2 Independent Scientific Review Panel. Report of Databases Funded through the Columbia River Basin Fish and Wildlife 

Program. ISRP 2000-3. May 11, 2000. 

3 Science Applications International Corporation. Recommendations for a Comprehensive and Cooperative Columbia

River Information Management System. Report to the NWPCC, April 30, 2003

65
• 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.

66
Appendix D. Sources of Critical Uncertainties and Research 

Recommendations for the Columbia River Basin 

The critical uncertainties identified in this document were generated from evaluation of 

independent science group reports, recommendations from national science groups, the fish and 

wildlife program, the biological opinions, and other regional research plans 

Research Recommendations from the Council’s 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 (SRG) 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 (Council Document SRG 93-2). 

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 described the critical ecological uncertainties that identify 

important gaps in knowledge of the resources and functional relationships that determine fish 

and wildlife productivity in the Columbia River ecosystem. The SRG also 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.” With some 

exceptions, the six uncertainties were programmatic in scale. Phrased as questions, the 

uncertainties are: 

 

1. What are the key assumptions in the fish and wildlife program, and are they scientifically 

 valid?

2. Can salmonid populations in the Columbia River be increased and sustained over the long 

 term, given the multitude of biological, physical, and cultural constraints?

3. Can the diversity of anadromous salmonid stocks be sustained over the long term?

4. What are the relative contributions of habitat loss, harvest, predation, and mainstem passage to 

 reduced riverine survival and production of anadromous salmonids and other fishes targeted 

 in the program?

5. To what extent are hatchery production and supplementation programs detrimental to wild 

 salmonid productivity and stock diversity?

6. 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 (ISG) to provide an 

ongoing evaluation of the program on its scientific merits. Importantly, the Council made clear 

67
that uncertainties should be used to guide the prioritization and funding of research efforts 

conducted under the program. To provide for this guidance the Council created the Independent 

Scientific Review Panel (ISRP) for the purpose of reviewing projects proposed for funding under 

the program. The Council and NOAA Fisheries also jointly created the Independent Scientific 

Advisory Board (ISAB) to provide advice to both agencies, and the Council created a separate 

panel of economists to offer independent economic advice and analysis regarding fish and 

wildlife issues. This is the Independent Economic Advisory Board (IEAB). 

The ISRP recommended in its review of the previous draft research plan (April, 2002), that 

development of a long-term research plan would be facilitated by a workshop with members of 

the ISRP, ISAB and IEAB organized to identify critical uncertainties and research 

recommendations. During February 2003, the ISAB, ISRP, and the IEAB met for a workshop 

and discussed the elements of the research plan. 

The challenge of determining and compiling a definitive list of critical uncertainties and research 

recommendations was managed in the following way. An initial listing of critical uncertainties 

and research recommendations was drawn from the prior publications and recent reports of the 

Council’s science review groups (see next section). Members were then polled for what they 

considered the primary key uncertainties facing the basin. These were then discussed at the 

workshop, which provided a forum for the cross-pollination of ideas regarding critical 

uncertainties and research recommendations. One conclusion of the workshop was that many 

research areas outlined in the ISG's Return to the River (1996) were still not being addressed in 

the basin. Consequently, it was recommended that the list of research items identified at the 

meeting and in Return to the River might provide adequate guidance for an initial research 

agenda. Thus, the recommendations in this research plan were developed from prior efforts and 

updated with the current thinking of the three independent science groups. Because the 

recommendations arise from competing sources, some of them appear to support a particular 

perspective. 

State of the Science Documents 

The fish and wildlife program calls for the initiation of projects to review the current state of the 

science in key research areas. This effort may include the use of reports, surveys, conferences, 

and journals. The program identifies the ISAB as the body charged with developing a series of 

reports to survey past research and summarize the state of the science in key areas. In recent 

years the ISAB and the ISRP have completed several reviews that evaluate the state of the 

science underpinning specific topics. In light of the timeliness of these reports, and the research 

recommendations they contain, their findings collectively shaped the profile of research needs 

addressed in this plan. These reviews include: 

Review of Research, Monitoring, and Evaluation Plan for the NOAA-Fisheries 2000 Federal 

Columbia River Power System Biological Opinion (January, 2003) 

Review of Harvest Management (January 2005) 

Review of Strategies for Recovering Tributary Habitat (ISAB 2003-2) 

68
Review of Salmon and Steelhead Supplementation (ISAB 2003-3) 

Review of the Action Agencies' Draft Estuary Plan (ISRP 2003-13) 

 

Review of Fiscal Year 2004 Pre-proposals for the US Army Corps of Engineers' Anadromous 

Fish Evaluation Program (ISRP 2003-14) 

Review of Salmon Recovery Strategies for the Columbia River Basin (ISAB 2001-7) 

ISG Return to the River Report (NPCC 2000-12) 

Research Recommendations From a National Perspective 

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 here and in Chapter I. 

In November 2000, the National Science and Technology Council, Committee on Environment 

and Natural Resources (CENR), released From the Edge: Science to Support Restoration of 

Pacific Salmon. 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. These include: 

1. Definition of critical ecosystem features for the full life cycle of salmonid species and stocks. 

2. Quantitative definition and assessment of risks (natural and human caused) during upstream,

 downstream, and estuary/ocean life stages. 

3. Clarification of fundamentals of biological diversity in salmon species, races, and stocks. 

69
4. Development of remedial technologies that work with nature rather than replacing it. 

5. Clarification of the regional variation in the physical, biological, social, cultural, and 

 economic environments of salmon. 

6. Development of quantitative indicators and analytical methods to assess the status of salmon, 

 characterize risk factors, and evaluate out-comes of remediation efforts to improve 

 environmental conditions or reduce risks. 

70
Appendix E. FY 04 Research Projects Profile 

_______________________________ 

w:\sw\research draft plan 7.doc 

71
Appendix E. FY 04 Research Projects Profile

Topic PPID Title 

Habitat BM2002199202604 Investigate Life History of Spring Chinook Salmon and Summer Steelhead in 

the Grande Ronde River Basin and Monitor Salmonid Populations and Habitat

Habitat BM2002199608300 CTUIR Grande Ronde Subbasin Restoration 

Habitat BM2002199701501 Imnaha Smolt Survival and Smolt to Adult Return Rate Quantification 

Habitat BM2002199801003 Spawning distribution of Snake River fall chinook salmon 

Habitat BM2002199801004 Monitor and EvaluateYearling Snake River Fall Chinook Released Upstream Of 

Lower Granite Dam

Habitat CG2001000021009 Assess current and potential salmonid production in Rattlesnake Creek 

associated with restoration efforts

Habitat CP2002000025010 Regional Stream Conditions and Stressor Evaluation 

Habitat CP2002000025055 Echo Meadows Artificial Recharge Extended Groundwater and Surface Water 

Modeling

Habitat CP2002000025069 John Day Salmonid Recovery Monitoring Program 

Habitat CP2002198402100 Protect and Enhance Anadromous Fish Habitat in The John Day Subbasin 

Habitat CP2002198506200 Passage Improvement Evaluation 

Habitat CP2002199000501 Umatilla Basin Natural Production Monitoring and Evaluation Project 

Habitat CP2002199102900 Understanding the effects of summer flow augmentation on the migratory 

behavior and survival of fall chinook salmon migrating through L. Granite Res.

Habitat CP2002199106100 Swanson Lakes Wildlife Area (SLWA) 

Habitat CP2002199206200 Yakama Nation - Riparian/Wetlands Restoration 

Habitat CP2002199404200 Trout Creek Habitat Restoration Project 

Habitat CP2002199406900 Estimate production potential of fall chinook salmon in the Hanford Reach of 

the Columbia River.

Habitat CP2002199705300 Toppenish-Simcoe Instream Flow Restoration and Assessment 

Habitat CP2002199801600 Monitor Natural Escapement & Productivity of John Day Basin Spring Chinook 

Habitat CP2002200002600 Rainwater Wildlife Area 

Habitat HP2001000023074 Lower Columbia River and Estuary Habitat Assessment and Mapping Project 

Habitat IN2001000022050 Habitat Diversity in Alluvial Rivers 

Habitat IS2003199800200 Snake River Native Salmonid Assessment 

Habitat IS2003200000900 Logan Valley Wildlife Mitigation Project/ O&M 

Habitat IS2003200002700 Malheur Wildlife Mitigation Project 

Habitat LC2003199206800 Implement Willamette Basin Mitigation Program 

Page 1 of 4
Topic PPID Title 

Habitat MC2002000024009 Assess Feasibility of Enhancing White Sturgeon Spawning Substrate Habitat, 

Kootenai R., Idaho

Habitat MS2002199102800 Monitoring smolt migrations of wild Snake River sp/sum chinook salmon 

Habitat MS2002199107100 Snake River Sockeye Salmon Habitat and Limnological Research 

Habitat MS2002199107300 Idaho Natural Production Monitoring and Evaluation 

Habitat MS2002199303501 Enhance Fish, Riparian, and Wildlife Habitat Within the Red River Watershed 

Habitat MS2002199405000 Salmon River Habitat Enhancement M & E 

Habitat WP2001199001800 Evaluate Rainbow Trout/Habitat Improvements Of Tribs. To Lake Roosevelt 

Harvest Management LC2003199306000 Select Area Fishery Evaluation Project 

Harvest Management WP2001199404300 Monitor, Evaluate, Research and Model the Lake Roosevelt Fishery Hatchery Effectiveness BM2002000027002 Assess Salmonids in the Asotin Creek Watershed 

Hatchery Effectiveness BM2002199700900 Evaluate Potential Means of Rebuilding Sturgeon Populations in the Snake 

River Between Lower Granite and Hells Canyon Dams

Hatchery Effectiveness BM2002199800702 Grande Ronde Supplementation: Lostine River O&M and M&E 

Hatchery Effectiveness BM2002199800703 Facility O&M And Program M&E For Grande Ronde Spring Chinook Salmon 

and Summer Steelhead

Hatchery Effectiveness BM2002199800704 Northeast Oregon Hatcheries Implementation (ODFW) 

Hatchery Effectiveness BM2002199801001 Grande Ronde Basin Spring Chinook Captive Broodstock Program 

Hatchery Effectiveness BM2002199801006 Captive Broodstock Artificial Propagation 

Hatchery Effectiveness CC2003199604000 Evaluate The Feasibility And Risks Of Coho Reintroduction In Mid-Columbia 

Hatchery Effectiveness CG2001199506325 Yakima/Klickitat Fisheries Project Monitoring And Evaluation (Klickitat Only) 

Hatchery Effectiveness CG2001199902400 Bull trout population assessment in the Columbia River Gorge, WA. 

Hatchery Effectiveness CP2002000025007 Determine lamprey species composition, larval distribution and adult 

abundance in the Deschutes Subbasin

Hatchery Effectiveness CP2002000025059 Develop Progeny Marker for Salmonids to Evaluate Supplementation 

Hatchery Effectiveness CP2002000025062 Growth Rate Modulation in Spring Chinook Salmon Supplementation 

Hatchery Effectiveness CP2002000025093 Characterize Genetic Differences and Distribution of Freshwater Mussels 

Hatchery Effectiveness CP2002198902401 Evaluate Juvenile Salmonid Outmigration and Survival in the Lower Umatilla 

River Basin

Hatchery Effectiveness CP2002199000500 Umatilla Fish Hatchery Monitoring and Evaluation 

Hatchery Effectiveness CP2002199402600 Pacific Lamprey Research and Restoration 

Hatchery Effectiveness CP2002199506325 Yakima/Klickitat Fisheries Project Monitoring And Evaluation 

Hatchery Effectiveness CP2002199802000 Assess Fish Habitat and Salmonids in the Walla Walla Watershed in 

Washington

Hatchery Effectiveness CP2002200001900 Tucannon River Spring Chinook Captive Broodstock Program 

Hatchery Effectiveness IM2001000021008 Evaluation of the Banks Lake Fishery 

Page 2 of 4
Topic PPID Title 

Hatchery Effectiveness IM2001000021029 A cooperative approach to identifying the role of forage quality in affecting 

physical condition....of mule deer in north central Washington.

Hatchery Effectiveness IM2001199502700 Develop and Implement Recovery Plan for Depressed Lake Roosevelt White 

Sturgeon Populations.

Hatchery Effectiveness IS2003199405400 Tools for Managing Bull Trout Populations Influenced by Nonnative Brook Trout 

Invasions

Hatchery Effectiveness IS2003199701900 Evaluate The Life History of Native Salmonids In The Malheur Basin 

Hatchery Effectiveness LC2003200001200 Evaluate factors limiting Columbia River gorge chum salmon populations. 

Hatchery Effectiveness LC2003200001400 Evaluate habitat use and population dynamics of lampreys in Cedar Creek 

Hatchery Effectiveness MC2002000024019 Research, Monitor, and Restore Native Species 

Hatchery Effectiveness MC2002198806400 Kootenai River White Sturgeon Studies and Conservation Aquaculture 

Hatchery Effectiveness MC2002198806500 Kootenai River Fisheries Recovery Investigations 

Hatchery Effectiveness MC2002199004400 Implement Fisheries Enhancement Opportunities on the Coeur d'Alene 

Reservation

Hatchery Effectiveness MC2002199404700 Lake Pend Oreille Fishery Recovery Project 

Hatchery Effectiveness MC2002199404900 Improving the Kootenai River Ecosystem 

Hatchery Effectiveness MC2002199500400 Mitigation for the Construction and Operation of Libby Dam 

Hatchery Effectiveness MC2002199700400 Resident Fish Stock Status Above Chief Joseph and Grand Coulee Dams 

Hatchery Effectiveness MC2002200000400 Monitor and protect bull trout for Koocanusa Reservoir. 

Hatchery Effectiveness MS2002000028061 Safety-Net Artificial Propagation Program (SNAPP) 

Hatchery Effectiveness MS2002198335003 Nez Perce Tribal Hatchery Monitoring And Evaluation 

Hatchery Effectiveness MS2002198709900 Dworshak Dam Impacts Assessment and Fisheries Investigation 

Hatchery Effectiveness MS2002198909800 Idaho Supplementation Studies 

Hatchery Effectiveness MS2002198909801 Evaluate Supplementation Studies in Idaho Rivers (ISS) 

Hatchery Effectiveness MS2002198909802 Evaluate Salmon Supplementation Studies in Idaho Rivers- Nez Perce Tribe 

Hatchery Effectiveness MS2002198909803 Salmon Supplementation Studies in Idaho- Shoshone-Bannock Tribes 

Hatchery Effectiveness MS2002199005500 Steelhead Supplementation Studies in Idaho Rivers 

Hatchery Effectiveness MS2002199107200 Redfish Lake Sockeye Salmon Captive Broodstock Program 

Hatchery Effectiveness MS2002199204000 Redfish Lake Sockeye Salmon Captive Broodstock Rearing and Research 

Hatchery Effectiveness MS2002199604300 Johnson Creek Artificial Propagation Enhancement Project 

Hatchery Effectiveness MS2002199700100 Captive Rearing Project for Salmon River Chinook Salmon 

Hatchery Effectiveness MS2002199703000 Chinook Salmon Adult Abundance Monitoring 

Hatchery Effectiveness MS2002199902000 Analyze the Persistence and Spatial Dynamics of Snake River Chinook Salmon 

Hatchery Effectiveness MS2002200002800 Evaluate Status of Pacific Lamprey in the Clearwater River Drainage, Idaho 

Hydropower CP2002000025053 Evaluate bull trout movements in the Tucannon and Lower Snake rivers 

Page 3 of 4
Topic PPID Title 

Monitoring and Evaluatio CP2002000025049 Numerically Simulating the Hydrodynamic and Water Quality Environment for 

Migrating Salmon in the Lower Snake River

Monitoring and Evaluatio MS2002000028001 Evaluate Factors Influencing Bias and Precision of Chinook Salmon Redd 

Counts 

Natural Variation and Ocean Productivity

CE2003199801400 Survival and Growth of Juvenile Salmonids in the Columbia River Plume 

Predation MC2002000024001 Lake Pend Oreille Predation Research 

Page 4 of 4