Technical Report 2006–1

COASTAL HABITATS IN 

PUGET SOUND: 

A Research Plan in Support of the 

Puget Sound Nearshore Partnership

Prepared in support of the 

Puget Sound Nearshore Partnership

November 2006

Guy Gelfenbaum, U.S. Geological Survey 

Tom Mumford, Washington State Department 

 of Natural Resources

Jim Brennan, King County Department 

 of Natural Resources

Harvey Case, U.S. Geological Survey

Megan Dethier, University of Washington

Kurt Fresh, National Marine Fisheries Service

Fred Goetz, U.S. Army Corps of Engineers

Marijke van Heeswijk, U.S. Geological Survey

Thomas M. Leschine, University of Washington

Miles Logsdon, University of Washington

Doug Myers, Puget Sound Action Team

Jan Newton, University of Washington

Hugh Shipman, Washington State 

 Department of Ecology

Charles A. Simenstad, University of Washington

Curtis Tanner, U.S. Fish and Wildlife Service

David Woodson, U.S. Geological Survey
Recommended bibliographic citation:

Gelfenbaum, G., T. Mumford, J. Brennan, H. Case, 

M. Dethier, K. Fresh, F. Goetz, M. van Heeswijk, T.M., 

Leschine, M. Logsdon, D. Myers, J. Newton, H. Shipman, 

C.A. Simenstad, C. Tanner, and D. Woodson, 2006. Coastal 

Habitats in Puget Sound: A research plan in support of the 

Puget Sound Nearshore Partnership. Puget Sound Nearshore 

Partnership Report No. 2006-1. Published by the U.S. 

Geological Survey, Seattle, Washington. Available at 

http://pugetsoundnearshore.org.

All authors are members of either the U.S. Geological Survey 

or Puget Sound Nearshore Partnership’s Nearshore Science 

Team.

Technical subject matter of 

this document was produced 

by the U.S. Geological 

Survey and the PSNERP 

Nearshore Science Team, 

who are entirely responsible 

for its contents. Publication 

services were provided by the 

U.S. Geological Survey with 

financial support from the U.S. 

Army Corps of Engineers, 

Seattle District. This document 

may be freely copied and 

distributed without charge.

Cover: Oblique aerial photograph of Skagit River delta. 

(Photograph taken by Guy Gelfenbaum, U.S. Geological 

Survey, September 5, 2003.)

Acknowledgments

We thank members of the Puget Sound Nearshore Partnership 

Steering Committee, especially Bernie Hargrave and Tim 

Smith for their support of this effort. We thank Rob Koeppen 

for coordinating the external review process, the four 

reviewers, Jim Good, Oregon State University, Corvalis, OR; 

Kimberly Taylor, U.S. Geological Survey, Sacramento, CA; 

Ron Thom, Pacific Northwest National Laboratory, Sequim, 

WA; and Lynne Trujilo, California State University, San Jose, 

CA, for their thorough reviews, and Anne Kinsinger for her 

constructive comments on any earlier draft. We appreciate 

the excellent work by Linda Rogers and the staff of the U.S. 

Geological Survey Tacoma Publishing Service Center who 

provided editing, design, and publication services for the 

document.

    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1
A Research Plan in Support of the Puget Sound Nearshore Partnership     

Contents

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

2.  Introduction .............................................................................................................................. 1

Problem Statement ..................................................................................................................... 2

Need for a Sound-Wide Nearshore Science Plan ................................................................................. 4

Purpose, Scope, and Approach ...................................................................................................... 5

Conceptual Model of Nearshore Ecosystem Processes ........................................................................... 7

3.  Description of Puget Sound ............................................................................................................ 8

Environmental Setting .................................................................................................................. 8

Nearshore Environments............................................................................................................... 10

Marine Biota ........................................................................................................................... 10

Cultural Setting ........................................................................................................................ 11

4.  Research Goals ........................................................................................................................... 12

Goal 1:  Understand Nearshore Ecosystem Processes and Linkages to Watershed and Marine Systems.................. 12

Problem Statement ............................................................................................................... 12

Existing Work ..................................................................................................................... 12

Objectives ........................................................................................................................ 12

Relevance and Impact............................................................................................................ 13

Hypotheses and Studies ......................................................................................................... 13

Goal 2:  Understand the Effects of Human Activities on Nearshore Ecosystem Processes ................................. 14

Problem Statement ............................................................................................................... 14

Existing Work ..................................................................................................................... 15

Objectives ........................................................................................................................ 15

Relevance and Impact............................................................................................................ 15

Hypotheses and Studies ......................................................................................................... 15

Goal 3:  Understand and Determine the Incremental and Cumulative Effects of Restoration and Preservation

Actions on Nearshore Ecosystems ................................................................................................ 16

Problem Statement ............................................................................................................... 16

Existing Work ..................................................................................................................... 16

Objectives ........................................................................................................................ 17

Relevance and Impact............................................................................................................ 17

Hypotheses and Studies ......................................................................................................... 17

Goal 4:  Understand the Effects of Social, Cultural, and Economic Values on Restoration and Protection of the

Nearshore ........................................................................................................................... 18

Problem Statement ............................................................................................................... 18

Existing Work ..................................................................................................................... 18

Objectives ........................................................................................................................ 18

Relevance and Impact............................................................................................................ 19

Hypotheses and Studies ......................................................................................................... 19
II    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Goal 5:  Understand the Relations of Nearshore Processes to Important Ecosystem Functions Including

Human Health and Protection of At-Risk Species .............................................................................. 21

Problem Statement ............................................................................................................... 21

Existing Work ..................................................................................................................... 21

Objectives ........................................................................................................................ 22

Relevance and Impact............................................................................................................ 22

Hypotheses and Studies ......................................................................................................... 22

Goal 6:  Understand the Roles of Information—Its Representation, Conceptualization, Organization, and

Interpretation—in Restoring Nearshore Ecosystem Processes ............................................................... 23

Problem Statement ............................................................................................................... 23

Existing Work ..................................................................................................................... 23

Objectives ........................................................................................................................ 24

Relevance and Impact............................................................................................................ 24

Hypotheses and Studies ......................................................................................................... 24

5.  Strategy for Achieving Research Goals................................................................................................ 25

6.  Implementation of Research Plan ...................................................................................................... 26

7.  References Cited ........................................................................................................................ 27

8.  Further Reading ........................................................................................................................... 33

Appendix 1.  Goals of the Puget Sound Nearshore Ecosystem Restoration Program ................................................ 36

Appendix 2.  Executive Summary of “Application of ‘Best Available Science’ in Ecosystem Restoration:

Lessons Learned from Large-Scale Restoration Efforts in the U.S.” ............................................................... 37

Appendix 3.  Research Questions for Early-Action Projects and Demonstration Projects .......................................... 38
A Research Plan in Support of the Puget Sound Nearshore Partnership     III

The purpose of this research plan is to identify high-priority 

research goals and objectives and delineate the critical 

questions and information gaps that need to be addressed to 

provide natural-resource managers and policy- and decisionmakers with tools to effectively undertake restoration planning 

and adaptive management of the nearshore ecosystems of 

Puget Sound.

Puget Sound is the second largest estuary in the United 

States, supporting abundant fish and wildlife populations 

and a vibrant economy. The Sound is home to more than 

200 species of fishes, including several native salmon species 

and 10 species of marine mammals, including orca whales. 

Major port facilities located here support billions of dollars 

of trade between the United States and the rest of the world. 

Military installations of National importance depend on the 

Sound. The overall health of the Puget Sound estuary has 

steadily decreased as human population and development has 

increased in the Puget Sound Basin. Impairment of nearshore 

processes and degradation of ecosystem functions in the 

Sound, extending along more than 2,000 miles of shoreline, 

is believed to be a critical factor in the declining nearshore 

ecosystem health of Puget Sound. However, the complex 

role of geological, biological, and hydrological processes 

in maintaining nearshore ecosystem health remains poorly 

understood.

In response to these critical issues, the Washington 

Department of Fish and Wildlife and U.S. Army Corps of 

Engineers joined with other State natural resource agencies, 

other Federal agencies, Tribes, the commercial sector, nongovernmental organizations, universities, and numerous local 

governments to form the Puget Sound Nearshore Ecosystem 

Restoration Project (PSNERP). PSNERP represents a 

science-based approach to restoring and preserving nearshore 

ecosystems of the Puget Sound and to preventing additional 

damage. There is a fundamental need for restoration projects 

at a landscape scale to achieve sustainable, long-term 

restoration of the entire system. It is critically important that 

(a) both individual nearshore restoration and preservation 

actions be coordinated regionally and prioritized on the 

basis of their expected impact on the Sound; and (b) largescale restoration programs such as envisioned by PSNERP 

must be strategically designed and located for maximum 

impact. To enable the selection of optimum management 

options, the physical and biological processes that create and 

maintain nearshore ecosystems must be well understood so 

that the regional impacts of proposed small-scale restoration 

and preservation options can be anticipated and evaluated. 

This requires that the processes be understood at multiple 

spatial and temporal scales, knowledge that is currently 

limited at any scale. Once management options have been 

1. Executive Summary

implemented, outcomes must be monitored to verify how 

well restoration and preservation projects have achieved their 

intended results and to guide adjustments as needed through 

adaptive management. This adaptive management approach 

to ecosystem rehabilitation requires a clear understanding of 

the ecological function of nearshore Puget Sound. To support 

this science-based approach and guide scientific research in 

support of nearshore ecosystem restoration in Puget Sound, 

the USGS and PSNERP Nearshore Science Team developed 

six high-priority goals: 

Goal 1—Understand nearshore ecosystem processes and 

linkages to watershed and marine systems.

Goal 2—Understand the effects of human activities on 

nearshore ecosystem processes.

Goal 3—Understand and predict the incremental and 

cumulative effects of restoration and preservation actions 

on nearshore ecosystems.

Goal 4—Understand the effects of social, cultural, 

and economic values on restoration and protection of 

nearshore ecosystems.

Goal 5—Understand the relations of nearshore processes 

to important ecosystem functions including human health 

and protection of at-risk species.

Goal 6—Understand the roles of information—its 

representation, conceptualization, organization, and 

interpretation—in restoring nearshore ecosystem 

processes.

Natural resource managers need to have reliable predictive 

tools and information about the effects of different 

management actions on the ecosystem in order to help make 

wise restoration and preservation decisions. Such tools and 

information will

• Reduce the risk of unintended consequences associated 

with uncertainty.

• Provide an assessment of the potential interactive 

effects of multiple actions at various spatial and 

temporal scales.

• Allow selection of beneficial restoration and 

preservation actions.

• Provide direction for management decisions by 

suggesting which action or combination of actions is 

most likely to meet specific objectives within specific 

limitations.
IV    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

The strategy for achieving these goals includes conducting 

both inter- and multi-disciplinary research incorporating 

such scientific disciplines as geology, hydrology, biology, 

geography, oceanography, atmospheric science, and social 

science. Elements in a research approach should include such 

commonly agreed-upon techniques as the use of conceptual 

and numerical models, reference sites, and careful scientific 

peer review, not only of the results and products, but of 

research proposals.

The overarching goal of this research plan is to help reduce 

uncertainty in decisions regarding what and how much 

to protect and restore. This goal will be accomplished 

as individual academic researchers and local entities, as 

well as State resource agencies and the Federal and Tribal 

research community understand the information needs, 

seek funding, and develop specific research plans. Multiple 

avenues of implementation should be followed, including: 

(1) prioritization of funding for Demonstration Projects and 

Early-Action Projects to learn from planned and opportunistic 

restoration activities. Federal, State, and local agencies that 

fund restoration activities should actively seek opportunities 

to monitor and study the changes that occur as a result of the 

restoration actions; (2) directing and focusing ongoing agency 

science efforts to seek opportunities to leverage internal 

funding, as in the successful Coastal Habitats in Puget Sound 

(CHIPS) science program; (3) communicating information 

needs to the academic and private research community through 

reporting at national, regional, and local scientific conferences 

and workshops such as the Georgia Basin / Puget Sound 

Research Conference; and (4) collaborating through sharing 

of existing and new data and information, coordinating the 

collection of new data and information, prioritizing research 

needs, and pooling and leveraging resources. Progress in 

restoration will accelerate only if there are opportunities to 

learn from restoration efforts that are ongoing. This requires 

adding hypothesis-based research and monitoring components 

to restoration projects while they are in the design phases. 

This will require a commitment of funding research at a 

level directly proportional with the level of restoration funds. 

Continued failure to appropriately support research and 

monitoring in association with funded restoration projects 

leaves the restoration and resource agency community short on 

informed vision and is an opportunity lost.
A Research Plan in Support of the Puget Sound Nearshore Partnership    

The beautiful and productive inland marine waters and 

shorelines of Puget Sound1 in Washington State are 

considered a National treasure. This fjord-like arm of the 

Pacific Ocean, nestled between the Olympic and Cascade 

Mountains, contains more than 8,000 square kilometers 

(2 million acres) of marine waters and nearshore 

environment, and more than 33,000 square kilometers 

(8.3 million acres) of watershed with 4,020 kilometers 

(2,500 miles) of shoreline as the interface between the 

land and water.

Roughly 4 million people, 70 percent of the Washington 

State population, live in the Puget Sound watershed, 

concentrated in the metropolitan areas of Seattle, Tacoma, 

Everett, Bellingham, and Olympia. The population is 

growing by about 50,000 people per year (1.5 percent per 

year) and is expected to reach 5.33 million before 2020 

and double by 2040 (Puget Sound Regional Council, 

2004). To visualize this, one might imagine the current 

(2005) Puget Sound watershed’s population spaced 

evenly along the shoreline; they would be only 3 feet 

apart, jostling nearly shoulder to shoulder. Under current 

projections, the 2040 population would be squeezed back 

to back.

Despite these population pressures, Puget Sound is still 

home to tremendous biological richness that includes 

more than 200 species of fish, 100 species of birds, 26 

different marine mammals, and perhaps 7,000 species 

of marine invertebrates, including the world’s largest 

octopuses and more than 70 kinds of sea stars. This 

biological richness is supported by an equally diverse 

community of primary producers, with more than 

625 species of marine algae (seaweeds), 6 species of 

seagrasses, and hundreds of species of phytoplankton. 

These resources provide goods and services of high 

economic value to the people of Washington State and 

the United States. Shellfish growing areas in Puget Sound 

contribute 70 percent of shellfish harvested in Washington 

State. Annual shellfish production in Puget Sound from 

1979 to 1993 increased from about 4.5 to 9.6 million 

pounds; wholesale value (not adjusted for inflation) 

more than quadrupled during the same period. Shellfish 

production in Puget Sound has helped make Washington 

State the second largest oyster-producing region in the country 

now worth about $50 million per year (Puget Sound Action Team, 

2004). Geoduck harvest has generated $60 million of public funds 

through auctions of harvest quotas (Washington Department of 

Natural Resources, 2004). The total revenue from commercial fish 

harvesting in Puget Sound in 1998 was more than $12 million, 

and the industry employed nearly 900 people (Puget Sound Action 

Team, 2004).

The Sound also serves as one of the most important shipping 

and transportation routes in the world (Sommers and Canzoneri, 

1996). Taken together, the Ports of Seattle and Tacoma are the 

third largest container complex in the United States. More than 

$40 billion worth of goods travel through the ports of Puget Sound 

each year leading to tens of thousands of direct and indirect jobs 

(Trade Development Alliance of Greater Seattle, 2004).

Visitor and recreation activity in Puget Sound generates $5.2 

billion in revenue and 62,000 jobs (Puget Sound Action Team, 

2004). The 4 million people living in the Puget Sound watershed 

own nearly 500,000 boats, sailboats, and other watercraft that are 

moored in more than 280 marinas (Puget Sound Action Team, 

2004).

The Puget Sound shoreline provides tremendous allure as an 

esthetic amenity. Single-family residences on waterfront property 

now occupy nearly one-quarter of Puget Sound shorelines. 

Because coastal real estate near Puget Sound is limited, land value 

has tripled in some areas in the past 10 years (John L. Scott Real 

Estate, 2004).

Unfortunately, this bounty and beauty are in jeopardy.

2. Introduction

1Puget Sound is broadly defined to include Hood Canal and 

the U.S. portions of the Strait of Juan de Fuca and Georgia 

Strait.
    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Problem Statement

The apparent beauty and richness of Puget Sound 

belie real problems. Like other U.S. coastal 

ecosystems that suffer serious problems, the decline 

of the Puget Sound and its adjoining basin has 

been described as a death from a thousand cuts 

inflicted over the past 150 years. The cumulative 

effects of such activities as over harvesting, resource 

extraction, dredging, diking, filling, discharges of 

industrial and municipal wastes, deforestation, and 

paving are all taking their toll. Evidence is growing 

of declining fish and wildlife populations, toxic 

contaminants, eutrophication, habitat-loss, exotic 

species, and altered hydrologic regimes. 

The symptoms of these problems are a reduction 

in goods and services produced in Puget Sound, 

such as listed species or reductions in forage fish. 

However, the real problem to be addressed is change 

in the ecological processes that create and maintain 

directly, they also are subject to impacts from upland and marine 

environments—impaired water quality, invasive species coming from 

offshore, and most importantly, impacts downhill and downstream 

of the watershed, such as reduced water quantity and quality, altered 

sediment transport, and disrupted landscape linkages.

These visible effects and long-term impacts have been described and 

discussed in numerous documents (Wilson and others, 1994; West, 

1997; McMurray and Bailey, 1998; Washington Department of Natural 

Resources, 1998; Washington Department of Natural Resources, 2000; 

Heinz Center for Science, Economics, and the Environment, 2002; 

Mumford, 2002; Puget Sound Water Quality Action Team, 2002a; 

Puget Sound Action Team, 2002b; Puget Sound Action Team, 2004).

Multiple fish and wildlife species—including orcas, Chinook and chum 

salmon, diving birds, rockfish, and Pacific herring—have experienced 

dramatic population declines in recent years (West, 1997; Puget Sound 

Action Team, 2002). For example, the largest stock of Pacific herring 

in Washington State (the Cherry Point stock) declined by 84 percent 

over the past decade. Surf scoters declined by more than 50 percent 

and western grebes by more than 85 percent over the past 25 years. 

Common murres and marbled murrelets also have declined more than 

50 percent during this period (Nysewander and others, 2001; Puget 

Sound Action Team, 2005).

The number of marine species listed or proposed to be listed under 

Endangered Species Act and State regulations continues to increase 

and now includes bull trout, Puget Sound Chinook salmon, summer 

chum salmon, rockfish, birds, and marine mammals such as orca 

(National Oceanic and Atmospheric Administration Fisheries, 2004; 

Northwest Salmon Recovery Planning, 2004; Washington Department 

of Fish and Wildlife, 2004b).

2Puget Sound nearshore ecosystems encompass the 

bluffs, beaches, tide flats, estuaries, rocky shores, 

lagoons, salt marshes, and other shoreline features 

and shallow water habitats of the marine and estuarine 

areas of Washington State east of Cape Flattery and 

north to the Canadian border.

Figure 1. Conceptual model of relation of process, structure, habitat, biological 

resources, and good and services.

Processes

Structure

Habitats

Functions

STRESSORS

GOODS

AND

SERVICES

Biological

Resources

Stop / increase / change

Change

Harvest / Cultivate

Behavior

Dredge / pave

PSNRPfig01

habitats, which in turn produce the ecosystem 

resources that are so highly valued (fig. 1).

Direct loss of the historical nearshore ecosystems 

has been profound. It is estimated that 73 percent 

of the original salt marshes of the Sound have been 

destroyed, as have virtually all river delta marshes in 

urbanized areas. More than 800 of the 2,500 miles 

(33 percent) of shoreline have been modified in the 

Puget Sound region (Puget Sound Action Team, 

2002a, Puget Sound Update 2002: p. 27. Figure 2-13 

Shoreline Modifications and Table 2-2 Shoreline 

Modifications by county). The percentage of 

armored shoreline more than doubled in Totten Inlet 

and more than tripled in Nisqually Reach between 

1977 and 1993 (Morrison and others, 1994). There 

has been a nearly complete loss of eelgrass habitat 

in Westcott Bay and several other small embayments 

(Mumford and others, 2003; Wyllie-Echeverria and 

others, 2003).

The cumulative effects of these multiple humaninduced stressors is overwhelming the ability of 

naturally occurring ecosystem processes to maintain 

structures, biological resources, and ultimately the 

goods and services provided by the ecosystem. 

Although nearshore2 ecosystems have been affected 
A Research Plan in Support of the Puget Sound Nearshore Partnership     

The number and diversity of the species in decline in Puget 

Sound suggest systemic rather than isolated problems. 

Because nine of the ten Puget Sound species identified as 

endangered or threatened rely on nearshore environments, 

the declines are, at least in part, likely related to problems in 

nearshore ecosystems of Puget Sound. Although some of these 

declines are the result of over-harvesting, loss of habitat and 

degradation of water quality likely are the results of disruption 

of ecosystem processes supporting those habitats.

Other warning signals include the chemical contamination 

of marine food chains (Determan, 1999a; Schmidt and 

Johnson, 2001; Ross, 2003). Although overall discharge of 

toxic chemicals appears to be declining (Washington State 

Department of Ecology, 2004), persistent chemicals and fecal 

contamination continue to affect the ecosystem, especially in 

the higher portions of the food web in such animals as orcas 

(Wiles, 2004), salmon, and geoducks (Washington Department 

of Natural Resources, 2004). Some constituents, such as 

ambient concentrations of Polycyclic Aromatic Hydrocarbons 

(PAHs) in Puget Sound waters are equal to or greater than 

concentrations shown to be detrimental to fish eggs and 

embryogenesis (Carls and others, 1999; Heintz and others, 

1999).

Early signs of eutrophication are becoming more evident 

(Briker and others, 1999). There is an increase in the 

occurrence of green tides (Valiela and others, 1997; 

Frankenstein, 2000). The frequency and distribution of 

harmful algal blooms causing shellfish closures from paralytic 

shellfish poison (PSP) and domoic acid are increasing 

(Determan, 1999b). Hood Canal, a historically fragile area, has 

been plagued by an increase in hypoxia (Newton, 2004; Puget 

Sound Action Team, 2004; Washington State Department of 

Ecology, 2004). This is viewed as a sign of eutrophication, 

or over-enrichment of inorganic nitrogen (Thom and others, 

1988).

Another alarming trend is an increased threat of alien and 

invasive plant and animal species such as four species of 

Spartina (cordgrass), Sargassum, green crab, and dozens 

of poorly understood invertebrate species (Cohen and 

others, 1998; Cohen and others, 2001). Such species can 

cause extensive ecological damage and economic costs by 

depressing or eliminating valuable native species or requiring 

expensive measures to limit the species or its impact. The 

invasive tunicate, Didemnum lahillei, was discovered in Puget 

Sound in late 2004 and is causing alarm among biologists 

and the public. This tunicate forms dense mats over firm 

substrates, overgrowing sea scallops and mussels, and 

probably affecting numerous other species (http://www.nefsc.

noaa.gov/press_release/2004/news04.19.htm). 

Poorly documented but thought to be of great importance 

are the alterations to the hydrology of rivers, streams, and 

ground-water flow into Puget Sound (Staubitz and others, 

1997; Washington Department of Natural Resources, 1998). 

Little is known of inputs of nutrients and toxics by aerial 

deposition to the aquatic environment, and especially to the 

sea surface microlayer (Hardy and others, 1987a; Hardy and 

others, 1987b; Gardiner, 1992; Hardy, 1997).

Climate change will have profound effects in the future on the 

Puget Sound ecosystem (Mote and others, 1999; Whitfield 

and others, 2003). These include changes in the timing and 

quantity of freshwater inputs, changes in ocean circulation 

affecting upwelling, and sea-level change. The compounding 

affect that future climate change will have on Puget Sound 

ecosystems is largely unknown.

The presence of these multiple stressors are believed to 

be early signs of a system in serious decline. Many of the 

symptoms of declining ecosystem health described here 

were noted in other major estuarine environments such as 

Massachusetts (Valiela and others, 1997), Chesapeake Bay 

(The Chesapeake Bay Program, 2001; Boesch and Greer, 

2003), and the Baltic Sea (Gren and others, 2000). These 

symptoms became more widespread over time and were in fact 

early indicators of later, system-wide collapses.

Several nationally conducted review efforts, including the 

Heinz Center for Science, Economics, and the Environment 

(2002), the Pew Oceans Commission (2003), the U.S. 

Commission on Ocean Policy (2004), the Millennium 

Ecosystem Assessment (2005), and have come to a similar 

conclusion, “...America’s oceans are in crisis and the stakes 

could not be higher.” “Unfortunately, our use and enjoyment 

of the ocean and its resources have come with costs, and we 

are only now discovering the full extent of the consequences 

of our actions” (U.S. Commission on Ocean Policy, 2004). 

And the root cause is clear: “Our failure to properly manage 

the human activities that affect the Nation’s oceans, coasts, 

and Great Lakes is compromising their ecological integrity, 

diminishing our ability to fully realize their potential, costing 

us jobs and revenue, threatening human health, and putting our 

future at risk” (U.S. Commission on Ocean Policy, 2004).

Around Puget Sound, many scientists, as well as Federal and 

State resource agencies, fear the path the Sound is taking is 

similar to that observed in these other coastal settings. The 

nearshore region in particular is both ecologically sensitive 

and the region where many of the human impacts take place 

or are manifested. For example, docks and piers, dredging 

and filling, shoreline protection structures, waterfront 

development, stormwater outfalls, and beach harvesting are 

all located in the nearshore. As the interface between the 
    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

terrestrial and the marine, the nearshore concentrates much of 

what people value in the Sound, including the beaches, views, 

and entryway to boating and fishing. In addition, the impacts 

in this region are felt throughout the marine ecosystem. Direct 

removal of intertidal habitat, modification of valuable forage 

fish spawning grounds, and contamination of nearshore waters 

and sediments have both a direct and indirect effect on the 

larger Sound ecosystem.

This research plan is based on the premise that these many 

indicators of ecosystem stress are related to an underlying 

cause: disruption or elimination of the natural processes 

that control the delivery and distribution of sediment, water, 

energy, organic matter, nutrients, and other chemicals in Puget 

Sound’s nearshore environments. Because these nearshore 

processes are essential to the proper functioning of the Puget 

Sound ecosystem, restoring them is considered of highest 

priority.

Need for a Sound-Wide Nearshore Science

Plan

In response to these past and ongoing stresses on nearshore 

Puget Sound, the U.S. Army Corps of Engineers has 

joined State natural resource agencies, other Federal 

agencies, Tribes, the commercial sector, non-governmental 

organizations, universities, and numerous local governments 

to form the Puget Sound Nearshore Ecosystem Restoration 

Project (PSNERP). The PSNERP partnership is working to 

restore and preserve nearshore ecosystems to help rehabilitate 

the ecosystem health of Puget Sound and prevent additional 

damage in the future as the human population in the basin 

continues to increase (Appendix 1 describes PSNERP in 

greater detail). 

At the direction of the PSNERP Executive Committee, the 

PSNERP Nearshore Science Team was asked to produce a 

Strategic Science Plan. This research plan is one component of 

an overall science strategy supporting ecosystem restoration in 

Puget Sound. Other components include a peer-review plan, a 

monitoring plan, an information management plan, scientific 

workshops, and an outreach plan (fig. 2). Together, these 

components form the foundation of a science-based restoration 

plan that can help insure use of best-available science, broad 

communication, and adaptive management strategies that will 

lead to long-term success of the restoration activities.

Estuarine restoration projects are being undertaken in Puget 

Sound by various agencies and partners. A limited number of 

projects have been completed and still others are in planning 

stages. Examples of current projects include reconnection or 

improved connection of coastal wetlands to tidal influence 

through the removal of dikes or culverts in Skagit, Nisqually, 

Skokomish estuaries, and Hood Canal. Examples of completed 

projects include rehabilitation of tidal marshland in limited 

areas along the lower Duwamish River and at Deepwater 

Slough at the mouth of the South Fork of the Skagit River. 

Projects under consideration include restoration of tidal 

marshlands at the mouths of the Nisqually, Skagit, and other 

rivers. These projects generally are small (fewer than about 

300 acres) and planned and implemented as independent, local 

Figure 2. Relation of research plan described in this report to the Strategic Science Plan for PSNERP.

A Science Plan for PSNERP

Science Plan

Science

Workshops

GOAL 1:

Understand

nearshore

processes

GOAL 2:

Understand

effects of

human

activities

GOAL 3:

Understand

effects of

restoration

GOAL 4:

Understand

effects of

social

values

GOAL 5:

Understand

effects of

processes

on VECs

GOAL 6:

Understand

effects of

representation

of information

Monitoring

Plan

Research

Plan

Outreach

Plan

Peer-Review

Plan

Information

Management Plan
A Research Plan in Support of the Puget Sound Nearshore Partnership     

efforts. Although these smaller projects may have achieved 

important results at the local scale, there has been little 

consideration of how multiple small-scale efforts may affect 

each other or how they may cumulatively affect the restoration 

of the greater Puget Sound ecosystem.

There is, in addition, a critical need for restoration projects at 

a landscape scale to achieve sustainable, long-term restoration 

of the entire system. It is critical that (a) both individual 

nearshore restoration and preservation actions be coordinated 

regionally and prioritized on the basis of their expected impact 

on the Sound, and (b) large-scale restoration programs such as 

envisioned by PSNERP be strategically designed and located. 

To enable the selection of optimum management options, the 

processes that create and maintain nearshore ecosystems must 

be understood so that the regional impacts of proposed smallscale restoration and preservation options can be anticipated 

and evaluated. This requires that the processes be understood 

at multiple spatial and temporal scales, and this knowledge 

is currently limited at any scale. Once management options 

have been implemented, outcomes must be monitored to 

verify that restoration and preservation projects have achieved 

their intended results and can be adjusted as needed through 

adaptive management.

Many different agencies over the years have collected and 

analyzed monitoring data and scientific information for 

different aspects of the Puget Sound ecosystem, including 

nearshore habitat. To date, however, this information has not 

been integrated to develop a comprehensive understanding 

of nearshore ecosystems, including the natural and human 

factors that have changed conditions over time. Gaps in 

critical information must be identified to be able to anticipate 

ecosystem responses to different options for nearshore 

ecosystem restoration and preservation. 

Successful restoration and preservation of the Puget Sound 

nearshore involves a long-term societal commitment that 

requires substantial resources. Natural resource managers need 

to have reliable predictive tools and information about the 

effects of different management actions on the ecosystem in 

order to help make restoration and preservation decisions.

 Such tools and information will

• Reduce the risk of unintended consequences associated 

with uncertainty.

• Provide an assessment of the potential interactive effects 

of multiple actions at various spatial and temporal scales.

• Allow selection of beneficial restoration and preservation 

actions.

• Provide direction for management decisions by suggesting 

which action or combination of actions is most likely to 

meet specific objectives within specific limitations.

Purpose, Scope, and Approach

The purpose of this research plan is to identify high-priority 

research goals and objectives and important questions 

and information gaps that need to be addressed to assist 

natural-resource managers and policy and decision makers 

with restoration planning and adaptive management of 

nearshore ecosystems of Puget Sound. This plan relies heavily 

on the data and information gaps reports recently published 

by the Northwest Straits Commission (1999; 2000) and by 

King County Department of Natural Resources (2001). This 

plan identifies six overall goals, and strategies for achieving 

those goals through the collaboration of multiple partners. 

The research plan provides a prioritization for posing detailed 

and coordinated research questions by multiple agencies 

and organizations with the common goal of developing 

the scientific information and tools that support adaptive 

management of the Puget Sound nearshore (see table 1). 

The research goals, objectives, and hypotheses are presented 

in detail in Section 4. These objectives and hypotheses are 

formulated to support critical information needs through 

scientific studies. In addition, the research plan includes 

the development of research questions that could best be 

answered through detailed studies of nearshore ecosystem 

restoration projects. Appendix 3 lists important questions 

that could best be addressed through monitoring and analysis 

of Demonstration Projects and Early-Action Projects. 

Demonstration Projects are those restoration projects designed 

specifically to address important information needs that will 

ultimately help to decrease uncertainty in future restoration 

decisions. Early-Action Projects are those restoration projects 

designed primarily for restoration that also will serve to 

address major information needs.

The research questions identified in this plan focus on 

understanding the processes that create and maintain nearshore 

ecosystems and the natural and human factors that affect those 

processes. Current knowledge and understanding of nearshore 

ecosystem processes is limited, and the lack of understanding 

of the processes prevents natural-resource managers and 

policy and decision makers from effectively managing coastal 

ecosystems. 

The answers to questions identified in the research plan will 

explain observed ecosystem conditions by relating those 

conditions to natural and human factors, by defining the 

causes of spatial and temporal variations, and by predicting 

the effects of proposed nearshore restoration and preservation. 

Improved scientific information will assist decision makers 

in their efforts to balance the protection and restoration of 

the Puget Sound nearshore ecosystem with future sustainable 

development.
    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Research goal Examples of information needs

1. Understand nearshore ecosystem 

processes and linkages to 

watershed and marine systems

• Variability, rate, distribution, and quality of river and stream discharge to the nearshore, including sediment 

discharge

• Frequency, volume, and type of non-riverine sediment input to nearshore beaches

• Temporal and spatial variability of nearshore sediment erosion, transport, and deposition

• Rate, distribution, and quality of ground-water discharge to the nearshore

• Frequency, intensity, and type of nearshore disturbances resulting from storms and other episodic events 

(freshwater discharge, sediment and detritus sources and transport, plant and animal distributions)

• Spatial and temporal distributions of nearshore plants and animals, including the different stages of the life 

cycles of species

• Spatial and temporal variability of foodweb characteristics in the nearshore

• Spatial and temporal variability of marine waters from deep to shallow water, including temperature, salinity, 

turbidity, nutrients, other

• Causes of variability in foodweb characteristics, species distributions, physical, chemical, and other 

biological variables

• Linkages between physical, chemical, and biological processes in the nearshore

• Linkages between nearshore biological diversity and abundance and those factors elsewhere in the Puget 

Sound estuary and watersheds

2. Understand the effects of human 

activities on nearshore ecosystem 

processes

• Distribution of exotic species in Puget Sound

• Changes in the diversity and abundance of native species in response to the presence of exotic species

• Effects of individual and cumulative ecosystem stressors, both naturally occurring stressors and those 

resulting from human activities, including harvest, development, other

• Effects of land use on freshwater inputs to the nearshore, including contaminants, pathogens, nutrients, and 

sediments

• Effects of shoreline modifications and other development on beaches and nearshore substrates

• Effects of climate and sea-level change

• Distribution and fate of persistent contaminants in the nearshore foodweb

3. Understand and predict the 

incremental and cumulative effects 

of restoration and preservation 

actions on nearshore ecosystems

• Spatial and temporal scales at which effects of nearshore restoration can be measured 

• Nearshore physical, chemical, and biological effects of sample restoration projects, including dike breaching, 

dam removal, estuarine wetland restoration, other

• Short- and long-term ecological effects of restoration and preservation actions

4. Understand the effects of social, 

cultural, and economic values on 

restoration and protection of the 

nearshore

• Societal values associated with different aspects of the nearshore, including recreation, harvest, cultural 

significance, tourism, development, land use, other, and trends in those values

• Attitudes, perceptions and beliefs regarding restoration, and cost-benefit relationships of different restoration 

and preservation options, expressed in socially relevant terms

• Demographic patterns of use of shorezones, projected trends, and how they affect and are affected by 

restoration

• Governance and institutions for restoration

5. Understand the relationships of 

nearshore processes to important 

ecosystem functions such as

support of human health and 

at-risk species

• Cycling and accumulation of contaminants in the nearshore foodweb, of which humans and at-risk species 

are components

• Factors that alter parts of the foodweb relied on by at-risk species, such as orca whales, salmon, other

• Effects of restoration actions on nearshore foodweb characteristics

6. Understand the roles of 

information —its representation, 

conceptualization, organization, 

and interpretation—related to 

nearshore ecosystem processes on 

the preservation and restoration 

potential of Puget Sound

• Most effective methods to educate the public so it can engage in informed nearshore restoration 

decision-making

• Needs for information and tools that allow resource managers to analyze the costs and ecological impacts of 

different nearshore restoration and preservation options

• Most effective methods for storing and processing new and existing nearshore data and information for use 

by the public, decision-makers, and scientists

Table 1. Information needs for research goals.
A Research Plan in Support of the Puget Sound Nearshore Partnership     

Conceptual Model of Nearshore Ecosystem

Processes

A cornerstone to the development of this research plan is a 

conceptual model that describes key drivers in ecosystem 

change, and the inter-relationships among those drivers. 

Process-based nearshore restoration relies on a sound 

conceptual understanding of the complex interactions of 

multiple physical, chemical, and biological processes. 

This conceptual model of nearshore ecosystem processes 

developed by Puget Sound Nearshore Ecosystem Restoration 

Project (fig. 3) is one useful tool to help describe “how 

Puget Sound works” (PSNERP-NST Conceptual Model 

Working Group, 2004). One purpose of the model is to 

guide understanding of how ecosystem processes respond to 

specific stressors within and across the nearshore. Examples 

of such stressors are shoreline armoring, introduction of 

exotic species, and excess nutrient loading. Another purpose 

of the model is to help identify gaps in the understanding of 

critical processes, as well as interactions among processes. 

In some cases, specific processes or interactions are well 

known; in many other cases, little is known about what may 

be important processes. Successful restoration of coastal 

ecosystems depends on identifying and understanding these 

critical processes, the effects of these processes on a healthy 

functioning ecosystem, and the effects that human activities 

have on these processes.

Figure 3. Conceptual model of nearshore ecosystem processes developed by Puget Sound Nearshore Ecosystem Restoration Project 

(PSNERP) to support strategic restoration planning (from Simenstad et al. 2006). (O.M., organic matter.)

PSNERP Conceptual Model - Level 2.0

WATERSHED

(FORCING, INPUTS)

NEARSHORE

PUGET

SOUND

ATMOSPHERE

(FORCING, INPUTS)

OFFSHORE

UPLAND

LATERAL

(WITHIN NEARSHORE)

H2O

Animals

Sediments

Chemistry

Sediments

Chemistry

O.M.

Biota

Biota

Sediments

Chemistry

Shade

H2O

O2

O.M.

Nutrients

Evaporation

Nutrients

O2

O.M.

Nutrients

Heat

Wind Chemistry

Sediment

Biota

O2

E.T.

Particles

Heat

Sediments

Chemistry

Biota

Particles

H2O

Heat

Wind

Currents, Turbulance

Chemistry

Biota

AIR

BIOLOGY

WATER SEDIMENT
    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

3. Description of Puget Sound

Environmental Setting

The Puget Sound estuary is a glacial fjord 

(fig. 4) covering 7,250 square kilometers 

(2,800 square miles within a watershed of 

44,000 square kilometers (17,000 square 

miles). The Puget Sound estuary is connected 

and interdependent with Canadian waters and 

watersheds of the Strait of Juan de Fuca and the 

Strait of Georgia to the north. 

The region has a temperate maritime climate 

with average annual precipitation ranging from 

about 100 centimeters per year [cm/yr] [40 

inches per year (in/yr)] in the Puget Lowland 

to about 230 cm/yr (90 in/yr) in the mountains 

(Staubitz and others, 1997). 

from the deep fjord to the gently rolling elevated terrain of the 

Puget Sound Lowland. The lowlands are dissected by a system 

of rivers and coastal streams that supply freshwater, nutrients, 

and sediments to Puget Sound. Additional freshwater is 

supplied by diffuse ground-water discharge. Since sea level 

began to stabilize after the last glacial period, rivers and 

streams have built deltas, estuaries, and marshlands at their 

mouths. The coastal geomorphology continually evolves 

through landslide failures of coastal bluffs and longshore 

transport of sediments driven by wave action. This process 

combined with the irregular shorelines of Puget Sound leads to 

the segregation of beaches into many discrete littoral cells that 

each define a beach-sediment system with distinct sediment 

sources and sinks (Downing, 1983; Schwartz and others, 1989; 

Finlayson and Shipman, 2003).

Although some of these landscape-scale processes are 

gradual, the Puget Sound also is shaped by naturally 

occurring catastrophic events. For example, selected river 

deltas expanded rapidly following volcanic eruptions in the 

Cascade Range (Collins and others, 2003) and portions of 

the shoreline have been dramatically uplifted or submerged 

during earthquakes (Haugerud and others, 2003). River deltas, 

salt-marshes and estuaries also are shaped by large floods, and 

beaches and spits are altered and formed by severe storms. 

Nearshore ecosystems have evolved in response to these 

natural events and, in many cases, are maintained by them 

(King County Department of Natural Resources, 2001).

Puget Sound waters generally are cold, nutrient-rich, and 

support abundant marine life. Surface waters range in 

temperature seasonally from 7oC (45oF) to 13oC (55oF) 

and have an average salinity of 27 psu (practical salinity 

units). Deep waters are about 6oC (43oF) throughout the 

year and have an average salinity of 30 psu (Puget Sound 

Water Quality Authority, 1988), which approaches salinities 

of oceanic waters. The tidal range increases from about 2.5 

to 4.5 meters (8 to 15 feet) from northern to southern Puget 

(Gustafson and others, 2000).

Puget Sound was formed by glaciers that carved previously 

deposited glacial and interglacial sediments during the 

last glacial period about 10,000 to 14,000 years ago. This 

process created deep and narrow channels divided by islands 

and peninsulas that can be subdivided into several distinct 

oceanographic basins on the basis of water depths and 

circulation characteristics (fig. 1). As is typical for fjords, 

water depths in the Puget Sound increase rapidly from shore, 

with an average depth of 62 meters (205 feet) (Staubitz and 

others, 1997), and a maximum depth of about 370 meters 

(1,200 feet) (Burns, 1985; Puget Sound Water Quality 

Authority, 1987).

The glacial carving that shaped the deep channels of Puget 

Sound also helped shape the steep coastal bluffs, beaches, 

and relatively narrow, shallow marine terraces that form the 

terrestrial-marine interface of Puget Sound, transitioning 
A Research Plan in Support of the Puget Sound Nearshore Partnership     

Figure 4. Physiographic map of Puget Sound, with drainage basin and major oceanographic subbasins delineated.

Port 

Angeles

Everett

Bellingham

Victoria

Vancouver

Neah Bay

Olympia

Tacoma

Seattle

Anacortes

British Columbia 

Vancouver Island

Washington

OLYMPIC

MOUNTAINS

RANGE

CASCADE

San Juan

Islands

Cape

Flattery

Bremerton

Strait of Georgia

Strait of Juan de Fuca

Skagit River 

River 

Elwha 

River 

Fraser 

Hood Canal 

Skokomish

River 

SOUND PUGET

Duwamish

River

Cedar River

Green

River

White River

Nisqually River

Puyallup

River

Samish

River

Hoko 

River 

Dungeness River

Dosewallips River

Duckabush River

Hamma Hamma

River

Stillaguamish

River

Nooksack River

Snohomish R.

Skykomish River

Snoqualmie River

Deschutes River

North Fork

South Fork

Figure Location

WASHINGTON STATE

CANADA

UNITED STATES

EXPLANATION

MARINE SUBBASINS 

Strait

Whidbey Basin 

Central Puget Sound 

South Puget Sound 

Hood Canal 

Puget Sound watershed 

 boundary 

PSNERP base map from U.S. Geological 

Survey digital data 1:2,000,000, 1972 

Albers Equal-Area Conic Projection 

Standard parallels 47° and 49°, central meridian 122°

Washington shaded relief, USGS, 30 meter DEM 

British Columbia shaded relief, NASA, SRTM 90 meter

47°

124° 123° 122° 121°

48°

49°

0 25 50 75 MILES 

0 25 50 75 100 KILOMETERS 
10    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Nearshore Environments

Puget Sound contains a diverse assemblage of nearshore 

environments, each formed and maintained by a characteristic 

suite of geomorphic processes, and each associated with 

distinct aquatic and riparian ecosystems. Puget Sound’s vast 

shoreline of beaches and narrow marine terraces generate 

much of its intertidal and shallow subtidal ecosystems. 

The most common shoreline type consists of mixed 

sand and gravel beaches backed by high coastal bluffs. 

Rocky-bottom habitat is less common than soft-bottom 

habitat and is largely confined to northern Puget Sound. 

Other shoreline environments include large river deltas, tidal 

flats, salt-marshes, and estuaries (King County Department 

of Natural Resources, 2001). In addition to geomorphic 

and substrate characteristics, nearshore environments also 

are characterized by wave energy, water quality, aquatic 

vegetation, and faunal structure.

The nearshore environments of Puget Sound are maintained by 

a complex interplay of biological, geological, and hydrological 

processes that interact across the terrestrial-marine interface. 

Many of these processes have been significantly impacted by 

human activities, and nearshore habitats have been altered and 

lost since the start of industrial and agricultural development 

in the late 1800s (Bortleson and others, 1980). Dikes built to 

create farmland and reduce flooding have altered nearshore 

sedimentation patterns and eliminated the tidal influence that 

forms salt-marshes; dams built to manage water supplies and 

generate power have reduced the magnitude and frequency 

of floods and limited sediment inputs that sustain river 

deltas; and seawalls and bulkheads built to protect shoreline 

properties have reduced sediment supplies that feed beaches 

from naturally eroding bluffs. Examples of other changes in 

nearshore environments resulting from development include 

the elimination of small estuaries to create developable land, 

degradation of sediment quality due to the discharge of 

pollutants, generation of dangerously low oxygen levels from 

algal blooms fed by excess nutrient input, and modification 

of the structure of biological communities resulting from 

harvesting aquatic plants and animals and introducing exotic 

species. Successful restoration of coastal ecosystems depends 

on identifying, understanding, and restoring the nearshore 

ecosystem processes where possible.

Marine Biota

Puget Sound supports diverse communities of marine 

plant and animal species, ranging from phytoplankton and 

zooplankton to marine mammals (Simensted and others, 

1979).

The marine vegetation of Puget Sound includes many species 

of seaweed and seagrasses critical in providing food, shelter, 

and rearing habitat for numerous aquatic animals. Some 

of the more important plants include species of kelp (bull 

kelp, Nereocystis luetkeana, and giant kelp, Macrocystis 

integrifolia), surfgrass (Phyllospadix spp.) and native eelgrass 

(Zostera marina). Non-indigenous vegetation (Zostera 

japonica, Sargassum muticum, and Spartina spp.) is suspected 

of displacing native vegetation (Washington Sea Grant 

Program, 2000). Shoreline modifications, such as bulkheading, 

diking, and dredging and filling, also have adverse affects on 

native aquatic vegetation (Center for Marine Conservation, 

1998).

Assemblages of benthic invertebrates vary seasonally and 

annually throughout the Sound (Gustafson and others, 2000). 

These include polychaetes (worms), echinoderms (sand 

dollars, sea stars), mollusks (clams, snails), and crustaceans 

(crab, shrimp). Of these invertebrates, several are harvested 

commercially, such as Dungeness crab (Cancer magister), 

native littleneck clam (Protothaca staminea), Pacific geoduck 

(Panopea abrupta) and others, including non-indigenous 

species such as Pacific oyster (Crassostrea gigas) and Manila 

or Japanese littleneck clam (Venerupis philippinarum) 

(Washington Department of Fish and Wildlife, 2004a). 

More than 200 species of fish have been identified in Puget 

Sound (Palsson and others, 1997). These include resident 

species of demersal and pelagic fish that use Puget Sound 

habitats during a portion of their life cycle (Miller and 

Borton, 1980a; 1980b; 1980c). The most common of these 

are Chinook (Oncorhynchus tshawytscha), Coho (O. kisutch), 

chum (O. keta), pink (O. gorbuscha), and sockeye salmon 

(O. nerka), anadromous steelhead (O. mykiss), and cutthroat 

trout (O. clarki clarki) (Miller and Borton, 1980a; 1980b; 

1980c). Commercial marine fish species include Pacific hake 

(Merluccius productus), Pacific cod (Gadus macrocephalus), 

walleye pollock (Theragra chalcogramma), Pacific herring 

(Clupea harengus pallasi), spiny dogfish (Squalus acanthias), 

lingcod (Ophiodon elongatus), English sole (Pleuronectes 

vetulus) and various rockfish species (Sebastes spp.) (Miller 

and Borton, 1980a; 1980b; 1980c).
A Research Plan in Support of the Puget Sound Nearshore Partnership     11

Many marine birds depend on Puget Sound, the most common 

of which are rhinoceros auklet (Cerorhinca monocerata), 

glaucous-winged gull (Larus glaucescens), pigeon guillemot 

(Cepphus columba), cormorants (Phalacrocorax spp.), 

marbled murrelet (Brachyramphus marmoratus), and brant 

(Branta bernicla). 

In order of abundance, the most common species of marine 

mammals that live in Puget Sound year-round or migrate 

through the Sound for part of the year are harbor seal (Phoca 

vitulina), California sea lion (Zalophus californianus), 

Steller sea lion (Eumetopias jubatus), Northern elephant 

seal (Mirounga angustirostris), harbor porpoise (Phocoena 

phocoena), Dall’s porpoise (Phocoenoides dalli), orca 

(Orcinus orca), gray whale (Eschrichtius robustus), and minke 

whale (Balaenoptera acutorostrata) (Gustafson and others, 

2000).

Multiple fish and wildlife populations—including orcas, 

salmon, diving birds, rockfish, and Pacific herring— have 

experienced dramatic declines in recent years (West, 1997; 

Puget Sound Action Team, 2002). Marine species listed or 

proposed to be listed under Endangered Species Act and State 

regulations continues to increase. Bull trout, Chinook salmon, 

and Hood Canal summer chum salmon are currently listed 

as threatened under the Endangered Species Act. Several 

rockfish species, diving bird species, and orca whales also 

are depleted to the point where either State or Federal listing 

is being considered (National Oceanic and Atmospheric 

Administration Fisheries, 2004; Northwest Salmon Recovery 

Planning, 2004; Washington Department of Fish and Wildlife, 

2004b).

The diversity of the species in decline in Puget Sound suggests 

systemic rather than isolated problems. Because many of 

these declining species rely on nearshore environments, the 

declines are, at least in part, likely related to problems in 

nearshore ecosystems of Puget Sound. Although some of 

these declines are the result of overharvesting—direct losses 

through poor management—these declines also can be viewed 

as symptoms of underlying causes: loss of habitat, degradation 

of water quality, and in turn, from the disruption of ecosystem 

processes supporting those habitats. 

Human activities and development patterns have harmed, 

and continue to threaten, nearshore ecosystems by disrupting 

or eliminating the processes that control the delivery and 

distribution of sediment, water, energy, organic matter, 

nutrients, and other chemicals in Puget Sound’s nearshore 

environments. Exotic species that have been introduced have 

displaced native species and this phenomenon is likely to get 

worse in the future. 

Cultural Setting

Prior to permanent settlement by non-Native Americans in the 

mid-1800s, the Puget Sound Lowland was inhabited by Native 

Americans, who lived in small communities along rivers and 

saltwater shores. The population probably was about 10,000 

to 20,000 people (Washington State University, 2004), who 

lived on marine and terrestrial plants and animals harvested in 

the lowlands. In 1853, when the Territory of Washington was 

established, there were fewer than 5,000 settlers in the Puget 

Sound Lowland (Vaccaro and others, 1998). The lowlands 

population rapidly expanded to about 350,000 people by 1890, 

800,000 by 1960, and almost 4 million by 2000. By 2020, the 

population is expected to exceed 5 million (Transboundary 

Georgia Basin-Puget Sound Environmental Indicators 

Working Group, 2002). The rapid increase in population has 

been accompanied by extensive urbanization, agricultural 

development, and natural-resource extraction that have 

dramatically altered the pre-settlement landscape, much of it 

highly concentrated along Puget Sound’s shorelines. 

By the 2nd half of the 19th century, the effects of development 

on ecosystems were readily recognized. Congress established 

the National Fish Hatchery System in 1871 to produce fish 

for domestic consumption to replace declining native fish 

populations. In 1895, Washington State installed its first fish 

hatchery in southwest Washington to compensate for land-use 

changes that altered fish habitat (Washington Department of 

Fish and Wildlife, 2004c). At present, an extensive system of 

Tribal, State, and Federal fish hatcheries is operated in Puget 

Sound. With the passing of the Endangered Species Act in 

1973, the purpose of salmon and steelhead fish hatcheries 

in the Sound and elsewhere evolved to not only support 

sustainable harvest opportunities but also help recover and 

conserve naturally spawning fish populations (modified 

from Washington Department of Fish and Wildlife, 2000; 

2004c; and 2004d, U.S. Fish and Wildlife Service, 2004). 

There is no similar Federal or State-initiated cooperative 

management process for protecting and restoring coastal 

ecosystems. Nonetheless, many organizations and agencies 

are actively engaged in nearshore restoration and preservation 

efforts because they recognize the importance of doing so. 

In Puget Sound, these efforts generally are small-scale and 

not coordinated amongst each other. Scientific information 

on which to base restoration plans is limited, and followup monitoring to ascertain whether restoration efforts have 

their intended effects usually does not occur. For nearshore 

ecosystems to be restored and preserved so they will be selfsustaining without costly interventions in the future as the 

population and development in the Puget Sound Lowland 

continue to increase, it is critical that these efforts restore and 

preserve natural ecosystem processes and not solely ecosystem 

structure or function.
12    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

4. Research Goals

Problem Statement

Nearshore ecosystems functions that provide 

ecological and other “goods and services” 

ultimately depend on the interaction among 

physical, chemical, and biological processes that 

sustain desirable nearshore structure, attributes, 

and communities. These processes dictate 

the mode and strength of interactions among 

nearshore ecosystems and watershed, marine, 

and atmospheric systems. However, at present, 

our scientific understanding of these processes 

is insufficient to determine mechanisms of 

nearshore degradation or the likelihood of 

ecosystem restoration, particularly when 

multiple stressors are involved. 

and are much less understood categorically or mechanistically. 

Limited studies are being conducted on the faunal structure of 

Puget Sound beaches (e.g., on-going Washington Department 

of Natural Resources SCALE studies (Schoch and Dethier, 

2001), but none of these address the “forcing” processes 

that regulate faunal structure, or even whether the most 

important regulating factors are physical (e.g., wave exposure 

and sediment structure) or ecological (e.g., predators and 

competitors) across the range of Puget Sound’s nearshore 

environments. NearPRISM research (Puget Sound Regional 

Synthesis Model, 2004) is presently being conducted to 

describe the variation in Puget Sound beach geomorphologies 

and to ascertain some of the underlying physical processes. 

This work is conducted in concert with other Puget Sound 

Regional Synthesis Model (PRISM) research in watershed, 

marine, and atmospheric domains, but none of this research 

addresses biological responses to the processes being studied.

Objectives

Basic objectives of research to address this goal include:

1. Identify key nearshore ecosystem processes, which are 

defined as dominant and most human impacted, and set 

priorities for filling information gaps.

2. Characterize the spatial and temporal scales over which 

key ecosystem processes prevail and vary.

3. Define how physical and chemical processes interact and 

affect biological processes.

4. Define and evaluate the strengths of linkages between 

nearshore ecosystems and their associated watershed and 

marine systems.

Goal 1: Understand Nearshore

Ecosystem Processes and Linkages to

Watershed and Marine Systems

Existing Work

Previous investigations of Puget Sound have focused on the 

structure of nearshore ecosystems rather than the underlying 

nearshore ecosystem processes. When processes have been 

investigated, the objective has been to resolve responses 

to a stressor (e.g., excess nutrient input) rather than the 

mechanisms accounting for the stress. For example, there 

are a considerable number of investigations of intertidal 

benthic macroinvertebrate assemblages along Puget Sound 

and the Strait of Juan de Fuca (e.g., Long and others, 1983; 

Thom and others, 1984; King County Department of Natural 

Resources and Parks, 2002). Although these investigations 

included some assessments of corresponding biotic and 

abiotic beach characteristics (e.g., grain size, salinity, and 

contaminant concentrations), the actual processes structuring 

these assemblages and especially ecological processes 

have not been a focus of such investigations. Such studies 

typically are limited to a few nearshore ecosystems and sites, 

are short-term (Staude, 1979), and are seldom published 

in peer-reviewed scientific journals (exceptions include 

Armstrong and others, 1976 and 1981; Thom and others,

1976; Schoch and Dethier, 1996).

As a result of these limitations, fundamental nearshore 

processes in Puget Sound are understood at only the most 

general level. Some processes, such as critical physical 

processes of erosion and transport of sediments by waves 

that impact the beach, are somewhat understood conceptually 
A Research Plan in Support of the Puget Sound Nearshore Partnership     13

Relevance and Impact

Process-based restoration can only succeed by significantly 

increasing the understanding of the nearshore processes that 

are affected by restoration and their role in the broader Puget 

Sound landscape. A fundamental understanding of nearshore 

ecosystem processes and linkages to stressors in surrounding 

watershed and marine systems is critical to determine the 

impacts of and plans for the expected growth of the population 

and infrastructure of Puget Sound over the next 50 years. 

Hypotheses and Studies

The following are examples of high-priority hypotheses and 

corresponding studies that serve to illustrate how scientific 

investigations might be focused on critical linkages between 

nearshore ecosystems processes and adjoining watersheds and 

open waters of the Sound.

Hypothesis 1: Upland areas such as coastal bluffs and banks 

are the primary source of sediments that

nourish Puget Sound beaches.

Study 1a: Document the frequency, volume, 

and composition of non-river/stream 

sediment input to Puget Sound beaches.

Study 1b: Determine under what conditions 

and at what rates sediments are transported 

from the upper shore to the lower beach 

terrace.

Hypothesis 2: Eelgrass (Zostera marina) and certain benthic

invertebrate assemblages moderate wave energy

and affect nearshore sediment stability and

structure.

Study 2a: Evaluate the wave energy and 

sediment structure and mobility in nearshore 

areas with and without eelgrass.

Study 2b: Evaluate the effects of differences 

in eelgrass density, blade length, and 

epiphyte growth on wave energy.

Study 2c: Determine what benthic and 

epibenthic organisms are associated with or 

contribute to sediment stability.

Hypothesis 3: Nutrient-cycling processes in the nearshore

are regulated by the structure and turnover of

sediments in the lower intertidal platform.

Study 3: Document what sediment 

processes promote the greatest nutrient 

uptake and transformations of nitrogen and 

phosphorus species.

Hypothesis 4: Nearshore ecosystems are both influenced by

and have the capacity to significantly modify

the structure and processes of adjacent

watershed and marine systems. 

Study 4a: Determine the capacity of 

different beach biota to consume food 

particles, such as phytoplankton and detritus 

that originate in adjacent watershed and 

marine systems.

Study 4b: Evaluate the forcing of nearshore 

ecosystem processes by watershed and 

marine systems, and the nearshore mediation 

of those systems.

Study 4c: Characterize the nutrient 

dynamics in different nearshore 

environments, their linkages to watershed 

and offshore marine sources, and how 

restorative actions may affect nearshore 

nutrient dynamics.
14    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Goal 2: Understand the Effects of Human

Activities on Nearshore Ecosystem Processes

Problem Statement

Human activities are creating stressors or change agents 

(table 2) that affect nearshore ecosystem processes (table 3) and 

components (e.g., Newton and others, 2000). Many of these 

ecological processes are unmeasured or poorly understood. The 

linkages between processes, structures, stressors, and activities 

also are poorly understood; either conceptually or quantitatively. 

Much of the existing research and knowledge is about single 

stressors and responses. An emphasis on cumulative effects 

and multiple stressors, and the interactions among stressors and 

ecosystem response is needed. (See also Goal 3.)

The key to answering these and similar questions will be to 

develop predictive capability through understanding the linkages 

between past and present physiochemical and biological 

processes and then project this knowledge into the future. 

Knowledge about past and present ecosystem processes, when 

integrated with studies of land use and development activities, 

will equip decision makers with the tools to guide policy 

development and natural-resources management.

Regional

• Atmospheric and climatic

○ Deposition of precipitation 

○ Energy sources

• Geologic

○ Earthquake

○ Volcanic

○ Glacial

• Hydrological

○ Tidal

○ Sea-level rise

○ Freshwater

○ (Sea) wave

Local

• Hydrological

○ Tidal

○ Freshwater inflow 

○ (Wind) wave

• Sedimentologic/geomorphologic

○ Erosion

○ Accretion/entrainment

○ Transport 

Finite

• Geochemical transformation and translocation

○ Dissolved organic to particulate organic

○ Inorganic to organic form

○ Inorganic species change

○ Contaminant species change and uptake 

• Food web

○ Primary production and reproduction

○ Production of seeds and other propagules

○ Primary consumption

○ Excretion and respiration 

○ Decomposition and detritus consumption

○ Secondary and tertiary production

○ Consumption

○ Growth

○ Reproduction 

○ Predation 

○ Competition

• Ecological

○ Recruitment

○ Symbiosis

○ Behavior

Table 3. Nearshore ecosystem processes (from Simenstad, 2004).

Toxics

• Add toxic

• Contribute fecal coliform bacteria

• Increase marine debris

• Increase air deposition

• Increase sediment loadings

Input changes

 • Decrease sediment loading

 • Alter freshwater input

 • Alter runoff timing

 • Increase strength of peak flow

Ambient changes

 • Alter light transmissivity from turbidity

 • Cause shading (structures)

 • Produce noise

 • Create physical disturbance via intrusion

 • Change depth or shoreline slope

 • Alter sediment type, including via water transport

 • Physically disturb the sediments

 • Resuspend sediment

 • Reduce endemic benthic habitat area

 • Sea level change

 • Add constructed habitat

 • Alter seawater temperature regime

 • Impede water circulation

Biota

 • Extinction/threatening of marine species

 • Introduction of exotic marine species

 • Alter local marine species composition

 • Change marine organism abundance

Table 2. Stressors and change agents.
A Research Plan in Support of the Puget Sound Nearshore Partnership     15

improve human and ecosystem health by understanding the 

sources, transport, and fate of anthropogenic contaminants that 

are mediated by natural processes. 

Hypotheses and Studies

Hypothesis 1: Increased sediment and nutrient loading due

to silviculture, agriculture, septic systems, and

storm drains affect the processes, structure,

and function of nearshore ecosystems.

Study 1a: Document the frequency, volume, 

and composition of non-river/stream (bluff, 

bank) sediment input to beaches along Puget 

Sound.

Study 1b: Link land-use practices and water 

quality.

Study 1c: Determine the effects of increased 

stressors on nearshore plankton communities 

(e.g., derived from benthic and pelagic 

sources).

Hypothesis 2: Changes in fish abundance and habitats

in upstream reaches affect the productivity and

species composition of estuarine communities.

Study 2: Document the reduction of 

marine-derived nutrients (from gametes and 

carcasses of adult salmon) from before the 

1800s (fishing, dams, and urbanization) and 

link to productivity for salmon and other 

species of interest. 

Hypothesis 3: Diking and draining tidal delta ecosystems or

construction of jetties and piers in delta or

coastal areas affect coastal processes.

Study 3a: Collect and synthesize monitoring 

information from existing dike removal 

projects (Nisqually, Spencer I., JimmyCome_Lately, Skagit, etc.)

Study 3b: Document off-site changes in 

deltaic processes and delta morphology 

resulting from dike removal.

Hypothesis 4: Invasive species affect ecosystem processes.

Study 4: Document the effects of Spartina 

anglica invasion on community structure, 

sediment movement, and habitat functions 

(for fish, birds, and invertebrates).

Hypothesis 5: Multiple stressors act synergistically or 

cumulatively on nearshore processes.

Study 5: Changes in parasite loads, 

contaminant levels, and competition with 

invasive species have cumulatively reduced 

herring populations at Cherry Point.

Existing Work

Much of the existing data and information about the 

Puget Sound region is scattered and fragmented. This is 

partly because of the many institutions and jurisdictional 

boundaries associated with human and natural-resource 

management activities in the Sound. In the Puget Sound 

nearshore, many large multidisciplinary research projects 

were undertaken following the passage of legislation in 

the 1970s: National Environmental Policy Act, Clean 

Water Act, Comprehensive Environmental Response, 

Compensation, and Liability Act, Endangered Species 

Act, MESA (Simensted and others, 1979). As a result 

of this legislation, many of the existing research and 

monitoring projects have been mission oriented, and 

scientific efforts have been focused on environmental 

assessments, impact analysis, and regulatory compliance. 

Most research and monitoring projects have been 

based on resource or habitat. More recently, large-scale 

efforts, such as the University of Washington’s PRISM 

program (Puget Sound Regional Synthesis Model, 

2004) have focused on understanding the ecosystem 

through information synthesis, research and monitoring, 

modeling, and visualization of human effects. The 

proposed work would provide complementary scientific 

coverage of the nearshore waters of Puget Sound.

Objectives

Basic objectives of research to address this goal include:

1. Understand types and ranges of human activities and 

the relation to stressors/change agents the activities 

have created or caused.

2. Link stressors/changes to ecosystem structure 

processes.

3. Factor in the role of hypothetical changes in 

climate and sea level to ecosystem components and 

processes.

4. Use a holistic approach to consider multiple and 

cumulative activities and stressors/change agents 

as the link to multiple processes and ecosystem 

structure.

5. Consider human activities and their impacts over 

multiple temporal and spatial scales.

Relevance and Impact

Resource managers and politicians need objective 

scientific information to determine and guide the course 

and effectiveness of restoration projects and programs to 

address these issues and, ultimately, to restore ecosystem 

health and integrity in the Puget Sound. This work 

also will promote an understanding of human effects 

at multiple scales on the Puget Sound nearshore, and 
16    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Problem Statement

Effective restoration management of nearshore ecosystems 

requires an improved understanding of the interactive 

effects of multiple restorations, preservation, and other 

management actions and an increased ability to determine 

these effects. Incremental effects are those that emerge 

as a series of successive management actions and begin 

to build on each other. In some instances, initial actions 

may need to be taken to reinitiate ecosystem processes 

that are required to support future actions. Cumulative 

effects are those that result from the interaction between 

either successive or simultaneous actions. These effects 

may emerge as synergistic, being greater than or different 

from the additive effects of multiple actions considered 

separately. To date, evaluations and modeling of effects 

of restoration actions have been focused largely on single 

actions and the resultant effects within the boundaries of 

the project area. Expanded evaluations and ecosystem 

modeling are needed that determine short- and long-term hydrodynamic, sediment transport, and morphological change 

model to explore alternative restoration scenarios for the 

Deschutes River Estuary Feasibility Study (George and others, 

2005). 

Other examples include: 

• Models that simulate marine circulation (Kawase, 1998);

• Watershed and ground-water models that simulate 

freshwater discharge to Puget Sound for different land-use 

alternatives;

• Water-quality and sediment-transport models that simulate 

the loading of nutrients, contaminants, and sediments to 

Puget Sound for different land-use alternatives; and

• Models that examine the fate of those inputs once they 

enter the marine waters of the Sound. 

The existing models simulate conditions at a range of scales, 

with some models simulating conditions at the sub-watershed 

or river-mouth scale within specific watersheds (George and 

others, 2005) and others simulating conditions throughout 

the entire Puget Sound Basin. The integration of disparate 

numerical models into one unifying modeling system has 

started as part of the University of Washington’s Puget Sound 

Regional Synthesis Model (PRISM), as well as other more 

localized efforts.

Goal 3: Understand and Determine the Incremental and Cumulative Effects of Restoration and

Preservation Actions on Nearshore Ecosystems

incremental and cumulative effects at scales ranging from 

project areas to the greater Puget Sound.

Existing Work

Nearshore ecosystem restoration in Puget Sound has largely 

focused on estuarine wetlands, especially those associated 

with large river systems. Much of the work has occurred 

relatively recently, with few large projects more than 10 years 

old. Monitoring of these projects has evaluated structural 

responses, such as vegetation community changes, production 

of invertebrate prey resources important to salmonids, and 

the presence of targeted fish species within the project area 

(Cordell and others, 2001; Tanner and others, 2002; Hood 

and Hinton, 2003; Hood, in press). Although these results are 

useful in formulating hypotheses about the relation between 

restoration actions and ecosystem processes as evidenced by 

structural response, little direct investigation of these relations 

has been completed.

Over the past few decades, a number of numerical models 

have been and continue to be developed by different 

agencies and institutions that simulate selected ecosystem 

processes across the Puget Sound Basin at the landscape 

scale. For example, the U.S. Geological Survey developed a 
A Research Plan in Support of the Puget Sound Nearshore Partnership     17

Objectives

Basic objectives of research to address this goal include:

1. Determine ecosystem response to management actions 

using rigorous, hypothesis-based evaluation of restoration 

projects and other management actions.

2. Develop methods to test hypotheses about the effects of 

management actions on nearshore ecosystems, including 

short- and long-term effects at multiple spatial scales.

3. Determine the interactive and cumulative effects of 

multiple management actions on nearshore ecosystem 

processes.

4. Develop tools to project and evaluate the incremental 

and cumulative effects of possible future alternatives of 

restoration, protection, and other management actions on 

the condition of the Puget Sound nearshore.

Relevance and Impact

Nearshore restoration projects typically are costly and 

there may be significant uncertainty in the outcome, especially 

considering improvements to higher order ecosystem 

functioning. It is therefore important to be able to predict the 

outcome of restoration actions, and in particular the outcome 

of various restoration scenarios, to help decision makers select 

the most favored or likely to succeed scenario. Improving 

the understanding of restoration and preservation actions 

on nearshore ecosystem processes, structure, and function 

will provide the basis for better predictive models that can 

be used for selecting amongst several restoration scenarios 

or prioritizing one management action versus another. In 

fact, strategic restoration planning requires some ability to 

prioritize amongst various options, thus an improved ability to 

predict these linkages will always be needed.

The ability to predict the outcomes of various restoration 

scenarios provides managers, decision makers, and the public 

the ability to make informed decisions about which restoration 

action they prefer. For example, for the Deschutes River 

Estuary Feasibility Study, at least four restoration scenarios 

have been considered. Hydrodynamic and sediment transport 

models of each of the scenarios provides input for a biological 

assessment of the likely response to those different scenarios. 

Each of the scenarios can then be evaluated for physical, 

biological, and aesthetic response, and compared against 

the range of values expressed by the various interest groups. 

Decision makers can then make more informed choices.

Benefits from an improved understanding and prediction 

of incremental and cumulative effects of restoration and 

preservation actions will increase over time, as more and 

more restoration projects are carried out, and as the expected 

increase in population in the region requires evermore 

carefully balanced management of natural resources.

Hypotheses and Studies

Hypothesis 1: Management actions affect nearshore

ecosystems at multiple spatial and temporal

scales.

Study 1a: Assess the detectable effects 

on ecosystem processes at various spatial 

and temporal scales associated with large 

restoration actions (e.g., dike breaching in 

the Skagit or Nisqually River estuary and 

dam removal in the Elwha River system).

Study 1b: Conduct hypothesis-based 

evaluations of recently completed restoration 

projects by comparing projected and actual 

ecosystem responses.

Hypothesis 2: Multiple management actions have interactive

and cumulative effects on nearshore 

ecosystems.

Study 2a: Evaluate the interactive and 

cumulative effects of multiple restoration 

actions (e.g., restoration of estuarine 

wetlands of the Snohomish River).

Study 2b: Develop numerical models to 

simulate the incremental and cumulative 

effects of restoration and preservation 

actions.
18    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Problem Statement

Human activities and development patterns reflect the social, 

cultural, and economic values of the societies, communities, 

and individuals that resided in, used, and influenced these 

nearshore ecosystems over time. Therefore, restoration 

of nearshore processes must consider the social, cultural, 

and economic values held by Puget Sound residents. It is 

imperative to understand the motivation for those values and 

the degree of flexibility and willingness to change in order to 

bring about an improved future condition for the nearshore 

ecosystem. To date, little or no social science study of 

nearshore resource use and development has been conducted 

in the Puget Sound. In addition, current social science tools 

and methods are not adapted for complex systems and need to 

be refined and/or applied in innovative ways for developing, 

analyzing, and assessing qualitative and quantitative data.

Existing Work

A draft National Social Science Research Strategy for Marine 

Protected Areas (Wahle and others, 2003) has been developed 

by National Oceanic and Atmospheric Administration 

(NOAA) and the U.S. Department of Interior that may be 

appropriate for application to Puget Sound and PSNERP. The 

strategy was developed through a series of focused meetings, 

workshops, and reviews with broad stakeholder participation, 

and used several existing social science plans including: 

Usable Knowledge: A Plan for Furthering Social Science and 

the National Parks; A Social Science Plan for South Florida 

National Park Service Units; Report on the Socioeconomic 

Roundtable Convened by the Chequamegon and Nicolet 

National Forests; and the South Florida Action Plan for 

Applied Behavioral Sciences. 

A regional effort of more local relevance was from The Pacific 

Northwest Coastal Ecosystem Regional Study (PNCERS), 

in which they conducted a survey of resident’s attitudes on a 

number of natural resource issues in the Grays Harbor estuary 

on the West Coast of Washington (Pacific Northwest Coastal 

Ecosystems Regional Study, 2000).

Within the Puget Sound Basin, in a 2003 proposal funded by the 

U.S. Department of Energy, the Tulalip Tribes of Washington 

identified the need to document the “environmental and tribal 

social, cultural, and economic benefits” as part of a proposal 

to determine the feasibility of a Biomass-Powered Renewable 

Energy Generation project on Tribal lands in Snohomish 

County, Washington. (http://www.eere.energy.gov/tribalenergy/

projects/fy03_tulalip.html, accessed June 2005).

Objectives

The purpose of Goal 4 is to provide the scientific basis 

for better understanding the effects of social, cultural, and 

economic values on restoration and protection of the Puget 

Sound nearshore. The specific objectives are to:

1. Determine how human governance, institutions, and 

social/political processes affect important nearshore 

ecosystem attributes such as habitats or biotic 

components.

2. Determine how human use patterns directly or indirectly 

affect and are affected by nearshore ecosystem attributes. 

3. Determine how human attitudes, perceptions, and beliefs 

directly or indirectly affect and are affected by nearshore 

ecosystem attributes. 

4. Determine how economic and demographic trends affect 

nearshore ecosystem attributes and human values. 

5. Determine how communities (geographic and 

stakeholder) associated with nearshore marine areas in 

Puget Sound affect ecosystem attributes including how 

these communities relate to the use and conservation of 

these attributes.

6. Characterize and provide the science needed to protect 

cultural heritage and resources (historical and traditional 

artifacts) of the Puget Sound nearshore ecosystem.

7. Understand the role of the Puget Sound nearshore 

ecosystem in both historic and contemporary cultural 

heritage of Native American and non-Native American 

communities.

8. Understand ways to improve communication of scientific 

information regarding nearshore restoration, and ways 

that community attitudes, perceptions, and beliefs can 

shape and inform restoration science. 

Goal 4: Understand the Effects of Social, Cultural, and Economic Values on Restoration and

Protection of the Nearshore
A Research Plan in Support of the Puget Sound Nearshore Partnership     19

Relevance and Impact

Process-based restoration and protection of nearshore 

environments likely will not achieve acceptable performance 

levels without significant increases in understanding the 

behaviors of individuals and human institutions that use and 

manage ecosystem attributes. To date, the vast majority of 

research and literature on nearshore ecosystems has focused 

on natural science, with largely anecdotal social scientific 

references and few rigorous projects or programs evaluating 

the complexities of their socioeconomic social scientific 

aspects. As with any policy or management issue, decisions 

regarding nearshore ecosystems always involve tradeoffs 

between the natural and human environments. Both must be 

adequately described and analyzed and integrated for sound 

decision making processes to occur (National Research 

Council, 1995).

Hypotheses and Studies

Hypothesis 1: Local and regional governance, institutions, and 

social/political processes and policies directly 

affect important nearshore ecosystem attributes 

such as habitats or biotic components and 

constrain restoration opportunities.

Study 1a: Examine the nature 

of intra-agency, interagency, and 

intergovernmental interactions in relation 

to nearshore restoration and protection 

planning, management and evaluation in 

order to design optimal structures and avoid 

inter-jurisdictional incompatibilities and 

conflict.

Study 1b: Explore alternative models for 

meaningful integration of the public into 

decision making about nearshore restoration 

and protection.

Study 1c: Evaluate information, resources, 

legal authorities, processes, and structures 

that are needed to plan, manage, and 

evaluate a site or network of nearshore 

restoration and protection areas and 

effectiveness of past designation processes.

Study 1d: Analyze and understand 

governmental and nongovernmental 

institutional cultures and how they influence 

and constrain decision making.

Hypothesis 2: Human use patterns directly or indirectly affect 

nearshore ecosystem attributes and constrain or

condition restoration opportunities.

Study 2a: Collect baseline data on human 

ecology of use at various spatial and 

temporal scales. 

Study 2b: Assess the ecology of nearshorerelated use patterns by conducting studies 

of the legislative institutional, social, 

environmental, and economic dimensions 

of decision making, as well as of legal and 

historic frameworks that depict the “rights 

and responsibilities” of resource use.

Study 2c: Assess the historical political 

ecology of nearshore-related use patterns by 

conducting studies combining biophysical 

and human dimensions data describing 

patterns of human use from prehistoric to 

present time.

Hypothesis 3: Human attitudes, perceptions, and beliefs 

directly or indirectly affect nearshore 

ecosystem attributes and constrain or condition 

restoration opportunities.

Study 3a: Collect data on constituents and 

stakeholders’ attitudes, perceptions, and 

beliefs regarding habitats, species, spaces, 

and ecological processes, relationships 

between people and restoration and 

protected areas, current environmental 

status, and the effects of restored and 

protected areas on quality of life. 

Study 3b: Assess traditional and local 

knowledge regarding habitats, species, 

spaces and ecological processes, develop 

validation frameworks and incorporation of 

traditional and local ecological knowledge, 

and assess the value manager’s place on this 

knowledge.

Study 3c: Assess the conditions under 

which people volunteer collective action 

in the name of ecological restoration and 

protection and how they perceive cause and 

effect linkages of these actions, including 

primary, secondary, and cumulative impacts.

Study 3d: Examine aesthetic ideals as they 

derive from or drive human/environment 

interactions and assess the relations 

between aesthetics and the development and 

maintenance of sense of place.

Study 3e: Assess individuals’ and 

community’s principles and ethics regarding 

the environment, and examine how “ways 

of thinking” influence decision making and 

behavior regarding restored and protected 

areas.
20    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Hypothesis 4: Economic conditions and trends affect 

nearshore ecosystem attributes.

Study 4a: Develop a regional inventory 

of socioeconomic data and analyses on 

groups and measures pertinent to restored 

and protected areas including: commercial 

and recreational fisheries, shore-side 

support industries and coastal communities 

and associated infrastructure; coastal 

development; associated tourism and 

recreation and non-consumptive use and 

existence value. 

Study 4b: Adapt and apply cost benefit 

analysis to restored and protected nearshore 

areas, including definition of costs and 

benefits; give consideration to basic groups 

(recreational, business, and tourism, etc.), 

different kinds of Resource Protection Areas 

(RPAs), specific scenarios, cultural values, 

and net costs and benefits to current and 

future generations.

Study 4c: Develop methods for estimating 

non-market values, in order to compute total 

economic value. 

Hypothesis 5: Communities (geographic and stakeholder) 

associated with nearshore areas affect 

ecosystem attributes and are in turn shaped by 

real of or perceived ecosystem attributes.

Study 5a: Develop descriptive and 

explanatory information regarding 

social, cultural, and economic aspects 

of communities and stakeholder groups 

of particular regions and subregions in 

association with particular habitat or 

ecosystem characteristics.

Study 5b: Develop community capacity and 

skills related to issues such as determining 

the best ways to empower communities to 

articulate and develop their own visions and 

tools, and to assess existing capacity and 

skills in relation to environmental protection.

Study 5c: Analyze community decision 

making patterns and processes, determining 

indicators of community resiliency and 

identifying sources of power as they 

influence political change.

Study 5d: Identify mechanisms designed 

to reach marginalized groups, determining 

incentives for community compliance 

with ecosystem restoration guidelines, 

determining which management structures 

and processes allow for flexibility and 

adaptation, and impacts of various 

management practices on communities. 

Study 5e: Assess the historic social 

construction of RPAs, and interdisciplinary 

studies of RPA “successes and failures.”

Study 5f: Develop and test means for 

protecting maritime cultural resources 

including archeological, historical and 

ethnographic resources, including the 

creation of databases for these resources.
A Research Plan in Support of the Puget Sound Nearshore Partnership     21

Problem Statement

Nearshore ecosystems support or provide a large number of 

valuable attributes or goods and services. These goods and 

services are collectively referred to here as Valued Ecosystem 

Components (VECs). Some structural features of nearshore 

ecosystems, such as low gradient beaches, are valued because 

these beaches can be directly enjoyed by humans (e.g., a beach 

to walk on and water to swim in). Nearshore environments 

provide habitat and other supporting functions for many 

species of plants, fish, and wildlife for part or all of their life 

cycles. Some of these species are valued because they are 

commercially and recreationally harvested or because they can 

simply be viewed (e.g., eagles). Salmon are the most obvious 

example of a valued ecosystem biotic component that is 

economically important. 

The number and types of VECs is dynamic. VECs that are 

valued today may decrease in value in the future while other 

ecosystem goods and services may increase in value. The 

ability of nearshore ecosystems to support and sustain VECs 

depends on the interaction of a wide variety of physical, 

geological, chemical, and biological processes. These 

ecosystem processes create and maintain structural features 

(e.g., habitats) of the ecosystems specifically important to 

different species in different ways, which then support the 

ecosystem functions that are valued. In addition, ecosystem 

processes in some cases can directly support functions, such 

as human health. 

The basic intent of this goal is to understand the interactions 

among ecosystem processes, structure (i.e., attributes defining 

habitat for particular organisms), and functions because these 

interactions generate VECs. Because attributes of nearshore 

ecosystems that are valued will be dynamic, the study of the 

interaction between processes, structure, and function must 

be similarly dynamic and incorporate our changing values. 

We generally have some knowledge of many VECs associated 

with nearshore ecosystems including habitats that they occupy, 

trophic relations, and so on. Much of this information is 

descriptive. For example, we understand much about how 

salmon use nearshore ecosystems. In addition, we understand 

in a general sense how ecosystem processes may work. We 

lack a quantitative understanding of the rates, frequency, 

duration, and magnitude at which many processes operate and 

the linkages between processes, structure, and function. The 

lack of such knowledge is critical because increasing human 

activity has significantly modified many nearshore ecosystem 

processes and thereby compromised their ability to support 

important structural and functional aspects of ecosystem. 

Existing Work

Basic information is available on many of the species of plants 

and animals that use nearshore ecosystems and the functions 

their nearshore habitats may provide for these species. For 

example, we understand the types of nearshore environments 

that constitute Pacific herring, Pacific sand lance, and surf 

smelt requirements for spawning habitats, and we know some 

of the key habitats of juvenile salmon. The functions of their 

nearshore habitats vary both within and among species as a 

function of time of year, size, and so on. Some species such 

as eelgrass are associated with specific nearshore habitats for 

much or all their lives while other species depend on nearshore 

habitats only for parts of their lives. However, the relative 

role or importance of nearshore ecosystems in “producing” 

Goal 5: Understand the Relations of Nearshore Processes to Important Ecosystem Functions

Including Human Health and Protection of At-Risk Species

Valued Ecosystem Components

(VECs)

• Salmon

• Forage fish

• Native shellfish

• Eelgrass and kelp

• Coastal forests

• Beaches and bluffs

• Orcas

• Marine and shore birds

• Great Blue Herons 
22    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

these VECs for many of the VECs associated with nearshore 

ecosystems for parts of their life cycles. For example, Puget 

Sound salmon populations have experienced widespread 

declines and these declines are not due to changes in any one 

ecosystem they occupy. Although degradation of nearshore 

ecosystems plays a role in declines of these populations, 

recovery of this VEC will require actions across a broader 

landscape. 

Although human health can be affected by nearshore 

processes in several ways, a primary concern is with 

consumption of contaminated fish and invertebrates. Many 

of these contaminants are known, where they can be found 

in the water and in sediments, and how they enter nearshore 

ecosystems (e.g., stormwater runoff). Although the structure 

of many nearshore food webs based on diet studies are well 

understood, structure of these food webs need to be quantified. 

Furthermore, how most contaminants enter food webs, how 

the contaminants are processed or cycled, and how they 

eventually end up in nearshore biota are not clear. 

Objectives

To address this science goal, a greater understanding of 

ecosystem processes is needed, what nearshore ecosystem 

attributes are important features of VEC habitats, and how 

VECs use their habitats. Thus, the ability to address this 

science goal will depend in part on the science conducted to 

address other goals in this research plan. Conceptually, the 

major objectives of work conducted under this goal will be 

to focus on defining linkages between ecosystem processes, 

ecosystem structure, and ecosystem functions. Support of 

human health and support of species in decline such as salmon 

and orca whales will be an initial focus of the research plan.

More specifically, the following objectives are identified: 

1. Determine how nearshore processes directly affect the 

quantity and quality of nearshore habitats. 

2. Determine the direct linkages between nearshore 

processes and key VECs. 

3. Determine how changes in ecosystem processes such as 

those brought about restoration or development affect 

nearshore habitats and other VECs. 

4. Understand how variability in nearshore habitats affects 

the ability of these ecosystems to support VECs, such as 

salmon, orca whales, and baitfish.

5. Determine the role of nearshore ecosystems in supporting 

key ecosystem components.

6. Determine economic values in relation to VECs and other 

aspects of the restoration process.

Relevance and Impact

Process-based restoration must be based on a significant 

increase in our understanding of nearshore ecosystem 

processes. By defining those attributes that are of most 

importance, attention can be focused on defining linkages 

between specific nearshore processes in specific regions. 

With this type of understanding, we can better understand 

what restoration actions to take. Planning for Puget Sound 

population and infrastructure growth over the next 50 years, 

and specifically along the shorelines, will not solve many 

of the predictable impacts without such a fundamental 

understanding of the relations between nearshore ecosystem 

processes and attributes of these systems that are most valued. 

Understanding how food webs function is especially critical 

because it will help track how contaminants enter food webs 

and how they are cycled, which will aid in the evaluation and 

management of Puget Sound water- and sediment-quality 

issues.

Hypotheses and Studies

Hypothesis 1: Nearshore processes and key VECs are directly 

and indirectly linked.

Study 1a: Develop and populate numeric 

models (e.g., using bioenergetics approaches 

of food web relations) to define pathways of 

contaminant uptake.

Study 1b: Determine the beach and bluff 

processes that are necessary for successful 

forage fish spawning.

Hypothesis 2: Changes in ecosystem processes brought about 

by restoration or development affect nearshore 

habitats and other VECs.

Study 2a: Determine which nearshore 

processes are affected by bulkheading, and 

how those altered processes affect nearshore 

habitats that support salmon and herring.

Study 2b: Determine the affect of dike 

breaching and/or removal on intertidal 

wetland processes and how those restored 

processes may affect juvenile salmon 

survival.

Hypothesis 3: Impaired or stressed ecosystem processes 

impact human health.

Study 3a: Determine how contaminants are 

processed and cycled and how they end up 

in biota we consume.

Study 3b: Investigate the role altered ground 

water and surface hydrology play in the 

development of harmful algal blooms.
A Research Plan in Support of the Puget Sound Nearshore Partnership     23

Problem Statement

There is no specific research regarding how information is presented and 

organized in support of process-based restoration of the Puget Sound 

nearshore ecosystem. A formal framework is needed that addresses: (1) the 

acceptance of analysis and conclusions drawn by science-based restoration 

research; (2) guidance for public policy; and (3) public support for longterm, system-wide restoration.

With data as the principle building block in constructing a knowledge 

pathway to informed decisions, the tasks required to manage large and 

complex database systems have become a central focus of many planning 

and research activities. Numerous initiatives need to be developed, both 

query-based and autonomous learning systems, to satisfy the information 

needs of many potential users, including individual investigators, decision 

makers, project managers, and publicly active collaborative groups. 

Existing Work

Data represent specific values, objects, or ideas that can 

convey meaningful information when properly interpreted. 

This distinction (interpretation to convey meaning) propels 

the task of “information management” into both technical 

(operative) research domains. Information systems seek to 

combine data access in a timely manner with quality and 

appropriate context. The body of knowledge that informs the 

usefulness of information is referred to as information science. 

In recent years, scientists have developed strategies for 

the management and visualization of data in an effort to 

“reconceptualize” both spatial and temporal patterns in 

ecosystem data. Little is known of (1) how visual-spatial 

abilities are invoked when analyzing geographically or 

temporally distributed data; (2) how to design inquiry 

experiences that connect users with data from field 

instruments (e.g., remotely sensed data, continuous monitoring 

data, high resolution measurements); (3) how to link the users’ 

interpretation of data with discipline-specific theories; and 

(4) what types of skills are necessary to support inquiry using 

visualization of scientific data in the classroom, boardroom, or 

courtroom.

As Latour (1990) has explained, scientists do not spend the 

majority of their time working with observations. Rather, 

they work most often with representations of observations 

including tables, graphs, drawings, mathematical formulae, 

maps, and output from instruments or models. These 

representations serve as a language of science (Garfinkel and 

others, 1981; Knorr-Cetina and Amann, 1990); however, users 

Goal 6: Understand the Roles of Information—Its Representation, Conceptualization,

Organization, and Interpretation—in Restoring Nearshore Ecosystem Processes

seldom participate in creating these representations and thus 

may have trouble following the language (Roth and McGinn, 

1998). Yet ecosystem scientists rely on the users to construct 

meaning from various forms of data representation. The 

ultimate effective use of data on nearshore ecosystems requires 

a theoretical foundation for facilitating those cognitive 

reconstructions.
24    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Objectives

Both basic and applied research in information science share 

a common set of fundamental questions that are relevant 

to a broad range of communities (academic, governmental, 

professional, and the public-at-large). These specific 

objectives are:

1. Determine how choices of measurements affect 

misconceptions regarding ecosystem processes.

2. Determine how the accessibility and exchange of data 

(driven by trends in technology) impact the distribution 

of knowledge and the socioeconomic benefit of improved 

information.

3. Determine how the design of an information distribution 

system or the inequality in interpretive skills may 

ultimately restrict access to that information and thus 

affect the success of individual restoration projects.

Relevance and Impact

The long-term results of an information science research 

program that addresses the complexities of nearshore 

ecosystem studies are:

• A theoretical model of how “learners” use various visualspatial-temporal abilities to make meaningful connections 

between actions and consequences in the nearshore 

ecosystem.

• A greater understanding of the knowledge and skills 

needed by users (program managers, project designers, 

decision makers, teachers, researchers, and the involved 

public) to support scientific inquiry of the nearshore 

ecosystem.

• A generalized model for constructing long-term 

information services.

Hypotheses and Studies

Hypothesis 1: Exaggeration in visual representations of 

spatial data creates misconceptions about 

ecosystem process relations. 

Study 1: Investigate how misconceptions 

about linkages between nearshore ecosystem 

processes and physical structure vary among 

people at different educational levels. Design 

a questionnaire to administer to selected 

K-12, high-education, and to attendees to 

existing nature center sites that investigates 

the impact of graphic representation of the 

nearshore. 

Hypothesis 2: Increased access to real-time information about 

nearshore physical conditions prior to project 

design will (a) alter project design, and 

(b) increase potential for successful restoration 

of processes. 

Study 2: Using a case study approach, 

investigate the strategic role that access to 

data and information plays in restoration 

projects that use adaptive management as a 

design tool.

Hypothesis 3: The errors that propagate when data recorded 

at different spatial scales are aggregated are less

significant in forming misconceptions than the 

aggregation of data at different temporal scales. 

Study 3: Select a series of field 

measurements that may be acquired across 

a gradient of both space and time scales 

(such as temperature and wave energy). 

Develop and administer (both pre and post) 

a survey questionnaire for the data collector, 

analyst, and “learner” that investigates the 

significance of measurement units and 

resolution in portraying nearshore processes. 

Record attributes of nearshore processes 

taken in different units, projections, and 

protocols may result in a cumulative error 

that leads to misinterpretation of ecosystem 

relations. 
A Research Plan in Support of the Puget Sound Nearshore Partnership     25

The PSNERP Research Plan research goals are complex, 

interrelated, and span a range of scientific disciplines. 

To achieve the goals, both inter- and multi-disciplinary 

research in such disciplines as geology, hydrology, biology, 

geography, oceanography, atmospheric science, and social 

science are required. Much of the research described here 

will be fundamental to understanding nearshore ecosystems 

anywhere, and thus will have wide applicability, although 

other research will be more applied and site-specific. 

The plan was developed with input from scientists and 

managers to assure that all research will be useful, relevant, 

and relate directly to the needs of natural-resource managers 

and policy and decision makers. The plan encourages building 

decision support tools that assist resource managers to better 

relate scientific studies to end users. Study designs should be 

flexible to take advantage of research opportunities that vary 

in relation to active restoration, preservation, and adaptive 

management of nearshore ecosystems. For example, if 

researchers have advance knowledge of a pending restoration 

action (an Early-Action Project), the area to be restored could 

serve as a “living laboratory” for learning about the effects 

of the restoration on nearshore ecosystem processes. Lessons 

learned in one restoration site can be applied in other similar 

sites yet to be restored to ensure optimum restoration based on 

the best available science (see Appendix 2). In order to take 

advantage of “living-laboratory” opportunities, it is critical 

that restoration, preservation, and adaptive-management 

actions be communicated among decision makers and 

scientists in Tribal, local, State, and Federal agencies and that 

monitoring and scientific analyses of the actions be conducted 

in collaboration when possible.

The fundamental ecosystem processes that this plan seeks to 

elucidate occur at multiple spatial and temporal scales, ranging 

from local to regional over periods of hours to decades and 

longer. This range of scales should be addressed by short- and 

long-term small- to landscape-scale studies and monitoring. 

Long-term monitoring at multiple spatial scales is particularly 

important to understanding and predicting cumulative effects 

of multiple restoration and preservation actions. Studies will 

synthesize and integrate new data and existing information 

collected for other purposes in the past but that contain 

important information for understanding nearshore ecosystem 

processes.

Rather than dictate or suggest specific research approaches, 

these should be left to the principle investigator(s). However, 

elements in a research approach should include such 

commonly agreed-upon techniques as the use of conceptual 

and numerical models, reference sites, and careful peer review, 

not only of the results, but of research proposals. 

5. Strategy for Achieving Research Goals
26    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

The overall goal of this research plan is to help reduce 

uncertainty in decisions regarding what and how much 

to protect and restore. This goal will be accomplished as 

individual academic researchers and local entities, as well as 

State resource agencies and the Federal and Tribal research 

community understand the information needs, seek funding, 

and develop specific research plans. Especially important to 

the success of this goal will be the prioritization of funding 

for Demonstration Projects and Early-Action Projects to learn 

from opportunistic and planned restoration activities. Federal, 

State, and local agencies that fund restoration activities should 

actively seek opportunities to monitor and study the changes 

that occur as a result of the restoration actions. Because there 

is little incentive for a local entity to fund monitoring and 

research studies, State and Federal agencies, through the 

auspices of restoration programs such as PSNERP and the 

Puget Sound and Adjacent Waterways (PSAW) should fund 

such activities. Another avenue for encouraging studies to 

address the research goals and objectives described in this plan 

is to direct and focus ongoing agency science efforts. National 

Oceanic Atmospheric and Atmospheric Administration, the 

U.S. Geological Survey (USGS), Washington Department of 

Natural Resources, and others all have staff with the expertise 

to address important information needs. Agency research 

programs could seek opportunities to leverage internal funding 

by augmenting ongoing studies with additional funds from 

large restoration programs, individual restoration projects, 

or local entities. The USGS, for example, has successfully 

directed its research efforts by funding the Coastal Habitats 

in Puget Sound (CHIPS) project. This multi-disciplinary 

project includes studies of ecosystem processes of large river 

deltas, effects of urbanization on nearshore ecosystems, and 

effects of dam removal on nearshore ecosystems. Washington 

Department of Natural Resources has augmented an ongoing 

effort directed at monitoring eelgrass. Another avenue for 

encouraging research on Puget Sound nearshore issues is 

to communicate the information needs to the academic and 

private research community through reporting at scientific 

conferences. Conferences such as the Georgia Basin Puget 

6. Implementation of Research Plan

Sound Research Conference, the Restore America’s Estuaries 

conference, the Estuarine Research Federation conference 

amongst others are excellent forums to inform scientists of the 

interesting and important issues in Puget Sound.

Implementation of this research plan depends upon close 

collaboration of multiple Tribal, local, State, and Federal 

agencies, universities, non-governmental organizations, and 

private industry. Many of these groups contributed to this plan 

through the PSNERP partnership and jointly identified the 

research goals described herein. Collaboration through sharing 

of existing and new data and information, coordinating the 

collection of new data and information, prioritizing research 

needs, and pooling and leveraging resources to achieve the 

research goals will benefit all interested parties.

The research plan is best used for posing detailed and 

coordinated research questions by individual researchers or 

lead entities, or multiple agencies and organizations with 

the common goal of developing the scientific information 

and tools that support adaptive management of nearshore 

Puget Sound. Because the Plan identifies complex 

research needs, encompassing several fields of scientific 

study, implementation will not be quick or inexpensive. 

Implementation of the plan will take multiple years, and 

funding should be sought from multiple sources. By the same 

token, restoration and preservation activities should not wait 

for the research studies identified in the plan to be complete. 

Just as restoration and preservation activities will be ongoing 

for a long time, so should research continue to improve 

understanding and to reduce uncertainty. In fact, progress will 

accelerate if there are opportunities to learn from restoration 

efforts that are ongoing, and by adding hypothesis-based 

research and monitoring components to restoration projects 

that are currently in the design phases. 

This research plan should be considered a living document 

that will be updated as significant scientific findings or new 

organizational structures or opportunities warrant refinements 

or changes of the plan.
A Research Plan in Support of the Puget Sound Nearshore Partnership     27

Armstrong, J.W., C.P. Staude, R.M. Thom, and K.K. Chew. 

1976. Habitats and relative abundances of the intertidal 

macrofauna at five Puget Sound beaches in the Seattle area. 

Syesis. 9:277-290.

Armstrong, J.W., R.M. Thom, and K.K. Chew. 1981. 

Impact of a combined sewer overflow on the abundance, 

distribution, and community structure of subtidal benthos. 

Marine Environmental Research. 4:3-23.

Boesch, D.F., and J. Greer (eds.). 2003. Chesapeake Futures: 

Choices for the 21st Century. Chesapeake Research 

Consortium, Inc., Edgewater, Maryland. 160 p.

Bortleson, G.C., M.J. Chrzastowski, and A.K. Helgerson. 

1980. Historical changes of shoreline and wetland at eleven 

major deltas in the Puget Sound Region, Washington. U.S. 

Geological Survey Hydrologic Investigations Atlas, HA617, 11 sheets.

Burns, R. 1985. The shape and form of Puget Sound. 

Washington Sea Grant Program. University of Washington 

Press. Seattle, Washington. 100 p.

Carls, M.G., S.D. Rice, and J.E. Hose. 1999. Sensitivity of fish 

embryos to weathered crude oil. Part I. Low level exposure 

during incubation causes malformations, genetic damage, 

and mortality in larval Pacific herring (Clupea pallasi). 

Environmental Toxicology and Chemistry 18:481-493.

Center for Marine Conservation, 1998, Marine resources. A 

citizen’s guide to the northwest straits, 40 p.

Cohen, A.N., C. Mills, H. Berry, M. Wonham, B. Bingham, 

B. Bookheim, J. Carlton, J. Chapman, J. Cordell, L. Harris, 

T. Klinger, A. Kohn, C. Lambert, G. Lambert, K. Li, D. 

Secord and J.Toft. 1998. Puget Sound Expedition: A rapid 

assessment survey of non-indigenous species in the shallow 

waters of Puget Sound. Prepared for the Nearshore Habitat 

Program, Aquatic Resources Division, Washington State 

Department of Natural Resources. Olympia, Washington 

and U.S. Fish and Wildlife Service, Lacey, Washington. 

Available at URL: http://www2.wadnr.gov/nearshore/

textfiles/pdf/exotics1998.pdf, accessed June 2005.

Cohen, A.N., H.D. Berry, C.E. Mills, D. Milne, 

K. Britton-Simmons, M.J. Wonham, D.L. Secord, 

J.A. Barkas, B. Bingham, B.E. Bookheim, J. E. Byers, 

J.W. Chapman, J.R. Cordell, B. Dumbauld, A. Fukuyama, 

L.H. Harris, A.J. Kohn, K. Li, T.F. Mumford Jr., 

V. Radashevsky, A.T. Sewell, K. Welch. 2001. Washington 

State Exotics Expedition 2000. A rapid survey of exotic 

species in the shallow waters of Elliot Bay, Totten and Eld 

Inlets, and Willapa Bay. Prepared for the Nearshore Habitat 

Program, Aquatic Resources Division, Washington State 

Department of Natural Resources. Olympia, Washington. 

Available at URL: http://www2.wadnr.gov/nearshore/

textfiles/pdf/exotics2000.pdf, accessed June 2005. 

Collins, B.D., D.R. Montgomery, and A.J. Sheikh. 2003. 

Reconstructing the historical riverine landscape of the 

Puget Lowland. p. 79-128 in D.R. Montgomery, 

S.M. Bolton, D.B. Booth, and L. Wall (eds.), Restoration 

of Puget Sound Rivers. University of Washington Press, 

Seattle, Washington.

Cordell, J.R., L.M. Tear, and K. Jensen. 2001. Biological 

monitoring at Duwamish River Coastal America restoration 

and reference sites: A seven-year retrospective. University 

of Washington, School of Aquatic Fishery Sciences 

SAFS-UW-0108. Seattle, Washington. 75 p. Available 

at URL: http://www.fish.washington.edu/research/

publications/pdfs/0108.pdf, accessed June 2005.

Determan, T.A. 1999a. Trends in fecal coliform pollution 

in eleven Puget Sound embayments. Office of Shellfish 

Programs. Washington Department of Health. Olympia, 

Washington. 102 p.

Determan, T.A. 1999b. Temporal and spatial distribution of 

paralytic shellfish poisoning in Puget Sound. Olympia, 

Washington. Office of Shellfish Programs, Washington 

State Department of Health. Olympia, Washington. 

Downing, J. 1983. The coast of Puget Sound: Its processes 

and development. University of Washington Press, Seattle, 

Washington. 126 p.

Finlayson, D. and H. Shipman. 2003. Puget Sound drift cells: 

The importance of waves and wave climate. Puget Sound 

Notes No. 47, p. 1-4. Puget Sound Action Team. Olympia, 

Washington. Available at URL: http://www.psat.wa.gov/

Publications/psnotes_pdf/ps_notes_47.pdf, accessed June 

2005.

Frankenstein, G. 2000. Blooms of ulvoids in Puget Sound. 

Puget Sound Water Quality Action Team. Olympia, 

Washington.

Gardiner, W.W. 1992. Sea surface films: deposition and 

toxicity in intertidal habitats. M.S. Thesis. Western 

Washington University. Padilla Bay National Estuarine 

Research Reserve Reprint Series No. 16. 

Garfinkel, H., M. Lynch, and E. Livingston. 1981. The work 

of discovering science construed with materials from 

the optically discovered pular. Philosophy of the Social 

Sciences 11:131-158.

George, D., G. Gelfenbaum, G. Lesser, B. Barnard, 

S. Morrison, P. Lund. 2005, The Deschutes Estuary 

Restoration Feasibility Study: development of a processbased morphological model. Puget Sound Georgia Basin 

Research Conference Proceedings.

7. References Cited
28    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Gren, I.-M., R.K. Turner, and F. Wulff (eds.). 2000. Managing 

a sea: The ecological economics of the Baltic. Earthscan 

Publications, Inc. London, England.

Gustafson, R.G., W.H. Lenarz, B.B. McCain, C.C. Schmitt, 

W.S. Grant, T.L. Builder, and R.D. Methot. 2000. Status 

review of Pacific Hake, Pacific Cod, and Walleye Pollock 

from Puget Sound, Washington. U.S. Department of 

Commerce, NOAA Technical Memorandum 

NMFS-NWFSC-44, 275 p. Available at URL: http://www.

nwfsc.noaa.gov/publications/techmemos/tm44/tm44.htm, 

accessed July 12, 2004. 

Hardy, J.T. 1997. Biological effects of chemicals in the 

sea-surface microlayer. Pages 339-370 in P. Liss and 

R. Duce (eds.), The Sea Surface and Global Change. 

Cambridge University Press, United Kingdom.

 Hardy, J.T., E.A. Crecelius, C.W. Apts, and J.M. Gurtisen. 

1987a. Sea-surface contamination in Puget Sound: Part II. 

Concentration and distribution of contaminants. Marine 

Environmental Research. 23:251-271.

Hardy, J.T., S.L. Kiesser, L.D. Antrim, A.I. Stubin, R. Kocan, 

and J.A. Strand. 1987b. The sea-surface microlayer of Puget 

Sound: Part I. Toxic effects on fish eggs and larvae. Marine 

Environmental Research. 23:227- 249.

Haugerud, R.A., D.J. Harding, S.Y. Johnson, J.L. Harless, 

C.S. Weaver, and B.L. Sherrod. 2003. High-resolution lidar 

topography of the Puget Lowland, Washington—A Bonanza 

for Earth Science. GSA Today. 13(6): 4-10.

Heinz Center for Science, Economics, and the Environment. 

2002. The State of the Nation’s Ecosystems: Measuring 

the lands, waters, and living resources of the United States. 

Cambridge University Press, United Kingdom. 270 p. 

Available at URL http://www.heinzctr.org/ecosystems/intro/

toc.shtml, accessed June 2005.

Heintz, R.A., J.W. Short, and S.D. Rice. 1999. Sensitivity of 

fish embryos to weathered crude oil: Part II. Incubating 

downstream from weathered Exxon Valdez crude oil 

caused increased mortality of pink salmon (Oncorhynchus 

gorbuscha) embryos. Environmental Science and 

Technology. 18:494-503.

Hood, G. in press. Deepwater slough restoration project 

monitoring report. Skagit Systems Cooperative. La Conner.

Hood, G., and S. Hinton. 2003. Baseline Monitoring: 

Planning, Design, and Prediction for Estuarine Habitat 

Restoration. Puget Sound Georgia Basin Research 

Conference Proceedings, 14 p.

John L. Scott Real Estate. 2004. San Juan Island Office. 

Available at URL http://johnlscottsji.com/P53.cfm, accessed 

July 22, 2004.

King County Department of Natural Resources and Parks. 

2002. Water quality status report for marine waters, 2001. 

Marine and Sediment Assessment Group, King County 

Department of Natural Resources and Parks. Seattle, 

Washington.

King County Department of Natural Resources. 2001. 

Reconnaissance assessment of the State of the Nearshore 

Ecosystem: Eastern shore of Central Puget Sound, including 

Vashon and Maury Islands (WRIAs 8 and 9). Available 

at URL: http://dnr.metrokc.gov/wlr/watersheds/puget/

nearshore/sonr.htm, accessed June 2005.

Knorr-Cetina, K.D., and K. Amann. 1990. Image dissection in 

natural scientific inquiry. Science, Technology, and Human 

Values. 15(3):259-283.

Kawase, M. 1998. A numerical model of Puget Sound 

circulation. Proceedings Puget Sound Conference, 

p. 209-216.

Latour, B. 1990. Drawing things together. p. 19-68 in

M. Lynch and S. Woolgar (eds.). Representations in 

Scientific Practice. MIT Press, Cambridge, Massachusetts.

Long, E.R., A.B. Benedict, R.D. Everitt, B.S. Miller, 

C.F. Nyblade, C.A. Simenstad, S.M. Speich, T.R. Wahl, 

and H.H. Webber. 1983. A synthesis of biological data 

from the Strait of Juan de Fuca and northern Puget Sound. 

U.S. Environmental Protection Agency EPA-600/7-82-004. 

Washington, D.C. 295 p.

McMurray, G.R., and R.J. Bailey (eds.). 1998. Change in 

Pacific Northwest Coastal Ecosystems. NOAA Coastal 

Ocean Program. Decision Analysis Series No. 11. 

Troutdale, Oregon. 342 p.

Millennium Ecosystem Assessment. 2005. Ecosystem and 

Human Well-Being: Synthesis, Island Press, Washington, 

D.C.

Miller, B.S., and S.F. Borton. 1980a. Geographical distribution 

of Puget Sound fishes: Maps and data source sheets. 

Volume 1. Family Petromysontidae (Lampreys) 

through Family Syngnathidae (Pipefishes). University 

of Washington, Fisheries Research Institute. Seattle, 

Washington. 681 p.

Miller, B.S. and S.F. Borton. 1980b. Geographical distribution 

of Puget Sound fishes: Maps and Data Source Sheets. 

University of Washington, Fisheries Research Institute. 

Seattle, Washington. v. 2.
A Research Plan in Support of the Puget Sound Nearshore Partnership     29

Miller, B.S., and S.F. Borton. 1980c. Geographical distribution 

of Puget Sound fishes: Maps and data source sheets. 

Volume 3. Family Cottidae (sculpins) through Family 

Molidae (Molas). University of Washington, Fisheries 

Research Institute. Seattle, Washington.

Morrison, S.W., J.K. Kettman, and D. Haug. 1994. Inventory 

and characterization of shoreline armoring, Thurston 

County, Washington, 1977-1993. Coastal Erosion 

Management Studies Volume 3. Shorelands and Coastal 

Zone Management Program, Washington Department of 

Ecology. 

Mote, P., D. Canning, D. Fluharty, R. Francis, J. Franklin, A. 

Hamlet, M. Hershman, M. Holmberg, K.G. Ideker, 

W. Keeton, D. Lettenmaier, R. Leung, N. Mantua, E. Miles, 

B. Noble, H. Parandvash, D.W. Peterson, A. Snover, and 

S. Willard. 1999. Impacts of variability and change in 

the Pacific Northwest. A Report of the Pacific Northwest 

Regional Assessment Group, for the U.S. Global Change 

Program. By the JISAO/.SMA Climate Impacts Group, 

University of Washington, Seattle. JISO Contrib. 

No. 175. 109 p.

Mumford, T. F. Jr. 2002. Emerging issues: Changing 

paradigms, unseen trends, neglected science. In

T.W. Droscher (ed.). Proceedings of the 2001 Puget Sound 

Research Conference. Puget Sound Action Team. Olympia, 

Washington. 9 p. Available at URL http://www.psat.wa.gov/

Publications/01_proceedings/sessions/oral/7b_mumfo.pdf, 

accessed June 2005.

Mumford, T.F., Jr., S. Wyllie-Echeverria, R.T. Thom, and 

D.E. Penttila. 2003. Loss of eelgrass (Zostera marina L.) in 

small embayments, Puget Sound, Washington: Similarity 

to worldwide early signs of collapse. Proceedings of the 

Estuarine Research Foundation Conference. Estuaries 

on the Edge: Convergence of Ocean, Land and Culture. 

Sept. 14-18, 2003. Seattle, Washington. Available at URL 

http://fish.washington.edu/news/erf/Program_9-17.pdf. 

(abstract only).

National Research Council (NRC), 1995a. Improving 

Interactions Between Coastal Science and Policy: 

Proceedings of the Gulf of Maine Symposium, National 

Academy Press.

National Research Council (NRC), 1995b. Science, Policy, 

and the Coast: Improving Decisionmaking, National 

Academy Press.

Newton, J. 2004. Hood Canal dissolved oxygen concentrations 

at historically low values during winter 2003-2004. 

Available at URL: http://www.hoodcanal.washington.

edu/observations/winterconditions03-04.html, accessed July 

2004.

Newton, J., T. Mumford, J. Dohrmann, J. West, R. Llanso, 

H. Berry, and S. Redman. 2000. A conceptual model 

for environmental monitoring of a marine system. 

Developed for the Puget Sound Ambient Monitoring 

Program. Olympia, Washington. 12 p., 2 appendixes. 

Available at URL: http://www.psat.wa.gov/Publications/

conceptual%20model.pdf, accessed June 2005.

Northwest Salmon Recovery Planning. 2004. Final report 

of updated status of listed ESUs of salmon and steelhead. 

Available at URL: http://www.governor.wa.gov/gsro/

publications/sosreport/2004/puget.pdf, accessed June 2005. 

Northwest Straits Commission. 1999. Report from the 

Northwest Straits Workshop to identify gaps and 

information needs. Available at URL: http://www.nwstraits.

org/PageID/162/default.aspx, accessed June 2005. 

Northwest Straits Commission. 2000. Northwest Straits 

Overview: A Science Gap Report References. Available at 

URL: http://www.nwstraits.org/PageID/162/default.aspx, 

accessed June 2005. 

Nysewander, D.R., J.R. Evenson, B.L. Murphie, and 

T.A. Cyra. 2001. Status and trends for a suite of key 

diving marine bird species characteristic of greater Puget 

Sound, as examined by the Marine Bird Component. Puget 

Sound Ambient Monitoring Program (PSAMP). Poster 

presentation for Puget Sound Research Conference, 

Feb. 12-14, 2001, Bellevue, Washington.

Pacific Northwest Coastal Ecosystems Regional Study. 2000. 

Coastal Resident Survey, Basic Summary of Responses.

Palsson, W.A., J.C. Hoeman, G.G. Bargmann, and 

D.E. Day. 1997. 1995 status of Puget Sound bottomfish 

stocks (revised): Washington Department of Fish and 

Wildlife, Report No. MRD97-03. Olympia, Washington. 

98 p.

Pew Oceans Commission. 2003. America’s Living Oceans: 

Charting a course for sea change. A Report to the Nation. 

Pew Ocean’s Commission, Arlington, Virginia.

PSNERP-NST (Puget Sound Nearshore Ecosystem 

Restoration Program, Near-Shore Science Team) 

Conceptual Model Working Group. 2004. Conceptual 

model for assessing restoration of Puget Sound nearshore 

ecosystems: Conceptual Model Narrative. Available at 

URL: http://sal.ocean.washington.edu/nst/private/products/

conceptmodel/CM%20narrative%20(121702)_HMS.doc, 

accessed July 2004.

Puget Sound Action Team. 2004. Puget Sound Index. 

Available at URL: http://www.psrc.org/datapubs/pubs/

trends/d7jul04.pdf, accessed June 2005. 
30    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Puget Sound Action Team. 2005. State of the Sound, 2004. 

Puget Sound Action Team, PSAT 05-01, Olympia, 

Washington.

Puget Sound Regional Council. 2004. Population change and 

net migration. Puget Sound Trends No. D7. Available at 

URL: http://www.psrc.org/datapubs/pubs/trends/d7jul04.

pdf, accessed July 2004.

Puget Sound Regional Synthesis Model. 2004. “What is 

PRISM?” University of Washington. Available at URL: 

http://www.prism.washington.edu/, accessed July 23, 2004. 

Puget Sound Water Quality Action Team. 2002a. 2002 Puget 

Sound Update: Eighth Annual Report of the Puget Sound 

Ambient Monitoring Program. Puget Sound Water Quality 

Action Team. Olympia, Washington.

Puget Sound Water-Quality Action Team. 2002b. Puget Sound 

Georgia Basin Ecosystem Indicators Report. Terrestrial 

Protected Areas. Available at URL: http://wlapwww.gov.

bc.ca/cppl/gbpsei/terrestrial/graph1.html, accessed July 22, 

2004.

Puget Sound Water Quality Authority. 1987. Puget Sound 

Environmental Atlas, Volumes 1 and 2. Prepared by EvansHamilton, Inc. and D.R. Systems, Inc. Seattle, Washington.

Puget Sound Water Quality Authority. 1988. State of the 

Sound 1988 report. Puget Sound Water Quality Authority. 

Seattle, Washington. 225 p.

Ross, P.S. 2003. Life at the top of the food chain: 

Seabirds, seals and whales as sentinels of environmental 

contamination in Puget Sound and Georgia Basin (abs.). In

T.W. Droscher and D.A. Fraser (eds.). Proceedings of the 

2003 Georgia Basin/Puget Sound Research Conference. 

Available at URL: http://www.psat.wa.gov/Publications/03_

proceedings/PAPERS/ORAL/4e_ross.pdf, accessed June 

2005.

Roth, W.M., and M. McGinn. 1998. Inscriptions: Toward 

a theory of representing as social practice. Review of 

Educational Research. 68(1):35-59.

Schmidt M., and P. Johnson. 2001. Toxics in the Puget Sound 

food web. People for Puget Sound. Seattle, Washington. 

Available at URL: http://www.pugetsound.org/index/cmsfilesystem-action?file=publications/2001_toxics_food_web.

pdf, accessed June 2005.

Schoch, G.C., and M. Dethier. 1996. Scaling up: the statistical 

linkage between organismal abundance and geomorphology 

on rocky intertidal shorelines. Journal of Experimental 

Marine Biology and Ecology, v. 201; Number 1/2, 

p. 37-72.

Schoch, G.C., and M. Dethier. 2001. The intertidal biota 

of Puget Sound gravel beaches: Part 1. Spatial and 

temporal comparisons between 1999 and 2000, and Part 2. 

Recommendations for future sampling. Washington State 

Department of Natural Resources Nearshore Habitat 

Program, Olympia, Washington.

Schwartz, M.L., R.S. Wallace, and E.E. Jacobsen. 1989. 

Net shore-drift in Puget Sound. Engineering Geology in 

Washington, Volume II. Olympia, Washington. Washington 

Division of Geology and Earth Resources Bulletin 78. 

p. 1137-1145.

Simenstad, C. 2004. Nearshore processes. Paper prepared 

for PSNERP NST (Puget Sound Nearshore Ecosystem 

Restoration Program, Near-Shore Science Team). 5 p. 

Available at URL: http://sal.ocean.washington.edu/nst/

private/review/NearshoreProcessesDFT1.doc, accessed 

July 22, 2004.

Simenstad, C.A., M. Logsdon, K. Fresh, H. Shipman, and J. 

Newton. 2006. Conceptual Model for Assessing Restoration 

of Puget Sound Nearshore Ecosystems. Puget Sound 

Nearshore Partnership. Tech. Re. 2006-03. Olympia, 

Washington. 43 p.

Simenstad, C.A., B.S. Miller, C.F. Nyblade, K. Thornburgh, 

and L.J. Bledsoe. 1979. Food web relationships of northern 

Puget Sound and the Strait of Juan de Fuca; a synthesis 

of available knowledge. U.S. Environmental Protection 

Agency, Washington, D.C., Report #EPA-600/7-79-259. 

335 p. 

Sommers, P., and D. Canzoneri. 1996. The Sound Economy: 

Puget Sound Region’s industries and their relationship to 

the Sound. People for Puget Sound. Seattle, Washington. 

Available at URL: http://www.pugetsound.org/index/cmsfilesystem-action?file=publications/1996_industries_report.

pdf, accessed June 2005. 

Staubitz, W.W., G.C. Bortleson, S.D. Semans, A.J. Tesoriero, 

and R.W. Black. 1997. Water-quality assessment of the 

Puget Sound Basin, Washington—Environmental setting 

and its implications for water quality and aquatic biota. U.S, 

Geological Survey Water-Resources Investigations Report 

97-4013. 76 p. Available at URL: http://pubs.er.usgs.gov/

pubs/wri/wri974013, accessed June 2005.

Staude, C.P. 1979. Changes in the intertidal macrofauna and 

macroflora near Seattle’s West Point Sewage Treatment 

Plant from 1971 to 1975. M.S. Thesis. University of 

Washington, 161 p.

Tanner, C.D., J.R. Cordell, J. Rubey, and L.M. Tear. 2002. 

Restoration of freshwater intertidal habitat functions at 

Spencer Island, Everett, Washington. Restoration Ecology. 

10(3):564-576.
A Research Plan in Support of the Puget Sound Nearshore Partnership     31

The Chesapeake Bay Program. 2002. Where are we and 

where are we going? Available at URL: http://www.

chesapeakebay.net/pubs/Snapc2k.pdf, accessed June 2005. 

Thom, R.M., J.W. Armstrong, C.P. Staude, K.K. Chew, and 

R.E. Norris. 1976. A survey of the attached marine flora 

at five beaches in the Seattle area, Washington. 

Syesis. 9:267-275.

Thom, R.M., R. Albright, C.A. Simenstad, J. Hampel, 

J. Cordell, and K.K. Chew. 1984. Intertidal and shallow 

subtidal benthic ecology. v. IV in K.K. Chew and 

Q.J. Stober (eds.). Renton sewage treatment plant study: 

Seahurst baseline study. FRI-UW-8413, Final Report to 

Municipal. Metro. Seattle, Fish. Res. Inst., University of 

Washington, Seattle, Washington. 172 p.

Thom, R.M., A.E. Copping, and R.G. Albright. 1988. 

Nearshore primary productivity in central Puget Sound: 

A case for nutrient limitation in the nearshore systems 

of Puget Sound. Proceedings of the First Annual Puget 

Sound Research Conference. Puget Sound Water Quality 

Authority. Seattle, Washington. p. 378-391.

Trade Development Alliance of Greater Seattle. 2004. Trace 

Stats & Information: http://www.seattle.gov/tda/trade_info/

stats_info.htm.

Transboundary Georgia Basin-Puget Sound Environmental 

Indicators Workgroup. 2002. Georgia Basin-Puget Sound 

Ecosystem Indicators Report. Georgia Basin Ecosystem 

Initiative Pub. No. EC/GB- 01-034, Washington Department 

of Ecology Pub. No. 02-01-002.

U.S. Commission on Ocean Policy. 2004. An Ocean Blueprint 

for the 21st Century, Final Report. Washington D.C.

U.S. Fish and Wildlife Service. 2004. Critical habitat proposed 

for Washington’s Coastal Puget Sound population of bull 

trout. News Release, June 22, 2004. Available at URL: 

http://pacific.fws.gov/bulltrout/jcs/documents/cps_NR.pdf, 

accessed June 2005.

Vaccaro, J.J., A.J. Hansen, and M.A. Jones. 1998. 

Hydrogeologic framework of the Puget Sound aquifer 

system, Washington and British Columbia. U.S. Geological 

Survey Professional Paper 1424-D. 77 p.

Valiela, I., J. McClelland, J. Hauxwell, P.J. Behr, D. Hersh, 

and K. Foreman. 1997, Macroalgal blooms in shallow 

estuaries: controls and ecophysiological and ecosystem 

consequences. Limnology and Oceanography.

42(5, Part 2):1105-1118.

Wahle, C., S. Lyons, K. Barba, L. Bunce, P. Fricke, E. 

Nicholson, M. Orbach, C. Pomeroy, H. Recksiek, and J. 

Uravitch, 2003. A Social Science Research Strategy for 

Marine Protected Areas, NOAA Marine Fisheries Service.

Washington State Department of Ecology. 2004. Chemicals 

in Washington State summary report 2002. Toxics release 

inventory and tier two - Emergency and hazardous chemical 

inventory. Hazardous Waste and Toxics Reduction Program 

Publication Number 04-04-020. 95 p. Available at URL: 

http://www.ecy.wa.gov/pubs/0404020.pdf, accessed June 

2005.

Washington State Department of Ecology. 2004. Oxygen at 

historic low in Hood Canal waters. News release, June 8, 

2004. Available at URL: http://www.psat.wa.gov/News/

releases/DOE_04_106.htm, accessed June 2005.

Washington Department of Fish and Wildlife. 2000. The 

dual role of Washington’s hatcheries: conservation of wild 

stocks, sustainable fisheries. Washington Department of 

Fish and Wildlife Fact Sheet. July 2000. Available at URL: 

http://wdfw.wa.gov/factshts/hatcheries.htm, accessed 

July 20, 2004.

Washington Department of Fish and Wildlife. 2004a. Species 

of concern. Available at URL: http://wdfw.wa.gov/wlm/

diversty/soc/concern.htm, accessed June 2005.

Washington Department of Fish and Wildlife, 2004b, 

Shellfish: Available at URL: http://wdfw.wa.gov/fish/

shelfish/beachreg/1clam.htm, accessed July 19, 2004.

Washington Department of Fish and Wildlife. 2004c. 

Hatcheries program overview: Available at URL: http://

wdfw.wa.gov/hat/overview.htm, accessed July 20, 2004.

Washington Department of Fish and Wildlife. 2004d. Hatchery 

Scientific Review Group Press Conference, Remarks 

by Jeffrey Koenings, WDFW Director, April 23, 2004: 

Available at URL http://wdfw.wa.gov/depinfo/director/

apr2304.htm, accessed July 20, 2004.

Washington Department of Fish and Wildlife. 2004e. 

Hydraulic project approval: Available at URL: http://wdfw.

wa.gov/hab/hpapage.htm, accessed April 17, 2005.

Washington Department of Natural Resources. 1998. 

Changing our water ways: Trends in Washington’s Water 

Systems. Olympia, Washington. 133 p.

Washington Department of Natural Resources. 2000. Our 

changing nature: Natural Resource Trends in Washington 

State. Olympia, Washington. 75 p.

Washington Department of Natural Resources. 2004. The 

Geoduck Program: Managing a valuable natural resource 

for Washington citizens. Available at URL: http://www.

dnr.wa.gov/htdocs/adm/comm/fs04_176.htm, accessed 

June 2005. 
32    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Washington Sea Grant Program. 2000. Draft Northwest Straits 

overview: A science gap report. Prepared for the Northwest 

Straits Commission, revised April 2000. Washington Sea 

Grant Program, Office of Marine and Environmental and 

Resource Programs, University of Washington, Seattle. 

65 p. 

Washington State University. 2004. Penn Cove water festival 

past and present: Washington State University’s Extension 

Program for Island County. Fort Casey State Park, Whidbey 

Island, Washington. Available at URL: http://www.

beachwatchers.wsu.edu/whidbey/waterfest/, accessed 

July 19, 2004.

West, J.E. 1997. Protection and restoration of marine life 

in the inland waters of Washington State. Prepared for 

the Puget Sound/ Georgia Basin International Task Force 

Washington Work Group on Protecting Marine Life. 

Puget Sound/Georgia Basin Environmental Report Series 

Number 6. 154 p. Available at URL: http://www.psat.

wa.gov/Publications/west_protect_restor.pdf, accessed 

June 2005. 

Whitfield, P.H., D. Fraser, and S. Cohen. 2003. Climate 

change impacts on water in Georgia Basin/Puget Sound 

— Special Issue. Canadian Water Resources Journal 

28(4): 523-529. Available at URL: http://www.cwra.org/

Publications/CWRA_-_CWR_Journals/CWRA_-_Journal_

Contents/2003_Vol_28_4_/2Whitfield.pdf, accessed 

June 2005. 

Wiles, G.J. 2004. Washington State status report for the 

killer whale. Washington Department of Fish and Wildlife 

Program. Olympia, Washington. Available at URL: http://

wdfw.wa.gov/wlm/diversty/soc/status/orca/final_orca_

status.pdf, accessed June 2005.

Wilson, R.C.H., R.J. Beamish, F. Atkins, and J. Bell. (eds.) 

1994. Review of the marine environment and biota of 

Strait of Georgia, Puget Sound and Juan de Fuca Strait. 

Proceedings of the BC/Washington Symposium on 

the Marine Environment. Nanaimo, British Columbia 

January 13-14, 1994. Produced for the Marine Science 

Panel of the British Columbia/Washington Environmental 

Cooperation Council. Canadian Technical Report of 

Fisheries and Aquatic Sciences No. 1948. 390 p.

Wyllie-Echeverria, S., T. Mumford, J. Gaydos, and S. Buffum. 

2003. Zostera marina declines in San Juan County, 

Washington. Westcott Bay Taskforce Mini-Workshop, 

July 26, 2003. Roche Harbor, San Juan Island, Washington. 

18 p. Available at URL: http://mehp.vetmed.ucdavis.edu/

pdfs/eelgrassrpt.pdf, accessed July 22, 2004.
A Research Plan in Support of the Puget Sound Nearshore Partnership     33

Aschersleben, G., T. Bachmann, and J. Musseler (eds.). 1999. 

Cognitive contributions to the perception of spatial and 

temporal events. Advances in Psychology 129. Elsevier. 

Amsterdam. 

Bricker, S.B., C.G. Clement, D.E. Pirhalla, S.P. Orlando, and 

D.R.G. Farrow. 1999, National estuarine eutrophication 

assessment: Effects of nutrient enrichment in the Nation’s 

estuaries: National Ocean Service, National Oceanic and 

Atmospheric Administration, Special Projects Office and 

the National Centers for Coastal Ocean Science. Silver 

Spring, Maryland. 71 p. 

British Columbia/Washington Marine Science Panel. 1994. 

The shared marine waters of British Columbia and 

Washington: A scientific assessment of current status and 

future trends in resource abundance and environmental 

quality in the Strait of Juan de Fuca, Strait of Georgia, and 

Puget Sound. Report to the British Columbia/Washington 

Environmental Cooperation Council. 

Broadhurst, G. 1998. Impacts and threats to nearshore habitat. 

Chapter 2 in Puget Sound Nearshore Habitat Regulatory 

Perspective: A Review of Issues and Obstacles. Prepared 

for the Puget Sound/Georgia Basin International Task Force 

Work Group on Nearshore Habitat Loss. Available at URL: 

http://www.psat.wa.gov/shared/taskforce7.html, accessed 

June 2005.

Bull, P. 2002. Communication under the microscope: The 

theory and practice of microanalysis. Psychology Press. 

Routledge, London.

Chrisman, N. 1997. Exploring geographic information 

systems. John Wiley and Sons, New York.

Colich, F. 2003. Trace metals concentrations in stormwater 

runoff from the Evergreen Point Floating Bridge in the 

Seattle, Washington Area. In T.W. Droscher and 

D.A. Fraser (eds.). Proceedings of the 2003 Georgia 

Basin/Puget Sound Research Conference. Vancouver, 

British Columbia. March 31-April 3, 2003. Available at 

URL: http://www.psat.wa.gov/Publications/03_proceedings/

PAPERS/POSTER/p4_coli.pdf, accessed February 2004.

Collins, B.D., and A.J. Sheikh. 2005. Historical 

Reconstruction, Classification, and Change Analysis of 

Puget Sound Tidal Marshes. Project Completion Report 

to: Washington Department of Natural Resources, 120 p. 

Available at URL: http://www.pugetsoundnearshore.org/

techical_papers/historical_shoreline_dnr.pdf.

Davis, J., J.S. Labenia, D.H. Baldwin, B. French, and 

N.L. Scholz. 2003. Sublethal effects of the carbamate 

insecticide—carbaryl—on coastal cutthroat trout (abs.).

In T.W. Droscher and D.A. Fraser (eds.). Proceedings of 

the 2003 Georgia Basin/Puget Sound Research Conference. 

Vancouver, British Columbia. March 31-April 3, 2003. 

Available at URL: http://www.psat.wa.gov/Publications/03_

proceedings/PAPERS/POSTER/p4_davis.pdf, accessed 

February 2004.

Dutch, M., S. Aasen, and E.R. Long. 2003. PCB aroclor 

concentrations in Puget Sound sediments. In T.W. Droscher 

and D.A. Fraser (eds.). Proceedings of the 2003 Georgia 

Basin/Puget Sound Research Conference. Vancouver, 

British Columbia. March 31-April 3, 2003. 14 p. Available 

at URL: http://www.psat.wa.gov/Publications/03_

proceedings/PAPERS/POSTER/p4_dutc1.pdf, accessed 

February 2004.

Dutch, M., S. Aasen, and E.R. Long. 2003. PCB congener 

concentration in Puget Sound sediments In T.W. Droscher 

and D.A. Fraser (eds.). Proceedings of the 2003 Georgia 

Basin/Puget Sound Research Conference. Vancouver, 

British Columbia. March 31-April 3, 2003. 14 p. Available 

at URL: http://www.psat.wa.gov/Publications/03_

proceedings/PAPERS/POSTER/p4_dutc2.pdf, accessed 

February 2004.

Ebbert, J.C., S.S. Embrey, R.W. Black, A.J. Tesoriero, and 

A.L. Haggland. 2000, Water quality in the Puget Sound 

Basin, Washington and British Columbia, 1996-98: United 

States Geological Survey Circular 1216, 31 p. 

Erickson, A., T. Klinger, S.C. Fradkin. 2003. A pilot study of 

the effects of human trampling on rocky intertidal areas in 

Olympic National Park, USA. In T.W. Droscher and D.A. 

Fraser (eds.). Proceedings of the 2003 Georgia Basin/Puget 

Sound Research Conference. Vancouver, British Columbia. 

March 31-April 3, 2003. 6 p. Available at URL: http://www.

psat.wa.gov/Publications/03_proceedings/PAPERS/ORAL/

10f_eric.pdf, accessed February 2004.

EVS Environment Consultants. 2003. Status, trends, 

and effects of toxic contaminants in the Puget Sound 

environment. Prepared for the Puget Sound Action Team, 

Olympia, Washington. EVS Consultants. EVS Project 

No. 02-1090-01, 249 p. 

Gilkeson, L. 2003. Environmental trends in British Columbia, 

2002 (abs.). In T.W. Droscher and D.A. Fraser (eds.). 

Proceedings of the 2003 Georgia Basin/Puget Sound 

Research Conference, Vancouver, British Columbia. 

March 31- April 3, 2003. 1 p. Available at URL: http://

www.psat.wa.gov/Publications/03_proceedings/PAPERS/

POSTER/p8_gilke.pdf, accessed February 2004.

8. Further Reading
34    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Konrad, C.P. 2003. Streamflow metrics for linking landscape 

changes to the condition of stream ecosystems in the Puget 

Sound Basin (abs.). In T.W. Droscher and D.A. Fraser 

(eds.). Proceedings of the 2003 Georgia Basin/Puget 

Sound Research Conference, Vancouver, British Columbia. 

March 31-April 3, 2003. 1 p.

Leung, L.R., and W.T. Pennell. 2003. An end-to-end 

assessment of climate change impacts on water resources 

in the Western North America (abs.). In T.W. Droscher and 

D.A. Fraser (eds.). Proceedings of the 2003 Georgia Basin/

Puget Sound Research Conference, Vancouver, British 

Columbia. March 31-April 3, 2003. 1 p.

McKechnie, L.M., and K.E. Pettigrew. 1998. Theories for the 

new millennium: The deployment of theory in LIS research. 

In E. Toms (ed.). Information Science at the Dawn of the 

Millennium. Proceedings of the 26th Annual Conference of 

the Canadian Association for Information Science. Ottawa, 

Ontario. June 3-5, 1998. p. 125-142). 

McKechnie, L.M., and K.E. Pettigrew. 2002. Surveying the 

use of theory in library and information science research: A 

disciplinary perspective. Library Trends. 50(3):406-417. 

McKechnie, L.M., K.E. Pettigrew, and S.L. Joyce. 2000. The 

origins and contextual use of theory in human information 

behavior research. In L. Hoglund (ed.). The New Review 

of Information Behaviour Research: Studies of Information 

Seeking in Context 2:47-63. Graham Taylor, London, 

United Kingdom.

McMurray, G.R., and R.J. Bailey ( eds.). 1998. Change in 

Pacific Northwest Coastal Ecosystems. Pacific Northwest 

Coastal Ecosystems Regional Study (PNCERS). 

Washington, D.C. U.S. Department of Commerce (NOAA 

Coastal Ocean Program Decision Analysis Series No. 11). 

Leckie, G.I., K.E. Pettigrew, and C. Sylvain. 1996. Modeling 

the Information Behavior of Professionals: Library 

Quarterly, v. 66, no. 2, pp 161-193. 

Mote, P. 2001. There goes the rug. In Puget Sound Research 

2001: Plenary session and Panel Discussion. Challenges 

Facing Puget Sound and the Georgia Basin Scientists. 

p. 2-9. Available at URL: http://www.psat.wa.gov/

Publications/01_proceedings/keynote/plenary.pdf, accessed 

June 2005. 

Nysewander, D.R., J.R. Evenson, B.L. Murphie, and 

T.A. Cyra. 2003. Trends observed for selected marine bird 

species during 1993-2002 winter aerial surveys, conducted 

by the PSAMP Bird Component (WDFW) in the Inner 

Marine Waters of Washington State. In T.W. Droscher and 

D.A. Fraser (eds.). Proceedings of the 2003 Georgia Basin/

Puget Sound Research Conference, Vancouver, British 

Columbia. March 31-April 3, 2003. 11 p. Available at URL: 

http://www.psat.wa.gov/Publications/03_proceedings/

PAPERS/POSTER/p1_nysew.pdf, accessed February 2004.

O’Neill, S.M., and J. West. 2003. PCB accumulation in 

marine and anadromous fishes of the Puget Sound and 

Strait of Georgia (abs.). In T.W. Droscher and D.A. Fraser 

(eds.). Proceedings of the 2003 Georgia Basin/Puget 

Sound Research Conference. Vancouver, British Columbia. 

March 31-April 3, 2003. 1 p. Available at URL: http://

www.psat.wa.gov/Publications/03_proceedings/PAPERS/

ORAL/4e_oneil.pdf, accessed February 2004.

Pettigrew, K.E., and L.M. McKechnie. 2001. The use of theory 

in information science research. Journal of the American 

Society for Information Science and Technology.

52(1):62-73.

Puget Sound Task Force. 1970. Comprehensive study of 

water and related land resources, Puget Sound and adjacent 

waters, State of Washington, appendix III, hydrology 

and natural environment: Pacific Northwest River Basins 

Commission. Vancouver, Washington. 205 p. 

RE Sources. 2002. State of the North Sound and Straits. 

Bellingham, Washington. A Report from RE Sources and 

the North Sound Baykeeper. Bellingham, Washington. 38 p. 

Available at URL: http://www.re-sources.org/pdf/state_of_

the_sound.pdf, accessed July 19, 2004.

Reed, L., K. Lynch, K. Paulsen, B. McMillan, M. Myers, 

G. Ylitalo, J. Labenia, T. Collier, and N. Scholz. 2003. 

High rates of pre-spawn mortality in Coho Salmon 

(Oncorhynchus kisutch) from urban streams in the Puget 

Sound Basin (abs.) In T.W. Droscher and D.A. Fraser 

(eds.). Proceedings of the 2003 Georgia Basin/Puget 

Sound Research Conference. Vancouver, British Columbia. 

March 31-April 3, 2003. 1 p. Available at URL: http://

www.psat.wa.gov/Publications/03_proceedings/PAPERS/

POSTER/p8_reed.pdf, accessed February 2004.
A Research Plan in Support of the Puget Sound Nearshore Partnership     35

Reynolds, C.J. 2003. Hydrologic and climatic impacts of a 

changed climate on Georgia Basin, British Columbia (abs.). 

In T.W. Droscher and D.A. Fraser (eds.). Proceedings of 

the 2003 Georgia Basin/Puget Sound Research Conference. 

Vancouver, British Columbia. March 31-April 3, 2003. 

Available at URL: http://cgrg.geog.uvic.ca/abstracts/

ReynoldsHydrologicThe.html, accessed February 2004.

Schaeken, W., G. De Vooght, A. Vandierendonck, and 

G. d’Ydewalle (eds.). 2000. Deductive reasoning and 

strategies. (p. 191-207). xiv, 321 p.

Sobol, M.G., and G. Klein. 1989. New graphics as 

computerized displays for human information processing, 

IEEE Transactions on Systems, Man and Cybernetics 

19:893-898.

Snohomish County. Bibliography of marine resources issues, 

updated March 2004. Available at URL: http://www.

co.snohomish.wa.us/publicwk/swm/Marine/mrcbib.htm, 

accessed July 19, 2004.

Sobocinski, K. L. 2003. The impact of shoreline armoring on 

upper beach fauna of central Puget Sound. M.S. Thesis. 

School of Aquatic and Fishery Sciences. University of 

Washington. Seattle.

Sobocinski, K.L., J.R. Cordell, C.A. Simenstad, and

 J. Brennan. 2003. The impact of shoreline armoring 

on upper beach fauna of Central Puget Sound (abs.). In

T.W. Droscher and D.A. Fraser (eds.). Proceedings of the 

2003 Georgia Basin/Puget Sound Research Conference. 

Vancouver, British Columbia. March 31-April 3, 2003. 

Available at URL: http://www.psat.wa.gov/Publications/03_

proceedings/PAPERS/ORAL/10d_sobo.pdf, accessed 

June 2005.

Trainer, V.L., Bich-Thuy L. Eberhart, J.C. Wekell, 

N.G. Adam, L. Hanson, F. Cox, and J. Dowell. 2003. 

Increased magnitude, frequency and geographical spread 

of harmful algal blooms in Puget Sound (abs.). In T.W. 

Droscher and D.A. Fraser (eds.). Proceedings of the 

2003 Georgia Basin/Puget Sound Research Conference. 

Vancouver, British Columbia. March 31-April 3, 2003. 1 p. 

Available at URL: http://www.psat.wa.gov/Publications/03_

proceedings/PAPERS/ORAL/4f_train.pdf, accessed 

June 2005.

Vandierendonck, A., G. De Vooght, C. Desimpelaere, and V. 

Dierckx. (2000). Model construction and elaboration in 

spatial linear syllogisms. In W. Schaeken, G. De Vooght, 

A. Vandierendonck & G. d’Ydewalle (eds.). Deductive 

reasoning and strategies (p. 191-207). New York: Lawrence 

Erlbaum Associates.

West, J.E. 2002. Protection and restoration of marine life in 

Puget Sound and the Georgia Basin revisited: 1996-2002. 

Keynote Address, 1st Biennial Marine Ecosystem Health 

Program Science Symposium. September 6, 2002, Rosario 

Resort, Orcas Island, Washington. Program and Abstracts. 

Available at URL: http://mehp.vetmed.ucdavis.edu/pdfs/

scisympproc02.pdf, accessed June 2005. 

Windschitl, M., and B. Winn. 2000. Learning from virtual 

worlds. In B. Fishman and S. O’Connor-Divelbliss (eds.), 

Proceedings of the Fourth International Conference of the 

Learning Sciences. Erlbaum. Mahwah, New Jersey.
36    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

PNSERP partners have identified the following goals:

1. Rehabilitate ecosystem natural processes that create 

and maintain habitats in Puget Sound and watershed 

to fully support, with minimal ongoing human 

intervention, natural aquatic and associated terrestrial 

biotic communities and habitats in ways that favor native 

members of those communities.

2. Protect and/or restore functional habitat types in Puget 

Sound nearshore and watershed for ecological and public 

values such as supporting species and biotic communities, 

ecological processes, recreation, scientific research, 

aesthetics, and other beneficial human uses. (Define from 

CWA, DNR, SMA)

3. Prevent future listings and achieve recovery of at-risk 

native species dependent on Puget Sound as the first step 

toward establishing large, self-sustaining populations of 

these species; support similar recovery of at-risk native 

species in the Puget Sound and the watershed above the 

Appendix 1. Goals of the Puget Sound Nearshore Ecosystem

Restoration Program

estuary; and minimize the need for future endangered 

species listings and reversing downward population trends 

of native species that are not listed.

4. Prevent the establishment of additional non-native 

species and reduce the negative ecological and economic 

impacts of established non-native species in Puget Sound 

nearshore and watershed.

5. Improve and/or maintain water- and sediment-quality 

conditions that fully support healthy and diverse aquatic 

nearshore ecosystems in Puget Sound and watershed; 

and eliminate, to the extent possible, toxic impacts to 

nearshore aquatic organisms, wildlife, and people.

6. Increase the understanding of the natural processes and 

functions of the Puget Sound nearshore. 
A Research Plan in Support of the Puget Sound Nearshore Partnership     37

By F. Brie Van Cleve, Charles Simenstad, Fred Goetz, and Tom Mumford

Product of the Puget Sound Nearshore Ecosystem Restoration Project.

Nearshore Science Team. Lessons Learned Working Group. (Version December 19, 2003).

Available at URL: http://www.cev.washington.edu/lc/PSNERP/lessons_learned.pdf, accessed June 2005.

The Puget Sound Nearshore Ecosystem Restoration Project (PSNERP) proposes to restore degraded shoreline 

ecosystems of Puget Sound. In the process of providing scientific direction for PSNERP, the Nearshore Science 

Team (NST) sought to more clearly define the role and position of scientific input into large restoration programs 

such as PSNERP. As part of the planning phase of this program, the NST conducted a “lessons learned” exercise to 

characterize the role of science in five other large-scale programs around the country. These programs including the 

Chesapeake Bay Program, the Comprehensive Everglades Restoration Plan, the California Bay-Delta Authority, the 

Glen Canyon Adaptive Management Program, and the Louisiana Coastal Areas Ecosystem Restoration Program. 

The NST’s goal was to better understand how science is incorporated into program management and organizational 

structure, such that the “best available science” is realized. This document summarizes lessons learned by the NST 

about maximizing the best available science in conceptualizing, designing and implementing large-scale restoration.

The NST found that maintaining the independence of science from policy pressures in order to assure legitimacy and 

quality facilitated the incorporation of best available science into restoration actions. The NST found that the strongest 

assurance for scientific credibility was rigorous peer review, both internal and external to the organizational structural. 

“Vertical integration” was an effective tool to coordinate science with other sectors of the program. Several programs 

had successful strategies for educating stakeholders about science issues with publications and web sites. Although 

they all acknowledged the need for rigorous adaptive management, one program in particular demonstrated that 

adaptive management is a powerful tool that can only be effectively used if all involved understand it; this suggests 

that education and information dissemination are important and often neglected aspects of adaptive management. The 

NST found that these programs often struggled with fundamental cultural differences between science and policy and, 

at times, had difficulty estimating scientific resource requirements for true ecosystem management and restoration. In 

spite of difficulties encountered by these programs, the NST was encouraged by the numerous innovative approaches 

being employed to meet the challenges inherent in large-scale restoration. These observations hopefully will guide 

the utilization of science in PSNERP’s Feasibility Study Phase and throughout the General Investigation Study. The 

NST intends this document to stimulate interest in improving the role of science in ecosystem restoration and provide 

present and future restoration practitioners with practical advice gained from predecessor programs.

Appendix 2. Executive Summary of “Application of ‘Best Available

Science’ in Ecosystem Restoration: Lessons Learned from Large-Scale

Restoration Efforts in the U.S.”
38    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

November 3, 2005

The following represents a list of research questions developed by the Nearshore Science Team (NST) of PSNERP. They were 

developed with the following process:

1. Each member of the NST was asked to provide five questions that they felt could be addressed with an EARLY-ACTION

RESTORATION PROJECT and five questions that could be addressed with DEMONSTRATION RESTORATION 

PROJECTS (definitions provided below). Two additional categories were added: data base analyses and research 

approaches.

2. No effort was made to constrain members by subject or scale. 

3. Questions were compiled and organized by management measure. As a result, there were some questions that did not fit any 

management measure and were included in the first section. Questions were organized based upon management measure 

and topic, generally corresponding to processes.

4. Additional questions were added that were developed during “Science Morning” discussions by the NST.

5. The list was edited to reduce the number of redundancies and improve the organization.

The following are caveats associated with this list.

1. The list of research questions is not comprehensive. It is strictly limited to what the NST considered could be answered with 

restoration projects. 

2. The NST has not prioritized the list.

3. The NST did not focus on conservation or protection as a management measure.

4. Some questions could not be easily categorized and were left blank. Additional categories such as “comparative analyses” 

may be warranted.

5. There was no external review.

6. Questions vary in scope and scale and do not necessarily lend themselves to discrete studies.

Early-Action Projects (EA): Projects that are in the works that could exploited for research needs. 

Examples of EA projects include Capitol Lake and Seahurst Park. An EA project is one that has been 

designed and implemented for restoration but does not have an objective to promote science. They may 

have asked what should be monitored or what are research opportunities. The NST has little opportunity to 

modify the project design so it is more opportunistic. Some projects will not address a particular question 

because of how they are being implemented and in general they are not set up with control or reference 

sites. 

Demonstration Project (DEMO): A DEMO project is one in which scientists would design the 

restoration action to examine some explicit hypotheses. DEMO projects would involve the participation 

of scientists in the design of the project. Basically, these projects are designed as science-based projects. 

These projects would include reference and control sites for hypothesis testing. 

Data Base (DB): This means either analysis of existing data sets or existing projects. It can include a 

retrospective analysis and comprehensive survey. This can include monitoring of existing projects and 

review or existing monitoring data. SRFB project review, U.S. FWS, NOAA, Corps projects.

Research (RES): This refers to questions that are primarily of a research nature that may need to be 

addressed outside the restrictions of a restoration project.

Appendix 3. Research Questions for Early-Action Projects

and Demonstration Projects
A Research Plan in Support of the Puget Sound Nearshore Partnership     39

Management

measure

General

topic or issue

addressed

Question Approach

General—Independent of a Management Measure or Comprised of Multiple Measures

1.  Oceanographic Processes

a. What is the relationship between nearshore and offshore oceanographic processes? DEMO

2.  Relationships of Biotic Communities and Shore Types

a. Can we link shore types to biotic communities and extrapolate over large spatial scales? DB

3.  Pocket Estuary Related

a. Does the physical and biological structure of small estuaries change predictably with variation in tidal 

prism, freshwater input, tidal range, and sediment fluxes? DEMO, EA

b. How rapidly, if at all, does this shore form respond to natural or anthropogenic changes in these 

factors? DEMO

c. Develop classification of pocket estuaries and impairments and develop stratified approach to carrying 

out and evaluating specific restoration actions. DB

4.  Riparian Processes

a. What types and extent of vegetation (types, age structure, density, continuity) are needed to provide 

various riparian functions? How do we quantify the various marine riparian functions? EA

b. What scale of revegetation is needed to restore, enhance, or replace lost functions (especially where 

there are constraints [e.g., urban]), and do small-scale restoration and enhancement projects work? EA

5.  Food Web Processes

a. Determine change in primary productivity and organic input into Totten Inlet. Hwy 101 removal at 

Kennedy Creek/Totten Inlet. EA

b. What is the status of primary production in the nearshore. Are nutrients, light or other factors limiting? DEMO, RES

c. How do nearshore-offshore gradients in food webs vary and is there a pattern with various shoreline 

types? DEMO, RES

d. What is the relative contribution of algal versus vascular plant versus phytoplankton production? DEMO

6.  Climate Change

a. Are climate shifts changing the food web of Puget Sound on annual or decadal scales and if so, what 

adjustments should be made to a strategic restoration plan to accommodate such a change? DEMO

b. Do we see elements of climate change in Puget Sound? If so, what are they? DEMO

c. How does land use and other human activities affect nutrient loading into the nearshore? Are there 

effects of eutrophication in the nearshore? EA

7.  Landscape Scale Effects of Protection/Restoration

a. Is there a logical restoration sequence such that we can insure that the various parts (actions) “fit” 

together to deliver an “appropriate” ecosystem response at multiple spatial and temporal scales of 

analysis? How do we undertake? PHASE restoration? EA

b. At what scales can we detect physical, chemical and biological signals from restoration actions 

conducted at various scales? EA, DEMO

c. What are the time scales for habitat restoration actions to become fully functional and does this vary 

with the type of restoration action? EA

d. Do systems that have been the targets of multiple restoration actions show evidence of interactive or 

cumulative effects? For example, at least 10 restoration projects have been completed in the Duwamish 

River estuary over the past decade (Simenstad and others, in press). Is there any evidence that these 

multiple actions are beginning to “add up” to a sum greater than that of the individuals. How would we 

detect such a response if it were occurring? DB

e. Do biota, especially those identified as VEC’s, integrate the effects of multiple restoration actions 

across regional or other higher order scales of spatial analysis? How does this occur? DEMO

f. To what extent do particular life histories of specific organisms rely on the spatial configuration 

of habitats? This exercise, if pursued, might best begin with construction of appropriately specific 

Conceptual Models for relationships between biota (including especially VEC’s). EA

g. Can we model what climate change effects (e.g., SST, runoff, changes in wind) would be most 

important to nearshore communities, processes, and structures? DEMO
40    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Management

measure

General

topic or issue

addressed

Question Approach

General—Independent of a Management Measure or Comprised of Multiple Measures—Continued

8.  Social Values and Nearshore Ecosystems

a. What are the relative social preferences between private and public ownership of waterfront property in 

Puget Sound? EA

b. Which ecosystem services do people value most from Puget Sound? EA

c. What do people perceive as the biggest threat to Puget Sound? EA

d. How much are people willing to pay to restore the health of Puget Sound? EA

e. What are the relative social preferences between protection of existing functional nearshore areas 

through acquisition or regulation and how do those compare with restoration? EA

f. Is restoration as effective as regulatory reform (strengthening regulations and enforcement to prevent 

further harm)? EA

g. What do people really need to know about the problems and solutions and are we actually providing 

enough information (types and quantity) to gain acceptance and affect human behavior? EA

h. How big a geographic area should be covered in public process notification, review, and comment of 

restoration proposals?

i. How should effects of restoration outcomes be communicated, e.g. What metrics should be used?

j. What will affect public acceptance or rejection of restoration projects such as dike removal?

9.  (VECs)

a. Define stage-to-stage survival and growth rate estimates from freshwater to ocean entry for juvenile 

chinook salmon? EA

b. How does variability in site-scale habitat features (e.g., water depth and vegetation characteristics) and 

landscape-scale habitat features affect juvenile salmon and other VEC performance? EA

c. What are the processes that affect how juvenile salmon disperse throughout deltaic and shoreline 

habitats of Puget Sound? EA

d. There is no difference in mean residence time of juvenile salmon in higher order tidal channel systems 

than in lower order channel systems. DEMO

e. What are the most important habitats and species and why are they “the most important”? Do we know 

enough about the biology of specified species to “prioritize” them? EA

f. There is no difference in forage fish spawning on created versus restoring beaches? DEMO

g. Is there an interaction between hatchery and wild salmon and does it affect outcomes of restoration?

10.  Information

a. Regardless of the process being examined, “in what ways can we represent the data that will be 

collected other scientists interested in linkages to other ecosystem processes? 

1. Restoration of Watersheds (FW)

1.  Sediment Processes

a. What are the sources and ultimate fates of waterborne sediments that reach Puget Sound and how do 

these vary temporally? DEMO

b. What are the sources of sediment available during marsh evolution in any delta? DEMO

c. What is the fate and transport of sediment pulses from the modifying operation of existing dams, and 

removal of dams and determine how far away sediments have measurable influence. (Howard Hanson 

Dam modification; Capital Lake/Elwha River Dam Removals?) EA

d. Deltas. How is the pattern/distribution of landscape elements on estuarine deltas controlled by longterm changes in the distribution of fluvial sediment across the landscape? (the Louisiana Problem) 

Selectively remove lower stem dikes in locations specifically chosen to test hypotheses about sediment 

distribution or landscape characteristics. DEMO

2  Hydrology

a. How has the reconfiguration (Duwamish) and re-alignment (Snohomish, Stillaguamish, Skagit, and 

Nooksack) of major river channels affected nearshore processes—sediment and organic transport and 

deposition, inshore and offshore? DB
A Research Plan in Support of the Puget Sound Nearshore Partnership     41

Management

measure

General

topic or issue

addressed

Question Approach

1. Restoration of Watersheds (FW)—Continued

3.  Nearshore Habitat Conditions—Continued

a. How do changes in land-use practices (either new development, or better control of runoff i.e. undevelopment) affect nearshore quality, local plankton communities, SAV, and via what mechanisms do 

changes happen? EA

b. What are the affects of dike removal on deltaic sediment process (channel morphology, sediment 

delivery)? Determine affects of dike removal on eelgrass populations associated with delta and nearby 

nearshore areas. Example is the Skokomish River dike removal. 

2. Beach Nourishment

1.  Sediment Processes

a. What site and environmental parameters control the sediment dynamics of a nourished beach? 

Different types of beaches would be examined. This could include monitoring beach nourishment 

experiments (e.g., Lincoln Park Beach and Seahurst), perhaps as a suite of sediment placements in the 

same general area, with accompanying environmental monitoring (waves and water levels). DEMO, EA

b. How do different sediment sizes respond to wave events?

c. What are controls on longshore transport rates? How does this vary in Puget Sound? 

d. How does beach orientation affect longshore and cross shore sediment transport?

2.  Hydrology

a. What beach characteristics influence the extent of wave runup?

3.  Performance of Nourishment Projects

a. What is the impact of different sediments sizes on longevity of the project, renourishment schedule.

b. Does sediment placed on the beach face move offshore?

c. Will a gravel beach project “acquire” sand if it is available?

d. What is the effect of the project on adjacent beaches?

4.  Impacts on Biota

a. What is the impact of burying a beach on the benthic community?

b. What conditions promote re-establishment of vegetation on the berm?

c. Will forage fish spawn on nourished beaches?

3. Bulkhead Removal

1.  Nearshore Habitat Conditions (e.g., Vegetation, Beach Profile)

a. How does removal of a bulkhead affect beach profile and sediment structure?. DEMO

b. How do changes in shoreline armoring affect eelgrass and other SAV? DB, EA

2.  Sediment Processes

a. What are the effects of bulkhead removal on beach sediment structure and processes both ‘upstream’ 

and ‘downstream’? DEMO

b. Does removal of bulkhead along a coastal bluff result in a change in the sediment supply for the beach? 

How much and when? What do we measure? DEMO, RES

c. What are the rates of sediment source reduction due to shoreline armoring? RES

d. How does presence of a bulkhead affect cross shore transport of sediment? What is the area of 

influence? Where are effects in relation to upper and lower beach? DEMO, EA

e. How does the depth of disturbance, due to wave events, vary between similar tidal elevations in front of 

and away from bulkheads? EA

3.  Hydrology

a. How do bulkheads and their removal impact beach hydrology? EA

b. How is wave action affected by the presence of a bulkhead? EA

4.  Approaches to Bulkhead Removal

a. At what scale does removal become meaningful/beneficial? How effective are alternative techniques 

and do they restore processes, structure, or functions? DB, DEMO
42    PUGET SOUND NEARSHORE PARTNERSHIP Technical Report 2006–1

Management

measure

General

topic or issue

addressed

Question Approach

3. Bulkhead Removal—Continued

4.  Approaches to Bulkhead Removal—Continued

b. Synthesize existing information on armoring trends and amount of passive erosion occurring in Puget 

Sound. DB

c. What other areas in the world with bulkheads can serve as models for Puget Sound? 

d. Can we separate effects of bulkhead removal from beach nourishment which often occur 

simultaneously? Is nourishment necessary after removal? EA, RES

5.  Riparian Zone Processes

a. Determine effects of bulkhead removal (bulkheading) on riparian-zone functions both ‘upstream’ and 

‘downstream’. DEMO

6.  VEC’s/Habitat

a. Are there habitat attributes created by a bulkhead removal that are useful to forage fish?

b. What are the linkages between shoreline armoring and key biota?

c. What kind of shifts occur in plant and animal communities after a bulkhead is removed?

4. Methods of Protecting Nearshore Ecosystems

1.  Effects of BMP’s and other Management Measures

a. How effective are buffers, setbacks, and other management measures (and what are the best 

recommendations for establishing such management actions)? EA, DB

5. Restoring Tidal Hydrology to Stream and River Deltas

A. Partial Restoration of Tidal Hydrology Tide Gates

1.  Effects on Water Quality

a. Does muted tidal action (e.g., water control structures, such as SRTG) result in unnatural water quality 

in emergent marsh tidal channels DEMO

B. Full Restoration- Dike Breaching or Removal

1.  Effects on Physical Habitat Characteristics (e.g., Channel Morphology)

a. Will dendritic tidal channel systems evolve more naturally complex plan-form structure (in erosive 

sediments) without intervention than with constructed tidal channels? DEMO

b. Will a new estuarine delta form within 50 years if the Puyallup River is diverted? DEMO

c. What is the difference between dike breaching and dike removal in geomorphic structure of a restoring 

wetland? DEMO

 d. Determine effects of dike removal and dike breaching on the development of channel morphology. EA

e. What are the differences in channel development between single breach, multiple breaches and full 

dike removal?

f. What are the effects of dike breaching or physical habitat characteristics outside the restoring marsh? DEMO

g. What sort of channel development will occur in the Nisqually NWR when dikes are removed (or 

breached)? DEMO

h. Should historic or remnant channels be reconnected or incorporated in marsh restoration?

i. Will predisking or plowing prior to dike removal affect location and speed of channel development? DEMO

2.  Effects on Biological Habitat Conditions

a. Is there a difference in natural vegetation recruitment and persistence between naturally-accreting 

recovering emergent marshes and sediment-supplemented recovering marshes? EA

b. What is the difference between dike breaching and dike removal in vegetation recruitment, and fish 

utilization of a recovering wetland? EA

c. What is the effect of wood on fish utilization and fish habitat attributes (e.g., prey resources, vegetation, 

etc.) of recovering emergent marshes? DEMO

d. Does the reduced channel complexity associated with diked systems cause sedimentation of eelgrass 

beds? EA

e. How do we monitor changes in bird use and what do we compare it to?
A Research Plan in Support of the Puget Sound Nearshore Partnership     43

Management

measure

General

topic or issue

addressed

Question Approach

5. Restoring Tidal Hydrology to Stream and River Deltas—Continued

B. Full Restoration-Dike Breaching or Removal—Continued

3.  Sediment Processes

a. How is the pattern/distribution of landscape elements on estuarine deltas controlled by long-term 

changes in the distribution of fluvial sediment across the landscape? Compare the morphology and 

distribution of existing and historic environments between deltas with diked and undiked portions. 

4.  Food Web Processes

a. There is no difference in source of organic matter supporting food webs of restoring emergent marsh 

wetlands than in natural emergent marsh wetlands. DEMO

5.  Effects on Sediment Quality

a. What is the difference in surface sediment contamination in restoration sites in urbanized estuaries 

compared to non-urbanized sites? EA
PSNERP and the Nearshore Partnership

The Puget Sound Nearshore Ecosystem Restoration Project

(PSNERP) was formally initiated as a General Investigation 

(GI) Feasibility Study in September 2001 through a cost-share 

agreement between the U.S. Army Corps of Engineers and the 

State of Washington, represented by the Washington Department 

of Fish and Wildlife. This agreement describes our joint interests 

and responsibilities to complete a feasibility study to

“...evaluate significant ecosystem degradation in 

the Puget Sound Basin; to formulate, evaluate, and 

screen potential solutions to these problems; and 

to recommend a series of actions and projects that 

have a federal interest and are supported by a local 

entity willing to provide the necessary items of local 

cooperation.”

The current Work Plan describing our approach to completing this 

study can be found at:

http://pugetsoundnearshore.org/documents/StrategicWorkPlanfinal.

pdf

Since that time, PSNERP has attracted considerable attention and 

support from a diverse group of individuals and organizations 

interested and involved in improving the health of Puget Sound 

nearshore ecosystems and the biological, cultural, and economic 

resources they support. The Puget Sound Nearshore Partnership

is the name we have chosen to describe this growing and diverse 

group, and the work we will collectively undertake that ultimately 

supports the goals of PSNERP, but is beyond the scope of the 

GI Study. Collaborating with the Puget Sound Action Team, 

the Nearshore Partnership seeks to implement portions of their 

Work Plan pertaining to nearshore habitat restoration issues. We 

understand that the mission of PSNERP remains at the core of our 

partnership. However, restoration projects, information transfer, 

scientific studies, and other activities can and should occur to 

advance our understanding, and ultimately, the health of the 

Puget Sound nearshore beyond the original focus and scope of the 

ongoing GI Study. As of the date of publication for this Technical 

Report, our partnership includes participation by the following 

entities:

Interagency Committee for Outdoor Recreation

King Conservation District

King County

National Wildlife Federation

NOAA Fisheries

Northwest Indian Fisheries Commission

People for Puget Sound

Pierce County

Puget Sound Action Team

Salmon Recovery Funding Board

Taylor Shellfish Company

The Nature Conservancy

U.S. Army Corps of Engineers

U.S. Environmental Protection Agency

U.S. Geological Survey

U.S. Fish and Wildlife Service

University of Washington

Washington Department of Ecology

Washington Department of Fish and Wildlife

Washington Department of Natural Resources

Washington Public Ports Association

Washington Sea Grant

WRIA 9