Independent Scientific Review Panel

for the Northwest Power Planning Council

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

isrp@nwppc.org

Review of Draft 

Clearwater Subbasin Plan

ISRP 2003-3

February 19, 2003
Review Team

ISRP

Charles C. Coutant

Susan Hanna

Nancy Huntly

William Liss 

Lyman McDonald

Brian Riddell

Richard Whitney

Richard N. Williams

Peer Review Group

Jack Griffith

Ray White

Staff

Erik Merrill
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

ISRP Review of Draft Clearwater Subbasin Plan

I. Executive Summary.................................................................................................................... 1

II. General Review Comments........................................................................................................ 2

Preamble ........................................................................................................................................2

Regional Recommendations ............................................................................................................3

Development of Subbasin Plans......................................................................................................................................... 3

Allocation of Time and Resources..................................................................................................................................... 4

Clearwater Review Summary: Answers to Council Questions............................................................4

Consistency with the FWP and its Scientific Foundation.............................................................................................. 5

Internal Consistency, Scientific Soundness, and Thoroughness of the Plan............................................................... 5

Consistency with the Provincial- and Basin-level Program........................................................................................... 8

Consideration of Alternative Management Responses................................................................................................... 8

Plan for Assessing Progress toward Subbasin Goals ...................................................................................................... 8

Adaptive Management and the Subbasin Plan................................................................................................................. 8

Broad Participation in Developing the Clearwater Subbasin Plan ............................................................................... 9

III. Specific Comments and Recommendations on the Three Main Components—Assessment, 

Inventory, and Management ......................................................................................................... 11

The Subbasin Assessment.............................................................................................................11

General Format and Content............................................................................................................................................. 11

Documentation of Methods............................................................................................................................................... 12

Quantitative Approaches to the Assessment .................................................................................................................. 12

Limiting Factors and Completeness of the Assessment............................................................................................... 13

Potential Management Units (PMUs).............................................................................................................................. 14

Choice of Focal Species..................................................................................................................................................... 15

Out-of-Basin Effects........................................................................................................................................................... 15

Riparian Habitats and Wetlands....................................................................................................................................... 16

Socio-economic Themes.................................................................................................................................................... 16

Specific Review Comments on the Assessment............................................................................................................ 16

The Inventory...............................................................................................................................18

The Management Plan ..................................................................................................................19

General and Summary Comments..............................................................................................19

Review Comments on Sections of the Management Plan.............................................................22

A Vision for the Subbasin ............................................................................................................................................ 22

Goals ................................................................................................................................................................................ 22

Biological Objectives for Fish and Wildlife ............................................................................................................. 23

Working Hypothesis...................................................................................................................................................... 24

The Component Hypotheses, Objectives, and Strategies........................................................................................ 25

Strategies......................................................................................................................................................................... 29

Comments on Specific Parts of the Objectives-and-Strategies Material.............................................................. 31

Research, Monitoring and Evaluation Plan (RM&E).............................................................................................. 33

Specific Comments on the Aquatics RM&E.................................................................................................... 36

Specific Comments on the Terrestrial RM&E Section ................................................................................... 38

General Guidance on Research, Monitoring, and Evaluation........................................................................ 39

References..................................................................................................................................... 43
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

1

ISRP Review of Draft Clearwater Subbasin Plan

I. Executive Summary

The draft Clearwater Subbasin Plan represents a major new step in the Council’s Fish and 

Wildlife Program. It is the first of approximately 60 forthcoming subbasin plans intended to 

provide for each subbasin up-to-date biological assessments of fish and wildlife populations, a 

synthesis of past and ongoing fish and wildlife management activities, identification of factors 

currently limiting fish and wildlife production, a description of strategies to address the limiting 

factors, and a prioritization framework for future fish and wildlife activities in the face of limited 

resources. 

Development of the Clearwater Subbasin Plan is laudable for several reasons: a) Clearwater 

subbasin planners organized an aggressive effort to draft a subbasin plan and submit it ahead of 

schedule; b) the Policy Advisory Committee (PAC) brought diverse public and private interests 

together for subbasin planning; c) the planners attempted to include socio-economic factors in 

the subbasin plan, and d) the initial portion of the Clearwater assessment describes the subbasin 

setting and its general environmental conditions thoroughly and well, and will provide a rich 

source of reference material for people working in this subbasin.

However, the draft Clearwater Subbasin Plan is not complete enough to be consistent with the 

Fish and Wildlife Program (FWP) and, in its current form, does not constitute a viable subbasin 

plan. The Plan does not fully and clearly set forth the desired direction for the subbasin or 

describe clear, problem-solving approaches (i.e., strategies) to restoration and protection. With 

limited funding, it is essential for objectives and strategies to be prioritized within the subbasin in 

order to facilitate project selection by the Council and allocate funding resources efficiently. 

The Clearwater Subbasin Plan does not describe explicit linkages between the Assessment, 

Inventory, and Management Plan, and consequently does not provide an overall coordinated 

plan. The Assessment, which does a thorough job of describing physical features of the subbasin, 

needs to more thoroughly describe fish and wildlife resources quantitatively (status, abundance, 

distribution, productivity, etc). To accomplish this, the planners will need greater input from 

existing fisheries expertise within the basin than was evident in the draft plan. The Assessment 

should culminate in a rigorous analysis of factors currently limiting fish and wildlife production 

in the subbasin. The Inventory presents a comprehensive list of existing actions, as well as some 

past and planned activities, but needs to be expanded into a document that analyzes how well 

present activities are addressing the needs of fish and wildlife populations, and provides 

interpretative conclusions from the Inventory as a whole. The Management Plan and its 

components need to be more closely connected to the Assessment’s limiting factors analysis and 

to biological and environmental objectives. The subbasin plan should develop a prioritized 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

2

restoration, production, protection, and research agenda reflecting the critical uncertainties and 

limiting factors, at the level of detail described in the Council’s Technical Guide. 

The Plan does not present analysis or justification of its priorities and allocations of effort. About 

25% of the Clearwater Subbasin Management Plan’s strategy items seem directed toward 

making human activity less damaging, about 1% to habitat protection, and about 27% to active 

restoration. Preventing, halting, and reducing harmful processes logically take precedence over 

repair and can foster passive restoration, which can be most economical. Alternative strategies 

and their costs, consequences, and contingencies are rarely presented, but are needed to judge 

overall scientific soundness of the Plan. 

The Clearwater Subbasin Management Plan has the beginnings of a solid structural foundation 

and can be revised and expanded into a viable subbasin plan. To do this, the Assessment, which 

has a strong geologic and habitat base, needs to link habitat with fish or wildlife status and 

distributions in order to identify priority “potential management units” (PMUs) or “assessment 

units” (AUs) for classes of restoration or preservation actions. The reviewers felt that the AU 

and PMU approach, if linked quantitatively with historical and present fish and wildlife 

distributions and abundances, and with limiting factors, could link the Assessment with the 

Management Plan and facilitate the integrated subbasin plan intended by the Fish and Wildlife 

Program. 

II. General Review Comments

Preamble 

On November 13, 2002, the Council accepted delivery of the Draft Clearwater Subbasin Plan 

that is intended to guide future fish and wildlife projects in the Clearwater River subbasin of 

Idaho. The Draft Clearwater Subbasin Plan is the first to be completed since the Council called 

(in 2000) for development of subbasin plans to guide implementation of its Fish and Wildlife 

Program in the future. Upon submittal of the draft plan, the Council initiated this independent 

scientific review as called for in the Fish and Wildlife Program. On November 21 and 22, the 

Clearwater planners briefed the ISRP on the draft plan with specific focus on the technical 

approach to the subbasin assessment. This report includes the ISRP’s review of the three 

elements of the draft plan (assessment, inventory, and management plan) and impressions from 

the briefing.

The Clearwater planners are expected to consider the ISRP review and submit a final subbasin 

plan to the Council as a recommendation to adopt the plan as a fish and wildlife program 

amendment. The Council then will conduct its own review and undertake a formal rulemaking 

process, including a public comment period, before making a final decision to adopt the plan into 

the fish and wildlife program.
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

3

The ISRP recognizes that the Draft Clearwater Subbasin Plan is the initial attempt in the region 

to develop a comprehensive subbasin plan. The Clearwater planners had no precedent subbasin 

plans and no previous reviews by the ISRP and other regional entities to provide them guidance. 

Furthermore, they were in the process of developing the Clearwater Plan even as the criteria for 

planning, as set forth in the Northwest Power Planning Council’s 2000 Columbia River Basin 

Fish and Wildlife Program (Council document # 2000-19) and its technical appendix, were being 

developed and approved by the Northwest Power Planning Council. In this sense, the Clearwater 

planning effort is different from other ongoing planning efforts within the basin. 

While the ISRP recognizes these special circumstances faced by the Clearwater planners, the 

decision was made to review this plan as we would future subbasin plans. The ISRP wanted 

other subbasin planners to have a clear sense of how the ISRP would review subbasin plans, the 

ISRP’s expectations for each plan, and the criteria we would be using to evaluate the plans. The 

Fish and Wildlife Program (FWP) recognizes the need and importance of flexibility in planning 

processes at the subbasin levels. However, as noted in the Technical Guide for Subbasin Planners 

(hereafter called Technical Guide), there are basic requirements for content that all subbasin 

plans must meet. Subbasin plans adopted into the Council’s 2000 Fish and Wildlife Program 

must be consistent with the standards set out in Section 4(h) of the Northwest Power Act. The 

Act requires that for a subbasin plan to be adopted as part of the 2000 Program, the Council must 

find that the measures identified in the plan meet four criteria. Specifically, the plan should: 1) 

complement existing and future activities of federal and state fish and wildlife agencies and 

Indian tribes; 2) be based on the best available scientific information; 3) use least-cost 

alternatives when there exist equally effective means of achieving biological objectives; and 4) 

be consistent with the legal rights of Indian tribes in the region. Additionally, subbasin plans 

should also be consistent with other applicable laws, mainly the Endangered Species Act and the 

Clean Water Act. 

The criteria of the Northwest Power Act are concerned with general categories of content for 

subbasin plans. These content categories relate to the general functions that the plans must serve. 

Specific guidance for the content of subbasin plans is provided in the Technical Guide. While the 

content of subbasin plans needs to be uniform across the Columbia River Basin, the specifics of 

that content will vary across subbasins reflecting differences in visions, objectives, data and 

scientific knowledge.

Regional Recommendations

Development of Subbasin Plans

The ISRP recommends that subbasin planners follow the Technical Guide for Subbasin Planners 

(Council Document #2001-20) and refer to the Subbasin Planning Assessment Template in the 

Technical Appendix of the 2000 FWP. These documents have been reviewed and approved by 

regional entities. They define a comprehensive structure for an assessment that allows flexibility 

in completing recommended elements of the assessment and can be adapted to local problems 

and conditions. They also present a useful format for subbasin plans and describe how the 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

4

subbasin vision, objectives, assessment, and inventory are to be linked together into the subbasin 

management plan. Additional support and planning assistance is available from the Council’s 

subbasin planning website (www.subbasins.org). Additional assistance in the use of EDT as an 

assessment tool is provided through an EDT website found at www.edthome.org. 

Allocation of Time and Resources

It is important that subbasin planners consider the limited timeframe and funding for the 

development of their subbasin management plan. Planners should allocate time and effort from 

the outset for each major component of the plan, because there is a threat of spending too much 

effort in the assessment and not allocating adequate time for developing the management plan 

and an integrated set of linkages between vision, objectives, assessment, inventory, and 

strategies. Other assessment considerations include the choice of focal species, reliance on 

existing data (there should be no primary data collection as part of the plan preparation), and 

extensive engagement of local experts so that the assessment reflects the full range of scientific 

knowledge in the subbasin. 

Clearwater Review Summary: Answers to Council Questions 

The 2000 Fish and Wildlife Program calls for independent scientific review of proposed 

subbasin plans to help ensure that subbasin plans direct successful fish and wildlife and habitat 

actions. In an August 2002 Notice of Request for Recommendations (for subbasin plans), the 

Council further described its expectations for the independent scientific review. The Council 

specified that scientific reviewers evaluate whether subbasin plans were consistent with the FWP 

and its Scientific Principles. The Council also identified a list of seven additional considerations 

to assist in evaluating the scientific soundness of subbasin plans: 

1. Do the assessments appear to be thorough and substantially complete? 

2. Are the subbasin goals, objectives, and strategies scientifically appropriate in light of the 

assessment and inventory of existing activities? 

3. Does the plan demonstrate a linkage between the strategies, the biological objectives, the 

subbasin vision and the assessment? 

4. Are the goals, objectives, and strategies consistent with those adopted in the program for 

the province and/or basin levels? 

5. Do the plans demonstrate that alternate management responses have been adequately 

considered?

6. Does the proposed subbasin plan include a procedure for assessing how well subbasin 

objectives are being met over time? 

7. Does the plan provide a scientifically supportable procedure for refining the biological 

objectives as new information becomes available about how fish, wildlife and the 

environment interact, and in relationship to how the plans are implemented over time? 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

5

Consistency with the FWP and its Scientific Foundation

The Council first asked the ISRP to evaluate the Clearwater Subbasin Plan for its consistency 

with the Scientific Foundation adopted as part of the Program and with the requirements for 

“biological objectives” as described in the program. The core of the Council’s Scientific 

Foundation is a set of eight Scientific Principles:

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

characteristics of their ecosystem. 

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

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

hierarchically.

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

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

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

7. Ecological management is adaptive and experimental.

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

actions. 

In general, the Clearwater Subbasin Management Plan is not complete enough to be consistent 

with the Fish and Wildlife Program (FWP) and, in its current form, does not constitute a viable 

subbasin plan. The Plan does not fully and clearly set forth the desired direction for the subbasin 

or describe clear, problem-solving approaches to restoration and protection. Furthermore, the 

Plan lacks explicit linkages between the Assessment, Inventory, and Management Plan. 

The plan shows some consistency with the eight principles of the FWP, but stronger linkages to 

the FWP’s Scientific Foundation need to be developed as the subbasin plan is revised. The 

Management Plan falls short in conforming to Principle 1 because it does not adequately link the 

characteristics of the ecosystems (described in the Assessment), and how those characteristics 

will be managed, with abundance, productivity, and diversity of organisms. It also falls short of 

Principle 4 because it does not adequately discuss in the management context how habitats 

develop and are maintained by physical and biological processes; Principles 2 and 3 may also 

require more explanation in this regard. The Plan is weak in addressing Principle 7, adaptive and 

experimental ecosystem management. The plan does not convey a clear picture of how adaptive 

management would be applied in the Clearwater Subbasin. Finally, the Plan does not explicitly 

address biological diversity (Principle 6, and its relationship with Principle 5).

Internal Consistency, Scientific Soundness, and Thoroughness of the Plan

The set of seven considerations from Council asked the ISRP to evaluate the internal 

consistency, scientific soundness, and thoroughness of the Clearwater Subbasin Plan and its 

component parts. Internal consistency means there is scientific support for the conclusion that 

the strategies proposed in a subbasin plan will in fact address the problems identified by the 

subbasin assessment. The Council’s first three considerations also address these issues. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

6

In general, the Clearwater Subbasin Plan and its assessment do not demonstrate internal 

consistency. For some topics, the assessment is quite comprehensive in presenting background 

information. The inventory appears to be a thorough listing of projects and programs underway 

historically and currently. However, the overall plan and assessment do not provide sufficient

quantitative evaluation of fish and wildlife species and their habitats. The assessment 

emphasized habitat classification and evaluation but failed to make solid linkages to the 

abundances and distributions of fish and wildlife species’ that are of concern for ESA and 

resource management. The analysis of limiting factors was cursory, yet it should be the heart of 

the assessment. Limiting factors – the problems impeding desired biological conditions –

provide a foundation for linking the assessment and the inventory together into an integrated 

management plan. 

Throughout, the Clearwater Subbasin Management Plan fails to develop clear operational 

pathways toward biological outcomes. The essential purpose of a management plan is to set forth 

“the strategies that will be implemented at a local level” (FWP 2000, p 41). The Clearwater 

Subbasin Management Plan’s strategies, while related in a general way to the objectives, are not 

related in an explicit way. The strategies are worded so generally that, together with the 

objectives, they do not constitute a meaningful scientifically based management plan. 

The 2000 FWP also explicitly calls for prioritization of biological objectives (FWP, p. 41). The 

Clearwater Subbasin Management Plan lacks a prioritized framework for the objectives. Every 

subbasin management plan will include numerous objectives and strategies that have varying 

levels of importance for restoring fish and wildlife within a subbasin. With limited funding it is 

essential for these objectives and strategies to be prioritized so that effort can be efficiently 

directed and to facilitate project selection by the Council. 

The internal consistency and linkages between the Plan’s three parts are handicapped by 

inconsistent, and sometimes non-traditiona l, use of terms including: goals, objectives, 

hypotheses, and strategies. Subbasin planners need to refer to the Council’s 2000 FWP and the 

Technical Guide for definitions that are most pertinent to developing subbasin plans. 

Planners should also refer to the ISRP flow chart provided below that illustrates the general 

linkages needed to create an internally consistent plan. The ISRP has presented this figure to the 

Council’s Level Three Regional Coordinating Group and to the Clearwater planners. One 

important note on the flow chart is that existing projects should be described in the inventory and 

compared against strategies identified in the management plan for gaps. This linkage would 

allow plan reviewers and users to understand the implementation status of strategies and identify 

unimplemented strategies, or gaps. Such linkage would be especially useful for the next project 

solicitation, review, and selection process. Including these specific linkages in the subbasin plan 

does not mean that specific projects will be adopted as amendments to the Fish and Wildlife 

Program; they will not. Decisions to implement specific projects will be made through the 

project review and selection process.
7

Spawning habitat loss due to development in 

headwaters, passage problems at culverts, 

high water temperature in lower reaches, 

extinct coho run

Establish protected and rebuilt selfsustaining fish runs; maintain genetic 

integrity; reconnect habitats

Type 1, Population: Return 5,000 spring 

chinook & 1,000 coho

Type 2, Habitat: Water temperature <70 in 

lower reaches

Build from Strength - protect all actively spawning 

redds 

Restore Ecosystem - recover riparian functions in 

lower reach

Artificial Production - restoration of coho run

Habitat Acquisition in Culvert Replacement 

Headwaters and Fencing Exclosure

198504501 200100001

Coho Reintroduction (RFP)

Indicators: water temperature, sediment load, redd 

and juvenile counts

Performance Standards: lower reach water 

temperatures not to exceed 70 

Vision

Strategy

Projects

(To Implement

Plan)

Monitoring

& Evaluation

Objectives

Assessment
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

8

Consistency with the Provincial- and Basin-level Program 

The Council’s next question was to evaluate whether the goals, objectives, and strategies 

proposed in the Clearwater Subbasin Plan were consistent with those adopted in the program for 

the province and/or basin levels.

The Council’s 2000 Fish and Wildlife Program provides only general descriptions for basin-level 

(pp. 13-34) and province-level (pp. 35-38) goals, objectives, and strategies, noting that these will 

be developed at a future time. Therefore, it is not surprising that the Clearwater Subbasin 

Management Plan contains little information relating its proposed activities to province and basin 

level objectives. Nevertheless, given the FWP’s emphasis (pp. 13-38) on building from subbasin 

level management plans upward into provincial and basin level objectives, the Clearwater 

Subbasin Management Plan might have taken the initiative to describe how those linkages might 

occur. 

Consideration of Alternative Management Responses

Next, the Council asked the ISRP to determine whether the Clearwater Subbasin Plan 

demonstrated that alternate management responses had been adequately considered.

The Clearwater Subbasin Management Plan seldom proposes actions from an array of alternative 

options. Additionally, actions proposed in the plan lack specificity. Strategies are presented, for 

example to use a mix of hatchery and natural production within the subbasin, without a rationale 

as to why they are the best approach, or a description of what alternative strategies might be 

employed. Finally, no management responses are suggested, proposed, or discussed in the 

management plan, such as predictions of how focal species abundance would change in response 

to a proposed activity. 

Plan for Assessing Progress toward Subbasin Goals

The Council’s next question focused on accountability and self-assessment. The ISRP was asked 

to determine whether the Clearwater Subbasin Plan included a procedure for assessing how well 

subbasin objectives are being met over time.

In general, the Assessment, Inventory, and Management Plan do not provide an overall 

coordinated plan for research, monitoring, and evaluation in the subbasin. The Clearwater 

Subbasin Management Plan should include provisions for implementation monitoring as well as 

Tier 1 (trend and routine), Tier 2 (statistical), and Tier 3 (research) monitoring. The RM&E 

program needs to be more closely connected to a limiting factors analysis and the biological and 

environmental objectives. A prioritized research agenda reflecting the critical uncertainties and 

limiting factors should be developed and presented with the detail described in the Technical 

Guide. The research topics in the present plan are vague and unfocused. Additionally, no 

research is proposed to address the socioeconomic objectives.

Adaptive Management and the Subbasin Plan

Finally, the Council asked the ISRP to determine whether the subbasin plan provided a 

scientifically supportable procedure for refining the biological objectives as new information 

becomes available about how fish, wildlife, and the environment interact, and in relationship to 

how the plans are implemented over time. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

9

The Clearwater Subbasin Management Plan seems to imply use of adaptive management, but 

does not include a procedure for conducting it. The plan does not provide an explicit description 

of how the objectives would be refined on the basis of new information. How will such adaptive 

management feed into prioritization of research? The plan contains 20 pages (about 21% of the 

material) on research, much of it for monitoring and evaluation, but it does not say how the 

knowledge gained will be used. The plan does not include a synthesis of the current information 

and a statement of biological objectives at the level needed to facilitate adaptive management. 

Thus the Plan is not currently in the form envisioned by the FWP.

Broad Participation in Developing the Clearwater Subbasin Plan

The 2000 FWP, the 2000 Subbasin Assessment Template (part of the 2000 FWP Technical 

Appendices), the 2001 Technical Guide for Subbasin Planners (Council document #2001-20), 

and the individual contracts to lead entities emphasize that the subbasin planning effort is to be a 

locally led process with assured participation by and collaboration with fish and wildlife 

managers, local governments, interest groups, stakeholders, and other state and federal land and 

water resources managers. The Technical Guide emphasizes that the plan development process 

should be broadly participatory such that the technical expertise in the subbasin contributes to the 

scientific base of the plan and policy makers, managers and planners communicate local 

concerns, conditions, and priorities. Broad participation and buy-in at local levels is critical if 

subbasin plans are to be implemented successfully. The Technical Guide also points out the 

importance of assembling a group of local or state technical experts to work on the assessment as 

a subbasin technical team. The team should have the biological, physical, and management 

expertise to refine, validate, and analyze data and should work in close interaction with the 

policy group. 

The Policy Advisory Committee (PAC) established by Clearwater subbasin planners was 

designed to represent major public and private interests within the subbasin, and it had oversight 

over the planning process. This concept is laudable. It is unclear, however, how much direct 

involvement these diverse interests had in the actual planning process. It is especially unclear 

how much technical input was provided by local biologists and resource managers in developing 

the Clearwater Subbasin Management Plan. The expertise of state and federal agencies on 

matters of landscape processes, stream habitat, and wild fish populations does not seem as well 

represented as needed for a workable plan. Additionally, it is not clear that private landowners 

were sufficiently involved in development of the plan. For example, Potlatch Corporation is a 

major landowner within the basin and has extensive data on subbasin resources, yet we did not 

see that those data were used in the assessment or management plan. 

A subbasin plan will be strongest when the technical assessment teams include numerous local 

biologists who are experienced in basic ecology and in management of the region’s natural 

resources, especially in the practicalities of management to benefit fish and wildlife populations 

and terrestrial and aquatic habitat. The Clearwater planning did not seem to have enough of this 

participation, particularly in the aquatic technical team. The Clearwater Subbasin Management 

Plan lists only two aquatic personnel and a “spatial ecologist”, whereas the terrestrial team 

included six biologists and a GIS analyst. From earlier annual and provincial reviews, the ISRP 

is well aware of the substantial fisheries expertise in the Clearwater Subbasin, and adequate use 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

10

and reliance of that expertise was not evident in the Clearwater Subbasin Plan. The plan would 

have benefited from substantial participation by state, tribal, and federal natural resource 

agencies, as well the Potlatch Corporation, via commitment of data, expertise, and possibly 

personnel time. 

A management plan developed for a subbasin will affect diverse interests and should reflect the 

collective goals and objectives of these various interests, contain their knowledge, and represent 

their buy-in to a coordinated strategic plan for the subbasin. Too much reliance on subcontractors 

without concomitant participation by local stakeholders and technical experts can result in a plan 

that lacks integration, comprehensive context, and broad support. Valuable roles for 

subcontractors include gathering relevant background information and drafting the assessment 

and inventory sections. If subcontractors or consultants are used in the development of the 

subbasin management plan, their roles should be those of facilitating exchange of ideas and of 

representing the group’s objectives and agreements in the document in a format that can be 

implemented. 

The potentially extensive role of subcontractors in the Council’s subbasin planning effort raises 

the need for the Council and the subbasin planning level 1, 2, and 3 coordination groups to be 

vigilant in their educational outreach to local groups, technical experts, and fish and wildlife 

managers, to motivate participation in the process at a high level. In addition, the Council and 

the coordination groups should closely track the process to ensure that the subcontractors are 

securing meaningful local participation and taking advantage of the wealth of expertise and 

information present in the subbasin.

Finally, the ISRP recommends that subbasin planners follow the Subbasin Planning Assessment 

Template in the Technical Appendix of the 2000 FWP and the Technical Guide for Subbasin 

Planners (Council Document #2001-20). These documents have been reviewed and approved by 

regional entities. They define a comprehensive structure for an assessment that allows flexibility 

in completing recommended elements of the assessment and can be adapted to local problems 

and conditions. They also present a useful format for subbasin plans and describe how the 

subbasin vision, objectives, assessment, and inventory are to be linked together into the subbasin 

management plan. Having a common format helps writers, reviewers, and implementers to 

locate topics readily. Additional support and planning assistance is available from the Council’s 

subbasin planning website (www.subbasins.org). 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

11

III. Specific Comments and Recommendations on the Three Main 

Components—Assessment, Inventory, and Management 

In the sections that follow, the ISRP provides more specific comments on each of the major 

sections of the Clearwater Subbasin Plan: the Assessment, Inventory, and Management Plan. 

The Subbasin Assessment

Guidance for the Assessment (and the subbasin plan in general) comes from the 2000 FWP, the 

Program’s Technical Appendix, a detailed 13-page Subbasin Planning Assessment Template

(www.nwcouncil.org/library/2000/2000-19/TechAppC/SubbasinAssessmentTemplate.pdf), and 

the Technical Guide for Subbasin Planners (www.nwcounc il.org/library/2001/2001-20.pdf). 

Because this is the first subbasin plan submitted and reviewed, the ISRP assessed the extent to 

which the Clearwater assessment followed guidelines provided by the Template and the 

Technical Guide, although primary emphasis was placed on guidelines from the Technical 

Guide. For development of the remaining Columbia Basin subbasin plans, the ISRP recommends 

following the content and format recommendations in the Technical Guide. Attention to the 

Technical Guide should result in subbasin plans that are adequate for the ISRP review, and the 

Council’s planning and amendment process. 

General Format and Content

The 2000 FWP does not contain specific criteria or required scientific elements of a subbasin 

assessment, but refers planners to the Subbasin Planning Assessment Template in the Program’s 

Technical Appendix. In further defining the process, the Council developed a Technical Guide 

for Subbasin Planners. The guide was non-mandatory to allow some flexibility among subbasins, 

but provides a common structure and format. The ISRP assessed the extent to which the 

Clearwater assessment followed these formats.

The initial portion of the Clearwater assessment describes the subbasin setting and its general 

environmental conditions thoroughly and well, and will provide a rich source of reference 

material for people working in this subbasin. However, much of the remainder of the assessment 

is incomplete and does lay an adequate scientific and technical foundation for a functional 

management plan. 

The subbasin description incorporates topics 1, 2.1 – 2.3, and 3.1 in the Template and topic A.1 

in the "Technical Guide. The Clearwater assessment did not follow the exact topic heading or 

sequence given in either suggested format, but did succeed in describing the setting in an orderly 

and generally thorough manner. This portion of the assessment is lengthy, detailed, and useful. 

However, data sources for figures and tables in the subbasin description and throughout the 

management plan ne ed to be better documented. Good historical summaries are provided in 

several sections. The salient land uses that shape the subbasin (roads, agriculture, grazing, 

mining, and dams) are summarized. Almost half the subbasin has some protected status as a 

roadless or wilderness area. The assessment divides the subbasin into eight biophysical 

“assessment units” (AUs) about the size of a 4th field HUC. Each assessment unit is 

characterized on the basis of its geology, precipitation, dominant land use, primary land 

ownership, predominant landform, and elevation. Later in the assessment, Ecovista used another 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

12

organizing scheme whereby 6th field HUCs were characterized by 22 or more variables into 

“potential management units” (PMUs). 

Documentation of Methods

Greater documentation of methods, literature citations, and development of the assessment tool is 

needed throughout the Assessment to provide a solid foundation for the Management Plan. 

Methods and procedures used to assess fish and wildlife populations and their habitats need to be 

documented or references given to literature so that they can be repeated elsewhere and in the 

future for the Clearwater Subbasin. Decisions made in developing the analytical tools also need 

to be documented. For example, with respect to EDT, justification is needed for each “rule” 

(supporting literature, studies, data, expert opinion, best judgment of the modeler, etc). It 

appeared that many critical decisions on inputs into the Ecovista assessment tool reside only 

within the Ecovista team; they are not described in the assessment. At a minimum, this reliance 

on the expert opinion of the assessment team should be described and the methods used should 

be included, perhaps in an appendix. Better, scientific literature should be cited to support, 

suggest, or define questions about the assumptions used. 

The EDT Primer (www.edthome.org) provides strong advice to “begin documenting information 

sources early and diligently.” This advice extends beyond EDT to all data endeavors. The 

ecological structure of a subbasin is always complex and will be described by many different 

sources of information. Much of the value of an assessment lies in its complete and explicit 

documentation of the sources of information and the rationale for inferences made. 

Documentation is especially important because the subbasin plans are iterative documents and 

will need to be revisited as new information is presented, such as that generated by NOAA 

Fisheries’ Technical Recovery Teams.

Quantitative Approaches to the Assessment 

A quantitative approach is essential in subbasin planning, especially for determining limiting 

factors and the expected response of fish and wildlife species to management actions. The 

Clearwater Subbasin Plan should place greater emphasis on more detailed quantitative analysis 

of available data, particularly as related to fish and wildlife populations. 

Subbasins will differ in the quantity and quality of existing data and in the kinds of analyses that 

have been done before planning was initiated. Subbasin planners are not expected to engage in 

collection of primary data in the field, but rather to use information that has already been 

compiled. The planners should make optimal use of existing data and analyses in developing the 

subbasin plan. The analytical methods that are appropriate for developing the assessment include 

expert opinion, expert systems, and empirical models. These same tools are useful for 

establishing a prioritization of efforts. The ISRP expects that one or more of these procedures 

will be used in prioritization of efforts. 

• Expert opinion involves compiling the opinions of knowledgeable experts such as local 

managers and scientists. Expert opinion is often the least reliable of the decision-support 

tools because it is subjective and assumptions generally are not explicitly identified or 

substantiated. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

13

• Expert systems represent a more formal decision-support tool that utilizes both 

quantitative information and expert opinion. This method attempts to make underlying 

assumptions explicit. Expert systems that have been used in the Columbia River basin 

include the Interior Columbia Basin Ecosystem Management Plan’s (ICBEMP) Baysian 

belief network (Quigley and Arbelbeide 1997) and Ecosystem Diagnosis and Treatment 

(EDT; Mobrand Biometrics 1999). 

• Empirical models use quantitative information to develop associations between fish and 

wildlife population performances (e.g., extinction, abundance) and environmental 

conditions. They have been used extensively in the Columbia River basin. The utility of 

empirical models depends in part on the quality and quantity of available data. 

A good approach would be to utilize a variety of analytical methods for developing subbasin 

plans. Subbasin planners should clearly specify which types of analytical methods were used in 

the assessment and should include use of quantitative methods as one of their tools. The 

Independent Scientific Advisory Board (ISAB) is in the final stages of preparing a report titled 

“A Review of Strategies for Tributary Habitat Recovery.” That report contains more detailed 

discussion of the use of expert systems and models in subbasin planning. The full report of the 

ISAB will be available on the Northwest Power Planning Council website by April 2003. 

We also feel it is important to comment on the role of prediction in using various empirical 

models as an assessment tool. For example, EDT is most useful as a tool for comparing 

alternative management scenarios, rather than as a predictor of actual fish or wildlife population 

responses to various management actions. As such, EDT is useful in “predicting” actions that 

are most likely to provide benefits to fish and wildlife populations, but is not an appropriate tool 

to predict absolute values, such as total production capacity or productivity of stocks. 

Limiting Factors and Completeness of the Assessment 

While the initial portion of the Clearwater assessment provided a thorough description of the 

subbasin setting and its general environmental conditions, the assessment lacked sufficient 

quantitative evaluation of fish and wildlife species and their specific habitat conditions. 

Population abundance and productivity were not adequately addressed. Virtually no quantitative

data on fish productivity were presented. Instead, the subbasin planners attempted to use data on 

aquatic invertebrate abundance as a surrogate for fish productivity, but this falls short of 

providing a connection to numbers of fishes.

The rest of the assessment summarizes biological information. The Council’s Technical Guide 

calls for a list of native and non-native fish and wildlife and their legal status, and also special 

status plants. The Clearwater assessment does this, with a separate CD of 340 vertebrate species 

in the appendix and a text table of the 30-plus species of fishes. Reviewers noted the good 

identification of vegetative cover types and their related plant species in the assessment, as well 

as a list of plant species with special status (in an appendix), but not a comprehensive plant 

species list.

The analysis of limiting factors was cursory; yet, it should be the heart of the assessment. The 

identification of limiting factors – the problems that impede desired biological conditions – is 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

14

intended to provide a foundation for working hypotheses concerning ecological response to 

human interventions. These hypotheses then shape the objectives and strategies presented in the 

management plan, which will in turn provide the basis for Council recommendations on project 

funding. The assessment offers general speculation as to limiting factors based on exceedingly 

large land/water units, but it did not partition limiting factor analysis by fish life stage, as the 

Technical Guide suggests. A quantitative assessment of focal species-habitat relationships 

(including identification of important habitat features and processes, etc.) was not accomplished. 

Population dynamics of focal species in other subbasins could be incorporated into the 

assessment to provide context and fill in information gaps, but were not. 

The Clearwater Assessment authors speculate regarding limiting factors in only a very general 

but largely meaningless way based on exceedingly large (AU) land/water units (Table 58). They 

produce a long list of possible limiting factors, ranked on a 1-through-3 scale. This process so 

reduced information that its value is questionable. There should be documentation for the utility 

of the 1-through-3 rankings of limiting factors. The simple term, “importance rating”, would 

seem to be more in accordance with established terminology for ecological investigations. The 

text (p 343) says the ratings were “assigned” depending on the degree to which they “are 

thought” to limit the species involved. This seems to overly rely on professional judgment, 

without substantiation of its basis in data: Whose judgment was involved – the primary author, 

the technical team, or others? Would other people, given the same information that the authors 

had, come to the same conclusions? The rating process should be explained more explicitly and 

the data upon which ratings are based provided in an appendix.

Potential Management Units (PMUs)

The assessment bases much of its analysis on the identification and aggregation of Potential 

Management Units (PMUs). The assessment describes PMUs as groups of HUCs (either 

contiguous or noncontiguous) intended to characterize areas that have similar themes regarding 

species distributions, disturbance regimes, and other characteristics that will influence future 

subbasin scale restoration or recovery planning. This approach could be useful for prioritizing 

actions; however, the assessment states that PMUs were defined largely in a subjective manner 

and were not delineated in a species-specific manner due to a lack of comprehensive distribution 

and status information for some species, the heavy reliance on landscape level characteristics 

used to define them, and the potential for altered species distributions in the future (through 

reintroductions or habitat improvement). The subjective PMU delineation process should be 

clarified. It is not clear why a statistical process (e.g., cluster or ordination analysis) was not 

used to look for association of like attributes. Use of such a technique would allow 

documentation of existing grouping, as well as replication of results by future analysts, neither of 

which can be done with the subjective process that apparently was used. 

The final section of the Clearwater Assessment, the synthesis/interpretation described in the 

technical guidelines, is not complete; the assessment does not clearly link PMUs or aggregations 

of PMUs with AUs and with fish or wildlife status and distributions to prioritize specific PMUs 

or AUs for restoration or preservation actions. This is a critical shortcoming in both the 

Assessment and the Management Plan. The Plan should identify for each focal species where 

stronghold populations exist and should be protected, where restoration efforts are apt to be most 

effective, and what types of restoration actions are most prudent. The reviewers felt that the AU 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

15

and PMU approach, if linked solidly with historical and present fish and wildlife distributions 

and abundances, could link the Assessment with the Management Plan and facilitate the 

integrated subbasin management plan intended by the Technical Guide. 

Choice of Focal Species

The choice of focal species is critical to an assessment and a limited number must be selected 

due to limitations on time, budget, and analytical tools. The Technical Guide suggests that focal 

species be chosen on the basis of special ecological, cultural, or legal status, and that they be 

indicators of ecosystem health. It recommends that focal species should include one or more 

wildlife, resident fish, and anadromous fish species. In general, planners are able to deal 

effectively with a maximum of five focal species. In the Clearwater plan, the selection of 12 

terrestrial focal species is problematic both in sheer number and in species choice. The 

Clearwater subbasin focal species are endangered plants and big game species. This selection is 

counter to the advice of the Technical Guide and overlooks the approach of the Fish and Wildlife 

Program, which emphasizes a network of species and an ecosystem approach. 

There is a precedent for using a tractable number of focal species, especially with Environmental 

Impact Statements conducted under the National Environmental Policy Act (NEPA). Typically, 

keystone and endangered and threatened species are selected as focal species. Subbasin plans are 

ecosystem plans, so some attention must also be given to other non-focal species; these non-focal 

species, however, need not be described and considered with the same population-level of detail 

that is required for focal species. Attention to non-focal species provides a biological context for 

the focal species and serves to draw attention to unanticipated consequences of a management 

plan that uses focal species to make many central decisions. The choice of focal species needs to 

be made carefully to ensure that they represent the ecosystem. For example, stream habitat in the 

Grande Ronde subbasin is primarily suitable for cool or warm water species, so if bull trout were 

chosen as a focal species, they would not be representative of the entire system. 

Out-of-Basin Effects

The management plan contends that out-of-basin effects are the primary factors limiting 

recruitment of anadromous spawners to the Clearwater. This assertion needs to be scientifically 

justified and documented in the assessment. Adult passage data are available for the lower Snake 

River, as are data on reach survival of juvenile outmigrants. Given the asserted importance of 

out-of-basin factors, it would be useful to know how much improvement in anadromous fish 

populations would accrue if the objectives of the management plan were accomplished. The 

assessment and subsequent management plan need to deal more explicitly with out-of-basin 

factors. 

For example, the dominant limiting factor for lamprey in the Clearwater system may be 

difficulties with upstream passage by migrating adults at hydroelectric projects, rather than 

habitat limitations within the Clearwater subbasin. The assessment ought to point out that this 

finding probably has identified the single most important factor limiting the abundance of 

lamprey in the subbasin. Then, when it comes to prioritizing actions to restore lamprey in the 

subbasin, highest priority ought to be given to improving passage conditions for lamprey at the 

mainstem ladders. Actions that might be suggested within the subbasin are of much lower 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

16

priority – in fact they may be of no particular importance in restoring abundance of lamprey, 

particularly in the absence of mainstem actions to improve passage. The Plan should say so. 

While out-of-basin factors also affect Clearwater salmon and steelhead populations, within-basin 

factors such as water quality, habitat type, quantity, and quality, and the blockage of historical 

spawning areas also effect salmonid production in the subbasin. Out-of-basin effects 

conceivably could negate any actions within the subbasin. For example, unless offshore and 

lower river fisheries are regulated to allow specified numbers of fish to elude the fisheries, it is 

unlikely that goals established for the subbasin will be achieved, regardless of actions within the 

subbasin. A strong subbasin plan would endeavor to partition recovery potential for anadromous 

stocks into the fraction that would be expected from in-basin vs. that from out-of-basin 

expenditures of effort. Another approach might be for the subbasin plan to provide a sensitivity 

analysis of “out-of-basin” factors on subbasin goals; i.e., what is needed outside the subbasin to 

achieve their goals?

Riparian Habitats and Wetlands

Riparian habitats and wetlands are essentially ignored in the aquatic assessment. The discussion 

of wildlife habitat in the Management Plan acknowledges the importance of riparian areas, but 

that discussion (of black cottonwood vegetative cover type) suffers from a lack of any 

description of the previous quality and quantity of those resources. Similarly, management 

objectives identify the desire of managers to restore 500 acres of historical wetlands and to 

protect/restore 300 miles of riparian habitat, but these objectives are not based on documented 

needs or problems and so neither the realism of the specific objectives nor their priority can be 

judged.

The absence of information on riparian habitat is particularly noteworthy given the Technical 

Guide’s explicit discussion of the contribution of subbasin assessments to the NMFS and 

USFWS development of recovery plans for ESA listed species. The Guide presents a draft list of 

seven questions that concern habitat that NMFS has identified as important to recovery planning 

and that assessments should be able to answer. Riparian habitat is one of these. 

Socio-economic Themes

Section 3.10 “Population and Land Uses” contains information that could be used as a basis for 

forming socio-economic objectives and strategies (Hypotheses 18-20 in the management plan) 

that tie in to the biological objectives. For example, what effect will changes in grazing, 

agricultural production, and participation in the Conservation Reserve Program likely have on 

the proposed restoration strategies? How will the social and economic environment of the 

Clearwater Subbasin affect the likelihood of success of strategies to recover fish, wildlife, and 

plant communities? These objectives and strategies should be developed through broad interest 

group participation under the guidance of a qualified economist or social scientist. 

Specific Review Comments on the Assessment

1. The description of the subbasin's geology is well done for general descriptive purposes, but 

does not address the important question of which assessment units have a higher fish production 

potential (see comments on productivity below). Specifically, for example, it is important to 

identify the extent to which parent rock contains calcium and magnesium constituents that lead 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

17

to greater stream productivity. Unfortunately, Table 3 lumps carbonate with shale (as schist), 

and the single category "granite" is similarly too broad.

2. The Technical Guide requests an assessment of fish "productivity" and as a result the authors 

of the assessment gathered data on aquatic invertebrate abundance to use as a surrogate for fish 

abundance. The assessment confuses the terms productivity and production and states that 

productivity is defined as the rate of production. Actually, fish production (the weight of fish 

tissue generated over a certain period of time, including that of those individual fish that die 

during the period) is a standard, directly calculated measure of population performance, as is 

"standing stock", the weight of fish present at a point in time. More importantly, the attempt to 

provide a foundation for an assessment of aquatic productivity using data collected on 

macroinvertebrates falls short of establishing what is desired – a connection to numbers of fishes 

identified in Table 2. 

The discussion of fish productivity, and the generation of that new macroinvertebrate data, is 

flawed because (a) the approach requires the assumption that fish production in the Clearwater 

subbasin is food-limited (more invertebrates will mean more fish), which is not necessarily true, 

(b) it ignores the relative quality of various invertebrates as fish food, and (c) it ignores much 

more extensive efforts to attempt to do the same thing elsewhere (i.e., the Salmon subbasin). A 

simpler, cheaper, and more powerful procedure would have been to directly assess fish 

abundance at a variety of sites, or to simply make use of a measure of edaphic potential, such as 

specific conductance of stream water. A substantial body of literature has demonstrated a 

connection between geological constituents of watersheds (e.g. sedimentary strata v. granitic 

strata) and the resulting abundance of fishes (and macroinvertebrates too). There is no need to 

repeat that work to establish the relationship, only to determine where the particular stream reach 

within the Clearwater subbasin fits into the picture already developed in the literature. Of course 

the result is only a rough estimate, but certainly the best that can be expected at this stage, and 

certainly adequate for planning purposes.

3. The significance of the modeled thermal limitation parameter, MWMT, is useful but should 

be described more clearly. Is it not intended as an estimate of the mean of daily water 

temperature maxima during the warmest week of the year at a given point in a stream? If so, this 

should be said. Moreover, the terminology is needlessly confusing and is expressed in 

inconsistent form. Thus, even though the actual parameter being calculated might be valid and 

useful in considering thermal limitations, many readers, including plan users and evaluators, may 

misunderstand its meaning. The first time MWMT appears (1st paragraph in the section 

“Temperature Limitations (modeled)” on p 354), it is called “mean weekly maximum 

temperature,” but further on, in the captions for Table 61 and Figure 101, it is called “maximum

weekly maximum temperature” (italics added). Only the correct term should be used, whichever 

it is. The section on MWMT should be made simpler and clearer. Is there any ecological value 

in this parameter, any appropriate references to its use?

4. On page 283 it is stated with respect to interpreting the results of applying the method for 

estimating smolt carrying capacity (cited as NWPPC 1989) that there is “...little discernable 

pattern with regard to high or low production areas.” This finding calls out for further discussion, 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

18

as it suggests that either the NWPPC method or the method of defining high and low production 

areas is inadequate (or both). What is the explanation? 

In this regard, the paragraph discussing Chapman’s (1981) findings and the comparison with the 

NWPPC estimate deserves a more in-depth examination, as well. Because Chapman’s estimate 

relates to “pristine conditions”, it ought to be reasonable to conclude that his numbers would be 

near carrying capacity. And because his estimate includes areas no longer available to salmon, 

his number might be expected to be higher than those derived from the NWPPC process. Why 

are they not higher? The subject should be examined more fully, because the bottom line ought 

to provide some guidance as to what might reasonably be expected to be produced in the 

subbasin, as compared to what is currently being produced, and that is a primary subject that 

ought to be dealt with in some detail in the text.

5. On page 286 there is a discussion of fall chinook counts at Lewiston Dam. The fact that the 

ladder was determined to be inadequate for passage should be mentioned here – and it is 

mentioned in a later section.

6. On page 326 primary factors limiting salmonid populations in the subbasin are identified. It 

should be brought out that out-of-basin effects have a significant effect on the populations – to 

the point that within basin effects may be secondary. Fishing is a good example, as noted above. 

The text brings this out well on page 328 where it says that it is unlikely that improvement within 

the subbasins alone can increase survival enough to ensure recovery of listed salmonid 

populations. This statement belongs at the beginning of the section or the beginning of the Plan. 

It now appears on page 9 of the Plan as the first item in the discussion, which is good.

7. Effects of draw down of Dworshak Dam on resident fishes downstream of the dam should be 

enlarged upon. With 47 m of drawdown and periodic releases purportedly to benefit juvenile and 

adult salmon migrating in the lower mainstem, there are bound to be some adverse effects on 

resident fishes in the Clearwater below Dworshak Dam. These effects are not discussed here, but 

are discussed in the management plan.

The Inventory

The draft Clearwater Subbasin Inventory presents brief descriptions of the subbasin’s activities 

toward fish and wildlife recovery, as well as of applicable policies and plans. This constitutes a 

comprehensive list of existing actions, as well as some past and planned activities. 

As noted in the Technical Guide, the inventory of existing projects will be most valuable when it 

is reviewed in the context of the limiting factors identified in the assessment. The purpose of 

reviewing existing projects is to evaluate those projects against actions needed to address 

limiting factors – identifying gaps. The “gap analysis” will then guide the development of 

management strategies. 

The draft Clearwater Subbasin Inventory needs to be expanded from the present simple listing 

into a document that analyzes how well present activities are addressing the needs of fish and 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

19

wildlife populations. Toward this it would be advisable to (a) more completely follow the 

Inventory requirements set forth in the 2000 FWP, as outlined in the Technical Guide, and (b) 

include a new, interpretive, summary section which draws conclusions from the Inventory as a 

whole. 

As recommended in the Technical Guide, the inventory should, but this draft plan does not, 

include a synopsis of accomplishments or failures of each activity, related to established goals 

and objectives where possible; identify limiting factors or ecological processes the activity is 

designed to address; and identify relationship to other activities in the subbasin. For example, the 

Inventory’s extensive Table 4 contains few synopses of results, even for projects that have been 

underway for four or more years. Without the synopses of results, the inventory cannot form a 

meaningful part of the subbasin plan. Correspondingly, a required item for the inventory is a 

statement of objectives for existing projects and programs. Most project and program 

descriptions in the Inventory contain objectives, but seldom in quantitative or target-date terms. 

Sources, methods, and procedures used to compile the Inventory must be given in sufficient 

detail so that the inventory can be repeated in the future and future results compared by 

quantitative methods to the present inventory. 

The Management Plan

General and Summary Comments

The 2000 Fish and Wildlife Program characterizes the management plan as “the heart of the 

subbasin plan.” It is supposed to “reflect what is learned in the assessment and inventory work,” 

and, on that basis, merge “policy, legal, and ecological considerations” and set forth “the 

strategies that will be implemented at a local level” (FWP 2000, p 41). The Draft Clearwater 

Subbasin Management Plan does not satisfy these requirements adequately and is of limited 

utility in recovering key populations of fish and wildlife. The draft Management Plan does not 

follow the FWP criteria in important ways. It does not, for the most part, enunciate true 

strategies, draw sufficient connection with the Assessment and Inventory, or adequately show 

how policy, legal, and ecological considerations are merged. As a result, the Management Plan 

does not present what should constitute the main aspect of any management plan for biological 

resources: clear explanations of how the objectives, i.e., quantifiable benefits to focal species, are 

to be accomplished.

The FWP concedes that basin-scale biological and environmental objectives must be general and 

qualitative but “should become increasingly quantitative and measurable at the province and 

subbasin levels” (p. 16 and 41). The Technical Guide notes that the vision expressed by a plan is 

qualitative and should reflect the conditions, values, and priorities of a subbasin in a manner 

consistent with the Council’s Program vision for the Columbia River Basin. The biological 

objectives, however, are benchmarks that should be quantitative expressions of biological and 

physical changes needed to address the limiting factors and achieve the vision. 

The biological and environmental objectives in the present draft of the management plan are 

general and mostly qualitative. In only a few cases does the management plan give quantitative 

objectives and timeframes for accomplishing the objectives. The authors of the management plan 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

20

assert that they lacked sufficient data and information to develop quantitative objectives. The 

objectives in this management plan apparently are designed as just a first step, namely to develop 

methods and acquire the necessary data and information. Thus, the management plan is 

essentially a proposal to conduct the needed background work, rather than a plan with specific 

management objectives that will be accomplished within a specified timeframe. Although there 

are undoubtedly important information gaps, the management plan should provide more specific 

objectives and strategies based on information given in the assessment, even if many are 

tentative. 

The Clearwater Subbasin Management Plan does not describe clear, problem-solving approaches

to the subbasin’s restoration and protection needs. It should present the array of needs, each in 

straightforward terms: Here’s the problem; here’s the result needed (the objective); and here’s 

the solution (a strategy). The management objectives and strategies are vague and incomplete. 

The strategies should provide the core operational guidance but do not. A management plan 

should contain framework guidance about procedures to be followed under certain contingencies. 

It should also contain specifics about actions and regulations that will be taken to meet the 

objectives. These two elements are missing from this plan, which fails to develop clear 

operational pathways toward biological outcomes. The essential purpose of a management plan 

is to set forth “the strategies that will be implemented at a local level” (FWP 2000, p 41). The 

management plan’s strategies are not explicitly related to the objectives. The strategies are 

worded too generally to constitute a meaningful scientifically based management plan. Each 

strategy should consist of an integrated set of actions (FWP 2000), a logical sequence of actions 

for performance. The strategies should be explained in terms of their effects on the ecology and 

population dynamics of the focal (and perhaps non-focal) species.

The 2000 FWP explicitly calls for prioritization of biological objectives (FWP, p. 41). The 

Clearwater Subbasin Management Plan lacks a prioritized framework for the objectives. Every 

subbasin management plan will include numerous important objectives and strategies for 

restoring fish and wildlife within a subbasin. With limited funding, it is essential for these 

objectives and strategies to be prioritized so that effort can be efficiently directed and to facilitate 

project selection by the Council. Additionally, there is no indication in the Plan of how needed 

information will be acquired through adaptive management. In its current form, the management 

plan has limited utility for directing protection and restoration efforts in the Clearwater Basin and 

for project selection and funding allocations. It does not establish a strategic prioritizing 

framework for allocating limited funding toward specific actions or objectives within the 

subbasin. Stronger linkage between the Assessment and the Management Plan could lead to 

rearrangement of the subject matter discussed in the Clearwater Subbasin Management Plan, 

according to the “pyramid” of actions identified in the analysis given in the Assessment. It 

appears that a given category or type of AU possesses characteristics in terms of potential action 

types, and these can be prioritized. 

The plan does not, but should, justify that the proposed actions represent appropriate allocation 

of effort for getting the recovery job done with dispatch and efficiency. The plan should explain 

of the connections between the assessment, the objectives, proposed investigations, and actual 

recovery work. About 25% of the Clearwater Subbasin Management Plan’s strategy items seem 

directed toward making human activity less damaging; these include measures to alter land use 

or resource use, as well as education. The highest proportion of strategy items, 36%, involve 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

21

studies (mainly field investigations, some stating evaluation), other development of information, 

and development of study methods. Active restoration (mostly of fish or wildlife habitat but also 

artificial fish propagation for “supplementation” or mitigation) accounts for 27% of the items; 

habitat protection for 1%; development of restoration methods for 3%; and coordination, other 

administration, and program development for 9%. Generally, changing human activities so that 

they do less harm is the most essential category of effort in a habitat-based program for fish and 

wildlife recovery. Preventing, halting, and reduc ing harmful processes logically take precedence 

over repair and can foster passive restoration, taking advantage of the self-healing power of 

nature and allowing self-regeneration of habitat and of fish and wildlife populations. Letting 

nature do the work can be most economical. 

Throughout the Management Plan, failure to provide substantiation from pertinent, basic 

literature, and from the Assessment, violates scientific soundness. The management plan 

sometimes refers readers to the Assessment, but usually without specific reference to where in 

the Assessment the pertinent information exists; section and subsection numbers should always 

be given, usually also page numbers. The elements of the management plan need to be directly 

related to the watershed Assessment and Inventory; both these and the primary scientific 

literature should be used and referenced to justify the hypotheses, objectives, and strategies. 

Information from the Assessment need not always be reiterated in the management plan, but the 

planners should—for every hypothesis, and probably for every objective and most strategies—

specifically reference the assessment tables, figures, pages or section numbers—and in some 

cases paragraphs—that support the items. 

The Plan omits several significant administrative issues. It is unclear precisely how the

coordination of both ongoing and new activities will take place. Further, a management plan 

usually should reflect the approach a public entity (which holds authority to make management 

decisions) will take to achieve certain objectives and legislative mandates. This plan is different 

in that there is no specified action authority and no particular specific mandates under which that 

authority would act. It is not clear what motivation will ensure that actions are taken.

In general, the Assessment, Inventory, and Management Plan fail to provide an overall 

coordinated plan for research, monitoring, and evaluation in the subbasin. The management 

plan should include provisions for implementation monitoring as well as Tier 1 (trend and 

routine), Tier 2 (statistical), and Tier 3 (research) monitoring. The research, monitoring, and 

evaluation program needs to be more closely connected to a limiting factors analysis and to 

biological and environmental objectives. The Plan should develop a prioritized research agenda 

reflecting the critical uncertainties and limiting factors, with the detail described in the Technical 

Guide. The research topics in the present plan are vague and unfocused, and inventory is 

sometimes confused with research. Additionally, no research is proposed to address the 

socioeconomic objectives.

The ISRP recommends the following 5 actions to aid in the development of an improved 

Management Plan: 

1. Thorough adherence to the Council’s Technical Guide for subbasin plans. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

22

2. More direction of the planning by experts in the biological science of the subject. 

3. Greater inclusion on the planning team of biologists who are experienced in basic 

ecology and in management of the region’s natural resources, especially in the 

practicalities of management to benefit wild populations and stream habitat. 

4. Increased participation by private, state, and federal natural resource managers via 

commitment of data, expertise, and personnel time. 

5. More incorporation of fundamental knowledge about the ecology of the species and 

ecosystems targeted in the planned recovery efforts, with documentation of the scientific 

literature sources for that knowledge. This requires ample use of primary sources, not 

just gray literature.

Review Comments on Sections of the Management Plan 

ISRP comments on specific parts of the Clearwater Subbasin Management Plan are organized 

below according to the plan elements specified in FWP (2000, p 41), as well as plan elements 

added by the authors. 

A Vision for the Subbasin

The vision statement is a properly comprehensive expression of broad objectives. 

Goals

This helpful section (3.2) of the Clearwater Subbasin Management Plan contains nine goal 

statements, each begun with a verb such as respect, protect, or promote. Expressed are some 

general purposes and general actions, together representing a code of conduct for participating 

parties. It provides excellent, overarching guidelines for proceeding with action in the subbasin. 

The next logical step is to specify the desired results of potential actions; Table 2 in the next 

section is a beginning to do this (see the comments below on hypotheses, objectives, and 

strategies). 

The label “Goals” for this section, however, introduces an avoidable element of confusion. 

Fundamentally, the words goal and objective carry the same meaning, so it is best to avoid the 

word, goal, and stick with objective, unless some special need exists for using goal and both 

terms are defined. Moreover, most of this section’s items do not represent a goal (a desired end 

product or status), but rather state general, belief-based modes of operation to which all parties 

should commit. Respecting, protecting, promoting, etc. are actions, not products or outcomes, 

unless the performance of actions rather than attainment of results is the purpose, which should 

not be the case. It would be more appropriate to call the items (and the section) “Guiding 

Principles” since the actual desired end products or outcomes of the management plan are 

embodied in the objectives presented in a later section. If labeled “Principles,” then readers 

would be more likely to accept them as the very general guidance that they are, and would not 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

23

expect the rest of the Clearwater Subbasin Management Plan necessarily to refer back to them, 

although they should be consistent with them.

The 2nd item—on protecting, enhancing, and restoring habitats—should be augmented to include 

recognition that, beyond sustaining and recovering “aquatic and terrestrial species diversity,” 

proper habitat work leads to recovering population abundances. Also, native species should be 

specified. Thus, the statement could be recast as follows (italics show additions): Protect, 

enhance, and restore habitats in ways that will sustain and recover native aquatic and terrestrial 

species diversity and abundance to ecologically appropriate levels with emphasis on . . . (etc.). 

Doing this lends further, essential purpose to the statement and makes it more consistent with 

basin biological objectives (FWP 2000, p 16).

The 8th item should be revised to include the all-important activity of deciding what to do as 

follows: Develop a scientific foundation for diagnosing biological problems, for designing 

projects to deal with those problems, for prioritizing projects, and for monitoring and evaluation.

A 10th item should be added: that of commitment to adaptive management. An outcome of the 

evaluations mentioned in the 8th item should be alteration of further management to better 

achieve objectives. 

Biological Objectives for Fish and Wildlife

The present Clearwater Subbasin Management Plan combines the Objectives element with the 

FWP’s next specified element, Strategies, in major section 3.3, entitled “Hypotheses, 

Objectives and Strategies.” The section should tell what will be done and why. It should be the 

main explanation and guidance of management, the core of the subbasin plan. The present draft 

is insufficient. The section is shorter (barely 19 pages) than the subsequent section on research, 

monitoring and evaluation (21 pages) and, more importantly, its content is less substantial in 

many respects, less detailed, and less logically expressed than the research material. This 

indicates too little attention to the primary management goal of a management plan. The section 

needs to be substantially developed and improved. 

The section states hypotheses that express problems (conditions the planning team views as 

negatively affecting resources), states objectives to be achieved in overcoming or reducing the 

problem, and states strategies for meeting the objectives. This basic organization—objectives 

(intended outcomes) following from problem statements (diagnoses), and strategies (plans of 

action) following from objectives — is logical. However, the content lacks much critical detail 

and does not meet criteria set forth in FWP (2000) as outlined earlier in this report. 

The Clearwater Subbasin Management Plan states: “To avoid redundancy, the readers are 

referred to the Clearwater Subbasin Assessment for supporting data and information used to 

develop the following components. Only in cases where information is considered critical to the 

immediate understanding of the stated hypothesis, objective, or strategy is that information 

reiterated in this section.” This approach does not draw direct connections with the Assessment 

upon which the hypotheses, objectives, and strategies should be based and leaves the reader in 

the position of having to hunt through the Assessment to find supportive evidence and further 

pertinent detail. The organization limits understanding and use of the subbasin plan, and it does 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

24

not evidence that the Plan is in fact wisely drawn from the information in the Assessment. 

Information from the Assessment need not always be “reiterated”, but the authors should, for 

every hypothesis, and probably for every objective and most strategies, specifically reference the 

Assessment tables, figures, pages, or section numbers—and in some cases paragraphs—that 

support the items. The hypotheses, objectives, and strategies must be justified through reference 

to the Assessment and to the primary scientific literature. Without this, the soundness of the Plan 

cannot be evaluated. 

Working Hypothesis

The Clearwater Subbasin Management Plan’s section 3.3 contains a first subsection entitled 

“Working Hypothesis” before the second and main subsection, “Component Hypotheses, 

Objectives and Strategies.” This subsection does not state a hypothesis, but rather 14 premises 

in paragraph form. The premises can be listed as follows (paraphrased for the most part): 

a. Human activities have harmed ecosystems of the subbasin (with some specific categories 

of activity mentioned).

b. Many species are at risk and, absent proper management, may be further compromised.

c. Out-of-subbasin factors and in-subbasin habitat factors limit the subbasin’s anadromous 

fishes.

d. The major practice of releasing hatchery-produced anadromous fishes “is not thought to 

limit persistence of existing stocks” and “is a valuable tool” in the subbasin. (This 

appears to be the only category of management mentioned in the list or in the Clearwater 

Subbasin Management Plan.)

e. Genetic introgression, deteriorated habitat, and loss of fluvial population components 

limit or threaten resident fishes.

f. “Better understanding and combined consideration of economic, biologic, and flood 

control needs” can lessen impacts of Dworshak Dam operations on resident and 

anadromous fishes.

g. Dworshak Dam’s operations and secondary effects harm wildlife resources.

h. Habitat alterations of certain (specified) kinds have harmed the subbasin’s terrestrial 

species.

i. Urban and rural development and introduced plants have harmed plant and wildlife 

populations in the subbasin.

j. Anthropogenic changes in habitat complexity have reduced habitat condition for various 

plants and animals. (This is essentially a rewording of item a?)

k. Reduced and lost anadromous fish runs have altered nutrient cycling, thereby harming 

terrestrial plants and animals.

l. Integrating the Management Plan with existing programs will yield benefits beyond those 

associated with individual plans or programs.

m. Achieving the Management Plan’s objectives requires interagency coordination of 

policies.

n. Restoring and protecting ecosystems will have economic benefits and detriments, which 

the elements of this Management Plan can balance. 

Most of these statements are reasonable, but they stand as a list of assertions, requiring 

documentation, e.g., by reference to the Assessment and other literature for credibility. 

Interposing hypotheses or premises between the Assessment and the Management Plan’s 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

25

objectives could be a sound idea, but it should be shown how each major item derives from the 

Assessment, from the Inventory, or from principles of ecology, economics, sociology, or another 

pertinent basic field.

Many of the next subsection’s “Component Hypotheses” are redundant with the first subsection 

(c, d, e, f, k, l, and specifics of a). Although the introduction to the “Component Hypotheses” 

says they are “derived from the above working hypothesis [sic],” they appear to be mainly 

repetition. The “Component Hypotheses” and the objectives under them should instead derive 

from the Assessment. FWP (2000) stipulates that a management plan’s biological objectives be 

“responsive to the subbasin assessment findings.” For this section to serve as useful background, 

its points should be developed more fully and should be integrated with each other.

One premise of the “Working Hypothesis” needs to be carefully evaluated: “Hatchery production 

of anadromous fish is not thought to limit persistence of existing stocks within the Clearwater 

subbasin, . . .” This assertion runs contrary to the preponderance of scientific knowledge; thus 

the Plan needs to include greater justification on that issue; i.e. what is it about stocks and 

hatchery practices in the Clearwater subbasin that would lessen the potential for negative 

interactions between wild and hatchery produced fish? It is well substantiated that imposing 

hatchery-produced salmonids, anadromous or otherwise, on wild salmonid populations can cause 

detriments in terms of pathogenic interactions (Coutant 1998; Goede 1986; Goede 1994; Moffitt 

et al. 1998), ecologic interactions (Bachman 1984; McMichael et al. 1999; McMichael et al. 

1997; Nickelson et al. 1986; Sholes and Hallock 1979), and, where interbreeding is involved, 

genetics (Hindar et al. 1991). The Management Plan’s assertion that hatchery fish do not affect 

anadromous stocks in the Clearwater ignores the probability that the genetic introgression 

mentioned in the very next sentence as limiting or threatening to resident fish could also affect 

anadromous fish; that introgression derives from fish introduced from hatcheries breeding with 

wild fish. It is also inconsistent with the existence of the Clearwater Subbasin Management 

Plan’s proposed research program V. on interactions between hatchery and wild anadromous 

stocks (Clearwater Subbasin Management Plan, p 35), with “Strategy” III.A.1 on continuing “to 

develop stock specific knowledge of interactions between hatchery and wild fish,” and with 

“Strategy” III.B.1 on impacts of coho reintroduction on other species.

The Component Hypotheses, Objectives, and Strategies

For the Management Plan to be effective in guiding managers toward end products, this section 

needs to state problems more clearly, rather than “hypotheses”, sharpen the objectives (desired 

outcomes), and most importantly bolster the content and form of strategy statements. This 

section does not draw on the standard, fundamental literature concerning ecology and restoration 

of wild aquatic and terrestrial fauna, and it does not adequately refer to the subbasin Assessment 

and Inventory. There is no indication that the hypotheses and their objectives and strategies are 

listed in a prioritized order.

This section’s content is particularly inadequate with respect to fish, because the material 

insufficiently specifies species and life history stages, does not adequately relate to population 

processes, and misses important stream habitat components and processes. Table 2 is a start 

toward considering focal species among the fishes; the objectives and strategies should more 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

26

often show how recovery of each species is to be achieved and what the crucial life history stages 

are. 

With respect to the relationships of population processes of wild fish to stream habitat, this 

section refers five times to natural fish production or productivity, defining neither term, and too 

seldom deals with the processes involved, such as reproduction, body growth, survival, 

predation/harvest, competition, and movement/migration. 1 The subsequent section on research 

and monitoring mentions population processes more frequently, but consideration of these 

matters should enter prominently into the action plan.

Important functions of the riparian zone are not adequately considered. “Component 

Hypothesis” 10 states that loss of wetland and riparian habitats “has negatively impacted native 

terrestrial focal species,” five of these specified by name. The “Hypothesis” does not mention 

that riparian habitat loss affects fish, but then, under its Objective C (protect and restore an 

additional 300 miles of riparian habitat . . .), the first “Strategy” item specifies giving “first 

priority to riparian habitats along streams that support . . . salmonids.” This interjection of a fish 

item, as the first priority, into an effort “hypothesized” for solely terrestrial species is 

inappropriate. Objectives of protecting and restoring wetland and riparian habitat are important 

for terrestrial and aquatic species and coordinated effort to restore habitat for both is surely in 

order. The Management Plan should emphasize the importance of riparian conditions for stream 

fishes, include it prominently in problem statements and objectives, and treat it in much more 

substantial detail.

This section should be more specific about stream habitat components, such as channel forms 

(pools, riffles, etc.), and habitat processes, such as riparian plant succession, large woody debris 

recruitment, the functions of such debris and other large, relatively stable elements in channels, 

and the channel-forming action of flow regimes. The aquatic parts could be more useful if 

reorganized according to the ecological needs of focal species and how habitat functions to meet 

those needs—or how it could function better if anthropogenic impairment were reduced. There is 

much attention to summer water temperature; the appropriateness of this is undoubted, but 

should be shown by specific reference to the Assessment’s geographic analysis (where do the 

problems exist?) and to thermal requirements of the species of concern. Unfavorably cold water 

in winter is probably also a problem that should enter into objectives and strategies for 

improving thermal conditions or winter habitat.

Component Hypotheses

This core subsection of the Management Plan consists of 20 “Component Hypotheses” (which 

could be re-labeled as “Problems”). These are organized into three very general categories:

1. Biological: six hypotheses—three dealing with anadromous fishes, two with resident 

fishes, and one with terrestrial species. (Of the six, item III on coordination of hatchery 

and natural production is the only one stated as a hypothesis, but it is probably not a 

testable hypothesis. The problem to be solved is not clear.)

 

1

 Natural reproduction is alluded to via the terms spawner or spawning only 5 times, growth is mentioned once, 

survival once other than ocean survival and in relation to Dworshak Reservoir, predation never, competition twice, 

movement/migration twice 2 other than in relation to Dworshak, and rearing once. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

27

2. Environmental: 11 hypotheses—one affecting fish, eight affecting terrestrial species, and 

two affecting both aquatic and terrestrial species. 

3. Socioeconomic: three hypotheses. (These are indeed expressed as hypotheses, not as 

statements of problems to be solved. Associated problems should be defined.)

The items in this section need to be more clearly related to the Assessment and should make 

better use of specific biology of focal species or considerations of biodiversity. Only two of the 

ten hypotheses dealing with fish or other aquatic subjects contain definite information from the 

Assessment, one of these being Hypothesis 2, containing Table 2. Presentation and use of 

material such as exists in Table 2 is central to the subbasin planning and implementation effort. 

This approach should be enlarged to include not just fishes, but all features of the landscape (e.g., 

habitat attributes) and its associated biota that are the desired end products of actions, and the 

specific parts of the Assessment that support information should be referenced. Then, the 

strategies that follow should explain operations in ways that show managers how to reach the 

desired, quantified end products. The aquatic hypotheses and objectives should identify the 

species at issue more often than they do because objectives should state desired outcomes, and 

the outcomes for a fish and wildlife recovery program should be in terms of the species involved. 

Six of the eight aquatic hypotheses do not mention the species, however, 11 of the 22 objectives 

beneath these six do. The plan needs objectives and strategies that are species-specific and lifestage-specific because the life histories and habitat requirements of each species differ. 

Sometimes species that have similar habitat requirements at a life stage can be grouped. 

Most of the nine hypotheses dealing with terrestrial issues are more detailed, mentioning 

individual species and apparently incorporating findings from the Assessment, but still not 

referencing the latter by page or section number. This section’s terrestrial items usually identify 

species in the hypothesis (a problem statement), and then state objectives that deal with the 

ecological and human-generated processes that affect those species. This approach would also be 

beneficial in the aquatic items. 

The socioeconomic hypotheses, objectives, and strategies show no connection to the Assessment 

and need strengthening. These require expansion and greater detail as well as references to 

existing economic evaluation tools. Although research is proposed to address information gaps 

related to other objectives and strategies, none is associated with the socioeconomic objectives. 

The material in the socioeconomic section often seems platitudinous; this might be reduced by 

identifying end products and showing their relationship to actually getting things done, i.e., 

accomplishing fish and wildlife recovery. Education per se is not adequately considered; public 

understanding and enthusiasm for the overall program are essential. 

Objectives

There are five anadromous fish objectives, eight resident fish objectives, two terrestrial species

objectives, and 30 environmental objectives, most of which are somewhat vague and lack 

substantiation of the appropriateness or priority of the objective, failing to provide rationale from 

either the primary scientific literature or from the Assessment. Most of the problems for 

terrestrial wildlife are covered under the environmental category, which may represent a more 

habitat-oriented approach by the terrestrial planning team. Some environmental objectives list 

specific targets (e.g., restore 500 acres of historic wetlands, and protect/restore 300 miles of 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

28

riparian habitat), but give no basis for the targets. Specific rationale should be provided for target 

amounts of habitat to be restored, as should their priority and their likely locations. 

It is unclear whether there is agreement between IDFG and CRITFC with respect to the 

anadromous fish objectives: 

1) Increase naturally spawning adult number within 25 years to specific numbers. 

2) Improve subbasin habitat to increase fish production.

3) Establish index streams.

4) Optimize use of hatchery fish: Use a mix of hatchery and natural production strategies.

5) Restore coho.

Analysis and models should be given to support the high harvest rates that are targeted. 

Comparisons between existing returns and proposed targets should be given in greater detail. 

The use of index streams needs to be reconciled with the ISRP’s recommendation for 

probabilistic sampling. Better description of what constitutes optimal use of hatchery fish is 

needed. The scale of production proposed for hatchery chinook and steelhead in the Clearwater 

subbasin is large, and figures into the attainment of objective number 1 above. The subbasin 

management plan would benefit from greater justification of the scale of effort and better 

descriptions of the safeguards and monitoring that will be used to protect wild stocks in the 

subbasin (e.g., steelhead in the Lochsa and Selway rivers). 

Many of the Management Plan’s objectives specify quantified achievement levels and times, as 

an objective should, but others lack this. To enable evaluation, each objective should include 

such quantified criteria and times (or footnoted explanation of why it is not appropriate). Each 

quantification should be referenced to the appropriate Assessment section, table, or graph and/or 

other document that contains the data for it and that show the method by which it was calculated. 

The subsection’s second introductory paragraph, which discusses this matter, should document 

methods used to quantify levels and times. It is stated that where sufficient data were lacking, 

objectives designate timelines for developing the criteria; however, the timelines are not 

provided for all objectives that lack quantified criteria. Each objective should be reworked to 

meet standards of quantifiability and achievement date, and to reference these to the Assessment.

Some statements of objective diverge into matters of method. Objectives should be statements of 

desired outcomes; methods to accomplish the objectives belong in the strategies. For example, 

Objective I.A.: “Increase the number of naturally spawning adults to achieve goals in Table [2] 

within 25 years ... by ameliorating or mitigating the manageable limiting factors, or provide data 

key to out-of-basin efforts to improve limiting factors. Progress toward goals will be assessed at 

least every 2 generations” (italics added to highlight methods). The objective here is to increase 

the number of naturally spawning adults to achieve Table 2’s goals within 25 years. The methods 

part of the statement should be covered in a sequence of steps that constitutes a strategy for 

achieving the objective. Other examples include Objective II.A and III.B. Objective II.A should 

read: “Improve anadromous fish survival,” omitting the rest of the present lengthy statement, but 

adding species and saying how much survival is to be improved by what date. Objective III.B 

also contains a method statement that should be in its strategy instead.
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

29

Strategies

The greatest shortcoming of the section on “Component Hypotheses, Objectives, and Strategies” 

involves its strategies. These generally fail to develop clear operational pathways toward 

biological outcomes. The essential purpose of a management plan is to set forth “the strategies 

that will be implemented at a local level” (FWP 2000, p 41). The Clearwater Subbasin 

Management Plan’s strategies are only generally, rather than explicitly, related to the objectives, 

and they are worded too generally to constitute a management plan. 

The instructions on strategies stipulate that the management plan include (a) an explanation 

linking the strategies to the established subbasin biological objectives and vision and the 

subbasin assessment; (b) an explanation of how and why the strategies presented were selected 

over other alternative strategies (e.g. passive restoration strategies v. intervention strategies); and 

(c) a proposed sequence and prioritization (FWP 2000, p 41). The Management Plan does not 

incorporate these important elements. The Management Plan occasionally refers to linkages with 

the Assessment, but does not identify and explain them. Alternative strategies are not given. 

Activity lists do not have a proposed sequence. Prioritization, particularly a framework for 

spatial prioritization, is discussed in a special Management Plan section; however, each strategy 

(set of actions toward an objective) outlined should show the method by which efforts will be or 

have been prioritized. Vague statements such as: “Address relevant issues delineated under 

‘Prioritization of efforts’ section” are not helpful.

Most of the “strategies” are not adequately developed. Often, a “strategy” is stated as a single 

activity, which may name a strategy, but does not provide adequate operational guidance. The 

Technical Guidelines define strategies as “sets of actions to accomplish the biological 

objectives.” Further, strategies are “plans of action to accomplish the biological objectives” and 

“in developing strategies, the program takes into account . . . the desired outcomes . . . [and] the 

physical and biological realities expressed in the scientific foundation” (FWP 2000, p 19). It 

follows from this that each strategy should consist of an integrated set of actions, in the form of a 

logical sequence of actions for performance, probably often cast as a decision tree involving ifthen branches (or terminations) and statement of contingencies that would trigger them. A 

decision tree also tends to reveal logical alternative options in a strategy, and the circumstances 

in which they would apply. 

Further, the logical series of actions in each strategy should explicitly describe the design for 

achieving measurable benefits for target species at specific life stages. The strategies should be 

explained in terms of their effects on measurable biological objectives, e.g., the behavioral 

ecology or population dynamics of species, and, where appropriate, in terms of genetics. The 

Clearwater Subbasin Management Plan’s activity-lists, in which the items are labeled as 

strategies, should be thoroughly reexamined and reworked to come up with genuine strategies. In 

some cases, a list of “strategies” that the Management Plan presents under an objective could 

constitute a strategy if the list itself were labeled as the strategy and the present items (and often 

others) were shown as steps in a sequence that constitutes a procedure toward achievement of the 

objective. In all cases, the linkage of steps, and possible alternatives, should be explained. 

For example, the material under “Component Hypothesis 2” (labeled also as item II) could be 

restated along the lines of the following framework:
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

30

Problem 2: Habitat quantity and quality limit anadromous fish production in 

parts of the subbasin (reference to supporting information in assessment here or 

below).

Objective 2A: Increase rearing-stage survival2 of spring chinook salmon to a 5-

year mean of __%3 by the period 2010-2015.

Strategy (all of the following apply specifically to spring chinook salmon):

1. Analyze habitat factors that limit survival in each PMU that they inhabit. 

(Statements of known or likely habitat problems—from the Assessment—could 

be worked in here.)

2. Analyze for each PMU alternative kinds of habitat restoration, and from among 

them prescribe sub-strategies and methods likely to overcome the limiting factors. 

(This could involve a number of decision nodes and branches; for example, 

different general, potentially appropriate approaches to habitat restoration.)

3. Prioritize PMUs according to probable benefit/cost effectiveness of habitat 

restoration for the specified survival level (the expected, quantified biological 

result vs. the sum of logistic costs, labor costs, etc.).

4. Consider, on the basis of predicted benefit/cost, whether to proceed with any of 

the work. If not worthwhile, cancel the project (a possible termination branch on 

the decision tree) or reassess methods (a back-loop).

5. Identify the PMUs (or streams) in which to restore habitat in the first management 

cycle of __ years.

6. Select a probabilistic sample of streams (rather than index sites) from among 

those in item 4 for monitoring of habitat and fish-population. Begin monitoring at 

least one year (preferably several years) before habitat work starts, and continue 

monitoring in a sample of years on each stream for at least 7 years after its habitat 

work is complete.

7. Apply the habitat restoration prescriptions developed in item 2 to the streams 

selected in item 4.

8. Evaluate the levels of habitat and biological response achieved 7 years after 

habitat work was complete.

9. Use adaptive management in the next management cycle of __ years (and in 

similar management elsewhere), apply the lessons of what works and what does 

not.

At the end of this itemized strategy, insert a paragraph explaining such matters as the aspects of 

spring chinook salmon habitat use (behavior) at the rearing stage(s), as well as the habitat 

deficiencies in the subbasin (and their causes), that lie at the root of the problem; why the 

survival level specified in the objective level was chosen (how calculated or based on literature 

as sufficient for recovery of the species?); linkages in the strategy, where not obvious; and the 

 

2

 Survival is the parameter stated in the present Management Plan, so it is applied in this example, but with further 

specification of rearing survival in order to make it more meaningful in terms of life history. Perhaps some other 

survival or production parameter would be more appropriate.

3

The Assessment should state current survival rate for spring chinook, and show what it could be under desired 

environmental conditions, but does it? (The same applies to the other species of Table 2.)
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

31

alternative strategies or steps that were considered and why they are or are not thought to be 

feasible. Then go on to state objectives 2B, 2C, etc., each covering another species from Table 2 

and the special strategy required for it.

The ISRP suggests that all other strategy lists of the Clearwater Subbasin Management Plan 

should be revised according to the above comments.

Sometimes an item listed as a “strategy” more properly expresses an objective that ought to be 

followed by a step-wise strategy showing how it will be accomplished. For example, under 

Objective X.C on protection of riparian habitats, “strategies” 3, 4, and 5 seem to be major 

objectives (indeed, programs), each calling for a strategy (and for consideration of alternative 

strategies) to achieve it. A further example: Under Objective XI.B, the four items could together 

constitute an excellent, integrated strategy, particularly if it were shown a bit more explicitly how 

some of these measures follow from or otherwise relate to each other. And with regard to item 1, 

how should the managers encourage establishment of riparian pasture systems, etc.? What are the 

proven methods for such encouragement under the sorts of conditions that exist in the subbasin? 

Intended users of the Clearwater Subbasin Management Plan should be able to see guidance on 

such matters.

Comments on Specific Parts of the Objectives-and-Strategies Material

The sections of the Management Plan that deal with aquatic species and habitats are not 

sufficiently oriented to focal species. Objectives and strategies intended to affect fish seldom 

specify species, and outlined actions are not related to the special habitat needs and behaviors of 

the various fishes and their life stages. The plan also gives insufficient attention to the highly 

important riparian issues involved in habitat for salmonid fishes, including the roles of woody 

debris produced by riparian vegetation. Indeed, completely missing from the Management Plan 

are such common terms in considering stream fish habitat and its restoration as riffle, hiding 

cover, woody debris (or LWD), log, tree, and bush. Even the word pool occurs only once and 

only in a research context. Also appearing only once—and in no objective or strategy—are the 

word, gravel, and the term, cover, in the sense of shelter for fish. This is supposed to be “a 

habitat-based program” (FWP 2000, p. 13), yet the Management Plan does not adequately deal 

with major aspects of stream habitat characteristics and functions and does not come to grips 

with the practical, on-the-ground realities of habitat restoration for fish. One could conclude 

from reading the management plan that very little is known about habitat conditions and fish 

populations in the Clearwater basin. This is hardly the case, as the assessment should have 

demonstrated.

There seems to be a tendency to blame the anadromous fish scarcity on “Out-of-subbasin 

factors...[that] are the primary factors limiting recruitment of anadromous spawners to the 

Clearwater subbasin” (“Component Hypothesis” 1). Howeve r, the long lists of high priority 

issues with low or moderate opportunity for improvement in Tables 4, 5, and 6 would seem to 

indicate a major contradiction. 

In the present Management Plan, item 4 of the strategy list for Objective II.A, that on Dworshak 

Dam operations, seems a special case that deserves a separate objective and step-wise strategy.
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

32

The present Objective II.A says that improved anadromous fish survival is to be attained in part 

“through quantifiable improvements outlined for individual habitat components under 

Environmental Objectives (defined below).” However, no objective in the Environmental 

category mentions quantification of survival rates. Did the authors intend to place such emphasis 

on survival per se? What about reproduction and body growth?

In the strategy for Objective I.A there should be an item making it clear that data will be 

provided to fishery managers outside of the subbasin to guide their appropriate regulation of 

fisheries to ensure adequate returns of anadromous fishe s to the subbasin.

Objective III.B refers to recovery and harvest objectives that are spelled out in Table 2. 

Logically, these ought to be consistent with information provided in the Assessment. The 

discussion should provide a link between the Assessment and the Plan at this point. The 

Objective mentions “timelines delineated in Table 2”; that table contains no timelines.

“Strategy” III.B.1 is very vague. It needs much expansion to show how it is supposed to meet the 

objective.

“Strategy” III.C.1 is “Continue coho restoration efforts.” What are those efforts? This expresses 

no strategy.

“Component Hypothesis” 4 outlines threats to long-term persistence of resident fishes. Some of 

these apply to anadromous fishes, as well. Appropriately parallel items should be added in the 

anadromous category of problems, objectives, and strategies.

“Strategy” IV.C.1: This item should be omitted. Experts often have difficulty with field 

characters to distinguish hybrids of rainbow trout and cutthroat trout, so a public education 

campaign to increase angler ability to do this will be difficult to accomplish. Also, it is not 

explained why this should be done. What action would be taken on the basis of the information 

gained?

“Strategy” IV.C.4: If anglers identify hybrids, then what? Why should they do this?

“Strategy” IV.D.4: Why do this? What would the reasonable extent of effort on this in view of 

more urgent needs elsewhere? What would be the priority of such an effort? An intent to avoid 

competition with bull trout is expressed in this item; avoiding competition with other native 

salmonids, such as redband trout should also be considered.

“Strategy” VII.B.2: Rather than “maximizing” the activity, it would be better to optimize it by 

prioritizing barrier removals to maximize results.

“Strategy” VII.E.6: Replace the term, “glory holes,” with a description that outside readers will 

understand.

“Strategy” VII.G.1 mentions “habitat improvement efforts.” This is too vague. What are they?
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

33

“Strategy” VII.G.2 mentions “appropriate measures.” This is also much too vague. What might 

those measures reasonably consist of—or, for those already being done, what are they? 

Anywhere else that “appropriate measures,” “representative samples,” and such terms are used, 

the actual items should be specified instead.

Item XVIII (the first of three in the “socioeconomic” category): This set of objectives and 

strategies is not particularly socioeconomic. It deals with attributes, which, as sound natural 

resource management, should pervade the biological and environmental categories; parts of the 

present Management Plan for which this is not the case should be corrected. 

Objective XIX.A and its “strategy”: Once these things are accomplished, what will be done with 

the output? How will it be integrated into future management? Prioritize what?

Objective XIX.B: “Account for” these in doing what? The strategy list does not clearly relate to 

the statement of objective. The objective statement does not express an outcome.

“Strategy” XIX.B.1 would develop measures to evaluate the economic effectiveness and 

efficiency of implementing the Plan. To accomplish this would require that all actions be 

evaluated on a common basis, e.g., number of salmon or other benefits expected to be produced. 

To simply measure the relative costs of projects in dollar amounts would overlook the value of 

the relative benefits to various sectors of the community. In other words, this sounds easy, but 

promises to be very difficult.

Research, Monitoring and Evaluation Plan (RM&E)

One of the questions asked of the ISRP was “Does the proposed subbasin plan include a 

procedure for assessing how well subbasin objectives are being met over time?” In general, the 

answer to this question is “no”. However, as the introduction’s 4th paragraph indicates, current 

RM&E programs described in the Inventory “likely incorporate many of the RM&E needs 

identified in this section”. A list of ongoing research/monitoring projects is given in Table 4 of 

the Inventory and brief summaries of the projects are included. Unfortunately, the Assessment, 

Inventory, and Management Plan fail to fully summarize and analyze the ongoing 

research/monitoring projects. The readers should be shown in each research/monitoring proposal 

the aspects of the proposal that are met and unmet in existing projects and in what ways the 

proposal would fill gaps of knowledge. 

Development of the Clearwater Subbasin Plan offers a unique opportunity to better coordinate 

long-term monitoring of aquatic and terrestrial resources using common data collection 

procedures, storage of data in a system of distributed databases with common format and to fill 

data gaps to allow statistical inferences to be drawn to large subsections of the subbasin. In 

general, the Assessment, Inventory, and Management Plan do not provide an overall coordinated 

plan for research and monitoring in the subbasin and to promote the use of common methods 

throughout the subbasins of the Columbia Basin.

The introductory discussion on RM&E states that the section was developed in response to 

limiting factors identified in the Assessment and associated vision, hypotheses, objectives, and 

strategies sections of the Management Plan. RM&E material does not refer to specific pages, 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

34

tables, or figures in the Assessment. The “goals” sections names no limiting factors, and the 

hypotheses, objectives, and strategies should derive from the limiting factors identified in the 

Assessment. It would be well for the planning team to rework their ideas on how the proposed 

research and monitoring relates to limiting factors. The plan should tie the RM&E back to the 

limiting factors and objectives, which may be difficult given the objectives are very general. 

There is apparently no research that can be tied back to socio-economic hypotheses. 

In general, the RM&E section of the Management Plan is vague and unfocused. For example, 

the terrestrial section often confuses inventory with research. It is important to separate data 

collection and evaluation of research, Tier 3, from Implementation Monitoring, Tier 1 (trend or 

routine) monitoring, and Tier 2 (statistical monitoring) of large areas and over long time periods. 

Evaluation is an important part of all three processes and there must be a perceived need and 

clear procedure for analysis of data being collected. Granted that there is a perceived need and 

clear procedure for analysis of data being collected, plans for evaluation of the data are less 

important for Tier 1 and Tier 2 monitoring than Tier 3, because Tier 1 and Tier 2 data should 

have a long shelf life (in the range of 50 to 100 years minimum). In fact, the methods for 

evaluation of Tier 1 and 2 data in the future, say 2025, probably have not been conceived. On 

the other hand, Tier 3 research data are often for relatively short term evaluation of specific 

research projects and must have well defined plans for analysis and evaluation. To help 

distinguish between the different types of monitoring, we repeat some of our programmatic 

issues from the rolling reviews of the Provinces. 

Implementation Monitoring is monitoring of task completion in a specific project. For 

example, miles of stream fenced, number of culverts removed, completion of reports, irrigation 

diversions maintained, etc. Implementation monitoring is often given in proposals to the 

Council’s Fish and Wildlife Program. Implementation monitoring results must be presented for 

projects, but sound science requires that project results also be measured in terms of benefits to 

fish and wildlife. In addition to Implementation monitoring, all projects should also include one 

of the following types of monitoring in proposals and plans for observational studies or 

experiments. 

Tier 1 (trend or routine) monitoring obtains repeated measurements, usually representing a 

single spatial unit over a period of time, with a view to quantifying changes over time. Changes 

must be distinguished from background noise. For example, temperature of water entering and 

leaving a habitat improvement site might be measured in August every third year for a 21-year 

period. This can be a low level of monitoring on individual project sites or on a large area. For 

example, the ISRP anticipates that aerial photography or data layers in a GIS would be used for 

long term trend monitoring of riparian and other terrestrial habitat over time. In general, Tier 1 

monitoring does not establish cause and effect relationships (i.e., is not research) and does not 

provide statistical inductive inferences to larger areas or time periods. It is not necessarily 

expensive or time consuming. However, Tier 1 mapping or trend monitoring on similar projects 

replicated over time and space can provide compelling evidence for general conclusions. Also, 

aerial photography or data layers in a GIS yields a census of the study area thus eliminating the 

need for spatial sampling and classical statistical analysis at the scale studied. Unfortunately, the 

aerial photography or data layers often have unknown measurement errors which may limit their 

usefulness for detecting changes and trends when compared to future data.
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

35

Tier 2 (statistical) monitoring provides statistical inferences to parameters in the study area as 

measured by certain data collection protocols (i.e., The Methods in a report). These inferences 

apply to areas larger than the sampled sites and to time periods not studied. The inferences 

require both probabilistic selection of study sites and repeated visits over time. A good model is 

the Oregon Plan for Salmon and Watersheds Monitoring Program 

(http://www.nwr.noaa.gov/pcsrf/Moore/) as implemented in the Oregon coastal coho streams. 

The Oregon Plan, successfully implemented for estimation of coho distribution and abundance, 

applied a rigorous design for probabilistic site selection to answer key monitoring questions. 

Individual proposals can support larger Tier 2 statistical monitoring projects such as the Oregon 

Plan by using the same field methods and methods to select study sites that contribute 

information to Tier 2 statistical monitoring. Most large projects should implement sampling 

designs that allow Tier 2 statistical monitoring or contribute data to statistical monitoring. Tier 2 

statistical monitoring will be required for estimation of parameters such as number of spawners 

in the escapement, juvenile production, acres of noxious weed present, etc.

Tier 3 (research) monitoring is for those projects or groups of projects whose objectives 

include establishment of mechanistic links between management actions and salmon or other fish 

or wildlife population response. Bisbal (2001) defines this level of effort as effects or response 

monitoring; the repeated measurement of environmental variables to detect changes caused by 

external influences. The key words here are “establishment of mechanistic links” and “detect 

changes caused by external influences.” Tier 3 research monitoring requires the use of 

experimental designs incorporating “treatments” and “controls” randomly assigned to study sites. 

Generally, the results of Tier 3 research monitoring qualify for publication in the refereed 

scientific literature. Examples of Tier 3 monitoring would include: 1) projects to evaluate the 

effects of different levels of fertilization on growth and survival of juvenile salmonids with 

streams selected randomly for reference and treatment; 2) projects to evaluate the survival rates 

of adult salmonids caught and released from tangle nets; 3) projects to evaluate the survival rates 

of juveniles migrating past a dam at different levels of spill and turbine passage; 4) projects to 

evaluate the swimming ability of lamprey during upstream migration; 5) projects to evaluate the 

effectiveness of various land restoration or management techniques, etc.

Large scale observational studies that involve “treatment-control”, “before-after” or “beforeafter-control-impact (BACI)” designs fall under Tier 1 or 2 trend monitoring and do not establish 

cause and effect relationships as in Tier 3 research monitoring. A good example in the 

Clearwater Subbasin is the Idaho Supplementation Study (ISS) on chinook salmon. With a large 

number of replications, as in the ISS, compelling evidence for general conclusions based on 

regression-correlation type analyses can be obtained. However, the ISRP cautions that 

maintaining the essential elements of a large-scale observational study over a long period of time 

is a difficult task. For example, in the ISS there have been changes in the original design that 

will make interpretation of the data difficult.

Reference to the Clearwater Subbasin Management Plan’s “hypotheses” (i.e., to problem 

statements) is by number. The functional relationship of the proposed investigation to the 

resource problem is not discussed, and it is not said what managers are supposed to do with the 

expected research results in order to achieve fish or wildlife recovery. It would add much to the 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

36

meaning of the program statements, if an item were added to each on the types of results 

expected, the envisaged applicability to management, and how this could benefit fish or wildlife. 

Because reference to those matters and to the Assessment are missing, readers cannot judge 

appropriateness of the proposed RM&E subjects except on the basis of their prior knowledge 

about natural resource ecology and the Clearwater Subbasin.

Specific Comments on the Aquatics RM&E

Many of the proposed research topics in this section of the Management Plan are vague and 

unfocused and should be expanded. 

Some specific comments and questions are:

1. The research items should be carefully examined to indicate which are actually research 

projects with a limited life (Tier 3) and which are long term Tier 1 or 2 monitoring projects. 

For example, the ISRP judges that Item I.3 “Develop appropriate intensity and spatial 

distribution of monitoring to estimate parr carrying capacity” is a limited life research 

project, but Item I.2 “Determine migration characteristics and timing of smolts outmigrating 

from the subbasin and assess hatchery:wild ratio” has components that probably should 

involve long term Tier 1 or 2 monitoring.

2. In proposed research item I.2, we agree with the authors of the Management Plan that “Sites 

should be distributed probabilistically within a PMU, ensuring that both “good” and “bad” 

sites are appropriately represented.” However, this statement immediately follows and 

contradicts the statement that the plan is to “Establish or use preexisting index sites to gather 

baseline, trend, and comparative data.” Item IV.2 “Develop/expand index areas” is correctly 

identified as Tier 1 and 2 monitoring with new sites to be collected by probabilistic 

procedures. This approach yields a 100% sample from the stratum “index sites” and a 

probabilistic sample from the rest of the area. Statistical inference would involve estimation 

of a parameter on the larger area not in the index sites combined with data from the index 

sites. 

3. The ISRP recommends that a general protocol for probabilistic selection of aquatic sites be 

developed and included in the subbasin plan and that new sites be overlapped with existing 

index sites for a few years, say 5 to 10 years. In our judgment, the best model to follow in 

development of probabilistic sampling plans is the EPA EMAP strategy in the “Oregon Plan” 

as implemented in the Oregon and Washington coastal coho streams and in the Yakima 

Subbasin. Details for implementation of a probabilistic sampling procedures are not trivial 

and should be developed in the Subbasin Plan to the point that scientists working for 

management agencies can apply the procedures with help from, say Don Stevens, 

Department of Statistics, Oregon State University. 

4. In addition to contact with the Department of Statistics at Oregon State University or entity 

with similar expertise, we recommend that the authors review the plans for status (Tier 2) 

monitoring of fish and habitat being developed by the Action Agencies (Bonneville Power 

Administration (BPA), Corps of Engineers (Corps), and Bureau of Reclamation (BOR) and 

the NMFS) in their RME Plan (see the BPA Draft Report “Research, Monitoring & 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

37

Evaluation, For the NMFS 2000 FCRPS Biological Opinion”). Plans are being developed 

for implementation of the EPA EMAP probabilistic selection of sites in a pilot project in the 

Salmon Subbasin. Every effort should be made to include the same site selection protocols 

and data collection methods in the Clearwater Subbasin. This is a unique opportunity to 

promote the collection of research and monitoring data with common methods throughout 

not only the Snake River Basin, but the entire Columbia Basin. 

5. Proposed Research II.4 is to study temperature impacts of Dworshak Dam operations on 

downriver fish populations. An ISRP comment on the Assessment brings out that the 

Assessment does not mention this aspect of the situation. Again this points to the need for 

stronger linkage between the Assessment and the Management Plan. It is not clear if this 

proposal intended to include the possibility of studying effects on juvenile salmonids in the 

lower Clearwater River and Columbia River mainstem.

6. Proposed Research III.1 to study a minimum flow requirement would involve evaluating the 

accuracy of existing stream gauge data. Past work on this subject suggests that the data 

should include hourly records. In most cases, the continuous records are simplified to daily or 

longer averages. Such averages may be meaningless if there are water withdrawals or 

interruptions upstream.

7. Proposed Research V.1 is on genetic interactions of hatchery and wild fish. It is said in the 

M&E item that effects of interactions on “fitness” will be measured, but fitness is not 

defined, and it is not said how it would be measured. Definition and measurement of 

“fitness” is likely to be one of the most difficult steps in this process, if it is even possible.

8. Proposed Research V.2 on assessing interactions between reintroduced and native 

anadromous salmonid populations say under M&E: “Using appropriate methods, assess 

habitat use . . .” Methods should be specified or referenced for all such proposed research.

9. Same Proposed Research, next paragraph, item a) deals with comparing growth rates 

between native and introduced species. What are the species? Are the fish to be examined 

wild or hatchery-produced or both?

10. Proposed Research VI.1, item c involves “population status monitoring of fluvial x resident 

genetic interchange.” What is this, exactly? What is population status supposed to mean 

here? What does the “x” mean? Why do this? What sort of output is supposed to result, and 

how would it be used in restoration?

11. Proposed Research VI.2 on effectiveness of planting sterile rainbow trout. A subject not 

discussed is the extent of competition for food and space of these fish with fish already 

resident in the river. 

12. Proposed Research VI.3 concerns lamprey studies. These seem superfluous given that the 

primary limiting factor for lamprey abundance is passage at the mainstem dams. Factors 

within the subbasin are not likely to have any effect at all, and even if they do, it is unlikely, 

given the low abundance of lamprey, that the effects within the subbasin could be measured. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

38

Genetic analysis seems especially unlikely to lead to any results that would lead to 

restoration actions. Perhaps the Plan should propose participating in or encouraging studies 

by the Corps of Engineers to find a solution to the passage problem.

13. Proposed Research VIII.2 on profiling anadromous salmonid genetics. What will be done 

with the information that results from this? How will it be used in restoration?

14. Proposed Research VIII.3 to study out of basin factors affecting smolt outmigration success. 

While it is necessary and desirable for subbasin participants to be kept informed on these 

subjects and to assist where possible, it seems redundant to fund studies under the subbasin 

heading that are more logically organized as part of the Mainstem and Systemwide 

component of the FWP. 

15. Proposed Research VIII.6 to study effects of unclipped hatchery fish on natural production. It 

is regrettable that there are unclipped fish being released. However, it is not clear how 

unmarked hatchery fish can be identified with any degree of reliability when they spawn in 

the river.

Specific Comments on the Terrestrial RM&E Section

The ISRP is less critical of the research/monitoring proposals in the terrestrial section than we 

are of those in the aquatic section, primarily because of the more detailed analyses of terrestrial 

issues presented in the Assessment and Inventory. However again, readers should be shown in 

each research/monitoring proposal the aspects of the proposal that are met and unmet in existing 

projects and in what ways the proposal would fill one or more gaps of knowledge. The 

hypotheses, objectives, and strategies should derive from the limiting factors identified in the 

Assessment and the proposed research/monitoring should be more clearly tied back to both.

In the Proposed Research IX.1, it is unfortunate that there does not exist a good model for Tier 2 

statistical sampling and inventory of terrestrial components of the subbasin. The National 

Resources Inventory (NRI) studies long-term changes in cultivated agricultural lands, but not 

forest or grazing lands. The Forest Service has its Forest Inventory and Analysis program, but it 

does not extend and is not really appropriate for many terrestrial parameters. The Bureau of 

Land Management apparently has little to mimic. The EPA Environmental Monitoring and 

Assessment Procedure (EMAP) is helping some of the states instigate valid probabilistic 

sampling for certain aquatic parameters. In short, there is not a good existing program on which 

the Tier 2 terrestrial monitoring might be attached or modeled after.

The Clearwater Subbasin is in a position, as the first subbasin to go through the planning process 

of the Council’s FWP, to help implement a coordinated Tier 2 terrestrial monitoring program for 

estimation of key terrestrial parameters over the subbasin and to influence the direction of 

terrestrial monitoring for the entire Columbia Basin. The ISRP recommends that a general 

protocol for probabilistic selection of sites be developed and included in the subbasin plan. 

During the province reviews by the ISRP, the Albeni Falls Workgroup prepared a Draft 

Monitoring and Evaluation Plan for the Albeni Falls Wildlife Mitigation Project, dated August 

2001(see www.nwcouncil.org/library/isrp/isrp2001-4AlbeniFalls.pdf). In the Upper and Middle 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

39

Snake Provinces, the Southern Idaho Wildlife Mitigation projects (199505700 though 03) have 

adopted the Albeni Falls M&E Plan for use in southern Idaho in wetland cover types and were in 

the process of expanding that plan to include techniques for monitoring upland habitat and 

wildlife species. We encourage the authors of the terrestrial section of the Clearwater Subbasin 

Plan to work closely with the Albeni Falls Workgroup, the Confederated Salish and Kootenai 

Tribes, and the Southern Idaho Wildlife Mitigation projects to develop common site selection 

procedures and data collection protocols for terrestrial monitoring. This is a unique opportunity 

to promote the use of common terrestrial monitoring methods within the Columbia Basin.

General Guidance on Research, Monitoring, and Evaluation to Evaluate Effectiveness of 

Habitat Restoration Activities 

The Independent Scientific Advisory Board (ISAB) is in the final stages of preparing a report 

entitled “A Review of Strategies for Tributary Habitat Recovery.” That report contains pertinent 

information on design of Tier 2 and 3 research and monitoring studies to evaluate the effects of 

actions intended to recover or improve tributary habitat for fish and wildlife. For consistency, 

we repeat some of that information and give recommendations that are particularly relevant to 

RM&E of tributary habitat improvement techniques that might be implemented in the individual 

subbasins. Please note that at the time of preparation of the review of the Clearwater Subbasin 

Plan, the ISAB report is still in draft format and minor changes in the following paragraphs may 

exist in the final version. The material is written primarily for RM&E on fish populations and 

aquatic habitat; however, the basic principles apply equally well to terrestrial wildlife and 

habitat. Pertinent text from the ISAB report is presented below in italics: 

Understanding the effect of habitat conditions on salmon population performance requires 

replicated observational studies or intensive research level experiments to be conducted at large 

spatial and long temporal scales. Very few evaluation efforts for tributary habitat that have been 

implemented to date in the Columbia River basin meet these criteria. Considerable expense and 

effort are required to establish studies or experiments that can enhance our understanding of 

habitat-population relationships and thus provide a sound basis for the development of tributary 

habitat restoration efforts. 

Two general approaches, i.e., philosophies, of conducting field studies exist to collect empirical 

data for evaluation of the effectiveness of tributary habitat restoration activities. The first 

approach seems to be consistent with that currently promoted by the Action Agencies (Bonneville 

Power Administration (BPA), Corps of Engineers (Corps), and Bureau of Reclamation (BOR) 

and the NMFS) in their RME Plan (see the BPA Draft Report “Research, Monitoring & 

Evaluation, For the NMFS 2000 FCRPS Biological Opinion”). For example, a large number of 

pairs of sites (e.g., watersheds) might be located where the primary difference is that one 

member has a certain habitat improvement (e.g., grazing by livestock is excluded by fencing of 

streams) and the other does not. Future changes in management would be uniformly applied to 

both members of a pair. Enough pairs of sites are obtained to generate acceptable power for 

standard statistical tests to detect important differences in the estimated indicator variable(s). 

Given the number of pairs involved, parameters that can be monitored by Tier 1 or 2 methods 

within a reasonable budget are limited; perhaps, to estimates of spawners entering the 

watersheds and smolts leaving. The design of such a study will be similar to that used in the 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

40

large scale “treatment-control” observational Idaho Supplementation Study (ISS). With a large 

number of replications of treatment and control sites (e.g., watersheds), compelling evidence for 

general conclusions based on regression-correlation type analyses can be obtained. However, 

the ISAB cautions that maintaining the study design for a large number of replications over a 

long period of time is a difficult task. For example, in the ISS there have been changes in the 

original design that will make interpretation of the data difficult. Furthermore, this design 

requires study of essentially one factor at a time, e.g., fencing. Study of the interactions between 

two different types of habitat improvements (e.g., fencing and placement of large wood) would 

double the number of required sites in a 2x2 factorial design.

The second approach is to focus evaluations in a few watersheds in each subbasin, a monitoring

approach the state of Washington has termed Intensive Watershed Monitoring (IWM). The basic 

premise of IWM is that cause-effect relationships in complex systems can best be understood by 

concentrating monitoring and research efforts at a few locations. Closely spaced measurements 

in space and time are often required to develop a thorough understanding of the processes 

responsible for habitat or fish population response to a management action. Concentration of 

effort can focus sufficient resources and research expertise to begin to tease apart some of the 

complex interactions governing system response to restoration activities. 

There are obvious advantages and disadvantages to each approach. The first (e.g., ISS) attempts 

to drawn inferences based strictly on the design of the study to a very large area by, e.g., 

spreading a large number of pairs of sites over the target region. Obviously, the inference would 

be stronger if Tier 3 monitoring with random assignment of treatments and controls is used, but 

this requirement for cause and effect conclusions is likely not practical. Inferences are usually 

based on correlation-regression type analyses and confidence is gained in the conclusions as the 

numbers and geographical distribution of the study sites are increased. The primary 

disadvantages of the approach are costs and logistical difficulties in dealing with a large number 

of sites in a large area over a long time period.

The second approach (e.g., IWM) limits inferences to a small number of sites with limited 

geographical coverage, but with intense study of more parameters and their relationships. 

Again, randomization of treatment and control to relatively large watersheds is probably not 

practical, but perhaps some randomization can take place on streams within the larger units. 

Inferences concerning applicability of the conclusions to large regions are based on professional 

judgment. The primary disadvantages are costs, limited inductive inferences to large regions, 

and logistical difficulties of dealing with long-term studies.

The scientific debate between the relative advantages and disadvantages of these two 

philosophies will not be settled here. However, based on our collective judgment, we 

recommend the IWM philosophy for the evaluation of effectiveness of tributary habitat actions. 

This approach to research and monitoring has a proven history of effectiveness. Some of the 

earliest intensive watershed monitoring efforts were instituted by the Forest Service in the 1950s 

to better understand watershed responses to logging. ............
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

41

Intensive Watershed Monitoring is a method of achieving the level of sampling intensity 

necessary to determine the response of salmon to a set of management actions, but admittedly in 

limited numbers of areas. ..................

Further discussion of the Intensive Watershed Monitoring philosophy for conducting research to 

evaluate effectiveness of tributary habitat actions will shortly be available in the ISAB report 

referenced above. The report will be posted on the Northwest Power Planning Council website 

in the late winter of 2002-2003.

It is not easy to condense the advice given by the various government agencies to a simple set of 

recommendations on research and monitoring for the effectiveness of habitat restoration actions 

in a subbasin. Further, the situations in different parts of a subbasin are likely to require different 

approaches, e.g., evaluation of effectiveness of habitat actions on forest lands might be integrated 

with the U.S. Forest Service monitoring procedures, while evaluation on private lands may 

require development of survey procedures. We believe the following bullets contain the 

essential elements for development of an appropriate RM&E plan in subbasin planning:

• First, develop a sound Tier I trend monitoring procedure based on remote sensing, 

photography, and data layers in a GIS. Landscape changes in terrestrial and aquatic habitat and 

land use should be monitored for the smallest units possible. Accuracy and precision of data 

layers in the GIS should be evaluated using “blind” classification of randomly selected units by 

on-the-ground verification during field visits.

• Second, cooperate with Columbia Basin-wide attempts to develop common Tier 2 

probabilistic (statistical) site selection procedures for population and habitat status monitoring

and common protocols for on-the-ground or remotely sensed data collection. In so far as 

possible, measurement of indicator variables should be collocated on the same sites. Status 

Monitoring plans are being developed by the Action Agencies for implementation of the EPA 

EMAP probabilistic selection of aquatic sites in a pilot project in the Salmon Subbasin (BPA 

Draft Report “Research, Monitoring & Evaluation, For the NMFS 2000 FCRPS Biological 

Opinion”). Every effort should be made to include the same site selection protocols and data 

collection methods in the Clearwater Subbasin. This is a unique opportunity to promote the 

collection of research and monitoring data with common methods throughout not only the Snake 

River Basin, but the entire Columbia Basin. Status of fish and wildlife populations and habitat 

would be evaluated in a long-term biological monitoring program.

• Third, as data are obtained in a wildlife or fish population and habitat status monitoring 

program, develop empirical models for prediction of current abundance or presence-absence of 

focal species. Potential predictor variables include not only physical habitat variables (flow, 

temperature, etc.), but also measures of habitat recovery actions that are currently in place or are 

implemented in the future. Use the empirical models to evaluate the relative importance of 

physical factors and habitat improvements and to predict abundance or presence-absence 

throughout major sections of the subbasin. If adequate coverage exists with current study sites, it 

may be advisable to conduct initial analyses on current data as part of the assessment plan. 

However, a shift to probabilistically selected sites should be made as soon as possible to avoid 

inherent biases in subjectively selected and non-collocated study sites.
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

42

• Fourth, make your best judgment based on the assessment and inventory as to whether 

any new research in the spirit of the Intensive Watershed Monitoring approach should be 

instigated immediately. This step can be based on expert systems and existing data if adequate 

coverage of the subbasin (or part thereof) exists and if unique research needs exist in the 

subbasin. However, a subbasin plan will be an ever-changing document as new information 

becomes available. The ISRP judges that most new unique intensive research to be implemented 

in a subbasin should arise as a result of interaction of the Assessment and Inventory with new 

data arising in population and habitat status monitoring. 

The ISRP judges that the approach in these four steps is the most likely to accomplish a 

successful long term RM&E program. An extensive long term status monitoring program 

identifies important and unexplained trends and changes, i.e., identifies the intensive research 

that if conducted would explain the “why.” Tier I trend monitoring by remotely sensing 

procedures and Tier 2 statistical monitoring provide indications of trend and change in indicator 

variables, but the “why” of certain trends and changes is not well understood. For example, the 

status monitoring may indicate that a major and unexpected increase in juvenile fish production 

occurred in a watershed with high summer water temperature and low flow during the period 

2010 to 2020. Why? A population of bull trout is detected in an area where current knowledge 

and logic indicate they should not exist. Why? 

We do not recommend an intensive research project to explain, “why changes occurred” on 

every habitat improvement project, but rather periodic economical monitoring on individual 

projects to indicate benefits to fish and wildlife. We grant that replicated and coordinated data 

on habitat actions can provide compelling evidence for their effectiveness, but, in general, 

individual projects should depend on the Action Agency’s status monitoring program (or in the 

unlikely event the Action Agency’s status monitoring program is not implemented, a similar 

regional effort with standard protocol) to establish changes and trends in populations and habitat 

on a larger scale and their relationships to actions intended to improve habitat.

The basic elements of our recommendations that can be implemented in the near term in a 

subbasin are: 1) ensure the existence of sound Tier 1 level monitoring using modern GIS (Step 1) 

and 2) put a major effort into cooperation with and development of a probabilistic Tier 2 status 

monitoring program as recommended by the Action Agencies for the Upper Salmon subbasin 

(Step 2). Step 3 and perhaps step 4 depend on collection of data in the future. 
ISRP 2002-3 Review of Draft Clearwater Subbasin Plan

43

References

Bachman RA. 1984. Foraging behavior of free-ranging wild and hatchery brown trout in a 

stream. Transactions of the American Fisheries Society 113(1):1-32.

Bisbal, G. A. 2002. The best available science for the management of anadromous salmonids in 

the Columbia River Basin. Canadian Journal of Fisheries and Aquatic Sciences 59:1952-

1959.

Coutant CC. 1998. What is "normative" for fish pathogens? A perspective on the controversy 

over interactions between wild and cultured fish. Journal of Aquatic Animal Health 10:101-

106.

Goede RW. 1986. Management considerations in stocking of diseased or carrier fish. In: Stroud 

RH, editor. Fish culture in fisheries management. Bethesda, Maryland: American Fisheries 

Society. p 349-355.

Goede RW. 1994. Aquaculture/disease/wild fish. In: Wiley RW, Hubert WA, editors. Wild trout 

and planted trout: balancing the scale. Laramie: Wyoming Game and Fish Department.

Hindar K, Ryman N, Utter F. 1991. Genetic effects of cultured fish on natural fish populations. 

Canadian Journal of Fisheries and Aquatic Sciences 48(5):945-957.

McMichael GA, Pearsons TN, Leider SA. 1999. Behavioral interactions among hatchery-reared 

smolts and wild Oncorhynchus mykiss in natural streams. North American Journal of 

Fisheries Management 19:948-956.

McMichael GA, Sharpe CS, Pearsons TN. 1997. Effects of residual hatchery-reared steelhead on 

growth of wild rainbow trout and spring chinook salmon. Transactions of the American 

Fisheries Society 126:230-239.

Moffitt CM, Stewart BC, LaPatra SE, Brunson RD, Bartholomew JL, Peterson JE, Amos KH. 

1998. Pathogens and diseases of fish in aquatic ecosystems: implications for fisheries and 

management. Journal of Aquatic Animal Health 10:95-100.

Nickelson TE, Solazzi MF, Johnson SL. 1986. Use of hatchery coho salmon (Oncorhynchus 

kisutch) presmolts to rebuild wild populations in Oregon Coastal streams. Canadian Journal 

of Fisheries and Aquatic Sciences 43:2443-2449.

Sholes WH, Hallock RJ. 1979. An evaluation of fall-run chinook salmon, Oncorhynchus 

tshawytscha, to yearlings at Feather River Hatchery, with a comparison of returns from 

hatchery and downstream releases. California Fish and Game 64:239-255.