United States

Department of

Agriculture

Forest Service

Pacific Northwest

Research Station

General Technical

Report

PNW-GTR-625

January 2005

A Review of Protocols for

Monitoring Streams and

Juvenile Fish in Forested

Regions of the Pacific

Northwest

Scott A. Stolnack, Mason D. Bryant, and Robert C. Wissmar
The Forest Service of the U.S. Department of Agriculture is dedicated to the

principle of multiple use management of the Nation’s forest resources for sustained yields of wood, water, forage, wildlife, and recreation. Through forestry

research, cooperation with the States and private forest owners, and management

of the National Forests and National Grasslands, it strives—as directed by Congress—to provide increasingly greater service to a growing Nation.

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USDA is committed to making the information materials accessible to all USDA

customers and employees

Authors

Scott A. Stolnack is a research associate and Robert C. Wissmar is a professor,

School of Aquatic and Fishery Sciences, University of Washington, P.O. Box

355020, Seattle, WA 98195; and Mason D. Bryant is a research fisheries biologist,

U.S. Department of Agriculture, Pacific Northwest Research Station, Forestry

Sciences Laboratory, 2770 Sherwood Lane, Suite 2A, Juneau, AK 99801-8545.
Abstract

Stolnack, Scott A.; Bryant, Mason D.; Wissmar, Robert C. 2005. A review of

protocols for monitoring streams and juvenile fish in forested regions of the

Pacific Northwest. Gen. Tech. Rep. PNW-GTR-625. Portland, OR: U.S. Department of Agriculture, Forest Service, Pacific Northwest Research Station.

36 p.

This document reviews existing and proposed protocols used to monitor stream

ecosystem conditions and responses to land management activities in the Pacific

Northwest. Because of recent work aimed at improving the utility of habitat survey

and fish abundance assessment methods, this review focuses on current (since

1993) monitoring efforts that assess stream habitat conditions and juvenile fish use.

It does not focus on protocols specifically intended to monitor trends in fish

populations for salmon recovery efforts, other fish life-history stages (e.g., salmonid smolt monitoring or spawner surveys), or approaches designed to monitor

water quality or sources of pollution. We provide an overview of agency monitoring protocols, adaptive management, and types of monitoring, and briefly review

the core habitat characteristics thought to be most sensitive to forest management

practices. Finally, we summarize a selection of protocols in use in the Pacific

Northwest in light of those core habitat characteristics.

Keywords: Monitoring, aquatic habitat, riparian ecosystems, adaptive management,

forest practices.
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A Review of Protocols for Monitoring Streams and Juvenile Fish...

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Introduction

This document reviews existing and proposed protocols used to monitor stream

ecosystem conditions and responses to land management activities in the Pacific

Northwest. We define a monitoring protocol as a set of directions and guidelines

that address specific objectives and provide methods designed to obtain data sets

that can be used to detect trends or changes in habitat conditions and fish use. This

review focuses on current (since 1993) monitoring efforts that assess stream habitat

conditions and juvenile fish use. It does not focus on protocols specifically intended to monitor trends in fish populations for salmon recovery efforts, other fish

life-history stages (e.g., salmonid smolt monitoring or spawner surveys), biotic

indexes, or approaches designed to monitor water quality or sources of pollution.

However, we recognize that some of these approaches may contain specific recommendations that apply to protocols for assessing stream habitat conditions and

juvenile fish use (MacDonald et al. 1991).

This review consists of several sections. We begin by presenting the methods

used to locate relevant stream monitoring protocols and our criteria for selecting

the monitoring protocols that we evaluated as most relevant. We then provide an

overview of agency monitoring protocols, adaptive management, types of monitoring, and a summary of the core habitat characteristics thought to be most sensitive

to forest management practices. Finally, we provide a comparison of current

protocols in light of those core habitat characteristics.

Methods

This document was compiled by conducting reviews of published and gray literature and by performing Web-based searches of protocols and databases. Databases

used for the Web search included the National Technical Information Service,

Cambridge Scientific Abstracts, Aquatic Sciences and Fisheries Abstracts, and

Google. In addition, various agency Web sites including the U.S. Environmental

Protection Agency (EPA), U.S. Department of the Interior (USDI) National Park

Service, U.S. Department of Agriculture Forest Service (FS), Columbia River InterTribal Fish Commission, British Columbia Ministry of Sustainable Resource

Management, and state agencies from California, Oregon, Washington, and Idaho,

were searched for the most recent documents and updates. Agencies, including

those currently conducting protocol reviews of their own, were also contacted (e.g.,

Johnson et al. 2003, Lanigan 2002). References in the retrieved documents were

searched for additional sources.
GENERAL TECHNICAL REPORT PNW-GTR-625

2

Because of the recent work aimed at improving the utility of habitat survey and

fish abundance assessment methods (e.g., Kaufmann et al. 1999, Kurtz et al. 2001,

Reeves et al. 2003, Thompson 2003), several stream monitoring protocols are

currently or were recently under revision. We have focused our attention on the

recently revised protocols (1993 or later) published or proposed by agencies

operating in forested regions of Washington, Oregon, Idaho, California, and British

Columbia.

Our criteria for screening the retrieved documents included how recently the

document had been published or updated, as well as the scope, level of detail, and

potential application of the protocol (or significant parts of it) for assessing influences of forest land use practices on stream habitats and juvenile salmonids.

A list of documents was compiled by using EndNote software (ISI

ResearchSoft),1

 then further refined to 37 documents that we determined to be the

most relevant (see appendix). Of that refined list, five of the most recent were

selected for side-by-side comparison (tables 1 and 2). Where possible, URLs are

provided so that readers can navigate to the documents in question and view them

in detail.

Overview of Agency Monitoring Protocols

The issues involved in monitoring streams, rivers, and watersheds are not new.

For aquatic ecosystems, monitoring activities commonly involve repetitive (e.g.,

yearly) surveys that assess changes in select physical and ecological characteristics.

Regier (1976) describes monitoring processes as evolving from descriptive natural

history studies to more quantitative approaches. Most monitoring of streams has

involved surveys and assessments of changing environmental characteristics at the

habitat scale (e.g., changes in composition of pool and riffle types, large woody

debris [LWD] size and quantity), select landscape-scale characteristics (e.g.,

channel gradients of reaches), and use by fish (Duff and Cooper 1978; Kershner et

al. 2003; Medsser et al. 1991; Platts et al. 1987; Rinne 1985; Roni, in press; USDA

FS 2001). An underlying goal of these monitoring efforts is to identify and understand effects of human perturbations on ecosystems or parts of ecosystems. These

effects may result from land management practices, such as timber management in

forested watersheds, or from the implementation of restoration and rehabilitation

1

 The use of trade or firm names in this publication is for reader information and does not

imply endorsement by the U.S. Department of Agriculture of any product or service.

Text continues on page 11

An underlying goal

of these monitoring

efforts is to identify

and understand

effects of human

perturbations on

ecosystems or parts

of ecosystems.
A Review of Protocols for Monitoring Streams and Juvenile Fish... 3

Table 1—General characteristics of five major protocols

Protocol

AREMP EPA-EMAP USGS-NWQA FS EPA-RBP

Title Aquatic and Riparian Environmental Revised protocols for Stream Inventory Rapid

Effectiveness Monitoring Monitoring and sampling algal, Handbook, Levels bioassessmentPlan for the Northwest Assessment Program— invertebrate, and fish 1 & 2. Region 6, protocols for use inForest Plan Surface Waters: communities as part of Version 2.2 streams and

Western Pilot Study the National Water- wadeable rivers:Field Operations Quality Assessment periphyton,Manual for Wadeable Program (NWQAP) macroinvertebratesStreams (EMAP) and fish (RBP)

Author AREMP 2003 Peck et al. 2001 Moulton et al. 2002 USDA FS 2002 Barbour et al. 1999

(unpublished draft)

Agency Interagency EPA USGS FS EPA 

Purpose Watershed ecological National ecological Water quality status Stream channel, Water quality

conditions: status and conditions: status and and trends riparian, and assessment: rapidtrends trends aquatic ecosystem biosurvey

conditions

Spatial scale Regional  6th-field HUC Western US  stream Basin  segment  Watershed  Reach 

subwatershed  reach segment  reach reach  microhabitat reach

Statistical Random sample of 6th-field Random sample of Subjective (not defined Stratified random “Targeted or

design HUC watersheds  points on 1:100,000 in protocol) at reach level probabilistic” (not

random sample of reaches scale “blue-line” stream (watershed defined in protocol)

network selection not

defined)
GENERAL TECHNICAL REPORT PNW-GTR-625

4 Table 1—General characteristics of five major protocols (continued)

Protocol

AREMP EPA-EMAP USGS-NWQA FS EPA-RBP

Features Physicochemical, habitat; Physicochemical, Periphyton, macro- Physical, fish Physicochemical,

sampled periphyton, benthic habitat; periphyton, invertebrates, and fish habitat; periphyton,(see table 2) macroinverts, and fish benthic macroinverts, (for habitat, see benthic

assemblages and fish assemblages; Fitzpatrick et al. 1998) macroinverts, and

fish tissue fish assemblages

Explicit Yes—pilot program Yes Recommended Minimum standards Yes

QA/QC established

Comments Synthesis of protocols from Protocol used by many Fixed sites; Multimetric

EPA, USGS, FS, and BPA NW state and local “representative” fish assessment protocol

agencies samples; extensive (Index of Biotic

basin characterization Integrity)with GIS

URL http://www.fs.fed.us/pnw/ http://www.epa.gov/emap/ http://water.usgs.gov/ http://www.epa.gov/

pubs/gtr577.pdf html/pubs/docs/ nawqa/protocols/ owow/monitoring/rbp/

groupdocs/surfwatr/field/ OFR02-150/OFR02- wp61pdf/rbp.pdf

ewwsm01.html 150.pdf

Note: Features sampled are described in more detail in table 2.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

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Table 2—Features sampled by five core protocols

AREMP EAP—EMAP USGS—NWQA FS EPA—RBP

Sampling Eight randomly Randomly selected Habitat and physical Stream/watershed Not defined in

strategy selected reaches index site. characteristic selection process not protocol.

within each sample Sample 40X avg. protocols from defined in thissubwatershed. bankfull width (min. Fitzpatrick et al. protocol.Reach length = 20X 150 m) from central (1988).avg. bankfull width index point. 10 percent of all fast-(150 m min., 500 m 11 transects. Subjective site and slow-water unitsmax.). 11 transects. selection measured (minimum

10 of each type).

20X avg. bankfull

width (min. 150 m,max. 300 m).11 transects.

Physical

habitat:

Channel

cross Nonconstrained Wetted width Wetted channel Four equidistant Estimated width,section reaches: initial cross measured at 21 width, bankfull bankfull depth depth.

section is monumented equally spaced cross channel width, bank measurements at EMAP protocoland an additional sections. height and channel each measured fast- optional.10 systematic Four equally spaced features measured at water unit.(nonmonumented) depth measurements each transect; bankcross sections are taken at each stability index at each Flood-prone widthplaced at 1/10 of the transect (11 transects transect. measured.reach length. total).

Optional: Five

Constrained reaches: transects that best

Six systematic represent the(nonmonumented) geomorphology arecross sections are selected (one each atplaced at 1/5 of the upstream andreach length. downstream ends of

reach—one or both

Cross sections are benchmarked).

measured with a laserrange finder; 11transects aremeasured innonconstrainedreaches and 6 inconstrained reaches.
GENERAL TECHNICAL REPORT PNW-GTR-625 6 Table 2—Features sampled by five core protocols (continued) AREMP EPA—EMAP USGS—NWQA FS EPA—RbP Longitudinal Longitudinal profile Measured at 100 Measured at Not collected. Estimated reach profile measured (x, y, z equally spaced transects. length. coordinates) by using a intervals (150 in laser range finder and streams less than 2.5 EMAP protocol an electronic compass, m wide) along optional. following the thalweg. centerline between Shots are taken on an first and last transect. increment about 1/100 of the sample site length. Additional measurements taken at pool tail crests, maximum pool depth,

and pool head.The same protocol isused in all samplereaches, constrainedor nonconstrained.

Pool frequency Pool defined as being Part of channel unit Length of pools Pool defined as being Percentage of reach

and length longer than the characterization; greater than 50 longer than the represented by

average wetted width. pool-forming percent of channel average wetted width stream morphologyHabitat unit has to elements noted. width measured and unless unit is a types (riffle, run,span channel. mapped. plunge pool. Habitat pool).

unit has to span EMAP protocolchannel. optional.

Pool depth Pool tail crest, max Part of longitudinal Part of longitudinal Maximum pool tail Not measured.

pool depth, and pool and cross-sectional and cross-sectional crest and maximum EMAP protocolhead locations measurements. measurements pool depth. optional.measured with laserrange finder.

Stream Calculated as the rise Water surface slope Calculated from Calculated from High gradient

gradient of the streambed and bearing maps or GIS; also 1:24,000 maps. (riffle/run) vs. low

divided by the length of measured along measured along gradient (glide/pool).the sampling segment longitudinal profile. longitudinal profile EMAP protocol(slope of streambed, with clinometer or optional.

not water surface). hand level.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

7

Table 2—Features sampled by five core protocols (continued)

AREMP EPA—EMAP USGS—NWQA FS EPA—RbP

Sinuosity Calculated by using Compass bearings Calculated from Calculated from Scale of 0 to 20.

longitudinal profile along longitudinal maps or GIS. 1:24,000 maps. EMAP protocoldata. Sum of lengths profile. optional.between thalwegpoints at each transectdivided by straight-linedistance.

Discharge Measured with flow Measured with flow Mean water-column Derived from velocity Surface velocity

meter or neutral meter (D60), neutral velocity at three measurements; 25 measured at thalweg.buoyant object if buoyant object, or points along each velocity EMAP protocolstream too small. Ten time-filling procedure transect. measurements optional.cells measured for depending on depth across channel.meter measurements. of stream; 15 to 20

intervals for metermeasurements.

Bankfull Calculated at each Depth of thalweg Water depth at three Bankfull width and High-water mark

width: transect. Eleven depth measured each 1/100 points along each depth measured at measurement only.

depth measurements of reach; bankfull transect. each measured fast- EMAP protocol

between and including channel and incision water unit. optional.

bankfull points at each height.transect to determinemean depth.

Substrate Similar to EMAP. Substrate size and Size and Wolman pebble count Estimated

Percentage of fines in embeddedness embeddedness at two points in compositionpool tail areas by using visually estimated at estimated at three stream reach in (percentage).Klamath grid (max. 12 four equally spaced points along each “normal” fast-waterpools). points along each transect. stream units.

transect.

Optional: Wolman

pebble count.
GENERAL TECHNICAL REPORT PNW-GTR-625

8 Table 2—Features sampled by five core protocols (continued)

AREMP EPA—EMAP USGS—NWQA FS EPA—RbP

Large wood Count wood if min. Tallied between each Tallied for each Estimated area,

length 

≥ 3 m and at transect. Sorted into channel unit as small, density.

least 0.3 m diameter at one of 12 diameter- medium, or large. EMAP protocold.b.h. Length and class categories. optional.

d.b.h. estimated.Length and d.b.h.measured on first 10pieces in reach andevery 5th piece

thereafter. Notelocation in channel.Jams of more than 5pieces not measuredbut presencedocumented.

Other Total Kjeldahl N, Bank angle, undercut Water quality. Length of unstable Temperature,

chemical total P, temperature, distance at each banks (above bankfull conductance,and physical dissolved oxygen, pH, transect. stream margin), dissolved oxygen,

parameters conductivity. Sampled temperature, pH, turbidity.

at lowest point in Major cations and entrenchment ratio.subwatershed on anions, nutrients,federal land. total Fe and Mn,

turbidity, color, pH,

Entrenchment ratio. dissolved organic

carbon, temp.(conductivity anddissolved oxygenoptional).
A Review of Protocols for Monitoring Streams and Juvenile Fish...

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Table 2—Features sampled by five core protocols (continued)

AREMP EPA—EMAP USGS—NWQA FS EPA—RbP

Biological

sampling:

Periphyton/ EMAP field and lab 11 transects Five samples from Not collected. Two samplingphytoplankton analysis protocol. collecting substrate each of five locations approaches

samples from in riffles distributed described.dominant habitat type throughout reach; Representativeon transect. All five macrophyte habitats sampled.samples collected samples.into one composite Quantitative Qualitative listing ofsample. phytoplankton, aquatic biota;Three lab samples microalgae; composite samplesprepared: composite samples. collected.ID/enumeration,chlorophyll, andbiomass.

Benthic Two subsamples in Two types of Qualitative and Not collected. All riffles/runs in

macroinverte- each of four riffles in samples: “reach- semiquantitative representative reachbrates reach by using kick net. wide” samples samples taken from sampled. Samples

These eight sub- collected at each each habitat type in combined.samples combined transect and reach and combined. into single sample combined; “targetedfor reach. riffle” samples (eight)

combined fromseparate, riffle-onlysamples. Modified D-frame kicknet.
GENERAL TECHNICAL REPORT PNW-GTR-625

10Table 2—Features sampled by five core protocols (continued)

AREMP EPA—EMAP USGS—NWQA FS EPA—RbP

Fish and Single pass with Single pass with Two-pass electro- Minimum: Sample Representative

aquatic electroshocker at each electroshocker fishing and seining to every measured stream reachamphibians site between transects. between transects determine length, slow-water unit and sampled with singleTen to twenty percent along entire sample weight, and every other fast-water pass electrofishing.

of fish measured, reach. Largest and abnormalities. All unit. Snorkel,condition estimated by smallest specimens channel units and electroshock, hookusing displacement. measured. Voucher habitat features are and line, or seining.Snout-vent lengths specimens and tissue sampled. Weigh and Amphibians noted.measured for all samples collected. measure at least 30aquatic amphibians, Seining used where individuals of eachSnorkeling used to electrofishing not species. determine fish/amphibians appropriate. Jaccard Voucher specimenspresence where coefficient used to collected.threatened/endangered assess samplingfish species present. adequacy.

Other biological Terrestrial amphibians. Riparian canopy Riparian canopy Avg. width of inner/

parameters cover at each cover at each outer riparian zone,

transect by using transect by using successional class,densiometer; densiometer; overstory, understory.vegetation structure, dominant riparianareal cover vegetation; instreamestimation. habitat cover; bank

Instream fish cover stability index; bankand human influence angle, substrate,estimates; channel vegetative cover.constraint. 

Source: Adapted from Lanigan (2003).
A Review of Protocols for Monitoring Streams and Juvenile Fish...

11

programs. Common landscape approaches include watershed-scale (km2) assessments developed and implemented to evaluate environmental conditions and

management actions that can influence fish habitats (Collins and Pess 1997,

Morrison and Marcot 1995). They also can be used to monitor natural disturbance

events (e.g., wildfires and floods). The ability to detect and explain change can be

the most instructive outcome of a monitoring program (MacDonald et al. 1991).

Major issues warranting monitoring are habitat degradation, compliance with

regulations related to sensitive and endangered species (e.g., the Endangered Species Act, National Environmental Policy Act), and the implementation of agency

policies or management plans. In the Pacific Northwest, some pertinent examples

of management plans and actions with provisions for monitoring stream ecosystems include efforts of the FS, the states of Oregon and Washington, and local

watershed management councils. The FS examples include the Northwest Forest

Plan (NWFP) for the Pacific Northwest (FEMAT 1993) and the Tongass Land

Management Plan (USDA FS 1997) for southeast Alaska.

The FEMAT (1993) report contains interagency scientists’ recommendations

resulting from President William Clinton’s Forest Summit in 1993. It focuses on

the influences of forest and other resource management practices in the Pacific

Northwest and includes an aquatic conservation strategy for restoring salmon

stocks, habitats, streams, and riparian ecosystems. Recommendations include

provisions for monitoring strategy objectives.

Goals of the Tongass plan include “the maintenance or restoration of the

natural range and frequency of aquatic habitat and stream channel and bank

conditions” in the Tongass National Forest (USDA FS 1997). A common monitoring objective for aquatic ecosystems is determining the effectiveness of fish and

riparian standards and guidelines in maintaining or improving fish habitats (USDA

FS 1995, 1997).

The state of Oregon is involved in several monitoring programs. Oregon’s

Coastal Landscape Analysis and Modeling Study (CLAMS), an interagency

program, uses monitoring as one tool in a set of analyses to link ecological, economic, and social factors with forest management policies and practices in coastal

Oregon watersheds.2

 The Oregon Plan for Salmon and Watersheds has provisions

for monitoring spawning salmonids, smolt outmigration, and the effects of habitat

modifications on juvenile salmonids (IMST 1999, Solazzi et al. 2003).

2

 Cooperative effort of Oregon State University, USDA Pacific Northwest Research Station,

Oregon Department of Forestry, and the National Commission on Science for Sustainable

Forestry. http://www.fsl.orst.edu/clams/intro.html. (January 6, 2004).
GENERAL TECHNICAL REPORT PNW-GTR-625

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The Washington State Department of Natural Resources (WSDNR) (Grizzel et

al. 2000, Pleus et al. 1999, Schuett-Hames et al. 1999) and the Skagit Watershed

Council (2000) provide two examples of management strategies based on basinwide analysis programs designed to assess influences of land uses on stream

systems and fish use of habitats. For WSDNR, the monitoring of stream ecosystems is the responsibility of the Cooperative Monitoring, Evaluation, and Research

Program (CMER). The CMER program is conducting a number of effectiveness

studies that must incorporate some stream classification scheme (e.g., Montgomery

and Buffington 1993). They are especially interested in a classification that is

sensitive to watershed inputs (e.g., wood and sediment) (e.g., Grizzel et al. 2000).

They are also conducting effectiveness studies for evaluating new prescriptions

relating to riparian buffer zones, channel erosion problems, road runoff, and other

environmental concerns. The CMER program is currently selecting monitoring

sites that are representative of the range of variables of interest (e.g., stream

physical processes and ecological sensitivities). A major goal of the WSDNR

monitoring is to benefit that agency’s ongoing adaptive management efforts.

The Skagit Watershed Council in western Washington is an example of a local

watershed council that is evaluating and improving aquatic resources throughout a

large river drainage. The council’s strategy is designed to address stream ecosystem

questions relating to flooding, sediment supply, riparian functions, floodplain functions, and habitat connectivity. Assessments have been made of habitat losses to

help prioritize actions required to restore habitat-forming processes. This information was used to make decisions based on proposed project effectiveness relative

to costs and likelihood of success (Skagit Watershed Council 2000). This approach

allows monitoring of the amount of available habitat created by projects (e.g.,

removal of culvert blockages and other impediments to habitat formation and fish

movement).

Adaptive Management

Adaptive management is a strategy for dealing with the risks associated with

resource management decisions derived from imperfect data (Anderson et al. 2003,

Holling 1978, Ralph and Pool 2003, Walters 1986). In theory, adaptive management is founded on considering land use activities as experimental manipulations

implemented within the framework of a well-documented monitoring program. The

intent of the concept is to gain perspectives into the response of ecosystems

inhabited and used by humans.

Information obtained by the different Forest Service monitoring approaches,

along with research and other new information, provides a basis for adaptive
A Review of Protocols for Monitoring Streams and Juvenile Fish...

13

management strategies. Adaptive management can occur when policies and management actions are changed in response to new knowledge provided by monitoring programs. Adaptive management has been adopted by many land management

agencies and particularly within the FS; however, it has not been universally

applied (Stankey et al. 2003). Ralph and Pool (2003), Stankey et al. (2003), and

Anderson et al. (2003) discuss many of the challenges in applying adaptive management and propose some solutions. The most effective adaptive management

plans include specific links with monitoring programs that can be used to evaluate

management prescriptions. Ideally, provisions can be made to use data obtained

through repetitive long-term monitoring as feedback information for revising management plans and actions (Wissmar 1993). In summary, adaptive management

plans that include monitoring programs as integral components can provide information to managers on “what works and what does not work.”

Types of Monitoring

Many monitoring approaches have been applied to fluvial ecosystems by authors

and agencies. For example, MacDonald et al. (1991) identify several monitoring

approaches and define parameters that can be used to evaluate effects of forestry

activities on stream chemical (e.g., water quality), physical (e.g., channel characteristics), and select biotic conditions. Examples of other historically significant

approaches include (1) prescriptions designed to assess the effectiveness of best

management practices in protecting water and stream quality (NCASI 1988), (2)

rapid bioassessment protocols for evaluating benthic macroinvertebrates and fish

populations in streams and rivers (USEPA 1989), and (3) biological criteria

(USEPA 1990). These approaches range from rapid inventories (e.g., Barbour et al.

1999, Dolloff et al. 1993) to those that require extensive field surveys and statistical rigor (e.g., Peck et al. 2001, Reeves et al. 2003).

Forest management plans that include provisions for monitoring streams

generally define four primary types of monitoring designed to provide information

to assess if management actions meet the objectives of the prescribed standards and

guidelines (USDA FS 1994, 1997; USDA and USDI 1994).

1. Baseline monitoring is analogous to an inventory. This prescription is used to

establish existing conditions within a geographic area or ecosystem for planning or future comparisons. Commonly it may be applied to obtain a “natural

range” of conditions for streams and watersheds to capture much of the temporal variability of the system(s) of interest.

Adaptive management plans that

include monitoring

programs as integral

components can provide information to

managers on “what

works and what does

not work.”
GENERAL TECHNICAL REPORT PNW-GTR-625

14

2. Implementation monitoring is designed to determine if prescribed standards

and guidelines were indeed carried out. For example, when riparian buffer

strips of specific widths and distances are prescribed, implementation monitoring determines if they were created and meet the given criteria.

3. Effectiveness monitoring is more complex and is applied to determine the

effect of a management prescription. In the case of the buffer strip example,

this includes assessing if the buffers can maintain stream temperatures within

the range of natural variation expected for stream ecosystems, sustain recruitment of large wood to stream channels, or maintain windfirm characteristics

of trees (i.e., trees do not blow down a few years after logging). Effectiveness

monitoring may involve research to obtain additional information (USDA FS

1994, 1997; USDA and USDI 1994).

4. Validation monitoring is designed to determine if underlying assumptions are

sound. Validation monitoring determines the accuracy of an assumed causeand-effect relationship between management activities and the resource

being managed (i.e., Does maintaining large woody debris actually help fish?).

Validation monitoring may also require research to obtain information (USDA

FS 1994, 1997; USDA and USDI 1994).

Baseline, implementation, and effectiveness monitoring have been specified in

fish habitat assessments prepared for the Tongass National Forest (USDA FS

1995). The USDA Forest Service and the USDI Bureau of Land Management have

developed and adopted implementation, effectiveness, and validation monitoring

approaches for evaluating the Aquatic Conservation Strategy of the NWFP for

federal forests in the Pacific Northwest (USDA FS 1994, 1997; USDA and USDI

1994). These monitoring approaches were designed to ensure that management

actions meet the objectives of the prescribed standards and guidelines and comply

with laws and management policy. General objectives of FS monitoring include (1)

determining if best management practices have been implemented, (2) determining

the effectiveness of management practices at multiple scales (e.g., local habitats

and watersheds), and (3) validating whether ecosystem functions and processes

have been maintained (USDA FS 1994, 1997; USDA and USDI 1994).

In some FS management plans, monitoring approaches are accompanied by an

evaluation question and include general descriptions of standards and guidelines

(key items to be monitored). For stream systems, some major items to be measured

for implementation monitoring can include width and integrity of riparian reserves.

Important measurements obtained through effectiveness monitoring for streams
A Review of Protocols for Monitoring Streams and Juvenile Fish...

15

commonly include pool frequency and quality, substrate composition, coarse

woody debris frequency and quality, and water temperature (USDA FS 1994,

1997; USDA and USDI 1994).

Core Habitat and Salmon Characteristics Sensitive to

Forest Practices

Hicks et al. (1991) listed a number of forest practices that have effects on salmonid

abundance and habitat condition. Those practices that altered the riparian and

stream habitats by removing stream canopy or large woody debris, or by adding

logging slash, had potentially negative effects on salmonids, such as increasing

water temperatures, lowering dissolved oxygen levels, and increasing inputs of fine

sediments to channels. Large pieces of wood are essential for creating and maintaining pools for fish habitat and for storing sediment (Bilby et al. 2003, Hicks et

al. 1991, Montgomery et al. 1995). Timber harvest from hillsides or road construction can accelerate erosion, alter streamflow regimes and habitats, and present

physical obstructions. Increased fine sediment levels can have a detrimental effect

on different salmonid life history stages (Hicks et al. 1991, Meehan 1991).

The well-documented long-term studies at Carnation Creek, British Columbia,

and the Alsea watershed, Oregon, have identified a number of relationships

between forest management practices and salmonid populations and habitat conditions (Hall et al. 1987, Hartman and Scrivener 1990, Meehan 1991). In the Carnation Creek monitoring studies, for instance, those practices that increased stream

insolation, nutrients, and water temperature also increased the numbers and size

of juvenile coho salmon (Oncorhynchus kisutch) (Hartman and Scrivener 1990).

Increasing coho salmon size may result in early smoltification, which has been

implicated in higher marine mortality (Holtby et al. 1990). Those practices that

decreased streambank stability and abundance of large woody debris or changed

the spawning gravel composition had negative effects (Hartman and Scrivener

1990).

Oregon’s Independent Multidisciplinary Science Team (IMST 1999) listed

four categories of characteristics that affect salmonids. Intact riparian forests were

important in regulating stream temperature, nutrient inputs, and LWD inputs to

channels. Inputs of LWD into channels from riparian areas and land failures were

important for formation of stream habitats. Increased amounts of fine sediment

commonly reduce salmonid habitat quality, and roads may hinder fish passage at

stream-road crossings.
GENERAL TECHNICAL REPORT PNW-GTR-625

16

The number and quality of pools are also known to be important for fish

(Nickelson et al. 1992, Rosenfeld et al. 2000). In a series of experimental studies

in Washington, deep pools with brushy cover were found to be beneficial to juvenile salmonids (Quinn and Peterson 1994, 1996). Coho salmon abundance was

positively correlated with amount of pool habitat, and fish species richness

was positively correlated with habitat complexity (Quinn and Peterson 1994).

Likewise, Roni and Quinn (2001) reported juvenile coho salmon densities were

higher in both summer and winter in reaches treated with the addition of artificial

large woody debris.

In summary, juvenile coho salmon and other fish species seem to be most

sensitive to the following habitat characteristics. (See Bauer and Ralph [1999]

for an annotated bibliography of 334 literature citations related to salmon habitat

requirements.)

• Amount and size of large woody debris

• Number and quality of pools

• Changes in riparian vegetation

• Water temperature

• Nutrient level

• Streamflow regime

• Sediment transport regime

• Quality of spawning environment

• Road placement and structures (sediment sources, passage barriers)

• Streambank stability

Many of these habitat characteristics are interrelated, and alteration in one

characteristic (e.g., LWD) can affect another (e.g., pools). Forest practices that

have measurable effects on these characteristics (see references in Meehan 1991)

can differ with the range of management practices imposed on the watershed

(FEMAT 1993, Meehan 1991, USDA FS 1995).

Most of the affected habitat characteristics are well known and comprise

“core parameters” in monitoring protocols (Bain et al. 1999, Bauer and Ralph

2001, Gregory and Bisson 1997). Some habitat features that affect distribution

of juvenile coho salmon, such as stream-channel gradient, are not usually affected

by forest practices. However, differences in channel gradients of reaches can be

important in classification of habitats and the design of monitoring programs.

Recently Revised Monitoring Protocols

Many federal and state agencies are currently updating or developing monitoring

protocols. The Washington Department of Fish and Wildlife reviewed 112 documents containing 429 salmon habitat inventory and monitoring protocols in the
A Review of Protocols for Monitoring Streams and Juvenile Fish...

17

Pacific Northwest (Johnson et al. 2001). Current interagency efforts include the

preparation of a similar review of fish survey protocols (Johnson et al. 2003). The

FS Inventory and Monitoring Institute is presently developing guidelines for and

a searchable database of monitoring protocols, but none are currently available

(USDA FS 2003). The Forest Service national efforts also include an aquatic

ecological unit inventory protocol with a core set of sampling features and recommended protocol.3

 The USDI National Park Service is developing a national

framework for their inventory and monitoring efforts (National Park Service 2003).

Table 1 provides a brief overview of five protocols that were considered to be the

most current and applicable to this review.

Regional-scale, national water quality assessment programs that are already

in place, such as the EPA’s Environmental Monitoring and Assessment Program

(EMAP) and the USGS National Water Quality Assessment Program (NWQAP)

(Lazorchak et al. 1998, Meador et al. 1993, Moulton et al. 2002, Peck et al. 2001)

have useful components for monitoring forest land use practices and regional

comparisons. These documents often provide a basis for other agencies’ development of monitoring programs. The EPA’s revised Rapid Bioassessment Protocol

(RBP) is another large-scale monitoring protocol (Barbour et al. 1999). Its features

are less quantitative and thus less useful for scientifically rigorous studies.

Two monitoring plans are currently being coordinated by the FS for the Northwest Forest Plan area under the Interagency Regional Monitoring Program for the

Pacific Northwest. They include the Aquatic and Riparian Effectiveness Monitoring Plan (AREMP) and the PACFISH/INFISH plan to monitor the aquatic and

riparian resources related to biological opinions for bull trout, salmon, and steelhead (Kershner et al. 2003, Reeves et al. 2003). As an interagency program, the

AREMP is developing a regional synthesis of protocols from the EPA, USDI

Geological Survey, FS, and Bonneville Power Administration. The AREMP contains core components that are by design either directly compatible or translatable

to other protocols (AREMP 2003, Reeves et al. 2003). The AREMP sampling

design is directly applicable to monitoring forest land use practices and is applicable across different geographical regions. The AREMP protocol appears to be

the most current synthesis of watershed monitoring that has been published to date.

The PACFISH/INFISH plan evaluates the effect of land management activities

on aquatic and riparian communities at multiple scales. It was developed for Forest

3 Roper, B. 2003. Personal communication. Aquatic ecologist, U.S. Department of

Agriculture, Forest Service, Rocky Mountain Research Station, Forestry Sciences

Laboratory, 860 North 1200 East, Logan, UT 84321.

The AREMP protocol

appears to be the

most current synthesis of watershed

monitoring that has

been published to

date.
GENERAL TECHNICAL REPORT PNW-GTR-625

18

Service Regions 1, 4, and 6 (Northern, Intermountain, and Pacific Northwest,

respectively), and other federal and state agencies (Kershner et al. 2003). This

protocol does not collect fish presence or abundance data. However, other methods

of the PACFISH/INFISH plan are similar to the AREMP protocol, and the plans

will develop compatible documents.

The FS Region 6 Stream Inventory Handbook was recently revised in parallel

with the AREMP effort and contains “core data standards” developed by the NWFP

interagency team mentioned earlier (USDA FS 2002). According to the document,

it is the “aquatic companion” to the FS Integrated Resource Inventory and is compatible with Oregon Department of Fish and Wildlife and Washington Timber, Fish,

and Wildlife aquatic inventories (USDA FS 2002).

Other watershed-specific protocols (e.g., Bain and Stevenson 1999, Dambacher

et al. 2001, Moore et al. 2000) have been based on the above federal protocols and

earlier approaches (Dolloff et al. 1993, Hankin and Reeves 1988). Still others, such

as the Salmonid Life Cycle Monitoring Project of the Oregon Plan (Solazzi et al.

2003) and the state of Washington’s Index Watershed Monitoring Program (Seiler

et al. 2002), use counts from smolt traps as an index of regional watershed conditions or salmonid abundance. Although salmon smolts can provide a useful indicator of watershed conditions (Seiler et al. 2002, Solazzi et al. 2003), monitoring

protocols that use smolts were not the focus of this review.

For a comprehensive listing of habitat assessment protocols in use in the

Pacific Northwest, see Johnson et al. (2001). Bain et al. (1999) summarize attributes measured in 31 stream assessment protocols in use in North America but

do not list the protocols by name.

Data Quality

Some researchers have been critical of previous survey and monitoring efforts

because data collected were not always quantitative or reproducible and therefore

of questionable use for management purposes (Peterson and Wollrab 1999, Spence

et al. 1996). Bauer and Ralph (2001) provide a thorough summary of concerns with

commonly assessed habitat attributes and offer suggestions for increasing measurement precision. Roper et al. (2002) provide some tools to evaluate consistent

measures of habitat. Kaufmann et al. (1999) identify several habitat variables, such

as width-to-depth ratio and residual depth, that were either precise or moderately

precise as described by signal-to-noise ratio (Kaufmann et al. 1999). Archer et al.

(2004) found the least amount of observer variability in descriptions of stream

reach, streambank, and cross-section characteristics.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

19

Peterson and Wollrab (1999) analyzed the data collected with established FS

protocols and found inconsistent and subjective procedures for sampling fish and

habitat attributes, biased site-selection criteria, and problems in following established quality assurance and quality control measures. Spence et al. (1996), however, found two federal monitoring programs (EMAP and NWQAP) to be more

quantifiable than other efforts. Stream surveys that require walking all reaches in

the study area (e.g., Dolloff et al. 1993) can dictate efforts that result in qualitative

rather than quantitative measurements (Spence et al. 1996).

Some agencies have initiated quality-assurance-and-control (QA/QC) programs

to ensure that field teams can be adequately trained in the use of protocols and to

assess the variability in performances of different teams’ results (Gallo et al. 2003).

Others recommend checks to ensure that the quality of the data remains high but

provide no clear direction (Moulton et al. 2002). As QA/QC efforts continue (e.g.,

Gallo et al. 2003), they should lead to a refinement of field techniques and more

dependable results.

Scale and Sampling Design

Regardless of their sampling intensity, strong sampling designs should account for

or reduce variability among sites and increase applicability across different spatial

scales (Conquest and Ralph 1998, McDonald 2002). As part of the Oregon Plan for

Salmon in Watersheds, Stevens (2002) discusses characteristics of good sampling

design for assessing status and trends in juvenile salmonid abundance and other

factors. Likewise, in the state of Washington, the Department of Natural Resources

is evaluating the use of sampling and survey protocols (modeling and statistical)

developed by the USDI Fish and Wildlife Service (Thurow et al. 2004).

Two protocols considered in this review have a statistical design that allows

for landscape-scale inferences (Peck et al. 2001, Reeves et al. 2003). A third, the

FS Region 6 protocol, uses a stratified random sampling process at the reach level,

but watershed or stream selection criteria are not discussed in the protocol document (USDA FS 2002). Two other protocols use subjective (or undocumented) siteselection criteria and, without application of statistical selection procedures, are of

limited use beyond the habitat unit scale (Barbour et al. 1999, Fitzpatrick et al.

1998, Moulton et al. 2002, USDA FS 2002). Other protocols (generally intended

for monitoring restoration projects) are site or reach specific. Although many

subjective or site-specific protocols have elements that relate to land use practices

in forested watersheds, the current, large-scale synthesis documents (e.g., Peck et

al. 2001, Reeves et al. 2003) offer the benefits of widespread use, foundations

based on current science, and applicability across different spatial scales.
GENERAL TECHNICAL REPORT PNW-GTR-625

20

Level of Complexity and Relevance

Rapid surveys have the benefits of speed and relative simplicity but sacrifice

quantitative measurement. For example, the EPA’s RBP (Barbour et al. 1999) only

estimates stream channel width and depth, characterizes stream gradient as either

high or low rather than measuring directly or deriving from maps, and uses qualitative measurements of aquatic biota (although more rigorous measurements are

optional). The FS basinwide visual estimation technique uses visual observations

with periodic measurements to calibrate for observer bias (Dolloff et al. 1993).

Although this type of “calibration” seems promising, questions have been raised

about the validity of underlying assumptions used to standardize the data

(Thompson 2003).

At the other end of the spectrum, the USGS NWQAP and the EPA EMAP

perform extensive monumented surveys of stream cross-sectional transects and

longitudinal profiles, bank and channel morphology, as well as laboratory analyses

of water quality, periphyton, macroinvertebrates, and fish tissue, with concomitant

increase in time and expense. The AREMP protocol is similar to EMAP in its

measurement of most habitat and biotic attributes.

The FS Region 6 protocol (USDA FS 2002) uses a combination of estimated

and measured parameters to monitor stream habitats. Stream gradient and sinuosity

are calculated from 1:24,000 maps. Maximum pool tail crest and maximum pool

depth are measured directly, and large wood is estimated visually (USDA FS 2002).

Large wood is counted as large, medium, or small. In contrast, EMAP uses 12

diameter-class categories for wood, and AREMP directly measures a subset of

wood in the stream channel.

Comparison of Protocols

Based on our survey of the literature regarding stream monitoring protocols in use

in the Pacific Northwest, we consider the following five to be the most comprehensive and widely distributed; they contain provisions for monitoring habitat and

biological characteristics considered sensitive to management practices. These

protocols are products of ongoing federal and state research and therefore seem to

be the most up to date and useful for monitoring land use practices in forested

watersheds.

• The Aquatic and Riparian Effectiveness Monitoring Plan for the Northwest

Forest Plan (Reeves et al. 2003).

• The FS Region 6 Stream Inventory Handbook (USDA FS 2002).
A Review of Protocols for Monitoring Streams and Juvenile Fish...

21

• EPA Environmental Monitoring and Assessment Program—Surface Waters:

Western Pilot Study (Peck et al. 2001).

• USGS National Water Quality Assessment Program (Moulton et al. 2002).

• EPA Rapid Bioassessment Protocol (Barbour et al. 1999).

These five protocols are listed in tables 1 and 2 to facilitate side-by-side

comparison.

Conclusions

Stream monitoring programs of differing geographic scale and scientific rigor have

been developed and implemented by various federal and state land management

agencies. Most of the protocols reviewed contain common objectives for monitoring stream habitat conditions, fish use, and influences of land management activities. They generally rely on published research to define relationships between

habitat characteristics and the presence of fish, usually salmonids. Some features

may be quantified by field work in one protocol, and maps or GIS data in another.

Protocols that emphasize speed and simplicity can sacrifice quantitative measurements and rely on subjective evaluations, whereas protocols that require many

measurements and greater detail are more time consuming and expensive. Few

protocols exist that are easy to apply, quantitatively adequate, and relatively

inexpensive.

Quality-control issues, such as consistency of measurements among observers,

have been addressed in some, but not all, protocols. Repeatability within a protocol

should be an important consideration for all monitoring protocols. Consistency

among protocols would bring added value and strength to management through a

larger database and broader scope of application. Recent efforts promote compatibility among the protocols used by large-scale monitoring programs in the Pacific

Northwest (Gallo et al. 2003, Lanigan 2003).

Several biological and physical characteristics of stream ecosystems seem to

be sensitive to land use activities. Pool abundance and quality were two of the

better documented measurements with respect to the presence of juvenile coho

salmon. The amount of large woody debris in streams was sensitive to timber

harvest activities and was an important habitat component related to salmonid

abundance. Watershed conditions such as poor road and drainage facilities (e.g.,

damaged culverts), excessive erosion, and inputs of sediments to channels were

common factors adversely affecting stream systems.

Clearly defined objectives are important elements in the sample design of

monitoring protocols, selection of physical and biological characteristics to be

Few protocols exist

that are easy to apply,

quantitatively

adequate, and

relatively inexpensive.
GENERAL TECHNICAL REPORT PNW-GTR-625

22

measured, and intensity of sampling. Comparisons of streams in different watersheds, including those not altered by logging, would provide a baseline of the range

of natural conditions and would help identify streams affected by these practices

(Roni et al. 2003).

Long-term monitoring programs can be important for coordinating efforts of

management organizations, decisionmakers, and researchers who intend to improve

and protect natural ecosystems. The ability of management policies to change over

time creates both opportunities and challenges for managing streams and can result

in continued policy improvements for managing ecosystems and watersheds.

Positive changes (e.g., through adaptive management) can result from new data.

English Equivalents

When you know: Multiply by: To find:

Meters (m) 3.28 Feet

Kilometers (km) .6215 Miles

Square kilometers (km2

) .386 Square miles

Literature Cited

Anderson, J.L.; Hilborn, R.W.; Lackey, R.T.; Ludwig, D. 2003. Watershed

restoration-adaptive decision making in the face of uncertainty. In: Wissmar,

R.C.; Bisson, P.A., eds. Strategies for restoring river ecosystems: sources of

variability and uncertainty in natural and management systems. Bethesda, MD:

American Fisheries Society: 203-232.

Aquatic and Riparian Effectiveness Monitoring Program [AREMP]. 2003.

Field protocol synopsis: 2003 field season. Corvallis, OR: U.S. Department of

Agriculture, Forest Service. 5 p. http://www.reo.gov/monitoring/watershed/

02fieldprotocol.pdf. (August 23, 2004).

Archer, E.K.; Roper, B.B.; Henderson, R.C. [et al.]. 2004. Testing common

stream sampling methods: How useful are these techniques for broad-scale,

long term monitoring? Gen. Tech. Rep. RMRS-GTR-122. Fort Collins, CO:

U.S. Department of Agriculture, Forest Service, Rocky Mountain Research

Station. 15 p.

Bain, M.B.; Hughes, T.C.; Arend, K.K. 1999. Trends in methods for assessing

freshwater habitats. In: Bain, M.B.; Stevenson, N.J., eds. Aquatic habitat

assessment. Bethesda, MD: American Fisheries Society: 193-200.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

23

Bain, M.B.; Stevenson, N.J., eds. 1999. Aquatic habitat assessment: common

methods. Bethesda, MD: American Fisheries Society. 224 p.

Barbour, M.T.; Gerritsen, J.; Snyder, B.D.; Stribling, J.B. 1999. Rapid

bioassessment protocols for use in streams and wadeable rivers: periphyton,

benthic macroinvertebrates and fish. 2nd ed. EPA 841-B-99-002. Washington,

DC: U.S. Environmental Protection Agency, Office of Water. http://

www.epa.gov/owow/monitoring/rbp/wp61pdf/rbp.pdf. (June 30, 2004).

Bauer, S.B.; Ralph, S.C. 1999. Appendix D: annotated bibliography for aquatic

habitat indicators and their application to water quality objectives within the

Clean Water Act. EPA-910-R-99-014. Seattle, WA: U.S. Environmental

Protection Agency, Region 10. 77 p. http://www.krisweb.com/biblio/

gen_usepa_baueretal_1999_ahibibli.pdf. (June 30, 2004).

Bauer, S.B.; Ralph, S.C. 2001. Strengthening the use of aquatic habitat indicators

in Clean Water Act programs. Fisheries. 26:14-24.

Bilby, R.E.; Reeves, G.H.; Dolloff, C.A. 2003. Sources of variability in aquatic

ecosystems: factors controlling biotic production and diversity. In: Wissmar,

R.C.; Bisson, P.A., eds. Strategies for restoring river ecosystems: sources of

variability and uncertainty in natural and managed systems. Bethesda, MD:

American Fisheries Society: 129-146.

Collins, B.; Pess, G.R. 1997. Critique of Washington state’s watershed analysis

program. Journal of the American Water Resources Association. 33: 997-1010.

Conquest, L.L.; Ralph, S.C. 1998. Statistical design and analysis considerations

for monitoring and assessment. In: Naiman, R.J.; Bilby, R.E., eds. River

ecology and management: lessons from the Pacific coastal ecoregion. New

York: Springer-Verlag: 455-475.

Dambacher, J.M.; Jones, K.K.; Li, H.W. 2001. The distribution and abundance

of Great Basin redband trout: an application of variable probability sampling

in a 1999 status review. Information Report 2001-08. Portland, OR: Oregon

Department of Fish and Wildlife. 26 p. http://oregonstate.edu/Dept/ODFW/

freshwater/inventory/pdffiles/Dambacher_et_al_Info_Report_2001-08.pdf.

(June 30, 2004).

Dolloff, C.A.; Hankin, D.G.; Reeves G.H. 1993. Basinwide estimation of habitat

and fish populations in streams. Gen. Tech. Rep. SE-GTR-83. Asheville, NC:

U.S. Department of Agriculture, Forest Service, Southeastern Forest Experiment Station. 25 p. http://www.trout.forprod.vt.edu/fishpubs/

dolloff1993_01.pdf. (June 30, 2004).
GENERAL TECHNICAL REPORT PNW-GTR-625

24

Duff, D.A.; Cooper, J.L. 1978. Techniques for conducting stream habitat surveys

on national resource land. Tech. Note. Denver, CO: U.S. Department of the

Interior, Bureau of Land Management. 73 p.

Fitzpatrick, F.A.; Waite, I.R.; D’Arconte, P.J. [et al.]. 1998. Revised methods

for characterizing stream habitat in the national water-quality assessment

program. Water-Resources Investigations Report 98-4052. U.S. Department

of the Interior, Geological Survey. http://water.usgs.gov/nawqa/protocols/

WRI98-4052/index.html. (June 30, 2004).

Forest Ecosystem Management Assessment Team [FEMAT]. 1993. Forest

ecosystem management: an ecological, economic, and social assessment.

Portland, OR: U.S. Department of Agriculture; U.S. Department of the Interior

[et al.]. [Irregular pagination].

Gallo, K.; Moyer, C.; Lanigan, S. 2003. Interagency regional monitoring: Northwest Forest Plan aquatic and riparian effectiveness monitoring program.

2002 annual report. Corvallis, OR: U.S. Department of Agriculture, Forest

Service. http://www.reo.gov/monitoring/watershed/docs/2002Report.pdf.

(June 30, 2004).

Gregory, K.J.; Bisson, P.A. 1997. Degradation and loss of anadromous salmonid

habitat in the Pacific Northwest. In: Stouder, D.J.; Bisson, P.A.; Naiman,

R.J., eds. Pacific salmon and their ecosystems. New York: Chapman and

Hall: 277-314.

Grizzel, J.; McGowan, M.; Smith, D.; Beechie, T. 2000. Streamside buffers and

large woody debris recruitment: evaluating the effectiveness of watershed

analysis prescriptions in the North Cascades Region. TFW Effectiveness

Monitoring Report. TFW-MAG1-00-003. Olympia, WA: Washington Department of Natural Resources. 38 p.

Hall, J.D.; Brown, G.W.; Lantz, R.L. 1987. The Alsea watershed study: a

retrospective. In: Salo, E.O.; Cundy, T.W., eds. Streamside management:

forestry and fishery interactions. Seattle, WA: University of Washington

Press: 399-416.

Hankin, D.G.; Reeves, G.H. 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.; Scrivener, J.C. 1990. Impacts of forestry practices on a coastal

stream ecosystem: Carnation Creek, British Columbia, Canada. Canadian

Bulletin of Fisheries and Aquatic Sciences. 223: 1-148.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

25

Hicks, B.J.; Hall, J.D.; Bisson, P.A.; Sedell, J.R. 1991. Responses of salmonids

to habitat changes. In: Meehan, W.R., ed. Influences of forest and rangeland

management on salmonid fishes and their habitats. Spec. Publ. 19. Bethesda,

MD: American Fisheries Society: 483-518.

Holling, C.S., ed. 1978. Adaptive environmental assessment and management.

New York: John Wiley. 377 p.

Holtby, B.L.; Andersen, B.C.; Kadowaki, R.K. 1990. Importance of smolt size

and early ocean growth to interannual variability in marine survival of coho

salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and Aquatic

Sciences. 47: 2181-2194.

Independent Multidisciplinary Science Team [IMST]. 1999. Recovery of wild

salmonids in western Oregon forests: Oregon Forest Practices Act rules and the

measures in the Oregon Plan for Salmon and Watersheds. Tech. Rep. 1999-1.

Salem, OR: Governor’s Natural Resources Office. 85 p.

Johnson, D.H.; O’Neal, J.; Knutzen, J. [et al.]. 2003. Protocols for counting

salmonids, resident fish, and lamprey in the Pacific Northwest. Olympia, WA:

Washington Department of Fish and Wildlife. 2 p.

Johnson, D.H.; Pittman, N.; Wilder, E. [et al.]. 2001. Inventory and monitoring of salmon habitat in the Pacific Northwest: directory and synthesis of

protocols for management/research and volunteers in Washington, Oregon,

Idaho, Montana, and British Columbia. Olympia, WA: Washington Department of Fish and Wildlife. 212 p.

Kaufmann, P.R.; Levine, P.; Robinson, E.G. [et al.]. 1999. Quantifying physical

habitat in wadeable streams. EPA/620/R-99/003. Washington, DC: U.S.

Environmental Protection Agency. 102 p. http://www.epa.gov/emap/html/pubs/

docs/groupdocs/surfwatr/field/phyhab.pdf. (June 30, 2004).

Kershner, J.L.; Coles-Ritchie, M.; Cowley, E. [et al.]. 2003. A plan to monitor

the aquatic and riparian resources in the area of PACFISH/INFISH and the

biological opinions for bull trout, salmon, and steelhead. Logan, UT: U.S.

Department of Agriculture, Forest Service, Fish and Aquatic Ecology Unit.

http://www.fs.fed.us/biology/resources/pubs/feu/pibo_final_011003.pdf.

(August 23, 2004).

Kurtz, J.C.; Jackson, L.E.; Fisher, W.S. 2001. Strategies for evaluating indicators based on guidelines from the EPA’s Office of Research and Development.

Ecological Indicators. 1: 49-60.
GENERAL TECHNICAL REPORT PNW-GTR-625

26

Lanigan, S. 2002. Monitoring watershed health: state-federal monitoring partnership. Sept. 2002 progress overview. Corvallis, OR: U.S. Department of Agriculture, Forest Service. http://www.reo.gov/monitoring/watershed/docs/

Overview_of_efforts_.html. (August 23, 2004).

Lanigan, S. 2003. Monitoring protocol attributes. http://www.reo.gov/monitoring/

watershed/docs/Attributesformonitoringcomparison_Master_Table.html.

(November 24, 2003).

Lazorchak, J.M.; Klemm, D.J.; Peck, D.V., eds. 1998. Environmental monitoring

and assessment program—surface waters: field operations and methods for

measuring the ecological condition of wadeable streams. EPA/620/R-94/004F.

Washington, DC: U.S. Environmental Protection Agency. [Pages unknown].

http://www.epa.gov/emap/html/pubs/docs/groupdocs/surfwatr/field/

ws_abs.html. (June 30, 2004).

MacDonald, L.H.; Smart, A.W.; Wissmar, R.C. 1991. Monitoring guidelines to

evaluate effects of forestry activities on streams in the Pacific Northwest and

Alaska. Seattle, WA: Region 10, U.S. Environmental Protection Agency. 166 p.

McDonald, T.L. 2002. Review of environmental monitoring: survey designs.

Environmental Monitoring and Assessment. 1: 1-16.

Meador, M.R.; Cuffney, T.F.; Gurtz, M.E. 1993. Methods for sampling fish

communities as part of the National Water-Quality Assessment Program. Rep.

93-104. Raleigh, NC: U.S. Department of the Interior, U.S. Geological Survey.

[Pages unknown]. http://water.usgs.gov/nawqa/protocols/OFR-93-104/

fish3.html. (June 30, 2004).

Medsser, J.J.; Linthurst, R.A.; Overton, W.S. 1991. An EPA program for monitoring ecological status and trends. Environmental Monitoring and Assessment.

17: 67-78.

Meehan, W.R., ed. 1991. Influences of forest and rangeland management on

salmonid fishes and their habitats. Spec. Publ. 19. Bethesda, MD: American

Fisheries Society. 751 p.

Montgomery, D.R.; Buffington, J.M. 1993. Channel classification, prediction of

channel response, and assessment of channel condition. Washington State

Timber/Fish/Wildlife Report TFW-SH10-93-002. Olympia, WA: Washington

Department of Natural Resources. 84 p.

Montgomery, D.R.; Buffington, J.M.; Smith, R.D. [et al.]. 1995. Pool spacing in

forest channels. Water Resources Research. 31: 1097-1105.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

27

Moore, K.; Jones, K.; Dambacher, J. 2000. Methods for stream habitat surveys,

version 10.1. Corvallis, OR: Oregon Department of Fish and Wildlife,

Corvallis Research Lab. [Pages unknown].

Morrison, M.L.; Marcot, B.G. 1995. An evaluation of resource inventory and

monitoring programs used in national forest planning. Environmental Monitoring and Assessment. 19: 147-156.

Moulton, S.R., II; Kennen, J.G.; Goldstein, R.M.; Hambrook, J. 2002. Revised

protocols for sampling algal, invertebrate, and fish communities as part of the

National Water-Quality Assessment Program. Rep. 02-150. Reston, VA: U.S.

Department of the Interior, U.S. Geological Survey. 75 p. http://water.usgs.gov/

nawqa/protocols/OFR02-150/OFR02-150.pdf. (August 23, 2004).

National Council for Air and Stream Improvement, Inc. [NCASI]. 1988.

Procedures for assessing the effectiveness of Best Management Practices in

protecting water and stream quality associated with managed forests. Tech.

Bull. No. 538. New York. 23 p.

National Park Service. 2003. Monitoring natural resources in our national parks.

U.S. Department of the Interior. http://science.nature.nps.gov/im/monitor/.

(November 25, 2003).

Nickelson, T.E.; Rodgers, J.D.; Johnson, S.L.; Solazzi, M.F. 1992. Seasonal

changes in habitat use by juvenile coho salmon (Oncorhynchus kisutch) in

Oregon coastal streams. Canadian Journal of Fisheries and Aquatic Sciences.

49: 783-789.

Peck, D.V.; Lazorchak, J.M.; Klemm, D.J., eds. 2001. Environmental monitoring

and assessment program—surface waters: Western pilot study field operations

manual for wadeable streams. Washington, DC: U.S. Environmental Protection

Agency. http://www.epa.gov/emap/html/pubs/docs/groupdocs/surfwatr/field/

ewwsm01.html. (June 30, 2004).

Peterson, J.T.; Wollrab, S.P. 1999. An analysis of potential stream fish and fish

habitat monitoring procedures for the inland Northwest. Annual report 1999 to

Bonneville Power Administration DOE/BP-25866-1. Portland, OR: Bonneville

Power Administration. 52 p. http://www.efw.bpa.gov/Environment/EW/EWP/

DOCS/REPORTS/HABITAT/H25866-1.pdf. (June 30, 2004).

Platts, W.S.; Armour, C.; Booth, G.D. [et al.]. 1987. Methods for evaluating

riparian habitats with applications to management. Gen. Tech. Rep. INT-221.

Ogden, UT: U.S. Department Of Agriculture, Forest Service, Intermountain

Forest and Range Experiment Station. 177 p.
GENERAL TECHNICAL REPORT PNW-GTR-625

28

Pleus, A.E.; Schuett-Hames, D.; Bullchild, L. 1999. TFW monitoring program

method manual for the habitat unit survey. TFW-AM9-99-003. Olympia, WA:

Washington Department of Natural Resources. 68 p.

Quinn, T.P.; Peterson, N.P. 1994. The effect of forest practices on fish populations. Final Report. TFW-F4-94-001. Seattle, WA: University of Washington,

Center for Streamside Studies. 157 p. http://www.krisweb.com/kriskootenai/

krisdb/html/krisweb/biblio/gen_tfw_quinnetal_1994_f494001.pdf. (June 30,

2004).

Quinn, T.P.; Peterson, N.P. 1996. The influence of habitat complexity and fish

size on over-winter survival and growth of individually marked juvenile coho

salmon (Oncorhynchus kisutch) in Big Beef Creek, Washington. Canadian

Journal of Fish and Aquatic Sciences. 53: 1555-1564.

Ralph S.C.; Pool, G.C. 2003. Putting monitoring first: designing accountable

ecosystem restoration and management plans. In: Montgomery, D.R.; Bolton,

S.; Booth, D.B.; Wall, L., eds. Restoration of Puget Sound rivers. Seattle, WA:

University of Washington Press: 226–247.

Reeves, G.H.; Hohler, D.B.; Larsen, D.P. [et al.]. 2003. Aquatic and riparian

effectiveness monitoring plan for the Northwest Forest Plan. Gen. Tech. Rep.

PNW-GTR-577. Portland, OR: U.S. Department of Agriculture, Forest Service,

Pacific Northwest Research Station. 71 p. http://www.fs.fed.us/pnw/pubs/

gtr577.pdf. (June 30, 2004).

Regier, H.A. 1976. Environmental biology of fishes: emerging science. Environmental Biology of Fishes. 1: 5-11.

Rinne, J.N. 1985. Physical habitat evaluation of small stream fishes: point vs.

transect, observation vs. capture methodologies. Journal of Freshwater Ecology. 3: 121-131.

Roni, P., ed. [In press]. Monitoring stream and watershed restoration. Bethesda,

MD: American Fisheries Society.

Roni, P.; Liermann, M.; Steel, A. 2003. Monitoring and evaluating fish response

to instream restoration. In: Montgomery, D.R.; Bolton, S.; Booth, D.B.; Wall,

L., eds. Restoration of Puget Sound rivers. Seattle, WA: University of

Washington Press. 318–339.

Roni, P.; Quinn, T. 2001. Density and size of juvenile salmonids in response to

placement of large woody debris in western Oregon and Washington streams.

Canadian Journal of Fisheries and Aquatic Sciences. 58: 282-292.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

29

Roper, B.B.; Kershner, J.L.; Archer, E. [et al.]. 2002. An evaluation of physical

stream habitat attributes used to monitor streams. Journal of American Water

Resources. 38: 1637-1646.

Rosenfeld, J.; Porter, M.; Parkinson, E. 2000. Habitat factors affecting the

abundance and distribution of juvenile cutthroat trout (Oncorhynchus clarki)

and coho salmon (Oncorhynchus kisutch). Canadian Journal of Fisheries and

Aquatic Sciences. 57: 766-774.

Schuett-Hames, D.; Pleus, A.E.; Smith, D. 1999. TFW Monitoring Program

method manual for the salmonid spawning habitat availability survey. TFWAM9-99-007. Olympia, WA: Washington Department of Natural Resources.

82 p.

Seiler, D.; Volkhardt, G.; Murdoch, A. [et al.]. 2002. 2002 index watershed

salmon recovery monitoring report. Olympia, WA: Washington Department

of Ecology. 48 p. http://www.ecy.wa.gov/pubs/0203061.pdf. (July 1, 2004).

Skagit Watershed Council. 2000. Application of the Skagit Watershed Council’s

strategy: basin analysis of the Skagit and Samish basins: tools for salmon

habitat restoration and protection. Mount Vernon, WA. 80 p.

Solazzi, M.F.; Johnson, S.L.; Miller, B. [et al.]. 2003. Salmonid life-cycle monitoring project 2002 report. OPSW-ODFW-2003-2. Portland, OR: Oregon

Department of Fish and Wildlife. 20 p. http://oregonstate.edu/Dept/ODFW/

progress-reports/annual2002ver2.pdf. (July 1, 2004).

Spence, B.C.; Lomnicky, G.A.; Hughes, R.M.; Novitzki, R.P. 1996. An

ecosystem approach to salmonid conservation. TR-4501-96-6057. Corvallis,

OR: ManTech Environmental Research Services Corp. [Not paged].

http://www.nwr.noaa.gov/1habcon/habweb/habguide/ManTech/front.htm.

(July 1, 2004).

Stankey, G.H.; Bormann, B.T.; Ryan, C. [et al.]. 2003. Adaptive management

and the Northwest Forest Plan: rhetoric and reality. Journal of Forestry. 101:

40-46.

Stevens, D.L., Jr. 2002. Sampling design and statistical analysis methods for the

integrated biological and physical monitoring of Oregon streams. OPSWODFW-2002-07. Portland, OR: Oregon Department of Fish and Wildlife.

14 p. http://oregonstate.edu/Dept/ODFW/spawn/pdf%20files/reports/

DesignStevens.pdf. (July 1, 2004).

Thompson, W.L. 2003. Hankin and Reeves’ approach to estimating fish abundance

in small streams: limitations and alternatives. Transactions of the American

Fisheries Society. 132: 69-75.
GENERAL TECHNICAL REPORT PNW-GTR-625

30

Thurow, R.F.; Peterson, J.T.; Larson, C.A.; Guzevich, J.W. 2004. Development of bull trout sampling efficiency models. Final Report to USDI Fish

and Wildlife Service Aquatic Resources Division. Boise, ID: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station. 68 p.

http://www.fs.fed.us/rm/boise/teams/fisheries/publications/

Thurow%20et%20al.%20Final%20Report%202004_2%20.pdf. (August 23,

2004).

U.S. Department of Agriculture, Forest Service [USDA FS]. 1994. Section 7,

fish habitat monitoring protocol for the upper Columbia River basin. Portland,

OR: Pacific Northwest Region, Intermountain Region, Northern Region. On

file with: Forestry Sciences Laboratory, 2770 Sherwood Lane, Suite 2A,

Juneau, AK 99802-1628. 61 p.

U.S. Department of Agriculture, Forest Service [USDA FS]. 1995. Report to

Congress: anadromous fish habitat assessment. R10-MB-279. Juneau, AK:

Alaska Region and Pacific Northwest Research Station. [Pages unknown].

U.S. Department of Agriculture, Forest Service [USDA FS]. 1997. Tongass

Land Management Plan Revision. Final Environmental Impact Statement.

Juneau, AK: Region 10 [Alaska]. http://www.tongass-seis.net/seis/index.html.

(August 23, 2004).

U.S. Department of Agriculture, Forest Service [USDA FS]. 2001. Fish and

aquatic stream habitat assessment. Chapter 20 FSH 2090-Aquatic Ecosystem

Management Handbook, R-10 amendment 2090-2001-1. Juneau, AK: Region

10 [Alaska]. [Not paged].

U.S. Department of Agriculture, Forest Service [USDA FS]. 2002. Stream

inventory handbook: levels 1 and 2. Region 6 version 2.2. Portland, OR:

Pacific Northwest Region. [Pages unknown].

U.S. Department of Agriculture, Forest Service [USDA FS]. 2003. Inventory

and Monitoring Institute. http://www.fs.fed.us/institute/. (November 25, 2003).

U.S. Department of Agriculture, Forest Service; U.S. Department of the

Interior, Bureau of Land Management [USDA and USDI]. 1994. Record of

Decision for amendments to Forest Service and Bureau of Land Management

planning documents within the range of the northern spotted owl. [Place of

publication unknown]. 74 p. [Plus attachment A: standards and guidelines].
A Review of Protocols for Monitoring Streams and Juvenile Fish...

31

U.S. Environmental Protection Agency [USEPA]. 1989. Rapid bio-assessment

protocols for use in streams and rivers: benthic macro-invertebrates and fish.

EPA/444/4-89-001. Washington, DC: Office of Water. [Pages unknown].

http://www.epa.gov/owowwtr1/monitoring/rbp/index.html. (August 23, 2004).

U.S. Environmental Protection Agency [USEPA]. 1990. Biological criteria. EPA/

440/5-90-004, Washington, DC. [Pages unknown]. http://www.epa.gov/

bioindicators/html/biolcont.html. (August 23, 2004).

Walters, C.J. 1986. Adaptive management of renewable resources. New York:

Macmillan. 374 p.

Wissmar, R.C. 1993. The need for long-term monitoring programs in forest

ecosystems of the Pacific Northwest. Environmental Monitoring and Assessment. 26: 219-234.
GENERAL TECHNICAL REPORT PNW-GTR-625

32

Appendix: Literature Identified as Most Relevant to

Protocols for Monitoring Streams and Juvenile Fish

Andersen, T. 2001. Kalispel resident fish project. Annual Report, Project No.

1995-00100 DOE/BP-37227-5. Portland, OR: Bonneville Power Administration. 75 p. http://www.efw.bpa.gov/Environment/EW/EWP/DOCS/REPORTS/

RESIDENT/R37227-5.pdf. (July 1, 2004).

Aquatic and Riparian Effectiveness Monitoring Program [AREMP]. 2003.

Field protocol synopsis: 2003 field season. Corvallis, OR: U.S. Department of

Agriculture, Forest Service. 5 p. http://www.reo.gov/monitoring/watershed/

02fieldprotocol.pdf. (August 23, 2004).

Armour, C.L.; Burnham, K.P.; Platt, W.S. 1983. Field methods and statistical

analyses for monitoring small salmonid streams. FWS/OBS-83/33. Washington, DC: U.S. Department of the Interior, Fish and Wildlife Service, Western

Energy and Land Use Team, Division of Biological Services, Research and

Development. 200 p.

Bain, M.B.; Stevenson, N.J., eds. 1999. Aquatic habitat assessment: common

methods. Bethesda, MD: American Fisheries Society. 224 p.

Barbour, M.T.; Gerritsen, J.; Snyder, B.D.; Stribling, J.B. 1999. Rapid

bioassessment protocols for use in streams and wadeable rivers: periphyton,

benthic macroinvertebrates and fish. 2nd ed. EPA 841-B-99-002. Washington,

DC: U.S. Environmental Protection Agency, Office of Water. http://

www.epa.gov/owow/monitoring/rbp/wp61pdf/rbp.pdf. (June 30, 2004).

British Columbia Ministry of Fisheries. 1999. Overview fish and fish habitat

inventory, methodology version 1.0. http://srmwww.gov.bc.ca/risc/pubs/

aquatic/overview/assets/overview.pdf. (October 31, 2003).

British Columbia Ministry of Fisheries. 2001. Reconnaissance (1:20,000)

fish and fish habitat inventory: standards and procedures, version 2.0.

http://srmwww.gov.bc.ca/risc/pubs/aquatic/recon/recce2c.pdf.

(October 31, 2003).

California Department of Fish and Game. 2003. California coastal salmonid

restoration monitoring and evaluation program: interim restoration effectiveness and validation monitoring protocols (draft). Fortuna, CA: California

Department of Fish and Game. 359 p. http://www.dfg.ca.gov/nafwb/pubs/2003/

200303_Interim_Protocol_Manual.pdf. (March 2003).

Coyle, T.; Karl, D.; Mendel, G. 2001. Assessment of salmonids and their habitat

conditions in the Walla Walla River basin. Annual report. BPA Report DOE/

BP-00000485-1. 108 p. http://www.efw.bpa.gov/Environment/EW/EWP/

DOCS/REPORTS/RESIDENT/R00000485-1.pdf . (July 1, 2004).
A Review of Protocols for Monitoring Streams and Juvenile Fish...

33

Dambacher, J.M.; Jones, K.K.; Li, H.W. 2001. The distribution and abundance

of Great Basin redband trout: an application of variable probability sampling in

a 1999 status review. Information Report 2001-08. Portland, OR: Oregon

Department of Fish and Wildlife. 26 p. http://oregonstate.edu/Dept/ODFW/

freshwater/inventory/pdffiles/Dambacher_et_al_Info_Report_2001-08.pdf.

(June 30, 2004).

Dolloff, C.A.; Hankin, D.G.; Reeves G.H. 1993. Basinwide estimation of habitat

and fish populations in streams. Gen. Tech. Rep. SE-GTR-83. Asheville, NC:

U.S. Department of Agriculture, Forest Service, Southeastern Forest Experiment Station. 25 p. http://www.trout.forprod.vt.edu/fishpubs/

dolloff1993_01.pdf. (June 30, 2004).

Dunham, J. 2000. Sampling protocol: bull trout habitat study (DRAFT). Boise,

ID: U.S. Department of Agriculture, Forest Service, Rocky Mountain Research

Station. 23 p.

Fitzpatrick, F.A.; Waite, I.R.; D’Arconte, P.J. [et al.]. 1998. Revised methods

for characterizing stream habitat in the national water-quality assessment

program. Water-Resources Investigations Report 98-4052. U.S. Department of

the Interior, Geological Survey. http://water.usgs.gov/nawqa/protocols/WRI98-

4052/index.html. (June 30, 2004).

Hankin, D.G. 1984. Multistage sampling designs in fisheries research applications

in small streams. Canadian Journal of Fisheries and Aquatic Sciences.

41: 1575-1591.

Hankin, D.G.; Reeves, G.H. 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.

Jones, M.L.; Stockwell, J.D. 1995. A rapid assessment procedure for the enumeration of salmonine populations in streams. North American Journal of Fisheries

Management. 15: 551-562.

Kershner, J.L.; Coles-Ritchie, M.; Cowley, E. [et al.]. 2003. A plan to monitor

the aquatic and riparian resources in the area of PACFISH/INFISH and the

biological opinions for bull trout, salmon, and steelhead. Logan, UT: U.S.

Department of Agriculture, Forest Service, Fish and Aquatic Ecology Unit.

[Pages unknown]. http://www.fs.fed.us/biology/resources/pubs/feu/

pibo_final_011003.pdf. (August 23, 2004).
GENERAL TECHNICAL REPORT PNW-GTR-625

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Lazorchak, J.M.; Klemm, D.J.; Peck, D.V., eds. 1998. Environmental monitoring

and assessment program—surface waters: field operations and methods for

measuring the ecological condition of wadeable streams. EPA/620/R-94/004F.

Washington, DC: U.S. Environmental Protection Agency. [Pages unknown].

http://www.epa.gov/emap/html/pubs/docs/groupdocs/surfwatr/field/

ws_abs.html. (June 30, 2004).

McCullough, D.A.; Espinosa, F.A. 1996. A monitoring strategy for application to

salmon-bearing watersheds. Tech. Rep. 96-5. Portland, OR: Columbia River

Inter-Tribal Fish Commission. 169 p. [plus appendices]. http://www.critfc.org/

tech/96-5report.pdf. (August 24, 2004).

Meador, M.R.; Cuffney, T.F.; Gurtz, M.E. 1993. Methods for sampling fish

communities as part of the national water-quality assessment program. Rep.

93-104. Raleigh, NC: U.S. Department of the Interior, U.S. Geological Survey.

[Pages unknown]. http://water.usgs.gov/nawqa/protocols/OFR-93-104/

fish3.html. (June 30, 2004).

Moore, K.; Jones, K.; Dambacher, J. 2000. Methods for stream habitat surveys,

version 10.1. Corvallis, OR: Oregon Department of Fish and Wildlife,

Corvallis Research Lab. [Pages unknown].

Moulton, S.R., II; Kennen, J.G.; Goldstein, R.M.; Hambrook, J. 2002. Revised

protocols for sampling algal, invertebrate, and fish communities

as part of the national water-quality assessment program. Rep. 02-150.

Reston, VA: U.S. Department of the Interior, U.S. Geological Survey. 75 p.

http://water.usgs.gov/nawqa/protocols/OFR02-150/OFR02-150.pdf.

(August 23, 2004).

Murphy, P.; Huntington, C.W. 1995. Updated stream survey methodology for the

Clearwater National Forest. Orofino, ID: Clearwater National Forest. [Pages

unknown].

Neilson, L.A.; Johnson, D.L., eds. 1983. Fisheries techniques. Bethesda, MD:

American Fisheries Society. 468 p.

Niemelae, E.; Julkunen, M.; Erkinaro, J. 1999. Revealing trends in densities of

juvenile Atlantic salmon, Salmo salar L., in the subarctic River Teno using

cluster analysis on long-term sampling data. Fisheries Management and

Ecology. 6: 207-220.

Oregon Coastal Salmon Restoration Initiative. 1997. OCSRI Conservation Plan.

Final plan. Salem, OR: Oregon Coastal Salmon Restoration Initiative. Chapter

16. On file with: Forestry Sciences Laboratory, 2770 Sherwood Lane, Suite

2A, Juneau, AK 99802-1628.
A Review of Protocols for Monitoring Streams and Juvenile Fish...

35

Overton, S.W.; McDonald, T.L. 1998. Regional estimation of juvenile coho

abundance in streams. West Technical Report 98-5. Cheyenne, WY: Western

EcoSystems Technology, Inc. On file with: Forestry Sciences Laboratory, 2770

Sherwood Lane, Suite 2A, Juneau, AK 99802-1628.

Peck, D.V.; Lazorchak, J.M.; Klemm, D.J., eds. 2001. Environmental monitoring and assessment program—surface waters: Western pilot study field operations manual for wadeable streams. Washington, DC: U.S. Environmental

Protection Agency. http://www.epa.gov/emap/html/pubs/docs/groupdocs/

surfwatr/field/ewwsm01.html. (June 30, 2004).

Peterson, J.T.; Wollrab, S.P. 1999. An analysis of potential stream fish and fish

habitat monitoring procedures for the inland Northwest. Annual report 1999 to

Bonneville Power Administration DOE/BP-25866-1. Portland, OR: Bonneville

Power Administration. 52 p. http://www.efw.bpa.gov/Environment/EW/EWP/

DOCS/REPORTS/HABITAT/H25866-1.pdf. (June 30, 2004).

Pleus, A.E.; Schuett-Hames, D.; Bullchild, L. 1999. TFW monitoring program

method manual for the habitat unit survey. TFW-AM9-99-003. Olympia, WA:

Washington Department of Natural Resources. 68 p.

Reeves, G.H.; Hohler, D.B.; Larsen, D.P. [et al.]. 2003. Aquatic and riparian

effectiveness monitoring plan for the Northwest Forest Plan. Gen. Tech. Rep.

PNW-GTR-577. Portland, OR: U.S. Department of Agriculture, Forest Service,

Pacific Northwest Research Station. 71 p. http://www.fs.fed.us/pnw/pubs/

gtr577.pdf. (June 30, 2004).

Seiler, D.; Volkhardt, G.; Murdoch, A. [et al.]. 2002. 2002 index watershed

salmon recovery monitoring report. Olympia, WA: Washington Department of

Ecology. 48 p. http://www.ecy.wa.gov/pubs/0203061.pdf. (July 1, 2004).

Solazzi, M.F.; Johnson, S.L.; Miller, B. [et al.]. 2003. Salmonid life-cycle

monitoring project 2002 report. OPSW-ODFW-2003-2. Portland, OR: Oregon

Department of Fish and Wildlife. 20 p. http://oregonstate.edu/Dept/ODFW/

progress-reports/annual2002ver2.pdf. (July 1, 2004).

Spence, B.C.; Lomnicky, G.A.; Hughes, R.M.; Novitzki, R.P. 1996. An ecosystem approach to salmonid conservation. TR-4501-96-6057. Corvallis, OR:

ManTech Environmental Research Services Corp. [Not paged].

http://www.nwr.noaa.gov/1habcon/habweb/habguide/ManTech/front.htm.

(July 1, 2004).
GENERAL TECHNICAL REPORT PNW-GTR-625

36

Stevens, D.L., Jr. 2002. Sampling design and statistical analysis methods for

the integrated biological and physical monitoring of Oregon streams. OPSWODFW-2002-07. Portland, OR: Oregon Department of Fish and Wildlife. 14 p.

http://oregonstate.edu/Dept/ODFW/spawn/pdf%20files/reports/

DesignStevens.pdf. (July 1, 2004).

U.S. Department of Agriculture, Forest Service. 1993. Stream inventory handbook: level 1 & 2. Version 7.0. Portland, OR: Pacific Northwest Region. [Pages

unknown].

U.S. Department of Agriculture, Forest Service. 2002. Stream inventory handbook: levels 1 and 2. Region 6 version 2.2. Portland, OR: Pacific Northwest

Region. [Pages unknown].
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