Independent Scientific Advisory Board

for the Northwest Power Planning Council, 

the National Marine Fisheries Service, 

and the Columbia River Basin Indian Tribes

851 SW 6th Avenue, Suite 1100

Portland, Oregon 97204

ISAB@nwppc.org

A Review of Strategies for Recovering 

Tributary Habitat

Robert E. Bilby

Peter A. Bisson

Charles C. Coutant 

Daniel Goodman

Robert Gramling 

Susan Hanna

Eric Loudenslager

Lyman McDonald 

David Philipp

Brian Riddell

March 31, 2003

ISAB 2003-2
ISAB 2003-2 Tributary Habitat

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ISAB Review of Strategies for Recovering Tributary Habitat

Contents

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

I. Introduction ....................................................................................................5

Status of Subbasin Planning ........................................................................................................6

Tributary Habitat Restoration Framework...................................................................................9

II. Establishing Biological Objectives................................................................ 13

a. Tributary habitat performance standards ...............................................................................14

b. Limiting factor determination................................................................................................26

III. Implementation Strategies ........................................................................... 30

IV. Implementation Incentives .......................................................................... 35

a. Environmental policy instruments.........................................................................................36

b. Federal agriculture-environmental incentive-based programs ..............................................37

c. Federal programs ...................................................................................................................38

d. Programs for environmental improvements ..........................................................................38

e. Effectiveness of incentive-based programs ...........................................................................38

V. Foundation for Habitat Recovery.................................................................. 39

VI. Monitoring and Evaluation.......................................................................... 41
ISAB 2003-2 Tributary Habitat

1

Executive Summary

Background

Whether tributary habitat improvements have achieved, or are likely to achieve, the goal of 

recovering conditions favoring the natural production of native salmonids in the Columbia River 

Basin is an open question, and a review of the approaches, assessment procedures, and 

implementation strategies for habitat improvement is therefore timely. In this report we examine 

several topics central to the recovery of tributary habitat: (1) the biological objectives related to 

habitat recovery, (2) the strategies for implementing restoration; (3) the incentives for 

implementing restoration; (4) the scientific foundation for habitat recovery; and (5) monitoring 

and evaluation. The objective of the review is to answer the question: What concepts and 

strategies should be incorporated in habitat recovery actions to improve their chances for 

success?

Biological Objectives

Biological objectives are important because they provide measurable targets for habitat recovery. 

Tributary performance standards are referenced in the All-H Report and are taken to mean the 

habitat conditions that would achieve biological recovery in an area of interest. These standards 

become the de facto biological objectives for tributary habitat. Fixed habitat standards (the 

traditional approach to habitat protection) do not easily account for natural environmental 

variation, differences in habitat requirements among species, or changes in habitat needs over a 

fishes’ life cycle. Additionally, managers often treat fixed standards as targets, tolerating habitat 

degradation until a danger threshold is exceeded and only then taking corrective action.

Habitat standards based on the distribution of conditions observed in unmanaged watersheds are 

more ecologically relevant, especially if they are expressed at appropriately large scales of space 

and time. Large spatial and temporal scales are required to account for the variety of conditions 

generated by natural disturbance and recovery. In many cases, decades or centuries might be 

required for habitat attributes within a degraded watershed to achieve a distribution of conditions 

comparable to those occurring in an unmanaged watershed. Therefore, performance standards 

are usefully articulated by comparing the distribution (median, range, and variance) of current 

habitat conditions to the desired distribution of habitat conditions (based on studies of reference 

watersheds), and tracking the rate at which conditions in a restored area converge on those 

observed in unmanaged landscapes. Standards expressed in this manner have the advantage of 

providing meaningful feedback on the efficacy of restoration much more realistically than a 

simple comparison of current conditions to a fixed set of habitat standards. While we 

acknowledge that the distribution of natural habitat conditions is often imperfectly known, and 

therefore do not advocate complete abandonment of habitat and water quality standards, we 

argue that a better understanding of natural variability provides a much more sound context for 

defining biological objectives for tributary habitat.
ISAB 2003-2 Tributary Habitat

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Implementation Strategies

With accurate data on habitat condition and sensitivity of fish populations to human actions, 

numerous analytical methods can be used to develop habitat recovery plans. Significant data 

gaps exist, however, and very few analytical methods have been sufficiently verified by field 

studies. As a consequence, several predictive methods have been developed to use incomplete 

data to relate tributary habitat to aquatic community condition or the abundance of target species. 

These methods are of three basic types: expert opinion, expert systems, and empirical models. 

Expert opinion has been most commonly applied in the Columbia Basin to habitat restoration 

projects. This approach is highly subjective and the assumptions underlying the opinions are 

often not field verified, or even made explicit. As a result, the products of such an approach are 

generally less helpful than more formal decision processes, especially those using quantitative 

information. Expert systems such as Ecosystem Diagnosis and Treatment (EDT) represent an 

improvement over undisciplined application of expert opinion. They provide a mechanism for 

objectively, and in some cases transparently, combining opinions from multiple scientists. They 

can also provide a clear indication of the assumptions underlying model predictions, if the 

process is properly documented. Parameterizing these models can provide a very good 

indication of significant data gaps, thus highlighting areas where more data are needed. 

However, model outputs must be interpreted with a full appreciation of the limitations imposed 

by the model structure and underlying assumptions; in most cases they have not been tested in 

the area to which they have been applied. Empirical models relate the abundance or occurrence 

of the species of interest to habitat attributes at a given location, and in this sense are directly 

applicable to restoration decisions because they are based on local data. In empirical models, 

associations between populations and habitat characteristics can be used to predict the 

distribution and abundance of a species or a species assemblage for locations where only habitat 

information is available. The predicted distribution directs protection and restoration actions to 

locations with the greatest potential (i.e., the appropriate suite of habitat conditions) to support 

target species. Empirical modeling techniques are informative when relatively complete data for 

fish populations and habitat are available, but they can be used even when data are incomplete. 

The ability to use empirical models has been enhanced by new statistical approaches and a 

steady improvement in remote sensing and spatial mapping technologies. 

Until the accuracy of various decision support approaches is properly evaluated on the ground, 

the ISAB believes the best approach to the development of habitat recovery plans is to use more 

than one analytical method. Policy makers can gauge the degree of scientific uncertainty by 

comparing the output from two or more analytical tools, understanding the assumptions made by 

each of them, and knowing the areas of agreement and disagreement. If multiple analytical 

techniques based on different assumptions and methods all point to the same locations and 

habitat conditions as being important factors limiting fish production, considerably more 

confidence can be placed in these conclusions. Application of multiple analytical procedures in 

the stressful context of subbasin assessment and planning may seem onerous to those required to 

complete these processes. Nonetheless, use of several approaches is one of the best methods of 

identifying the relationship between watershed condition and salmon recovery, and will help 

ensure that planned restoration actions address habitat conditions most likely to influence fish 
ISAB 2003-2 Tributary Habitat

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production. However, we emphasize that identification of useful analytical tools will require 

carefully designed comparisons of model outputs with actual habitat and fish population data.

Implementation Incentives

Once potential restoration locations and implementation strategies have been identified and 

prioritized, the question becomes how to ensure that strategies are implemented and restoration 

objectives are achieved. The successful implementation of tributary habitat improvements rests 

in large part on the incentives facing those with decision authority over tributary resources. In 

the case of publicly owned resources – either state or federal – mechanisms exist through various 

pieces of legislation, administrative rules and consultation procedures to motivate and coordinate 

restoration actions. Use of these should be acknowledged in the subbasin planning process.

Scientific Foundation for Habitat Recovery

Understanding large spatial and temporal-scale patterns is important in subbasin planning 

because restoration strategies need to identify the best sites for protection as well as the best 

candidates for restoration – those sites that have a likelihood of becoming highly productive at 

some future time. In preparing this report, the ISAB was briefed by scientists who have 

completed subbasin assessments that have been considered successful. Although the objectives 

of the assessments varied, the approaches that contributed to their success shared four common 

themes.

First, the assessments began with a thorough, systematic inventory of conditions within the 

drainage system. Instead of gathering as much data as possible and then attempting to make 

sense of it all, the investigators first identified the information needed to address their questions 

and then set up data collection programs to acquire it.

Second, successful assessments utilized measures of ecosystem functionality that extended 

beyond the stream to encompass whole watersheds. In each situation, rule sets were established 

that enabled investigators to make statements about the general ecological condition or “health” 

of an area based on combinations of environmental factors. This step was critical because it 

provided the context needed to assess the significance of habitat degradation at individual sites, 

as well as a means of judging the potential for effective restoration at different locations.

Third, the distribution and habitat requirements of target species over the entire freshwater life 

cycle were overlain on spatially referenced maps of watershed condition to allow for a 

landscape-scale comparison of life-history needs and habitat status. Superimposing fish 

population data on landscape condition allowed investigators to identify locations within 

subbasins where fish populations and ecosystem processes were robust or impaired.

Fourth, successful subbasin assessments all contained explicit strategies for habitat recovery

(e.g., rebuilding outward from core stronghold areas; reconnecting aquatic, riparian, and 

floodplain systems) and provided a means of forecasting future conditions based on projected 

human developments.
ISAB 2003-2 Tributary Habitat

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Monitoring and Evaluation

Understanding the effect of habitat conditions on salmonid population performance requires 

replicated observational studies or intensive research-level experiments at large spatial and 

temporal scales. Few evaluations of tributary habitat in the Columbia River basin have 

successfully adopted either approach. Monitoring has been categorized in a hierarchical 

sequence (Tier 1, Tier 2, or Tier 3) in the All-H Paper and repeated in the 2000 BiOp. For 

consistency, we discuss monitoring and make recommendations in terms of this hierarchical 

sequence. The three levels are: trend monitoring (Tier 1), statistical monitoring (Tier 2), and 

research monitoring (Tier 3). The value of research, monitoring and evaluation is greatly 

enhanced if these elements are integrated. The ISAB recommends that intensive watershed 

monitoring at selected locations be included in overall strategies for evaluating habitat 

improvement projects.
ISAB 2003-2 Tributary Habitat

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Tributary subbasins of the Columbia River are a complex mosaic of different land uses and 

ownerships.

I. Introduction

Tributary habitat improvement has been highlighted as one of the most important cornerstones 

for salmon recovery in the Columbia River Basin. Tributary habitat is emphasized in salmon 

recovery documents, the Fish and Wildlife Program and watershed planning. Many tributary 

habitat restoration efforts embrace the concept of returning altered streams to natural conditions. 

This emphasis is in contrast to many salmon recovery projects in the mainstem Columbia River 

that emphasize mitigation or artificial propagation as opposed to ecological restoration. In this 

sense, tributary habitat restoration may lead to somewhat more “normative” conditions (ISG 

2000) than those produced by recovery actions addressing the other Hs (hatcheries, harvest, and 

hydroelectric operations).

Whether tributary habitat improvements have achieved, or are likely to achieve, the goal of 

recovering conditions favoring natural production of native salmonids in the Columbia River 
ISAB 2003-2 Tributary Habitat

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Basin is an open question. As recommended in the 2000 FCRPS BiOp and All-H Paper 

(National Oceanic and Atmospheric Administration, National Marine Fisheries Service 2000), 

federal and state action agencies have committed to aggressive tributary habitat restoration partly 

in lieu of breaching the lower Snake River dams. Tributary restoration is to be coordinated 

through subbasin planning (www.nwcouncil.org/fw/subbasinplanning) to ensure that habitat 

recovery actions are complementary to the other Hs. NOAA Fisheries has indicated it will 

accept subbasin planning as a process for developing recovery plans for listed Pacific salmon 

ESUs in the Columbia River Basin (letter from Bob Lohn to Larry Cassidy: May 24,2002).

A review of the approaches, assessment procedures, and implementation strategies for tributary 

habitat improvement is therefore timely. In this report we examine several topics central to the 

recovery of tributary habitat under subbasin planning: (1) subbasin plan objectives related to 

habitat recovery; (2) strategies for implementing restoration; (3) incentives for implementing 

restoration; (4) scientific foundation for habitat recovery; and (5) monitoring and evaluation. 

The overall objective of the review is to answer the question: What concepts and strategies 

should be incorporated in habitat recovery actions to improve their chances for success?

Status of Subbasin Planning

The subbasin planning process is coordinated by the Northwest Power Planning Council. 

“In 2000, the Council adopted a set of amendments to the Program to begin what will 

eventually be a complete revision of the Program. In the first phase of the amendment 

process, completed in 2000, the Council reorganized the Program around a 

comprehensive framework of scientific and policy principles. The fundamental 

elements of the Program as revised are the vision, which describes desired 

accomplishments regarding fish and wildlife; basinwide biological objectives, which 

describe physical and biological changes needed to achieve the vision, consistent with 

the scientific principles; implementation strategies, which will guide or describe the 

actions needed to achieve the desired ecological conditions; and a scientific

foundation, which links these elements and explains why the Council believes certain 

kinds of actions should result in desired habitat conditions and why these conditions

should improve fish and wildlife populations in the desired way.

The Program amendments in 2000 set the stage for subsequent phases of the Program 

revision process, in which the Council will adopt more specific objectives and 

measures for the tributary subbasins, consistent with the framework elements already 

adopted. The Council intends to incorporate these specific objectives and measures 

into the program in locally developed subbasin plans for the 62 subbasins of the 

Columbia River (along with a coordinated plan for the mainstem Columbia and Snake 

rivers). The subbasin plans will become the source of specific actions and projects 

recommended by the Council for Bonneville funding and implementation, and will 

provide the context for the review of proposals for funding by the Council and the 

Independent Scientific Review Panel.”
ISAB 2003-2 Tributary Habitat

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The basic elements of a subbasin plan are described in a recent posting on the Council’s website: 

(www.nwcouncil.org/fw/subbasinplanning/admin/recommendations.htm)

 “Any subbasin plan adopted into the Program must consist of three general 

components:

• A subbasin assessment providing a description of historical and existing 

conditions;

• A clear and comprehensive inventory of existing projects and past 

accomplishments;

• A 10-15 year management plan with a vision, biological objectives and strategies 

for the subbasin.”

“...all recommendations for subbasin plans [are to] be submitted to the Council on or before 

Friday, May 28, 2004. This deadline seeks to provide the maximum amount of time 

available for developing recommendations while allowing for a Council amendment 

proceeding to adopt plans by the end of 2004.”

Before subbasin plans are formally submitted to the Council as recommendations, the Council 

has offered scientific review of final drafts subbasin plans. This will allow subbasin planners to 

receive input from the science review and make any changes that they decide are appropriate 

before submitting a final formal subbasin plan recommendation to the Council. The Independent 

Scientific Review Panel (ISRP) will conduct the reviews, during which they will answer the 

following questions:

 “Scientific review will evaluate proposed subbasin plans for their consistency with 

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

for “biological objectives” as described in the program. Scientific review will 

evaluate whether proposed plans are 1) internally consistent and 2) scientifically 

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

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

by the subbasin assessment. In evaluating whether subbasin plans are scientifically 

sound, the scientific review will be guided by the following considerations:

• Do the assessments appear to be thorough and substantially complete? 

• Are the subbasin goals, objectives, and strategies scientifically appropriate in light 

of the assessment and inventory of existing activities? 

• Does the plan demonstrate a linkage between the strategies, the biological 

objectives, the subbasin vision and the assessment? 

• Are the goals, objectives, and strategies consistent with those adopted in the 

program for the province and/or basin levels? 

• Do the plans demonstrate that alternate management responses have been 

adequately considered? 

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

subbasin objectives are being met over time? 
ISAB 2003-2 Tributary Habitat

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• 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? 

Once the subbasin plans are formally submitted, the Council will conduct its own review, which 

will include Council staff and public review. The Council staff will also facilitate analysis of the 

subbasin plans using the Ecosystem Diagnosis and Treatment tool, allowing the Council to 

evaluate and understand in a consistent way how different plans have incorporated assumptions 

about how fish and wildlife are affected by their environments.

The Columbia Basin Fish and Wildlife Authority (CBFWA) has completed reviews of each of 

the Columbia River Basin’s 11 geographic provinces, some of which align, more or less, with 

ESU boundaries, as part of the rolling review process for Fish & Wildlife Program Funding 

(www.cbfwa.org/province.htm). Included in the provincial reviews are assessments of the 

habitat conditions and fish populations in major tributary systems. This information will be 

incorporated into subbasin assessments and the inventory of existing and past projects. The 

NPPC has applied EDT to many of the tributaries in the Columbia Basin 

(www.edthome.org/Default.htm) for the purpose of assessing current habitat conditions at the 

sub-watershed (HUC-6) level, and for the purpose of comparing the model’s estimate of current 

productivity to what the sub-watershed could support under “best case” conditions. For an 

example of EDT output, see the model’s results for chinook salmon in the Chiwawa River, a 

tributary of the Wenatchee River subbasin at 

www.edthome.org/level2/viewer.asp?from=subbasinplanning&fldWatershed=Wenatchee.

To date, “subbasin plan workplans” have been approved for a majority of the Columbia River 

Basin subbasins, e.g., the Flathead River subbasin workplan 

(www.nwcouncil.org/fw/subbasinplanning/flathead/workplan.pdf). This workplan provides a 

roadmap for developing the full subbasin plan for the Flathead River system over a 14-month 

period, at a cost of approximately $150K. The Flathead workplan is to serve as the model for 

other subbasin plan workplans in the Columbia River Basin. Based on the Council’s schedule, 

all of the subbasin plans will be completed by 2005, in time for the 5-year interim review 

prescribed in the BiOp.

The first completed subbasin plan, for Idaho’s Clearwater River, was submitted to the Council on 

November 13, 2002 (www.nwcouncil.org/fw/subbasinplanning/clearwater/default.asp). The 

Clearwater plan was developed by the Clearwater Policy Advisory Committee, which included 

representatives of Idaho County, Potlatch Corporation, Nez Perce National Forest, the Nez Perce 

Tribe, U.S. Fish and Wildlife Service, Idaho Department of Environmental Quality, Idaho 

Department of Fish and Game, Idaho Department of Lands, Idaho Association of Conservation 

Districts, Clearwater National Forest, and NOAA Fisheries. The Independent Scientific Review 

Panel completed its review of the Clearwater subbasin plan on February 18, 2003

(www.nwcouncil.org/library/isrp/isrp2003-3.htm). The Clearwater planners are now reviewing 

the ISRP report and will make any changes that they decide are appropriate before submitting a 

final formal subbasin plan recommendation to the Council. The Council then will conduct its 
ISAB 2003-2 Tributary Habitat

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own review and undertake a formal rulemaking process, including a public comment period, 

prior to adopting the plan.

Tributary Habitat Restoration Framework

An overview of the procedure for developing subbasin plans for tributary habitat recovery is 

given at www.nwcouncil.org/fw/subbasinplanning/admin/guides/overview.htm. There are six 

steps in the process:

1. Assessment

An assessment forms the foundation for developing the subbasin vision, biological objectives 

and strategies. The initial assessment is based on existing information about the environmental 

conditions and fish and wildlife populations in the subbasin. A key element of the assessment 

will be information on the current and potential conditions in each subbasin. From this 

assessment, the subbasin plan will identify limiting factors and factors for decline for key fish 

and wildlife populations in the subbasin, including ESA-listed populations. Where the 

assessment identifies significant data gaps, the subbasin plan should identify the data need and 

measures necessary to meet those needs. The assessment should address the question, "What are 

the problems that keep fish and wildlife populations within the subbasin from reaching full 

potential?"

Examples of limiting factors and factors for decline

• Water quality problems in the lower river (temperature and sedimentation) 

• Passage barriers at culverts and falls (late summer) 

• Lack of adequate screening 

• Overwinter habitat is insufficient 

• Lack of juvenile rearing habitat 

• Low fish or wildlife abundance 

• Reduced biological function of habitat above blockages 

2. Vision

The intention of the Council’s subbasin planning effort is to define the environmental and 

biological goals specific to fish and wildlife within the Columbia River Basin. The Council 

anticipates a 10-15 year timeframe as the planning window. A vision statement is qualitative, and 
ISAB 2003-2 Tributary Habitat

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should reflect the policies, legal requirements and local needs, given the ecological realities 

within a subbasin. The vision will provide the guidance and priority for implementing actions in 

the future. The vision for the subbasin should address the question, "What are you trying to 

achieve overall?" -- a collective desire to accomplish certain things.

Examples of collective goals forming the vision

• Restore fish runs 

• Maintain genetic integrity 

• Protect and restore wildlife habitat 

• Increase harvestable populations of fish

• Increase escapement to the spawning grounds 

• Rebuild fish runs to achieve ESA delisting 

3. Biological Objectives

Biological objectives have two components: (1) biological performance, describing responses of 

populations to habitat conditions, described in terms of capacity, abundance, productivity and 

life history diversity, and (2) environmental characteristics, which describe the environmental 

conditions or changes sought to achieve the desired population characteristics. Objectives should 

be specific, measurable, and quantifiable. The initial assessments along with the vision will guide 

the focus of the biological objectives. For each major limiting factor, there should be a biological 

objective that describes the extent of improvement that the plan will call for. In addition, for each 

key population, specific biological objectives should describe the improvements planned for that 

population. These objectives will serve as a benchmark to evaluate progress toward the subbasin 

vision, and should have measurable outcomes. The questions that should be addressed through 

the biological objectives are "What target species need to be addressed?" "What number is 

achievable, and in what time frame?" Immediate, interim, and long-term biological objectives 

should be considered.

Examples of biological objectives

• 2,700 summer steelhead return to spawn by 2006; 

• 5,000 spring Chinook return to harvestable levels by 2008. 

• Increase winter rearing habitat by 10%. 
ISAB 2003-2 Tributary Habitat

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4. Strategies

Strategies describe the actions needed to address the limiting factors and therefore achieve the 

biological objectives. The strategies identified in the subbasin plans form the basis for Council 

funding recommendations to the Bonneville Power Administration. Implementation strategies 

will vary depending on the current condition of the populations and habitat, and the biological 

objectives identified for the species and life stages of interest. Strategies should be formulated to 

address the question, "What are the generic or overarching actions ne eded to address the limiting 

factors?"

Examples of strategies

• Improve water quality in the lower river 

• Restore passage through a particular barrier 

• Restore riparian habitat in a particular stream reach 

Strategies will be implemented through specific projects and/or actions. Projects proposed for 

funding will not be identified within the subbasin plan. When a plan is approved, it will form the 

basis for project selection within the subbasin. Projects will be developed through the regional 

project funding process. Projects proposed for funding will undergo independent scientific 

review as to how they fulfill the strategies and biological objectives in the subbasin plan.

An example of a strategy with related projects

Strategy

Projects (submitted through province review)

Restore fish 

Build a fishway at Sunny Creek

Passage

Increase instream flows - upgrade Sunny Farm diversion

5. Research, Monitoring, and Evaluation

Each subbasin plan will contain a monitoring and evaluation plan that will show whether the 

actions taken to implement the subbasin plan are achieving their objectives. Each monitoring and 

evaluation plan should answer the questions "How will we evaluate progress toward the 

biological objectives?" "How will it be measured?" "Who will conduct the monitoring and 

evaluation work?" and “What is the timeframe for such work?" The information gained through 
ISAB 2003-2 Tributary Habitat

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monitoring and evaluation allows for the examination of the effectiveness of actions taken so that 

actions may be refined over time.

In addition, each subbasin plan will contain a set of research questions (agenda) that will address 

critical uncertainties related to stated goals, biological objectives, and strategies that will become 

part of a larger research plan for the basin. The research agenda recognizes conditions and 

situations identified within a subbasin that will require specific research in order to help resolve 

specific management uncertainties.

6. Appendices

The background information and supporting documentation used in subbasin plan development 

can be included as technical appendices to the plan. Components of the technical appendices 

should include:

ß Assessment and limiting factors data and information; 

ß Project listings and summaries -- inventory of existing projects, program and past 

accomplishments; 

ß Subbasin summaries developed for the Council; 

ß Maps, excerpts, and other relevant documents. 
ISAB 2003-2 Tributary Habitat

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Wildfires, floods, and even volcanic eruptions are examples of natural disturbances that often 

cause short-term damage, but are needed to sustain complex aquatic habitats and long-term 

productivity. Accommodating natural disturbances often conflicts with the notion of fixed 

habitat standards.

II. Establishing Biological Objectives

The vision for each subbasin will be articulated by local, state, tribal, and federal policy-makers, 

addressing each of the Hs, within the context of the overarching mandates for fish and wildlife 

recovery in the Columbia River Basin. Subbasin plans are expected to contain clear statements 

of the biological objectives for each major tributary system, including population recovery 

targets for key species and expected improvements in habitat. The biological objectives 

developed in each subbasin plan are important because they provide measurable targets for 

habitat recovery. Biological objectives for habitat will emerge from four major considerations:

• Tributary habitat performance standards

• Limiting factor determination

• Definition of the “habitat template” (in EDT, for example, the habitat template is defined 

as the “hypothetical potential state where conditions are as good as they can be within the 

watershed”)

• Association of fish populations with habitat conditions

These four issues are closely related. Tributary performance standards are referenced in the AllH Report (Vol. 2, pp. 13-14) and are taken to mean the specific habitat states that would achieve 

biological recovery in an area of interest. These standards become the de facto biological 

objectives for tributary habitat. Development of realistic and achievable tributary habitat 

performance standards is crucial; without them, prioritization of restoration efforts is unclear and 

prediction of population response to habitat restoration will be highly uncertain.
ISAB 2003-2 Tributary Habitat

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a. Tributary habitat performance standards

What are the merits of fixed habitat targets (e.g., TMDLs, minimum dissolved oxygen 

concentrations, maximum stream temperature and sediment levels), as opposed to managing for 

the “distribution of natural conditions”?

Habitat standards have been with us for decades, especially since enactment of the Clean Water 

Act in 1972. They usually appear in regulations as, for example, maximum allowable water 

temperature or minimum levels of dissolved oxygen. Environmental targe ts, e.g., the number of 

pieces of large wood per unit length of stream or minimum instream flows, are used as a basis 

for habitat restoration decisions and to justify land and water use restrictions. In many 

management schemes, these standards serve as indicators of fish habitat condition and as 

barometers of management performance (USDA Forest Service/USDI Bureau of Land 

Management 1995).

In many cases the application of environmental standards and performance thresholds will divert 

attention from the real issue – managing watersheds in such a way that ecological processes 

supporting aquatic productivity and diversity are restored and conserved. Habitat standards have 

often failed to protect salmon because they are taken as fixed and do not focus on dynamic 

processes that create and maintain ecologically complex and resilient watersheds (Reeves et al. 

1995; Bisson et al. 1997). Fixed habitat standards do not easily account for environmental 

variations, differences in habitat requirements among species, or temporal changes in habitat 

requirements over a fishes’ life cycle. Additionally, managers often treat standards as targets, 

tolerating habitat degradation until a danger threshold is exceeded and only then taking some 

corrective action. This approach is inappropriate because the general trend is to homogenize 

habitat rather than maintain the complexity of conditions that support biological diversity at 

multiple scales. In addition, applying generic assumptions about environmental thresholds, often 

obtained from laboratory studies, can lead to unrealistic habitat standards (Shirvell 1989). 

Variation in environmental conditions has been identified as an important component of their 

habitat requirements for some species of wildlife. Erickson et al. (2003) studied habitat selection 

by alder flycatchers (Empidonax alnorum) on the Innoko National Wildlife Refuge in west 

central Alaska. Locations of breeding alder flycatchers were gathered by walking 

systematically-located transects, orientated perpendicular to the river channel, within the flood 

plain of the Innoko River during the 2000 and 2001 breeding seasons. Data from these surveys 

were used to construct a habitat selection function to predict the likelihood of the presence of 

alder flycatchers from habitat condition (Manly et al. 2002). Candidate predictor variables 

included both physical site descriptors such as slope, aspect, elevation, and distance to the river, 

and vegetation characteristics inferred from LandSat imagery. The variables with the highest 

importance in predicting the presence of the birds were elevation and two LandSat-derived 

attributes: the band 4 value and standard deviation of the band 3 value. In this example it 

appeared that the birds were responding to both the average condition of the site and the degree 

of variation in habitat conditions. 

Productive habitat for fish and wildlife exhibits complex structural diversity in space and time. 

Populations persist under these variable conditions because they have a complex structure of 

sub-populations, some strong and some vulnerable, distributed across a wide array of habitats. 
ISAB 2003-2 Tributary Habitat

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Extirpation in one area can be compensated, in time, by emigration from an adjacent subpopulation. Similarly, low production in one area may be compensated by above average 

production in adjacent areas. Scientists can only make educated guesses regarding the optimal 

population structure and habitat patterns for a successful population. Projects to improve 

watershed processes that produce productive natural habitat for fish and wildlife probably are 

beneficial in most situations, but by themselves, are likely to make only minor contributions to 

restoration of the structure needed by a successful population of wildlife or fish. We recommend 

that attention be focused on identifying, as soon as possible, the overall spatial array of 

watersheds and habitat units needed to protect important populations. 

Habitat standards have been used in modeling systems. However, major sources of error can 

arise from modeling fish distribution and abundance from a limited number of physical habitat 

variables without considering the full array of ecological interactions that are potentially 

controlling factors. For example, the Instream Flow Incremental Methodology (IFIM) has been

widely employed to estimate usable rearing habitat at different discharge levels (Bovee and 

Cochnauer 1977; Milhouse et al. 1981). IFIM modeling is often used to establish minimum 

instream flows in connection with the management of regulated rivers, despite objections to its 

accuracy if the model is not adequately calibrated with local biophysical data (Annear and 

Conder 1984; Mathur et al. 1985; Kondolf et al. 2000). Habitat-based population models can be 

useful, but may not yield accurate predictions about population responses to ecosystem change 

unless parameterized with data from populations in question (Fausch et al. 1988). 

Proponents of environmental standards often regard spatial and temporal variation as a sampling 

problem and ignore variation in habitat requirements within or among species. An alternative 

view is that variation is an important part of the spatial and temporal landscape that deserves a 

place in environmental planning. Natural disturbances create spatial and temporal variability 

essential for maintaining the distribution of habitat conditions necessary to support high levels of 

aquatic productivity and diversity (Reeves et al. 2002). Large natural disturbances such as 

wildfires and floods often result in short-term habitat loss and population stresses (e.g., through 

inputs of fine sediment or spawning gravel scouring) but over longer cycles of disturbance and 

recovery are important contributors of wood, coarse sediment, and other structural roughness 

elements to streams. As streams recover from a disturbance, habitat conditions change and 

biological communities utilizing the stream also change. Disturbance itself may be directly 

important as part of the environmental template for evolution. The maintenance of genetic and 

phenotypic variation and plasticity in life history characteristics that allow populations to persist 

in the face of natural and anthropogenic disruption of habitats may depend on habitats naturally 

varying in space and time (Poff and Ward 1990; Reice et al. 1990). Large natural disturbances 

create complex mosaics of aquatic and floodplain habitats necessary for different fish life history 

stages. They also create a full range of environmental conditions needed to maintain biodiversity 

at spatial scales ranging from the stream reach to the province.
ISAB 2003-2 Tributary Habitat

16

The short-term impact of wildfire often includes increased fine sediment and elevated stream 

temperature, but ecological recovery can be rapid and the long-term benefits of fire include 

recruitment of large wood and coarse sediment for habitat formation.

Suppose a habitat performance standard was determined to be the percent of old growth 

coniferous forest. Old growth forests are known to be important for fish and wildlife, and the 

percent of old growth remaining in the Columbia River Basin is now far below historic average 

levels, so this might be a reasonable choice. What were historical levels and how could we set 

old growth landscape targets? Some of the best work has been done in the Pacific coastal 

ecosystem in the range of the northern spotted owl, an old growth-associated species. Vegetation 

specialists, climatologists, and geographers have attempted to reconstruct the percentage of old 

growth forests in the Oregon Coast Range using disturbance simulation models (Wimberly et al. 

2000). Their findings are relevant to the question of applying standards at different geographic 

scales (Figure 1). 

In Figure 1, the upper graph illustrates long-term variation in the percentage of old growth forest 

at the province scale beginning at present and extending back 3,000 years. The average 

percentage of old growth at 500-yr intervals ranges from about 40% to 55%. However, the 

middle and lower graphs reveal an increase in temporal variability with successively smaller 

landscape units. Most of this simulated variability is due to large wildfires, forest disease 

outbreaks, and climate change. Wimberly et al. (2000) conclude “Until we can estimate ranges 

of historical landscape variability more accurately, it will be difficult to substantiate an argument 

for their use as precise forest management goals”.
ISAB 2003-2 Tributary Habitat

17

Figure 1. Percent of old growth coniferous forest over the past 3,000 years in the Oregon Coast 

Range based on simulation modeling. From Wimberly et al. (2000) reprinted with 

permission from the Society for Conservation Biology.

Although this analysis is a computer simulation of the Oregon Coast Range, it shows how much 

landscape conditions can vary under natural disturbance regimes. There is no reason to believe 

many areas of the Columbia River Basin have been any less variable. Attempting to define an 

old growth habitat performance standard, especially at the subbasin and smaller scale, becomes 

problematic because natural variation is so extreme over periods of decades to centuries as to 

make average conditions essentially meaningless. Similar patterns of variability are likely among 

many other environmental attributes.

Graph (a) in Figure 1 suggests some habitat parameters could vary within somewhat narrow 

limits at very large scales (province) and it is at this scale that applying standards makes the most 

sense. But even at this large scale, setting a standard based on an average condition over time 
ISAB 2003-2 Tributary Habitat

18

does not acknowledge the inherent natural variation. As a result, this type of standard only 

reflects “natural conditions” that occur for a very limited period of time. Using such a standard 

could be counterproductive to achieving biological objectives if temporal variation is important 

to biological productivity and diversity. In addition, targets generalized over very large 

landscapes and time scales may not be very helpful at the site level where habitat management 

decisions are most often made. How do we know if departure from desired conditions at the 

scale of a watershed, subwatershed, or stream reach merits restoration? Can generalized 

landscape target conditions be applied at the level of a subwatershed or stream reach?

Some environmental attributes are simply too variable at small spatial scales to be used as habitat 

standards or biological objectives. Two of the best examples are stream temperature and fine 

sediment concentration. Temperature varies along stream gradients from headwaters to mouth, 

due primarily to altitudinal changes in air temperature and increases in direct solar radiation as 

streams widen and both riparian and topographic shading decrease. Diel temperature change can 

be considerable where long-wave radiation loss cools stream water at night (Beschta et al. 1987). 

Inputs of ground water or hyporheic flows create localized cool water areas in what might 

otherwise be warm streams in summer (Bilby 1984). At any point in the drainage network or at 

any time of day, temperature can be highly variable, an exception being when flow is largely 

controlled by reservoir releases. Forward Looking Infrared (FLIR) surveys in the John Day 

River Basin has revealed numerous cool water zones in the mainstem associated with small 

tributaries and groundwater seeps (Bruce McIntosh, Oregon State University, personal 

communication). Salmonids have been shown to utilize pockets of cool water in Columbia 

Basin tributaries, enabling them to maintain a body temperature as much as 10oC lower than the 

average water temperature (Berman and Quinn 1991). Given the spatial and temporal variation 

in stream temperature and the possibility of behavioral thermoregulation by salmon, the 

biological meaning of a single-value temperature standard for protecting salmon habitat is 

questionable. 

Likewise, fine sediment deposits in stream channels are highly variable. There tends to be a 

gradual increase in deposited fine sediment in a downstream direction due to lessening gradients, 

but actual fine sediment levels at a particular site are dictated by local soils and geologic rock 

type, the abundance of large roughness elements such as large woody debris that retain sediment, 

geomorphic irregularities in the channel, inputs from natural and anthropogenic disturbances, 

and stream power (Everest et al. 1987; Megahan et al. 1992). At any given location there is 

often a wide range in fine sediment concentration within the stream channel that makes 

characterization of average conditions very difficult and not biologically meaningful. 

The spatial patchiness and temporal variability of both temperature and fine sediment requires 

that measurement of either of these parameters be undertaken with careful consideration of 

environmental heterogeneity. At present we are aware of no standardized sampling protocols for 

stream temperature that capture this heterogeneity in a way that can be interpreted ecologically. 

Even a thorough review of fine sediment in streams (Chapman 1988) concluded that relating fine 

sediment concentration to salmonid spawning success requires intimate knowledge of spawning 

locations so samples can be obtained from egg pockets, and further, that interpretation of 

resulting data be related to sediment tolerances of different species. Without this information, 

estimation of the effects of fine sediment on egg and alevin survival will be speculative.
ISAB 2003-2 Tributary Habitat

19

In the 15 years since Chapman’s review little has been done to improve sediment sample 

methods or to refine our understanding of sediment effects on salmon and trout. Some promising 

new technologies have been applied to temperature, including Forward Looking Infrared 

surveys. We conclude that sampling methods for temperature and sediment are currently too 

poorly developed to adequately characterize the variability in these parameters. Therefore, it is 

unlikely that standards at the scale of watersheds, subwatersheds, or stream reaches would be 

useful and it is highly doubtful they would be of much use at the province level. 

This same conclusion may well apply to other physical parameters associated with stream habitat 

(Poole et al. 1997). Standards are not available for many ecological attributes, and even in cases 

where standards have been established, their biological relevance may be questionable. Rigid 

performance standards for physical system attributes fail to account for the complex array of 

habitats required to support biological diversity at multiple scales of space and time; simple 

standards cannot encompass the dynamic processes that create and maintain ecologically 

complex and resilient watersheds (Bisson et al. 1997). Using fixed habitat standards and 

thresholds to assess current watershed condition and evaluate progress of restoration strategies 

potentially diverts attention from the primary objective of most restoration efforts – reestablishment of processes that support aquatic productivity and diversity.

Habitat standards based on the distribution of conditions observed in unmanaged landscapes are 

more ecologically relevant if they are expressed at appropriately large scales of space and time. 

Large spatial and temporal scales are required to account for the variety of conditions generated 

by natural processes of disturbance and recovery in unmanaged landscapes (Reeves et al. 1995; 

Bisson et al. 1997). In many cases, decades or centuries might be required for habitat attributes 

within a degraded watershed to achieve a range of conditions comparable to those exhibited by 

an unmanaged system. Therefore, performance standards may be more usefully articulated by 

coupling the potential range of parameter conditions (i.e., median, range, and variance) with a 

predicted rate of change from the current to the desired state. Standards expressed in this manner 

have the advantage of providing meaningful feedback on the efficacy of management actions 

much faster than simple comparison to a fixed set of habitat standards. 

“Distribution of natural conditions” standards require an understanding of conditions in 

watersheds with little human impact or watersheds with high-levels of natural production for the 

species of interest. Because unimpacted watersheds no longer exist in many areas, determining a 

natural range of conditions for many ecological attributes is often problematic. Two approaches 

to address this deficiency have recently been applied: 

• Modeling tools that predict distributions of conditions for some watershed attributes, such 

as forest stand ages or large wood in stream channels (Benda et al. 1998; Wimberley et 

al. 2000). These tools may prove useful for establishing desired outcomes for landscapes 

where no adequate reference information is available. 

• Historical information from a variety of sources to understand the range of variability in 

certain watershed conditions (Collins and Montgomery 2001). These historical 

reconstructions have been developed for a number of Puget Sound watersheds (Collins et 

al. 2003).
ISAB 2003-2 Tributary Habitat

20

In most cases, establishing desired distributions of conditions may be accomplished by linking 

empirical information from unmanaged watersheds to historical data using models that enable 

projections of the range of previous watershed conditions. An understanding of the range of 

conditions of a watershed through time provides a basis for establishing desired trends in 

monitored parameters in watersheds where habitat degradation has occurred. For example, 

maximum summer water temperatures recorded at multiple locations in an unimpacted or highly 

productive watershed might exhibit a frequency distribution as shown in Figure 2. If the 

distribution of water temperatures in a nearby degraded or low productivity watershed deviates 

significantly from the distribution of maximum temperatures in the unimpacted watershed, the 

desired outcome of a restoration program to address water temperature would be a gradual shift 

in this frequency distribution toward that observed in watersheds with the desired biological 

attributes. This approach acknowledges that a proportion of streams in a productive landscape 

will exhibit water temperatures different than those considered desirable for certain species. 

Natural temperature deviations are usually caused by disturbances that remove streamside 

vegetation, such as wildfires or floods. These periodic disturbances play a key role in 

maintaining long-term productivity of aquatic systems and are a vital process for maintaining 

watershed health (Bisson et al. 1997). Thus, warm water at some sites is not ecologically 

undesirable, and in fact may be needed for native species with higher temperature preferences 

than salmonids. Restoring an appropriate distribution of water temperatures in a developed 

watershed would represent a management goal more realistic and biologically meaningful than a 

single, fixed water temperature value.

Stream channels are highly variable. Understanding the distribution of natural conditions in 

relatively unaltered watersheds is important for establishing realistic habitat goals and trends.
ISAB 2003-2 Tributary Habitat

21

An understanding of the distribution of natural conditions of a watershed through time provides a 

basis for establishing desired trends in monitored parameters in watersheds where habitat 

degradation has occurred. For example, maximum summer water temperatures recorded at 

multiple locations in an unimpacted or highly productive watershed might exhibit a frequency 

distribution as shown in Figure 2. If the distribution of water temperatures in a nearby degraded 

or low productivity watershed deviates significantly from the distribution of maximum 

temperatures in the unimpacted watershed, the desired outcome of a restoration program to 

address water temperature would be a gradual shift in this frequency distribution toward that 

observed in watersheds with the desired biological attributes. This approach acknowledges that a 

proportion of streams in a productive landscape will exhibit water temperatures different than 

those considered desirable for certain species. Desired distributions for various habitat 

parameters can be articulated in this manner. Wood abundance, pool frequencies, and other 

habitat attributes all exhibit spatial and temporal variation. This natural variation is caused by 

local differences in underlying physical features of the landscape, disturbance history, and 

dynamics of recovery processes. Attempts to restore most of these attributes will require long 

time periods to achieve the desired conditions. Evaluation of the effectiveness of a restoration 

effort may be more rapidly judged by tracking the direction and rate of movement of the 

distribution of conditions in a watershed towards the desired median, range, and variance.

Figure 2. Theoretical frequency distribution of average maximum daily water temperature in an 

impacted and an unimpacted watershed. 

0

10

20

30

40

6 10 14 18 22 26

Average Maximum Daily Water Temperature (oC)

% of Sites in a Watershed

unimpacted Impacted 

15oC temperature standard
ISAB 2003-2 Tributary Habitat

22

An illustration of this approach is provided by the following example. The data to estimate the 

natural distribution of large wood in forested streams were collected by Fox (2001). Wood in 

streams selected at random from areas of unlogged forest ranged widely in abundance (Figure 3). 

Even after accounting for the effects of channel size and forest type, natural wood loading varied 

by about a factor of 10. By measuring wood abundance (or a surrogate of wood abundance such 

as riparian forest age) at multiple sites in a managed landscape over time, the rate at which wood 

abundance in a restored watershed approaches the distribution of wood in a comparable 

reference watershed could be estimated. The evaluation could be further refined by developing 

an expected rate of change in riparian conditions or wood abundance using one of several 

predictive models for instream habitat that have recently been developed (Beechie et al. 2001; 

Welty et al. 2002).

Figure 3. Distribution of wood abundance in streams flowing through unmanaged forests in the 

western Washington Cascade Mountains of Washington State. Values are the median 

abundance (dark line) the 25th and 75th percentiles of the distribution (box) and the 5th and 

95th percentile of the distribution (whiskers). Data from Fox (2001).

0

50

100

150

200

250

0-6m 6-30m >30m

Wood Pieces/100m Channel Length

Channel Width Categories
ISAB 2003-2 Tributary Habitat

23

The high mobility of fishes, especially anadromous fishes, and the great degree of variation in 

population size they display over space and time complicates the process of evaluating their 

response to changes in aquatic habitat. Some of this variation is not related directly to freshwater 

habitat quality but to the variable effects of weather and flow conditions on survival and growth, 

or to factors impacting fish in the marine environment that affect the number of adults returning 

to spawn. Because this variability is not a direct product of the condition of freshwater habitat, it 

is difficult to account for when attempting to relate fish abundance to habitat condition.

The relationship between freshwater habitat and productivity of fish populations has traditionally 

been examined at very fine spatial scales (individual habitat units or short stream reaches) over 

short periods of time (one to five years). The goal of much of this research has been to establish 

an association between an environmental factor and a life-stage specific response, such as the 

effect of fine sediment on the survival of incubating eggs (Everest et al. 1987) or the relationship 

between the amount of pool habitat and densities of juvenile salmonids during summer or winter 

rearing periods (Reeves et al. 1989). Although these studies are important for clarifying the 

mechanisms by which various factors affect salmon populations, they cannot provide meaningful 

information about the broader biological consequences of a restoration action unless they are part 

of a large scale, integrated evaluation effort. 

Quantification of biological responses to restoration actions that affect the quality, quantity, or 

distribution of aquatic habitats is complicated by the diversity of habitat types required by 

salmon and trout to complete freshwater rearing (Table 1). The relative availability and 

distribution of the numerous habitat types required over the entire freshwater life cycle plays a 

key role in determining the survival rate and productivity of a fish population. Habitatpopulation relationships are further complicated as the relative importance of each habitat type 

can change from year-to-year due to variations in weather, abundance of fish spawning within 

the watershed and other factors. For example, smolt production can be dictated by spawning 

habitat availability and quality during years when scouring flood flows occur during egg 

incubation (Hartman and Scrivener 1990). However, when flows are moderate during egg 

incubation, population performance may be more influenced by the availability of food during 

spring and summer or adequate winter habitat. 

Can habitat targets be related to the abundance or diversity of fishes?
ISAB 2003-2 Tributary Habitat

24

Table 1. Changes in the habitat requirements of coho salmon during freshwater rearing. The 

changing requirements of the fish stress the need to develop monitoring designs that 

evaluate responses at a spatial scale large enough to encompass the full range of habitat 

types required by the fish to complete freshwater rearing.

Life History Stage Habitat

Spawning and egg incubation Gravel bedded riffles and pool tail outs in proximity of 

cover suitable for adult spawners (e.g., deep pools, undercut 

banks, debris jams)

Early fry rearing Low velocity with cover in close proximity to food source 

typically associated with shallow, channel margin habitat 

with cover from wood and overhanging vegetation

Summer rearing Pool habitat with cover in close proximity to food source 

typically associated with low gradient channels, pool/riffle 

morphology, streams in flood plain valley type 

Winter rearing Low velocity refuge with cover typically associated with 

off-channel habitat on floodplains including low gradient 

tributaries, secondary channels and ponds

The scale at which biological evaluations of restoration projects are conducted is dependent on 

the nature of the restoration effort and the biological responses being evaluated. Some biological 

responses can be evaluated at the reach level and related to application of a single restoration 

action. For example, the biological effects of an action designed to reduce the input of sediment 

at a road crossing can be evaluated by comparing sediment levels in spawning gravel and egg 

survival upstream and downstream of the road before and after implementation of the corrective 

action. 

The ultimate effectiveness of a restoration program is reflected by the performance of the fish 

through their entire period of freshwater residency. Therefore, performance must be evaluated at 

a scale sufficiently large to enable that species to complete freshwater rearing. There are 

numerous measures that can indicate biological response at this scale. For example, survival can 

be estimated by comparing the number of eggs deposited in a watershed to the number of smolts 

from that cohort that ultimately leave the watershed. These Tier 2 watershed-level assessments 

(2000 BiOp) ideally are coupled with evaluations of effects of Tier 1 site-level restoration 

projects on specific habitat types and life stages. Information collected at nested spatial scales 

provides both an indication of the cumulative success of all projects within a restoration program 

and relative efficacy of individual projects. 
ISAB 2003-2 Tributary Habitat

25

What is the risk that setting habitat targets favorable for one species might result in unfavorable 

conditions for other species?

In most cases, restoring natural features of streams and adjacent riparian areas will be sufficient 

to provide the physical template that supports productive aquatic ecosystems. However, in some 

situations habitat targets may be set to specifically enhance one or two species of interest. Such 

targets typically include percentages of pool habitat, levels of fine sediment, pieces of large 

wood, or the amount of overhead cover, and are based on laboratory or field studies showing that 

the target conditions were optimal for the species in question. But habitat requirements differ by 

species and life stage, and what may be optimal for one species at one time may be distinctly 

sub-optimal for others. What is the risk that setting habitat restoration goals based on a few key 

species will lead to a reduction of other, less commercially, recreationally, or culturally 

important organisms?

We are aware of no studies of habitat recovery in western North America in which significant 

losses of biodiversity occurred after restoration, and in some case studies, restoration of 

ecological function has led to development of more diverse aquatic communities (Frissell and 

Ralph 1998). However, there are numerous warnings in the ecological literature about the 

pitfalls of attempting to optimize stream habitat for certain species where such attempts run 

counter to natural stream conditions and the maintenance of natural species assemblages (Sedell 

and Beschta 1991). The following quotation from the National Research Council (1992) 

expresses a scientific consensus that attempting to optimize streams for target species often leads 

to unanticipated and often undesirable outcomes:

“Some fisheries biologists believe that ‘water and space are going to 

waste’ if they are not used by trout and that ‘even the best streams 

could be made better’ by producing more trout in them. To the 

ecologist interested in stream or river restoration, maximizing the 

ecosystem for trout, or any single species, is not the same as restoring 

the biotic structure and function of the stream [p. 229]”

There is a danger, of course, that attempting to restore stream conditions favorable for salmonid 

production will produce harmful effects on non-salmonid species. For the most part, this has not 

been conclusively demonstrated in the Columbia River Basin, in part because non-salmonid 

species are rarely monitored. Although the ISAB doubts that this will be an issue in most 

situations, we do acknowledge that the habitat requirements of some native species are quite 

different from the habitat needs of salmon and trout. Lamprey (Lampetra spp.), for example, 

spend the early years of their life cycles burrowing through fine grained substrates in search of 

fine particulate organic matter upon which they feed. These sediment and organic matter-rich 

stream substrates are needed by lamprey ammocoetes, but sand- and silt-dominated substrates 

are considered undesirable for salmonid production. Imposing habitat targets that would lead to 

significant reductions in fines in stream gravels, while undoubtedly beneficial for salmonids, 

would probably reduce habitat suitable for juvenile lampreys. Likewise, setting habitat targets 

that call for reducing stream temperatures may benefit juvenile salmon at the expense of cyprinid 
ISAB 2003-2 Tributary Habitat

26

and catostomid fishes that prefer slightly warmer water (Reeves et al. 1998). Such targets may 

be viewed as desirable by managers, but if a native non-salmonid were to be listed under the 

Endangered Species Act, habitat conflicts could arise.

Installing large wood in streams, excluding livestock, and planting trees in riparian zones 

(protected by plastic mesh tubes in the right photograph) are common techniques of active 

restoration. Active restoration projects are usually designed to address factors that are 

believed to limit natural productivity.

b. Limiting factor determination

Limiting factors are usually taken to mean those factors that constrain the production of a species 

of interest. Typically cited examples of limiting factors for stream-dwelling salmonids include 

high temperature, excessive levels of fine sediment in spawning gravels, and lack of suitable 

winter habitat. By implication, “fixing” these environmental factors will “lift the lid” on 

production and allow target populations to attain higher sustainable growth and abundance. 

What is the basis for believing that habitat factors limit salmonid populations in Columbia River 

Basin streams (i.e., lab studies, field experiments, research with closely-related species)?

The usual procedure for identifying limiting factors is to compare current conditions with 

published data on environmental tolerance. For example, if eggs of a particular species are 

known to undergo significant mortality when exposed to dissolved oxygen concentrations of less 

than 5.0 mg/L, and if intragravel oxygen levels in known spawning areas often fall below this 

threshold, then dissolved oxygen is believed to be a limiting factor. In another example, if 

stream temperatures exceed 24oC for multiple and/or extended periods during summer, 

temperature is believed to be a limiting factor because 24oC is commonly accepted as a lethal 

environmental threshold for most salmonid fishes (Bjornn and Reiser 1991).
ISAB 2003-2 Tributary Habitat

27

In reality, critical thresholds have been established for relatively few environmental parameters, 

and most of these are factors that directly affect survival. Most lethal thresholds have been 

established experimentally in the laboratory by varying the parameter of concern while holding 

other aspects of the environment constant, and determining the level that kills 50% of a batch of 

test fish in 96 hours. While this is a very precise way of establishing lethal thresholds, results 

from laboratory tolerance tests may not translate directly to survival in natural streams. Fishes 

have evolved various mechanisms of surviving temporarily adverse conditions, and there are 

case studies in the literature of salmon surviving, and even thriving, in circumstances where 

laboratory test results predict they would perish. Bisson et al. (1988), for example, documented 

juvenile coho salmon exhibiting high levels of production in streams draining post-eruptive 

Mount St. Helens during an unusually hot summer in which water temperature reached 29.5oC. 

Berman and Quinn (1991) found that adult chinook salmon sought pools with cool groundwater 

in order to maintain lower body temperatures while migrating through the relatively warm 

Yakima River. This is not to assert that high temperatures, elevated sediment, or depressed 

oxygen do not limit survival, but rather to point out that performance of fish in the field may 

differ from their performance in the laboratory.

The distinction between factors that may limit survival and factors that may limit individual 

growth rate is often blurred in practice. Most limiting factor assessments attempt to identify 

environmental features whose levels exceed critical survival thresholds, but there are always a 

number of other factors that can influence individual growth or population abundance without 

actually killing fish. These include factors that affect food resources and the amount of suitable 

rearing space. For example, Reeves et al. (1989) developed a model of assessing the factors 

limiting coho salmon in western Washington and Oregon. When they applied their model to data 

sets from Oregon coastal watersheds, Reeves et al. (1989) predicted that the amount of protected 

winter habitat was likely to be one of the most influential variables for this species.

Food availability is another factor likely to limit fish production in most locations without being 

directly lethal, but estimating the abundance of food resources in the field is very difficult. 

Nevertheless, we note that field experiments involving trophic manipulations in the Pacific 

Northwest (e.g., nutrient additions or salmon carcass introductions) have repeatedly been shown 

to boost the abundance of potential prey organisms, and consequently salmonid growth (Warren 

et al. 1964; Gregory 1980; Shortreed et al. 1984; Slaney et al. 1986; Bilby et al. 1998) while 

many attempts to restore physical habitats (e.g., creating pools or adding cover structures) have 

not produced unambiguous evidence that the restoration yielded increased populations (House 

and Boehne 1985; Frissell and Nawa 1992; Hilborn and Winton 1993; Reeves et al. 1997; Ward 

2000). We do not conclude from these studies that food availability is somehow more limiting to 

salmonid populations than the quality of the physical environment. The relative importance of 

food and space will depend on site-specific circumstances (Chapman 1966). Rather, we believe 

that food has been demonstrated in field studies to be an important limiting factor, and this 

aspect of the aquatic environment is often overlooked in limiting factor analyses because there 

are no easily measured indices of food abundance.

The ISAB feels that the emphasis of a limiting factor analysis should be on whether a 

watershed’s aquatic and riparian ecosystem processes are functionally impaired, as opposed to 

whether an environmental assessment reveals potentially dangerous conditions for a species of 

interest at the reach scale. Simply going to the field and observing high sediment concentrations 
ISAB 2003-2 Tributary Habitat

28

in spawning areas or measuring high stream temperatures during mid-summer sidesteps the real 

issues of evaluating whether (1) the conditions observed may be perfectly normal for the site, 

irrespective of their suitability for target species, (2) watershed processes, e.g., inputs and routing 

of water, sediment, nutrients, and organic material have been significantly disrupted by human 

activities, and (3) local fish populations have evolved adaptations that allow them to persist in 

what would be considered unfavorable conditions. Instead, the ISAB recommends that limiting 

factor analysis include an assessment of how well the stream system is ecologically connected to 

its watershed, how the stream has responded to natural and anthropogenic disturbances in the 

past, how current and potential future conditions are constrained by land and water use, and how 

fish respond to the current range of conditions. We believe an analysis centered more on an 

examination of ecosystem processes (e.g., erosion, flow regime, aquatic and riparian interactions, 

large wood recruitment, and storage and routing of sediment and organic material) will produce a 

more meaningful picture of the conditions likely to influence the productivity of fish 

communities than an assessment of individual reach factors and whether they exceed putative 

risk thresholds.

What is the basis for predicting that correcting limiting factors will lead to measurable increases 

in the productive capacity of fish populations in a stream?

Many studies have shown that habitat restoration projects result in local (i.e., reach-specific) 

increases in fish density, but very few have demonstrated sustained response to habitat 

improvement at the scale of a breeding population, such as what might occupy a 3rd- or 4th-order 

tributary. Does this mean there is little basis for the assumption that “if you build it, they will 

come?” Not necessarily, because three factors regularly confound the interpretation of habitat 

restoration monitoring.

The first factor is the high level of natural variation that exists within breeding populations from 

year to year. For stream-dwelling anadromous salmonids, interannual variability (as expressed 

by the coefficient of variation of abundance, CV) is typically 50% or more for small populations 

(National Research Council 1996). Resident salmonids tend to have somewhat lower levels of 

natural variability, but even with a conservative CV estimate of 25% annually, almost a decade 

of pre-and post-monitoring population data would be needed to detect a 50% population increase 

with 80% certainty (Bisson et al. 1997). Since such an increase would be very difficult to 

achieve with habitat improvement alone, that is, with no corresponding improvement in the other 

Hs (hatcheries, harvest, hydroelectric operations), statistical detection of a population-level 

response to habitat restoration will likely take several decades at best (Hilborn and Winton 1993; 

Botkin et al. 2000; Ham and Pearsons 2000). That kind of commitment to long-term stream 

salmonid population monitoring is necessary for evaluation of the effects of habitat 

improvement, but has occurred at only a few locations in North America.

The second problem commonly confounding the documentation of habitat restoration success is 

that the scale of restoration projects rarely matches the geographical distribution of the fish 

population that is meant to receive the benefits. Restoration is typically targeted at improving 

habitat in a stream reach that has been significantly damaged, but rarely do restoration projects 

affect more than a small fraction of the overall breeding or rearing area. One of the few 

watersheds in which comprehensive, population-wide habitat restoration has been attempted is 
ISAB 2003-2 Tributary Habitat

29

Fish Creek, a tributary of the Clackamas River (a Lower Columbia River watershed in Oregon). 

In this drainage, over 1,000 instream structures were placed in Fish Creek and its main 

tributaries, an off-channel pond was created for winter habitat, and road crossings that blocked or 

impeded fish passage were either made fully passable or obliterated. After about 15 years of 

intensive effort, the effects of restoration on steelhead and coho salmon are not completely clear 

(Reeves et al. 1997). Likewise, almost two decades of restoration of Vancouver Island’s Keogh 

River have proved insufficient to enable the effects of watershed-scale habitat improvement on 

steelhead to be differentiated from the effects of climate change (Ward 2000). These case 

studies emphasize the importance of long-term monitoring to evaluate the effects of habitat 

improvements.

Finally, the experimental design of most monitoring efforts to date has been deficient. Rarely 

are appropriate reference sites associated with treatment locations. One of the key factors 

complicating the interpretation of fish response to the watershed-level experiments conducted at 

Fish Creek (Reeves et al. 1997) and the Keogh River (Ward 2000) was the lack of an untreated, 

reference watershed. The problems with interannual variation in fish abundance caused by 

factors other than condition of freshwater habitat may be significantly reduced by the inclusion 

of reference sites. Most monitoring efforts also fail to consider response variables other than fish 

abundance. Variables such as smolts produced per spawning female, distribution of fish within 

the watershed, life history stage specific survival rates and growth rates all may be less variable 

and more sensitive to certain restoration approaches than fish density. However, these types of 

measures have rarely been used in assessing restoration efforts. 

The implication of this pessimistic assessment of the evidence for habitat restoration 

effectiveness is that we still have much to learn about the efficacy of different types of 

restoration projects. Additional intensively monitored population-scale restoration efforts are 

needed, as most existing long-term studies have taken place in coastal, rainforest-dominated 

watersheds, the results of which may not be directly applicable to interior semi-arid drainage 

systems. One way to carry this out is to establish a regional network of experimental watersheds 

(approximately HUC-6 in size) in which habitat improvement can be implemented at a scale that 

includes most of the freshwater life history stages of a population, and to apply restoration 

treatments in such a way that population changes can be distinguished from other natural and

anthropogenic sources of environmental variation (e.g., Walters et al. 1988, 1989). Such an 

effort will require a high level of organizational cooperation and coordination.
ISAB 2003-2 Tributary Habitat

30

A number of analytical tools have been used to guide implementation of restoration projects in 

small streams and large rivers. These tools attempt to relate habitat to fish abundance in a 

quantitative way so the outcome of restoration projects can be predicted.

III. Implementation Strategies

The purpose of a subbasin assessment is to provide the information necessary to underpin the 

habitat restoration strategy that is ultimately articulated in the subbasin plan. The assessment 

should include three key elements: the locations where restoration efforts are apt to be most 

effective, the types of restoration actions that are appropriate at a given location, and some 

indication of the expected fish response. With sufficient data on habitat condition and 

sensitivities to human actions and fish populations, there are numerous analytical methods that 

can be used to develop this information. However, data are never complete and the menu of 

available analytical tools has not yet been subjected to adequate field evaluations. Predictive 

methods have been utilized for relating tributary habitat to aquatic community condition or the 

abundance of key species when less than complete data are available. These techniques are of 

three basic types: expert opinion, expert systems, and empirical models. 

Expert opinion has been the method most commonly applied in the Columbia Basin in the 

development of habitat restoration projects prior to the implementation of the subbasin 

assessment and planning process. The expert opinion method involves compiling the opinions of 

local fish managers and scientists (i.e., knowledgeable experts) with regard to the sites within a 

subbasin that have the greatest restoration potential and the types of restoration actions that are 

suited to those locations. This approach is highly subjective and the assumptions underlying the 

opinions are often not field verified, or even made explicit. As a result, the products of such an 

approach are generally less helpful than those utilizing more formal decision processes, 

especially those with quantitative information.

Expert systems represent a formalized method of organizing and applying information and 

opinion. Most expert systems utilize quantitative information when available, but usually rely 

primarily on expert opinion. These approaches enjoy an advantage over more informal methods 
ISAB 2003-2 Tributary Habitat

31

of using expert opinion in that they attempt to make the assumptions underlying an opinion 

explicit and clear. In the Columbia River Basin, two expert systems have been used extensively 

to assess the response of fish populations to the application of various land management 

practices or restoration efforts: the Interior Columbia Basin Ecosystem Management Plan 

(ICBEMP) Bayesian belief network (Quigley and Arbelbeide 1997) and the Ecosystem 

Diagnosis and Treatment (EDT) method (Mobrand Biometrics 1999) endorsed by the Northwest 

Power Planning Council. 

The ICEBMP Bayesian Belief Network (BBN) assessment was based on a fairly simple “box 

and arrow” conceptual model of the effects of various land use practices on aquatic habitat 

condition and fish population status (Figure 4). The boxes, or nodes, of the model represented 

various ecosystem attributes, such as rate of sediment delivery or riparian condition. Nodes were 

connected to other nodes they impacted or that directly impacted them. Thus, sediment input 

and riparian condition were two of the nodes determining habitat capacity for salmon. In turn, 

factors such as grazing intensity or the frequency of fires would affect riparian condition, and 

road density and soil erosion would influence sediment input. Relationships between the nodes 

were quantified using empirical information, when available; however, in many cases data were 

not available. Therefore, causal connections among most of the nodes were inferred using 

opinion gathered from a panel of scientists with the appropriate expertise. The process of 

applying the expert opinion to the Bayesian Belief Network was highly formalized. Each node 

was assigned several possible states, usually expressed qualitatively. The conditional probability 

of the state of a node, given differing combinations of states of the input nodes, was estimated by 

each panel member and the average used to parameterize that set of conditions in the network 

(Figure 4). All node interactions throughout the model were parameterized in this fashion. The 

model was run for each of the 6th-code HUCs within the interior Columbia Basin for a number of 

species of salmon and trout to evaluate the response of aquatic habitats and fish populations to 

the application of several land management alternatives.
ISAB 2003-2 Tributary Habitat

32

Figure 4. Theoretical example of the process used to parameterize the ICEBMP Bayesian Belief 

Network. The interaction between riparian condition and sediment input can result in high, 

moderate or low habitat capacity. The probability (%) that a specific combination of the 

two input variables will produce a certain habitat capacity state is shown in the table. These 

probability values are the average of the probabilities assigned by each member of the 

expert panel that participated in the parameterization process. 

Riparian Habitat Condition

• Good

• Moderate

• Poor

Sediment Input

• High

• Moderate

• Low

Aquatic Habitat Capacity

• High

• Moderate

• Low

Sediment Riparian Habitat Capacity

Input Condition High Moderate Low

High Good 40 20 20

High Moderate 20 40 40

High Poor 5 15 80

Moderate Good 75 20 5

Moderate Moderate 40 50 10

Moderate Poor 20 50 30

Low Good 90 8 2

Low Moderate 75 20 5

Low Poor 30 50 20
ISAB 2003-2 Tributary Habitat

33

 

Ecosystem Diagnosis and Treatment is an expert system that has been widely used in the 

Columbia Basin, as well as elsewhere in the Pacific Northwest. Like the ICBEMP Bayesian 

network, EDT is based on a conceptual model of habitat condition and fish population response. 

However, the EDT model is far more complicated (i.e., it contains far more boxes and arrows) 

than the BBN system used in the ICBEMP analysis. EDT is designed to utilize fine-scale data 

on habitat condition. In the model for the entire Columbia Basin the habitat data (where 

available) were compiled for each subwatershed. In many watershed-scale applications of EDT, 

habitat data for each kilometer of stream reach are required. The biological response data 

required for EDT also are very detailed, including life stage-specific carrying capacity and 

survival values and how these are influenced by habitat change. The survival and capacity 

values for each life history stage in each stream reach are summed through the freshwater 

residency of the fish to estimate smolt production, and in the process develop a “survival 

landscape”. The EDT model also can include marine life stages of the fish, thereby enabling the 

projection of returning adults and population growth rates. For most subbasins, only a small 

proportion of the locally derived data required to parameterize EDT is available. Therefore, 

population capacity and survival values, as well as some of the habitat attributes, have been 

obtained through expert opinion. Because the fine-scaled nature of EDT requires a very large 

number of values to be derived by expert opinion, many of the assumptions made during the 

process of parameterizing the model are often not fully documented. Neither the ICBEMP-BBN 

nor EDT has been evaluated in a side-by-side comparison of model accuracy based on actual 

data.

The two expert system approaches represent an improvement over undisciplined application of 

expert opinion. They provide a mechanism for objectively, and in some cases transparently, 

combining opinions from multiple scientists. They can also provide a clear indication of the 

assumptions underlying the model predictions, if the process is properly documented. 

Parameterization of these models can provide a very good indication of key uncertainties in the 

system, thus highlighting areas where the collection of data might be most useful. However, 

their outputs must be interpreted with a full appreciation of the limitations imposed by the model 

structure and underlying assumptions, because both models have yet to be locally calibrated. 

Limitations in model structure can prevent the inclusion of key variables. For example, neither 

of the two expert systems addresses temporal population variability. Population response to 

factors such as variation in climate or periodic catastrophic events cannot be modeled, and it is 

becoming increasingly apparent that the productivity and diversity of stream-dwelling fishes is 

significantly influenced by temporal changes in habitat characteristics (Reeves et al. 1995). 

Nonetheless, these tools can provide information useful in developing a restoration plan. 

A third approach to assessing habitat-fish population relationships is empirical modeling, which 

for the most part is based on local data. Although these techniques are most informative when 

comprehensive data on fish populations and habitat conditions are available, they can be used 

even when data are incomplete. The ability to use empirical approaches has been enhanced by 

new statistical approaches and a steady improvement in remote sensing and spatial mapping 

technologies. Generally, empirical modeling relates the abundance or presence-absence of the 

species of interest to habitat attributes at a given location (Manly et al. 2002). From this 

comparison, associations between populations and habitat characteristics are developed and can 

then be used to predict the distribution and abundance of a species or a species assemblage for 
ISAB 2003-2 Tributary Habitat

34

locations where only habitat information is available. The predicted distribution can be used to 

direct protection and restoration actions to locations with the greatest potential (i.e., the 

appropriate suite of habitat conditions) to support target species. 

These types of analyses have been used in the Columbia Basin, and elsewhere, for many years. 

Recently, the application of new analytical approaches coupled with information generated by 

remote sensing and GIS has enabled the examination of these relationships at larger, more fishrelevant, spatial scales. A classification regression tree method (CART) has been used to 

identify relative strength of salmonid populations at a 6th-code HUC level across the entire 

interior Columbia Basin (Rieman et al. 1997; Thurow et al. 1997). In this application, the CART 

technique was applied to several thousand HUC 6 watersheds. The method evaluated habitat 

variables one at a time to identify the single variable most closely associated with fish abundance 

for the entire data set. This habitat variable was then used to segregate the HUC 6 watersheds 

into two condition classes and the process was repeated for each set of sites. The sites were 

segregated into an increasing number of classes, each associated with a habitat attribute that was 

responsible for that classification assignment. Ultimately, a broad-scale picture of the habitat 

attributes most closely associated with abundance of different species was generated.

The NOAA Fisheries Watershed Research Program has used the technique of hierarchical linear 

modeling to determine habitat–abundance associations for spring chinook salmon or steelhead in 

the Salmon River, Willamette River Yakima River, and Wenatchee River watersheds (Feist et al. 

in review; Steel et al. in prep.). This approach has been called the Salmon Watershed 

Assessment Method (SWAM). The method regresses habitat variables compiled at the reach or 

watershed level, and generated primarily from remotely sensed or geospatially-referenced data, 

against normalized fish population abundance values for each year of record. Habitat variables 

that consistently exhibit a significant association with abundance are identified. The variables 

exhibiting a significant association with fish abundance are used in a predictive model of 

capacity, and the model can then be applied to areas for which fish data are not available. Model 

outputs enable the identification of locations within a subbasin possessing habitat conditions 

needed to support large populations of the target species. Both CART and SWAM techniques 

provide habitat characterization of sites that support high fish densities. With this information, 

the potential of all tributaries within a subbasin to support species of interest can be predicted 

from habitat attributes. Similarly, logistic regression methods can be used to identify habitat 

conditions associated with the presence-absence of a particular life history stage of a species 

(Manly et al. 2002). 

The ability to use empirical assessment approaches, and the value of the output, is largely 

dependent upon the availability of appropriate local data. The most useful information is 

generated from fish population measures taken over a long period of time at multiple locations in 

a watershed, as well as comprehensive data on habitat condition and how that condition has 

changed over the period for which fish data are available. Unfortunately, these data are available 

for relatively few sites and must be interpreted with some caution. Estimates of fish abundance 

at multiple locations are largely restricted to spawner or redd counts. This life history stage may 

not be the most sensitive to freshwater habitat condition. Information on climate, land use 

patterns, and even channel characteristics, are available at many locations. But nutrient or 

riparian data may be much more difficult to obtain. Incomplete data may lead to erroneous 

conclusions about the relative importance of different habitat factors. 
ISAB 2003-2 Tributary Habitat

35

Until the accuracy of various decision support approaches is properly evaluated on the ground, 

the ISAB believes the best approach to the development of habitat recovery plans is to use more 

than one analytical method. Policy makers may be helped to gauge the degree of scientific 

uncertainty by comparing the output from two or more analytical tools, understanding the 

assumptions made by the analytical tools, and knowing the areas of agreement and disagreement 

among them. If multiple analytical techniques based on different assumptions and methods all 

point to the same locations and habitat conditions as being important factors limiting fish 

production, considerably more confidence can be placed in these conclusions. Areas where 

considerable divergence in model output occurs also provide worthwhile information. 

Attempting to understand why there are differences in model output can help identify areas 

where our current understanding of system function is incomplete and highlight those issues for 

which additional data are needed. We emphasize, however, that identification of useful 

analytical tools will require carefully designed comparisons of model outputs with actual habitat 

and fish population data.

Application of multiple analytical procedures in the stressful context of subbasin assessment and 

planning may seem onerous to those required to complete these processes. Nonetheless, use of 

multiple analytical approaches is one of the best methods of identifying key uncertainties in our 

understanding of the interaction between watershed condition and salmon recovery and will help 

ensure that planned restoration actions address habitat conditions that are controlling fish 

production. The difficulties in applying multiple analytical tools is somewhat alleviated by the 

fact that some of these analyses have already been completed for many subbasins and watersheds 

within the Columbia basin. The CART analyses and Bayesian Belief Network described above 

have been applied to all 6th Code subwatersheds in the Columbia Basin east of the Cascade 

Mountains. Numerous EDT evaluations have been completed. SWAM analyses have been 

conducted for the Salmon River, John Day River, Wenatchee River and Willamette River. 

Information from these completed analyses should be utilized in conjunction with output from 

modeling efforts undertaken during the process of subbasin assessment to provide the technical 

foundation for subbasin plans. These analyses can be continuously improved in subsequent 

subbasin assessments as new data become available and as improved analytical tools and models 

are developed. 

IV. Implementation Incentives

Once potential restoration locations and implementation strategies have been identified and 

prioritized, the question becomes how to ensure that strategies are implemented and restoration 

objectives are achieved. The successful implementation of tributary habitat improvements rests 

in large part on the incentives facing those with decision authority over the resources of concern. 

In the case of publicly owned resources – either state or federal – mechanisms exist through 

various pieces of legislation, administrative rules and consultation procedures to motivate and 

coordinate restoration actions. Although problems of inter-jurisdictional coordination do exist, 

they are mitigated by the fact that the incentives facing those making decisions over public land 

tend to be aligned with the public objectives of tributary habitat restoration.
ISAB 2003-2 Tributary Habitat

36

In contrast, when tributary resources are privately owned, no mechanism exists to naturally bring 

together the public demand for habitat improvements with the private supply of restoration 

actions. For goods and services exchanged through markets, the market aligns demand and 

supply through the responsiveness of price to changing conditions. But many of the 

environmental goods and services involved in tributary habitat – water quality, riparian 

vegetation, biodiversity- are amenities that remain outside a market. Something other than price 

has to encourage people to take certain actions so that private supply of environmental goods and 

services matches public demand.

a. Environmental policy instruments

The policy instruments used in the United States to encourage people to do the “right thing” for 

environmental resources fall into three general categories of motivation: regulatory coercion, 

economic incentives and moral suasion.

Regulatory coercion is the motivation found in state and federal regulatory programs that are 

based in enabling legislation and enforced through government authority. Compliance is a matter 

of law. Examples are water temperature standards and pollution TMDLs established under the 

Clean Water Act and land use controls established under the Endangered Species Act.

Economic incentives use self-interest as the motivation for action. Individuals are penalized for 

undesired actions or rewarded for desired actions, and have flexibility to select the type and 

magnitude of participation. Examples are charges for point-source pollution discharges (negative 

incentives) and payments for agricultural acreage set-asides (positive incentives).

Moral suasion uses the motivation of “doing the right thing” for the environment. A positive 

feeling of contributing to the public good underlies much volunteer work and voluntary actions. 

Examples are volunteer adopt-a-river programs and voluntary watershed councils. 

The type of policy instrument most appropriate for tributary habitat restoration depends on the 

context of the restoration. In general, restoration strategies will be multifaceted and will include 

resources regulated under mandatory programs as well as those without specific protections. To 

the extent that the resources are privately owned, strategies must go beyond regulatory coercion 

to motivate people on the basis of either suasion or self-interest. 

Voluntary programs are an increasing phenomenon in environmental restoration. The system of 

Oregon watershed councils is based on voluntary participation, as are many stream restoration 

projects and activities. Voluntary programs have the advantage of being low cost and flexible in 

testing new approaches, but they have the disadvantage of uncertain effectiveness (EPA 2001).

Incentive-based policy instruments can provide either positive incentives to encourage desired 

behavior or negative incentives to discourage environmentally harmful activities. Cost-share and 

incentive payment policies are frequently used as positive incentives to encourage changes in 

agricultural practices that will protect environmental resources or to take land out of agricultural 

production (USDA 2000). Some involve the government taking on partial legal interests in the 

land through conservation easements (Wiebe et al 1996). Pollution emission fees are negative 

incentives designed to increase the costs of undesired behavior. Compliance mechanisms like the 
ISAB 2003-2 Tributary Habitat

37

Wetland Conservation (“Swampbuster”) Program are a mix of positive and negative incentives, 

in which a basic level of environmental compliance is a condition of eligibility for other 

programs (USDA 2002a). 

The U.S. experience with environmental restoration has shown a number of benefits from 

applying the motivation of self-interest to induce environmentally desirable private behavior 

(Shogren and Tschirhart 2001). The experience most closely related to tributary habitat 

restoration is in the suite of federal incentive-based agriculture/environmental programs 

administered by the USDA. These programs use positive economic incentives to create changes 

in agriculture that will promote environmental goals. They operate on the basis of compensating 

producers for the cost of lost production opportunity brought by changing uses of agricultural 

land. Most would apply to tributary habitat restoration where riparian land is in agricultural 

production. 

b. Federal agriculture-environmental incentive-based programs 

The 2002 Farm Act continues the trend of increasing funding for agricultural programs targeted 

at achieving environmental benefits. In contrast to past conservation funding which emphasized 

the retirement of land from agricultural production, emphasis has shifted toward conservation 

actions on working land. Land retirement programs place a stronger emphasis on wetland 

restoration (USDA 2002b). The following are some examples of federal incentive-based 

agricultural programs that would apply to tributary habitat restoration. These programs would be 

compatible with the “range of natural conditions” management objectives.

Conservation Reserve Program (CRP): provides farm operators an annual per-acre rental 

payment and cost-sharing for establishing a permanent land cover, in exchange for retiring 

environmentally sensitive cropland from production for 10- to 15-years. Offered land is 

evaluated on the basis of an Environmental Benefits Index (EBI). 

Wetlands Reserve Program (WRP): provides cost sharing and/or long-term or permanent 

easements for restoration of wetland on private land. The 2002 Farm Bill increased the acreage 

cap 1.2 million acres (117%). The landowner voluntarily limits future use of the land, yet retains 

private ownership. 

Environmental Quality Incentives Program (EQIP): provides technical assistance, cost-sharing 

and incentive payments to assist livestock and crop producers with conservation and 

environmental improvements through 5-10 year contracts. It is targeted to watersheds, regions, 

or areas of special environmental sensitivity identified as priority areas. 

Wildlife Habitat Incentives Program (WHIP): provides cost-sharing assistance to landowners for 

developing habitat for upland wildlife, wetland wildlife, threatened and endangered species, fish, 

and other types of wildlife. WHIP funds are distributed to states based on their wildlife habitat 

priorities, which may include wildlife habitat areas, targeted species and their habitats, and 

specific practices.
ISAB 2003-2 Tributary Habitat

38

Conservation Security Program: this new program provides payments to producers for 

maintaining or adopting a wide range of structural and/or land management practices that 

address a variety of local and/or national resource concerns. 

Small Watershed Program: provides technical and financial assistance to states, local units of 

government, tribes, and other sponsoring organizations to voluntarily plan and install watershedbased projects on private lands for watershed protection, fish and wildlife habitat enhancement, 

and wetland restoration, among other purposes. 

c. Federal programs

Challenge Cost-Share Programs (CCS): The U.S. Forest Service provides funds and technical 

expertise for cooperative projects to improve aquatic habitat, fishing opportunities, and 

environmental education. The U.S. Fish and Wildlife Service also funds challenge cost-share 

programs targeted at conserving fish and wildlife resources and natural habitats on public and 

private lands. CCS funds must be matched by contributions of money, labor, equipment, or 

materials from conservation groups, private enterprises, individuals, schools, or other public 

agencies (USDA 2002c; USDI 2002).

d. Programs for environmental improvements

Some state actions for environmental restoration are the implementation of federal regulatory 

programs. For example, the Environmental Protection Agency delegates authority to the Oregon 

Department of Environmental Quality (DEQ) to conduct federal programs to implement the 

Clear Air Act, the Clean Water Act and the Resource Conservation and Recovery Act (control of 

hazardous waste). To implement the Clear Water Act, the DEQ maintains the 303(d) List of 

stream segments that do not meet the established water quality standards, established to protect 

native salmon and trout. In addition, the DEQ develops TMDLs (Total Maximum Daily Loads) 

for a range of pollutants delivered through both point and non-point sources. Management plans 

to restore streams and rivers bodies to water quality standards are then developed in cooperation 

with landowners (DEQ 2002). These programs are targeted to achieving fixed standards 

mandated by federal law. 

Other state programs for habitat recovery operate on a voluntary basis, but without the large 

component of economic incentives contained in federal programs. An example is the Oregon 

Watershed Enhancement Board (OWEB), which provides grants for watershed council support, 

watershed assessment and monitoring, watershed action plan development, watershed restoration 

project design and implementation, and watershed education and outreach projects. A funding 

directory for Watershed Enhancement is contained on the OWEB website 

(www.oweb.state.or.us/directory/fundingintro.html).

e. Effectiveness of incentive-based programs 

The growth in voluntary compliance with incentive-based programs in agriculture indicates that 

they have been popular with agricultural producers. They have also been effective in diminishing 

agricultural impacts on environmental resources. Incentive-based tools take account of basic 

principles of economic behavior in ways that tend to lead to more effective environmental 
ISAB 2003-2 Tributary Habitat

39

protection. A disadvantage of the agriculturally based incentive programs is that they do not 

apply to all crops, to parcels of land below a minimum size, or to land outside of agricultural 

production. In areas of rapid population growth and urbanization, similar incentive-based 

programs are needed to encourage nonagricultural participation in tributary habitat restoration. 

The principle of using compensation to provide an economic incentive for restoration actions 

applies across sectors and scale of ownership.

V. Foundation for Habitat Recovery

Recent studies have shown that there are significant inherent differences in the productivity of 

salmon streams. Research at the Northwest Fisheries Science Center suggests that most of the 

salmon production for a subbasin originates from a relatively small number of watersheds or 

mainstem reaches (Pess et al. 2002; Feist et al. in review). Geology, elevation, topography, 

surface and subsurface hydrology, and vegetation all seem to be influential. Likewise, land and 

water uses affect productivity. While there have been many investigations of the influence of 

local and reach-scale environmental factors on habitat suitability for salmonids, the importance 

of landscape-scale features has received far less attention. Furthermore, stream productivity and 

biological diversity is known to vary with climate cycles and large natural disturbances. 

Providing productive conditions for all species of interest may depend upon watersheds 

exhibiting a variety of habitat conditions produced by variations in the underlying physical 

attributes of stream reaches and the process of disturbance and recovery. The unavoidable 

conclusion is that salmonid productivity varies widely in both space and time, and it will never 

be possible, or desirable, to maintain all streams in a condition considered optimum for one 

species of fish.

Understanding large-scale spatial and temporal patterns is important in subbasin planning 

because restoration strategies need to identify the best sites for protection as well as the best 

candidates for restoration – those sites that have a likelihood of becoming highly productive at 

some future time. Subbasin planners will not have the resources to do everything everywhere; 

difficult decisions will be needed to apply limited resources to the most cost-effective restoration 

projects. In preparing this report, the ISAB heard from scientists who have completed subbasin 

assessments that have been considered successful. These assessments included analyses of the 

Skagit River (Washington) Basin, Oregon coastal watersheds, and the Willamette River Basin. 

Although the objectives of the assessments varied, the approaches that contributed to their 

successful completion shared four common themes. 

First, the assessments began with a thorough, systematic inventory of conditions within the 

drainage system. Instead of gathering as much data as possible and then attempting to make 

sense of it all, the investigators first identified the information needed to address their questions 

and then set up data collection programs to acquire it. In some cases, the information had 

already been obtained by other organizations, so data compilation became a matter of putting it 

into the proper format for analysis.
ISAB 2003-2 Tributary Habitat

40

Second, successful assessments utilized measures of ecosystem functionality that extended 

beyond the stream reach scale to encompass whole watersheds. In each situation, rule sets were 

established that enabled investigators to make statements about the general ecological condition 

or “health” of an area based on combinations of environmental factors. This step was critical 

because it provided the context needed to assess the significance of habitat degradation at 

individual sites, as well as a means of judging the potential for effective restoration at different 

locations. The rules (decision criteria) for linking watershed condition with ecological health 

and biological productivity may have been derived from the knowledge of local experts, 

scientific literature, or correlations between landscape features and fish abundance, but in all 

cases these rules were made explicit in the analytical process. This was important to 

understanding and interpreting results.

Third, the distribution and habitat requirements of target species over the entire freshwater life 

cycle were overlain on spatially referenced maps of watershed condition to allow for a 

landscape-scale comparison of life-history needs and habitat status. This step required that the 

seasonal distribution of fishes be known or inferred from reasonable models, a step that usually 

required field verification. Superimposing fish population data on landscape condition allowed 

investigators to identify locations within subbasins where both fish populations and ecosystem 

processes were healthy, fish populations or habitat conditions were depressed, or where both 

populations and habitats were impaired. Streams having strong populations and intact 

ecosystems became candidate “stronghold” watersheds that could serve as sources from which 

wild fish populations could be rebuilt in restored tributaries. Locations having weak populations 

but relatively high quality habitats could be made more productive by providing more spawning 

fish through changes in harvest management or improved access to these sites. Locations where 

populations were relatively (or potentially) abundant, but habitats were impaired, could become 

excellent candidates for restoration. Tributaries where populations were weak and habitat was 

degraded were recognized as locations in which restoration would be expensive and risky, unless 

both fish population access and sustainable habitat quality issues were addressed.

Fourth, successful subbasin assessments all contained explicit strategies for restoration (e.g., 

rebuilding outward from core stronghold areas; reconnecting aquatic, riparian, and floodplain 

systems) and provided a means of forecasting future conditions based on projected human 

developments in the area of interest. The best example was the Willamette River Basin 

assessment (www.orst.edu/dept/press/WillRivrBas.html), in which the influence of alternative 

land development patterns on the distribution and abundance of high quality aquatic habitats was 

modeled. The Willamette River Basin analysis (Hulse et al. 2002) utilized different 

combinations of active and passive restoration techniques in its visual projections of future 

habitat scenarios. It serves as a model of how a thoughtful subbasin assessment can be used to 

effectively inform restoration decision-making in the Columbia River Basin.
ISAB 2003-2 Tributary Habitat

41

Tracking the effects of habitat improvement projects is critical to judging their success, but 

monitoring and evaluation can be time -consuming and costly. How can monitoring and 

evaluation be organized to make the most of scarce resources?

VI. Monitoring and Evaluation

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. Few evaluations of tributary habitat in the Columbia Rive r 

Basin meet these criteria. 

Monitoring has been categorized in a hierarchical sequence (Tier 1, Tier 2, or Tier 3) in the 

NMFS All-H document (Conservation of Columbia Basin Fish: Final Basinwide Salmon 

Recovery Strategy, Volume 1, Table 4) and repeated in the 2000 BiOp. For consistency, we 

discuss monitoring and make our recommendations in terms of this hierarchical sequence. The 

three levels are: trend monitoring (Tier 1), statistical monitoring (Tier 2), and research 

monitoring (Tier 3).

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, the temperature of water entering 

and leaving a habitat improvement site might be measured in August every third year for a 21-

year period. Tier 1 monitoring can be applied to individual project sites or to a large area. For 
ISAB 2003-2 Tributary Habitat

42

applications involving large areas, the ISAB anticipates that remotely sensed, spatially 

referenced data would be used. For example, long-term trend monitoring of changes in riparian 

and other terrestrial habitat could be accomplished with aerial photography or LandSat imagery. 

In general, Tier 1 monitoring does not establish cause and effect relationships and does not 

provide statistically inductive inferences to larger areas or time periods. However, Tier 1 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 statistical analysis at the scale 

studied. However, many habitat attributes cannot be derived from remotely sensed data and 

measurement errors may limit the usefulness of remote sensing for detecting changes.

Tier 2 (statistical) monitoring provides statistical inferences to parameters in a study area as 

measured by certain data collection protocols. These inferences extend to larger areas and longer 

time periods than the sample. The inferences require both probabilistic selection of study sites 

and repeated visits over time. A good example is the process used to estimate abundance of 

spawning coho salmon coastal Oregon watersheds, described in the Oregon Plan for Salmon and 

Watersheds Monitoring Program (www.nwr.noaa.gov/pcsrf/Moore/). This method utilizes a 

rigorous design for probabilistic site selection to ensure that the locations where spawning coho 

salmon are enumerated are representative of all stream reaches. Evaluation of the effectiveness 

of habitat improvement projects will require Tier 2 statistical monitoring for some parameters, 

e.g., the number of redds in a watershed.

Tier 3 (experimental research) monitoring is often required to establish cause and effect 

relationships between management actions and 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. 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 include 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, and projects to evaluate the effectiveness 

of various land restoration or management techniques.

The value of research, monitoring and evaluation efforts is greatly enhanced if these elements are 

integrated. Tier 1 and Tier 2 monitoring results will help define the key issues that should be 

addressed with a more intensive Tier 3 effort. Results of the Tier 3 research will identify which 

habitat attributes are most informative for Tier 1 and 2 efforts. Implementing Tier 1 and 2 

monitoring without a corresponding Tier 3 effort would not provide conclusive information 

about the efficacy of various restoration approaches. However, without the more extensive Tier 

1 and 2 monitoring, there would a great deal of uncertainty regarding the extension of results 

from the geographically focused Tier 3 monitoring to sites not being studied. The actions listed 

below are the essential elements of a research, monitoring and evaluation plan to evaluate 

tributary habitat restoration.

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

obtained from sources such as aerial photography or satellite imagery. Changes in 
ISAB 2003-2 Tributary Habitat

43

terrestrial and aquatic habitat and land use should be monitored at the largest possible 

spatial scale using the “finest grained” data available.

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

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

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

common protocols for cost-effective “on the ground” or remotely sensed data collection 

of a limited number of indicator variables. Measurement of indicator variables should be 

done 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 John Day, Upper Salmon, and Wenatchee Subbasins (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 throughout the Columbia River Basin. 

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

Potential predictor variables include not only physical habitat variables, e.g., flow, 

temperature, etc., but also habitat recovery actions. The empirical models can be used to 

evaluate the relative importance of physical factors and habitat improvements and to 

predict abundance or presence-absence throughout major sections of a subbasin (Manly 

et al. 2002). 

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

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

identified in Tiers 1 and 2 monitoring. An extensive, long term status monitoring 

program can identify important and unexplained trends and changes. Tier 1 trend 

monitoring and Tier 2 statistical monitoring provide indications of trend and change in 

indicator variables. But because Tiers 1 and 2 monitoring efforts rely on low-intensity 

data collection over large areas, the reason for certain trends and changes is not well 

understood. For example, the status monitoring may indicate that a major increase in 

juvenile fish production occurred between 2010 and 2020 that cannot be attributed to 

habitat changes derived from Tier 1 or 2 monitoring. Why? A population of bull trout is 

detected in an area where modeling results based on current knowledge indicate they 

should not exist. Why? Answering these questions requires a more thorough 

understanding of the ecological processes governing fish population responses to habitat 

condition than can be obtained through Tiers 1 and 2 monitoring. As understanding the 

“why?” is often critical in identifying habitat protection and restoration priorities, Tier 3 

research monitoring should be included as part of the monitoring strategy.

There are two general approaches to Tier 3 field research to evaluate the effectiveness of 

tributary habitat restoration activities (i.e., to determine cause and effect relationships). The first 

approach is consistent with that promoted by the Action Agencies (Bonneville Power 

Administration (BPA), Corps of Engineers (Corps), and Bureau of Reclamation (BOR)), and 

NMFS in their RME Plan (see the BPA Draft Report “Research, Monitoring & Evaluation, for 

the NMFS 2000 FCRPS Biological Opinion”). In this approach a large number of pairs of sites 
ISAB 2003-2 Tributary Habitat

44

(e.g., watersheds) might be identified where the primary difference between members of each 

pair is that one has a certain habitat improvement (e.g., stream fencing to exclude livestock) and 

the other does not. Future management actions 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 (e.g., estimates of spawners entering the watersheds and smolts leaving). 

The design of such a study will be similar to that used in the large scale “treatment-control” 

observational Idaho Supplementation Study (ISS). General conclusions from this approach may 

be obtained using regression-correlation type analyses provided that a sufficiently large number 

of treatment and control sites are included in the study. 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 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 intensive research monitoring in a small number of watersheds 

in each subbasin, an approach the state of Washington has termed Intensive Watershed 

Monitoring (IWM). This approach is similar to the “Top-Down Monitoring” described in the 

RME plan (BPA Draft Report “Research, Monitoring & Evaluation, for the NMFS 2000 FCRPS 

Biological Opinion”). The basic premise of IWM is that cause and 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 understand 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 draw inferences about a very large area by monitoring a large number of pairs of sites over the 

target region. Obviously, the inferences 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, logistical difficulties in dealing with a large number of sites in a large area over a long 

time period, difficulty of locating suitable control (untreated) sites, and the ability to monitor 

only one factor at a time.

The second approach (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 studied watersheds. 

Inferences concerning applicability of the conclusions to large regions are based on professional 
ISAB 2003-2 Tributary Habitat

45

judgment. The primary disadvantages are cost, 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, we recommend that the IWM approach be used 

to begin to develop a better understanding of the causes of biological response to tributary 

habitat actions. The IWM 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. Research at 

these sites expanded over time to include water chemistry and biological responses to logging. 

Changes in the regulatory framework of forest management practices nationwide have been 

based on studies conducted at experimental watersheds such as the H.J. Andrews Experimental 

Forest in Oregon, the Hubbard Brook Experimental Forest in New Hampshire, and the Coweeta 

Experimental Forest in North Carolina.

The success of these efforts led to a number of intensive watershed monitoring efforts in the 

Pacific Northwest to evaluate the response of salmonid fishes to forest practices. The Alsea 

Watershed Study, which was initiated in the early 1960s and continues today, examined the 

response of coho salmon and cutthroat trout to various logging methods in three small 

watersheds in the Oregon Coast Range. Early results from this study provided some of the 

impetus for the revision of laws governing forest practices in Oregon and Washington in the 

early 1970s. In the 1970s an ambitious watershed-level project was initiated at Carnation Creek 

on Vancouver Island, British Columbia that evaluated the response of salmonids to logging of an 

old-growth forested watershed. The results of this study led to a revision of the forestry code for 

British Columbia and also influenced revisions of forest practice rules in other areas of the 

Pacific Northwest. Research on trophic effects of salmon and trout at the Keogh River on 

Vancouver Island have provided a vastly improved appreciation for the importance of nutrients 

and trophic processes in supporting salmon productivity (Ward and Slaney 1988). 

IWM 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. 

Evaluating biological responses is complicated, requiring an understanding of how various 

management actions interact to affect habitat conditions and how the ecosystem responds to 

these habitat changes. The response of fish is dependent on the relative availability of the habitat 

types that change through the period of freshwater rearing (Table 1), and the manner in which 

these habitat types are influenced by application of a management action. Additionally, the 

relative influence of each habitat type on fish survival changes from year to year due to 

variations in weather and flow, the abundance of fish spawning within the watershed, and other 

factors. For example, smolt production may be limited by spawning habitat during years when 

scouring flood flows occur during incubation and greatly decrease egg survival. When more 

benign flow conditions occur during egg incubation, smolt production may be influenced more 

by the availability of food during spring and summer, or by the availability of adequate winter 

habitat. Untangling the importance of various factors and predicting how these factors respond to 

land use actions or restoration efforts can only be accomplished with an intensive monitoring 

approach.
ISAB 2003-2 Tributary Habitat

46

A before vs. after, control vs. impact (BACI) study design often is well suited to address many of 

questions amenable to IWM. This type of design enhances the ability to differentiate treatment 

responses from responses due to factors not directly affected by the treatments (e.g., weather). 

This approach also implies that IWM efforts must include two or more watersheds, with at least 

one serving as a reference site where no experimental treatments are implemented during the 

study. Obviously, confidence in the generality of the conclusions is enhanced with random 

assignment of treatment and control status to the watersheds although this may not be practical in 

many applications. A calibration period prior to applying treatments is required to determine 

how the reference and treatment watershed compare in the key response variables prior to any 

habitat manipulation. The length of time required to develop this baseline will vary among 

watersheds. However, recent comparisons of adult salmon densities among multiple sites 

suggests that relative abundance, i.e., concordance of abundance patterns, is fairly consistent 

(Pess et al. 2002; Feist et al. in review), suggesting that a fairly short calibration period may 

suffice. The calibration period for sites with records of spawner abundance and smolt output 

would be much shorter than for watersheds where these data have not been collected. 

Treated and untreated sites can be paired at a multiple spatial scales within the IWM design, with 

the scale dependent on the question being addressed. In fact, reference sites for some reach-level 

projects could be located within the treated watershed. These reference sites would consist of 

streams comparable to the location where a restoration action is applied but where no habitat 

manipulation would occur during the period of evaluation. Questions that can be addressed at 

this finer scale include life-history specific biological responses or physical habitat responses to 

management actions. For evaluations of treatment effects at the scale of an entire watershed, a 

comparison with a nearby watershed that is not undergoing treatment is required. Therefore, the 

IWM approach does require sufficient management coordination to ensure that reference sites 

remain untreated through the duration of the study. This does not imply that any management 

activities in the reference watershed will compromise the integrity of the study. The validity of 

the study will be maintained as long as other management activities not directly related to the 

restoration projects being evaluated are similar at the reference and treated locations. For 

example, the effectiveness of restoration actions can be evaluated in watersheds being actively 

managed for commodity production provided that the type and intensity of agriculture or forest 

management activities in the treated and reference watersheds are comparable.

Fundamental to the IWM approach is the establishment of a set of overarching objectives that 

provide the context for the application of ecological restoration and to which individual projects 

can easily be related. As the goal of most habitat restoration efforts for salmon and trout is to 

improve the survival of fish through their entire period of freshwater residency, the objectives 

should relate to this outcome. Individual restoration projects should collectively contribute to the 

attainment of the objectives. To determine whether this is occurring, projects applied at the 

reach scale should be nested within, and clearly related to, the watershed-level objectives for 

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

among projects that is critical to assessing the efficacy of the restoration efforts. 

Implementation of intensive watershed monitoring should begin with an assessment of the 

current condition of the watershed. The assessment will provide some indication of the factors 

that might be influencing fish production in the watershed. For example, if the watershed 

assessment identifies a lack of large wood in streams, a testable hypothesis could be that lack of 
ISAB 2003-2 Tributary Habitat

47

pool habitat is limiting available rearing space. An experiment to evaluate this hypothesis might 

involve deliberate addition of wood to channel segments and measurement of the change in pool 

habitat and summer and winter rearing populations at these sites relative to populations at 

untreated reaches (reach-level evaluation). However, even if this analysis indicates an increase 

in the number of fish rearing at treated sites, it does not imply that wood addition projects will 

boost the overall productivity of fish populations. In order to determine whether the wood 

addition would actually change ecosystem capacity, rather than simply attracting fish to treated 

reaches that would have reared elsewhere, measures of watershed-level productivity are required. 

To evaluate watershed-scale responses to restoration, the treatments (e.g., wood additions) would 

need to be applied at enough locations that population responses can be detected. If the initial 

hypothesis is correct and pool habitats do have a controlling influence on fish production in the 

watershed, the number of smolts produced or survival rate from egg to smolt should increase. 

The number of treatment sites required to detect a watershed-level response can be evaluated as 

wood-addition projects are successively implemented. Due to the expense and labor involved in 

wood additions to channels, application of treatments will occur over a period of years. Small 

increases in density of rearing fish at the reach level would indicate that watershed-scale 

responses would only be discernible when a large number of sites had been so treated. A very 

dramatic density response to restoration at the reach level might suggest that changes in 

populations could be measurable with treatment of fewer sites. 

The minimum information required to evaluate watershed-level responses is numbers of 

spawning adult fish and smolt emigration. Counting fences or weirs at the downstream end of a 

watershed provide the most accurate measure of adult salmon returning to spawn (Botkin et al. 

2000). However, weirs are labor intensive and provide no information about spawner 

distribution within the watershed. Counts of adults on spawning grounds or mark-recapture 

estimates of spawning fish or carcasses conducted during the time of spawning is not as accurate 

as counts at weirs in determining breeding population size, but does provide information on 

distribution. Application of Tier 2 probabilistic techniques of reach selection, and frequent, 

consistent surveys of each reach are required to provide accurate spawner estimates. 

An improved statistical approach known as the USEPA Environmental Monitoring and 

Evaluation Program (EMAP) methods has been developed and implemented on the Oregon coast 

for coho salmon. Smolts leaving the watershed are sampled with traps, including fences or weirs 

that capture all emigrating smolts (although fences may become inoperable at high flows), or 

devices that capture a portion of the fish (scoop or screw traps). Partial sampling traps are easier 

to maintain and can be utilized in channels too large for weirs; however, these types of devices 

require frequent calibration to determine the proportion of smolts being captured. With adult and 

smolt data it is possible to calculate the survival rate of fish from spawning through smolting. 

The objective of nearly all salmon habitat restoration efforts is to increase this value. Regardless 

of the methods used to estimate adult salmon and smolt abundance, these measures are critical to 

any evaluation of fish response to tributary habitat restoration and should be included at all 

intensively monitored sites. 

Augmenting the smolt and spawner data with information on egg survival and the distribution, 

abundance, and survival of juvenile salmon from emergence through smolting can enable salmon 

response to individual restoration projects to be estimated at the scale of whole watersheds. 
ISAB 2003-2 Tributary Habitat

48

Capturing fish seasonally by electrofishing, seining or trapping at multiple locations across a 

watershed enables an estimate of species distribution, abundance, growth rate, and age class 

composition. If handling fish is not permitted because of ESA considerations, one alternative is 

a visual survey over a broad area (Hankin and Reeves 1988). Although this method does not 

provide data on fish species and size that are as accurate as methods that involve capturing fish, 

it is rapid and permits sampling the entire stream network in 6th-code HUC watersheds. A 

combination of the two approaches (capture and visual sampling), including a complete survey 

coupled with nested subsamples at selected sites where fish are captured and measured, would 

yield the most complete information.

Tagging salmon captured during stream sampling and subsequent recovery of tagged fish at 

smolt traps can provide additional information on survival of fish rearing in different parts of the 

watershed as well as the effectiveness of individual restoration projects. Differences in survival 

among reaches or habitat types indicates key mortality factors operating in the river, and aids in 

the identification of restoration efforts likely to have the greatest effect on salmon populations.

Collection of fish population data can be coupled with information on changing habitat 

conditions and climate. Salmonids are very sensitive to variations in flow, temperature, and 

other factors that are not directly influenced by restoration treatments, and interpretation of data 

can be enhanced by collection of this information. At a minimum, a recording flow gauge is 

required at the mouth of the reference and treatment watersheds. In addition, if some of the 

restoration efforts result in altered flow patterns, secondary flow gauges should be installed at 

locations where these efforts are undertaken. Weather stations recording precipitation and air 

temperature should be located near the downstream end of the watershed. Water temperature 

should be recorded year round at each gauging station and at all sites where the objective of a 

restoration action is to alter water temperature. Instruments to record flow, weather and water 

temperature information have improved dramatically in the last decade and costs have decreased. 

However, maintaining the instruments and the environmental databases are labor intensive. 

Thus, this type of sampling is well suited to the intensive watershed monitoring approach.

Habitat measurements should be collected concurrently with juvenile fish sampling; these data 

are especially important at sites where restoration projects will be implemented. Physical 

characteristics of the channel (e.g., pools and riffles), riparian vegetation, sediment in pools and 

spawning gravel, water quality (e.g., temperature, dissolved oxygen, and turbidity), and nutrient 

levels, are examples of habitat features that may be relevant to restoration efforts. Projects 

designed to increase pool habitat will focus on the physical attributes of the channel, while 

measures of nutrient levels, and primary and secondary production, would be appropriate 

measures of a salmon carcass project. The expense and effort needed to obtain the data 

necessary for evaluating the response of salmonids to habitat restoration is considerable, and this

supports an approach of focusing intensive monitoring efforts on a relatively few locations. It is 

likely to require several fish generations to get statistically supported answers to questions about 

the effectiveness of habitat restoration. However, by implementing these evaluations with clear 

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

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

obtained that will greatly improve our ability to promote salmon recovery.
ISAB 2003-2 Tributary Habitat

49

References

Annear, T. C., and A. L. Conder. 1984. Relative bias of several instream flow methods. North 

American Journal of Fisheries Management 4:531-539.

Beechie, T. J., B. D. Collins, and G. R. Pess. 2001. Holocene and recent geomorphic processes, 

land use, and fish habitat in two Puget Sound watersheds. Pages 37-54 in J. M. Dorva, D. 

R. Montgomery, B. Palcsak, and F. Fitzpatrick (eds.) Geomorphic processes and riverine 

habitat. American Geophysical Union, Washington, D. C. 

Benda, L. E., D. J. Miller, T. Dunne, G. H. Reeves, and J. K. Agee. 1998. Dynamic landscape 

systems. Pages 261-288 in R. J. Naiman and R. E. Bilby, editors. River ecology and 

management. Springer, New York, N.Y., USA.

Berman, C., and T. P. Quinn. 1991. Behavioural thermoregulation and homing by spring chinook 

salmon, Oncorhynchus tshawytscha Walbaum, in the Yakima River. Journal of Fish

Biology 39:301-312.

Beschta, R. L., R. E. Bilby, G. W. Brown, L. B. Holtby, and T. D. Hofstra. 1987. Stream 

temperature and aquatic habitat: fisheries and forestry interactions. Pages 191-232 in E. 

O. Salo and T. W. Cundy, editors. Streamside management: forestry and fishery

interactions. Institute of Forest Resources Contribution Number 57. University of

Washington, Seattle.

Bilby, R. E. 1984. Characteristics and frequency of cool-water areas in a western Washington 

stream. Journal of Freshwater Ecology 2:593-602.

Bilby, R. E., B. R. Fransen, P. A. Bisson, and J. K. Walter. 1998. Response of juvenile coho 

salmon (Oncorhynchus kisutch) and steelhead (Oncorhynchus mykiss) to the addition of 

salmon carcasses in two streams in southwestern Washington, U.S.A. Canadian Journal 

of Fisheries and Aquatic Sciences 55:1909-1918.

Bisbal, G.A. 2001. Conceptual design of monitoring and evaluation plans for fish and wildlife in 

the Columbia River ecosystem. Environmental Management 28(4): 433-453.

Bisson, P. A., J. L. Nielsen, and J. W. Ward. 1988. Summer production of coho salmon stocked 

in Mount St. Helens streams 3-6 years after the 1980 eruption. Transactions of the 

American Fisheries Society 117:322-335.

Bisson, P. A., G. H. Reeves, R. E. Bilby, and R. J. Naiman. 1997. Watershed management and 

Pacific salmon: desired future conditions. Pages 447-474 in D. J. Stouder, P. A. Bisson, 

and R. J. Naiman, editors. Pacific salmon and their ecosystems: status and future options. 

Chapman and Hall, New York.

Bjornn, T. C., and D. W. Reiser. 1991. Habitat requirements of salmonids in streams. American 

Fisheries Society Special Publication 19:83-138.

Botkin, D. B., D. L. Peterson, and J. M. Calhoun, technical editors. 2000. The scientific basis for 

validation monitoring of salmon for conservation and restoration plans. Olympic Natural 

Resources Center Technical Report. University of Washington, Olympic Natural

resources Center, Forks, Washington, USA. 82 p.
ISAB 2003-2 Tributary Habitat

50

Bovee, K. D., and T. Cochnauer. 1977. Development and evaluation of weighted criteria

probability of use curves for instream flow assessments: fisheries. Instream Flow

Information Paper Number 3, Cooperative Instream Flow Service Group, Fort Collins, 

Colorado.

Chapman, D. W. 1966. Food and space as regulators of salmonid populations in streams. 

American Naturalist 100:345-357.

Chapman, D. W. 1988. Critical review of variables used to define effects of fines in redds of 

large salmonids. Transactions of the American Fisheries Society 117:1-21.

Collins, B. D. and D. R. Montgomery. 2001. Importance of archival and process studies to 

characterizing pre-settlement riverine geomorphic processes and habitat in the Puget 

lowlands. Pages 227-243 in J. M. Dorva, D. R. Montgomery, B. Palcsak, and F.

Fitzpatrick (eds.) Geomorphic processes and riverine habitat. American Geophysical

Union, Washington, D. C. 

Collins, B. D., D. R. Montgomery, and A. J. Sheikh. 2003. Reconstructing the historic river 

landscape of the Puget lowland. Pages 79-128 in D. R. Montgomery, S. Bolton, D. B. 

Booth and L. Wall (eds.) Restoration of Puget Sound Rivers. University of Washington 

Press, Seattle and London.

DEQ (Department of Environmental Quality). 2002. Oregon Water Quality Program.

[www.deq.state.or.us/wq/] 

EPA (Environmental Protection Agency) 2001. The United States experience with economic 

incentives to protect the environment. EPA-240-R-01-011, January. National Center for 

Environmental Economics, Office of Policy, Economics, and Innovation, Office of the 

Administrator, U.S. Environmental Protection Agency, Washington, DC 20460.

Erickson, W.P, R. Nielson, R. Skinner, B. Skinner, and J. Johnson. 2003. Applications of

resource selection modeling using unclassified Landsat TM. Proceedings of the 2003 

International Conference on Resource Selection. Omnipress, Madison, Wisconsin.

Everest, F.H., R.L. Beschta, J.C. Scrivener, K V. Koski, J.R. Sedell, and C.J. Cederholm. 1987. 

Fine sediment and salmonid production: a paradox. Pages 98-142 in E.O. Salo and T.W. 

Cundy, editors. Streamside management: forestry and fishery interactions. Contribution 

Number 57, Institute of Forest Resources, University of Washington, Seattle,

Washington, USA.

Fausch, K. D., C. L. Hawkes, and M. G. Parsons. 1988. Models that predict standing crop of 

stream fish from habitat variables: 1950-85. USDA Forest Service General Technical 

Report, PNW-213, Pacific Northwest Experiment Station, Portland, Oregon, USA. 52 p.

Feist, B. E., E. A. Steel, G. R. Pess, and R. E. Bilby. in review. The influence of scale on salmon 

habitat restoration priorities. Animal Conservation.

Fox, M. J. 2001. A new look at the quantities and volumes of instream wood in forested basins 

within Washington State. M.S. thesis, University of Washington, Seattle, WA. 239 p.

Frissell. C. A., and R. K. Nawa. 1992. Incidence and causes of physical failure of artificial 

habitat structures in streams of western Oregon and Washington. North American Journal 

of Fisheries Management 12:182-197.
ISAB 2003-2 Tributary Habitat

51

Frissell, C. A., and S. C. Ralph. 1998. Stream and watershed restoration. Pages 599-624 in R. J. 

Naiman and R. E. Bilby, editors. River ecology and management: lessons from the 

Pacific Coastal Ecoregion. Springer-Verlag, New York, N.Y.

Gregory, S. V. 1980. Effects of light, nutrients, and grazing on periphyton communities in

streams. Ph.D. thesis, Oregon State University, Corvallis, Oregon. 151 p.

Ham, K. D., and T. N. Pearsons. 2000. Can reduced salmonid population abundance be detected 

in time to limit management impacts? Canadian Journal of Fisheries and Aquatic

Sciences 57(1):17-24.

Hankin, D. G., and G. H. Reeves. 1988. Estimating total fish abundance and total habitat area in 

small streams based on visual estimation methods. Canadian Journal of Fisheries and 

Aquatic Sciences 45:834-844.

Hartman, G. F., and J. C. Scrivener. 1990. Impacts of forestry practices on a coastal stream 

ecosystem, Carnation Creek, British Columbia. Canadian Bulletin of Fisheries and 

Aquatic Sciences 223: 148 p.

Hilborn, R., and J. Winton. 1993. Learning to enhance salmon production: lessons from the 

Salmonid Enhancement Program. Canadian Journal of Fisheries and Aquatic Sciences 

50:2043-2056.

House, R. A., and P. L. Boehne. 1985. Evaluation of instream enhancement structures for 

salmonid spawning and rearing in a coastal Oregon stream. North American Journal of 

Fisheries Management 5:283-295.

Hulse, D., S. Gregory, and J. Baker, editors. 2002. Willamette River Basin planning atlas:

trajectories of environmental and ecological change. Oregon State University Press, 

Corvallis, Oregon.

Independent Scientific Group (ISG). 2000. Return to the river 2000: restoration of salmonids 

fishes in the Columbia River ecosystem. Northwest Power Planning Council document 

2000-12, Northwest Power Planning Council, Portland, Oregon. 538 p.

Kondolf, G. M., E. W. Larsen, and J. G. Williams. 2000. Measuring and modeling the hydraulic 

environment for assessing instream flows. North American Journal of Fisheries

Management 20:1016-1028.

Manly, B.F.J., L.L. McDonald, D.L. Thomas, T.L. McDonald, and W.P. Erickson. 2002. 

Resource selection by animals: Statistical design and analysis for field studies, Second 

Edition. Kluwer Academic Publishers, Dordrecht. 221 pp.

Mathur, D., W. H. Bason, E. J. Purdy, Jr., and C. A. Silver. 1985. A critique of the Instream 

Flow Incremental Methodology. Canadian Journal of Fisheries and Aquatic Sciences 

42:825-831.

Megahan, W. F., J. P. Potyondy, and K. A. Seyedbagheri. 1992. Best management practices and 

cumulative effects from sedimentation in the South fork Salmon River: an Idaho case 

study. Pages 401-414 in R. B. Naiman, editor. Watershed management: balancing 

sustainability and environmental change. Springer-Verlag, New York, N.Y.
ISAB 2003-2 Tributary Habitat

52

Milhous, R. T., D. L. Wegner, and T. Waddle. 1981. User's guide to the physical habitat 

simulation system. Instream Flow Information Paper No. 11, FWS/OBS-81/43, U.S. Gov. 

Printing Office, Washington, D.C.

Mobrand Biometrics, Inc. 1999. The EDT method. Northwest Power Planning Council, Portland, 

Oregon (see www.edthome.org/sbp/default.htm).

National Oceanic and Atmospheric Administration, National Marine Fisheries Service (NMFS). 

2000. Conservation of Columbia Basin fish: all-H paper. US Department of Commerce, 

National Oceanic and Atmospheric Administration, National Marine Fisheries Service, in 

consultation with the Federal Caucus, Portland, Oregon. 3 vol.

National Research Council (NRC). 1992. Restoration of aquatic ecosystems. National

Academy Press, Washington, D.C. 552 p.

National Research Council (NRC). 1996. Upstream: salmon and society in the Pacific

Northwest. National Academy Press, Washington, D.C.

Pess, G. R., D. R. Montgomery, E. A. Steel, R. E. Bilby, B. E. Feist, and H. M. Greenberg. 

2002. Landscape characteristics, land use, can coho salmon (Oncorhynchus kisutch) 

abundance, Snohomish River, Wash., U.S.A. Canadian Journal of Fisheries and Aquatic 

Sciences 59:613-623.

Poff, N. L., and J. V. Ward. 1990. Physical habitat template of lotic ecosystems: recovery in the 

context of historical pattern of spatial heterogeneity. Environmental Management 

14:629-645.

Poole, G. C., Frissell, C. A., and Ralph, S. C. 1997. In-stream habitat unit classification; 

inadequacies for monitoring and some consequences for management. Water Resources 

Bulletin 33:879-896.

Quigley, T. M., and S. J. Arbelbeide, technical editors. 1997. An assessment of ecosystem 

components in the interior Columbia basin and portions of the Klamath and Great Basins: 

volume 3. General Technical Report PNW-GTR-405, United States Department of

Agriculture, Forest Service, Pacific Northwest Research Station, Portland, Oregon. 

Pages 1058-1713.

Reeves, G. H., L. E. Benda, K. M. Burnett, P. A. Bisson, and J. R. Sedell. 1995. A disturbancebased ecosystem approach to maintaining and restoring freshwater habitats of

evolutionarily significant units of anadromous salmonids in the Pacific Northwest.

American Fisheries Society Symposium 17:334-349.

Reeves, G. H., P. A. Bisson, and J. M. Dambacher. 1998. Fish Communities. Pages 200-234 in: 

R. J. Naiman and R. E. Bilby, editors. River ecology and management. Springer-Verlag, 

New York.

Reeves, G. H., K. M. Burnett, and S. V. Gregory. 2002. Fish and aquatic ecosystems of the 

Oregon Coast Range. Pages 68-98 in: S. D. Hobbs, J. P. Hayes, R. L. Johnson, G. H. 

Reeves, T. A. Spies, J. C. Tappeiner II, and G. E. Wells, editors. Forest and stream 

management in the Oregon Coast Range. Oregon State University Press, Corvallis,

Oregon.
ISAB 2003-2 Tributary Habitat

53

Reeves, G. H., F. H. Everest, and T. E. Nickelson. 1989. Identification of physical habitats 

limiting the production of coho salmon in western Oregon and Washington. United States 

Forest Service, General Technical Report PNW-GTR-245, Pacific Northwest Research 

Station, Portland, Oregon, USA.

Reeves, G. H., D. B. Hohler, B. E. Hansen, F. H. Everest, J. R. Sedell, T. L. Hickman, and D. 

Shively. 1997. Fish habitat restoration in the Pacific Northwest: Fish Creek of Oregon. 

Pages 335-359 in J. E. Williams, C. A. Wood, and M. P. Dombeck, editors. Watershed 

restoration: principles and practices. American Fisheries Society, Bethesda, Maryland.

Reice, S. R., R. C. Wissmar, and R. J. Naiman. 1990. Disturbance regimes, resilience, and 

recovery of animal communities and habitats in lotic ecosystems. Environmental

Management 14(5):647-659.

Rieman, B. E. and Myers, D. L. 1997. Use of redd counts to detect trends in bull trout 

populations. Conservation Biology 11(4):1015-1018.

Sedell, J. R., and R. L. Beschta. 1991. Bringing back the "bio" in bioengineering. American 

Fisheries Society Symposium 10:160-175.

Shirvell, C. S. 1989. Habitat models and their predictive capability to infer habitat effects on 

stock size. Pages 173-179 in C. D. levings, L. B. Holtby, and M. A. Anderson, editors. 

Proceedings of the National Workshop on Effects of habitat Alteration on Salmonid 

Stocks. Canadian Special Publication in Fisheries and Aquatic Sciences 105. 199 p.

Shogren, J. F. and J. Tschirhart. 2001. Protecting endangered species in the United States. 

Cambridge University Press, Cambridge, Massachusetts.

Shortreed, K. S., A. C. Costella, and J. G. Stockner. 1984. Periphyton biomass and species 

composition in 21 British Columbia lakes: seasonal abundance and response to wholelake nutrient additions. Canadian Journal of Botany 62:1022-1031.

Slaney, P. A., C. J. Perrin, and B. R. Ward. 1986. Nutrient concentration as a limitation to 

steelhead smolt production in the Keogh River. Proceedings of the Annual Conference of 

the Western Association of Fish and Wildlife Agencies 66:146-155.

Steel, E. A., B. E. Feist, D. Jensen, G. R. Pess, M. Sheer, J. Brauner, and R. E. Bilby. in prep. 

Using large-scale habitat models to understand steelhead (Oncorhynchus mykiss) 

distribution and prioritize barrier removals in the Willamette basin, OR, U.S.A.

Thurow, R. F., D. C. Lee, and B. E. Rieman. 1997. Distribution and status of seven native 

salmonids in the interior Columbia River Basin and portions of the Klamath River and 

Great Basins. North American Journal of Fisheries Management 17:1094-1110.

USDA (United States Department of Agriculture). 2000. Agricultural resources and

environmental indicators, 2000. Economic Research Service, Resource Economics

Division, U.S. Department of Agriculture, Washington, D.C.

USDA (United States Department of Agriculture). 2002a. Economic Research Service. Briefing 

Room: Conservation and Environmental Policies. 

[www.ers.usda.gov/briefing/ConservationandEnvironment/overview.htm]

USDA (United States Department of Agriculture). 2002b. Natural Resources Conservation 

Service. Farm Bill 2002. [www.nrcs.usda.gov/programs/farmbill/2002/index.html]
ISAB 2003-2 Tributary Habitat

54

USDA (United States Department of Agriculture). 2002c. U.S. Forest Service Challenge CostShare Agreements. [www.fs.fed.us/im/directives/fsh/1509.11/1509.11,60.txt]

USDA (United States Department of Agriculture) Forest Service, USDI (United States 

Department of the Interior) Bureau of Land Management. 1995. Environmental 

assessment for the implementation of interim strategies for managing anadromous fishproducing watersheds in eastern Oregon and Washington, Idaho, and portions of 

California. United States Department of Agriculture, Forest Service, Washington D.C.

USDI (United States Department of the Interior). 2002.U.S. Fish and Wildlife Service Challenge 

Cost Share Programs. [policy.fws.gov/055fw6.html]

Walters, C. J., J. S. Collie, and T. Webb. 1988. Experimental designs for estimating transient 

responses to management disturbances. Canadian Journal of Fisheries and Aquatic 

Sciences 45:530-538.

Walters, C. J., J. S. Collie, and T. Webb. 1989. Experimental designs for estimating transient 

responses to habitat alteration: is it practical to control for environmental interactions? 

Pages 13-20 in C. D. Levings, L. B. Holtby, and M. A. Anderson, editors. Proceedings of 

the National Workshop on Effects of Habitat Alteration on Salmonid Stocks. Canadian 

Special Publication of Fisheries and Aquatic Sciences 105.

Ward, B. R. 2000. Declivity in steelhead (Oncorhynchus mykiss) recruitment at the Keogh River 

over the past decade. Canadian Journal of Fisheries and Aquatic Sciences 57:298-306.

Ward, B. R., and P. A. Slaney. 1988. Life history and smolt-to-adult survival of Keogh River 

steelhead trout (Salmo gairdneri) and the relationship to smolt size. Canadian Journal of 

Fisheries and Aquatic Sciences 45: 1110-1122.

Warren, C. E., J. H. Wales, G. E. Davis, and P. Doudoroff. 1964. Trout production in an 

experimental stream enriched with sucrose. Journal of Wildlife Management 28:617-660.

Welty, J. J. T. Beechie, K. Sullivan, D. M. Hyink, R. E. Bilby, C. Andrus, G. Pess. 2002. 

Riparian Aquatic Interaction Simulator (RAIS): a model of riparian forest dynamics for 

the generation of large woody debris and shade. Forest Ecology and Management 162: 

299-318.

Wiebe, K., A. Tegene, and B. Kuhn. 1996. Partial interests in land: policy tools for resource use 

and conservation. ERS Agricultural Economic Report Number 744, United States 

Department of Agriculture, Washington, D.C.

Wimberly, M. C., T. A. Spies, C. J. Long, and C. Whitlock. 2000. Simulating historical 

variability in the amount of old forests in the Oregon Coast Range. Conservation 

Biology 14(1):167-180.

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