NOAA Technical Memorandum NMFS-NWFSC-130

Puget Sound 

Chinook Salmon Recovery

A Framework for the Development of 

Monitoring and Adaptive Management Plans

September 2015

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Northwest Fisheries Science Center
NOAA Technical Memorandum

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The Northwest Fisheries Science Center of NOAA’s

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imply endorsement by the National Marine Fisheries Service.

Reference this document as follows:

Puget Sound Recovery Implementation Technical Team. 

2015. Puget Sound Chinook salmon recovery: A framework 

for the development of monitoring and adaptive management 

plans. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-130.
NOAA Technical Memorandum NMFS-NWFSC-130

Puget Sound 

Chinook Salmon Recovery

A Framework for the Development of 

Monitoring and Adaptive Management Plans

Puget Sound Recovery Implementation Technical Team

Northwest Fisheries Science Center

2725 Montlake Boulevard East

Seattle, Washington 98112

September 2015

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Most NOAA Technical Memorandums

NMFS-NWFSC are available at the 

Northwest Fisheries Science Center

Web site, http://www.nwfsc.noaa.gov

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Table of Contents

List of Figures...............................................................................................................................................v

List of Tables..............................................................................................................................................vii

Executive Summary.....................................................................................................................................ix

Acknowledgments......................................................................................................................................xiii

Framework Structure ....................................................................................................................................1

Introduction ..............................................................................................................................................1

Purpose and Scope....................................................................................................................................2

The Open Standards Approach.................................................................................................................3

Elements of the Framework......................................................................................................................4

Regional-scale Application.......................................................................................................................6

Monitoring and Adaptive Management....................................................................................................6

Ecosystem Components................................................................................................................................8

Key Ecological Attributes and Indicators for Chinook Salmon .............................................................10

Background ........................................................................................................................................10

KEAs and Indicators..........................................................................................................................11

Key Ecological Attributes and Indicators for Freshwater Habitats........................................................16

Background ........................................................................................................................................16

Key Ecological Attributes and Indicators ..........................................................................................18

Key Ecological Attributes and Indicators for Estuarine and Marine Habitats........................................34

Background ........................................................................................................................................34

Estuarine and Marine Habitat Components........................................................................................34

Key Ecological Attributes and Indicators ..........................................................................................39

Key Ecological Attributes and Indicators for Species and Food Webs..................................................59

Background ........................................................................................................................................59

Key Ecological Attributes and Indicators ..........................................................................................61

Framework Process.....................................................................................................................................68

General Application of the Framework ..................................................................................................68

Open Standards Tools for Applying the Framework..............................................................................68

Process: Eight Steps for Applying the Framework.................................................................................79
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Regional-scale Application ..................................................................................................................... 81

Monitoring and Adaptive Management .................................................................................................. 82

Conclusion .................................................................................................................................................. 83

Glossary ...................................................................................................................................................... 85

Abbreviations.......................................................................................................................................... 85

Terms Related to Ecosystem Components ............................................................................................. 86

Chinook Salmon Life Stages .............................................................................................................. 86

Freshwater Habitats ............................................................................................................................ 87

Estuarine and Marine Habitats ........................................................................................................... 88

References ................................................................................................................................................... 93

Appendix A: Terminology Crosswalk ...................................................................................................... 111

Appendix B: Supporting Information for Select Elements ....................................................................... 113

Pressures ............................................................................................................................................... 113

Stresses ................................................................................................................................................. 131

Contributing Factors ............................................................................................................................. 141

Drivers .................................................................................................................................................. 141

Strategies .............................................................................................................................................. 141

Appendix C: Other Monitoring Projects and Programs ............................................................................ 145
v

Figures

Figure 1. Five general steps used to organize the Open Standards system..................................................3

Figure 2. Conceptual diagram of linkages between landscape controls, habitat characteristics, and 

biotic responses...........................................................................................................................................10

Figure 3. Schematic diagram of the life cycle of Puget Sound Chinook salmon and the freshwater, 

estuarine, and marine habitats associated with each life stage....................................................................11

Figure 4. Relationships between freshwater habitat ecosystem components and Chinook salmon life 

stages, as described in the framework and depicted in Miradi software.....................................................12

Figure 5. Relationships between estuarine and marine habitat ecosystem components and Chinook 

salmon life stages, as described in the framework and depicted in Miradi.................................................13

Figure 6. Freshwater habitat ecosystem components organized by habitat type and watershed scale 

or system type, as described in the framework and depicted in Miradi......................................................20

Figure 7. Conceptual diagram of linkages between landscape controls, ecosystem processes, and 

freshwater habitat conditions......................................................................................................................23

Figure 8. Estuarine and marine habitats, as described in the framework and depicted in Miradi..............37

Figure 9. Shoreline habitats typical to Puget Sound ..................................................................................38

Figure 10. Cross section of a beach showing typical nearshore marine habitat zones in the Puget 

Sound region ...............................................................................................................................................39

Figure 11. Ecosystem components and system types for component categories of freshwater habitats, 

estuarine and marine habitats, species and food webs, and salmonids, as described in the framework 

and depicted in Miradi ................................................................................................................................70

Figure 12. Generic portfolio of elements, as described in the framework and depicted in Miradi............71

Figure 13. Key to relationships between the portfolio of elements within a watershed conceptual 

model, as described in the framework and depicted in Miradi ...................................................................72

Figure 14. Taxonomy of sources of pressures developed by the Puget Sound Partnership and as 

described in the framework and depicted in Miradi....................................................................................73

Figure 15. Taxonomy of Chinook salmon stresses organized by Chinook salmon life cycle, as 

described in the framework and depicted in Miradi....................................................................................74

Figure 16. Taxonomy of habitat stresses organized by stress type, as described in the framework 

and depicted in Miradi ................................................................................................................................75

Figure 17. Example of a results chain addressing issues associated with culverts in salmon-bearing 

streams........................................................................................................................................................78
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Tables

Table 1. Fourteen ecosystem components associated with Chinook salmon recovery in the Puget 

Sound region .................................................................................................................................................8

Table 2. Chinook salmon life stages and their relationship to broad types of freshwater, estuarine, 

and marine habitats.......................................................................................................................................9

Table 3. Key ecological attributes (KEAs) and potential indicators for the Chinook salmon ecosystem 

component, organized by life cycle segments and events...........................................................................14

Table 4. KEAs and potential indicators for the Chinook salmon ecosystem component, organized 

by life cycle segments and events...............................................................................................................15

Table 5. Examples of ways in which abundance and productivity indicators for the Chinook salmon 

ecosystem component might be determined, either through direct measurements or calculations using 

other indicators............................................................................................................................................17

Table 6. Examples of ways in which spatial structure and diversity indicators for the Chinook salmon 

ecosystem component might be determined, either through direct measurements or calculations using 

other indicators............................................................................................................................................18

Table 7. Classification of freshwater habitats within Puget Sound watersheds.........................................19

Table 8. Priority KEAs for freshwater habitat components, organized by ecosystem process..................21

Table 9. Freshwater KEAs organized by ecosystem process and ecosystem component..........................22

Table 10. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at 

watershed and reach scales .........................................................................................................................24

Table 11. Classification of estuarine and marine habitats, showing the five largest hierarchical scales...35

Table 12. KEAs for estuarine and marine ecosystem components, organized by ecosystem process.......40

Table 13. Estuarine and marine KEAs organized by ecosystem process and ecosystem component .......41

Table 14. KEAs and example indicators for estuarine and marine ecosystem components, organized 

by component..............................................................................................................................................42

Table 15. KEAs and indicators for estuarine and marine components in the Skagit watershed................52

Table 16. Key ecological attributes, as related to Chinook salmon, for the species and food webs 

ecosystem component .................................................................................................................................60

Table 17. Examples of species and food webs indicators, grouped by KEA and relationship to 

Chinook salmon ..........................................................................................................................................63

Table 18. Examples of specific species or guilds that interact with Chinook salmon as predators, 

competitors, prey, etc., according to the literature......................................................................................65

Table 19. Eight-step outline for using the framework to develop a watershed-specific monitoring 

and adaptive management plan...................................................................................................................69
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Table 20. Example of a viability table for three indicators associated with two KEAs for 

Chinook salmon .......................................................................................................................................... 76

Table 21. Example of a viability table for four indicators associated with four KEAs for ecosystem 

components of freshwater, estuarine, and nearshore marine habitats ......................................................... 77

Table A-1. Crosswalk of terminology common to our framework, the Puget Sound Partnership, 

Open Standards, and Miradi software ....................................................................................................... 111

Table B-1. Taxonomy of Puget Sound pressure sources based on previous classifications .................... 114

Table B-2. Puget Sound stressors, the most proximate agents of change to Puget Sound ecosystems, 

including both human and natural processes that impair or degrade the system ...................................... 124

Table B-3. Stresses associated with KEAs of the Chinook salmon ecosystem component ..................... 132

Table B-4. Stresses associated with the KEAs of the habitat and species and food web ecosystem 

components ............................................................................................................................................... 134

Table B-5. Broad categories and examples of contributing factors that may exist in watersheds ........... 142

Table B-6. Broad categories and examples of drivers that may exist in watersheds ............................... 142

Table B-7. Categories of strategies common to both volumes of the Puget Sound Salmon 

Recovery Plan ........................................................................................................................................... 143
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Executive Summary

Chinook salmon (Oncorhynchus tshawytscha) were listed as threatened in Puget Sound 

under the U.S. Endangered Species Act (ESA) in 1999. In response, a coalition of public and 

private stakeholders, called the Shared Strategy for Puget Sound, developed a salmon recovery 

plan. The resulting Puget Sound Salmon Recovery Plan (hereinafter called the Recovery Plan) 

contained both regional (i.e., Sound-wide, Volume I) and local-scale (i.e., watershed-wide, 

Volume II) chapters. The Recovery Plan was submitted to the National Marine Fisheries Service 

(NMFS) in 2005, and in 2006 NMFS issued a required Supplement to the Recovery Plan, 

concluding that the Recovery Plan met the requirements of the ESA and adding addition 

elements. Among these, the supplement identified a critical need to develop and implement a 

rigorous monitoring and adaptive management framework to assess the effectiveness of actions 

and progress toward recovery.

This technical memorandum was developed by the Puget Sound Recovery

Implementation Technical Team (PS RITT) to provide a formal monitoring and adaptive 

management framework (hereinafter called the framework) for assessing Puget Sound Chinook 

salmon recovery. Monitoring and adaptive management have occurred at the watershed and 

regional scales as implementation of the Recovery Plan has proceeded. However, the lack of a 

formal framework has meant that there is no standardized vocabulary or shared common 

approach to articulate the key assumptions of the chapters in Volume II, test assumptions across 

chapters, or connect the local, watershed-scale information in Volume II with the regional-scale 

information in Volume I. This gap limits the collective ability of resource managers to assess the 

effectiveness of salmon recovery efforts across the region, identify uncertainties, and update 

priorities and actions in the Recovery Plan. Furthermore, the framework is intended to help 

salmon recovery managers formalize their local-scale monitoring and adaptive management

plans using a common approach.

We developed the framework using concepts taken from the Open Standards for the 

Practice of Conservation (hereinafter called Open Standards). Open Standards is a scalable, 

adaptable system widely used to design, manage, and monitor conservation projects. The 

framework builds on several interrelated categories of information, or elements. These elements 

are as follows:

• Ecosystem components—Species, ecological systems/habitats, or ecological processes 

that are chosen to represent and encompass the full suite of biodiversity in the project 

area for place-based conservation.

• Key ecological attributes (KEAs)—Patterns of biological structure and composition, 

ecological processes, environmental regimes, and other environmental constraints 

necessary for an ecosystem component to persist.

• Indicators—Measures of condition or status.
x

• Pressures—Factors delivering direct stresses to ecosystem components.

• Stresses—Altered or degraded KEAs.

• Contributing factors—Factors affecting human-induced actions, events, or natural 

processes that are not drivers or direct pressures, but that affect the condition of 

ecosystem components.

• Drivers—The ultimate human-induced actions, events, or natural processes that underlie 

or lead to one or more pressures.

• Strategies—A group of actions with a common focus designed to achieve specific 

objectives and goals.

These elements function as building blocks of conceptual models that describe the 

relationships between strategies, pressures on ecosystem components, and recovery goals and 

objectives in order to determine what kind and level of intervention is likely to be most effective. 

Open Standards includes companion Miradi software to create graphical depictions of these 

conceptual models. Miradi software is also used to develop results chains, which are diagrams 

derived from the conceptual models depicting assumptions or hypotheses that link short-, 

medium-, and long-term actions and results in an “if...then” fashion. Development of a 

monitoring and adaptive management plan consistent with the framework is not contingent on 

the use of the Miradi software, as we recognize other data management tools may already be in 

use in some watersheds.

We used the scientific literature on Pacific salmon and salmonid ecosystems and also the 

Recovery Plan chapters to describe the elements above for Chinook salmon in the Puget Sound 

region. We identify 14 ecosystem components and their associated KEAs. These ecosystem 

components are Chinook salmon, the two ecosystems—freshwater habitats, and estuarine and 

marine habitats—used by Chinook salmon, and finally, the species and food web processes upon 

which these salmon depend.

We provide example indicators of KEAs that can be tailored to the individual watershed 

recovery plans. The list of indicators presented in this document, provided as an example, is 

neither prescriptive nor all inclusive. However, we do recommend that watershed managers 

work together to develop common indicators in order to attain a common, region-wide measure 

of progress.

We identify linkages between major life cycle segments and events that represent the 

Chinook salmon ecosystem component and the habitat ecosystem components. Each life cycle 

segment and event is associated with habitat types these salmon use during particular life stages. 

This association is necessary to connect the habitat-related ecosystem components with the 

Chinook salmon ecosystem component in the framework. The habitat-related ecosystem 

components are organized into hierarchical watershed-, reach-, and habitat unit–scale 

classifications. These classifications are intended to include all habitats utilized by Chinook 

salmon across their life history or contributing to the formation and maintenance of their habitat. 

Our intent is that every habitat-forming ecosystem process should be incorporated in the 

framework regardless of whether the process occurs upstream, upslope, or otherwise outside of 

habitats accessible to Chinook salmon.
xi 

We catalog and describe 26 potential pressures based on modification of International 

Union of Conservation of Nature classification of pressures. This common list provides the 

foundation for pressure assessments within and across different watersheds. 

Applying the framework to develop watershed-specific monitoring and adaptive 

management plans requires a series of steps that builds on the technical information contained in 

the watershed chapters in Volume II of the Recovery Plan and new information gained since the 

chapters were prepared. These steps are as follows:

1. Develop a preliminary, watershed-specific conceptual model. 

2. Update the conceptual model with new information. 

3. Conduct a viability assessment. 

4. Assess pressures. 

5. Create results chains. 

6. Link results chains to monitoring. 

7. Develop a monitoring plan. 

8. Develop an adaptive management plan.

We describe the tools useful for completing these steps and suggest the use of Miradi software. 

Watershed planners may have other more appropriate or sophisticated tools that they wish to use 

for a given step. 

Collecting the information needed to evaluate the progress of salmon recovery across an 

evolutionarily significant unit and using it to adapt recovery strategies and actions is not simple. 

A successful approach to collecting information, evaluating actions, and informing decisions 

made at the local, regional, or national levels needs to provide consistency across multiple scales 

and geographies, while being flexible enough to capture unique differences. We know of no 

such approach elsewhere. The framework and process we describe here are designed to address 

this need for a scalable, flexible approach to managing recovery planning in a complex 

ecosystem. Use of this framework is intended to help managers describe and refine their 

assumptions regarding the magnitude and extent of recovery actions needed at the scale of the 

natural processes they are intended to affect, so that the actions produce expected responses that 

can be measured, evaluated, and improved. 
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Acknowledgments

This document draws on the insights and inputs of many people. In particular, Bob 

Warinner, Washington Dept. Fish and Wildlife, helped apply the framework described here to 

Chinook salmon recovery planning using data and information from the Skagit River watershed, 

and helped improve it through constructive feedback. Members of three lead entity watershed

groups―Skagit, San Juan, and Hood Canal―provided their time, data, knowledge, and 

comments throughout document development. From the Skagit group, we thank Shirley 

Solomon and Mary Raines; from the San Juan group, Barbara Rosenkotter, Laura Arnold, and 

the WRIA 2 Technical Advisory Team; and from the Hood Canal group, Richard Brocksmith 

and Scott Brewer. We also thank Aundrea McBride and Greg Hood, Skagit River System 

Cooperative, for help in developing the nearshore marine sections of this technical 

memorandum. We acknowledge Phil Roni, George Pess, Tim Beechie, and Sandie O’Neill, 

Northwest Fisheries Science Center (NWFSC); and Dave Beauchamp, University of 

Washington, for valuable suggestions during development of the manuscript. We thank Bruce 

Crawford and Scott Redman, Puget Sound Partnership; and Abby Hook, Hook Knauer LLP, for 

cross-referencing and incorporating the developing concepts into other ongoing projects; and we 

are grateful to Elisabeth Babcock and Alison Agness, National Marine Fisheries Service

Northwest Region (now West Coast Region), for their continuing review and support. We also 

thank our peer reviewers, Tim Beechie, Mike Ford, Kurt Fresh, Correigh Green, George Pess, 

and Casey Rice, NWFSC; Dave Beauchamp; Jeff Duda, U.S. Geological Survey; and Nick 

Salafski, Foundations of Success. And lastly, we thank Stacey Vynne, Puget Sound Partnership, 

for helping finalize the draft for submission to the technical memorandum series, and Ed 

Quimby, NWFSC, for editing and formatting this publication. 
xiv 
Framework Structure

Introduction

Chinook salmon (Oncorhynchus tshawytscha) were listed as threatened in the Puget 

Sound evolutionarily significant unit (ESU) under the U.S. Endangered Species Act (ESA) in 

1999 (NMFS 1999). In response to this listing, a coalition of local, state, federal, tribal, 

business, agricultural, and nonprofit organizations―the Shared Strategy for Puget Sound―in 

coordination with the Puget Sound Technical Recovery Team (PS TRT) appointed by the 

National Marine Fisheries Service (NMFS), established a process to develop a salmon recovery 

plan. Volume I of the resulting Puget Sound Salmon Recovery Plan (hereinafter called the 

Recovery Plan) (SSDC 2007) provides a regional-scale overview of recovery. Volume II of the 

Recovery Plan consists of individual chapters that describe information specific to each of the 14 

Chinook salmon watersheds the TRT identified in the Puget Sound region. In addition, there is a 

chapter on nearshore marine recovery relative to Chinook salmon. Volumes I and II of the 

Recovery Plan were submitted to NMFS for review in 2005.

1

 NMFS issued a supplement to the 

Recovery Plan in 2006, then finalized both documents the following year. The supplement 

identified the development of a rigorous monitoring and adaptive management framework as a 

critical component to Recovery Plan implementation that was left incomplete (NMFS 2006).

The Puget Sound Recovery Implementation Technical Team (PS RITT) was convened in 

2006 and consists of a team of independent volunteer scientists from the Northwest Fisheries 

Science Center (NWFSC), Northwest Indian Fisheries Commission (NWIFC), Washington 

Department of Fish and Wildlife (WDFW), Seattle City Light, and several consultants. This 

occurred after the PS TRT completed their work to define the populations of salmon listed under 

the ESA in the Puget Sound ESU and subsequently disbanded. The mission of the PS RITT is to 

“support the recovery of Pacific salmon [Oncorhynchus spp.] in Puget Sound to robust and 

harvestable levels by providing scientific support (e.g., original design and analyses, project 

review, literature review, and the scientific interpretation of independent studies) to the Puget 

Sound Salmon Recovery Council, watershed recovery groups, state and federal agencies, tribes, 

and other organizations and governments that are working to implement salmon recovery plans 

within the Puget Sound domain.” The technical aspects of this framework for recovery planning 

and development of monitoring and adaptive management plans for the Puget Sound Chinook 

Salmon ESU were developed by the PS RITT, while the policy and strategic aspects were 

adapted from the Conservation Measures Partnership’s Open Standards for the Practice of 

Conservation (hereinafter called Open Standards) (CMP 2007) by staff in the Puget Sound 

Partnership (PSP). In developing this framework, the authors relied on expert knowledge, 

published literature, informational reports, and unpublished data made available by state, tribal, 

and federal agencies.

 1 The document is online at http://www.nwr.noaa.gov/Salmon-Recovery-Planning/Recovery-Domains/PugetSound/PS-Recovery-Plan.cfm.
2

The PS RITT currently consists of Kirk Lakey (Chair, WDFW, Issaquah, WA), Kenneth 

P. Currens (Vice Chair, NWIFC, Olympia, WA), Greg Blair (ICF International, Seattle, WA), Ed 

Connor (Seattle City Light), Mike Parton (Environ Corporation, Olympia), and Melinda L.

Rowse (NWFSC, Seattle). Past members of the PS RITT include Norma Jean Sands (past Chair, 

NWFSC, retired), Kit Rawson (past Chair, Tulalip Tribes, present affiliation Swan Ridge 

Consulting, Mount Vernon, WA), Krista Bartz (NWFSC, present affiliation National Park 

Service, Anchorage, AK), Eric Beamer (Skagit River System Cooperative, LaConnor, WA), 

Michael Blanton (WDFW, present affiliation PSP, Tacoma, WA), and Bill Graeber (Cardno 

Entrix, Seattle). In addition, PSP staff including Rebecca Ponzio (present affiliation Washington 

Environmental Council, Seattle) and Kari A. Stiles assisted the PS RITT and contributed to this 

technical memorandum.

Despite the lack of a formal framework from 2006 to 2013, monitoring and adaptive 

management have occurred at the local (i.e., watershed) and regional (i.e., Puget Sound) scales as 

part of the effort to implement the Recovery Plan. At the local scale, this work has focused 

primarily on site-specific monitoring of habitat restoration projects and salmon. In some 

watersheds, it has also included the development of monitoring and adaptive management plans. 

At the regional scale, this work has fallen into three categories: monitoring of salmon by the state 

and tribal comanagers, nascent habitat monitoring programs that address state-wide questions,

and a draft monitoring and adaptive management plan associated with Volume I. For this third 

category, the draft was written but never finalized (SSDC 2007), and no comparable approach 

associated with Volume II was developed.

These efforts to conduct monitoring and adaptive management help address specific 

needs at both the local and regional scales, but there is currently no way to 1) uniformly frame 

the assumptions stated in the various chapters in Volume II, 2) incorporate new monitoring 

information regarding these assumptions, 3) test similar assumptions across multiple watersheds, 

or 4) connect the local-scale information in Volume II with the regional-scale information in 

Volume I. Additionally, we are limited in our ability to assess the effectiveness of individual 

salmon recovery efforts and to identify uncertainties and priorities for change across the Puget 

Sound region. In response, we developed a science-based structure and process or framework

for creating local-scale monitoring and adaptive management plans (hereinafter called the 

framework) that will allow consistency across the Puget Sound region.

Purpose and Scope

This framework allows inclusion of watershed-specific conditions by incorporating 

information stated in Volume II of the Recovery Plan. It also enables the monitoring and 

adaptive management plans for individual watersheds to be compared via common terminology 

and principles. Our purpose in developing the framework was to retain the individual salmon 

recovery approaches developed for each watershed while also providing the consistency required 

for a regional-scale assessment of Chinook salmon recovery.

In this report, we define parameters important to Chinook salmon and the ecosystems that 

support them. We also define linkages of anthropogenic impacts (social and economic) to 

Chinook salmon and the ecosystems on which they depend. The process can be applied via eight 

steps to develop monitoring and adaptive management actions and plans within each watershed 
3

(see the companion guidance document produced by Long Live the Kings and PSP, titled 

Chinook Monitoring and Adaptive Management Project Toolkit (hereinafter called the Toolkit) 

(LLTK and PSP 2014). These watershed-scale monitoring and adaptive management plans will 

give us the ability to track changes in Chinook salmon population performance and habitat 

change, and to inform management decisions on all scales (watershed, cross-watershed, and 

regional). The framework is currently developed for Chinook salmon, but can be adapted to 

other salmonid species such as summer chum salmon (O. keta) and steelhead (O. mykiss), both of 

which are also listed as threatened in Puget Sound.

The Open Standards Approach

We designed the framework to be consistent with the Open Standards document (CMP 

2007). The Open Standards approach provides a scalable, adaptable system for assembling the 

concepts, methods, and terminology widely used in the design, management, and monitoring of 

conservation projects. This approach is intended to facilitate shared learning among disparate 

conservation projects and to guide the development and implementation of effective monitoring 

and adaptive management plans. More specifically, the Open Standards approach is designed to 

help practitioners identify conservation targets, actions related to those targets, the status of those 

targets, and ways to measure or monitor changes, then ultimately to adapt actions.

Open Standards encompasses five main steps commonly applied to conservation projects: 

1) conceptualize the project; 2) plan actions and monitoring; 3) implement actions and 

monitoring; 4) analyze, use, and adapt monitoring information; and 5) capture and share learning 

with stakeholders (Figure 1). These steps form an iterative cycle that can be refined and adapted 

over time as new information is developed and shared—a true adaptive management process.

Figure 1. Five general steps used to organize the Open Standards system. (Adapted from CMP 2007.)
4

As described above, Volume II of the Recovery Plan contains 14 watershed (local scale) 

chapters and a chapter describing nearshore marine salmon recovery. These chapters include 

Chinook salmon recovery goals and prioritized management actions and monitoring needs. 

Additional work has also been implemented in the watersheds since the plans were approved in 

2007. Our framework is designed to incorporate all of this information into a common language 

and format by applying Step 1 and Step 2 of the Open Standards approach. Monitoring plans 

will then be developed and implemented by applying Step 2 and Step 3 of the Open Standards 

approach. In Step 4, data gained through implementation of monitoring plans and actions will be 

used to evaluate the impacts of projects and to adapt the plans accordingly. Finally, Step 5, the

critical step identified in the Open Standards approach to monitoring and adaptive management,

addresses the importance of sharing project lessons and products with stakeholders and project 

partners. Development and use of this framework is also intended to improve sharing of 

information among and between project partners and stakeholders throughout all steps. Our 

framework provides a scientific basis for evaluating the status of Recovery Plan implementation 

in a common format that may be used by managers and policy leaders region-wide.

The Open Standards approach includes a companion software package called Miradi, 

which practitioners can use to develop, visualize, and track these steps. Miradi, an open source 

software package, is available for free (https://miradi.org/download). We used this software to 

create a template containing all of the components of our framework that are described within 

this document. The template is a Miradi file intended for use as a starting point by practitioners 

who are developing watershed-specific monitoring and adaptive management plans. However, 

practitioners need not use Miradi or this template to apply the framework.

Elements of the Framework

Our framework defines several interrelated categories of information or elements based 

on the Open Standards approach. The elements are: ecosystem components, key ecological 

attributes (KEAs), indicators, pressures, stresses, contributing factors and drivers, and strategies

and associated actions. Brief definitions of the elements are listed below and adapted from 

Salafsky et al. (2008) and FOS (2009). In order to improve consistency with terminology used 

by the PSP, some element names differ from those used in Open Standards. Therefore, the 

elements are listed below by framework name with the corresponding Open Standards or Miradi 

name included in italics, if different (see Appendix A for a detailed crosswalk of terminology 

common to this framework, Open Standards, and Miradi).

1. Ecosystem components (Conservation targets). These components are the things we care 

about conserving. They can be individual species, habitat types, ecological processes, or 

ecosystems chosen to encompass the full breadth of conservation objectives for a specific 

project. In our framework, ecosystem components are priorities for salmon recovery, 

such as Chinook salmon or their natal estuary habitats.

2. Key ecological attributes. These attributes are the characteristics of an ecosystem 

component that, if present, would support a viable component but, if missing or altered, 

would lead to loss or degradation of the component over time. KEAs can be used to 

assess the status of a component, develop protection and restoration objectives for 

conservation, and focus monitoring and adaptive management programs. In our 
5

framework, KEAs are characteristics necessary for salmon recovery, such as the 

abundance and productivity of Chinook salmon or the tidal hydrology of estuary habitats.

3. Indicators. Indicators are specific units of information measured over time that document 

changes in the status of a KEA or another element (e.g., a pressure). Indicators can be 

measured directly or computed from one or more directly measured variables. Indicators 

should be measurable, precise, consistent, and sensitive (TNC 2007). In our framework, 

indicators are metrics to assess salmon recovery, such as the annual number of Chinook 

salmon spawners for a population or the length of tidal channel habitat in an estuary.

4. Pressures (Direct threats). These are the proximate human activities or processes that 

have caused, are causing, or may cause the destruction, degradation, or impairment of 

ecosystem components. Natural phenomena are also regarded as pressures in some 

situations. Pressures include both stressors and the sources of stressors. In our 

framework, pressures are proximate limitations on salmon recovery, such as commercial 

harvest of Chinook salmon or levees and tide gates in estuary habitats.

5. Stresses. Stresses are attributes of an ecosystem component’s ecology that are impaired 

directly or indirectly by human activities. They are equivalent to altered or degraded 

KEAs. Stresses are not pressures, but rather degraded conditions or symptoms that result 

from pressures. In our framework, stresses are symptoms of limitations on salmon 

recovery, such as reduced Chinook salmon spawner abundance or altered tidal hydrology 

in estuary habitats.

6. Contributing factors (Factors). These factors describe the context for why a pressure 

becomes a concern. They are the underlying, human-induced actions or events―usually 

social, cultural, political, institutional, or economic―that enable or otherwise add to the 

occurrence or persistence of pressures. Contributing factors encompass indirect threats, 

existing conditions, and root causes, as well as opportunities. Therefore, they can have 

either negative or positive effects. A political or legal constraint in the regulatory system 

that allows transportation corridors to damage the tidal hydrology of an estuary 

exemplifies a contributing factor with a negative effect.

7. Drivers (Factors). Drivers are similar to contributing factors in that they represent the 

conditions underlying the occurrence or persistence of a pressure. For the purposes of 

this framework, we distinguish between drivers, which tend to be outside the scope of 

strategies and actions in the local-scale recovery plans (e.g., climate change, market 

forces), and contributing factors, which are addressed by specific strategies and actions 

(e.g., lack of public awareness, deficient funding). Furthermore, drivers differ from 

contributing factors in that they also include nonhuman events and forces such as natural 

disasters. Combined, drivers and contributing factors can be thought of as the ultimate 

limitations on salmon recovery.

8. Strategies and actions (Strategies and activities). Strategies are groups of actions 

designed to achieve specific conservation goals, pressure reduction objectives, or 

intermediate outcomes. Collectively, they reduce pressures, capitalize on opportunities, 

or restore natural systems. In our framework, strategies and their associated actions are 

approaches to address limitations on salmon recovery, such as increasing habitat 

protection.
6

We drew from existing documents to define elements 4–8 (Appendix B). Elements 1–3 

are developed in the Ecosystem Components section of this document, where we have identified 

14 ecosystem components associated with Chinook salmon recovery in the Puget Sound region, 

and defined KEAs and potential indicators for each component. This provides the essential 

technical relationships associated with salmon recovery to inform a monitoring and adaptive 

management framework. In the Framework Process section of this document, we provide 

general and specific examples of the application of these elements to generate local-scale and 

regionally consistent monitoring and adaptive management plans to guide Chinook salmon 

recovery. Further development of these elements and this process are available in the Toolkit 

(LLTK and PSP 2014) during the first implementation phase (June 2013 to June 2014) in 

applying the framework to recovery planning in the local watersheds.

Regional-scale Application

The use of this framework enables information regarding Chinook salmon recovery to be 

summarized and assessed at local watershed scales, but also combined to assess recovery at the 

regional scale, as well as across multiple watersheds. For example, we can have greater 

confidence and better understand regional priority pressures by evaluating the key pressures from 

all 14 watersheds (i.e., utilizing our framework), rather than if regional pressures are only 

analyzed at a larger regional scale. In addition, our framework allows us to report on the status 

of habitat types (e.g., how floodplain habitats are currently functioning across the ESU) by 

analyzing the results of explicitly stated goals across all 14 watersheds. And we will be able to 

compare monitoring results across multiple watersheds, for example, on a specific strategy such 

as education and outreach or habitat restoration. Comparing information on monitoring across 

multiple watersheds can help inform watershed practitioners where and how they may more 

effectively work together, or how the tools and techniques to implement strategies may be 

correlated across watersheds.

Monitoring and Adaptive Management

Generally defined, monitoring is the act of collecting and evaluating information needed

to answer questions related to how well a conservation project or strategy is working, and helps 

identify the conditions under which actions are likely to succeed or fail (Stem et al. 2005, CMP 

2007). A monitoring plan defines which information needs to be collected, then describes how 

and where it will be collected, who will collect it, and how it will be analyzed and summarized 

for decision makers. Several types of monitoring can be incorporated into a monitoring plan 

(USDA and USDI 1994), including:

• Implementation monitoring. This type of monitoring tracks whether proposed actions 

were executed or accomplished as designed, answering questions such as: Were priority 

projects implemented? If so, when and by whom? If not, why not?

• Status and trends monitoring. This describes current conditions and changes over time in 

the organisms and habitats we care about, by answering questions such as: What is 

current spawner abundance? Has it increased or decreased since listing? Has riparian 

forest cover increased or decreased since listing?
7

• Effectiveness monitoring. This type of monitoring evaluates whether implemented 

actions achieved the desired outcomes. By definition, it assesses the operational 

effectiveness of management actions, answering questions such as: Did side channels 

form following the removal of bank armor? Did residual pool depth increase after the 

installation of logjams? Were the objectives of a management action met?

• Validation monitoring. This determines whether the assumed cause-and-effect 

relationships between management actions and outcomes are valid. It answers questions 

such as: Will side channels form if bank armor is removed? Do pool depths increase if 

logjams are installed? Effectiveness and validation monitoring are related and

complementary, since it is necessary to know that 1) actions are being achieved 

(effectiveness monitoring) and 2) the effect is caused by the action, as hypothesized 

(validation monitoring). 

As described above, there is a need to track and manage all of these types of monitoring 

throughout the Puget Sound Chinook Salmon ESU in order to assess and comply with recovery 

status and goals. By organizing information (including current assumptions, working 

hypotheses, recovery goals, recent research, and planned restoration actions), then applying it to 

this framework, watershed groups will have the ability to specifically define monitoring goals 

and activities (including the four types of monitoring described above), and thus devise their 

watershed monitoring plans. These plans will vary depending on the conditions and 

characteristics of each watershed, and the current status of knowledge and specific actions being 

pursued. The mechanism for how this will be achieved through application of the framework is 

further defined below, and also in the Toolkit guidance document. 

Many methods, or protocols, exist for collecting the information needed for each type of 

monitoring (e.g., see https://salmonmonitoringadvisor.org/ or http://monitoringmethods.org/). 

We do not address which specific protocols should be employed in the application of this 

framework to devise monitoring and adaptive management plans. However, many other 

monitoring-related projects are currently underway in the Puget Sound region (Appendix C). 

Our framework was developed alongside—both in context of and providing context for—these 

other projects. 

Adaptive management is “learning by doing,” then applying what has been learned to 

improve the “doing.” Anderson et al. (2003) identify three approaches: active adaptive 

management, passive adaptive management, and evolutionary problem solving. Each approach 

emphasizes different considerations for how to implement directed changes from learning by 

doing, and each has different strengths and weaknesses. The defining qualities of an effective 

adaptive management plan are: 1) the approaches used are scientifically based and produce 

measured outcomes, 2) measured outcomes are compared against expected outcomes, and 3) 

management actions are modified according to what was learned (Anderson et al. 2003). 
8

Ecosystem Components

Defining ecosystem components is the first task outlined in the Open Standards approach 

(Figure 1). Our framework identifies four broad categories of ecosystem components relevant to 

the recovery of Chinook salmon in the Puget Sound region. These categories are: 1) Chinook 

salmon, 2) their freshwater habitats, 3) their estuarine/marine habitats, and 4) the other species 

and food webs related to Chinook salmon. Fourteen ecosystem components are identified within 

these four categories (Table 1).

Greene and Beechie (2004), Greene et al. (2005), Scheuerell et al. (2006), and both 

volumes of the Recovery Plan (SSDC 2007) define and document life cycles and life history 

stages for Puget Sound Chinook salmon. Based on this work, we identify five major life cycle 

segments for them, each of which encompasses one or more life cycle events (Table 2). The 

Chinook salmon ecosystem component includes these life cycle segments and events. Each life 

cycle segment or event is associated with habitat types (Table 2 and see also the Glossary). 

Through this association, we connect habitat ecosystem components with the Chinook salmon 

ecosystem component in our framework.

Identifying ecosystem components for habitats used by Chinook salmon involves 

classification. The ecological literature contains numerous efforts to classify environments and 

habitats. Review of the history and development of these classifications (e.g., Naiman et al. 

1992, Montgomery and Buffington 1997, Lombard 2006) suggests several key conclusions: 

Table 1. Fourteen ecosystem components associated with Chinook salmon recovery in the Puget Sound 

region. Components are divided into four broad categories.

Category Ecosystem component

Chinook salmon Chinook salmon 

Freshwater habitat Upland

Channel >50 m bankfull width

Channel <50 m bankfull width

Side channel

Nonchannel lakes and wetlands

Estuarine and marine habitat 

(including nearshore and 

offshore marine)

Natal Chinook estuary

Coastal landform

Bluff-backed beach

Pocket estuary (embayment)

Rocky pocket estuary

Rocky beach

Offshore marine system

Species and food webs Species and food webs
9

Table 2. Chinook salmon life stages and their relationship to broad types of freshwater, estuarine, and marine habitats. The table entries show 

which life stages use each habitat type during particular life cycle segments and events. Detailed definitions of life stages are provided in 

the Glossary.

Life cycle

Freshwater habitat

Estuarine 

habitat (natal 

Chinook)

Nearshore marine habitat Offshore marine 

habitat (offshore 

Channel system)

Nonchannel 

lakes and

Segment Event wetlands

Drift cell 

system

Rocky 

shoreline

Reproduction Spawning Spawner Spawner

Egg 

deposition

Egg Egg

Larval 

development

Egg 

development

Egg, alevin Egg, alevin

Growth and 

migration

Freshwater 

rearing

Fry, parr, 

yearling

Fry, parr, 

yearling

River 

outmigration

Fry, parr, 

yearling

Fry, parr, 

yearling

Natal estuary 

rearing

— — Fry, parr, 

yearling

Estuary 

outmigration

— — Fry, parr, 

yearling

Nearshore 

rearing

— — — Fry, parr, 

yearling

Fry, parr, 

yearling

Transition to 

offshore

— — — — — Parr, yearling, 

subadult

Open water 

rearing

— — — — — Subadult

Maturation Coastal 

migration

— — — Adult Adult Adult

Spawning 

migration

Migration to 

spawning

location

Adult Adult Adult
10

1) hierarchical classifications best encompass the various ecological processes and attributes 

operating at different spatial and temporal scales; 2) physical, process-based classification 

systems offer a unifying approach for understanding landscape controls on habitat-forming 

processes and the effects on habitat characteristics; and 3) no existing classification system 

adequately links physical controls and processes with biological controls and processes (e.g., 

zoogeography, community structure, species interactions, population dynamics). Nevertheless, 

conceptual diagrams linking physical controls and processes to biological responses (Figure 2) 

have been used to describe freshwater, estuarine, and marine habitats (e.g., Bartz et al. 2006, 

Fresh 2006, Simenstad et al. 2006) and to plan salmon recovery actions (Beechie et al. 2003a). 

Therefore, our framework employs existing classifications and conceptual diagrams to identify 

habitat-related ecosystem components, but applies them to Chinook salmon recovery in Puget 

Sound.

Key Ecological Attributes and Indicators for Chinook Salmon

Background

McElhany et al. (2000) listed four parameters for evaluating Pacific salmonid populations 

that fit the definition of KEAs: abundance, productivity or population growth rate, diversity, and 

spatial structure. Because the topic of the document was the criteria for a population to be 

viable, these four have become known in the salmon recovery community as viable salmonid 

population (VSP) parameters. There is obviously, then, a close relationship between determining 

whether a population is a VSP and determining viability status in the Open Standards system. 

Applying a classification of KEAs often used by Open Standards practitioners (TNC 2007), the 

VSP parameters can be categorized as size (abundance), condition (productivity and diversity), 

and landscape context (spatial structure).

Figure 2. Conceptual diagram of linkages between landscape controls, habitat characteristics, and biotic 

responses. Dashed lines indicate overlap with the habitat-related and species-related ecosystem 

subcomponents. (Adapted from Beechie et al. 2003b.)
11

Another essential paradigm for understanding salmon population performance is the basic 

life cycle model. Although all organisms have a life cycle, the migratory and semelparous nature 

of Pacific salmon make the life cycle particularly useful for analyzing the factors that contribute 

to persistence, especially because particular life stages can be associated with particular habitats 

(Figure 3). It is convenient to regard the overall population growth rate as the product of 

survival rates between life stages through an entire life cycle. This basic model has been the 

foundation of salmon population management for many years (e.g., Paulik 1973). Its central 

position today is illustrated by the fact that the life cycle is the organizing principle for two key

references for Pacific salmon, Groot and Margolis (1991) and Quinn (2005). As stated above, 

our framework identifies several major life cycle segments and events for Puget Sound Chinook 

salmon. Table 2, Figure 4, and Figure 5 depict the relationship between these segments/events 

and various freshwater, estuarine, and nearshore marine habitat types.

KEAs and Indicators

We define Chinook salmon KEAs to correspond with the VSP parameters described by 

McElhany et al. (2000). We include three aspects of productivity (survival rate, fish growth, and

population growth), two aspects of diversity (life history and genetic), abundance, and spatial 

structure. These seven KEAs are important throughout the Chinook salmon life cycle (Table 3

and Table 4).

Figure 3. Schematic diagram of the life cycle of Puget Sound Chinook salmon and the freshwater, 

estuarine, and marine habitats associated with each life stage.
12

Figure 4. Relationships between freshwater habitat ecosystem components and Chinook salmon life 

stages, as described in the framework and depicted in Miradi. Also see Table 2 for a description 

of relationships between habitats and Chinook salmon life stages.
13

Figure 5. Relationships between estuarine and marine habitat ecosystem components and Chinook 

salmon life stages, as described in the framework and depicted in Miradi software. Also see 

Table 2 for a description of relationships between habitats and Chinook salmon life stages.
14 

Table 3. KEAs and potential indicators for the Chinook salmon ecosystem component, organized by life cycle segments and events (first and 

second rows, respectively). Half of the life cycle events―“spawning” to “natal estuary rearing”―are shown in this table; the rest are in 

Table 4. The cell entries under each life cycle event are indicators.

KEA

Reproduction

Larval development (egg 

development)

Growth and migration

Freshwater 

rearing

River 

Spawning Egg deposition outmigration Natal estuary rearing

Abundance No. of spawners

No. of female spawners

Hatchery contribution to 

spawning population

No. of redds

No. of eggs

Biomass of eggs

No. of emergent 

fry

No. of juveniles 

by life history 

type (including

hatchery)

No. of river 

outmigrants by 

life history type 

(inclu. hatchery)

No. of fry, parr

Hatchery contribution 

to estuary population

Productivity―

survival rate

— Size of eggs Emergent fry 

per spawner

Stream survival 

rate

Outmigrants per 

spawner

— 

Productivity―

fish growth

Avg. size at age — Avg. size of 

emergent fry

River residence 

time

Avg. size of fry, 

parr, yearlings

Estuary growth rate

Estuary residence time

Productivity―

population 

growth

Spawners per broodyear 

spawner

Intrinsic spawners per 

broodyear spawners

Eggs per female — — Outmigrants per 

spawner

— 

Spatial 

structure

Distribution of 

spawners within/among 

subbasins

No. of subbasins 

with high redd 

density

— Distribution of 

rearing within/

among freshwater habitats 

— Distribution of rearing 

within/among estuary 

habitats

Life history 

diversity

Age structure of 

spawners

Timing of spawning

— Timing and size 

at emergence

No. and 

frequency of 

freshwater life 

history types

Age structure of 

outmigrants

Outmigration 

timing

Estuary residence time

Genetic 

diversity

Effective population 

size

Alleles per locus

Gene flow

— — — — No. of populations 

using estuary habitats 

(based on genetic stock 

identification)
15 

Table 4. KEAs and potential indicators for the Chinook salmon ecosystem component, organized by life cycle segments and events (first and 

second rows, respectively). Half of the life cycle events―“estuary outmigration” to “migration to spawning location”―are shown in this 

table; the rest are in Table 3. The cell entries under each life cycle event are indicators.

KEA

Growth and migration

Maturation (coastal 

migration)

Migration to 

spawning location

Estuary 

outmigration Nearshore rearing

Transition 

to offshore Open water rearing

Abundance No. of estuary 

outmigrants

Hatchery contribution 

to estuary outmigrants

Density of fry, parr, 

yearlings

Hatchery contribution 

to nearshore

Density of 

parr, 

yearlings

— No. of recruits

Terminal run no.

No. of upriver migrants

Hatchery contribution 

to upriver migrants

Productivity―

survival rate

— Nearshore survival 

rate

— Interannual survival 

rate

Ocean survival rate

Recruits per 

outmigrant

Maturation rate by age

Spawners per upriver 

migrant

Productivity―

fish growth

Size distribution of 

fry, parr, yearlings

Size distribution of 

fry, parr, yearlings

Nearshore growth rate

Nearshore residence 

time

Size 

distribution 

of parr, 

yearlings

Avg. size at age

Annual growth rate

Avg. size at age Avg. size at age

Productivity―

population 

growth

— — — — Recruits per spawner Upriver migrants per 

spawner

Spatial 

structure

— Distribution of rearing 

within/among 

nearshore habitats

No. of drift cells with 

rearing

— Distribution of 

rearing in the ocean

Distributions among 

offshore regions 

within Puget Sound

No. of coastal 

migration routes

— 

Life history 

diversity

Outmigration timing Nearshore residence 

time

Timing of nearshore 

residence

— — Age structure of 

fishery recruits

Timing of return to 

terminal areas

Age structure of upriver 

migrants

Timing of upriver 

migration

Genetic 

diversity

— No. of populations 

using nearshore 

habitats (based on 

genetic stock

identification)

— — — — 
16

Indicators for each KEA (i.e., VSP parameter) and relevant life cycle segment and event 

are listed in Table 3 and Table 4. Indicators are not designated in all table cells because some are 

problematic to measure (e.g., abundance of subadults) or redundant (e.g., genetic diversity 

measures at different life stages). However, future applications could include indicators in cells 

that currently have none or indicators that are shown here may need to be modified.

Based on further assessment of the difficulty or redundancy of measuring certain 

indicators, we reduced the list of indicators to a fundamental set (Table 3 and Table 4). We 

considered both feasibility of measurement and possible relationships between the KEAs. A 

subset of the indicators from the full list may be applicable in any single watershed. Choice of 

indicators remains a decision to be made at the local watershed management scale.

Some indicators are directly measurable, while others are computed from additional 

measurements, which may or may not be indicators in the framework (Table 5 and Table 6). For 

example, the average size at age of spawners (an indicator of productivity) is directly 

measureable from escapement samples. Likewise, the number of spawners (an indicator of 

abundance) is directly measureable through a full census, although it is often estimated from two 

other indicators: number of redds and sex ratio of spawners. The number of spawners is also 

used in conjunction with the number of fish recruited to fisheries (another abundance indicator) 

to compute recruits per spawner (a productivity indicator). Other indicators are not directly 

measurable, nor are they computable from additional measurements appearing elsewhere in the 

framework. Three indicators of genetic diversity—effective population size, alleles per locus, 

and gene flow—exemplify this in that each depends on allele frequencies determined from 

genetic analyses of tissue samples taken from spawners or juveniles. These indicators are 

ascribed to the spawning life cycle event when individual populations are assumed to be 

segregated (Table 3), but in theory, they could be measured at any life stage. It is noteworthy 

that, while methods for measuring and calculating abundance and productivity indicators are 

generally well established in salmon management, there are few comparably vetted methods for 

diversity and spatial structure indicators (see Fresh et al. 2009). Stresses (i.e., altered KEAs) to 

Chinook salmon at specific points in their life cycle are identified in Appendix B (Table B-3).

Key Ecological Attributes and Indicators for Freshwater Habitats

Background

We define five ecosystem components for the freshwater habitats relevant to Chinook 

salmon recovery: uplands, large channels (main channels >50 m bankfull width [BFW]), small 

channels (main channels <50 m BFW), side channels (secondary channels in main channel 

floodplain), and other floodplain water bodies (lacustrine and palustrine habitats) (Table 1, Table 

7). We recognize that these ecosystem components and their associated key ecological attributes 

occur at multiple spatial and temporal scales (Frissell et al. 1986); however, we focus at the 

hierarchical scale of individual watersheds and smaller segments (reaches and habitat units, 

defined in kilometers and meters, respectively) for this framework (Figure 6, Table 7). At the 

watershed scale, we utilize habitat classification systems described by Beechie et al. (2003a, 

2003b, 2005), Bisson et al. (1988), and Cowardin et al (1979). Beechie et al. (2005) described 

habitat types for large rivers. Bisson et al. (1988) identified habitats and channel hydraulics of 

smaller streams, and Cowardin et al. (1979) categorized wetland and deep water habitats. Each 
17

Table 5. Examples of ways in which abundance and productivity indicators for the Chinook salmon 

ecosystem component might be determined, either through direct measurements (DM) or 

calculations using other indicators. Potential methods for obtaining some indicators are provided.

KEA Indicator Computed from Potential method

Abundance No. of spawners DM, dam or weir counts, no. of 

female spawners, no. of redds

Full census (for DM), counts 

reduced for in-river mortality, 

redd surveys expanded for fish 

per redd

No. of river 

outmigrants by life 

history type

DM, smolt trap or weir counts Full census (for DM), markrecapture studies (trap 

efficiency studies)

No. of fry, parr (in 

estuaries)

Density of fry, parr by habitat 

type; total area by habitat type

—

No. of recruits No. of natural-origin spawners, 

coded-wire tag recoveries, fishery 

contribution by stock

Cohort reconstruction models

Terminal run no. Terminal area harvest, no. of 

spawners

—

Productivity―

survival rate

Stream survival 

rate

No. of spawners, eggs per female 

spawner, no. of river outmigrants

—

Nearshore 

survival rate

DM Acoustic tagging studies, sizeselective % of total mortality 

est. by comparison of scale 

size-at-circuli distributions at 

this life stage to subsequent life 

stages (offshore juv. and adult)

Ocean survival 

rate (smolt-toadult returns)

No. of river outmigrants, no. of 

recruits

Size-selective % of total 

mortality est. by comparison of 

scale size-at-circuli 

distributions at this life stage to 

subsequent life stages (adults)

Spawners per 

upriver migrant

DM, no. of spawners, no. of 

upriver migrants

Tagging studies (for DM)

Productivity―

fish growth

Avg. size of fry, 

parr, yearlings

DM (scale or otolith backcalculations for size at circuli)Trapping studies (in 

freshwater, estuarine, and 

nearshore habitats)

Estuary residence 

time

DM (scale or otolith backcalculations for size at circuli)Marking studies

Avg. size at age DM(scale or otolith backcalculations for size at circuli)Escapement samples, terminal 

fishery samples

Productivity―

population 

growth

Spawners per 

broodyear 

spawner

No. of spawners, age structure of 

spawners

—

Eggs per female Avg. spawner size at age, 

fecundity by size from hatcheries

—

Outmigrants per 

spawner

No. of river outmigrants, no. of 

spawners

—

Recruits per 

spawner

No. of recruits, no. of spawners —
18

Table 6. Examples of ways in which spatial structure and diversity indicators for the Chinook salmon 

ecosystem component might be determined, either through direct measurements (DM) or 

calculations using other indicators. Potential methods for obtaining indicators are provided.

KEA Indicator Computed from Potential method

Spatial 

structure

Distribution of spawners 

within/among subbasins

DM, no. of redds (by 

location)

Full census (for DM), 

inferred from redd surveys 

Distribution of rearing 

within/among freshwater 

habitats

No. of juveniles by life 

history type (per freshwater 

habitat type)

Snorkel surveys or 

electrofishing in 

freshwater habitats

Distribution of rearing 

among/within nearshore 

habitats

Density of fry, parr, 

yearlings (per nearshore 

habitat type)

Trapping studies (via 

beach seine, purse seine, 

tow net)

Life history 

diversity

Age structure of spawners DM Analysis of scales sampled 

from spawners

Timing of spawning DM Redd surveys

No. and frequency of 

freshwater life history types

DM Analysis of scales or 

otoliths from spawners

Outmigration timing DM, smolt trap or weir 

counts

Full census (for DM), 

mark-recapture studies

Estuary residence time DM Trapping studies in 

representative habitats

Age structure of fishery 

recruits

DM Analysis of scales sampled 

from terminal fisheries

Timing of return to terminal 

areas

DM Records of terminal 

fishery catch

Genetic 

diversity

Effective population size Genotypes of spawners, no. 

of spawners

Genetic analysis of tissue 

samples

habitat is further subdivided into finer scales of organization: reaches and habitat units (Table 7) 

(Cowardin et al. 1979, Bisson et al. 1988, Beechie et al. 2005). Bisson et al. (1988) described 

rapid and cascade habitats in addition to those unit-scale habitats described by Beechie et al. 

(2005). Cowardin et al. (1979) classified wetland and deep water habitats as riverine, lacustrine, 

and palustrine, with further breakdown into subsystem and class categories. Not all Puget Sound 

watersheds contain each of these habitats. Also, if other habitats in a watershed do not fall into 

this classification system (and are deemed important to Chinook salmon) we urge individual 

watershed groups to modify the framework as necessary, preferably so modifications nest within 

this classification scheme.

Key Ecological Attributes and Indicators

We use a basic conceptual diagram in which high-level landscape controls govern 

ecosystem processes, which in turn affect the physical, chemical, and biological characteristics 

of freshwater habitats (Figure 2) (Spence et al. 1996, Beechie and Bolton 1999, Roni et al. 2002). 

We incorporate and define these ecosystem processes in our framework as KEAs (Table 8 and 

Table 9). For convenience, we follow Beechie et al. (2003a) in organizing these KEAs into 
19

Table 7. Classification of freshwater habitats within Puget Sound watersheds. Ecosystem components 

(in italics) representing habitat types important to Chinook salmon recovery are defined at various 

scales; see the Glossary for more information. (Modified from Beechie et al. 2003b [all scales], 

Cowardin et al. 1979 and Beechie et al. 2005 [reach and habitat unit scale], Montgomery and 

Buffington 1997 and Beechie et al. 2006a [reach scale], and Bisson et al. 1988 [habitat unit 

scale].)

Watershed scale Reach scale Habitat unit scale

Upland Upland Not described in this document Not described in this document

Floodplain Channel Channel >50 m BFW

Confined

Straight

Unconfined

Meandering

Island-braided

Braided

Mid channel

Pool

Glide

Riffle (boulder/cobble or 

cobble/gravel)

Edge

Bar

Bank (natural or hardened)

Backwater (alcove)

Channel <50 m BFW

Confined

Bedrock

Colluvial

Unconfined

Alluvial

Cascades

Step pool

Plane bed

Pool riffle

Dune ripple

Pool

Glide

Riffle

Rapids

Run

Cascades

Side channel

Unconfined

Alluvial

Step pool

Plane bed

Pool riffle

Dune ripple

Pool

Glide

Riffle

Rapids

Run

Nonchannel 

lakes and 

wetlands

Lake

Pond

Reservoir (i.e., lacustrine habitat)

Littoral

Limnetic

Wetland (i.e., palustrine habitat) Emergent wetland

Scrub-shrub wetland

Forested wetland
20

Figure 6. Freshwater habitat ecosystem components (italicized) organized by habitat type and watershed 

scale or system type, as described in the framework and depicted in Miradi software.

watershed-scale and reach-scale processes. Watershed-scale processes are those with multiple, 

widely distributed sources, whereas reach-scale processes are those that affect one or more 

adjacent reaches.

Chinook salmon at various life stages depend on freshwater habitats that are maintained 

when both watershed-scale and reach-scale processes are healthy, intact, and functioning 

properly. A healthy ecosystem with a diversity of habitat types promotes a diversity of Chinook 

salmon life history types and population resilience (McElhany et al. 2000, Fresh et al. 2009, 

Greene et al. 2010). Changes and interactions between physical, chemical, and biological 

processes at the watershed and reach scales control the complexity and diversity of habitats 

(Figure 7) (Beechie et al. 2010). KEAs and their associated indicators should have the ability to 

detect gradations of ecosystem process and function and should be applicable across all spatial 

and temporal scales appropriate for the process. The following descriptions of watershed-scale 

and reach-scale processes provide context for our defined KEAs. Table 10 lists these KEAs, as 

well as some associated KEA and pressure indicators. The indicators are presented as examples 

and are neither prescriptive nor all inclusive. A list of stresses or altered KEAs is included in 

Appendix B (Table B-4).
21

Table 8. Priority KEAs for freshwater habitat components, organized by ecosystem process.

Ecosystem process KEA (generic)*

I. Sediment dynamics I-1 Sediment delivery

I-2 Sediment transport and storage

II. Hydrology II-3 High-flow hydrological regime

II-4 Low-flow hydrological regime

III. Organic matter III-5 Organic matter–inputs

III-6 Organic matter–retention/processing

IV. Riparian IV-7 Spatial extent and continuity of riparian area

IV-8 Riparian community structure

IV-9 Riparian function

V. Nutrient supply V-10 Nutrient concentrations (high, low)

V-11 Water quality

V-12 Nutrient cycling/flux

VI. Floodplain-channel 

interactions

VI-13 Floodplain connectivity

VI-14 Floodplain structure and function

VII. Habitat connectivity VII-15 Habitat connectivity

* To be used in development of adaptive management and monitoring plans, the KEAs included here need to be 

adapted to specific components. Examples of component-specific KEAs and indicators are in Table 9 and Table 10.

I. Sediment dynamics

Sediment dynamics include the processes that supply, transport, and deposit sediment 

within freshwater watersheds. Upland and riparian hillslopes and streambanks are the primary 

sediment supply locations within a watershed. Mass wasting (landslides and debris flows), 

surface erosion, and bank erosion result in sediment supply to these aquatic habitats. Riverine 

features are formed (e.g., bars, islands, plane-bed channels) as a result of deposition (or 

accretion) of sediment, and disappear as a result of further downstream transport of these 

sediments (Church 2002). Local variation in sediment delivery rates, routing, and composition 

determines the type and quality of habitat (Sullivan et al. 1987). For example, sediment supply 

affects water quality, and the development and persistence of structures used for salmon 

reproduction and cover (Poff et al. 1997). Transport of sediment (suspended and bedload) occurs 

along a continuum of reaches within the watershed. Sediment input and output must be adequate 

to form and maintain habitat-type diversity and complexity. Sediment supply affects the 

distribution and productive capacity of spawning, incubating, and freshwater rearing life stages 

of Chinook salmon (Dauble et al. 2003).

Various low-gradient habitats (pools, riffles, dune riffles, etc.) are lost over time if 

sediment supply is altered or increased. Sediment supply dynamics can be altered in three 

general ways:

1. Increased delivery of sediments to stream channels from mass wasting or upslope erosion 

(e.g., related to groundcover/canopy loss, road-related sediments, surface water and 

groundwater rerouting);
22 

Table 9. Freshwater KEAs organized by ecosystem process and ecosystem component (italicized). Roman numerals correspond to ecosystem 

processes in the text; Arabic numbers refer to the associated KEAs. Table cells containing these numerals and numbers (e.g., I-2) are 

considered priority KEAs for monitoring and adaptive management of Puget Sound salmon recovery. Table cells containing an asterisk 

(*) are considered potential KEAs.

Ecosystem 

process Upland

Floodplain

Channel

Nonchannel lakes 

Channel >50 m bankfull width Channel <50 m bankfull width and wetlands

Side 

channel

Straight

MeanderingIslandbraided BraidedLake, pond, 

reservoir Bedrock Colluvial Alluvial Alluvial

Lake, pond, 

reservoir Wetland

Sediment 

dynamics

I-1 * I-1, 2 I-1, 2 I-1, 2 I-1, 2 * I-1, 2 I-1, 2 I-1, 2 I-2 I-2 

Hydrology — II-3, 4 II-3, 4 II-3, 4 II-3, 4 II-3, 4 II-3, 4 II-3, 4 II-3, 4 II-3, 4 II-4 II-3, 4

Organic 

matter

III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 III-5, 6 

Riparian — IV-7, 8,

9

* * * IV-7, 8 IV-7, 8,

9

— — IV-7, 8,

9

IV-7, 8, 9 IV-7, 8,

9

Nutrient 

supply

— V-10,

11, 12

V-10, 11, 

12

V-10,

11, 12

V-10,

11, 12

V-10, 11, 

12

V-10,

11, 12

V-10,

11, 12

V-10,

11, 12

V-10,

11, 12

V-10, 11, 

12

V-10,

11, 12

Floodplain/ 

channel 

interactions

— VI-13 VI-13, 14 VI-13, 

14 

VI-13, 

14 

VI-13 — — VI-13, 

14 

VI-13, 

14 

— VI-13, 

14 

Habitat 

connectivity

— VII-15 — — — VII-15 VII-15 — — VII-15 VII-15 VII-15 
23 

Figure 7. Conceptual diagram of linkages between landscape controls, ecosystem processes, and freshwater habitat conditions. The KEAs in our 

framework match the processes in this model. (Adapted from Roni et al. 2002.) 
24 

Table 10. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at watershed and reach scales.

Ecosystem process Scale KEA Example of KEA indicator* Example of pressure indicator

I. Sediment 

dynamics 

Watershed 1. Sediment 

delivery

2. Sediment 

transport and 

storage

Sediment budget and transport/storage 

regime (Madej 1992, Reid and Dunne 

1996) 

Sediment loading (rate) (Reid and Dunne 

1996) 

Substrate composition (relevant to Chinook 

spawning, egg incubation, and juvenile 

overwintering requirements) (SchuettHames and Pleus 1996, McHugh and Budy 

2005) 

Current frequency and volume of mass 

wasting (inventory) (Reid and Dunne 1996)

Road density (e.g., index of sediment 

loading)

Loss of substrate area suitable for 

Chinook spawning, egg incubation, 

juvenile overwintering

Historical frequency and volume of 

mass wasting (inventory) (Reid and 

Dunne 1996) (i.e., measured loss) 

Reach 1. Sediment 

delivery

2. Sediment 

transport and 

storage

Substrate composition (relevant to Chinook 

spawning, egg incubation, and juvenile 

overwintering requirements) (SchuettHames and Pleus 1996, McHugh and Budy 

2005) 

Sediment input (adjacent hillslopes and 

streambanks, or upstream sediment supply) 

(Reid and Dunne 1996) 

Patterns of sediment deposition (aggrading, 

degrading) (Madej 1992)

Total suspended sediment (weight/volume)

Length and percentage of armored 

channel bank, including riprap, 

bulkheads, docks/boat ramps, and 

marina areas

Amount of in-channel dredging 

Length, area, and percentage of log 

storage areas
25 

Table 10 continued. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at watershed and reach scales.

Ecosystem process Scale KEA Example of KEA indicator* Example of pressure indicator

II. Hydrology Watershed 3. High-flow 

hydrology regime

4. Low-flow 

hydrology regime

Area/basin discharge, (e.g.,TQMean, T0.5 Yr), 

threshold discharge, point discharge, 

groundwater recharge/discharge (Booth et 

al. 2004) 

Land cover including percentages of 

impervious surface area and vegetative 

cover

Hydrographic patterns unique to each 

watershed will determine specific measures 

and the seasonal patterns most affecting 

Chinook (e.g., 7-day low-flow and peakflow frequency, magnitude, and duration) 

(Dunne and Leopold 1978, Booth et al. 

2004, Beechie et al. 2006b) 

Groundwater elevation/flows

Regulated instream flow hydrograph

Volume of in-basin storage

Withdrawals and consumption 

Volume of out-of-basin transfer 

Volume and location of stormwater 

discharge and related alteration of 

natural hydrologic processes (e.g., 

infiltration, surface water and 

groundwater flow patterns) 

Reach 3. High-flow 

hydrology regime

4. Low-flow 

hydrology regime

Seasonal hydrological patterns:

Water depth and velocity

Area and type of habitat units (including 

seasonal variation) (Schuett-Hames et al. 

1994, Johnson et al. 2001)

Residual pool depth (Lisle 1987)

Stage/discharge/habitat relationships (e.g., 

low flow resulting in isolated habitats,

high velocities resulting in redd scouring) 

Scour depth in incubation habitats

Area of redd stranding due to natural or 

regulated flows

Area and connectivity of floodplain 

channels leading to stranding of 

juveniles during low-flow time 

periods 

Rapid decreases in flow stage (e.g., 

ramping of regulated flows) that 

isolate pools in floodplain channels 

and wetlands
26 

Table 10 continued. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at watershed and reach scales.

Ecosystem process Scale KEA Example of KEA indicator* Example of pressure indicator

III. Organic matter Watershed 5. Organic matter 

—input 

6. Organic matter 

—retention/ 

processing 

Structure (species composition and seral 

stage), continuity (width and length), and 

extent (area) of riparian systems; also see 

the Riparian process (IV) below 

Allocthonous recruitment from riparian 

vegetation 

Carbon and nitrogen cycling (flow), amount 

and sources of inputs; also see Nutrient 

process (V) below

Recruitment and transport rates of instream 

large woody debris (LWD)

Reduction of riparian forest cover

Changes in delivery of organic inputs 

from upslope areas 

Changes in delivery of organic inputs 

from upstream areas

Type and concentration of exogenous 

organic inputs

Reach 5. Organic matter 

—input 

6. Organic matter 

—retention/ 

processing 

Primary productivity and water chemistry 

(e.g., biological oxygen demand, total 

nitrogen concentration) 

Macroinvertebrate community structure (e.g., 

Index of Biological Integrity) (Karr 1991, 

Plotnikof 1994, Kleindl 1995, Karr and 

Chu 1997) 

Allocthonous recruitment from riparian 

vegetation

Recruitment and retention of instream LWD

Reduction of organic matter input or 

retention related to changes in area, 

community, and seral stage of 

riparian forest

Type and concentration of exogenous 

organic inputs

IV. Riparian Watershed 7. Spatial extent 

and continuity of 

riparian area

8. Riparian 

community 

structure

9. Riparian 

function 

Structure (species composition and seral 

stage), continuity (width and length), and 

extent (area) of riparian vegetation (species 

composition and seral stage)

Distribution of LWD concentrations and 

complexes (Wohl et al. 2010) 

Wood budget (Martin and Benda 2001, Abbe 

et al. 2003) 

Recruitment rate of LWD

Area of lost depositional/floodplain 

areas that historically or potentially 

supported riparian forests (Collins et 

al. 2003) 

Length and area of hydromodified bank 

(e.g., erosion, bank hardening, diking) 

Area and percentage of lost riparian 

forest cover

Limits and interruptions of LWD 

transport (Naiman et al. 2002)
27 

Table 10 continued. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at watershed and reach scales.

Ecosystem process Scale KEA Example of KEA indicator* Example of pressure indicator

IV. Riparian 

(continued) 

Reach 7. Spatial extent 

and continuity of 

riparian area

8. Riparian 

community 

structure

9. Riparian 

function 

Riparian area (extent) 

Riparian community species composition and 

structure (WFPB 1997, Johnson et al. 2001, 

Booth et al. 2002, Bowen and Waltermire 

2002, May 2003, Wohl et al. 2010) 

Size, species, and decay state of downed 

wood 

Area, condition, and seral stage of upslope 

LWD recruitment areas

Canopy closure (Schuett-Hames et al. 1994, 

Korhonen et al. 2006) 

Recruitment rate of LWD (Van Sickle and 

Gregory 1990, Naiman et al. 2002)

Length and area of hydromodified bank 

(e.g., erosion, bank hardening, diking) 

Loss of riparian vegetation area

Change and reduction in riparian and 

upslope vegetation community 

structure

Loss of late seral stage component for 

LWD recruitment to salmon habitats 

Conversion of riparian area for human 

uses (e.g., transportation, residential, 

and commercial structures)

V. Nutient supply Watershed 10. Nutrient 

concentrations 

(high, low) 

11. Water quality 

12. Nutrient 

cycling/flux

Baseline levels of nutrients (primarily 

nitrogen (N), phosphorus (P), and 

potassium (K) 

Water quality metrics, including temperature, 

dissolved oxygen (DO), pH, conductivity/ 

salinity 

Nutrient budget (types and sources of 

nutrient inputs)

Inventory of anthropogenic nutrient 

sources (locations and load levels)

Natural or artificial abundance of 

salmon carcasses

Clean Water Act, 303d status 

Water quality standards exceedance

Contaminants 

Reach 10. Nutrient 

concentrations 

(high, low) 

11. Water quality 

12. Nutrient 

cycling/flux

Nutrient concentrations, including total N, 

organic N, NH4, NO3, NOx, total P, organic 

P, particulate P, and ortho-PO4 (Levin et al. 

2010) 

Benthic community structure (Karr 1991, 

Plotnikoff 1994, Karr and Chu 1997) 

Toxics in water, freshwater fish, 

shellfish, and juvenile salmon (from 

point and nonpoint sources) (Beechie 

et al. 2003a, Levin et al. 2010) 

Biological water quality index 

(including toxics, fecal bacteria) 

(Levin et al. 2010)
28 

Table 10 continued. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at watershed and reach scales.

Ecosystem process Scale KEA Example of KEA indicator* Example of pressure indicator

VI. Floodplain/ 

channel 

interactions 

Watershed 13. Floodplain—

connectivity 

14. Floodplain— 

structure and 

function 

Length or area of potential floodplain 

development (gradient/confinement 

metrics)

Hyporheic connection intact (groundwater, 

lakes, ponds, wetlands) 

Historical and current distribution of utilized 

habitats for holding, spawning, and rearing 

Distribution of habitats for rearing juveniles

Distribution of habitats for prespawn holding 

(deep pools) and spawning (gravel riffles in 

main stem, side channel, and large 

tributaries)

Location, area, and elevation/topography of 

floodplain features over time (Montgomery 

and Buffington 1998, Collins et al. 2003, 

Rapp and Abbe 2003, Downs and Gregory 

2006)

Type and location of limits to juvenile 

and adult fish passage

Area of lost natural floodplain area 

(historical vs. current) 

Reach 13. Floodplain—

connectivity 

14. Floodplain— 

structure and 

function 

Length of natural bank

Depositional/transport state 

(aggradation/degradation rates)

Length of hydromodified bank

Depth of historical conditions (i.e., for 

comparison and planning)
29 

Table 10 continued. Freshwater ecosystem processes, KEAs, and examples of KEA and pressure indicators at watershed and reach scales.

Ecosystem process Scale KEA Example of KEA indicator* Example of pressure indicator

VII. Habitat 

connectivity 

Watershed 15. Habitat 

connectivity 

Availability and use of habitat patches for 

Chinook salmon (by life stage) 

Pathways (landscape) and movements 

(behavior) of Chinook salmon between 

habitat patches (i.e., for migration, rearing, 

feeding, etc.) (Kocik and Ferreri 1998, 

Bélisle 2005)

Temporal (future short- and long-term) 

accessibility (Price et al. 2010)

Historical vs. current connectivity patterns 

(Fullerton et al. 2010)

Correlation between abundance of Chinook 

salmon (by life stage) and size of required 

habitat types (Romero et al. 2009)

Adult and juvenile salmon passage 

barriers that limit distribution 

(inventory and passage assessment by 

life stage)

Access/limitations of nonindigenous 

species, pathogens, or contaminants 

Location and duration of low-flow 

barrier

Reach 15. Habitat 

connectivity

Local network connections (i.e., pathways), 

in which fish can access preferred habitat 

patches (Kocik and Ferreri 1998)

Distribution of suitable habitat patches 

(Benda et al. 2004a, 2004b, Ganio et al. 

2005, Fullerton et al. 2010) 

Thalweg profiles and metrics (Mossop and 

Bradford 2006) 

Size of habitat patches for specific life stages 

of Chinook salmon

Frequency and duration of floodplain 

inundation 

Restriction of access to floodplain 

channel 

* The suite of KEA indicators listed exemplifies what can be measured. Exclusion or apparent endorsement of any specific approach is unintentional.
30

2. Decreased delivery of sediments caused by the installation of a dam, channelization, bank 

hardening, or loss of floodplain connectivity;

3. Changes in sediment transport and storage due to either a) increases or decreases in 

abundance of woody debris or beaver dams, b) modified stream gradient and confinement 

(channelization, incision, head cutting), or c) remobilized stored sediments (channel 

avulsion, bank erosion).

Two KEAs were identified for sediment dynamics:

• KEA I-1. Sediment delivery, and

• KEA I-2. Sediment transport and storage.

II. Hydrology

Hydrology refers to the distribution, patterns, duration and magnitude of stream flows 

resulting from precipitation, evaporation, transpiration, runoff, and routing. Water is necessary 

to build and sustain the habitats required for complex aquatic species assemblages. Natural and 

managed hydrological regimes create and maintain aquatic habitats through bankfull flows 

(typically 1.5 to 2.0 year recurrence) and episodic flood flow events (Leopold 1994). The 

resulting aquatic habitats and their spatial distribution are dynamic and subjected to seasonal 

high and low flows that are a primary control on fish passage and timing, as well as the 

distribution and timing of fish rearing, growth (including condition), and survival (Poff et al. 

1997). Stream flow (high and low) provides hydraulic diversity (variation in water depths and 

velocities) that is dynamic both spatially (reach) and temporally (season, year). Diverse and 

complex habitat structure includes shallow-edge and low-velocity refugia for salmonids (Bain et 

al. 1988), as well as higher velocity areas for spawning or feeding. Connectivity of floodplain 

habitats is also very important for a fully functional hydrological regime (Fullerton et al. 2010).

Hydrology affects the distribution and timing of prespawning and spawning Chinook 

salmon entering freshwater habitats, as well as the dispersal of juvenile Chinook at various life 

stages to rearing habitats and their migration to estuarine, nearshore, and offshore marine 

habitats (McClure et al. 2008). Extreme hydrological events (floods, low flows) can have 

episodic or catastrophic impacts on the survival of adults and juveniles due to displacement, and 

cause density-dependent population controls on spawning and rearing (Waples et al. 2008). 

They can also have a major impact on the life history diversity and spatial structure of 

populations.

Two KEAs were identified for hydrology:

• KEA II-3. High-flow hydrological regime, and

• KEA II-4. Low-flow hydrological regime.

III. Organic matter

This watershed process focuses on the processing of organic matter from riparian 

vegetation, salmon carcasses, and other allochthonous inputs. All natural surface water contains 

dissolved and particulate organic matter, and the amounts can be surprisingly high (Hynes 1970). 
31

Some of this matter is deposited in low-velocity habitats (e.g., lakes, pools, and impoundments), 

while some is transported downstream and through the system (Hoover et al. 2010). Hynes 

(1970) concludes that there is likely a steady rain of minute particles of organic matter which 

ultimately forms food for animals. The type (dissolved and coarse/fine particulate matter) and 

amount of allochthonous organic matter inputs affect productivity at multiple trophic levels in 

the aquatic community (Vannotte et al. 1980, Bilby and Bisson 1992). Organic matter in aquatic 

systems is processed from a variety of source materials, ranging from logs (large woody debris

[LWD]) to leaves and even terrestrial insects. In rivers or streams with low light availability 

(i.e., streams shaded by riparian trees), aquatic food webs are often driven by detritus

―processed organic matter which cycles through all trophic levels (Odum 1984). In addition to 

food web support, detritus (particularly LWD) serves a structural function in combination with 

streamflow by affecting bed scour and creating hydraulic diversity (Frissel et al. 1986, Gregory 

et al. 1991, Gregory and Bisson 1997, Montgomery and Buffington 1997). Vegetation removal 

and bank armoring, along with floodplain development, can impede recruitment and processing 

of detritus (Pess et al. 2005).

Two KEAs were identified for organic input:

• KEA III-5. Organic matter―inputs, and

• KEA III-6. Organic matter―retention/processing.

IV. Riparian

Riparian vegetation affects streambank stability, sediment supply, delivery of LWD and 

organic litter, light and temperature (shading), composition of nutrients in aquatic habitats, and 

mediation of biotic interactions (Naiman and Décamps 1997). Riparian functions that depend on 

vegetation include maintaining instream water temperatures (through shade), bank stability 

(through vegetative root structure), primary food production (organic inputs through leaf litter 

and insects falling from trees over streams), recruitment of LWD, and sediment and nutrient 

trapping (Naiman and Décamps 1997). LWD recruitment sustains dynamic river morphology in 

forested floodplain river systems (Collins and Montgomery 2002, Naiman et al. 2010). This 

KEA is especially important in large mainstem, small mainstem, tributary, and off-channel 

habitats. Riparian function controls aquatic habitat quality and lost riparian function can result in 

Chinook salmon life stage–specific productivity limitations, regardless of habitat quantity.

Riparian functions affect the quality and quantity of complex rearing habitats for all 

Chinook salmon freshwater life histories (McCullough 1999). Ecological function in the context 

of Chinook salmon within riparian areas is dependent on the width of forest buffer adjacent to 

stream; that is, wood input increases with an increasing width of forest buffer (Sedell et al. 

1997). Other riparian functions (microclimate, litter fall, root strength, etc.) can be assessed in 

terms of stream buffer widths and continuity. Stream buffer width is typically impacted as a 

result of floodplain development causing riparian habitat loss, lack of continuity, bank 

hardening, and increased stream temperatures during low flow periods (Hauer et al. 2003).

Three KEAs were identified for riparian area function:

• KEA IV-7. Spatial extent and continuity of riparian area,
32

• KEA IV-8. Riparian community structure (e.g., species composition and seral stage), and

• KEA IV-9. Riparian function (e.g., recruitment, canopy closure, etc.).

V. Nutrient supply

Nutrients (e.g., nitrogen and phosphorous) are supplied naturally through the processing 

of organic matter by microbial and other biotic processes at lower trophic levels (Beechie et al. 

2003a, 2003b). Nutrients exert a strong control on primary productivity and the consequent 

diversity and abundance of the aquatic community. Changes in riparian areas, point and chronic 

source inputs, stream channels, and biotic assemblages alter the flux and uptake of nutrients 

(organic or inorganic), which are the chemical constituents in water required for biological 

processes (Ward 1992). Growth and survival of juvenile Chinook salmon are affected by the 

type and abundance of prey items and forage available. However, anthropogenic sources of 

nutrients (e.g., urban stormwater, septic systems, agricultural runoff) enrich aquatic systems with 

nutrients and supply contaminants that may locally affect aquatic biota (e.g., macroinvertebrate 

communities), as well as the suitability of habitats for rearing juvenile Chinook salmon (Booth et 

al. 2004). Urban development also influences the concentration and yield of compounds that 

naturally occur in surface waters. For example, nitrogen yields from urban basins were the same 

order of magnitude as agricultural basins, and an order of magnitude higher than the yield from 

less-developed, forested basins (Embrey and Inkpen 1998). Furthermore, chemical 

concentrations of pesticides and total phosphorous were more important than physical habitat 

features for identifying patterns of fish assemblages in low-gradient floodplain reaches of the 

Willamette River, Oregon (Waite and Carpenter 2000). Excess nutrients can shift aquatic 

communities away from preferred food items and reduce water quality to a level that can result 

in physiological stresses to rearing Chinook salmon juveniles.

Contaminants as referred to here can be organic or inorganic, and can be derived from 

natural or unnatural sources, but they essentially have deleterious impacts on water quality and

Chinook salmon growth, survival, or distribution. Water quality and contaminants are complex 

mechanisms that have profound impacts on the aquatic environment. They can vary greatly by 

watershed and by the degree of stress imparted. Contaminants can operate singly or in 

combination with other chemical constituents, affecting Chinook salmon directly or indirectly 

via their habitat or food supply.

Three KEAs were identified for nutrient supply:

• KEA V-10. Nutrient concentrations (high, low),

• KEA V-11. Water quality, and

• KEA V-12. Nutrient cycling/flux.

VI. Floodplain-channel interactions

Interaction of rivers and floodplains affects capacity to deliver, supply, and store water, 

sediment, and wood (Bolton and Shellberg 2001). This attribute is especially important in large 

mainstem habitats. Floodplains generally contain numerous sloughs, side channels, and other 

features that provide important spawning habitat, rearing habitat, and refugia during high flows 
33

(Beechie et al. 2001), and may be used by rearing salmonids for long periods of time. These offchannel areas provide an abundance of food with fewer predators than would typically be found 

in the river, and provide habitat for juvenile salmonids to hide from predators and conserve 

energy (Sandercock 1991). The importance of floodplain habitat to salmonids cannot be 

overstated. In the Skagit and Stillaguamish basins, more than half of the total salmonid habitat is 

contained within the floodplain and estuarine deltas, while this habitat encompasses only 10% of 

the total basin area (Beechie et al. 2001). Functional floodplains also moderate high flows by 

substantially increasing the area available for water storage (Ziemer and Lisle 2002). Water 

seeps into the groundwater table during floods, recharging wetlands, off-channel areas, shallow 

aquifers, and the hyporheic zone (Bolton and Shellberg 2001). Floodplains form in alluvial 

stream systems as a consequence of sediment input, sorting, transport, and storage. Floodplains 

are naturally subject to erosion and recruitment of stored sediments through channel migration 

and flood events (Pess et al. 2005). Connected floodplains provide instream habitat and support 

riparian processes. Secondary channels can have varied hydrologic connectivity with mainstem 

channels including direct surface water connections (periodic or continual), groundwater 

connections, or both (Gregory and Bisson 1997, Beechie et al. 2006b). These channels are 

classified based on a combination of hydrologic connection and gradient and confinement after 

Montgomery and Buffington (1997). The quantity and quality of available floodplain habitats 

can affect the life history diversity and spatial structure of Chinook salmon populations (Waples 

et al. 2009).

Human influence past and present has degraded watersheds and wetlands, diminished the 

amount of available floodplain, and fragmented remaining intact floodplains throughout Puget 

Sound (Beechie et al. 2001, Pess et al. 2003). Floodplain impacts include the direct loss of 

aquatic habitat from human activities (filling); disconnection of main channels from floodplain 

channels with dikes, levees, revetments, and roads; and reduction of lateral movement of flood 

flows with dikes, levees, revetments, and roads (Pess et al. 2005). Decreased abundance of 

LWD results in degraded aquatic habitat quality and area (e.g., pools) due to altered sediment 

and wood supplies (Montgomery et al. 2003, Wohl et al. 2010). Dikes and riprap are used to 

control channel movement and can cause channel incision, further isolating the channel and its 

hydrologic connectivity to the floodplain (Beechie et al. 2003a, 2003b, Collins et al. 2003).

Two KEAs were identified for the floodplain-channel interaction watershed process:

• KEA VI-13. Floodplain―connectivity (e.g., to the main channel), and

• KEA VI-14. Floodplain―structure and function.

VII. Habitat connectivity

Connectivity of habitats is necessary for the dispersal and migration of aquatic species

and, in the case of Chinook salmon, the development and expression of diverse life histories 

(Fullerton et al. 2010). Connectivity can be described as the availability or access to habitats that

are required by each Chinook life history stage. Furthermore, the growth performance and size 

attained by individuals within some (but not all) habitats and life stages can strongly influence 

survival in current or subsequent life stages. Loss of connectivity due to seasonal, episodic, or 

artificial limits on volitional movements introduces local controls that effectively decrease the 

area of productive habitat in a watershed. This KEA represents a biological view and 
34

synthesizes the sediment, hydrology, and floodplain dynamics of other KEAs. Side channels, 

off-channel wetlands, and tidal marshes are important habitats Chinook salmon use for feeding, 

rearing, refuge, and holding, given their connectivity to main migratory pathways.

Reconnection of isolated habitats is a primary objective in many restoration programs. 

Systematic methods can be used to restore habitats through barrier inventory, assessment, and 

allocation of funds to correct the fish passage problems. Cost-effectiveness of reconnection 

projects is easily determined by considering the habitat area restored, the average life span of a 

blockage (≈50 years), and the cost of the project (Pess et al. 2003).

One KEA was identified for habitat connectivity:

• KEA VII-15. Habitat connectivity.

Key Ecological Attributes and Indicators for Estuarine and 

Marine Habitats

Background

The need for a regionally consistent classification of estuarine and marine habitats is

apparent when the individual chapters in Volume II of the Recovery Plan are viewed as a whole. 

These watershed-specific chapters tend to classify habitat differently, despite proposing 

restoration and protection actions that often follow common themes. Also, not all chapters 

classify habitat based on natural processes and their controls. Instead, they use a mixture of 

natural processes, habitat types, and biota at various spatial and temporal scales in a priori 

assignments of habitat classes. These differences in classification among chapters would make 

regional-scale assessment of monitoring and adaptive management in estuarine and marine 

systems difficult.

Estuarine and Marine Habitat Components

To support Puget Sound–wide and cross-watershed assessments of Chinook salmon 

monitoring and adaptive management, we developed a comprehensive classification system for 

estuarine and marine habitats within Puget Sound that includes seven discrete ecosystem 

components (Table 11). Our classification system uses six hierarchical scales―broad habitats, 

system types, system subtypes, shoreline types, habitat zones, and vegetative zones. Six of the 

seven ecosystem components are defined at the scale of system subtype and a single ecosystem 

component, Offshore marine systems, is defined at the system-type scale (Table 11, Figure 8).

We consider the first four scales―broad habitats through shoreline type―to be 

geomorphic and process inferred, because the dominant natural process or combination of 

processes, acting on a specific estuarine or marine habitat, can be determined by the geomorphic 

signatures of those processes (including topographic relief) or previously mapped longshore 

drift. Thus when monitoring the health of a process, we do not measure or observe a process per 

se; rather we measure or observe a result created by a process (Shipman 2008, McBride et al. 

2009). The seven estuarine and marine ecosystem components can be linked to large-scale and 

small-scale landscape controls, natural processes, and biological responses based on a general 
35 

Table 11. Classification of estuarine and marine habitats, showing the five largest hierarchical scales with ecosystem components at various scales 

depicted in italics. Detailed definitions of select habitats are provided in the Glossary.

Broad habitat System type System subtype Shoreline type Habitat zone

Estuarine Major river 

system

Natal Chinook 

estuary

Drowned channel 

River-dominated (fan) 

delta

Tidal delta

Delta lagoon

Alluvial floodplain

Tidal channel (e.g., distributary and blind tidal channels, lagoon 

inlet/outlet)

Impoundment (e.g., lagoon, pond, lake) 

Tidally influenced wetland (e.g., salt marsh, scrub-shrub, 

forested) 

Tide flat, low tide terrace, subtidal flat

All other zones possible along delta margin

Nearshore 

marine

Drift cell 

system

Coastal 

landform

Barrier beach (spit, cusp, 

tombolo)

Backshore, beach face, tide flat, low-tide terrace, subtidal flat

Bluff-backed 

beach 

Sediment source beach

Depositional beach 

Beach seep

Plunging sediment bluff

Marine riparian zone

Bluff face

Backshore, berm, beach face, tide flat, low-tide terrace

Pocket estuary 

(embayment) 

Drowned channel lagoon

Tidal delta lagoon

Longshore lagoon

Tidal channel lagoon or 

marsh

Closed lagoon or marsh 

Open coastal inlet

Marine riparian zone

Tidal channel (e.g., distributary and blind tidal channels, lagoon 

inlet/outlet)

Impoundment (e.g., lagoon, pond, lake) 

Tidally influenced wetland (e.g., salt marsh, scrub-shrub, 

forested) 

Backshore, berm, beach face, tide flat, low-tide terrace

Rocky 

shoreline 

Rocky pocket 

estuary

Pocket beach lagoon 

Pocket beach estuary

Pocket beach closed 

lagoon or marsh 

Marine riparian zone

Tidal channel (e.g., distributary and blind tidal channels, lagoon 

inlet/outlet)

Impoundment (e.g., lagoon, pond, lake) 

Tidally influenced wetland (e.g., salt marsh, scrub-shrub, 

forested) 

Backshore, berm, beach face, tide flat, low-tide terrace

Rocky beach Veneered rock platform

Rocky shoreline

Plunging rocky shoreline 

Pocket beach

Marine riparian zone 

Plunging rocky cliff, cliff 

Rocky platform, backshore, berm, beach face, low-tide terrace
36 

Table 11 continued. Classification of estuarine and marine habitats, showing the five largest hierarchical scales with ecosystem components at 

various scales depicted in italics. Detailed definitions of select habitats are provided in the Glossary.

Broad habitat System type System subtype Shoreline type Habitat zone

Offshore 

marine

Offshore 

marine 

Bay/inlet — Water column habitat (At a minimum, stratify into shallow 

mixed layer vs. deeper waters. Juvenile salmon use the shallow 

mixed layer whereas larger salmon, other potential predators 

and competitors, and a much different zooplankton community 

use the deeper stratum during daylight, with some species 

migrating into the shallower layer during twilight-night 

periods) 

Epibenthic habitat 

Benthic habitat

Open basin — Water column habitat 

Epibenthic habitat 

Benthic habitat 
37

Figure 8. Estuarine and marine habitats (italicized), as described in the framework and depicted in 

Miradi software.

conceptual diagram that is applicable region-wide (Figure 2, Figure 7). In the estuarine and 

marine habitats of Puget Sound, controls and large-scale processes include geology, topography, 

bathymetry, wave energy, freshwater inflow, tidal range, and sea level rise. These controls and 

processes differ across the region and form the basis of seven geographic basins within the 

United States portion of the Salish Sea (see the map in the Glossary); the basin boundaries were 

chosen to follow natural breaks in geomorphology and large-scale hydrodynamic processes 

(Simenstad et al. 2011).

Landscape controls and large-scale processes generally are not influenced by the 

strategies and actions in the Recovery Plan, because they operate beyond the scope of the 

recovery planning area and its implementation period. However, they are considered in 
38

development of the estuarine and marine nearshore classification system and identification of 

KEAs, because they limit (or otherwise influence) the expression of the small-scale natural 

processes that form habitat. In estuarine and nearshore habitats in particular, these small-scale 

processes include tidal, fluvial, and wave energy dynamics that cause water, sediment, LWD, 

and other detritus to form geomorphic habitat types at a variety of spatial scales.

Habitat and vegetative zones comprise the fifth and sixth scales, respectively, of our 

classification system and are found across multiple system types, subtypes, and shoreline types. 

Habitat zones are related to elevation differences and natural process signatures easily illustrated 

in bird’s-eye or cross-section views of typical landforms (Figure 9 and Figure 10). They are also 

included in the final column of Table 11. Vegetative zones, the smallest level in our 

classification system (not shown in Table 10) are features that live or accumulate on habitat 

zones. Vegetation zones include: 1) vegetation (marine riparian vegetation [MRV], salt marsh, 

and submerged aquatic vegetation [SAV], including kelp, eelgrass [Zostera marina], macroalgae, 

etc.); 2) detritus (marine, estuarine, freshwater, and terrestrial detritus, including LWD); and 3) 

substrate (sediment). Specific vegetation zones are associated with specific habitat zones. For 

example, MRV is associated only with habitat zones higher in elevation than extreme high tide. 

SAV is associated only with lower intertidal or subtidal habitat zones to a depth determined by 

the lower limit of the photic zone. Some vegetative zones in our classification system (e.g., 

MRV, salt marsh, and SAV) are also biotic response variables in the conceptual diagram 

(Figure 2) and are a result of multiple ecosystem processes.

Figure 9. Shoreline habitats typical to Puget Sound. The illustration demonstrates the hierarchical 

relationships listed in Table 10, columns 3 through 5, specifically among system subtypes (e.g., 

natal Chinook estuary, bluff-backed beach, rocky beach, and pocket estuary), shoreline types 

(e.g., barrier beach, pocket beach lagoon), and habitat zones (e.g., alluvial floodplain, backshore, 

marine riparian zone). (Reprinted from Shipman 2008.)
39

Figure 10. Cross section of a beach showing typical nearshore marine habitat zones in the Puget Sound 

region. Habitat zones by system subtype are also listed in Table 10. (Reprinted from 

Johannessen and MacLennan 2007.)

Key Ecological Attributes and Indicators

To support development of watershed-scale and regional monitoring plans that track the 

status and condition of estuarine and marine systems, we have identified a set of KEAs (Table 

12) associated with six ecosystem process categories critical for Chinook salmon habitat 

formation and maintenance: coastal sediment dynamics, fluvial sediment dynamics, freshwater 

hydrology, tidal hydrology, tidal channel formation and maintenance, and detritus recruitment 

and retention. Two additional groups of KEAs have been developed to specifically address 

habitat connectivity and attributes that are influenced by multiple ecosystem processes. The set 

of KEAs was derived largely from a review of the Volume II chapters that include nearshore 

habitat, as well as several Puget Sound Nearshore Ecosystem Restoration Project technical 

reports (Finlayson 2006, Brennan 2007, Johannessen and MacLennan 2007, Mumford 2007, 

Penttila 2007, Shipman 2008, Clancy et al. 2009). The ecosystem process categories and 

associated KEAs listed in Table 12 are described below. Table 13 presents a summary of all 

KEAs organized by ecosystem process and ecosystem component. Table 14 expands on Table 

13 and provides a list of KEAs relevant to each estuarine or marine component, with example 

indicators for each KEA. Table 15 provides specific examples from the Skagit watershed and 

hypothetical examples for each component that illustrate how component-specific indicators and 

KEAs are derived from the generic KEAs listed in Table 12 and Table 13. KEAs also provide a 

framework for assessing the effects of pressures or stressors on ecosystem components. A list of 

stresses or altered KEAs is included in Appendix B (Table B-4).
40

Table 12. KEAs for estuarine and marine ecosystem components, organized by ecosystem process.

Ecosystem process KEA (generic)*

I. Sediment dynamics―

coastal

I-1 Coastal sediment dynamics in drift cells―condition

I-2 Coastal sediment dynamics in drift cells―landscape 

context

I-3 Coastal sediment deposition and accretion―extent

I-4 Coastal sediment deposition and accretion―condition of 

sediment

I-5 Coastal sediment deposition and accretion―condition of 

impoundment

I-6 Coastal sediment supply―extent

I-7 Coastal sediment supply―distribution

I-8 Coastal sediment dynamics―extent (size or volume) of 

wind and wave features

I-9 Coastal sediment dynamics―condition of wind and wave 

features

II. Sediment dynamics―

fluvial

II-10 Fluvial sediment dynamics―condition

III. Hydrological dynamics―

tidal

III-11 Tidal circulation―extent of biological activity

III-12 Tidal circulation―water condition

IV. Hydrological dynamics―

freshwater

IV-13 Freshwater hydrology―water condition (relative to 

physical and chemical parameters)

IV-14 Freshwater hydrology―condition (relative to freshwater 

input, stream discharge and flow)

V. Tidal channel formation 

and maintenance

V-15 Tidal channel formation and maintenance―extent of 

channels

V-16 Tidal channel formation and maintenance―connectivity 

of channels

VI. Detritus recruitment and 

retention

VI-17 Detritus recruitment and retention―extent

VI-18 Detritus recruitment and retention―extent of supply

VII. Habitat connectivity VII-19 Habitat connectivity condition

VIII. Multiple ecosystem 

processes

VIII-20 SAV beds―condition

VIII-21 SAV beds―extent

VIII-22 Estuarine habitats―extent

VIII-23 Estuarine habitats―condition

VIII-24 Estuarine habitats―distribution

VIII-25 Intertidal habitat zone―extent

VIII-26 Intertidal habitat zone―condition

VIII-27 Tidally influenced wetlands―extent

VIII-28 Tidally influenced wetlands―condition

VIII-29 Water quality

VIII-30 MRV―spatial extent and continuity

VIII-31 MRV―community structure

VIII-32 MRV―function

* To be used in development of adaptive management and monitoring plans, the KEAs included here need to be 

adapted to specific components. Examples of component-specific KEAs and indicators are in Table 13 and Table 

14.
41

Table 13. Estuarine and marine KEAs organized by ecosystem process and ecosystem component 

(italicized). Roman numerals correspond to ecosystem processes in the text; Arabic numbers 

refer to the associated KEAs. The table cells containing these numerals and numbers (e.g., I-2) 

are considered priority KEAs for monitoring and adaptive management of Puget Sound salmon 

recovery. The table cell containing an asterisk (*) is considered a potential KEA. 

Drift cell system Rocky shoreline

Ecosystem process

Natal 

Chinook 

estuary

Coastal 

landform

Bluffbacked 

beach

Pocket 

estuary

Rocky 

pocket 

estuary

Rocky 

beach

Offshore 

marine 

system

I. Sediment dynamics 

—coastal

* I-1, 2, 3, 

5, 8

I-1, 2, 3, 

6, 7, 8, 9

I-1, 2 I-4, 5, 6, 

7, 8, 9

I-4, 6, 7, 

8, 9

— 

II. Sediment dynamics 

—fluvial

II-10 — — II-10 II-10 — — 

III. Hydrological 

dynamics—tidal

III-11, 

12

III-11, 

12

III-12 III-11, 

12

III-11, 

12

III-11, 

12

III-11, 

12

IV. Hydrological 

dynamics—freshwater

IV-13, 

14

IV-13 IV-13 IV-13, 

14

IV-13, 

14

IV-13 IV-13

V. Tidal channel formation & maintenanceV-15, 16 — — V-15, 16 V-15, 16 — — 

VI. Detritus recruitment & retentionVI-17, 

18

VI-17, 

18

VI-17, 

18

VI-17, 

18

VI-17, 

18

VI-18 VI-18

VII. Habitat 

connectivity

VII-19 — — VII-19 VII-19 VII-19 — 

VIII. Multiple 

ecosystem processes

VIII-20, 

21, 22, 

23, 24, 

27, 28, 

29, 30, 

31, 32

VIII-21, 

25, 26, 

29, 30, 

31, 32

VIII-20, 

21, 25, 

26, 29, 

30, 31, 

32

VIII-20, 

21, 22, 

23, 24, 

27, 28, 

29, 30, 

31, 32

VIII-20, 

21, 22, 

23, 24, 

27, 28, 

29, 30, 

31, 32

VIII-20, 

21, 25, 

26, 29, 

30, 31, 

32

VIII-20, 

21, 29
42

Table 14. KEAs and example indicators for estuarine and marine ecosystem components, organized by 

component.

KEA Example indicator of KEA status or condition

Major river system: Natal Chinook estuary

II-10. Fluvial sediment dynamics—

condition

Sediment loading

Sediment accretion

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity

No. and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, dissolved oxygen (DO), pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition

Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-14. Freshwater hydrology—condition River or stream discharge rate and hydrograph (flow 

gauges and precipitation)

V-15. Tidal channel formation and 

maintenance—extent of channels

Extent (area, length, width) of blind or distributary 

channels

V-16. Tidal channel formation and 

maintenance—connectivity of channels

Connectivity of blind or distributary channels. Metrics 

should address connectivity within and between habitat 

types

VI-17. Detritus recruitment and retention—

extent 

Amount (quantity, size, volume, type) of detritus 

recruited or retained in the habitat zones. Measure in 

tidally influenced wetlands

VI-18. Detritus recruitment and retention—

extent of supply 

Recruitment of detritus from marine riparian vegetation 

(MRV)

VII-19. Habitat connectivity condition Extent (area, length, width) of bluff retreat

Extent (number, volume) of landslides

Extent (area, length) of coastal landforms over time

Distance between suitable habitats

Indicators should address connectivity within habitat 

types and between habitat types

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2)

Spatial extent and continuity (i.e., patchiness)

Function of submerged aquatic vegetation (SAV)

Substrate composition of SAV beds

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-22. Estuarine habitats—extent Amount (area in acres) of estuarine habitat (intertidal and 

subtidal) zones

Number of accessible (to Chinook salmon) pocket 

estuaries

VIII-23. Estuarine habitats—condition Elevation of estuarine habitats

Vegetation community composition
43

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Major river system: Natal Chinook estuary (continued)

VIII-24. Estuarine habitats—distribution Spatial distribution of defined estuarine habitats

Distance of pocket estuary from natal Chinook estuary

Distance between pocket estuaries or other estuarine 

habitats

VIII-27. Tidally influenced wetlands—

extent 

Amount (area in acres) of tidal wetland habitat

Number of pocket estuaries, and distance between them

VIII-28. Tidally influenced wetlands—

condition 

Vegetation community composition

Elevation of wetlands

Changes in tidal wetland accretion

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH

Nutrient load

Detritus load

Turbidity (sediment load—suspended)

VIII-30. MRV—spatial extent and 

continuity

Amount (area in acres, length, width) of MRV

Spatial extent and continuity (i.e., patchiness)

VIII-31. MRV—community structure Community structure (species composition)

Density (no. shoots/m2)

Seral stage

VIII-32. MRV—function Function of MRV (e.g., recruitment, canopy closure, 

etc.)

Drift cell system: Bluff-backed beach

I-1. Coastal sediment dynamics 

in drift cells—condition

Number of drift cells with functional sediment dynamics

Percent of drift cells with functional sediment dynamics

Percent feeder bluff

Rocky beach embeddedness

Rocky beach profile

Drift cell beach profile

I-2. Coastal sediment dynamics in 

drift cells—landscape context

Distribution of functional drift cells across landscape

I-3. Coastal sediment deposition and 

accretion—extent

Amount (area, volume) of sediment deposition or 

accretion (relative to historic) on coastal landform

I-6. Coastal sediment supply—extent Rate of sediment supply (e.g., landslide area on a bluffbacked beach over time)

Extent (length, expressed as % or count) of sediment 

source bluffs and transport zones that are functioning 

within drift cells

I-7. Coastal sediment supply—distribution Distribution of functioning sediment source bluffs and 

transport zones within drift cells

I-8. Coastal sediment dynamics—extent 

(size or volume) of wind and wave features

Amount (area, length, width) of bluff retreat

Amount (number, volume) of landslides

Amount (area, length) of coastal landforms over time

Extent and distribution of uninterrupted transport zones
44

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Drift cell system: Bluff-backed beach (continued)

I-9. Coastal sediment dynamics—condition 

of wind and wave features

Composition of SAV bed substrate 

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity

Number and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition

Temperature, salinity, DO, pH

Sediment load

Nutrient load

VI-17. Detritus recruitment and retention—

extent

Amount (quantity, size, volume, type) of detritus 

recruited or retained in the habitat zones. Measure in 

tidally influenced wetlands

VI-18. Detritus recruitment and retention—

extent of supply

Recruitment of detritus from MRV

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2)

Spatial extent and continuity (i.e., patchiness)

Function of SAV

Substrate composition of SAV beds

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-25. Intertidal habitat zone—extent Amount (area in acres, length) of intertidal and subtidal 

habitat zones

Number of accessible pocket estuaries

VIII-26. Intertidal habitat zone—condition Profile (slope and elevation) of intertidal zones (see 

Figure 10). Note: This is an indicator of tidal hydrology

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH

Nutrient load

Detritus load

Turbidity (sediment load—suspended)

VIII-30. MRV—spatial extent and 

continuity

Amount (area in acres, length, width) of MRV

Spatial extent and continuity (i.e., patchiness)

VIII-31. MRV—community structure Community structure (species composition)

Density (no. shoots/m2)

Seral stage

VIII-32. MRV—function Function of MRV (e.g., recruitment, canopy closure, 

etc.)
45

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Drift cell system: Coastal landform

I-1. Coastal sediment dynamics in drift 

cells—condition

Number of drift cells with functional sediment dynamics

Percent of drift cells with functional sediment dynamics

Percent feeder bluff

Rocky beach embeddedness

Rocky beach profile

Drift cell beach profile

I-2. Coastal sediment dynamics in drift 

cells—landscape context

Distribution of functional drift cells across landscape

I-3. Coastal sediment deposition and 

accretion—extent

Amount (area, volume) of sediment deposition or 

accretion (relative to historic) on coastal landform

I-5. Coastal sediment deposition and 

accretion—condition of impoundment

Width of tidal inlets for lagoons at or near equilibrium

Proportion of spits with overwash deposits

I-8. Coastal sediment dynamics—extent 

(size or volume) of wind and wave features

Amount (area, length) of coastal landforms over time

Extent and distribution of uninterrupted transport zones

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity

Number and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition

Temperature, salinity, DO, pH

Sediment load

Nutrient load

VI-17. Detritus recruitment and retention—

extent

Amount (quantity, size, volume, type) of detritus 

recruited or retained in the habitat zones. Measure in 

tidally influenced wetlands

VI-18. Detritus recruitment and retention—

extent of supply

Recruitment of detritus from MRV

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2)

Spatial extent and continuity (i.e., patchiness)

Function of SAV

Substrate composition of SAV beds

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-25. Intertidal habitat zone—extent Amount (area in acres, length) of intertidal and subtidal 

habitat zones

Number of accessible pocket estuaries

VIII-26. Intertidal habitat zone—condition Profile (slope and elevation) of intertidal zones (see 

Figure 10). Note: This is an indicator of tidal hydrology
46

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Drift cell system: Coastal landform (continued)

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH

Nutrient load

Detritus load

Turbidity (sediment load—suspended)

VIII-30. MRV—spatial extent and 

continuity

Amount (area in acres, length, width) of MRV

Spatial extent and continuity (i.e., patchiness)

VIII-31. MRV—community structure Community structure (species composition)

Density (No. shoots/m2)

Seral stage

VIII-32. MRV—function Function of MRV (e.g., recruitment, canopy closure, 

etc.)

Drift cell system: Pocket estuary

I-1. Coastal sediment dynamics in drift 

cells—condition

Number of drift cells with functional sediment dynamics

Percent of drift cells with functional sediment dynamics

Percent feeder bluff

Rocky beach embeddedness

Rocky beach profile

Drift cell beach profile

I-2. Coastal sediment dynamics in drift 

cells—landscape context

Distribution of functional drift cells across landscape

II-10. Fluvial sediment dynamics—

condition

Sediment loading

Sediment accretion

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity

Number and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition

Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-14. Freshwater hydrology—condition River or stream discharge rate and hydrograph

Presence/absence of freshwater input (pocket estuaries)

V-15. Tidal channel formation and 

maintenance—extent of channels

Extent (area, length, width) of blind or distributary 

channels

V-16. Tidal channel formation and 

maintenance—connectivity of channels

Connectivity of blind or distributary channels. Metrics 

should address connectivity within and between habitat 

types

VI-17. Detritus recruitment and retention—

extent

Amount (quantity, size, volume, type) of detritus 

recruited or retained in the habitat zones. Measure in 

tidally influenced wetlands
47

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Drift cell system: Pocket estuary (continued)

VI-18. Detritus recruitment and retention—

extent of supply

Recruitment of detritus from MRV

VII-19. Habitat connectivity condition Extent (area, length, width) of bluff retreat

Extent (number, volume) of landslides

Extent (area, length) of coastal landforms over time

Distance between suitable habitats

Indicators should address connectivity within habitat 

types and between habitat types

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2)

Spatial extent and continuity (i.e., patchiness)

Function of SAV

Substrate composition of SAV beds

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-22. Estuarine habitats—extent Amount (area in acres) of estuarine habitat (intertidal and 

subtidal) zones

Number of accessible (to Chinook salmon) pocket 

estuaries

VIII-23. Estuarine habitats—condition Elevation of estuarine habitats

Vegetation community composition

VIII-24. Estuarine habitats—distribution Spatial distribution of defined estuarine habitats

Distance of pocket estuary from natal Chinook estuary

Distance between pocket estuaries, or other estuarine 

habitats

VIII-27. Tidally influenced wetlands—

extent

Amount (area in acres) of tidal wetland habitat

Number of pocket estuaries, and distance between them

VIII-28. Tidally influenced wetland—

condition

Vegetation community composition

Elevation of wetlands

Changes in tidal wetland accretion

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH

Nutrient load

Detritus load

Turbidity (sediment load—suspended)

VIII-30. MRV—spatial extent and 

continuity

Amount (area in acres, length, width) of MRV

Spatial extent and continuity (i.e., patchiness)

VIII-31. MRV—community structure Community structure (species composition)

Density (no. shoots/m2)

Seral stage

VIII-32. MRV—function Function of MRV (e.g., recruitment, canopy closure, 

etc.)
48

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Rocky shoreline: Rocky beach

I-4. Coastal sediment deposition and 

accretion—condition of sediment

Composition (size and type) of sediment

Beach face and back shore width and area

I-6. Coastal sediment supply—extent Rate of sediment supply (e.g., landslide area on a bluffbacked beach over time)

Extent (length, expressed as % or count) of sediment 

source bluffs and transport zones that are functioning 

within drift cells

I-7. Coastal sediment supply—distribution Distribution of functioning sediment source bluffs and 

transport zones within drift cells

I-8. Coastal sediment dynamics—extent 

(size or volume) of wind and wave features

Amount (area, length) of coastal landforms over time

Extent and distribution of uninterrupted transport zones

I-9. Coastal sediment dynamics—condition 

of wind and wave features

Composition of SAV bed substrate

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity

Number and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition

Temperature, salinity, DO, pH

Sediment load

Nutrient load

VI-18. Detritus recruitment and retention—

extent of supply

Recruitment of detritus from MRV

VII-19. Habitat connectivity condition Extent (area, length, width) of bluff retreat

Extent (number, volume) of landslides

Extent (area, length) of coastal landforms over time

Distance between suitable habitats

Indicators should address connectivity within habitat 

types and between habitat types

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2)

Spatial extent and continuity (i.e., patchiness)

Function of SAV

Substrate composition of SAV beds

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-25. Intertidal habitat zone—extent Amount (area in acres, length) of intertidal and subtidal 

habitat zones

Number of accessible pocket estuaries

VIII-26. Intertidal habitat zone—condition Profile (slope and elevation) of intertidal zones (see 

Figure 10). Note: This is an indicator of tidal hydrology
49

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Rocky shoreline: Rocky beach (continued)

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH

Nutrient load

Detritus load

Turbidity (sediment load—suspended)

VIII-30. MRV—spatial extent and 

continuity

Amount (area in acres, length, width) of MRV

Spatial extent and continuity (i.e., patchiness)

VIII-31. MRV—community structure Community structure (species composition)

Density (no. shoots/m2)

Seral stage

VIII-32. MRV—function Function of MRV (e.g., recruitment, canopy closure, 

etc.)

Rocky shoreline: Rocky pocket estuary

I-4. Coastal sediment deposition and 

accretion—condition of sediment

Composition (size and type) of sediment

Beach face and back shore width and area

I-5. Coastal sediment deposition and 

accretion—condition of impoundment

Width of tidal inlets for lagoons at or near equilibrium

Proportion of spits with overwash deposits

I-6. Coastal sediment supply—extent Rate of sediment supply (e.g., landslide area on a bluffbacked beach over time)

Extent (length, expressed as % or count) of sediment 

source bluffs and transport zones that are functioning 

within drift cells

I-7. Coastal sediment supply—distribution Distribution of functioning sediment source bluffs and 

transport zones within drift cells

I-8. Coastal sediment dynamics—extent 

(size or volume) of wind and wave features

Amount (area, length) of coastal landforms over time

Extent and distribution of uninterrupted transport zones

I-9. Coastal sediment dynamics—condition 

of wind and wave features

Composition of SAV bed substrate

II-10. Fluvial sediment dynamics—

condition

Sediment loading

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity

Number and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition

Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-14. Freshwater hydrology—condition River or stream discharge rate and hydrograph (flow 

gauges and precipitation)

Presence/absence of freshwater input (pocket estuaries)
50

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component.

KEA Example indicator of KEA status or condition

Rocky shoreline: Rocky pocket estuary (continued)

V-15. Tidal channel formation and 

maintenance—extent of channels

Extent (area, length, width) of blind or distributary 

channels

V-16. Tidal channel formation and 

maintenance—connectivity of channels

Connectivity of blind or distributary channels. Metrics 

should address connectivity within and between habitat 

types

VI-17. Detritus recruitment and retention—

extent

Amount (quantity, size, volume, type) of detritus 

recruited or retained in the habitat zones. Measure in 

tidally influenced wetlands

VI-18. Detritus recruitment and retention—

extent of supply

Recruitment of detritus from MRV

VII-19. Habitat connectivity condition Extent (area, length, width) of bluff retreat

Extent (number, volume) of landslides

Extent (area, length) of coastal landforms over time

Distance between suitable habitats

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2)

Spatial extent and continuity (i.e., patchiness)

Function of SAV

Substrate composition of SAV beds

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-22. Estuarine habitats—extent Amount (area in acres) of estuarine habitat (intertidal and 

subtidal) zones

Number of accessible (to Chinook salmon) pocket 

estuaries 

VIII-23. Estuarine habitats—condition Elevation of estuarine habitats

Vegetation community composition

VIII-24. Estuarine habitats—distribution Spatial distribution of defined estuarine habitats

Distance of pocket estuary from natal Chinook estuary

Distance between pocket estuaries or other estuarine 

habitats

VIII-27. Tidally influenced wetlands—

extent

Amount (area in acres) of tidal wetland habitat

Number of pocket estuaries, and distance between them

VIII-28. Tidally influenced wetlands—

condition

Vegetation community composition

Elevation of wetlands

Changes in tidal wetland accretion

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH

Nutrient load

Detritus load

Turbidity (sediment load—suspended)

VIII-30. MRV—spatial extent and 

continuity

Amount (area in acres, length, width) of MRV

Spatial extent and continuity (i.e., patchiness)
51

Table 14 continued. KEAs and example indicators for estuarine and marine ecosystem components, 

organized by component. 

KEA Example indicator of KEA status or condition

Rocky shoreline: Rocky pocket estuary (continued)

VIII-31. MRV—community structure Community structure (species composition)

Density (no. shoots/m2) 

Seral stage

VIII-32. MRV—function Function of MRV (e.g., recruitment, canopy closure, 

etc.)

Offshore marine system

III-11. Tidal circulation—extent of 

biological activity

Primary productivity

Secondary productivity 

Number and species of organisms present (zooplankton, 

macrobiota, etc.)

III-12. Tidal circulation—water condition Temperature, salinity, DO, pH

Sediment load

Nutrient load

IV-13. Freshwater hydrology—water 

condition 

Temperature, salinity, DO, pH

Sediment load

Nutrient load

VI-18. Detritus recruitment and retention—

extent of supply

Recruitment of detritus from MRV

VIII-20. SAV beds—condition Community structure (species composition)

Density (no. shoots/m2) 

Spatial extent and continuity (i.e., patchiness) 

Function of SAV 

Substrate composition of SAV beds 

Elevation of SAV beds

VIII-21. SAV beds—extent Amount (area, length, width in acres) of any SAV, either 

eelgrass or kelp species

VIII-29. Water quality River discharge rate and hydrograph

Temperature, salinity, DO, pH 

Nutrient load

Detritus load

Turbidity (sediment load—suspended)
52

Table 15. KEAs and indicators for estuarine and marine components in the Skagit watershed.

KEA Indicator

Current 

status

Desired 

future 

status

Historical 

condition

Indicator description 

and method

Pocket estuary component

VIII-22. 

Estuarine 

habitat 

extent

Count of 

accessible* 

pocket estuaries 

within Skagit 

Bay

8 12 22 Count of accessible* pocket 

estuaries of Skagit Bay, GIS 

methods

VIII-22. 

Estuarine 

habitat 

extent

Extent of 

accessible* 

pocket estuary 

habitat within 

Skagit Bay

47.5 ha 311.5 ha 340.7 ha Sum of area of accessible* 

intertidal and subtidal habitat 

within pocket estuaries of Skagit 

Bay, GIS methods

VII-19. 

Habitat 

connectivity 

condition

Median distance 

between pocket 

estuaries

3.49 km Not 

specified

1.26 km Median distance along shoreline at 

mean of lower low water (MLLW)

between accessible* pocket 

estuaries within the Whidbey Basin,

GIS methods

VII-19. 

Habitat 

connectivity 

condition 

Median 

landscape 

connectivity of 

pocket estuaries 

within Skagit 

Bay

0.14 0.14 — Median landscape connectivity 

index (distance and complexity of 

fish migration pathways to 

accessible* pocket estuaries within 

Skagit Bay), methods described in 

Beamer et al. 2005

Natal Chinook estuary component

VIII-22. 

Estuarine 

habitat 

extent

Accessible* 

tidally 

influenced 

wetlands within 

the Skagit 

estuary

3,118.0 

ha

4,232.6 

ha

11,483.0 

ha

Sum of area of tidally influenced 

wetlands in the Skagit estuary, 

remote-sensed methods

VIII-22. 

Estuarine 

habitat 

extent

Accessible* 

distributary 

channel area 

within the 

Skagit estuary

851.7 ha 895.8 ha 1,223.8 ha Sum of area of accessible*

distributary channels in the Skagit 

estuary, remote-sensed methods

VIII-22. 

Estuarine 

habitat 

extent

Accessible* 

blind channel 

tidal area within 

the Skagit 

estuary

62.7 ha 110.8 ha 1,158.0 ha Sum of area of accessible* blind 

tidal channels in the Skagit estuary, 

remote-sensed methods with 

subsample of channels field 

measured

VII-19. 

Habitat 

connectivity 

condition 

Median 

landscape 

connectivity of 

blind channels 

within the 

Skagit estuary

0.0190 0.0246 — Median landscape connectivity 

index (distance and complexity of 

fish migration pathways to 

accessible* blind channels within 

the Skagit estuary), methods 

described in Beamer et al. 2005

*Accessible = Accessible to juvenile Chinook salmon rearing; pocket estuaries and natal estuarine habitat are

sufficiently exposed to tidal hydrology to allow access to and use of habitat by juveniles.
53

I. Sediment dynamics―coastal

Coastal sediment dynamics comprise the processes that supply, transport, and deposit 

shoreline sources of sediment within estuarine and marine systems. This includes coastal 

sediment dynamics associated with drift cells, major river systems, and rocky shorelines. We 

also include wind/wave processes in each system, which are a primary energy source for 

movement of coastal sediment.

Within drift cell systems, bluff-backed beaches are the sediment supply shore forms 

(Keuler 1988). Sediment transport and deposition also occur at bluff-backed beaches (Finlayson 

2006, Johannessen and MacLennan 2007). Coastal landforms (e.g., spits, tombolos, cuspate 

forelands) are deposition (or accretion) shore forms where there is a net gain and storage of 

sediment (Shipman 2008). Pocket estuaries with lagoon habitat formed behind coastal landforms 

are a byproduct of healthy drift cell sediment dynamics. Lagoon habitat is lost over time if 

coastal landforms erode away due to lack of sediment supply or blocked sediment transport 

within the drift cell. Sediment supply dynamics can be disturbed in two general ways:

1. Oversupplied sediment caused by a) an increase in bluff erosion (due to sea level rise or 

an uptick in storm frequency), b) loss of stabilizing bluff vegetation, or c) rerouting of 

surface water or groundwater such that slope failure and erosion increase; or

2. Undersupplied sediment caused by a) a change in the geologic material exposed to 

natural erosion, b) armoring/bulkheading toes of sediment bluffs such that sediment 

sources are isolated from wave energy, or c) blocking sediment transport such that 

sediments are moved to deeper water instead of proceeding down drift.

Two KEAs related specifically to coastal sediment dynamic processes associated with 

drift cells were identified:

• KEA I-1. Coastal sediment dynamics in drift cells―condition, and

• KEA I-2. Coastal sediment dynamics in drift cells―landscape context.

Additional attributes of coastal sediment dynamics that are not exclusively related to drift cell 

systems are discussed below.

Not all Puget Sound shorelines are drift cell systems. Major river systems and rocky 

shorelines respond differently to the influence of wave energy. Rocky shorelines erode 10 to 100 

times more slowly than bluff-backed beaches (Keuler 1988). These shorelines thus have little or 

no beach area and no appreciable longshore sediment transport. The exception along rocky 

shorelines is the pocket beach (i.e., a beach in a small rocky embayment). Sediment for the 

pocket beach is locally derived rather than delivered via longshore sediment dynamics. Variable 

erodibility in rock or sediment types (e.g., a friable slate unit sandwiched between hard quartzite, 

glacial-carved valley with till deposits), tectonic weaknesses (fractures or faults), and upland 

erosional weaknesses (mechanical erosion by ice, water, or trees) can make a rocky shoreline 

segment more susceptible to onshore wave erosion. Over time this susceptibility can evolve into 

an embayment with a wave-cut platform and a beach—a pocket beach. Beach sediments come 

from the eroding rock immediately upslope.
54

A pocket beach can be considered a closed system because all sediment within the

embayment evolves from the embayment itself. At some point, the issue of scale blurs the 

boundaries between very short drift cells and closed-system pocket beaches. As pocket beaches 

age and erosion cuts deeper into the rocky shoreline, upland fluvial processes and erosion are 

more likely to intersect the pocket beach shoreline. Additionally, the energy of the system 

decreases as the deepening pocket beach forms a more protected shoreline. This decreased 

energy keeps sediment in the system longer, rather than washing it offshore. Deepening plus 

stream sediment and water inputs and sloughing of upland eroded sediment can lead to the 

evolution of small drift cells and coastal landform development (berms, spits, tombolos) within 

the low-energy embayment. Changes in sea level can hasten beach development or destroy 

beaches. These systems are fragile because of their minimal sediment input and slow evolution 

process.

Five KEAs related to all coastal sediment dynamic processes were identified:

• KEA I-3. Coastal sediment deposition and accretion―extent,

• KEA I-4. Coastal sediment deposition and accretion―condition of sediment,

• KEA I-5. Coastal sediment deposition and accretion―condition of impoundment,

• KEA I-6. Coastal sediment supply―extent, and

• KEA I-7. Coastal sediment supply―distribution.

Healthy drift cell and rocky shoreline pocket beach systems require wind-driven waves to 

move coastal sediments. If waves are blocked from recruiting or moving sediment, all 

components of the drift cell and sediment source/deposition areas in pocket beaches are impacted 

(see KEA I and KEA II). Localized impediments to wave energy (e.g., jetties) will change local 

sediment dynamics, causing the silting in of enclosed areas and the scouring of areas where 

waves are refracted (adding erosive energy to the wave). Submerged aquatic vegetation (SAV) 

is impacted by substrate changes and by changes in wave energy regime. Some types of SAV 

(e.g., certain kelps) depend on wave energy and would be negatively impacted by structures that 

block it, while other types of SAV (e.g., eelgrass) could be eroded by increases in wave energy.

Two KEAs related to wind and wave–driven coastal sediment dynamics were identified:

• KEA I-8. Coastal sediment dynamics―extent (size or volume) of wind and wave 

features, and

• KEA I-9. Coastal sediment dynamics―condition of wind and wave features.

II. Sediment dynamics―fluvial

Fluvial sediment dynamics include deposition and erosion of sediment from fluvial 

sources. In estuaries, these dynamics are driven by the fluvial energy of the entering river or 

stream as its discharge fluctuates. Actual sediment load of specific rivers or streams, a function 

of watershed conditions upstream, is covered in the subsection above on Key Ecological 

Attributes and Indicators for Freshwater Habitats. Changes in freshwater hydrology alter the 

energy and thus the sediment-carrying capacity of a river or stream. Lower discharge results in 

finer sediment and less sediment overall delivered to an estuary. Higher discharge has the 
55

opposite effect, with more sediment delivered and a coarser sediment component included. Too 

much sediment builds estuaries to higher elevation habitat zones, while sediment starvation leads 

to lower elevation habitat zones and the possible loss of marsh, lagoon, and channels. Fluvial 

processes also assist in distributary channel formation (see KEA V-15, Tidal channel formation 

and maintenance―extent of channels, and KEA V-16, Tidal channel formation and 

maintenance―connectivity of channels).

Fluvial sediment dynamics can bury or erode SAV. This may happen naturally; however,

anthropogenic changes in the watershed can impact both water quantity (i.e., discharge, see KEA 

III) and water quality (i.e., salinity). Salinity and to some extent temperature will determine if, 

where, and what SAV can survive in estuaries and marine nearshore systems.

One KEA related to fluvial sediment dynamics was identified:

• KEA II-10. Fluvial sediment dynamics―condition.

III. Hydrological dynamics―tidal

Tidal processes (e.g., timing and magnitude) form tidal circulation patterns (e.g., 

direction and velocity of currents) within the marine basins of Puget Sound. Tidal circulation 

affects salinity patterns, sediment transport, detrital transport, organismal movements, and 

patterns in primary and secondary production within marine basins. Water masses from separate 

sources (e.g., specific rivers, marine basins, or beyond) may differ in salinity, temperature, or 

suspended sediment concentration—and thus density. Tidal fronts form where water masses of 

contrasting density meet but do not mix immediately. These fronts trap and concentrate organic 

material and become a focus of primary and secondary production. Water masses from separate 

sources may also differ in dissolved oxygen (DO) and in nutrient and pollutant loads, which may 

cause differences in productivity. Tidal circulation can be affected by withdrawing water 

upstream, rerouting river outlets, and building structures such as jetties, causeways, dikes, groins, 

and marine hydropower installations.

Tides are fundamental to the structure and function of estuaries. Tidal circulation affects 

salinity patterns, sediment transport, detrital transport, organismal movements, and patterns in 

primary and secondary production. Tidal circulation, along with tidal inundation of estuarine 

wetlands, also affects the physical structure of habitats (e.g., by changing distributary channel 

and blind tidal channel geometry and sediment sorting in benthic habitats). Consequently, these 

processes affect floral and faunal community composition and function throughout estuaries. 

Tidal inundation is impacted by dikes, culverts, tide gates, and fill. Tidal circulation can be 

affected by withdrawing water upstream, rerouting river outlets, and building structures such as 

jetties, causeways, dikes, and groins.

Tidal inundation of beaches (i.e., rocky, bluff-backed, and coastal landform beaches) and 

estuaries determines the area and elevation of habitat and vegetative zones. Structures that 

intercept rising water and prevent tides from encroaching on land disrupt tidal hydrology and 

displace tidally determined habitats and ecological communities that otherwise would have been 

present. These structures include dikes, fill, bulkheads, and other features built within the 

intertidal zone.
56

Two KEAs related to tidal hydrological dynamics were identified:

• KEA III-11. Tidal circulation―extent of biological activity (relative to primary and 

secondary productivity), and

• KEA III-12. Tidal circulation―water condition (relative to physical and chemical 

parameters).

IV. Hydrological dynamics―freshwater

Freshwater discharge introduces sediment, nutrients, detritus, and pollutants to estuaries 

downstream. Discharge also alters estuarine water quality variables, such as temperature, 

salinity, DO, and pH. Anthropogenic activities that modify freshwater hydrology (via changes in 

water quantity or quality) will impact estuaries at river or stream mouths. For example, land 

clearing or development may cause silt deposition in the estuary (see KEA VIII-23) and 

degraded water quality may impact estuarine fish, vegetation, and other wildlife.

Anthropogenic activities that modify freshwater hydrology will impact the nearshore and 

offshore marine water column within Puget Sound’s marine basins as well as its estuaries. 

Increased water column turbidity due to land clearing, elevated contaminant loading due to 

development, and adverse changes in salinity and temperature due to water withdrawal or loss of 

riparian vegetation exemplify some potential impacts. Freshwater inputs can drive habitat 

diversity and complexity; alternatively, they can deliver the upland’s problems to the marine 

environment.

Two KEAs related to freshwater hydrological dynamics were identified:

• KEA IV-13. Freshwater hydrology―water condition (relative to physical and chemical 

parameters), and

• KEA IV-14. Freshwater hydrology―condition (relative to freshwater input, stream 

discharge, and flow).

V. Tidal channel formation and maintenance

Distributary channels are the framework upon which large river estuaries or deltas are 

built. As a river delivers sediment to its delta, the delta progrades and the river progressively 

divides into distributaries. Thus the processes of delta and distributary network formation are 

inextricably interrelated (Edmonds and Slingerland 2007, Stouthamer and Berendsen 2007). 

Distributaries are primarily formed by avulsion (Slingerland and Smith 2004) or channel 

bifurcation during mouth bar development and delta progradation (Edmunds and Slingerland 

2007). Avulsions are thought to be caused principally by channel aggradation, which leads to 

differences in elevation between a channel and its floodplain, thereby creating a gradient 

advantage for a potential avulsion channel relative to the original channel. Loss of channel 

capacity from channel infilling also contributes to avulsion (Makaske 2001, Slingerland and 

Smith 2004).

Distributary network geometry is potentially the most important factor controlling delta 

landforms (Coleman 1988, Syvitski et al. 2005) and related hydrological, geological, and 
57

ecological processes. Because distributary network geometry in deltas affects the spatial 

distribution of salinity gradients and sedimentation patterns and these affect vegetation 

distribution in turn, distributary network geometry also affects fish and wildlife distribution 

patterns through its effect on habitat. Anthropogenic engineering significantly influences 

distributaries and the growth and evolution of their associated deltas (Pasternack et al. 2001, 

Syvitski and Saito 2007). Direct human impacts include distributary blockage or excavation to 

redirect river discharge. Indirect impacts include system modifications such as 1) dam 

construction, which moderates seasonal flood pulses, causing sediment retention in reservoirs, 

and 2) water withdrawals, which effectively reduce the drainage area of the watershed (Syvitski 

2008).

Estuarine tidal channels are conduits for water, sediment, nutrients, detritus, and aquatic 

organisms, and thus link highly productive tidal marshes to the nearshore marine environment 

(Simenstad 1983, Odum 1984, Rozas et al. 1988, Pethick 1992, French and Spencer 1993). 

Tidal channels affect hydrodynamics (Rinaldo et al. 1999), sediment transport (French and 

Stoddart 1992), and the distribution and production of flora (Sanderson et al. 2000) and fauna 

(Levy and Northcote 1982, Halpin 1997, Williams and Zedler 1999, Hood 2002). Tidal channel 

formation and maintenance depend on tidal prism (i.e., the volume of water between low and 

high tides that flushes the channels during tidal exchange). Tidal prism can be impacted directly 

through the use of dikes and tide gates to limit flooding (Greene et al. 2012), or indirectly 

through the conversion of upslope marshes to farmland (Hood 2004). Sediment starvation can 

also result in marsh erosion, leading to the loss of tidal channels (Hood 2007a).

Two KEAs related to tidal channel formation and maintenance were identified:

• KEA V-15. Tidal channel formation and maintenance―extent of channels, and

• KEA V-16. Tidal channel formation and maintenance―connectivity of channels.

VI. Detritus recruitment and retention

Detritus consists of a variety of materials, ranging from decaying SAV to marsh plants in 

subtidal and intertidal habitats, or from leaves to logs (i.e., LWD) in upland habitats. Food webs 

in tidal marshes are largely based on detritus (Simenstad 1983, Odum 1984). In addition to 

providing food web support, detritus (particularly LWD) serves a structural function by affecting 

blind tidal channel morphology and beach morphology. Detritus also supplies perches for 

wildlife, beach microhabitat for invertebrates (Tonnes 2008), and nurse logs that affect 

vegetation community composition and succession (Hood 2007b). Sources of detritus include 

watersheds, marine riparian zones, tidal marshes, and intertidal/subtidal zones. Armoring of 

river banks and coastlines impedes recruitment of detritus.

Two KEAs related to detritus recruitment and retention were identified:

• KEA VI-17. Detritus recruitment and retention―extent, and

• KEA VI-18. Detritus recruitment and retention―extent of supply.
58

VII. Habitat connectivity

Connectivity of habitats is necessary for the dispersal and migration of aquatic species

and, in the case of Chinook salmon, the development and expression of diverse life histories 

(Fullerton et al. 2010). Connectivity can be described as the availability of or access to habitats 

that are required by each life stage. Beamer et al. (2005) defined landscape-scale habitat 

connectivity for juvenile Chinook salmon in a natal estuary and its adjacent nearshore marine 

basin in terms of the relative distances and pathways that salmon must travel to find habitat. 

Landscape connectivity was a function of the distance and complexity of the pathway that 

salmon must follow to reach certain types of habitats (e.g., blind tidal channels and pocket 

estuaries). Specifically, connectivity decreased as the distance and complexity of the pathway 

increased. Localized habitat connectivity, synonymous with the concept of habitat opportunity 

proposed by Simenstad (2000) and Simenstad and Cordell (2000), is applied to metrics reflecting 

a juvenile salmon’s ability to “access and benefit from the habitat’s capacity.” Differences 

between empirical values of metrics (e.g., tidal elevation, water velocity, and temperature) and 

suitability standards for these metrics (e.g., standards for suitable juvenile salmon habitat) have 

been used to infer differences in local connectivity between estuarine habitats (Bottom et al. 

2001). In tide-gated estuarine channel systems, additional data are needed to determine local 

connectivity, such as the percentage of time tide gate doors are open (Greene et al. 2012).

One KEA related to habitat connectivity was identified:

• KEA VII-19. Habitat connectivity condition.

VIII. Multiple ecosystem processes

Many attributes of estuarine and marine systems are dependent on the proper functioning 

of multiple ecosystem processes. The KEAs included in this multiple ecosystem process group 

primarily represent critical habitat types for Chinook salmon. Indicators of the health of these 

attributes provide information about the underlying habitat-forming processes and conditions. 

For example, natal estuaries are a critical habitat for juvenile ocean-type Chinook salmon, and 

the extent and condition of estuarine habitats are a function of tidal and freshwater hydrology, 

fluvial sediment dynamics, and other ecosystem processes. SAV beds provide direct habitat for 

juvenile Chinook salmon and many other species important to salmonid food webs. SAV 

distribution is limited by desiccation stress, salinity patterns, and water clarity. Likewise, 

spawning locations of forage fish (e.g., surf smelt [Hypomesus pretiosus], sand lance

[Ammodytes hexapterus], and Pacific herring [Clupea pallasii]) in intertidal habitat zones are 

limited by physiological constraints on egg survival related to desiccation, oxygenation, and 

temperature stresses. Tidal inundation directly affects all of these factors; it also indirectly 

affects them through tidal and wave energy effects on beach substrate composition. 

Consequently, distributions of SAV and forage fish spawning are constrained to certain substrate 

types and tidal elevations. Tidal inundation and energy can be affected by shoreline armoring 

and constrictions on tidal flows such as tide gates and other marine engineering.

Marine riparian vegetation (MRV) is also a factor that affects the quality of estuarine and 

nearshore marine intertidal, and wetland habitats. The relationships of MRV that directly affect 

Chinook salmon in estuarine and nearshore marine habitats are not well studied to date. We 

provide the context for work to be connected on this topic in KEAs VIII-30, VIII-31, and VIII-
59

32, but leave prioritization to the watersheds if this is an aspect stated in their recovery plan goals 

and thus their monitoring and adaptive management plans. For example, marine riparian areas 

have largely not been mapped and should be done to establish baseline. And it may be difficult 

to evaluate/rank MRV indicators now in the viability assessment, as benchmarks have yet to 

determined. See Brennan et. al. (2009) for additional guidance and references.

Thirteen KEAs related to multiple ecosystem processes were identified:

• KEA VIII-20. SAV beds―condition,

• KEA VIII-21. SAV beds―extent,

• KEA VIII-22. Estuarine habitats―extent,

• KEA VIII-23. Estuarine habitats―condition,

• KEA VIII-24. Estuarine habitats―distribution,

• KEA VIII-25. Intertidal habitat zone―extent,

• KEA VIII-26. Intertidal habitat zone―condition,

• KEA VIII-27. Tidally influenced wetlands―extent,

• KEA VIII-28. Tidally influenced wetlands―condition,

• KEA VIII-29. Water quality,

• KEA VIII-30. MRV―spatial extent and continuity,

• KEA VIII-31. MRV―community structure (e.g., species composition and seral stage), 

and

• KEA VIII-32. MRV―function (e.g., recruitment, canopy closure, etc.).

Key Ecological Attributes and Indicators for Species and 

Food Webs

Background

Nonnative species invasion, pollutant bioaccumulation, primary production, nutrient 

cycling, and biotic interactions such as predation, competition and disease represent food web 

processes. In many cases, these processes underlie constraints on the production of at-risk native 

fish populations (ISAB 2011, Rice et al. 2011). While these underpinnings are apparent in 

theory, they are often overlooked in the practice of recovery planning and implementation. For 

example, many studies quantify the effects of biotic interactions on salmonids in general (e.g., 

Groot and Margolis 1991, Fresh 1997, NMFS 1997, Sanderson et al. 2009), and on Puget Sound 

Chinook in particular (e.g., Arkoosh et al. 2004, Ruggerone and Goetz 2004, Hanson et al. 2010, 

Duffy and Beauchamp 2011). However, consideration of these effects varies widely among 

salmon recovery plans, from inclusion as a footnote to a focal point. The lack of systematic 

attention to the effects of biotic interactions and other food web processes is attributed in part to 

gaps in scientific data (Ruckelshaus et al. 2002). The gaps persist because many interactions are 

difficult to measure. Filling these gaps through targeted monitoring is an important need.
60

This subsection of the framework, like the habitat-related subsections above, relies on a 

simple conceptual diagram in which large-scale and small-scale processes affect habitat 

conditions, leading in turn to a biological response in Chinook salmon (Figure 2). Clearly this 

response does not exist in isolation, but rather in concert with other organisms. Biotic 

interactions occur between Chinook salmon and other species in all the life stages and habitats 

described above (Figure 4, Table 5, and Table 2). The intent of this subsection is not to identify 

every potential interaction with Chinook salmon or to document all possible linkages with 

Chinook salmon in aquatic food webs. Rather, the intent is to provide a placeholder in the 

framework, enabling watershed groups with concerns about species and food webs to include 

them in their monitoring and adaptive management plans.

This subsection of the framework is based on Chapter 1A of the 2010 Puget Sound 

Science Update. In this chapter, Levin et al. (2010) use the Open Standards system to evaluate 

indicators for ecosystem components corresponding to four of the partnership’s statutory goals 

(species and food webs, habitats, water quantity, and water quality). Here we tailor the parts of 

their work that relate to species and food webs, sound-wide, by adding four categories of 

ecological relationships to limit the range of species to include only those relevant to Chinook 

salmon as 1) predators, 2) competitors, 3) prey, or 4) symbiotically as pathogens, facilitators, etc. 

(Table 16). Which species fit best into each category depends on the Chinook life stage and 

habitat type of interest. For example, predators of adult Chinook spawning in freshwater habitats 

(e.g., black bears [Ursus americanus]) differ from predators of the eggs that the spawners release 

(e.g., torrent sculpins [Cottus rhotheus]). Predation by humans is excluded from this section

because it is included elsewhere (e.g., as a pressure, Appendix B). Interactions with hatchery 

fish (e.g., as potential predators, competitors, and pathogen vectors) are included here and in 

appendix Table B-4.

Table 16. Key ecological attributes, as related to Chinook salmon, for the species and food webs 

ecosystem component. The identity of the appropriate predator, competitor, prey, or other 

species depends on the Chinook life stage and habitat type of interest.

Ecological relationship to Chinook salmon KEA

Predator species Population size

Population condition

Competitor species Population size

Population condition

Prey species Population size

Population condition

Other species* Population size

Population condition

Food web Community composition

Energy and material flow

* Pathogens or facilitators (e.g., species that provide habitat for Chinook salmon).
61

Key Ecological Attributes and Indicators

Levin et al. (2010) identify four KEAs applicable to species and food webs. Two of the 

KEAs, population size and population condition, pertain to species; the other two, community 

composition and energy and material flow, relate to food webs. Each of these KEAs can be 

subdivided further. The rationale against doing so is to keep the framework as simple as 

possible, so that multiple indicators can apply to a single KEA and excessive data gaps can be 

avoided (Levin et al. 2010). In support of this rationale and in the interest of maintaining 

consistency, our framework uses identical KEAs with minor changes to their definitions.

Species KEAs

Population size is defined as the abundance of a population, measured as a number of 

individuals or total biomass (Levin et al. 2010). Changes in abundance over time are also 

included, measured as productivity or population dynamics like rates of birth, death, 

immigration, and emigration. Population condition includes various measures of population 

health, such as genetic diversity, phenotypic diversity, age structure, size structure, and spatial 

structure (Levin et al. 2010). It also incorporates two measures of health at the organismal level: 

physiological status (i.e., individual size and growth) and disease status (i.e., incidence of 

infection).

Population size and condition, thus defined, encompass the three types of KEAs often 

used by Open Standards practitioners: size, condition, and landscape context (TNC 2007). 

Population size and condition also include all four parameters (abundance, productivity, 

diversity, and spatial structure) used to describe viable populations of Chinook salmon 

(McElhany et al. 2000). Here those parameters are applied to other species. Some of these 

species have no delineated population structure or are rarely identified past the family or genus 

level, making groupings like “population” and “species” irrelevant. Still other species are both 

ESA-listed and directly responsible for Chinook mortality (e.g., orcas [Orcinus orca] and 

steelhead [Oncorhynchus mykiss]). As a result, trade-offs might occur between improvements in 

the status of these species and Chinook salmon.

Food web KEAs

While the species KEAs characterize single species or guilds, the food webs KEAs 

integrate multiple species at various trophic levels or they refer to ecological processes rather 

than species (Table 16). For example, community composition encompasses various measures 

of biodiversity, such as species diversity, trophic diversity, response diversity, and functional 

redundancy (Levin et al. 2010). Functional redundancy refers to the number of species that 

perform the same functional role in a food web (Lawton and Brown 1993). Response diversity 

represents the number of reactions functionally similar species exhibit when confronted with 

disturbance (Elmqvist et al. 2003).

Energy and material flows (i.e., via consumption) consist of processes such as primary 

production and nutrient cycling, as well as flows of organic and inorganic matter within food 

webs (Levin et al. 2010). Consumption is another key process―between trophic levels, along 

different energy pathways, and within and among habitats. The relative importance of food 
62

production, temporal food supply, and competition to growth (and thus size-selective survival), 

as well as the importance of predation within or beyond the Puget Sound region should be 

fundamental to our understanding of what limits production of Chinook salmon and other 

salmonids. 

Where anadromous salmon are concerned, these flows are not unidirectional, moving 

only upstream to downstream and eventually to the ocean. It is well documented that salmon 

subsidize freshwater and terrestrial food webs by redistributing organic matter and nutrients from 

marine ecosystems (reviewed by Naiman et al. 2009). It is also well documented that salmon 

transport persistent industrial pollutants (reviewed by ISAB 2011), and that Chinook salmon are 

particularly laden vectors (Hites et al. 2004, O’Neill and West 2009). Note that this KEA is also 

incorporated in the habitat-related sections of the framework, either directly (e.g., KEA V, 

Nutrient supply, of the freshwater ecosystem component) or indirectly (e.g., KEA VIII-29, Water 

quality, of the estuarine and marine ecosystem component). 

Indicators

Potential indicators for the species and food webs KEAs are listed in Table 17. As in 

Table 5 and Table 6, some indicators are directly measurable, whereas others are derived. 

Unlike Table 5 and Table 6, Table 17 does not target specific species. Instead, examples of 

specific species that interact with Chinook salmon according to the literature are provided in 

Table 18. This is not an exhaustive list of relevant species, nor is Table 17 a complete list of 

potential indicators. Moreover, we do not suggest that every indicator and species in these tables 

be monitored in all watersheds. Each watershed group will need to tailor its monitoring plan to 

include indicators deemed important at the local scale.
63 

Table 17. Examples of species and food webs indicators, grouped by KEA and relationship to Chinook salmon. 

Ecological relationship to Chinook salmon

KEA Predator species Competitor species Prey species Other species Food web

Population 

size

Abundance, 

biomass, or 

density of key 

predator 

populations 

Productivity of key 

predator 

populations 

Abundance, biomass, or 

density of key competitor 

populations 

Annual releases of hatchery 

salmonids 

Smolt-to-adult returns of 

hatchery salmonids 

Abundance of hatchery 

Chinook salmon spawning 

naturallya

Abundance of other 

salmonid populations 

spawning concurrently 

with Chinook salmona

Abundance, 

biomass, or 

density of 

preferred prey 

populations 

Abundance, 

biomass, or 

density of key 

facilitators

—

Population 

condition 

Spatiotemporal 

distribution of 

key predator 

populations 

Size structure of 

key predator 

populations 

Proportion (by 

weight) of 

Chinook salmon 

in the diets of key 

predator 

populations 

Spatiotemporal distribution 

of key competitor 

populations 

Size structure of key 

competitor populations 

Consumption demand of key 

competitor populations (in 

space and time), relative to 

that of juvenile Chinook 

salmon

Individual body mass, fork 

length, and marine growth 

for key competitor 

populationsb

Spatiotemporal 

distribution of 

key prey 

populations 

Proportion (by 

weight) of key 

prey types in the 

diet of juvenile 

Chinook salmon

Energy contribution 

of key prey types 

in juvenile 

Chinook salmonc

Prevalence of key 

pathogens in 

Chinook salmon

—
64 

Table 17 continued. Examples of species and food webs indicators, grouped by KEA and relationship to Chinook salmon. 

Ecological relationship to Chinook salmon

KEA Predator species Competitor species Prey species Other species Food web

Community 

composition 

— — — — Diversity of nonnative 

predator species

Response diversity of prey 

species 

Benthic index of biological 

integritya

Ephemeroptera, Plecoptera, 

and Trichoptera species 

richnessa

Species diversity and trophic 

diversity of catches by 

beach seine, tow net, etc.b

Average trophic level of fish 

caught by fisheriesb

Energy and 

material flow

— — — — Chlorophyll a concentration 

Stable isotope or fatty acid 

signatures of key species

Consumption demand on 

key prey by key predator 

guilds 

Pollutant concentrations of 

key species

a Indicator is specific to freshwater habitats (see Table 7). b Indicator is specific to marine habitats (see Table 10). c Energy contribution is calculated as the percentage of total joules consumed to support observed growth.
65

Table 18. Examples of specific species or guilds that interact with Chinook salmon as predators, 

competitors, prey, etc., according to the literature. 

Associated 

habitat

Ecological relationship 

to Chinook salmon Example and literature source

Freshwater Predator species Piscivorous mammals

Piscivorous birds 

Gulls (Larus spp.), Weitkamp and Ruggerone 2000a

Piscivorous fish

Salmonids 

Rainbow trout (Oncorhynchus mykiss), Tabor et al. 2004a

Brook trout (Salvelinus fontinalis), Levin et al. 2002b

Cutthroat trout (O. clarkii), Nowak et al. 2004,a Beauchamp

et al. 2007a

Nonsalmonids 

Northern pikeminnow (Ptychocheilus oregonensis), 

Rieman et al. 1991,b

 Tabor et al. 2004a

Smallmouth bass (Micropterus dolomieu), Rieman et al. 

1991,

b Tabor et al. 2004a

Competitor species Salmonids

Hatchery Chinook salmon, Peery and Bjornn 2004,b Weber 

and Fausch 2005b

Other salmonid species, Stein et al. 1972,b Hearn 1987b

Nonsalmonids

Prey species Aquatic and terrestrial insects

Diptera, Becker 1973,b Loftus and Lenon 1977,b Merz 2002,b

Koehler et al. 2006a

Small crustaceans

Cladocera, Craddock et al. 1976,

b Kjelson et al.1982,b

Koehler et al. 2006a

Gammarid amphipods, Muir and Emmett 1988b

Other species Pathogens

Renibacterium salmoninarum, Arkoosh et al. 2004,

a

 Rhodes 

et al. 2006,a

 Rhodes et al. 2011a

Facilitators

Estuarine Predator species Piscivorous mammals

Harbor seal (Phoca vitulina), NMFS 1997,a, c London et al. 

2002a

Piscivorous birds 

Caspian tern (Hydroprogne caspia), Collis et al. 2001b

Piscivorous fish

Salmonids 

Cutthroat trout, Simenstad et al. 1982,a

 Footen 2001,a Duffy 

and Beauchamp 2008a

Steelhead, Simenstad et al. 1982a

Nonsalmonids 

Staghorn sculpin (Leptocottus armatus), Footen 2001a

River lamprey (Lampetra ayresi), Ruggerone et al. 2004a
66

Table 18 continued. Examples of specific species or guilds that interact with Chinook salmon as 

predators, competitors, prey, etc., according to the literature.

Associated 

habitat

Ecological relationship 

to Chinook salmon Example and literature source

Estuarine 

(continued)

Competitor species Salmonids

Hatchery Chinook salmon, Levings et al. 1986b

Other salmonid species

Nonsalmonids

Threespine stickleback (Gasterosteus aculeatus), Spilseth 

2008b

Prey species Aquatic and terrestrial insects

Dipterans, Dunford 1975,

b Fresh et al. 1978,a Shreffler et al. 

1992,

a Duffy 2003a

Chironomids, Dunford 1975,

b Shreffler et al. 1992,a Duffy 

2003a

Hymenopterans, Duffy 2003a

Small crustaceans 

Cladocera, Dunford 1975,

b Shreffler et al. 1992,a Simenstad 

et al. 2003a

Euphausiids, Fresh et al. 1978,

a Duffy 2003a

Gammarid amphipods, Dunford 1975,

b Fresh et al. 1978,a

Shreffler et al. 1992,

a Duffy 2003a

Polychaetes, Duffy 2003a

Larval/juvenile fish 

Chum salmon (O. keta), Bax et al. 1978a

Other species Pathogens

Nanophyetus salmincola, Arkoosh et al. 2004a

Facilitators

Beaver (Castor canadensis), Pess et al. 2002,a Hood 2012a

Marine Predator species Piscivorous mammals

Orca, Hanson et al. 2010,

a

Sea lion (Zalophus californianus), NMFS 1997a, c

Piscivorous birds

Gulls, Ruggerone 1986b, c

Common merganser (Mergus merganser), Wood 1987b

Piscivorous fish

Salmonids

Coho salmon (O. kisutch), Fresh et al. 1981a

Cutthroat trout, Duffy and Beauchamp 2008a

Nonsalmonids

River lamprey, Beamish and Neville 1995b

Spiny dogfish (Squalus acanthias), Beamish et al. 1992b

Competitor species Salmonids

Hatchery Chinook salmon, Levings et al. 1986,b Duffy 2009,a

Rice et al. 2011a

Other salmonid species

Pink salmon (O. gorbuscha), Ruggerone and Goetz 2004a

Nonsalmonids

Pacific herring, Beauchamp and Duffy 2011a
67

Table 18 continued. Examples of specific species or guilds that interact with Chinook salmon as 

predators, competitors, prey, etc., according to the literature.

Associated 

habitat

Ecological relationship 

to Chinook salmon Example and literature source

Marine 

(continued)

Prey species Aquatic and terrestrial insects and arachnids

Insecta, Fresh et al. 1981,a Duffy 2003,a Duffy et al. 2010a

Arachnida, Duffy 2003a

Small crustaceans 

Gammarid amphipods, Duffy 2003,a Duffy et al. 2010a

Decapods, Fresh et al. 1981,a Duffy 2003,a Duffy et al. 2010a

Larval/juvenile fish

Pacific herring, Fresh et al. 1981,a Duffy et al. 2010a

Pacific sand lance, Fresh et al. 1981,a Duffy 2003,a Duffy et 

al. 2010a

Other species Pathogens

Lepeophtheirus salmonis, Waknitz et al. 2002,a Gardner and 

Peterson 2003b

Vibrio anguillarum, Arkoosh et al. 1998a

Facilitators

Common eelgrass, Thayer and Phillips 1977,a, c Phillips 1984b

a Source describes relationships observed in the Puget Sound region.

b Source describes relationships observed outside the Puget Sound region.

c Source does not identify salmon to the species level.
68

Framework Process

General Application of the Framework

We have introduced the framework structure above, its context in Puget Sound salmon 

recovery implementation, and its basis in the Open Standards approach. We also outlined the 

elements of the framework (ecosystem components, key ecological attributes, indicators, 

pressures, stresses, contributing factors, drivers, and strategies and their associated actions), and 

described the first three in detail in the Ecosystem Components section. The current section 

describes the Open Standards tools and eight steps to apply the framework for practitioners to 

develop watershed-specific monitoring and adaptive management plans (Table 19). 

Implementation of the framework is further elaborated upon in the Toolkit (LLTK and PSP 

2014). Miradi software can be used for tracking decisions and linking the elements of the 

framework, but this framework process is not contingent on any specific software package.

Open Standards Tools for Applying the Framework

Open Standards provides a common and systematic method for selecting the subset of 

key ecological attributes and indicators that are best suited for the purposes of monitoring and 

that can support adaptive management within a given watershed. This method starts by using the 

best available data on Chinook salmon populations to assess their status and trends, then 

employing the local watershed chapters of the Recovery Plan and other local and regional 

sources of scientific information to identify the ecosystem components that have the greatest 

influence on the long-term population viability of Chinook salmon in each watershed.

This process first involves developing and refining a list of ecosystem components, 

which we have defined in the previous section to include the Chinook salmon populations 

present in each watershed, as well as the freshwater, estuary, and nearshore marine habitats, and 

other species and food webs that are critical to the long-term health and persistence of these 

populations (Figure 11). Because these ecosystem components are much too broad to measure 

(e.g., estuary ecosystems), a list of KEAs is identified for each of the ecosystem components. 

KEAs are a limited set of the biological characteristics, habitat characteristics, and ecological 

processes that shape the natural variability of an ecosystem component over time and space 

(TNC 2007). KEAs are linked to ecosystem components through cause-and-effect relationships. 

KEAs are still typically too broad to measure in a cost-effective manner over time, so it is 

necessary to identify indicators that can be effectively measured over time and used to document 

changes in KEAs. Indicators are important because they inform managers of the status and 

changes in KEAs. In addition to the list of ecosystem components, KEAs, and associated 

indicators, we next list all possible elements (pressures, stresses, drivers, and strategies and 

actions) in the framework as described above in the first section and in Figure 12 and Figure 13. 

In addition, Figure 14 through Figure 16 provide a detailed construct of the defined pressures 
69

Table 19. Eight-step outline for using the framework to develop a watershed-specific monitoring and 

adaptive management plan.

Step Summary Resource Product

1 Develop a preliminary conceptual 

model by defining watershed-specific 

relationships between the elements 

from the generic portfolio of 

elements (Figure 12).

Generic portfolio of elements

Chapter of interest in Vol. II of 

the Recovery Plan

Preliminary 

watershed-specific 

conceptual model

2 Update the conceptual model to 

include new information gained since 

2005 and remove elements that are 

not relevant to the watershed.

Preliminary watershed-specific 

conceptual model

Chapter of interest in Vol. II of 

the Recovery Plan

Habitat work schedulea

Relevant information gained since 2005b

Three-year work plansc

Final watershedspecific conceptual 

model

3 Conduct viability assessment: 

Identify current status, recent trends, 

and desired future conditions of 

ecosystem components.

Chapter of interest in Vol. II of 

the Recovery Plan

Habitat work schedulea

Relevant information gained since 2005b

Three-year work plansc

Viability analysis, 

including 

indicators for 

ecosystem 

components

4 Assess pressures (pressure 

ratings/rankings): Assess the relative 

impact of each pressure on each 

ecosystem component.

Chapter of interest in Vol. II of 

the Recovery Plan

Habitat work schedulea

Relevant information gained since 2005b

Pressure rating and 

ranking

5 Create results chains: Identify the 

key pressures that have the largest 

impact on the ecosystem 

components.

Chapter of interest in Volume II of 

the Recovery Plan

Final watershed-specific conceptual model

Viability analysis

Pressure rating and ranking

Results chains

6 Link results chains to monitoring: 

Identify objectives and indicators for 

intermediate results in the results 

chains.

Results chains

This document

Indicators and 

objectives for 

implementation 

and effectiveness 

monitoring

7 Develop monitoring plan: Use the 

conceptual model, results chains, and 

viability and pressure ratings/

rankings, including indicators and 

objectives to develop a monitoring 

plan.

Conceptual model

Viability analysis

Pressure rating and ranking

Results chains

Monitoring plan

8 Develop adaptive management plan: 

The plan will describe the interval, 

participation and approach used to 

evaluate and make resource 

management decisions based on 

monitoring results. It may be used to 

update recovery implementation 

actions, the monitoring plan, and the 

watershed chapter recovery plan.

Conceptual model

Results chains

Monitoring plan

Adaptive 

management plan

a Availability of this resource (see http://hws.ekosystem.us/) will vary from watershed to watershed. b Availability of this resource (which includes monitoring, assessments, etc.) will vary from watershed to watershed. c Availability of this resource (see http://psp.wa.gov) will vary from watershed to watershed.
70

Figure 11. Ecosystem components (italicized) and system types for component categories of freshwater 

habitats, estuarine and marine habitats, species and food webs, and salmonids, as described in the 

framework and depicted in Miradi software.

(Figure 14) and stresses (Figure 15) to Chinook salmon and their habitats (Figure 16). This 

entire list is defined as the Portfolio of Elements for the watershed (Figure 11 through Figure 

16).

Next the process involves completing a viability assessment for each ecosystem 

component. The assessment is an Open Standards tool for defining current conditions and 

desired future healthy conditions for each of the KEAs, then setting appropriate and measurable 

goals for these healthy conditions. Viability assessments involve determining whether the 

current status of ecosystem components and their KEAs are in poor, fair, good, or very good
71

Figure 12. Generic portfolio of elements, as described in the framework and depicted in Miradi. See Appendix B for examples of the specific 

elements within each category. Also see Figure 11 and Figure 14 through Figure 16 for more detailed lists of components, pressures, and 

stresses. See Figure 13 for a key that illustrates the relationships between the elements within an individual conceptual model.
72 

Figure 13. Key to relationships between the portfolio of elements within a watershed conceptual model, as described in the framework and 

depicted in Miradi. Strategies can address contributing factors, pressures, or stresses. Contributing factors underlie the existence and 

persistence of pressures and are within the scope of the project. Drivers (e.g. climate change, population growth) underlie problems in the 

ecosystem, but are beyond the scope of the project. Drivers can be addressed through adaptation and mitigation strategies focused on their 

impacts (e.g., sea level rise, development patterns). 
73

Figure 14. Taxonomy of sources of pressures developed by the Puget Sound Partnership and as described 

in the framework and depicted in Miradi. Also see appendix Table B-1 for definitions of 

pressures.
74

Figure 15. Taxonomy of Chinook salmon stresses organized by Chinook salmon life cycle, as described 

in the framework and depicted in Miradi. Also see appendix Table B-3 for a list of stresses 

related to the Chinook salmon ecosystem component.

condition (Table 20). This is accomplished by establishing specific ranges of values for each of 

these ratings for each indicator. It is desirable to have established, scientifically defined 

thresholds, but this will not be possible for all indicators. When such information does not exist, 

best professional judgment must suffice for the near term so the process is not stalled, and 

effectively, this informs watershed partners and planners of gaps in data and knowledge. These 

indicator ratings are used to develop a simple viability assessment table (Table 21) for all of the 

KEAs, which can then be used to identify the KEAs. This process should be iterative, and 

through successive trials can be used to further refine the prospective list of KEAs, their 

indicators, and values/ratings. The viability assessment will be used to inform the prioritization 

of recovery actions, the focus of monitoring and adaptive management plans, and the 

distribution/use of limited resources.

A conceptual model is completed that develops the linkages between the most important 

pressures in a watershed and the relationship and impact of these threats to the ecosystem 

components (Figure 13). Using Miradi software, these linkages can be portrayed graphically and 
75

Figure 16. Taxonomy of habitat stresses organized by stress type, as described in the framework and 

depicted in Miradi. An example of a complete suite of habitat stresses for a single ecosystem 

component, Large channels, is included. Also see appendix Table B-4 for a list of stresses related 

habitat and species and food web ecosystem components.

the dynamic and complex nature of these linkages can be tracked more easily. Developing the 

conceptual model is an important component of the Open Standards process, since it provides the 

process for linking pressures and ecosystem components. Conceptual models can then be 

reduced to simple results chains that portray the links between chosen conservation strategies 

and actions and contributing factors, which cause reductions in pressures and stresses, to produce 

desired changes in the status of the ecosystem components and their respective KEAs and 

indicators (Figure 17). This process provides a method for determining the final subset of KEAs 

and indicators that will be the most useful for monitoring and adaptive management. From the 

refined list of KEAs and indicators determined in the preceding steps, a final list is determined 
76 

Table 20. Example of a viability table for three indicators associated with two KEAs for Chinook salmon. Current conditions and desired future 

conditions (i.e., Skagit Chinook salmon recovery goals) are shown at both the watershed scale and population scale. 

KEA

Life cycle 

event Indicator Population

Current condition Desired future conditiona Location 

in Skagit 

Value Status Value Status Vol. II

Abundance Natal estuary 

rearing

No. of parr in the 

Skagit natal estuary

All 2,250,000 Fair 3,600,000 Good Chap. 16, 

p. 284

Spawning No. of populations 

meeting “no. of 

spawners” recovery 

goals

All NCb NDc 6 out of 6 Very good Chap. 4, 

Lower Skagit NC ND 3,900–7,400 p. 21 d Very good

Upper Skagit NC ND 5,380–9,400d Very good

Lower Sauk NC ND 1,400–2,700d Very good

Upper Sauk NC ND 750–1,340d Very good

Suiattle NC ND 160–270d Very good

Upper Cascade NC ND 290–510d Very good

Productivity– 

survival rate

Coastal 

migration

No. of populations 

meeting “no. of 

recruits per spawner” 

recovery goals

All NC ND 6 out of 6 Very good Chap. 4, 

Lower Skagit NC ND 3.0–5.4 p. 21 e Very good

Upper Skagit NC ND 3.8–6.6e Very good

Lower Sauk NC ND 3.0–4.8e Very good

Upper Sauk NC ND 3.0–4.1e Very good

Suiattle NC ND 2.8–4.2e Very good

Upper Cascade NC ND 3.0–4.6e Very good

a Desired future conditions for population-specific indicators reflect population-specific recovery goals in the Skagit chapter. b NC = Not calculated.

c ND = Not determined.

d Number of spawners by population.

e Number of recruits per spawner by population.
77 

Table 21. Example of a viability table for four indicators associated with four KEAs for ecosystem components of freshwater, estuarine, and 

nearshore marine habitats. Current and desired future conditions are shown, with status rated on a scale of Poor–Fair–Good–Very Good. 

Ecosystem 

component KEAa KEA type Indicator

Current condition Desired future condition

Measure Status Measure Status Reference

Channels 

>50 m BFW 

(freshwater) 

VII-14. Habitat 

connectivity― 

condition of connected 

habitat

Condition Fragmentation of areas 

with high density of 

backwater and 

floodplain channels 

(i.e., high diversity 

floodplain habitat)

Fragmented; 

20 gaps 

across total 

high diversity 

area

Poor Not 

fragmented; 

no gaps 

across total 

high diversity 

area

Very 

good 

SSDC 

2007, 

Chap. 10, 

p. 117–

118 

Side 

channels 

(freshwater)

VI-12. Floodplain 

connectivity―extent 

of floodplain-channel 

interactions

Size Floodplain side 

channel length 

371.1 km Fair 442.6 km Good Chap. 10, 

p. 98, 

113–114

Size Floodplain side 

channel area

560 ha Fair 628 ha Good Chap. 10b

Natal 

Chinook 

estuaries 

(estuarine)

VII-16. Tidal 

hydrology―extent of 

blind channel exposed 

to natural processesc

Size Blind tidal channel 

area accessible to 

juvenile Chinook 

salmon

62.7 ha Poor 110.8 ha Good Beamer et 

al. 2005, 

App. D, 

p. 12, 41d

Pocket 

estuaries 

(nearshore 

marine)

XVI-37. Habitat 

connectivity― 

distribution 

(accessibility) of 

pocket estuary habitat 

for fish migration

Landscape 

context 

Mean distance 

between pocket 

estuaries

Not specified; 

could be 

calculated

— Not specified; 

could be 

calculated

— App. D, 

p. 15e

a KEAs are adapted from Table 9 for freshwater KEAs and Table 12 for estuarine and nearshore marine KEAs (this document).

b Updated information about habitat area was derived from Table 3 in Beamer et al. 2010. This report is based on data collected in 2006. c The indicator associated with this KEA (blind tidal channel area accessible to juvenile Chinook salmon) could instead be included as an indicator of a related 

KEA (XIII-26, Nearshore marine―blind tidal channel formation). Although the indicator provides information about multiple KEAs associated with natal 

Chinook estuaries, it should be associated with only one KEA per ecosystem component. d According to Appendix D, the historical condition of this indicator was 1,158.0 ha (very good). e According to Appendix D, the historical condition of this indicator was 1.26 km (very good).
78 

Figure 17. Example of a results chain addressing issues associated with culverts in salmon-bearing streams.
79

by selecting those that are most impacted by the pressures present in a watershed. Furthermore, 

the final subset of KEAs and indicators should be those that are linked through the results chain 

to feasible strategies and actions that can effectively reduce major threats over time, resulting in 

measurable improvements in the indicators (and thus KEAs and ecosystem components they 

represent) (Figure 17).

Each results chain includes intermediate results2 or expected changes and objectives or 

quantitative desired outcomes. Results chains also include goals or the desired future condition 

of an ecosystem component (Figure 17). These goals are expected to change as a result of 

implementing strategies, completing actions, and achieving intermediate results.

Pressure assessments provide a systematic, transparent, consistent way of describing our 

best assessment of the relative impacts of different pressures on different ecosystem components. 

An understanding of the relative impacts of different pressures is important for prioritizing 

recovery strategies, actions, and monitoring. We presume that pressures that are having the 

greatest potential impact on salmon and other ecosystem components are the most important to 

address for recovery. Likewise, understanding how much effort and resources it takes to change 

the impacts of pressures helps us allocate resources to recovery wisely. Using a systematic, 

consistent approach not only allows us to identify which pressures may be greatest and where, 

but it also allows us to identify where the uncertainty about the pressures is greatest. This can 

help focus monitoring programs on key pressures and help answer key policy questions. A 

detailed description of the methods for pressure assessment is too much to include in this 

document. However, the process generally uses published and unpublished scientific 

information and expert knowledge to estimate the scope, severity, and irreversibility of impacts, 

and to describe the uncertainty in these estimates.

Process: Eight Steps for Applying the Framework

We can use this framework to develop individual monitoring and adaptive management 

plans that are watershed-based and regionally consistent. The process for applying the 

framework within each individual watershed is described below (Table 19). These steps can 

guide the development of monitoring and adaptive management plans and are intended to be 

applied in an iterative manner. This process is further developed in the Toolkit document (LLTK 

and PSP 2014).

These steps involve interpreting the technical information present in recovery plans and 

updated scientific work. The science-related tasks are the focus of this document; however, 

accomplishing them depends on the participation of policy makers and managers through 

implementation of the following steps.

1. Develop preliminary watershed-specific conceptual model. This first step uses the 

Portfolio of Elements to document the conditions, relationships, and assumptions 

regarding what would be necessary for Chinook salmon recovery as stated in Volume II 

of the Recovery Plan (SSDC 2007). This includes goals, objectives, and assumptions 

 2 Intermediate results that specifically address changes in pressures and stresses are called pressure-reduction and 

stress-reduction results, respectively, in our Miradi template. Intermediate results that address changes in 

contributing factors are simply called intermediate results.
80

identified in the individual watershed chapters. These goals, objectives, and assumptions 

are relative to the ecosystem components and threats, stresses, pressures, and contributing 

factors that exist in the watershed. Initially, watershed managers identify a list of 

ecosystem components present in the watershed. The population(s) of Chinook salmon 

present in each watershed should be placed on this list first. The other ecosystem 

components placed on this list should be those that directly influence the long-term 

viability or health of the Chinook salmon population(s) present in the watershed. 

Because Chinook salmon use many different ecosystems during their life history, 

components should be included for each of the major ecosystems present within a 

watershed.

2. Update conceptual model. Modify the preliminary conceptual model to include any new 

information gained since 2005. This includes new scientific studies and completed 

restoration/recovery projects. Remove elements of the framework that are not relevant to 

the individual watershed. This step documents the evolution of information associated 

with the Recovery Plan and sets the work for the rest of the steps.

3. Conduct viability assessment. Identify the current status, recent trends, and desired 

future conditions of ecosystem components identified in Step 1 and Step 2. Information 

for this step is derived from individual watershed chapters in Volume II of the Recovery 

Plan, as well as information gained since the Recovery Plan was submitted. This step 

helps practitioners document and track the status of the ecosystem components of the 

Recovery Plan and sequence when and where to focus recovery efforts.

4. Assess pressures (pressure ratings/rankings). Assess the relative impact of each pressure 

on each of the ecosystem components. This helps practitioners understand which 

pressures should be the focus of the work for implementing the Recovery Plan. It is also 

a critical step for developing monitoring and adaptive management plans.

5. Create results chains. Using the conceptual model, viability assessment, and pressure 

ratings/rankings, identify the key pressures which have the largest impact on the 

ecosystem components to create results chains that define the goals, objectives, and

assumptions delineated in the conceptual model.

6. Link results chains to monitoring. Identify objectives and indicators for the intermediate 

results that are included in the results chains. This step identifies the types of monitoring 

(implementation, status and trends, effectiveness, and validation) needed to appropriately 

address Chinook salmon recovery.

7. Develop monitoring plan. Use the conceptual model, results chains, and viability and 

pressure ratings/rankings to develop a monitoring plan for salmon recovery. The types of 

monitoring included will depend on the results chains, that is, indicators of intermediate 

results pertain to implementation monitoring while indicators of ecosystem components 

pertain to both status and trends and effectiveness monitoring. The focus of monitoring 

in the plan will depend on the prioritization determined in the viability and pressure 

ratings/rankings. The monitoring plan will also include the specific methodology for 

measuring indicators.

8. Develop adaptive management plan. Develop an adaptive management plan that 

describes the interval, participation, and approach used to evaluate and make decisions 
81

based on the monitoring results. The adaptive management plan can then be used to 

amend recovery implementation actions, the monitoring plan, and the watershed chapter 

recovery plan.

Regional-scale Application

The application of this framework supports key decisions made at both the regional and 

watershed scales by using the same hierarchical structure as the recovery criteria for Puget Sound 

Chinook salmon adopted by NMFS. Although recovery criteria apply to the regional scale of the 

Puget Sound Chinook Salmon ESU, the criteria demand knowledge of the status of all the 

independent populations that occur in the watersheds and across different biogeographical 

subregions of Puget Sound (NMFS 2006). For example, two of the recovery criteria are: 1) 

“viability status of all populations in the ESU is improved from current conditions” and, 2) “two 

to four Chinook salmon populations in each of five biogeographical regions within the ESU 

achieve viability.” Population-based and watershed-based monitoring of Chinook salmon 

viability documented by this framework specifically allows assessment of the status of Chinook 

salmon at the subregional and regional (Puget Sound) scales, that is, consistent with the recovery 

criteria.

This framework also provides the information to assess threats to recovery at the 

watershed scale as well as across the ESU. For example, as part of recovery planning, the ESA

identifies factors that have to be evaluated in addition to the status of the species. These include:

1. The present or threatened destruction, modification, or curtailment of Chinook salmon 

habitat,

2. Overutilization for commercial, recreational, scientific, or educational purposes,

3. Disease or predation,

4. Inadequacy of existing regulatory mechanisms, and

5. Other natural or human-derived factors affecting continued existence of Chinook salmon.

The Final Supplement to the Shared Strategy’s Puget Sound Salmon Recovery Plan 

(NMFS 2006) provides additional descriptions of the evaluation of threats to habitat needed at 

both the watershed and Puget Sound scales. A variety of ecosystem functions (channel function 

and complexity, natural substrate and sediment processes, flows, floodplain functions, 

connectivity, nearshore processes, prey availability) and pressures (stormwater runoff, 

agricultural practices, urban and rural development, toxic contaminants, obstructions to fish 

migration, dredging, bank hardening, and forestry practices) are listed and need to be considered. 

The Final Supplement leaves the scientific and logistic questions of how, when, and where to do 

this unanswered. However, it specifically identifies the requirement to use technical tools that 

accurately assess the impacts of habitat management actions. This framework, consistent with 

the Final Supplement, includes a detailed list of KEAs and pressures and a systematic process for 

evaluating these. Information from the watersheds applied within the context of this framework 

will provide detailed insights into what factors are most important in a given watershed, as well

as across multiple watersheds.

Analysis of information developed from this kind of hierarchical framework also will 

help identify both shared and unique policy needs for addressing key pressures and allocating 
82

scarce resources. Because monitoring can be explicitly linked to where these questions occur, it 

allows monitoring to be designed to contribute information to policy solutions that advance 

salmon recovery more efficiently than either watershed-scale or regional monitoring can provide 

independently. For example, this information furnishes the basis for describing, prioritizing, and 

designing monitoring that might be needed across watersheds. It also identifies monitoring 

needs within single watersheds that are important to the Puget Sound ESU because those 

populations contribute to achieving the population-based regional recovery criteria. This latter 

circumstance is not easily addressed by monitoring frameworks based only on the regional scale.

Monitoring and Adaptive Management

The framework developed here provides a standard way of organizing and depicting the 

key relationships underlying the diverse recovery strategies in the 14 watershed chapters of 

Volume II of the Recovery Plan. Monitoring of the indicators (i.e., for KEAs or other ecosystem 

components) will provide information regarding the logic of the chapters’ recovery strategies, as 

well as the success of implementing of those strategies. In response to the information gained 

from monitoring, adaptive management will then consist of: 1) modification of the specified 

recovery actions to implement within the watershed chapters, and thus 2) modification of the 

Volume II Recovery Plan chapters themselves.

The first type of adaptation―modification of watershed chapter recovery actions―will 

occur when either research or monitoring provides new information which alters prior 

assumptions. For example, if monitoring data revealed that an exploitation rate target is 

repeatedly not attained, then harvest management implementation might be adjusted by altering 

annual fishing plans, thus improving preseason abundance forecasts or better enforcing 

regulations. This framework provides an organized, systematic process to determine the 

indicator(s) that will best evaluate actions implemented with the intent of achieving recovery 

goals.

The second kind of adaptation―modification of a watershed chapter―will occur when it 

becomes clear that the assumptions underlying the chapter’s basic strategies are no longer held. 

For example, if a strategy was based on the assumption that lack of good quality spawning 

habitat limited production, then that chapter might have emphasized a hatchery supplementation 

program to provide more incubation capacity than was available in the degraded natural 

environment. If, subsequently, population life stage validation monitoring suggested that 

estuarine rearing habitat capacity was a key limiting factor, then the chapter assumptions and 

goals would need to be revised to emphasize restoration of estuarine habitats.

NMFS offers guidance for applying the adaptive management principles of Anderson et 

al. (2003) to salmon recovery. The guidance lists the following essential features of an adaptive 

management plan: 1) revise management strategies regularly; 2) use conceptual or quantitative 

models to guide hypotheses, strategies, and actions; 3) identify a range of potential management 

actions; 4) track progress by monitoring and evaluation; 5) make decisions regarding strategies 

and actions through iterative learning; and 6) use stakeholder participation in adjusting strategies 

and actions (NMFS 2007). This framework will make it possible to apply these principles to 

salmon recovery across all 14 Puget Sound watersheds.
83

Conclusion

We present our framework as a method to systematically organize information and 

evaluate progress of Chinook salmon recovery across the Puget Sound ESU. It may be used to 

monitor and adapt recovery strategies and actions for the multiple Chinook populations. 

Chinook salmon have a very complex and diverse life history―they are migratory, depend on 

freshwater, estuarine, and marine habitats, and disperse widely. In addition, they are highly 

adaptable and can form metapopulations, from which individuals stray to newly available 

habitats (and populations) or alternately away from lost or damaged habitats. Actions affecting 

the recovery of Chinook salmon in the Puget Sound region likewise occur across a 

heterogeneous landscape and at multiple geographic scales. These actions are driven by human 

behaviors that reflect differences in local, regional, and national economies, community values, 

and available resources. Authorities who make decisions at multiple levels of government (e.g., 

local, regional, and national) and in multiple contexts (e.g., political, regulatory, and 

enforcement) influence the effectiveness of Chinook salmon recovery actions taken at each land 

use scale, whether local or regional.

A successful approach to collect information, evaluate actions, and inform decisions 

made at all land use scales needs to provide consistency across these multiple scales and 

geographies, while also retaining flexibility to capture unique differences. No such approach to 

monitoring, adapting, and improving salmon recovery efforts across multiple scales currently

exists. Recognizing this, NMFS specifically identified the development and implementation of 

such an approach as a requirement for approval of the Recovery Plan under the ESA (NMFS 

2006). Our framework was developed in response to the NMFS requirement. Successful 

implementation of the framework will require commitment from both technical experts and 

policy decision makers.

Our framework builds on a general strategic planning system called Open Standards for 

the Practice of Conservation (CMP 2007). Open Standards provides a common vocabulary for 

organizing descriptions of conservation strategies and actions, direct and indirect threats to the 

environment and species, and the attributes of a sustainable ecosystem. Lack of a common 

vocabulary hampers the communication and coordination that must occur if a monitoring 

approach is to include both local and regional recovery efforts (Hamm 2012). Open Standards 

also provides a hierarchical structure so that actions can be shared and coordinated between 

recovery plans and across different spatial and organizational levels. Despite the theoretical and 

practical advantages of Open Standards for conservation planning, applying it or similar systems 

to a problem as large and complex as Pacific salmon recovery at the scale of Puget Sound has not 

been done.

The process to incorporate information stated in the 2005 recovery plan chapter and the 

incorporation of information produced since 2005 provide the basis for development of the 

watershed-scale monitoring and adaptive management plans. Ultimately the RITT framework 
84 

will be applied across all watersheds in the Puget Sound region as applicable to Chinook salmon. 

The resulting monitoring and adaptive management plans will stand alone for each watershed 

and be the road map for local entities to pursue funding, engage in activities for salmon recovery, 

and maintain the ability to measure change (progress) and adapt management actions to support 

these changes. Also, given the consistent structure of the RITT framework, it will also be 

possible to evaluate the plans, recovery objectives and goals, and strategies across watersheds 

and across the region. 

Once the monitoring and adaptive management plans are developed, managers can use 

the information to observe: 1) how the plan is designed to achieve the desired goals for Chinook 

salmon recovery in the watershed; 2) where integration of various salmon recovery strategies 

may occur (i.e., within and across watersheds, and across the Puget Sound region); or 3) where a 

potential gap, lack of integration, or conflict between watershed strategies exists. The key to 

success of this process includes identifying indicators for ecosystem components and indicators 

for intermediate results of strategies and actions that are linked to ecosystem components. 

Commonality between watersheds regarding choice of indicators will help to make crosswatershed and regional evaluations. Thus use of this framework should allow plan implementers 

to track success or lack thereof. In the latter case, the objective would be to determine the cause 

of a problem so it can be corrected. This reflects what we define as adaptive management.
85

Glossary

This glossary has two subsections, one listing abbreviations and another listing terms 

related to ecosystem components. The latter list has terms grouped into three components: 

Chinook salmon life stages, freshwater habitats, and estuarine and marine habitats.

Abbreviations

BFW. For bankfull width. Channel width between the tops of banks on either side of a stream; 

tops of banks are the points at which water overflows its channel at bankfull discharge.

DO. For dissolved oxygen. The amount of oxygen that is present in the water, measured in 

milligrams per liter.

ESA. For U.S. Endangered Species Act of 1973. Passed by Congress, its purpose is to provide a 

means to conserve the ecosystems on which threatened and endangered species depend.

ESU. For evolutionarily significant unit. A population or group of populations that 1) is

substantially reproductively isolated from other populations, and 2) represents an important 

component of the evolutionary legacy of the species.

GIS. For Geographic Information System. A computer system for assembling, storing, 

manipulating, and displaying geographically referenced information.

KEA. For key ecological attribute. The characteristic of an ecosystem component that, if 

present, would support a viable component but, if missing or altered, would lead to loss or 

degradation of the component over time.

LWD. For large woody debris. A large piece of woody material such as a log or stump that 

intrudes into a stream channel.

MRV. For marine riparian vegetation.

NMFS. For National Marine Fisheries Service.

Open Standards. For Open Standards for the Practice of Conservation (CMP 2007).

PSP. For Puget Sound Partnership.

PS RITT. For Puget Sound Recovery Implementation Technical Team.

PS TRT. For Puget Sound Technical Recovery Team.
86

Recovery Plan. For Puget Sound Salmon Recovery Plan.

SAV. For submerged aquatic vegetation.

Toolkit. For Chinook Monitoring and Adaptive Management Project Toolkit.

TRT. For Technical Recovery Team.

VSP. For viable salmonid population. An independent population of any Pacific salmonid 

(genus Oncorhynchus) that has a negligible risk of extinction due to threats from 

demographic variation, local environmental variation, and genetic diversity changes over a 

long time frame.

WDFW. For Washington Department of Fish and Wildlife.

WDNR. For Washington Department of Natural Resources.

Terms Related to Ecosystem Components

Chinook Salmon Life Stages

Spawner. Sexually mature salmon at or very near locations where it will spawn, or in the act of 

egg deposition and fertilization.

Egg. A female gamete from the time of deposition in the substrate to hatching of an alevin.

Alevin. A juvenile life stage of salmon between hatching from an egg to emergence from the 

streambed substrate as a fry. The alevin stage is characterized by the presence of a yolk sac 

in varying degrees of absorption.

Fry. A juvenile stage of salmon between the alevin and parr stages. During the fry stage, the 

yolk sac has been absorbed and the fish has emerged from the streambed and is actively 

seeking food. Chinook salmon fry are generally between 30 and 50 mm fork length (Beamer 

et al. 2005, Fresh 2006).

Parr. A juvenile life stage of salmon (sometimes called fingerling) between the fry and yearling 

stages. Fish at this life stage often have visible parr marks and are actively feeding. Chinook 

salmon parr are generally between 50 and 90 mm fork length (Beamer et al. 2005, Fresh 

2006).

Yearling. A juvenile life stage of salmon between the parr and subadult stages, when fish are at 

least 1 year but not more than 2 years old. Chinook salmon yearlings outmigrating from the 

Skagit River are generally greater than 90 mm fork length (Beamer et al. 2005).

Subadult. A developmental life stage of salmon between the yearling and adult stages, when 

fish exhibit most morphological traits of adults but are not sexually mature. For Chinook 

salmon, subadults are sometimes called blackmouth and can range from 2 to 6 years old.
87

Adult. Sexually mature or maturing salmon, generally migrating toward natal locations.

Freshwater Habitats

Upland. Geomorphic surface with no defined channel. This surface may include isolated 

wetland.

Floodplain. The band of relatively level land adjacent to a stream channel that may become 

partly or fully inundated during periods of high flow—on average once every 1.5−2 years 

(Leopold et al. 1964).

Channel >50 m BFW. Mainstem channel (i.e., riverine habitat) with bankfull width greater 

than 50 m. Habitat formation in these channels is controlled by bank erosion and sediment 

deposition, leading to lateral movement. Reach-scale and habitat unit–scale classes are 

adapted from Montgomery and Buffington (1997) and Beechie et al. (2003a, 2005, 2006a).

Channel <50 m BFW. Mainstem and tributary channel (i.e., riverine habitat) with bankfull 

width less than 50 m. Habitat formation in these channels is driven by the relative 

magnitudes of sediment transport and supply, as slope, confinement, and position in the 

channel network also change. Reach-scale and habitat unit–scale classes follow Bisson et al. 

(1988), Montgomery and Buffington (1997), and Beechie et al. (2003a, 2003b, 2005).

Side channel. Active channel that is separated by stable islands from the main channel (i.e., 

large or small channel, as defined above). Side channels carry surface water at flows less 

than bankfull (Lestelle et al. 2005); however, some may become disconnected (dry) at one or 

both ends during periods of low flow, while others may remain connected (wetted).

Nonchannel lakes and wetlands. Deep-water or shallow-water, nonriverine habitats located in 

floodplains. These habitats may be lacustrine (lake, pond, or reservoir) or palustrine 

(wetland). Both lacustrine and palustrine habitats may be tidal or nontidal, as long as their 

ocean-derived salinity is less than 0.5 ‰. According to Cowardin et al. (1979), the defining 

characteristics of these habitats are as follows:

• Lacustrine habitats include deep-water and shallow-water bodies (i.e., lake, reservoir, 

pond, wetland) that are 1) located in topographic depressions or dammed channels and 2) 

not dominated by vegetation (areal coverage <30%), and c) larger than 8 ha in total area. 

Water bodies less than 8 ha in total area may be counted as lacustrine if they meet the 

first two criteria (1 and 2 above) and if their maximum water depth exceeds 2 m at low 

water, or if an active wave-formed or bedrock shoreline feature constitutes all or part of 

the water body boundary.

• Palustrine habitats include shallow water bodies (i.e., wetlands) that are either dominated 

by vegetation (i.e., areal coverage >30%) or lacking such vegetation but having 1) total 

areas less than 8 ha, 2) no active wave-formed or bedrock shoreline features, and 3) 

maximum water depths less than 2 m at low water.
88

Estuarine and Marine Habitats

Geographic basin. The broad habitat classes in our framework (i.e., estuarine, nearshore 

marine, and offshore marine habitat) exist within seven geographic basins encompassing the 

United States portion of the Salish Sea (see map of marine basins below). Basin boundaries 

are based on natural breaks in geomorphology and large-scale hydrodynamic processes. 

They are also chosen to be consistent with other classification efforts. The Puget Sound 

Nearshore Ecosystem Restoration Project (PSNERP) first defined the boundaries (Simenstad 

et al. 2011) by adapting previous delineations from Ebbesmeyer et al. (1984), Burns (1985), 

and Redman et al. (2005). The boundaries were used in PSNERP’s Strategic Needs 

Assessment (Schlenger et al. 2011), and they were later adopted by the Northwest Indian 

Fisheries Commission’s Salmon and Steelhead Habitat Inventory and Assessment Program

(McBride et al. 2009). They differ from the Action Areas adopted by the Puget Sound 

Partnership (see www.psp.wa.gov/aa_action_areas.php), which are politically rather than 

geomorphically or hydrodynamically defined.

Estuarine habitat. This broad habitat class includes only one system subtype: natal Chinook 

salmon estuaries. For the purposes of this framework, natal Chinook estuaries correspond to 

the “large river deltas” in PSNERP’s Change Analysis data set (Simenstad et al. 2011). 

PSNERP’s large river deltas include 16 deltas, 3 of which do not support natal populations of 

Chinook salmon in the Puget Sound ESU (Samish, Deschutes, and Quilcene rivers). The 

remaining 13 deltas are the natal estuaries for 20 of the 22 ESA-listed Puget Sound Chinook 

salmon populations (Ruckelshaus et al. 2006) (see map of marine basins and crosswalk table 

below). Two listed Chinook salmon populations (Cedar and Sammamish rivers) currently 

have no large river delta for their natal estuary; they use Salmon Bay and Shilshole Bay 

along the Lake Washington Ship Canal, both of which are classified as nearshore marine 

habitat within our hierarchical classification system. As state above, estuarine habitat 

includes one system subtype (Table 10). This subtype encompasses four shoreline types, 

selected (in part) to maintain consistency with previously published classifications (see 

classification systems table below).

Nearshore marine habitat. The area bounded by the upper limit of tidal influence and the 

lower limit of the photic zone (Figure 9). The lower limit of the photic zone varies by 

location and season, but is considered to range from 5 to 20 m in depth (Redman et al. 2005). 

This definition aligns with that used by PSNERP (after Goetz et al. 2004). Nearshore marine 

habitat includes 2 system types, 5 system subtypes, and 18 shoreline types (Table 10). As 

with the estuarine shoreline types, the nearshore marine shoreline types were chosen to be 

consistent with previously published classifications (see classification systems table below).

Offshore marine habitat. All areas deeper than the lower limit of the photic zone, extending 

from the water surface to the bottom (Redman et al. 2005). This includes all wet marine 

areas in Puget Sound not captured in the nearshore definition. System subtypes and habitat 

zones within the offshore marine habitat class (Table 10) were selected to align with Newton 

et al. (2000).
89 

Marine basins (A−G) and Chinook salmon populations (1−22) within the Puget Sound region. 

Abbreviations (A−G and 1−22) are explained in the crosswalk table below. 
90 

Crosswalk of the 16 large river deltas, 13 natal Chinook estuaries, and 22 independent populations of 

Chinook salmon in the Puget Sound region. The marine basin into which each delta/estuary 

drains is also provided. Abbreviations (A−G and 1−22) match those in the map above. 

Marine basin*

Large river 

delta name

Natal Chinook 

estuary? Population in the Puget Sound ESU

San Juan Islands and 

Georgia Strait (A)

Nooksack Yes North Fork Nooksack River (1), South Fork 

Nooksack River (2)

Samish No

Whidbey Island (B) Skagit Yes Lower Skagit River (3), Upper Skagit River 

(4), Lower Sauk River (5), Upper Sauk 

River(6), Suiattle River (7), Cascade River (8)

Stillaguamish Yes North Fork Stillaguamish River (9), South 

Fork Stillaguamish River (10)

Snohomish Yes Skykomish River (11), Snoqualmie River (12)

South Central Puget 

Sound (D)

Duwamish Yes Duwamish/Green River (15)

Puyallup Yes Puyallup River (16), White River (17)

South Puget Sound 

(E)

Nisqually Yes Nisqually River (18) 

Deschutes No

Hood Canal (F) Skokomish Yes Skokomish River (19)

Hamma 

Hamma

Yes Mid-Hood Canal rivers (20)

Duckabush Yes Mid-Hood Canal rivers (20)

Dosewallips Yes Mid-Hood Canal rivers (20)

Quilcene No

Strait of Juan de 

Fuca (G)

Dungeness Yes Dungeness River (21)

Elwha Yes Elwha River (22)

* One of the seven marine basins depicted in the map (C, North Central Puget Sound) is not included, as no 

deltas/estuaries drain into this basin. Likewise, 2 of the 22 Chinook salmon populations depicted in the map (13, 

Sammamish River and 14, Cedar River) are not included because they currently have no large river deltas for their 

natal estuarine habitat.
91 

Classification of estuarine and nearshore marine habitats in the framework (see Table 10), compared with 

three other classifications specific to Puget Sound (see Figure 8). Many local-scale (e.g., 

watershed-wide or county-wide) geographic information system (GIS) data sets use the 

Johannessen and MacLennan 2007 classification to define shoreline features, and at least two 

regional-scale GIS data sets use the Shipman 2008 and McBride et al. 2009 classifications.* 

Framework classification Other classification

System 

type

System 

subtype Shoreline type

Johannessen and

MacLennan 2007 Shipman 2008

McBride et al. 

2009

Major 

river 

system

Natal Chinook 

estuary

Drowned 

channel

Not addressed Open coastal inlet Drowned channel

Riverdominated (fan) 

delta

Not addressed Fan delta, riverdominated deltaFan delta, riverdominated delta

Tidal delta Not addressed Tide-dominated 

delta

Tide-dominated 

delta

Delta lagoon Not addressed Barrier estuary, 

wave-dominated 

delta

Delta lagoon, 

drowned channel 

lagoon, tidal delta 

lagoon

Drift cell 

system

Coastal 

landform

Barrier beach 

(spit, cusp, 

tombolo)

Accretion 

shoreform

Barrier Barrier beach

Bluff-backed 

beach

Sediment source 

beach

Feeder bluff, 

feeder bluff

(exceptional)

Bluff Sediment source 

beach

Depositional 

beach

Accretion 

shoreform

Bluff Depositional 

beach

Beach seep Not addressed Not addressed Beach seep

Plunging 

sediment bluff

Not addressed Not addressed Plunging 

sediment bluff

Pocket estuary 

(embayment) 

Drowned 

channel lagoon

Not addressed Barrier estuary Drowned channel 

lagoon

Tidal delta 

lagoon

Not addressed Barrier estuary Tidal delta lagoon

Longshore 

lagoon

Not addressed Barrier lagoon Longshore lagoon

Tidal channel 

lagoon (or 

marsh)

Not addressed Barrier lagoon Tidal channel 

lagoon

Closed lagoon 

and marsh

Not addressed Closed lagoon 

and marsh

Closed lagoon 

and marsh

Open coastal 

inlet

Not addressed Open coastal inlet Drowned channel
92

Classification systems table continued. Classification of estuarine and nearshore marine habitats in the 

framework (see Table 10), compared with three other classifications specific to Puget Sound (see 

Figure 8). Many local-scale (e.g., watershed-wide or county-wide) GIS data sets use the 

Johannessen and MacLennan 2007 classification to define shoreline features, and at least two 

regional-scale GIS data sets use the Shipman 2008 and McBride et al. 2009 classifications.*

Framework classification Other classification

System 

type

System 

subtype Shoreline type

Johannessen and

MacLennan 2007 Shipman 2008

McBride et al. 

2009

Rocky 

shoreline

Rocky pocket 

estuary

Pocket beach 

lagoon

Not addressed Barrier estuary Pocket beach 

lagoon

Pocket beach 

estuary

Not addressed Barrier estuary Pocket beach 

estuary

Pocket beach 

closed lagoon 

and marsh

Not addressed Pocket beach 

closed lagoon and 

marsh

Pocket beach 

closed lagoon and

marsh

Rocky beach Veneered rock 

platform

Not addressed Platform Veneered rock 

platform

Rocky shoreline Not addressed Platform Rocky shoreline

Plunging rocky 

shoreline

Not addressed Plunging Plunging rocky 

shoreline

Pocket beach Not addressed Pocket beach Pocket beach

* The two regional-scale GIS datasets are PSNERP’s Puget Sound Nearshore General Investigation (see 

http://www.nws.usace.army.mil/PublicMenu/Menu.cfm?sitename=PSNERP&pagename=Change_Analysis) and the 

Salmon and Steelhead Habitat Inventory and Assessment Project (see http://nwifc.org/about-us/habitat/sshiap/), 

which is comanaged by the Western Washington Treaty Indian Tribes and WDFW.
93

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Wood, C. C. 1987. Predation of juvenile Pacific salmon by the common merganser (Mergus merganser) 

on Eastern Vancouver Island. I: Predation during seaward migration. Can. J. Fish. Aquat. Sci. 

44:941–49. 

Ziemer, R. R., and T. E. Lisle. 2002. Chapter 3. Hydrology. In R. J. Naiman and R. E. Bilby (eds.), 

River ecology and management: Lessons from the Pacific coastal ecoregion, p. 43–58. SpringerVerlag, New York.
110 
111

Appendix A: Terminology Crosswalk

Table A-1. Crosswalk of terminology common to our framework, the Puget Sound Partnership (PSP), 

Open Standards for the Practice of Conservation (CMP 2007), and the Miradi software package. 

Framework terms are ordered alphabetically. (Definitions adapted from CMP 2007.)

Framework/PSP 

term

Open Standards/ 

Mirandi term Definition

Action Activity Activity that is associated with a particular strategy and 

designed to achieve desired intermediate results.

Conceptual model Conceptual model A box-and-arrow diagram that portrays the cause-and-effect 

relationships between strategies, drivers, contributing factors, 

pressures, stresses, and ecosystem components.

Contributing factor Factor Human-induced action or event that contributes to the 

persistence of one or more pressures. They can be indirect 

threats, existing conditions, underlying or root causes, or 

opportunities, and thus can be negative or positive in nature. 

They include social, cultural, political, institutional, and 

economic factors.

Driver Indirect threat Human-induced action, event, or natural process that 

contributes to the existence or persistence of one or more 

pressures. For the purposes of our framework, drivers are 

similar to contributing factors, but they are beyond the scope of 

that which can be addressed directly by salmon recovery plans. 

For example, drivers might include population growth, climate 

change, or global market forces. Recovery strategies and 

actions might address adaptation responses or mitigation of 

impacts (e.g., adaptation to sea level rise or altered precipitation 

patterns, mitigation of impacts of population growth, adaptation 

to altered economic base), but are unlikely to address drivers 

directly.

Ecosystem 

component

Conservation target Ecosystem components represent the focus of a protection, 

conservation, or recovery effort. They can be specific species, 

habitats, ecosystems, ecological processes, or aspects of human 

well-being and they are selected to represent the breadth of 

focus of a project or program.

Goal/target 

(framework and PSP 

terms, respectively)

Goal A measure of an ecosystem component or pressure, 

representing the desired future condition of the component or 

pressure.

Indicator (for an 

ecosystem 

component)

Indicator A measure of condition or status―in this case, of an ecosystem 

component.

Indicator (for 

intermediate results)

Indicator A measure of effectiveness or progress toward the objectives of 

intermediate results.

Indicator (for 

pressure)

Indicator A measure of condition or status―in this case, of a pressure.
112

Table A-1 continued. Crosswalk of terminology common to our framework, the Puget Sound Partnership 

(PSP), Open Standards for the Practice of Conservation (CMP 2007), and the Miradi software 

package. Framework terms are ordered alphabetically. (Definitions adapted from CMP 2007.)

Framework/PSP 

term

Open Standards/ 

Mirandi term Definition

Intermediate results Results or outcomes The desired or expected results (aka, changes to contributing 

factors) that would follow from the implementation of strategies 

and the completion of actions.

Key ecological 

attribute (KEA)

KEA Aspect of an ecosystem component’s biology that, if missing or 

altered, would lead to the loss of the component or its 

ecological integrity.

Objective (for 

intermediate results)

Objective A quantitative, time-bound measure associated with 

intermediate results, reflecting the desired future outcome.

Objective (for 

pressures)

Objective A quantitative, time-bound measure associated with the status 

of a pressure, representing the desired future condition of the 

pressure.

Pressure rating and 

ranking

Threat rating and 

ranking

A method used to rate and rank (prioritize) highest risk or 

highest priority pressures to ecosystem components. This 

method helps focus conservation efforts on the highest priority 

issues. Pressures can be rated based on the risk posed to an 

ecosystem component or their contribution to specific stresses 

associated with KEAs of components.

Pressure Direct threat Pressures are primarily human activities that directly affect 

ecosystem components or alter key ecological processes (e.g., 

hydrological dynamics) common to multiple ecosystem 

components. They include sources of stress (e.g., residential 

and commercial development) and associated stressors (e.g., 

habitat conversion due to development).

Results chain Results chain A diagram that portrays the logic of how and why individual 

strategies and actions are expected to affect contributing factors 

and pressures, thereby reducing stresses and producing desired 

changes in the status of ecosystem components. Building a 

results chain requires us to define how we would like the 

system to change―including desired outcomes and 

hypothesized theories of change (i.e., the “if-then” 

relationships)―and how we are going to measure progress 

toward objectives and goals.

Strategies Strategies or 

conservation actions

A group of conservation actions with a common focus designed 

to achieve specific objectives and goals (e.g., reducing 

pressures, exploiting opportunities, restoring natural systems).

Stress Stress A stress is equivalent to an altered or degraded KEA of an 

ecosystem component. It is an impaired aspect of the ecosystem 

and results directly from human activities or natural pressures 

on the ecosystem.

Viability analysis Viability assessment Viability assessment is a systematic method used to describe 

the current health and desired future health (aka goals) of 

ecosystem components using metrics specified by scientific 

research or best professional judgment when research does not 

exist. One or more indicators are identified for each KEA. 

Information about the current status and desired future status of 

each indicator is then used to determine which KEAs and which 

ecosystem components are in greatest need of attention.
113 

Appendix B: Supporting Information 

for Select Elements

The five selected elements in this appendix are pressures (Table B-1 and Table B-2), 

stresses (Table B-3 and Table B-4), contributing factors (Table B-5), drivers (Table B-6), and 

strategies (Table B-7).

Pressures 

A pressure taxonomy has been developed by the Puget sound Partnership (PSP) to 

support assessment of threats to Puget Sound ecosystems and identification of priority actions to 

reduce those threats. Pressures are defined as human activities or processes that have caused, are 

causing, or may cause the destruction, degradation, or impairment of ecosystem components. 

Pressures include both stressors, the most proximate agents of change to the ecosystem, and the 

sources of stressors. Table B-1 and Table B-2 identify the pressure–source and pressure–stressor 

classifications, respectively. These classifications represent a modest revision to the Pressure 

Taxonomy that was included in the 2012/2013 action agenda for Puget Sound (PSP 2012). They 

were revised through the Puget Sound Pressure Assessment Project (https://sites.google.com/site

/pressureassessment) to better capture sources of stress in Puget Sound and for better alignment 

with the International Union for Conservation of Nature threat taxonomy. 
114

Table B-1. Taxonomy of Puget Sound pressure sources based on previous classifications (IUCN 2001, 

Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source categories. 

Sources are the cause of stressors that in turn are the causes of stressed conditions in the 

ecosystem.

Source class Definition and exposition Puget Sound examples

1. Residential 

and commercial 

development

Human settlements or other nonagricultural land uses 

with a substantial footprint.

These sources of stress are tied to a defined and 

relatively compact area, which distinguishes them from 

those in 4, Transportation and service corridors, which 

have a long narrow footprint, and 6, Human intrusions 

and disturbance, which do not have an explicit footprint.

—

1.1. Housing 

and urban areas

Human cities, towns, and settlements including 

nonhousing development typically integrated with 

housing.

This class dovetails with 1.2, Commercial and industrial 

areas (including ports). As a general rule, however, if 

people live in the development, it should fall into this 

source class. This class does not include transportation 

and utility infrastructure, water use, shoreline armoring 

and overwater structures, or runoff and other pollution 

associated with any developed areas (see 4, 7, and 9).

Urban areas, suburbs, 

villages, ranchettes, 

vacation homes, 

shopping areas, offices, 

schools, hospitals, land 

reclamation, or 

expanding human 

habitation that causes 

habitat conversion or 

degradation in riverine, 

estuary, and coastal 

areas, etc.

1.2. 

Commercial and 

industrial areas 

(including 

ports)

Factories and other commercial centers.

Shipyards and airports fall into this class, whereas 

shipping lanes and flight paths fall under 4, 

Transportation and service corridors. Overwater 

structures and shoreline armoring associated with 

marinas and ports full under 7, Natural system 

modifications. Water use and dams are also covered 

under 7. For runoff and other pollution associated with 

commercial and industrial areas, see 9, Pollution.

Military bases, factories, 

stand-alone shopping 

centers, office parks, 

power plants, train 

yards, shipyards, ports, 

airports, landfills, etc.

1.3. Tourism 

and recreation 

areas

Tourism and recreation sites with a substantial footprint.

This class includes vacation housing/resorts and 

associated habitat effects of recreation areas. However, 

disturbance effects posed by recreational activities 

outside the footprint of developed areas are included in 

6.1, Recreational activities.

Ski areas, golf courses, 

resorts, ball fields, 

county parks, 

campgrounds, coastal 

and estuarine tourist 

resorts, etc.

2. Agriculture 

and aquaculture

Farming and ranching practices, expansion and 

intensification, including silviculture, mariculture and 

aquaculture (includes the impacts of any fencing around 

farmed areas).

The use of agrochemicals, rather than the direct 

conversion of land to agricultural use, should be included 

under 9.3, Agricultural and forestry effluents. Likewise 

in cases where conversion to agriculture causes increased 

runoff and hence sedimentation of rivers and lakes, that 

is also best treated under 9.3.

—
115

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

2.1. Annual and 

perennial 

nontimber crops

Crops planted for food, fodder, fiber, fuel, or other uses.

This class includes small-holder farming, agro-industry 

farming, and rotating agriculture.

—

2.2. Wood and 

pulp plantations

Stands of trees planted for timber or fiber outside of 

natural forests, often with nonnative species.

If it is one or a couple of timber species that are planted 

on a rotation cycle, it belongs here. If it is multiple 

species or enrichment plantings in a quasi-natural 

system, it belongs in 5.3, Logging and wood harvesting. 

This class includes small-holder and agro-industry 

plantations.

—

2.3. Livestock 

farming and 

ranching

Domestic terrestrial animals raised in one location on 

farmed or nonlocal resources (farming); also domestic 

or semidomesticated animals allowed to roam in the wild 

and supported by natural habitats (ranching).

This class includes small-holder grazing, ranching, or 

farming, and agro-industry grazing, ranching, or farming, 

and nomadic grazing. In farming, animals are kept in 

captivity; in ranching they are allowed to roam in wild 

habitats. Forage of wild resources for stall-fed animals 

falls under 5.2, Gathering terrestrial plants. If a few 

animals are mixed in a subsistence cropping system, it 

belongs in 2.1, Annual and perennial nontimber crops.

—

2.4. Marine and 

freshwater 

finfish 

aquaculture

Finfish raised in one location on farmed or nonlocal 

resources; also hatchery fish allowed to roam in the 

wild.

This class includes pressures associated with the 

location, intensification, or practice of finfish 

aquaculture. Farmed animals are kept in captivity; 

hatchery fish are put into wild habitats and are the 

aquatic equivalent of terrestrial ranching.

—

2.5. Marine 

shellfish 

aquaculture

Marine shellfish raised in one location on farmed or 

nonlocal resources.

This class includes pressures associated with the 

location, intensification, or practice of shellfish 

aquaculture.

—

3. Energy 

production and 

mining

Production of nonbiological resources.

Various forms of water use (for example, dams for hydro 

power) that involve alterations to hydrologic regimes 

should go in 7.2, Dams and water management/use.

—
116

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

3.1. Oil and gas 

drilling

Exploring for, developing, and producing petroleum and 

other liquid hydrocarbons.

Oil and gas pipelines go into 4.2, Utility and service 

lines. Spills (oil or other hazardous substances) 

associated with drilling or transportation of oil go in 9.2, 

Industrial and military effluents.

Oil wells, deep sea 

natural gas drilling, 

hydraulic fracking, etc.

3.2. Mining and 

quarrying

Exploring for, developing, and producing minerals and 

rocks.

Deforestation caused by strip mining should be included 

here if the motivation is access to minerals. It should be 

included in 5.3, Logging and wood harvesting, if the 

primary motivation is access to the trees. Sediment or 

toxic chemical runoff from mining is under 9.2, 

Industrial and military effluents.

Coal strip mines, 

alluvial gold panning, 

gold mines, rock 

quarries, sand/salt 

mines, coral mining, 

deep sea nodules, guano 

harvesting, dredging 

outside of shipping 

lanes, etc.

3.3. Renewable 

energy

Exploring, developing, and producing renewable energy.

Hydropower should be put in 7.2, Dams and water 

management/use.

Geothermal power 

production, solar farms, 

wind farms (including 

birds flying into 

windmills), tidal farms, 

etc.

4. 

Transportation 

and service 

corridors

Long narrow transport corridors and the vehicles that 

use them.

This includes transportation and utility corridors outside

of human settlements and industrial developments in 

terrestrial and aquatic environments. These corridors are 

associated with specific stressors including especially 

fragmentation of habitats and direct species mortality.

—

4.1. Roads and 

railroads 

(including 

culverts)

Surface transport on roadways and dedicated tracks.

Off-road vehicles are treated in the appropriate category 

in 6, Human intrusions and disturbance. If there are 

small roads associated with a major utility line, they 

belong in 4.2, Utility and service lines.

Highways, secondary 

roads, primitive roads, 

logging roads, bridges 

and causeways, fencing 

associated with roads, 

freight/passenger/

mining railroads, etc.

4.2. Utility and 

service lines

Transport of energy and resources.

Cell phone and other communication towers connected 

by small access roads belong here. If there are small 

utility lines using a road right of way, they belong in 4.1, 

Roads and railroads. Oil spills from pipelines go in 9.2, 

Industrial and military effluents.

Electrical and phone 

wires, aqueducts, oil and

gas pipelines, 

electrocution of wildlife, 

etc.
117 

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

4.3. Shipping 

lanes and 

dredged 

waterways

Transport on and in freshwater and ocean waterways.

This class includes vessel traffic as well as dredging and 

other activities that maintain shipping lanes. Wastewater 

discharge from tugs and nonmilitary cargo vessels is also 

included here. Anchor damage from dive boats belongs 

in 6.1, Recreational activities. Oil spills from ships go in 

9.2, Industrial and military effluents.

Canals, shipping lanes, 

whale-watching routes, 

wakes from cargo ships, 

etc.

4.4. Flight paths Air and space transport.

Airports fall into 1.2, Commercial and industrial areas.

Flight paths, jets 

impacting birds, etc.

5. Biological 

resource use

Consumptive use of “wild” biological resources; also 

persecution or control of specific species.

—

5.1. Hunting 

and collecting 

terrestrial 

animals

Killing or trapping terrestrial wild animals or animal 

products for commercial, recreation, subsistence, 

research or cultural purposes, or for control/persecution 

reasons.

This class focuses on animals that primarily live in a 

terrestrial environment, as well as those that live on the 

terrestrial/aquatic boundary. Hunting otters, beavers, 

amphibians, waterfowl, and sea birds belongs here. 

Hunting seals, whales and other marine mammals, and 

freshwater and marine turtles goes in 5.4, Fishing and 

harvesting aquatic resources. This also includes animal 

products that are traditionally “gathered,” such as honey, 

eggs, or insects or other slow moving targets.

Trophy hunting, beaver 

trapping, butterfly 

collecting, honey or bird 

nest hunting, etc.; pest 

control, hunting with 

dogs, wolf control, 

persecution of snakes 

because of superstition, 

etc.

5.2. Gathering 

terrestrial plants

Harvesting plants, fungi, and other nontimber/nonanimal 

products for commercial, recreation, subsistence, 

research or cultural purposes, or for control reasons.

This class focuses on plants, mushrooms, and other 

nonanimal terrestrial species except trees, which are 

treated in 5.3, Logging and wood harvesting. This 

source can have intentional and unintentional impacts on 

target and nontarget species.

Wild mushroom 

collection, forage for 

stall-fed animals, orchid 

collection, harvesting of 

flowers and greens, etc.; 

control of host plants to 

combat timber diseases, 

etc.
118

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

5.3. Logging 

and wood 

harvesting

Harvesting trees and other woody vegetation for timber, 

fiber, or fuel.

This includes subsistence-scale use and large-scale use, 

both of which can have intentional and unintentional 

effects on target and nontarget species. Felling trees to 

clear agricultural land belongs in 2, Agriculture and 

aquaculture. If it is a few timber species that are planted 

on a rotation cycle, it belongs in 2.2, Wood and pulp 

plantations. If it is multiple species or enrichment 

plantings in a quasi-natural system, it belongs here. 

Consider the specific product(s) harvested and the 

method used (e.g., clear cutting of hardwoods, selective 

commercial logging, pulp or woodchip operations, fuel 

wood collection, etc.).

—

5.4. Fishing and 

harvesting 

aquatic 

resources

Harvesting aquatic wild animals or plants for 

commercial, recreation, subsistence, research, or 

cultural purposes, or for control/persecution reasons; 

includes accidental mortality/bycatch.

This category focuses on all kinds of species that are 

primarily found in an aquatic environment as well as 

some species that live on the terrestrial/aquatic boundary. 

Hunting seals, whales and other marine mammals, and 

freshwater and marine turtles goes here. Hunting otters, 

beavers (Castor canadensis), amphibians, waterfowl, and 

sea birds belongs in 5.1, Hunting and collecting 

terrestrial animals. This class includes large-scale 

harvest and subsistence/small-scale harvest and can be a 

source of multiple stressors, including harvest 

(intentional), and discards or bycatch (unintentional). 

Note that associated stresses can be both ecosystem 

degradation and species mortality.

Commercial trawling, 

commercial long-line 

fisheries, whaling, seal 

hunting, turtle egg 

collection, live coral 

collection, seaweed 

collection, blast fishing, 

cyanide fishing, artisinal 

trawling, shark nets 

trapping nontarget 

species, loss of a 

species’ prey base due 

to overharvesting by 

humans of their prey, 

beach protection with 

shark nets, sharks and 

seals killed because they 

eat commercial fish 

species, etc.

6. Human 

intrusions and 

disturbance

Human activities that alter, destroy, and disturb habitats 

and species associated with nonconsumptive uses of 

biological resources.

Nonconsumptive use means that the resource is not 

removed (i.e., multiple people can use the same resource, 

e.g., birdwatching). These pressures typically do not 

permanently destroy habitat except perhaps in extremely 

severe manifestations.

—
119

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

6.1. 

Recreational 

activities

People spending time in nature or traveling in vehicles 

outside of established transport corridors, usually for 

recreational reasons.

This class includes wastewater discharged from 

recreational vessels. It does not include work involving 

consumptive use of biodiversity. For example, 

disturbance impacts from loggers or hunters would

appropriately be in category 5, Biological resource use. 

Vehicles in established transport corridors go in 4, 

Transportation and service corridors. The development 

of activities at permanent recreational or tourist facilities 

(such as hotels and resorts) belongs under section 1.3, 

Tourism and recreation areas, rather than here.

Off-road vehicles, 

motorboats, 

motorcycles, jet skis, 

snowmobiles, ultralight 

planes, dive boats, 

whale watching, 

mountain bikes, hikers, 

cross-country skiers, 

hang gliders, 

birdwatchers, scuba 

divers, pets brought into 

recreation areas, temporary campsites, caving, 

rock climbing, etc.

6.2. War, civil 

unrest, and 

military 

exercises

Actions by formal or paramilitary forces without a 

permanent footprint.

This class focuses on military activities that have a large 

impact on natural habitats, but are not permanently 

restricted to a single area. It also includes wastewater 

discharged from military vessels. Development and 

operation of permanent military bases goes under 1.2, 

Commercial and industrial areas.

Armed conflict, mine 

fields, tanks and other 

military vehicles, 

training exercises and

ranges, defoliation, 

munitions testing, etc.

6.3. Work and 

other activities

People spending time in or traveling in natural 

environments for reasons other than recreation or 

military activities.

Law enforcement, drug 

smugglers, illegal 

immigrants, species 

research, vandalism, etc.

7. Natural 

system 

modifications

Actions and structures that convert or degrade habitat in

service of “managing” natural or seminatural systems.

This class deals primarily with changes to natural 

processes such as fire, hydrology, and sedimentation, 

rather than land use. Thus it does not include pressures 

relating to agriculture (which should be under 2, 

Agriculture and aquaculture), or infrastructure (1, 

Residential and commercial development and 4, 

Transportation and service corridors).

—

7.1. Fire and 

fire suppression

Suppression or increase in fire frequency or intensity 

outside its natural range of variation.

This class focuses on the human activities that lead to 

either not enough fire or too much fire in the ecosystem 

in question. If fire escapes from established agricultural 

lands, it belongs here, if fire is used to clear new 

agricultural lands, it belongs in 2, Agriculture and 

aquaculture. It also includes damaging “natural” fires in 

systems that have lost their natural resilience.

Inappropriate fire 

management, escaped 

agricultural fires, arson, 

campfires, fires for 

hunting, fire suppression 

to protect homes, etc.
120

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

7.2. Dams and 

water management/use

Changing water flow patterns from their natural range 

of variation, either deliberately or as a result of other 

activities.

This class focuses on the human activities that lead to 

either not enough water or too much water in the 

ecosystem in question. Note that homogenizing flows to 

a constant level may be outside the “natural range of 

variation.” This includes surface water diversion, 

channelization, ditching, artificial lakes, groundwater 

pumping, dam construction, release of too little or cold 

water from dam operations, sediment control, dikes, 

levees, floodgates and tide gates, etc. Dredging belongs 

in 4.3, Shipping lanes.

—

7.2.1.

Abstraction of 

surface water

Diverting or withdrawing surface water. —

7.2.2.

Abstraction of 

ground water

Pumping or other extraction of groundwater. —

7.2.3. Dams Construction or operation of dams used to generate 

hydropower or manage how and when water flows 

through a system.

Impacts associated with dams include conversion/loss or 

degradation of habitat, altered hydrology, and altered 

connectivity.

—

7.2.4. 

Freshwater 

levees, 

floodgates, tide

gates

Levees and floodgates along freshwater systems to 

manage the hydrologic flow in a system.

Impacts associated with levees and floodgates include 

conversion/loss or degradation of habitat, altered 

hydrology, and altered connectivity.

—

7.2.5. Marine 

levees, 

floodgates, tide

gates

Levees and tide gates along marine water systems to 

manage or exclude marine water into the freshwater 

system.

Impacts associated with levees and tide gates include 

conversion or degradation of habitat, altered hydrology, 

and altered connectivity.

—

7.3. Freshwater 

shoreline 

infrastructure

Armoring of freshwater shorelines and overwater 

structures that alter, destroy, and disturb habitats and 

species via a nonconsumptive use, including industrial, 

commercial, and recreational marinas, ports, and 

shipyards.

Runoff from impervious surfaces or other water 

pollution should go in 9.1.

—
121

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

7.4. Marine 

shoreline 

infrastructure

Armoring of marine shorelines and overwater structures 

that alter, destroy, and disturb habitats and species via a 

nonconsumptive use, including industrial, commercial, 

and recreational marinas, ports, and shipyards.

Runoff from impervious surfaces or other water 

pollution should go in 9.1.

—

9. Pollution Introduction of exotic or excess materials or energy from 

point and nonpoint sources.

—

9.1 Domestic 

and urban waste 

water

— —

9.1.1. Domestic 

and commercial 

sewage

— —

9.1.1.1. 

Domestic and 

municipal 

wastewater to 

sewer

Discharges from municipal wastewater treatment plants 

(WWTPs) into hydrologic systems.

This class includes waterborne sewage that includes 

nutrients, pathogens, toxic chemicals, and sediments. 

Discharges from combined sewer overflows (CSOs) are 

included here. Onsite sewage systems (OSSs) go in 

9.1.1.2. This class does not include wastewater 

discharged from recreational and other vessels (see 4.3, 

6.1, and 6.2) or biosolids applied in terrestrial 

environments (see 9.3).

—

9.1.1.2. 

Domestic and 

commercial 

wastewater to 

OSSs

Discharges from OSSs.

This class includes sewage and leachates (nutrients, toxic 

chemicals or sediment) from residences and commercial 

facilities not connected to a municipal system (septics, 

small private systems, and everything with a drain field).

—

9.1.2. Runoff 

from residential 

and commercial 

lands

Introduction of exotic or excess material into hydrologic 

system due to surface water loading and runoff from the 

built environment.

This class includes runoff from commercial and 

residential lands, transportation facilities and corridors, 

as well as hull cleaning and other pollution from marina 

infrastructure and land-based boat maintenance practices 

(i.e., National Pollutant Discharge Elimination System–

regulated activities that occur in marinas and shipyards). 

Loading from septic systems (OSSs) goes in 9.1.1.2, 

CSOs go in 9.1.1.1, runoff from other activities (e.g.,

agriculture, timber harvest) goes in 9.3, and industrial 

runoff goes in 9.2.4.

—
122 

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

9.2. Industrial 

and military 

effluents

Waterborne pollutants from industrial and military 

sources including mining, energy production, and other 

resource extraction industries that include nutrients, 

toxic chemicals, or sediments.

The source of the pollution is often far from the 

system—an extreme example is the heavy metals that 

migrating eels bring to the Sargasso Sea. Often the 

pollutants only become a problem when they 

bioconcentrate through the food chain.

—

9.2.1. Oil spills Accidental, episodic, or potentially catastrophic spill of 

oil and hazardous waste in aquatic and terrestrial 

environments.

This class includes oil spills from pipelines, vessels, 

marine terminals, and industrial facilities. It does not 

include chronic or other frequent, smaller pollution 

events related to normal operations of vehicles, vessels, 

etc. (see 9.1.2).

—

9.2.2. Seepage 

from mining

Waterborne pollutants from mining, including nutrients, 

toxic chemicals, or sediments.

—

9.2.3. Industrial 

wastewater

Discharge from industrial WWTPs into hydrologic 

systems.

This class includes waterborne sewage that includes 

nutrients, pathogens, toxic chemicals, and sediments. 

Loading from municipal and domestic WWTPs goes in 

9.1.1.1, septic systems (OSSs) go in 9.1.1.2, CSOs go in 

9.1.1.1, runoff from other activities (e.g., agriculture, 

timber harvest) goes in 9.3, and industrial runoff goes in 

9.2.4.

—

9.2.4. Industrial 

runoff 

Introduction of exotic or excess material into hydrologic 

system due to surface water loading and runoff from 

industrial lands. 

This class includes runoff from industrial facilities and 

lands. Runoff from other lands (residential and 

commercial) goes in 9.1.2, loading from septic systems 

(OSSs) goes in 9.1.1.2, CSOs go in 9.1.1.1, runoff from 

other activities (e.g., agriculture, timber harvest) goes in 

9.3, and industrial runoff goes in 9.2.4.

—
123

Table B-1 continued. Taxonomy of Puget Sound pressure sources based on previous classifications 

(IUCN 2001, Salafsky et al. 2008). Minor modifications by the PSP resulted in eight source 

categories. Sources are the cause of stressors that in turn are the causes of stressed conditions in 

the ecosystem.

Source class Definition and exposition Puget Sound examples

9.3. Agricultural 

and forestry 

effluents

Waterborne pollutants from agricultural, silvicultural, 

and aquaculture systems that include nutrients, toxic 

chemicals, or sediments and the effects of these 

pollutants on the site where they are applied.

This class also includes pollutants added by biosolids, 

herbicide, and pesticide application. Wind erosion of 

agricultural sediments or smoke from forest fires goes in 

9.5, Airborne pollutants.

Nutrient loading from 

fertilizer runoff, manure 

from feedlots, nutrients 

from aquaculture, etc.; 

soil erosion from 

overgrazing, increased 

runoff and hence 

sedimentation due to 

conversion of forests to 

agricultural lands, etc.; 

herbicide runoff from 

orchards, etc.

9.4. Garbage 

and solid waste

Rubbish and other solid materials including those that 

entangle wildlife.

This class generally is for solid waste outside of 

designated landfills; landfills themselves should go in 

1.2, Commercial and industrial areas. Likewise, toxins 

leaching from solid waste (e.g., mercury leaking out of a 

landfill into groundwater) should go in 9.2, Industrial 

and military effluents.

Municipal waste, litter 

from cars, flotsam and

jetsam from recreational 

boats, waste that 

entangles wildlife, 

construction debris, etc.

9.5. Airborne 

pollutants

Atmospheric pollutants from stationary and mobile 

sources.

This class includes smog and ozone, the specific sources 

of which can be difficult to determine and difficult to 

address.

Smog from vehicle 

emissions, factory 

smoke emissions, coal 

burning, wind 

dispersion of pollutants 

or sediments, smoke 

from forest fires or 

woodstoves, etc. 

Associated stressors can 

include acid rain, excess 

nitrogen deposition, 

radioactive fallout.

9.6. Release of 

excess energy 

(light, heat, 

sound)

Inputs of heat, sound, or light that disturb wildlife or 

ecosystems.

These inputs of energy can have strong effects on some 

species or ecosystems.

Lamps attracting 

insects, beach lights 

disorienting turtles, etc.; 

heated water from 

power plants, damaging 

atmospheric radiation 

resulting from ozone 

holes, etc.; noise from 

highways or airplanes, 

sonar from submarines 

that disturbs whales, etc.
124

Table B-2. Puget Sound stressors, the most proximate agents of change to Puget Sound ecosystems, 

including both human and natural processes that impair or degrade the system. The 39 stressor 

classes are grouped into 26 higher level categories.

Code Name Description

01 Habitat conversion due to 

human land use change

—

01.1 Conversion of land cover 

for residential, 

commercial, and industrial 

use

Conversion of land cover to one dominated by residential, 

commercial, or industrial development. In the terrestrial and 

nearshore environments, sources include residential and 

commercial development; in the marine environment, consider 

conversion for marinas and other marine uses. Agriculture 

and aquaculture (see 01.2) and dredging (see 01.3) are 

assessed separately. Stress associated with disturbance due to 

human activities (including in developed areas) is addressed 

separately (see 07). Terrestrial habitat fragmentation (see 02),

shoreline hardening (see 03), and barriers to terrestrial animal 

movement and migration (see 06) are addressed as separate 

stressors. Pollution impacts are assessed through separate 

stressors (see 22 through 23). Note that conversion can be a

step-wise process where, for example, native forest land is 

converted to managed forests, which are then under stress for 

further conversion to agriculture or residential and commercial 

development.

01.2 Conversion of land cover 

for natural resource 

production

Conversion of land cover to one dominated by natural 

resource production, such as through agriculture and timber 

production in terrestrial environments and aquaculture in 

marine and nearshore environments. This stressor has to do 

with the reduction in extent and quality of habitat due to 

conversion. Stress associated with disturbance due to human 

activities (including in developed areas) is addressed 

separately (see 07). Terrestrial habitat fragmentation (see 02), 

shoreline hardening (see 03), and barriers to terrestrial animal 

movement and migration (see 06) are addressed as separate 

stressors. Pollution impacts are assessed through separate 

stressors (see 22 through 23). Note that conversion can be a

step-wise process where, for example, native forest land is 

converted to managed forests, which are then under stress for 

further conversion to agriculture or residential and commercial 

development.

01.3 Conversion of land cover 

for transportation and

utilities

Conversion of land cover to one dominated by transportation 

and service corridors. This stressor has to do with the 

reduction in extent and quality of habitat due to conversion, 

including conversion by dredging. Stress associated with 

disturbance due to human activities (including in developed 

areas) is addressed separately (see 07). Terrestrial habitat 

fragmentation (see 02), shoreline hardening (see 03), and 

barriers to terrestrial animal movement and migration (see 06) 

are addressed as separate stressors. Pollution impacts are 

assessed through separate stressors (see 22 through 23).
125

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories.

Code Name Description

02 Terrestrial habitat 

fragmentation

Division of contiguous habitat into smaller, discontiguous 

patches or different habitat types. Sources of this stressor 

include development of lands for agriculture, residential, 

commercial, or industrial uses, or roads and utility corridors. 

Expressions of this stressor will depend on the endpoint one is 

assessing. For example, bobcat (Lynx rufus) and certain small 

passerine birds may have minimum patch size requirements on 

the order of 25 ha and 3 ha, respectively. Landscapes in 

which habitat patches are predominantly smaller than these 

minimums are unlikely to support these species. Disturbance 

due to human activities (see 07) and habitat conversion (see 

01) are evaluated as separate stressors.

03 Shoreline hardening Change of shoreline habitat or features to conditions that 

reduce habitat extent or disrupt shoreline processes. The 

primary source of this stressor is the construction of shoreline 

infrastructure that produces a hard linear surface along the 

beach or streambank to reduce erosion (e.g., seawalls, 

revetments, riprap, and rock piles). Habitat conversion for 

residential, commercial and industrial development, and other 

uses is evaluated separately (see 01).

04 Shading of shallow water 

habitat

Decreased light transmitted into shallow waters. This stressor 

causes species stresses related to productivity or altered 

predator-prey relationships. The primary source of this 

stressor is construction of overwater and onshore structures.

05 Fish passage barriers —

05.1 Dams as fish passage 

barriers

Dams that block or impede movements and migrations of fish 

and other aquatic animals. This stressor is intended to 

evaluate only effects on fish and other aquatic species; effects 

on flow regulation (see 12) and physical processes (see 13) are 

evaluated as separate stressors. Fish passage barriers created 

by culverts and other structures are evaluated as separate 

stressors (see 05.2).

05.2 Culverts and other fish 

passage barriers

Structures other than dams that block or impede movements 

and migrations of fish and other aquatic animals. Includes 

structures in, alongside, and across water bodies. This stressor 

is intended to evaluate only effects on fish and other aquatic 

species; effects on flow regulation (see 12) and physical 

processes (see 13) are evaluated separately. Fish passage 

barriers created by dams are evaluated as separate stressors 

(see 05.1).
126

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories.

Code Name Description

06 Barriers to terrestrial 

animal movement and 

migration

Structures that block or impede movements and migrations of 

terrestrial animals such as roads and utility infrastructure. 

Expressions of this stressor will depend on the endpoint one is 

assessing. For example, for terrestrial species such as elk

(Cervus elaphus), a strong expression of the stressor may be 

structures such as multilane roads; for avian species a strong 

expression of the stressor may be energy infrastructure such as 

wind turbines. Disturbance due to human activities (see 07) 

and terrestrial habitat fragmentation (see 02) are evaluated as 

separate stressors.

07 Species disturbance—

terrestrial and freshwater

—

07.1 Terrestrial and freshwater 

species disturbance in 

human-dominated areas

Alteration in the feeding, breeding, or resting behaviors of fish

or wildlife due to human presence or activities associated with 

landscapes dominated by man-made structures, such as light 

and sound disturbances associated with developed areas. 

Includes artifacts and debris associated with human activities, 

except pollution impacts are evaluated through separate 

stressors (see 22 through 23).

07.2 Terrestrial and freshwater 

species disturbance in 

natural landscapes

Alteration in the feeding, breeding, or resting behaviors of fish 

or wildlife and adverse impacts on plant communities due to 

human presence or activities in more natural landscapes, such 

as disturbance associated with recreation and vehicle traffic on 

forest roads. Includes artifacts and debris associated with 

human activities, except pollution impacts are assessed 

through separate stressors (see 22 through 23).

08 Species disturbance—

marine

Alteration in the feeding, breeding, or resting behaviors of 

marine birds, fish, or other aquatic species due to human 

presence or activities (e.g., recreation, vessel traffic, military 

exercises) or artifacts and debris associated with activities,

except pollution impacts (see 22 through 23) and derelict 

fishing gear (see 09) are assessed through separate stressors.

09 Derelict fishing gear Mortality associated with entanglement in abandoned nets and 

other fishing gear.

10 Increased frequency and 

magnitude of storm flow

—

10.1 Altered peak flows from 

land cover change

Altered peak flows into and in surface waters related to 

changes in land cover and the associated surface hardening,

and associated impacts, such as changes in sediment and 

debris delivery. Stress from pollution impacts is evaluated 

separately (see 22 through 23). Altered peak flow from 

climate change is evaluated separately (see 10.2).
127

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories.

Code Name Description

10.2 Altered peak flows from 

climate change

Altered peak flows into and in surface waters related to 

changes in precipitation volume and timing due to climate 

change and associated impacts, such as changes in sediment 

and debris delivery. Stress from pollution impacts is 

evaluated separately (see 22 through 23). Altered peak flow 

from land cover change is evaluated separately (see 10.1).

11 Reduction in base flows —

11.1 Altered low flows from 

land cover change

Reduction of low flows in surface waters related to changes in 

land cover and the associated surface hardening and changes 

in hydrology. Other reductions of low flows are evaluated 

separately (see 11.2 and 11.3).

11.2 Altered low flows from 

climate change

Reduction of low flows in surface water related to changes in 

precipitation volume and timing due to climate change,

resulting in reduced glacial coverage and snowpack or 

changes in the timing and rate of snowmelt. Other reductions 

of low flows are evaluated separately (see 11.1 and 11.3).

11.3 Altered low flows from 

withdrawals

Reduction of low flows in surface waters related to water 

withdrawals for human use and consumption. Other 

reductions of low flows are evaluated separately (see 11.1 and 

11.3).

12 Flow regulation—

prevention of flood flows

Modification of flood flows by flow regulation in river and 

stream systems. Sources of this stressor are the impoundment 

of water by dams and the operation of dams for flood control 

or hydroelectric power production. These structures may also 

be barriers to movement and migration of fish and aquatic 

animals, evaluated separately (see 05.1).

13 Structural barriers to water, 

sediment, debris flow 

(including flood flows)

—

13.1 In-channel structural 

barriers to water, sediment, 

debris flows

Structures that block or restrict movement of water, sediment, 

or debris flow in the river or stream channel and associated 

impacts, such as changes in sediment and debris delivery. 

These structures may also be barriers to movement and 

migration of fish and aquatic animals, evaluated separately 

(see 05.2). Impacts associated with dams also are evaluated 

separately (see 05.1 and 12).

13.2 Other structural barriers to 

water, sediment, debris 

flows

Structures that block or restrict movement of water, sediment, 

or debris flow into the floodplain, such as levees, and 

associated impacts, such as changes in sediment and debris 

delivery. These structures may also be barriers to movement 

and migration of fish and aquatic animals, evaluated 

separately (see 05.2). Impacts associated with dams also are 

evaluated separately (see 05.1 and 12).
128

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories.

Code Name Description

14 Animal harvest Removal of fish, invertebrates, or wildlife for human use. 

This stressor includes intentional harvest or removals only and 

is meant to assess the effect of intentional harvest on species. 

Sources of this stressor include fishing, hunting, and 

collections in support of species’ management or 

investigation. Stress from bycatch is evaluated separately (see 

15). Stress from disturbance associated with harvest activities 

also is evaluated separately (see 07.2).

15 Bycatch Removal of nontarget species of fish, invertebrates, or wildlife 

caught during commercial or recreational fishing.

16 Plant harvest —

16.1 Timber harvest Removal of timber for human use. The strong expression of 

this stressor is clear cutting. Stress from harvest of other types 

of plants is evaluated separately (see 16.2). Stress associated 

with disturbance is evaluated separately (see 07.2).

16.2 Nontimber plant harvest Removal or harvest of nontimber plants, including 

mushrooms, floral greens, food plants, algae, and aquatic 

plants, for human use. Stress from timber harvest is evaluated 

separately (see 16.1). Stress associated with disturbance is 

evaluated separately (see 07.2).

17 Increase in native species —

17.1 Predation from increased 

native species

Increased predation resulting from the increase/spread of 

native fish, wildlife, invertebrates, or plants. Includes 

increased predation from synanthropic species such as corvids

(Corvidae), gulls (Larus spp.), cowbirds (Molothrus spp.), 

raccoon (Procyon lotor), and native species from hatcheries.

17.2 Displacement by increased 

native species

Displacement or decrease in abundance or decrease in 

population growth rates resulting from the increase/spread of 

native fish, wildlife, invertebrates, or plants. Includes 

displacement by synanthropic species such as corvids, gulls, 

cowbirds, raccoon, and native fish species released from 

hatcheries.

18 Introduction of new or 

increase in nonnative 

species

—

18.1 Predation from nonnative 

species

Increased predation resulting from the addition or increase of 

nonnative fish, wildlife, domestic animals and pets, 

invertebrates, or plants.

18.2 Displacement by 

nonnatives

Displacement or decrease in abundance or decrease in 

population growth rates resulting from the addition or increase 

of nonnative fish, wildlife, domestic animals and pets, 

invertebrates, or plants.
129

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories.

Code Name Description

18.3 Nonnative genetic material Introduction and spread of extra or new genetic material that 

includes transgenetic material introduced through a variety of 

genetic engineering methods and purposes (e.g., genetically 

modified agricultural crops), intentional or unintentional 

hybridization of different species because of management 

actions, and hybridization of introduced, exotic shellfish or 

fish with native forms through aquaculture.

19 Disease and parasite 

introduction, spread, or 

amplification

—

19.1 Spread of disease and 

parasites to native species

Introduction, spread, or amplification of disease or parasites 

from human and animal waste, aquaculture, or nonnative 

species to native species. This is meant to assess the effects of 

diseases and parasites that affecting species other than 

humans; diseases affecting humans are evaluated separately 

(see 19.2).

19.2 Introduction, spread, or 

amplification of human 

pathogens

Introduction, spread, or amplification of disease-causing or 

parasitic organisms to humans. Sources of this stressor 

include release human and animal waste. This is intended to 

evaluate effects on humans due to, for example, degradation in 

water quality and the associated degradation in the quality of 

aquatic species (e.g., shellfish) consumed by people.

20 Air pollution —

20.1 Air pollution from mobile 

sources

Presence or loading of chemicals or particles in the 

atmosphere that can cause discomfort, disease, or death to 

humans and harm the natural environment, (including via 

deposition to land and water) resulting from mobile sources,

such as car, truck, and vessel traffic. Noise and light pollution 

are evaluated separately (see 07.1).

20.2 Air pollution from 

stationary sources

Presence or loading of chemicals or particles in the 

atmosphere that can cause discomfort, disease, or death to 

humans and harm the natural environment, (including via 

deposition to land and water) resulting from stationary 

sources, such as industrial and commercial emissions. Noise 

and light pollution are evaluated separately (see 07.1).

21 Persistent toxic chemicals 

in aquatic systems

—

21.1 Point source, persistent 

toxic chemicals in aquatic 

systems

Presence or loading of persistent toxics from point sources. 

Sources of this stressor include activities that generate 

wastewater that is discharged from municipal and industrial 

sewers and treatment plants. Include stress from persistent 

chemical cycling here (e.g., PCB and Hg cycling). Stress 

from nonpoint sources is evaluated separately (see 21.2).
130

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories.

Code Name Description

21.2 Nonpoint source, persistent 

toxic chemicals in aquatic 

systems

Presence or loading of persistent toxics from nonpoint sources, 

such as runoff from developed areas and roads, including from 

historic (legacy) sources and small (<10 gallon) spill events. 

Sources of this stressor include activities that contribute 

pollutants to surface water runoff, including that discharged 

through stormwater conveyance systems. Stress from point 

sources is evaluated separately (see 21.1).

22 Nonpersistent toxic 

chemicals in aquatic 

systems

—

22.1 Point source, nonpersistent 

toxic chemicals in aquatic 

systems

Presence or loading of nonpersistent toxics from point sources, 

including historic sources and small spill (<10 gallons) events. 

Sources of this stressor include activities that generate 

wastewater that is discharged from municipal and industrial 

sewers and treatment plants. Stress from nonpoint sources is 

evaluated separately (see 22.2).

22.2 Nonpoint source, 

nonpersistent toxic 

chemicals in aquatic 

systems

Presence or loading of nonpersistent toxics from nonpoint 

sources, such as runoff from developed areas and roads, 

including from historic (legacy) sources and small (<10 

gallon) spill events. Sources of this stressor include activities 

that contribute pollutants to surface water runoff, including 

that discharged through stormwater conveyance systems. 

Stress from point sources is evaluated separately (see 22.1).

23 Large spills Spills of large amounts of oil and hazardous substances (>100 

gallon). Sources include large oil spills from large events 

related to vessels (including derelict vessels), road and rail 

traffic, pipelines, and industrial facilities. Stress from smaller,

more routine spills and releases, such as those that might occur 

at gas stations and marinas, is evaluated separately (see 21 and 

22).

24 Conventional water 

pollutants

—

24.1 Point source conventional 

water pollutants

Presence or loading of nutrients, sediment, turbidity, and 

oxygen demanding substances from point sources. Sources of 

this stressor include activities that generate wastewater that is 

discharged from municipal and industrial sewers and treatment 

plants. Stress from nonpoint sources (see 24.2) and 

temperature changes (see 24.3) are evaluated separately.

24.2 Nonpoint source 

conventional water 

pollutants

Presence or loading of nutrients, sediment, turbidity, and 

oxygen demanding substances from nonpoint sources. 

Sources of this stressor include activities that contribute 

pollutants, including that discharged through stormwater 

conveyance systems. Stress from point sources (see 24.1) and 

temperature changes (see 24.3) are evaluated separately.
131 

Table B-2 continued. Puget Sound stressors, the most proximate agents of change to Puget Sound 

ecosystems, including both human and natural processes that impair or degrade the system. The 

39 stressor classes are grouped into 26 higher level categories. 

Code Name Description

24.3 Changes in water 

temperature from local 

causes

Changes in water temperature. Changes in temperature of 

marine water from human-caused climate change (see 26.4) is 

evaluated separately.

25 Harmful algal blooms Presence of biological and chemical agents associated with 

blooms of algae in marine and freshwater systems.

26 Climate change Environmental stressors associated with increased gas 

concentrations in atmosphere.

26.1 Changing air temperature Changes in air temperature resulting from increased 

greenhouse gas concentrations in atmosphere. This is a 

proximate agent on terrestrial species and a source of other 

stressors. Stress associated with changing water temperature 

(see 24.3) and changes in air temperature associated with the 

built environment (see 07.1) are evaluated separately.

26.2 Changing precipitation 

amounts and patterns 

Changes in amount, form, and quantity of precipitation. This 

is a proximate agent on terrestrial systems and species, but an 

indirect influence (e.g., via altered flows) on other endpoints 

and a source of other stressors. Changes in peak (see 10) and 

base (see 11) flows associated with changing precipitation are 

evaluated separately.

26.3 Sea level rise The rise in sea level in Puget Sound related to human-induced 

climate change.

26.4 Changing ocean condition Changes in water temperature, patterns and magnitude of 

upwelling events, nutrient and oxygen levels, and decrease in 

pH of Puget Sound waters related to increased greenhouse gas 

concentrations in the atmosphere and human-induced climate 

change.

Stresses 

Stresses are equivalent to altered key ecological attributes (KEAs) of ecosystem 

components. Stresses are not pressures, but rather degraded conditions that result from 

pressures. For example, reduced population size is a stress that might result from the pressure of 

unsustainable fishing. Table B-3 and Table B-4 list stresses related to KEAs of the 14 ecosystem 

components in the framework. 
132

Table B-3. Stresses associated with KEAs of the Chinook salmon (Oncorhynchus tshawytscha) 

ecosystem component. Examples of indicators that reflect the health of (or stress to) associated 

KEAs are also included.

KEA Associated stress (altered KEA) Example indicator

Abundance Reduced abundance of spawners No. of subbasins meeting spawner 

abundance targets

Reduced abundance of eggs Redd abundance, egg biomass

Reduced abundance of emergent fry No. of emergent fry

Reduced abundance of juveniles No. of parr

Reduced abundance of river outmigrants No. of parr outmigrants, no. of river 

yearling outmigrants

Reduced abundance of estuary juveniles No. of parr in natal estuary

Reduced abundance of estuary 

outmigrants

No. of estuary outmigrants

Reduced abundance of nearshore 

juveniles

No. of parr

Reduced abundance of coastal migrants No. of management units meeting targets

Reduced abundance of upriver migrants No. migrating upriver

Productivity—

survival rate

Reduced egg survival Egg size

Reduced emergent fry survival Emergent fry survival rate

Reduced river outmigrant survival River outmigrants per spawner

Reduced juvenile survival in estuaries Estuary survival rate of fry, parr, yearling

Reduced subadult survival in open water Interannual survival rate by age

Reduced coastal migrant survival Maturation rate by age, marine survival

Reduced upriver migrant survival In-river survival rate

Productivity—

fish growth

Reduced growth of spawners Size of spawners at given age

Reduced growth of emergent fry Size of emergent fry

Reduced growth of freshwater juveniles River residence time of fry, parr, 

yearlings

Reduced growth of river outmigrants Size of fry, parr, yearlings at outmigration

Reduced growth of estuary juveniles Growth rate or residence time of fry, parr

Reduced growth of estuary outmigrants Size of fry, parr, yearlings

Reduced growth of nearshore juveniles Nearshore rearing size, growth rate, or 

residence time of fry, parr

Reduced growth of juveniles 

transitioning to offshore

Transition to offshore size of parr, 

yearling

Reduced growth of open water subadults Size of open water subadults, open water 

annual growth rate by age

Reduced growth of coastal migrants Size of coastal migrant fishery recruits at 

age

Reduced growth of upriver migrants Size of upriver migrants at age

Productivity—

pop. growth

Reduced spawner population Broodyear spawners

Reduced egg population No. of eggs per female, egg biomass per 

female

Reduced river outmigrant population River outmigrants per spawner

Reduced coastal migrant population No. of subbasins meeting targets for 

fishery recruits per spawner
133 

Table B-3 continued. Stresses associated with KEAs of the Chinook salmon (Oncorhynchus 

tshawytscha) ecosystem component. Examples of indicators that reflect the health of (or stress 

to) associated KEAs are also included.

KEA Associated stress (altered KEA) Example indicator

Spatial 

structure

Reduced spatial distribution of spawners No. of subbasins occupied by spawners

Reduced spatial distribution of egg 

deposition

No. of subbasins with high redd density

Reduced spatial distribution of 

freshwater juveniles

Distribution of fry, parr rearing among 

lowland, mainstem, headwaters

Reduced spatial distribution of estuary 

juveniles

Distribution of rearing among natal 

estuary habitat types

Reduced spatial distribution of nearshore 

juveniles 

No. of drift cells with rearing, distribution 

of nearshore rearing among/within habitat 

types

Reduced spatial distribution of open 

water juveniles

Distribution of rearing in the ocean

Reduced spatial distribution of coastal 

migrants

No. of coastal migration routes

Life history 

diversity

Reduced life history diversity of 

spawners

Spawning timing, spawner age

Reduced life history diversity of 

emergent fry

Timing and size of emergent fry at 

emergence (swim-up)

Reduced life history diversity of 

freshwater juveniles

Diversity of fry, parr river residence times

Reduced life history diversity of river 

outmigrants

Diversity of outmigration timing, age 

structure of river outmigrants

Reduced life history diversity of estuary 

juveniles

Diversity of estuary residence times

Reduced life history diversity of estuary 

outmigrants

Diversity of estuary outmigration timing

Reduced life history diversity of 

nearshore juveniles

Diversity of nearshore residence times

Reduced life history diversity of coastal 

migrants

Age structure of fishery recruits, timing of 

coastal migrant return to terminal areas

Reduced life history diversity of upriver 

migrants

Age structure of upriver migrants, 

diversity of upriver migration timing

Genetic 

diversity

Reduced genetic diversity of spawners Spawner effective population size, alleles 

per locus, or gene flow rate

Reduced genetic diversity of nearshore 

juveniles

No. of populations rearing in nearshore 

habitats
134

Table B-4. Stresses associated with the KEAs of the habitat and species and food web ecosystem 

components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Freshwater habitats category

Upland I-1. Sediment dynamics–sediment delivery Altered sediment delivery

III-5. Organic matter–inputs Altered organic inputs

Channel 

>50 m BFW

I-1. Sediment dynamics–sediment delivery Altered sediment delivery

I-2. Sediment dynamics–transport and 

storage

Altered sediment transport and storage

II-3. Hydrology–high-flow hydrological 

regime

Altered high-flow regime

II-4. Hydrology–low-flow hydrological 

regime

Altered low-flow regime

III-5. Organic matter–inputs Altered organic inputs

IV-7. Riparian–spatial extent and 

continuity of riparian area

Degraded riparian structure and function

IV-8. Riparian–community structure Degraded riparian structure and function

IV-9. Riparian–function Degraded riparian structure and function

V-10. Nutrient supply–nutrient 

concentrations (high, low)

Altered nutrient concentrations

V-11. Nutrient supply–water quality Altered nutrient inputs, cycling, and flux

V-12. Nutrient supply–nutrient cycling/flux Altered nutrient inputs, cycling, and flux

VI-13. Floodplain-channel interactions–

connectivity

Degraded floodplain structure and 

connectivity

VI-14. Floodplain-channel interactions–

structure and function

Degraded floodplain structure and 

connectivity

VII-15. Habitat connectivity Degraded habitat connectivity

Channel 

<50 m BFW

I-1. Sediment dynamics–sediment delivery Altered sediment delivery

I-2. Sediment dynamics–transport and 

storage

Altered sediment transport and storage

II-3. Hydrology–high-flow hydrological 

regime

Altered high-flow regime

II-4. Hydrology–low-flow hydrological 

regime

Altered low-flow regime

III-5. Organic matter–inputs Altered organic inputs

IV-7. Riparian–spatial extent and 

continuity of riparian area

Degraded riparian structure and function

IV-8. Riparian–community structure Degraded riparian structure and function

IV-9. Riparian–function Degraded riparian structure and function

V-10. Nutrient supply–nutrient 

concentrations (high, low)

Altered nutrient concentrations

V-11. Nutrient supply–water quality Altered nutrient inputs, cycling, and flux

V-12. Nutrient supply–nutrient cycling/flux Altered nutrient inputs, cycling, and flux

VI-13. Floodplain-channel interactions–

connectivity

Degraded floodplain structure and 

connectivity
135

Table B-4 continued. Stresses associated with the KEAs of the habitat and species and food web 

ecosystem components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Freshwater habitats category (continued)

Channel 

<50 m BFW 

(continued)

VI-14. Floodplain-channel interactions–

structure and function

Degraded floodplain structure and 

connectivity

VII-15. Habitat connectivity Degraded habitat connectivity

Side 

channel

I-1. Sediment dynamics–sediment delivery Altered sediment delivery

I-2. Sediment dynamics–transport and 

storage

Altered sediment transport and storage

II-3. Hydrology–high-flow hydrological 

regime

Altered high-flow regime

II-4. Hydrology–low-flow hydrological 

regime

Altered low-flow regime

III-5. Organic matter–inputs Altered organic inputs

III-6. Organic matter–retention/processing Altered organic retention and processing

IV-7. Riparian–spatial extent and 

continuity of riparian area

Degraded riparian structure and function

IV-8. Riparian–community structure Degraded riparian structure and function

IV-9. Riparian–vegetation, including 

wetland

Degraded riparian structure and function

V-10. Nutrient supply–nutrient 

concentrations (high, low)

Altered nutrient concentrations

V-11. Nutrient supply–water quality Altered nutrient inputs, cycling, and flux

V-12. Nutrient supply–nutrient cycling/flux Altered nutrient inputs, cycling, and flux

VI-13. Floodplain-channel interactions–

connectivity

Degraded floodplain structure and 

connectivity

VI-14. Floodplain-channel interactions–

structure and function

Degraded floodplain structure and 

connectivity

VII-15. Habitat connectivity Degraded habitat connectivity

Nonchannel 

lakes and 

wetlands

I-1. Sediment dynamics–sediment delivery Altered sediment delivery

I-2. Sediment dynamics–sediment transport 

and storage

Altered sediment transport and storage

II-3. Hydrology–high-flow hydrological 

regime

Altered high-flow regime

II-4. Hydrology–low-flow hydrological 

regime

Altered low-flow regime

III-5. Organic matter–inputs Altered organic inputs

III-6. Organic matter–retention/processing Altered organic retention and processing

IV-7. Spatial extent and continuity of 

riparian area

Degraded riparian structure and function

IV-8. Riparian community structure Degraded riparian structure and function

IV-9. Riparian function Degraded riparian structure and function

V-10. Nutrient supply–nutrient 

concentrations (high, low)

Altered nutrient concentrations

V-11. Nutrient supply–water quality Altered nutrient inputs, cycling, and flux
136

Table B-4 continued. Stresses associated with the KEAs of the habitat and species and food web 

ecosystem components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Freshwater habitats category (continued)

Nonchannel 

lakes and 

wetlands 

(continued)

V-12. Nutrient supply–nutrient cycling/flux Altered nutrient inputs, cycling, and flux

VI-13. Floodplain-channel interactions–

connectivity

Degraded floodplain structure and 

connectivity

VI-14. Floodplain-channel interactions–

structure and function

Degraded floodplain structure and 

connectivity

VII-15. Habitat connectivity Degraded habitat connectivity

Estuarine and marine habitats category

Natal 

Chinook 

estuary

II-10. Fluvial sediment dynamics–condition Altered fluvial sediment dynamics

III-11. Tidal circulation–extent of 

dependent biological activity

Reduced tidal circulation

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

IV-14. Freshwater hydrology–condition Altered freshwater hydrology

V-15. Tidal channel formation and 

maintenance–extent of channels

Reduced distributary channel formation 

and maintenance

V-16. Tidal channel formation and 

maintenance–connectivity of channels

Reduced connectivity of tidal channels

VI-17. Detritus recruitment and retention–

extent

Altered detritus recruitment and retention

VI-18. Detritus recruitment and retention–

extent of supply

Altered detritus recruitment and retention

VII-19. Habitat connectivity–condition Altered habitat connectivity

VIII-20. Submerged aquatic vegetation 

(SAV) beds–condition

Altered SAV beds

VIII-21. SAV beds–extent Altered SAV beds

VIII-22. Estuarine habitats–extent Altered estuarine habitat area

VIII-23. Estuarine habitats–condition Altered estuarine habitat

VIII-24. Estuarine habitats–distribution Altered estuarine habitat

VIII-27. Tidally influenced wetlands–

extent

Altered tidal hydrology

VIII-28. Tidally influenced wetlands–

condition

Altered tidal hydrology

VIII-29. Water quality Altered water quality

Coastal 

landform

I-1. Coastal sediment dynamics in drift 

cells–condition

Altered coastal sediment dynamics

I-2. Coastal sediment dynamics in drift 

cells–landscape context

Altered coastal sediment dynamics

I-3. Coastal sediment deposition and 

accretion–extent

Altered coastal sediment dynamics
137

Table B-4 continued. Stresses associated with the KEAs of the habitat and species and food web 

ecosystem components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Estuarine and marine habitats category (continued)

Coastal 

landform 

(continued)

I-5. Coastal sediment deposition and 

accretion–condition of impoundment

Altered coastal sediment dynamics

I-8. Coastal sediment dynamics–extent 

(size or volume) of wind and wave 

dependent features

Altered coastal sediment dynamics

III-11. Tidal circulation–extent of 

dependent biological activity

Reduced tidal circulation

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

VI-17. Detritus recruitment and retention–

extent

Altered detritus recruitment and retention

VI-18. Detritus recruitment and retention–

extent of supply

Altered detritus recruitment and retention

VIII-21. SAV beds–extent Altered SAV beds

VIII-25. Intertidal habitat zone–extent Altered intertidal habitat

VIII-26. Intertidal habitat zone–condition Altered intertidal habitat

VIII-29. Water quality Altered water quality

Bluff-backed 

beach

I-1. Coastal sediment dynamics in drift 

cells–condition

Altered coastal sediment dynamics

I-2. Coastal sediment dynamics in drift 

cells–landscape context

Altered coastal sediment dynamics

I-3. Coastal sediment deposition and 

accretion–extent

Altered coastal sediment dynamics

I-6. Coastal sediment supply–extent Altered coastal sediment dynamics

I-7. Coastal sediment supply–distribution Altered coastal sediment dynamics

I-8. Coastal sediment dynamics–extent 

(size or volume) of wind and wave 

dependent features

Altered coastal sediment dynamics

I-9. Coastal sediment dynamics–condition 

of wind and wave dependent features

Altered coastal sediment dynamics

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

VI-17. Detritus recruitment and retention–

extent

Reduced detritus recruitment and 

retention

VI-18. Detritus recruitment and retention–

extent of supply

Reduced detritus recruitment and 

retention

VIII-20. SAV beds–condition Altered SAV beds

VIII-21. SAV beds–extent Altered SAV beds
138

Table B-4 continued. Stresses associated with the KEAs of the habitat and species and food web 

ecosystem components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Estuarine and marine habitats category (continued)

Bluff-backed 

beach 

(continued)

VIII-25. Intertidal habitat zone–extent Altered intertidal habitat

VIII-26. Intertidal habitat zone–condition Altered intertidal habitat

VIII-29. Water quality Altered water quality

Pocket 

estuary

I-1. Coastal sediment dynamics in drift 

cells–condition

Altered coastal sediment dynamics

I-2. Coastal sediment dynamics in drift 

cells–landscape context

Altered coastal sediment dynamics

II-10. Fluvial sediment dynamics–condition Altered fluvial sediment dynamics

III-11. Tidal circulation–extent of 

dependent biological activity

Reduced tidal circulation

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

IV-14. Freshwater hydrology–condition Altered freshwater hydrology

V-15. Tidal channel formation and 

maintenance–extent of channels

Reduced distributary channel formation 

and maintenance

V-16. Tidal channel formation and 

maintenance–connectivity of channels

Reduced connectivity of tidal channels

VI-17. Detritus recruitment and retention–

extent

Reduced detritus recruitment and 

retention

VI-18. Detritus recruitment and retention–

extent of supply

Reduced detritus recruitment and 

retention

VII-19. Habitat connectivity–condition Degraded habitat connectivity

VIII-20. SAV beds–condition Altered SAV beds

VIII-21. SAV beds–extent Altered SAV beds

VIII-22. Estuarine habitats–extent Altered tidal hydrology

VIII-23. Estuarine habitats–condition Altered tidal hydrology

VIII-24. Estuarine habitats–distribution Altered tidal hydrology

VIII-27. Tidally influenced wetlands–

extent

Altered tidal hydrology

VIII-28. Tidally influenced wetlands–

condition

Altered tidal hydrology

VIII-29. Water quality Altered water quality

Rocky 

pocket 

estuary

I-4. Coastal sediment deposition and 

accretion–condition of sediment

Altered coastal sediment dynamics

I-5. Coastal sediment deposition and 

accretion–condition of impoundment

Altered coastal sediment dynamics

I-6. Coastal sediment supply–extent Altered coastal sediment dynamics

I-7. Coastal sediment supply–distribution Altered coastal sediment dynamics
139

Table B-4 continued. Stresses associated with the KEAs of the habitat and species and food web 

ecosystem components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Estuarine and marine habitats category (continued)

Rocky 

pocket 

estuary 

(continued)

I-8. Coastal sediment dynamics–extent 

(size or volume) of wind-dependent and 

wave-dependent features

Altered coastal sediment dynamics

I-9. Coastal sediment dynamics–condition 

of wind-dependent and wave-dependent 

features

Altered coastal sediment dynamics

II-10. Fluvial sediment dynamics–condition Altered fluvial sediment dynamics

III-11. Tidal circulation–extent of 

dependent biological activity

Reduced tidal circulation

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

IV-14. Freshwater hydrology–condition Altered freshwater hydrology

V-15. Tidal channel formation and 

maintenance–extent of channels

Reduced distributary channel formation 

and maintenance

V-16. Tidal channel formation and 

maintenance–connectivity of channels

Reduced connectivity of tidal channels

VI-17. Detritus recruitment and retention–

extent

Reduced detritus recruitment and 

retention

VI-18. Detritus recruitment and retention–

extent of supply

Reduced detritus recruitment and 

retention

VII-19. Habitat connectivity condition Degraded habitat connectivity

VIII-20. SAV beds–condition Altered SAV beds

VIII-21. SAV beds–extent Altered SAV beds

VIII-22. Estuarine habitats–extent Altered tidal hydrology

VIII-23. Estuarine habitats–condition Altered tidal hydrology

VIII-24. Estuarine habitats–distribution Altered tidal hydrology

VIII-27. Tidally influenced wetlands–

extent

Altered tidal hydrology

VIII-28. Tidally influenced wetlands–

condition

Altered tidal hydrology

VIII-29. Water quality Altered water quality

Rocky 

beach

I-4. Coastal sediment deposition and 

accretion–condition of sediment

Altered coastal sediment dynamics

I-6. Coastal sediment supply–extent Altered coastal sediment dynamics

I-7. Coastal sediment supply–distribution Altered coastal sediment dynamics

I-8. Coastal sediment dynamics–extent 

(size or volume) of wind-dependent and 

wave-dependent features

Altered coastal sediment dynamics

I-9. Coastal sediment dynamics–condition 

of wind-dependent and wave-dependent 

features

Altered coastal sediment dynamics
140

Table B-4 continued. Stresses associated with the KEAs of the habitat and species and food web 

ecosystem components.

Ecosystem 

component KEA* Associated stress (altered KEA)

Estuarine and marine habitats category (continued)

Rocky 

beach 

(continued)

III-11. Tidal circulation–extent of 

dependent biological activity

Reduced tidal circulation

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

VI-18. Detritus recruitment and retention–

extent of supply

Reduced detritus recruitment and 

retention

VII-19. Habitat connectivity condition Degraded habitat connectivity

VIII-20. SAV beds–condition Altered SAV beds

VIII-21. SAV beds–extent Altered SAV beds

VIII-25. Intertidal habitat zone–extent Altered intertidal habitat

VIII-26. Intertidal habitat zone–condition Altered intertidal habitat

VIII-29. Water quality Altered water quality

Offshore 

system

III-11. Tidal circulation–extent of 

dependent biological activity

Reduced tidal circulation

III-12. Tidal circulation–dependent water 

condition

Reduced tidal circulation

IV-13. Freshwater hydrology–dependent 

water condition

Altered freshwater hydrology

VI-18. Detritus recruitment and retention–

extent of supply

Reduced detritus recruitment and 

retention

VIII-20. SAV beds–condition Altered SAV beds

VIII-21. SAV beds–extent Altered SAV beds

VIII-29. Water quality Altered water quality

Species and food webs category

Species and 

food webs

Population size–predators Increased predator abundance

Population size–competitors Increased competitor abundance

Population size–prey Decreased prey abundance

Population size–other species Increased abundance of other species

Predator population condition–predators Altered predator population condition

Competitor population condition–

competitors

Altered competitor population condition

Prey population condition–prey Decreased prey population condition

Other species population condition–other 

species

Altered population condition of other 

species

Energy and material flow Altered energy and material flow

Community composition Altered community composition

* KEA numbers for habitat ecosystem components (e.g., I-2) correspond to those in Table 8 through Table10 and 

Table 12 through Table 14. Species KEAs specify the ecological relationship to Chinook salmon.
141 

Contributing Factors

Contributing factors are the underlying, human-induced actions or events that enable or 

otherwise add to the occurrence or persistence of pressures. They are used primarily to identify 

the expected intermediate results in results chains. Table B-5 lists broad categories of 

contributing factors and some examples of how these categories may manifest in watersheds. 

The list of categories and examples is intended as a starting point for watershed groups to 

consider why pressures are problematic to Chinook salmon recovery. 

Drivers 

Drivers are similar to contributing factors in that both elements represent the conditions 

underlying the occurrence or persistence of a pressure. For the purposes of this framework, we 

distinguish between drivers and contributing factors by defining drivers as conditions that tend to 

be outside the scope of strategies and actions in the local-scale chapters of Volume II of the 

Puget Sound Salmon Recovery Plan (SSDC 2007). Therefore, most chapters do not include 

drivers (Table B-6); however, they may be incorporated into results chains to identify 

intermediate results.

Strategies 

A strategy is a set of conservation actions with a common focus. When such actions are 

combined, they result in reduction of threats, developed capacity, or restoration of natural 

systems (FOS 2009). A well-designed strategy meets several criteria, including 1) linked 

between one or more ecosystem components; 2) focused―that is, it outlines specific courses of 

action to be executed; 3) feasible― that is, it can be accomplished given existing resources and 

constraints; and 4) appropriate― that is, it is consistent with site-specific social, cultural, and 

biological norms. Table B-7 lists categories and associated definitions of strategies found in 

Volume I and Volume II of the Puget Sound Salmon Recovery Plan (SSDC 2007). 
142 

Table B-5. Broad categories and examples of contributing factors that may exist in watersheds.

Category Example

Social (expectations and 

perceptions) 

The public’s lack of long-term perspective on the issues

Lack of public and political support for habitat protection and restoration

Education materials that need to be more broadly distributed and used

Outreach programs that need to be more broadly applied

Legal (regulations/policies 

and enforcement)

Inconsistencies in and between regulations or policies

Understaffed enforcement programs

Disparate application of regulations

Lack of thorough reviews because regulators are overburdened

Lack of enforcement

Technical (information and 

alternatives)

Lack of data regarding changes over time

Lack of information sharing

Concentration of technical information in few sectors or organizations

Expense of technical experts

Monetary (capital and 

capacity)

Expense of work

Limited capacity, given the amount of work

Lack of capital funds

Institutional Reliance on historical actions and approaches

Lack of support for work

Inconsistent decision-making process

Table B-6. Broad categories and examples of drivers that may exist in watersheds.

Category Example

Climate change Changes in air temperature and precipitation

Sea level rise

Ocean acidification

Extreme weather events (e.g., storms, droughts, heat waves)

Market forces Trade balance (import/export)

State and federal budget forecasts

Human population growth Immigration to Puget Sound

Distribution of human population

Human preferences Driving patterns

Consumption patterns
143 

Table B-7. Categories of strategies common to both volumes of the Puget Sound Salmon Recovery Plan 

(SSDC 2007). Definitions are derived from various sources.

Strategy Category Definition Source

Improve and increase 

habitat protection 

Habitat 

protection 

Safeguarding existing physical habitat and 

habitat forming processes through voluntary 

approaches (incentives or technical assistance), 

regulatory mechanisms, or acquisition.

SSDC 2007 

Improve and increase 

habitat restoration

Habitat 

restoration 

Enhancing degraded or restoring lost habitat 

through on-the-ground action, sometimes 

preceded by acquisition.

FOS 2009 

Manage hatcheries to 

support wild Chinook 

salmon populations 

Hatchery 

management

Artificially producing Chinook salmon to 

harvest or rebuild natural-origin stocks without 

impeding the rebuilding of those stocks (via 

other strategies) to levels that will sustain 

fisheries, enable ecological functions, and 

support treaty-reserved fishing rights.

WDFW and 

PSTT 2004

Manage harvest to 

support recovery of 

wild Chinook salmon 

populations 

Harvest 

management

Allowing some mortality of listed Chinook 

salmon so that fisheries directed at harvestable 

runs of other species or hatchery-produced 

Chinook are possible. The overall rate of 

fishery-related mortality to listed Chinook is 

kept at or below an amount that does not 

impede the rebuilding of these stocks to levels 

that are consistent with the capacity of properly 

functioning habitat and that will sustain 

fisheries, enable ecological functions, and 

support treaty-reserved fishing rights.

PSIT and 

WDFW 2010 

Improve and increase 

assessments

Assessment Filling data gaps and improving strategies as 

new data and information are acquired. 

SSDC 2007, 

Vol. II, San 

Juan chapter

Improve and increase 

research

Research Gaining fuller scientific knowledge or 

understanding of a subject through basic or 

applied study.

NSB 2010 

Improve and increase 

education 

Education Increasing public awareness and knowledge 

about environmental issues, and providing 

the skills necessary to make informed 

environmental decisions and take responsible 

actions.

EPA 2011 

Improve and increase 

outreach

Outreach Disseminating information about an issue and, 

in some cases, requesting that specific action 

be taken, without necessarily teaching how to 

analyze the issue.

EPA 2011 
144 
145

Appendix C: Other Monitoring Projects and 

Programs

Our framework has been developed alongside other monitoring-related work underway in

the Puget Sound region. Local-scale monitoring projects and programs―too numerous to list 

here―vary depending on the needs identified within each watershed and the funding available. 

Current regional-scale monitoring projects and programs include but are not limited to:

• Salmonid Work Group, Puget Sound Ecosystem Monitoring Program (PSEMP). Led by 

Bruce Crawford, this group has completed an assessment of current monitoring of salmon

(Oncorhynchus spp.) and steelhead (O. mykiss) and is working to define elements of a 

comprehensive monitoring strategy for salmon habitat. The recently completed viable 

salmonid population (VSP) assessment examined monitoring of the VSP parameters for 

ESA-listed salmonids in the Puget Sound region (PSEMP 2012). It documented ongoing 

VSP monitoring efforts in the region, evaluated the quality of the resulting data, and 

identified key monitoring gaps (Crawford and Rumsey 2011). This assessment was 

undertaken by the National Marine Fisheries Service (NMFS) and funded by the 

Environmental Protection Agency (EPA). The proposed habitat monitoring program 

includes remote sensing, on-the-ground monitoring of habitat in streams, nearshore, and 

estuarine areas using a probabilistic design, and intensive habitat monitoring for specific 

watersheds to complement existing monitoring for salmon and steelhead.

• Intensively Monitored Watersheds Project. It evaluates salmonid responses to land 

management and habitat restoration, based on the premise that the complex relationships 

underlying those responses are best understood by concentrating monitoring efforts in a 

few locations. Monitoring sites are located in three small stream complexes that focus on 

coho salmon (O. kisutch), steelhead, and cutthroat trout (O. clarkii) monitoring and two 

larger basins that focus on Chinook salmon (O. tshawytscha) in the Skagit and 

Wenatchee rivers. The project, a joint effort of the Washington Department of Ecology, 

Washington Department of Fish and Wildlife, NMFS, EPA, Lower Elwha Klallam Tribe, 

and Weyerhaeuser Company, is funded by the Washington Salmon Recovery Funding 

Board (http://www.ecy.wa.gov/programs/eap/imw/index.html).

• Washington Department of Ecology’s Status and Trends Monitoring for Watershed 

Health and Salmon Recovery (WSHR) program. It uses a probabilistic sampling design 

to select river and stream sites for monitoring. The rotating panel design divides the state 

into eight status and trend regions with two sampled each year. The Puget Sound basin, 

first sampled in 2009, was sampled again in 2013. From each of 50 sites, samples will be 

collected for vertebrates, invertebrates, habitat, and water chemistry. WSHR supports 

standard protocols for monitoring rivers and streams, training on these protocols, the 

Washington Master Sample site set, and the STREAM database for managing stream 

habitat data (http://www.ecy.wa.gov/programs/eap/stsmf).
146

• Regional Stormwater Monitoring Program (RSMP). The PSEMP Stormwater Work 

Group will implement the RSMP with funding from western Washington municipal 

stormwater permittee contributions. Status and trend monitoring for small streams and 

nearshore areas in the Puget Sound basin will be collected using a probabilistic sampling 

design. For streams, 100 randomly selected sites will be sampled during the 4–5 years of 

the permit cycle; 50 sites will be inside Urban Growth Areas (UGAs) and 50 outside. 

Water quality, invertebrate, sediment, habitat, and streamflow data will be collected. For 

nearshore areas, fecal coliform data will be collected monthly at 50 sites in the UGAs, 

sediment chemistry every 5 years at 50 sites in UGAs (to compare with PSEMP locations 

outside UGAs), and Mussel Watch Program data at 30–50 sites near stormwater outfalls 

(to be compared with Mussel Watch Program sites away from outfalls). In addition, a 

prioritized list of recommended study topics for effectiveness monitoring is being 

developed (http://www.ecy.wa.gov/programs/wq/stormwater/municipal/rsmp.html).

• U.S. Geological Survey (USGS) National Streamflow Information Program, Cooperative 

Water Program, Groundwater Resources Program, and National Water Quality 

Assessment Program. The USGS collects, compiles, and publishes hydrologic data from 

surface water stations that measure stream discharge and stage for rivers and streams; 

elevation and storage for lakes and reservoir; groundwater levels in wells; and chemical 

and physical data for streams, lakes, springs, and wells. Most streamflow data and 

selected other data are available in real time via satellite telemetry. Monitoring data from 

all USGS programs are available through the National Water Information System. 

Konrad and Voss (2012) evaluated the streamflow-gaging network in the Puget Sound 

basin for its capacity to monitor stormwater in rivers and small streams (http://pubs.usgs

.gov/sir/2012/5020).
Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center

NOAA Technical Memorandum NMFS-NWFSC129 Hard, J.J., J.M. Myers, E.J. Connor, R.A. Hayman, R.G. Kope, G. Lucchetti, A.R. Marshall, 

G.R. Pess, and B.E. Thompson. 2015. Viability criteria for steelhead within the Puget Sound distinct 

population segment. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-129, 332 p. NTIS 

number PB2015-105188.

128 Myers, J.M., J.J. Hard, E.J. Connor, R.A. Hayman, R.G. Kope, G. Lucchetti, A.R. Marshall, 

G.R. Pess, and B.E. Thompson. 2015. Identifying historical populations of steelhead within the 

Puget Sound distinct population segment. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC128, 155 p. NTIS number PB2015-103741.

127 Roni, P., G.R. Pess, T.J. Beechie, and K.M. Hanson. 2014. Fish-habitat relationships and the 

effectiveness of habit restoration. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-127, 

154 p. NTIS number PB2014-108836.

126 Russell, S., and M.S. Ruff. 2014. The U.S. whale watching industry of Greater Puget Sound: A 

description and baseline analysis. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-126, 

171 p. NTIS number PB2014-105939.

125 Sloan, C.A., B.F. Anulacion, K.A. Baugh, J.L. Bolton, D. Boyd, R.H. Boyer, D.G. Burrows, D.P. 

Herman, R.W. Pearce, and G.M. Ylitalo. 2014. Northwest Fisheries Science Center’s analyses of 

tissue, sediment, and water samples for organic contaminants by gas chromatography/mass spectrometry 

and analyses of tissue for lipid classes by thin layer chromatography/flame ionization detection. U.S. 

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-125, 61 p. NTIS number PB2014-104055.

124 Anderson, L.E., and S.T. Lee. 2013. Washington and Oregon saltwater sportfishing surveys: 

Methodology and results. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-124, 61 p. NTIS 

number PB2014-101405.

123 Ward, E.J., M.J. Ford, R.G. Kope, J.K.B. Ford, L.A. Velez-Espino, C.K. Parken, L.W. LaVoy, 

M.B. Hanson, and K.C. Balcomb. 2013. Estimating the impacts of Chinook salmon abundance and 

prey removal by ocean fishing on Southern Resident killer whale population dynamics. U.S. Dept. 

Commer., NOAA Tech. Memo. NMFS-NWFSC-123, 71 p. NTIS number PB2013-110079.

122 Frame, E., and K. Lefebvre. 2013. ELISA methods for domoic acid quantification in multiple marine 

mammal species and sample matrices. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-122, 

20 p. NTIS number PB2013-109341.

Most NOAA Technical Memorandums NMFS-NWFSC are available at the

Northwest Fisheries Science Center Web site, http://www.nwfsc.noaa.gov