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Sound Science: 

Synthesizing Ecological and Socio-economic 

Information about the Puget Sound Ecosystem 

Observable, widespread declines in the status of species, habitats, and ecosystem function 

in marine and terrestrial environments have led to calls for ecosystem-scale management 

strategies as a solution for what ails watersheds and our coastal oceans (Pew 2003, 

USCOP 2004). At the core of most descriptions of system-wide approaches to natural 

resource management is the fundamental importance of considering both factors that 

drive human behavior and the choices we make regarding our use of natural resources, 

and a full range of potential consequences of human actions on the natural system. It is 

clear that implementing such an approach in coastal communities will require 

understanding not only the biology of terrestrial, estuarine, and marine ecosystems, but 

also how humans fit into the system as consumers, competitors, and producers. Such a 

perspective facilitates strategies designed to explicitly consider how biological, social and 

political factors cumulatively affect the goods and services provided by watershed and 

coastal ocean environments. 

In Puget Sound, we have an exciting opportunity to apply the principles encouraged by 

the national ocean commissions due to the leadership of Governor Christine Gregoire. 

The Puget Sound Partnership established by the Governor will set goals for Puget Sound 

“.....to ensure that the Puget Sound forever will be a thriving natural system, with clean 

marine and fresh waters, healthy and abundant native species, natural shorelines and 

places for public enjoyment, and a vibrant economy that prospers in productive harmony 

with a healthy Sound.” In particular, the Governor asks that the Partnership develop 

recommendations for what actions are needed to”...preserve the health, goods and 

services needed by the year 2020 to ensure that the Puget Sound’s marine and fresh 

waters will be able to support healthy populations of the native species, as well as water 

quality and quantity to support both human needs and ecosystem functions.” 

This document is designed to provide a broadly supported characterization of the Puget 

Sound ecosystem. This characterization can support the development of an action plan 

for achieving ecosystem-based goals for Puget Sound. It can also provide a foundation 

upon which prioritization of funding for research and monitoring in Puget Sound can be 

conducted. Because of Governor Gregoire’s leadership in Puget Sound, we are in the 

enviable position of having a motivated, intelligent and action-oriented audience for this 

document. The messages we include here are supported by a broad scientific community, 

which increases greatly the odds that the decisions made by the Puget Sound Partnership 

will be based on sound science. 
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Purpose and Scope 

The Puget Sound is one of the defining natural features of Washington State (Figure 1). 

However, with over 40 species currently listed as threatened, endangered, or as 

candidates for state and federal endangered species lists, declining populations of food 

fishes, birds, and over a dozen Superfund sites within the Sound, it is clear that this area 

has suffered many insults. These impacts are likely to increase, as the human population 

in the Puget Sound region is expected to double within the next 20 years. Past and 

ongoing impacts to the ecosystem affect not only our recreational enjoyment of the 

region, but also human health, fishing, shoreline development, and other economic 

pursuits (PSAT 2005; Table a). 

Figure 1. Insert map of Puget Sound region 

Table a. Insert table with list of major impacts from PSAT, other assessments 

In order to meet the Puget Sound ecosystem goals of economic and environmental health, 

a system-wide perspective is needed. Achieving these multiple goals requires both that 

they be clearly articulated and that policy-makers have access to assessments of indirect 

or potentially unanticipated impacts of management actions on the ecosystem (Box 1—

urchin barrens), and of potential biological, social and economic tradeoffs between 

potential management strategies. Science can be instrumental in informing wise 

decisions in both of these areas. For example, effects of management actions can be 

translated into “ecosystem goods and services” resulting from ecosystem structural 

elements such as species and habitats (Box 2). These goods and services can be used as 

common currencies for comparison among alternative sets of ecosystem-scale actions, 

allowing the public and policy makers to explicitly consider how changes in ecosystem 

attributes translate into changes in the services provided by the system. Such a 

framework also allows consideration of trade-offs among multiple ecosystem objectives 

and ways to achieve them. In addition, scientists can develop decision support tools that 

can help organize information to explore ecosystem-level consequences of management 

actions. By combining ecological estimates of how ecosystem structure and function 

maintain services with economic estimates of the services’ values to humans (e.g., 

commercial and recreational fishing, shoreline stabilization, cultural heritage, existence 

of wild species), ecosystem management strategies can be developed so that human 

actions serve to maintain those values. 

Box 1--Insert Box showing pictures of urchin barrens and kelp forests—brief story of the 

role of otters and other top predators in structuring food webs and habitats. 
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Box 2--Include list of examples of ecosystem services and how they are just more formal 

statements of human visions for coastal ecosystems. 

The Figure below is from the National Research Council (2004) and shows conceptually 

how human actions can cause changes in the ecosystem structure and function, which in 

turn result in different outputs of goods and services from the system. Valuing the 

ecosystem services and looking at the cost-effectiveness of alternative approaches to 

achieving ecosystem objectives can inform wise management strategies for achieving 

ecosystem goals. 

The multiple goals of thriving natural systems and vibrant human communities in the 

Puget Sound region suggests a more integrated approach to managing Puget Sound. We 

are fortunate to have a wealth of existing scientific work, assessments and planning that 

already have been done—together, this base of information already can start us on a path 

towards an ecosystem-scale action plan for achieving Puget Sound goals. As a first step 

toward supporting ecosystem goals and strategies to achieve them in the Puget Sound 

region, we provide here an overview of the Puget Sound ecosystem, key science needs 

for more effective management and currently identifiable threats to the system. 

 

In the first section, we describe the components of the Puget Sound ecosystem, including 

humans and their effects as part of the system, and characterize linkages between those 

components. This section summarizes what we know about the Puget Sound 

ecosystem—its structure, function, and the goods and services it could provide. We 

know a lot about some parts of the ecosystem—the species, habitats upon which they 

depend and the processes that maintain those habitats. For some species, habitats, and 

processes, we have a fairly good understanding of how human actions threaten their 

persistence and function. However, we know less about the complex food web 

Human actions 

(private, public) 

Ecosystem 

structure & 

function 

Ecosystem 

goods & 

services 

Values* 

Ecological production 

Economic valuation 

*e.g., harvesting, water supply, recreation, 

transportation, aesthetics, flood, erosion, and pollution 

control, human health, cultural heritage, species and 

biodiversity preservation. 
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relationships among species and how the cumulative effects of human actions interact to 

impact the ecosystem. Our understanding of how Puget Sound produces ecosystem 

goods and services, and how to assign values to those goods and services is in its infancy. 

In this section, we also highlight those key threats that clearly have a significant impact 

on ecosystem elements. We also identify key information needs, defined as gaps that, if 

filled, would substantially improve our ability to anticipate ecosystem responses to 

environmental variation and human actions, and therefore our ability to manage for 

specific ecosystem goals. 

In the second section of the document, we summarize how both biological and social 

science tradeoffs can be assessed in decision frameworks for ecosystem approaches to 

management in Puget Sound. We illustrate these ideas with a transparent and clear 

decision framework that can be used to organize what we know about the natural and 

socio-economic systems to develop short-term management strategies for achieving 

ecosystem goals. These decision frameworks are designed to adapt strategies over time 

as our understanding improves of how the ecosystem functions, the relative cost 

effectiveness of alternative actions and how changes in ecosystem functions lead to 

changes in the goods and services. 

Finally, in the last section, we identify key findings that can contribute to developing both 

short and long-term action plans and ultimately to achieving Puget Sound goals identified 

by the region. This section highlights the conclusions from this synthesis and points 

towards how these findings might inform the charges facing the Puget Sound Partnership. 
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The Puget Sound Ecosystem: Biological, Physical and Human 

Components 

Overview

The U.S. Puget Sound includes the waters that extend from the mouth of the Straits of 

Juan de Fuca east including the San Juan Islands and south to Olympia (Figure 2). It is a 

large, complex estuary that covers an area of approximately 2,330 km2

, includes about 

3,700 km of shoreline, and is fed by thousands of streams and rivers that drain a total 

land area of about 35,500 km2. Based primarily upon geomorphology, extent of 

freshwater influence and oceanographic conditions, Puget Sound can be sub-divided into 

five major basins: North Puget Sound, the Main basin, Whidbey Basin, South Puget 

Sound and Hood Canal. Each of these basins differs somewhat in such features as 

temperature regimes, water residence and circulation, biological conditions, depth 

profiles and contours, processes, species, and habitats. On average, the Puget Sound has 

a depth of 62.5m, but ranges to nearly 300m at its deepest. This depth is the result of 

relatively recent geologic events, as 10,000 years ago, mile-thick glaciers pushed 

southward into the basin, carving deep fjords and depositing sediments hundreds of 

meters thick. 

The physical features of the Puget Sound support a diverse array of plants and animals. 

There are at least 100 species of birds, 26 species of marine mammals, 200 species of 

fish, and thousands of species of plants and invertebrates that can be associated with the 

waters of Puget Sound. While some of these species are biological invaders (e.g., 

Spartina), most of the species of Puget Sound are native species that include both 

residents and transient or migratory species. 

Both physical and biological features of the landscape have changed in response to 

ongoing settlement and increased population in the area. Land use changes have 

continued to convert the natural landscape to residential, commercial and industrial use. 

Between 1991 and 1999 alone, 73 more square miles of land was developed and 241 

square miles of forested lands were lost (PSAT 2005). Approximately 1/3 of the 

shoreline of Puget Sound has been impacted with bulkheads or overwater structures, 

much of it as a result of residential development. A wide variety of contaminants can be 

found in the waters, sediments, and biota of Puget Sound ranging from metals (copper) to 

organic chemicals (PAHs, PCBs). Some areas are so contaminated (e.g., Eagle Harbor 

and portions of the Puyallup and Green river estuaries) that they have qualified for 

SuperFund cleanup. 

In this section we describe the Puget Sound ecosystem in more details. We address six 

elements in particular: 1) habitats and physical factors that drive habitat types and 

distribution; 2) global processes, such as climate; 3) local, marine physical and chemical 

processes, including circulation; 4) interactions between freshwater or terrestrial systems 

and the marine system; 5) food webs, species interactions and individual species’ 

biology; and 6) socio-economic factors influencing the ecosystem. These elements are 
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linked in a conceptual model of the system (Figure 2). Global processes, and marine and 

freshwater or terrestrial processes all affect habitat distribution and availability as well as 

food webs and other species interactions. All can be affected by external natural or 

anthropogenic mechanisms, either directly or indirectly. Finally, the interaction of all 

these elements provides tangible or intangible “goods” that are valued by humans. For 

each element, we also identify “key” science needs or gaps – those pieces of information, 

that if obtained, would allow more effective management of the system -- and, where 

currently available information allows, key threats to that element. 

 
Natural mechanisms and anthropogenic activities

e.g., shoreline modification and dredging, 

discharges and spills, water flow alteration, 

logging, agriculture, upland development, 

biological resource harvest and culture, shipping, 

climate change, introduction of exotic and 

invasive species

Marine, freshwater and terrestrial processes

e.g., physical, chemical and biological processes such as 

element cycling, sediment transport, circulation and tides, 

primary and secondary production

Food web and 

species 

dynamics

Habitat types

and distribution

Status of ecosystem and its services

Figure 2. Natural and anthropogenic drivers of changes in ecosystem processes, structure & function; and the resulting ecosystem goods and services

Human valuation of goods and services and 

costs of management
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Puget Sound Habitat Types and Distribution

The marine ecosystems of Puget Sound are distributed across a mosaic of habitat types 

that support a rich array of species. In our conceptual model (Figure 2), Puget Sound 

habitat types and distribution are influenced by physical and chemical processes in the 

marine and freshwater realms, and both influence and are influenced by species 

interactions. Habitat types and their distribution also mediate many of the goods and 

services valued by humans. In this section, we provide an overview of habitats and 

species typical of Puget Sound for use as a general reference throughout this document. 

The goal of this section is not to develop a detailed taxonomy or typology of habitat 

types, but instead to provide a framework for discussing major habitat types and linking 

them to the physical and biological processes that have the potential to shape or modify 

them. We first identify several key physical attributes of marine habitats in Puget Sound, 

and then briefly describe some of the species characteristic of each habitat and impacts of 

the human activities that take place in each. Several more complete treatments of habitat 

exist, for example, Dethier’s Habitat Classification Scheme. More comprehensive 

treatments of the marine flora and fauna can be found in Kozloff 21983). The natural 

history of the region is described in Kruckeberg (1991). 

Key physical attributes of marine habitats in Puget Sound include depth and factors such 

as light and temperature that are correlated with depth, substrate type, water properties 

(temperature, salinity, nutrients), and hydrodynamic regime. A primary division in our 

characterization is those habitats that exist in the water column vs. those that are 

associated with a substrate. Depth and its correlates influence both benthic and pelagic 

community composition through physical (e.g., light, temperature), and biological (e.g., 

food web) processes. Within both water column and benthic habitats, we further 

distinguish between habitat types found at different depths. Finally, substrate type is a 

primary determinant of community composition, and we identify areas of different 

substrate. Water properties throughout the Sound influence planktonic communities and 

the food webs they support. Hydrodynamic regimes, especially those driven by tidal 

forcing, interact with other physical and biological attributes to shape habitats and their 

characteristic biological communities Disturbance events, both natural and 

anthropogenic, also exert control over species interactions, habitats, and ecosystem form 

and function. 

We first describe characteristics of the pelagic realm, defining the water column as 

habitat, then proceed to describe several key benthic habitats. 

The Water Column 

The water column comprises the aqueous habitat in which planktonic and demersal 

organisms exist. For convenience, the water column often is divided into the euphotic 

(lighted) and aphotic (unlighted) zones. The bulk of primary production occurs within 

the euphotic zone, which extends to variable depths, depending on water clarity and 
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penetration of sunlight. Phytoplankton are most abundant in the euphotic zone, where 

they form the basis of marine food webs. Areas of upwelling or vigorous tidal mixing can 

support blooms of large centric diatoms that can lead to trophic intensification that 

supports dense feeding aggregations of fish, birds, and mammals. In other areas, for 

example Hood Canal and Port Susan, injection of nutrients can cause phytoplankton 

blooms that lead to hypoxia or anoxia, in some cases causing mortality among fish and 

invertebrates. Where it occurs, hypoxia is generally a characteristic of deeper waters. 

Nearshore waters are tightly linked to upland areas via freshwater inputs. Terrigenous 

sources of sediment, toxicants, and pollutants all are delivered to nearshore waters in 

suspension or solution via fluvial, stormwater, or municipal inputs. These can remain 

entrained in surface layers until the lower-salinity surface waters are mixed with deeper 

waters. Tidal forcing causes nearshore low-salinity water masses to mix with those 

further from shore to form water masses of intermediate characteristics. Mixing occurs in 

both horizontal and vertical dimensions, through the formation and dissipation of tidal 

eddies and through upwelling at sills, and results in redistribution of terrestrially-derived 

particles and solutes throughout the water column. Some particles—for example, 

terrigenous sediments carried in the Fraser River plume—influence pelagic ecosystems 

via attenuation of light in the upper water column, with consequent impacts on primary 

productivity. Conversely, terrestrially-derived solutes tend to impact pelagic ecosystems 

via physiological or metabolic pathways that can have negative consequences for marine 

organisms. PCBs, dioxins, and other endocrine disruptors can act in this fashion to 

increase the incidence of disease in vertebrates within Puget Sound. 

Trophic webs link nearshore pelagic areas to those further offshore and in deep basins. 

For example, middle trophic species such as herring, surf smelt, and sandlance use 

nearshore areas for feeding and reproduction; they in turn are preyed upon by piscivorous 

fish which ultimately are consumed by birds and mammals. Ontogenetic shifts, for 

example transitions from larval or juvenile to adult phases, also serve to link shallow 

nearshore areas with deeper offshore areas. For example, larvae of some rockfish 

(Sebastes spp) species appear to spend a portion of their planktonic life history in surface 

waters. Juveniles recruit to shallow (<20 m) benthic areas, while adults inhabit deeper 

areas. Detrital and microbial food webs provide additional important linkages between 

shallow nearshore areas and deeper offshore areas. 

Benthic habitats 

Beaches

Puget Sound's beaches are formed from sediment supplied by the erosion of coastal bluffs 

and redistributed by wave action and littoral drift. They are composed of mud, sand, 

gravel, or cobble, or a mixture of these. Sandy beaches tend to be unstable and typically 

support relatively few species and relatively low biomass. Among the more conspicuous 

species on sandy beaches are beachhoppers, small amphipods that consume drift algae 

deposited by tides and which are themselves consumed by shorebirds. Like sandy 

beaches, gravel beaches tend to be unstable and support relatively few species. Stability 

tends to increase as grain size increases and cobbles become larger and more numerous. 
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In such areas, epibenthic algae and small invertebrates become more abundant, and 

infaunal invertebrates become more numerous and diverse. In northern regions of Puget 

Sound, mixed-substrate beaches support opportunistic algal species, for example, the sea 

lettuce Ulva, as well as epibenthic barnacles and littorine snails, and infaunal 

polychaetes, arthropods, and molluscs. In southern regions of Puget Sound, epibenthic 

barnacles, snails, and the Pacific oyster dominate such beaches. Edible clams occupy the 

low intertidal zone on some beaches. 

Humans interact with beaches in many ways. Beaches are preferred sites for many 

recreational activities, including beachwalking and clamming, and they offer staging 

areas for activities such as SCUBA diving and kayaking. Upland areas adjacent to 

beaches are preferred for residential development; in many areas of Puget Sound, 

residential development has led to beach hardening in efforts to protect homes and other 

buildings. 

Rocky habitats

Rocky shores are composed of bedrock or a mixture of boulder and cobble substrates and 

tend to occur in areas where sediments do not accumulate. Rocky substrates tend to be 

more stable than sediment-dominated habitats, and the biological communities that 

develop on rocky shores reflect this. Some species are very long-lived, reaching ages of 

several decades or more; other species create highly persistent patches composed of 

multiple, short-lived individuals. Still other species are short-lived and highly 

opportunistic, taking advantage of space opened through physical disturbance or by 

mortality of longer-lived individuals. The rockweed Fucus gardneri is abundant on rocky 

shores throughout the region, where it grows mixed among several species of barnacles. 

Fucus communities support a rich array of small grazers and their predators. 

In lower intertidal and shallow subtidal areas, Fucus is replaced by several species of 

kelp that support a different but equally rich community of grazers and predators. Urchins 

and abalone are among the species found in association with kelp communities; both 

species have declined sharply due to human removals for food, and abalone now are a 

conservation target in rocky areas where they once were abundant. 

Deep rocky habitats are characterized by the absence of kelps and other large seaweeds, 

and by the presence of benthic suspension feeders and multiple species of fish, including 

several species of rockfish (Sebastes spp.). Adult rockfish tend to associate with emergent 

rocky substrates (bedrock, boulders), to which they appear to have high site fidelity. Site 

fidelity, coupled with characteristics of delayed reproduction, extreme longevity, and 

susceptibility to fishing-induced embolism, combine to make rockfish highly vulnerable 

to overfishing. Populations of most species of rockfish in Puget Sound have declined 

sharply, and most now are conservation targets. 

Humans interact with natural communities on rocky shores through recreation and 

through shoreline development. Both can have negative impacts where the disturbance is 

frequent or severe. For example, beachwalkers unintentionally can cause mortality of 

seaweeds and invertebrates through trampling, and the construction of docks, piers, and 
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beachfront homes can modify the physical environment in ways that reduce habitat 

quality for rocky-shore organisms. 

Estuaries, Deltas, and Bays 

In an oceanographic sense, the entire Puget Sound constitutes a single large estuary, 

characterized by fluvial forcing that establishes an estuarine circulation pattern typified 

by the efflux of low-salinity water at the surface and influx of more saline oceanic water 

at depth. In a more vernacular sense, Puget Sound is comprised of multiple smaller 

estuaries, each created by one of the numerous rivers that drain into Puget Sound. These 

smaller estuaries contribute disproportionately to the overall productivity of Puget Sound. 

Their shallow expanses of well-lighted water promote the growth of phytoplankton, 

seagrass, and seagrass epiphytes. These form the basis of important nearshore food webs, 

provide habitat essential to juveniles of several important species (e.g., out-migrating 

salmon smolt), and export particulate and dissolved organic matter to offshore areas. 

Deltas are formed in areas where rivers deposit large amounts of sediment in nearshore 

areas. Deltas are characterized by their soft sediments and brackish waters, both of which 

influence the species that occupy deltaic areas. Rooted vegetation—for example, marsh 

grasses such as invasive Spartina, and native species such as Salicornia or pickleweed—

tend to be more common in deltas than in other areas of Puget Sound. Marsh plants are 

important to the development of nearshore food webs, including those important to 

migratory birds. 

Bays share several important characteristics with small estuaries—they tend to be 

shallow, well-lighted, and highly productive, and they often support the growth of 

eelgrass and associated communities. Not all bays are supplied by rivers, however, and 

bays therefore can differ from small estuaries in their physiographic and oceanographic 

characteristics. Although many bays are characterized by soft-sediment habitats, some 

bays in the northern and western areas of Puget Sound are rocky, or are a mixture of softsediment and rocky habitats. 

Estuaries, deltas, and bays all are highly desirable and heavily utilized for a variety of 

human activities. Recreational uses include boating and fishing (including crabbing and 

clamming). Commercial uses include aquaculture, fishing, and the construction of 

facilities (e.g., docks) and the modification of habitat (e.g., dredging) to support such 

activities. 

Figure 3. A panel figure with photos of several different habitat types. 

Interactions between Habitats and Other Ecosystem Elements 

 

Aquatic organisms have adapted to variability in the natural environment by evolving life 

history strategies that reduce their reliance on a particular habitat or optimize their 
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opportunities for successful reproduction (Gross 1987). As an example, Pacific salmon 

integrate habitats and ecosystems from headwater streams and uplands to the estuary, 

Puget Sound, and thousands of miles into the ocean by active migration and homing. 

During this migration the salmon transition through various food webs (Keeley and Grant 

2001) initially feeding on aquatic and terrestrial invertebrate drift (or zooplankton) in 

freshwater, benthic and epibenthic taxa such as amphipods and copepods as well as 

mysids, cumaceans, isopods, polychaetes, and shrimp in shallow nearshore waters 

(Kaczynski et al. 1973, Simenstad et al. 1982, Duffy 2003), and planktonic and neustonic 

taxa such as crab larvae, larvacean, Euphausiids, and fish in deeper nearshore waters 

(e.g., Simenstad et al., 1980; summarized in Duffy 2003). 

Other species such as the bull trout and coastal cutthroat trout are also anadromous, but 

have a much more limited seaward migration and much greater reliance on the nearshore 

waters of Puget Sound. Marine birds such as seabirds, waterfowl, and shorebirds 

similarly integrate habitats over a wide geographic expanse and ecologic range through 

their migrations. Habitat or ecosystem change in one of the connected habitats therefore 

affects the other connected habitats through its impact on the condition or behavior of 

migratory species. Loss of estuary habitat, poor ocean conditions for salmon, or excess 

harvest result in fewer spawners returning to streams, reduced contribution of marine 

nutrients from salmon carcasses to the streams and associated riparian and terrestrial 

community, and lower productivity in these habitats and communities. Reduced numbers 

of salmon also have a direct effect on their predators including orcas, pinnipeds, and 

bears. 

The nearshore of Puget Sound provides very important habitat to shorebirds, waterfowl, 

shellfish, finfish, and numerous other biota. Armstrong et al. (1976) found hundreds of 

species of invertebrates and Thom et al. (1976) found 157 species of algae in the 

intertidal zone of five beaches within the central Puget Sound. Community studies for 

eelgrass, saltmarshes, tidal channels, and coastal sand dunes reveal that numerous species 

use nearshore habitats for part or all of their lives (Canning and Shipman, 1995). Many 

of the animals that spend some time on or in beaches are there to feed, reproduce, rear, or 

rest. 

Physical processes also influence habitat distribution and abundance. Currents, including 

tidal currents, affect substrate and determine whether particular areas are depositional or 

erosional habitats, and thereby affect the structure and productivity of the biotic 

community. Winds affect water column mixing. Upland watersheds have distinct effects 

on many estuarine and marine habitats and species through flow (hydrograph and effect 

on salinities downstream), turbidity, and temperature, and delivery of sediments, 

nutrients, and contaminants and these effects vary among seasons and basins. For 

example, two-thirds of the freshwater reaching Puget Sound enters the main basin 

through the Skagit and Snohomish rivers via the Whidbey Basin with smaller amounts 

contributed by Lake Washington and Duwamish and Puyallup rivers (Strickland 1983). 

The amount of freshwater delivered into the Sound is determined by runoff and snowmelt 

which vary seasonally. 
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Dams have disrupted the natural connectivity within watersheds and between watersheds 

and the estuary/ocean in Puget Sound as in other parts of the PNW and the world. Two 

dams on the Elwha River (Strait of Juan de Fuca; dams slated for removal within the next 

few years) starved the lower river, estuary, and associated nearshore areas of sediment for 

nearly a century, reducing gravel and finer substrate habitats in these downstream areas 

and correspondingly depleting salmon and bivalve populations (Wunderlich et al. 1994). 

Forage fishes, marine birds, marine mammals, and other species no doubt also have been 

affected but the effects are unquantified. Monitoring to evaluate dam removal should 

shed light on the former impacts on these other biota (Triangle Associates, Inc. 2004). 

Current and Potential Threats to Puget Sound Habitats 

 Coastal Development

Coastal development has fundamentally changed the landscape of the Puget Sound. 

Shorelines have been converted to commercial or residential uses; wetlands have been 

dredged or filled; hydrological systems disrupted by diking or channeling. Since 

European settlement, Puget Sound had lost 58% of its intertidal habitat (Hutchinson 

1988); the Duwamish, Lummi, Puyallup, and Samish River deltas have lost 92% of their 

intertidal marshes (Simenstad et al. 1982, Levings and Thom 1994); and at least 76% of 

the wetlands around Puget Sound have been eliminated, converted to industrial uses in 

urban areas and to farmland in rural areas. The mudflats associated with the deltas of 

these estuaries have also substantially declined. About 30% of Puget Sound’s beaches 

now are armored; in some areas, nearly 100% of the shoreline is armored. Armoring 

reduces the supply of sediment to beaches, leading to narrowing and coarsening, 

increased scour, and erosion of adjacent areas. These physical changes have negative 

consequences for littoral species and for ecosystem health. 

Invasive Species

Non-native invasive species (NIS) cause negative impacts to receiving environments via 

habitat alteration, resource competition, food web interactions, and pathogenesis. Among 

the known NIS in Puget Sound are vascular plants (Spartina spp., Sargassum muticum, 

Zostera japonica) and marine invertebrates (several sea squirts, bivalves, drilling snails 

and zooplankton). Other non-native species are present but not yet obviously invasive 

(e.g., Atlantic salmon and American shad), and still others are cryptogenic (of unknown 

origin, e.g., some sea lettuce species). Alteration of habitat by NIS already has occurred, 

for example conversion of tidal flats to vegetated meadows via sediment accretion by 

Spartina spp.; loss of native understory kelp species due resource pre-emption by 

Sargassum; and loss of intertidal Fucus due to interactions with Pacific oysters. 

Evidence from San Francisco Bay and other west coast estuaries suggests that NIS will 

increase in Puget Sound, with increasing negative consequences for native systems. 

Additional threats to be fleshed out: 

• Contamination of water and sediment 

• Anthropogenic hydrological modifications in watersheds affecting both water and 

sediment 
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• Human population growth (and concomitant impacts to habitats and habitatforming processes) 

• Changes in physical habitat-forming processes (e.g. currents, sediment delivery) 

due to changes in climate 

Key Science Needs 

• Data to describe and quantify linkages between ecosystem processes, habitat 

structure and organism response. 

• Characterization of deep benthic and pelagic habitats, including their biota and 

human impacts. 

• Understanding of likely effects of climate change on habitat-forming processes 

and habitat distribution 

• Description and quantification of single and multiple stressor effects on habitat 

quality, quantity and distribution (including habitat modification, invasive 

species, etc.) 

Note to reviewers: Both key threats and science needs will require greater description, 

and will be modified in response to reviewer comments. 

Influence of Climate and Other Global Processes on the Puget Sound Ecosystem

That climatic variation underlies the dynamics of many populations, communities and 

ecosystems is hardly a new idea. In our conceptual model (Figure 2), we include 

climatic variation as a natural process influencing these elements. Inter-annual (e.g., El 

Niño events) and inter-decadal climate variability (e.g., climate regimes) generate 

substantial changes in precipitation and winds that effect changes in primary production, 

which in turn propagate throughout. In marine systems, climatic processes like El Nino 

Southern Oscillation (ENSO) have substantial ecological and fisheries consequences in 

the short term, while climate regimes described by the Pacific Decadal Oscillation (PDO) 

have longer lasting consequences. To better manage Puget Sound marine resources and 

anticipate indirect consequences of our actions, or respond effectively to natural variation 

in the system, we need to understand the mechanisms through which climate affects these 

systems and incorporate that knowledge in to our prediction and management. 

Climate and oceanography are clearly linked through coupling and positive feedback in 

the overall processes of global heat redistribution. The two are also linked in their effects 

on marine ecosystems. Large-scale climate patterns effect changes in physical 

oceanography that in turn influence population dynamics and ecosystem function. Since 

oceanography is the mechanism through which climate affects marine populations, it is 

appropriate to investigate jointly their impact on Puget Sound ecosystems. Better 

understanding the influence of climate on marine populations is important for making 

better short and long-term predictions, evaluating the past effects of human impacts, 
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determining remediation approaches to current problems, and defining our expectations. 

In this endeavor defining the mechanisms through which climate affects population and 

ecosystem dynamics is essential. 

The El Niño Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) – Key 

ecosystem drivers 

A primary oceanographic mechanism through which ENSO and the PDO regimes 

influence marine ecosystems is through the disruption of coast upwelling, which 

influences water temperature and nutrient availability. Wind-driven coastal upwelling in 

the eastern margins of the world’s oceans results in highly productive fisheries. El Nino 

events and warm regimes disrupt this upwelling through both the weakening of upwelling 

favorable winds and the deepening of the thermocline due to relaxed traded winds, 

resulting in reduced nutrient availability and consequently lower primary productivity. 

These oceanographic effects propagate through the biological side of the system 

devastating fisheries yields. The ramifications are more complex than simple changes in 

abundance or biomass based on productivity. They include changes in assemblage 

structure and the distributions of species in depth, latitude, on-shore vs. off-shore location 

as well. For example, changes in the strengths of the Alaska and California currents 

under different PDO conditions affect the relative abundance of northern and southern 

copepods, which in turn influences recruitment success of some of their predators. 

Climate Change and its potential effects on Puget Sound 

There is a strong consensus that human activities have induced and will continue to cause 

profound climate change through global warming. This change has and will continue to 

impact marine ecosystems, and the challenge that we face is to manage marine resources 

in the face of this change. Climate change may manifest as increases in the frequency 

and intensity of extreme events like El Nino, submarine eruptions that cause fish kills, 

and anoxic events due to changes in ocean circulation. Changes may also occur as the 

result of more general changes in the ocean system like a general warming and changes 

in productivity. Predicting the impacts of these changes on the ecosystem and related 

fisheries is an important task and requires an understanding of the mechanisms though 

which climate and oceanography affect fish stocks. 

The Climate Impacts Group at the University of Washington published two important 

reports (Snover et al. 2005; Mote et al. 2005) for the Puget Sound Action Team that 

document the evidence that climate change has and will continue to occur. Further, these 

reports document a number of potential impacts that climate change may have on the 

Puget Sound ecosystem. Here, we highlight several of their key findings. 

Based on extensive review of climate records, the UW Climate Impacts Group concluded 

that there is compelling evidence for climate change in the Puget Sound Region. 

Evaluation of temperature records, for instance, shows that nearly every climate record in 

the Pacific Northwest shows evidence of substantial warming. On average temperature 

increased about 2.3o

F from 1900 to 2000. While changes temperature shows a clear 

warming trend, changes in precipitation are more variable—so variable that, to date, any 
16

trend in precipitation cannot be distinguished from the recorded long-term variability in 

the system. 

Climate models predict an average rate of warming of 0.34o

C per decade through 2040 

(with some models projecting a rate as low as 0.2o

C and as high as 0.5oC per decade). 

Even though projected changes in precipitation are presently unclear, changes in 

temperature will have significant impacts on snowpack and stream flow, thus altering 

freshwater input into Puget Sound. The UW Climate Impacts Group work shows that the 

timing of water input into the Sound has changed substantially with more water entering 

the Sound earlier than historically. For instance, with warmer temperatures and less 

snowpack, the amount of water currently entering Puget Sound between June-September 

has declined by 18% as compared to the historical record. Additionally, most of the 

glaciers in the region have been retreated for 50-150 years, affecting flow rates in some 

systems. Overall, we can expect reduced spring snowpack, earlier spring snowmelt, 

increased winter flow and decreased summer flow. 

Water temperature, salinity, density, dissolved oxygen, and nutrients are influenced by 

climate-related fluctuations in the Pacific Oceans, freshwater input and local weather. 

While human activities around Puget Sound clearly affect these attributes of water 

quality, climate change may potentially exacerbate these problems. For instance, rises in 

sea level associated with climate warming could affect nutrient levels in surface waters 

via increased leakage from septic systems. 

Such changes can have significant impacts on the Puget Sound system. For example, 

changes in flow along with changes in temperature, solar radiation, winds can affect 

density gradients within the water column and thus promote or inhibit stratification 

(layering)in Puget Sound. Any factor that mixes water masses (e.g., winds, tidal 

circulation) will decrease stratification, and factors that increase density differences (e.g., 

fresh water input to the surface, high solar radiation) produce or maintain stratification. A 

typical model of estuarine stratification is of two layers: relatively warm, fresh water 

overlying colder, more saline water with separation marked by a distinct pycnocline 

(region of highest density gradient). 

The intensity and persistence of the density stratification of a water column is a key 

factor with wide–ranging effects. The development of stratification within the water 

column is significant because of the physical barrier it presents with respect to vertical 

water movement. Turbulent eddies, driven by winds and tides, cause vertical mixing of 

phytoplankton, DO, nutrients, etc. If, however, the water is stratified, that is, its density 

increases significantly with depth, then the ability of turbulent eddies to accomplish 

vertical mixing will be greatly decreased. This is particularly true at the pycnocline, the 

region of greatest density change, which is often observed in the top several meters of the 

water column. Thus, stratification effectively isolates the surface water from the deep 

water. When stratification is intense, two environmental conditions can be affected: 

surface waters can become depleted of nutrients (dissolved nitrogen and phosphorus) and 

bottom waters can become depleted of oxygen. This is due to phytoplankton growth in 

the surface water that will deplete ambient nutrients, with no re-supply from nutrient-rich 
17

deep waters, and to the decomposition of the organic material in the bottom water that 

will consume oxygen, with no re-supply from oxygen-rich surface water. 

While reduced river input to Puget Sound–Georgia Basin could be hypothesized a priori 

to increase salinity of the receiving marine waters, marine water properties are affected 

by weather–related forcing on a substantial scale. For example, the 2000–2001 drought 

period and its associated increase of estuarine salinity lead to higher density surface 

layers and weaker stratification, with a percent reduction in stratification averaging ~50% 

for Puget Sound–Georgia Basin and the outer Washington coast estuaries. Furthermore, a 

result of the higher salinity surface waters and weaker vertical density gradient is a 

decreased outflow velocity through the Strait of Juan de Fuca. In fact, flow was affected 

by a factor of four between drought and normal flow years; the reduced seaward flow 

presumably translates to longer residence times in the estuary. Implications of this could 

be substantial to ecosystem–level processes. First, marine water quality conditions, such 

as low dissolved oxygen concentrations, which are maintained by density stratification, 

could be affected. A reduction in stratification could lead to less probability of low 

oxygen because of increased mixing (less of a seawater density gradient to overcome). 

Alternatively, the reduced exchange velocity and an increased water residence time in the 

estuary could lead to lower oxygen concentrations because of increased time when 

respiration dominates before exiting the system. 

Although stratification is necessary for phytoplankton growth it also optimizes the 

chances for low DO concentrations. Conditions favorable for phytoplankton growth are 

sufficient light and nutrients and some degree of stratification (i.e. to prevent mixing out 

of the euphotic zone). Under such conditions, phytoplankton biomass increases in the 

upper layer of the water column and nutrients are consumed as growth continues. 

Without a replenishing source, surface nutrient concentrations decrease and can limit 

phytoplankton growth, causing a decrease in their biomass. When a nutrient source is 

available to surface waters, however, phytoplankton production will never reach a 

nutrient-limited state. Nutrient input can occur naturally through mixing, but the mixing 

also causes light limitation thus preventing significant population increase. 

Eutrophication (external increase in nutrient supply to system) of nutrient-limited 

stratified waters can result in very large algal blooms and, after these sink, a 

correspondingly large DO debt in bottom waters. However, the physical stratification of 

the water receiving the nutrient input is important, as inputs to well-mixed water columns 

have no immediate effect. 

Attributes of the saltwater in Puget Sound are a function of climate conditions in the 

coastal ocean. As discussed above, coastal waters are highly influenced by coastal 

upwelling, and thus any affect of global climate change on upwelling can have profound 

influences on the ecosystem of Puget Sound. Exactly, how global warming will affect 

the crucial wind patterns that drive upwelling is currently unclear. 

One of the best understood and most predictable components of climate change is sea 

level rise. Globally sea level has been increasing at a rate of abut 1-2 mm per year. How 

this global average is translated to Puget Sound is the by-product of a host of geological 
18

factors. For example, land in some regions of south Puget Sound land are sinking more 

than 2mm per year, while land does not appear to be sinking in regions of north Puget 

Sound. Thus, we might expect net sea level rise in south Puget Sound to be greater than 

the global average. Additionally, some climate models predict shifts in winds that could 

increase sea level rise by an additional 20cm in some regions of the Sound. 

Consequences of climate change for the Puget Sound Ecosystem. 

While a number of human activities clearly have had profound impacts on the ecosystem 

in the Sound, climate change probably has had little impact on the ecosystem relative to 

other risk factors. However, the consequences of future climate change are significant. 

Warmer temperatures may increase the productivity of plankton in surface waters. As 

discussed above this could lead to decreases in dissolved oxygen (DO). Depletion of DO 

in the water column can have a serious impact on marine ecosystems. The degree of 

impact will be dependent upon the intensity of the DO depletion as well as the temporal 

and spatial stability/persistence of the depressed DO levels. In addition, the effects of 

DO depletion are both organism and habitat-specific. Certain species of fish are stressed 

by environmental conditions of DO concentrations just under 5 mg/L. Other species may 

not exhibit stress at 2.0 mg/L. Benthic infauna and, particularly, molluscs are more 

resistant to hypoxia. 

Continuous or even intermittent hypoxic events may result in a shift in species 

composition. Fish may move away from the depleted area, or have higher susceptibility 

to disease. Motile species that are affected will attempt to leave the hypoxic area. 

Sedentary species may be killed outright, or exhibit significant changes in reproductive 

rates and larval recruitment. The species composition of a given area may also shift in 

response to changes in predator-prey relationships. Hypoxic conditions can initiate 

behavioral changes and physiological stresses. The diel pattern of vertical migration 

exhibited by some zooplankton to avoid predation can be interrupted. Copepods have 

been found to remain in the pycnocline in an attempt to avoid a bottom layer of lowoxygenated water. Hypoxia may also inhibit the hatching of zooplankton eggs, thereby 

reducing larval recruitment, and suppress metabolic rates. 

Thus, the net effect of oxygen depletion in marine waters may be a shift in species 

composition, a decrease in population numbers and species diversity with a resulting 

decrease in amount and type of biomass, a disruption of the usual predator-prey 

interaction, and a shift in the expected trophic pathways. These combined effects can 

result in reduced availability and subsequent harvest of marine resources. 

Rising sea level will also contribute to significant ecosystem changes. Salt marshes, for 

example, are among the world’s most productive habitats and support a number of 

important species and provide important ecosystem services. As discussed elsewhere, 

salt marshes in Puget Sound have declined dramatically as the result of a number of 

human activities. To date, climate has had little impact on remaining marshes because 

the rate of accretion of sediments in salt marsh has kept pace with the modest rise of sea 
19

level. However, as the rate of sea-level rise increases, accretion in salt marshes will not 

be able to match the pace resulting in their flooding and subsequent demise. 

In addition to salt marshes, other nearshore biogenic habitats such as eelgrass and bull 

kelp are at risk. Because optimal eelgrass productivity occurs within a narrow band of 

temperature and salinity, climate change is likely to affect the spatial extent of eelgrass 

meadows. For instance, if winter temperatures warm, then eelgrass productivity might 

increase; unless temperatures become too high in which case eelgrass would become 

stressed. Similarly, bull kelp may be negatively affected by increased water temperature. 

On the other hand, increased levels of CO2 may increase growth of kelp. 

How climate change will affect upper trophic levels in the Puget Sound ecosystem is 

complex and not well understood. Fish, seabirds and marine mammals can be affected by 

climate change though changes in the metabolic budget of animals, changes in habitat, 

availability of food, or changes in patterns of circulation that affect larval dispersal. 

Growth and reproduction in fish is governed by how much energy they require to 

maintain their basal metabolism and available food resources. When temperatures rise, 

the energy required to simply stay alive increase and thus the amount of energy available 

to growth and reproduction will be less. Lower rates of growth and reproduction means 

that the resiliency of these populations to perturbations (including fishing) is reduced. 

This is compounded since many fish species directly or indirectly use habitat such as kelp 

or seagrass beds that may also be declining. 

Many marine fish and invertebrates produce pelagic larvae that are dispersed by currents. 

Since these small larvae have limited swimming abilities, changes in patterns of 

circulation may affect where and when offspring are delivered. 

Certainly, changes in the food web as a consequence of climate change can be expected, 

but exactly how such changes will be manifested is unclear. We know that shifts in the 

PDO are accompanied by large shifts in the flow of energy through food webs, but how 

global climate change will affect food web dynamics is still a matter of speculation. 

Using climate information in natural resource management 

While climatic variability may be viewed by some as simply background noise, the twists 

and turns in the ongoing dialogue between the ocean and marine species has important 

implications for how we manage resources in Puget Sound. For example, scientists 

frequently determine the maximum sustainable yield of fish stocks based on average 

conditions over a number of years. Clearly, conditions during El Niño episodes are not 

average, making predictions based on average environments error prone. What do we 

need to do to better manage Puget Sound’s marine resources in the face of the irregular 

climatic rhythms such as El Niño or the PDO? We first require accurate predictions of 

climate events, and we then need to understand how different fish species respond to 

changing marine conditions so that we can alter our management schemes accordingly. 
20

Although we are not there yet, scientists have made great strides in recent years. 

Climatologists now use computer models to predict what ocean conditions will prevail 

several years into the future. The results of such models are by no means perfect, but 

they do give a better indication of the conditions that fish will face, rather than simply 

assuming conditions will be average. The Peruvian anchoveta provides a good example 

of how such El Niño forecasts might be used in marine resource management. Since 

1983, El Niño forecasts have been issued in Peru. Typically, these forecasts would 

predict one of four possibilities: (1) average conditions; (2) a weak El Niño with some 

disruption of the upwelling system; (3) a major El Niño that strongly interferes with 

upwelling, or (4) cooler than normal waters offshore (also known as La Niña). Once the 

forecast is issued, fisheries scientists and government officials can decide on the 

appropriate levels of harvest. 

The ability to use forecasts to alter management requires some understanding of the 

mechanisms by which climate affects the marine species or habitats being managed. The 

response of managers to an impending El Niño would certainly vary if the effects of the 

El Niño were based on changes in DO, food resources, migratory patterns, juvenile 

survival, etc.. While there is a copious literature describing the impacts of climate on the 

productivity of marine species, much of this work has simply described patterns, but not 

the underlying processes producing the patterns. Clearly, the management of Puget 

Sound for species affected by climate needs to be tuned to the biology of the species of 

interest. Attention to such biological processes in concert with accurate climate models 

will begin to give resource managers the tools they need to protect the ecosystem of 

Puget Sound. 

Key Science Needs 

1. We know very little about how and why Puget Sound species are affected by 

climate. Detailed studies of how climatic variation affects such parameters as 

rates of growth, reproduction, survival, migratory patterns, feeding habitats is 

crucial. 

2. Thus far, the effects of climate on ecology have focused on single-species effects. 

That is, how does climatic variation affect patterns of abundance of one species. 

We have very little understanding of how climate will affect ecological 

communities. For instance, how does climate affect the strengths of food web 

linkages or competitive interactions. 

3. While models predict changes in the timing of freshwater input into Puget Sound, 

less well documented are studies of how these changes in flow may affect marine 

water properties in the Puget Sound–Georgia Basin and, in turn, what effects on 

circulation, timing of phytoplankton blooms, and water quality might be 

anticipated. We lack a comprehensive and quantitative understanding of how 

variation in forcing by rivers, ocean, and local weather affect physical and 

biological processes, as well as their coupling, in the Puget Sound–Georgia Basin 

region. 
21

Physical and chemical processes in the Puget Sound Ecosystem

The goods and services provided by marine ecosystems rely on maintenance of processes 

that are described by highly dynamic and interacting physical, chemical and biological 

elements of the freshwater/terrestrial and marine environments. Structural elements of 

the ecosystem, such as food webs and the distribution of habitat types, are affected by 

how well processes such as nutrient cycling, sediment supply, and fresh- and saltwater 

flows are functioning (Fig. 2). In order to protect or restore key food web elements and 

habitat types in Puget Sound, we must understand how processes contribute to the 

underlying causes of species and habitat dynamics (Beechie et al. 2003, Gelfenbaum et 

al. 2006). If we skip over understanding these mechanistic linkages, we run the risk of 

designing restoration strategies that will not be sustainable. For example, adding gravel 

to streams or planting new eelgrass meadows in nearshore areas often do not result in 

habitat improvements if upstream or up-current flow and sediment delivery problems are 

not addressed. To avoid unsuccessful band-aid approaches to achieving Puget Sound 

ecosystem goals, we need to understand how these processes affect food web linkages 

and habitat distributions, and to identify sources of impaired processes. In this section, 

we briefly define what we know about physical and chemical processes in the marine 

waters of Puget Sound, key sources of their impairment, and important science gaps that, 

if filled, will improve our ability to design protection and restoration strategies for the 

Puget Sound ecosystem. We focus here on marine processes, since a discussion of how 

freshwater and terrestrial processes affect the functioning of the Puget Sound ecosystem 

is covered in the next section. 

Figure 4. Include a map of Puget Sound showing marine sub-basins and drift cell 

locations. 

Summary of processes 

Circulation and Upwelling

Water movement plays an important role in shaping both the beaches and the health of 

Puget Sound. Studies of Puget Sound circulation have indicated that the important 

characteristics of the flow include estuarine circulation, wind and tidal influences, and 

bottom water intrusions. Topography and variations in the amount and density of 

saltwater coming into the entrance of the Strait of Juan de Fuca also affect circulation 

characteristics. 

Numerous rivers flow into Puget Sound, diluting the ocean waters and creating gradients 

of fresh and salt water. The irregular bottom topography, tides, and winds cause mixing 

and complex currents in the Sound. Superimposed on the tidal currents is estuarine 

circulation caused by the surface outflow of fresh water from river runoff and deep 

inflow of salt water from the ocean. The average flow in most of Puget Sound is 

characterized by a typical two-layer estuarine circulation, where dense oceanic water 

flows inland to replace salt water diluted by river water flowing on the surface back out 

to the ocean (Figure 5). Deep, dense salt water enters Puget Sound through Admiralty 
22

Inlet, and part flows south into the Main Basin and part flows north up into Whidbey 

Basin. The resulting landward-flowing water replaces the bottom water of Puget Sound 

and keeps it from becoming stagnant, and the outflowing surface water flushes Puget 

Sound. The amount of water in each layer depends on amount of salt- and freshwater 

entering the Sound and the degree of mixing caused by tidal and wind forcing. Mixing 

over the Admiralty Inlet sill plays a major role in this process. A conceptual flow model 

of Puget Sound suggests that considerable seaward-flowing surface water from the Main 

Basin is mixed downward into the bottom water entering at the southern end of the 

Admiralty Inlet sill. This process returns the downward mixing surface water back into 

Puget Sound, but as part of the deep water below the sill. This process, known as 

refluxing, means that some fraction of the water and its dissolved and suspended 

constituents will not leave the basin immediately, but will make additional trips through 

Puget Sound. 

The fresh water flows reaching each of the four major sub-basins of Puget Sound differ 

because of the size and nature of the watersheds. Sixty percent of the total fresh water 

entering the Sound flows into the Whidbey Sub-basin from the drainages of the largest 

rivers in the area--the Skagit, Stillaguamish, and Snohomish watersheds. These rivers 

collectively drain about 50 percent of the Sound. The main Sub-basin receives 20 

percent of the fresh water entering the Sound from the Puyallup, Green/Duwamish, 

Sammamish, and Cedar rivers. Hood Canal receives 10 percent of the fresh water 

entering the Sound through a number of minor rivers (i.e., Skokomish, Dosewallips, 

Duckabush, and Hamma Hamma). The Southern Sub-basin receives less than 10 percent 

of the drainage into the Sound even though it has a large drainage area. It is fed mostly by 

small rivers and streams (the only major rivers are the Nisqually and the Deschutes) 

(PSAT, 1988). 

Two major forces, winds and bottom water intrusions, can cause significant variations in 

the circulation observed in Puget Sound. Northward winds augment the outflowing 

surface water, and southward winds impede and sometimes reverse the surface flow. 

These effects at the surface result in compensating flows in the opposite direction. 

Bottom water intrusions appear as denser salt water crossing the Admiralty Inlet sill 

replaces the deep water in the Main Basin. The intrusions propagate southward along the 

Main Basin and also displace the bottom waters of Whidbey Basin as they move 

northward along Possession Sound. 

The characteristics of saltwater coming into Puget Sound are determined in large part by 

climate conditions along Washington’s Pacific Ocean coast. Summertime winds from the 

north drive coastal upwelling along the Pacific coast, bringing cold, salty and nutrientrich deep water to the surface. Periods of weak or southerly winds following upwelling 

events frequently sweep the upwelled waters along the coast into the Strait of Juan de 

Fuca. The strength and timing of coastal upwelling varies considerably from weeks to 

decades and has an effect on circulation and water quality within Puget Sound (Snover et 

al., 2005). 
23

Changes in Puget Sound circulation patterns can have important implications for the 

exchange of water between Puget Sound and the ocean. Exchange helps flush the deep 

basins of the Sound and prevents the depletion of dissolved oxygen from organic decay. 

Exchange also plays a critical role in governing the fate and effects of contaminants that 

enter Puget Sound. A recent study (Newton et al, 2003) found that, during the 2000-2001 

drought in the Puget Sound region, the reduced river flows led to a significant decrease in 

the exchange between Puget Sound water and the Pacific Ocean. This had consequences 

for larval and plankton dispersal, as well as water quality. 

More on implications of changes in circulation and upwelling: effects on species, 

habitats, ecosystem services; influences of human activities on circulation and upwelling. 

Element Cycling and Stratification 

Element cycling in Puget Sound is driven by physical processes and such processes 

interact with species that use and generate chemical elements of the water. Nutrient 

concentrations in the upper layers of the ocean tend to be lower than in the deeper waters 

due to the utilization by phytoplankton in the euphotic (i.e., sunlight-rich) zone. 

Increased concentrations of nutrients occur in deeper waters due to the release of 

nutrients back into solution during the decay of detrital material sinking from the upper 

layers. Replenishment of nutrients in the upper layers can be accomplished through 

upwelling, vertical diffusion from other areas, and contributions from land through rivers 

and streams. Certain nutrients, including nitrogen and phosphorus, are necessary for 

phytoplankton growth. Low nitrogen levels typically limit phytoplankton growth in 

marine waters, and phosphorus tends to limit plant growth in freshwater. 

The process of vertical mixing between surface and underlying waters is a major driver of 

nutrient and phytoplankton dynamics, which in turn affect dissolved oxygen (DO) levels. 

Stratification refers to the horizontal layering of water masses due to density differences. 

Ambient air temperature, solar radiation, fresh water input from both precipitation and 

river flow, surface winds, internal waves, and tidal circulation are some of the factors that 

influence stratification in a water column (Newton et al. 2002). Water density increases 

with decreasing temperature or with increasing salinity. Any factor that mixes water 

masses (e.g., winds, tidal circulation) will decrease stratification, and factors that increase 

density differences (e.g., fresh water input to the surface, high solar radiation) produce or 

maintain stratification (Fig. 5). 

The development of stratification within the water column is significant because of the 

physical barrier it presents with respect to vertical water movement. For example, 

turbulent eddies, driven by winds and tides, cause vertical mixing of phytoplankton, DO, 

and nutrients. If, however, the water is stratified, then the ability of turbulent eddies to 

accomplish vertical mixing will be greatly decreased. This is particularly true at the 

pycnocline, which is often observed in the top several meters of the water column. Thus, 

stratification effectively isolates the surface water from the deep water. When 

stratification is intense, two environmental conditions can be affected: surface waters can 

become depleted of nutrients (dissolved nitrogen and phosphorus) and bottom waters can 
24

Figure 5: Simplified representation of two-layer circulation and tidal mixing in Puget Sound (courtesy of 

Mitsuhiro Kawase, University of Washington). The pycnocline is a transition layer between higher-salinity 

waters at depth and lower- salinity waters on the surface. 

become depleted of oxygen. Conditions favorable for phytoplankton growth are sufficient 

light and nutrients and some degree of stratification (i.e. to prevent mixing phytoplankton 

out of the euphotic, or light-rich, zone). Under such conditions, phytoplankton biomass 

increases in the upper layer of the water column and nutrients are consumed as growth 

continues. Without a replenishing source, surface nutrient concentrations decrease and 

can limit phytoplankton growth, causing a decrease in their biomass. When a nutrient 

source is available to surface waters, however, phytoplankton production will never reach 

a nutrient-limited state. Eutrophication (an increase in external nutrient supply to system) 

of nutrient-limited stratified waters can result in very large algal blooms and, after the 

algae sink and decay, a correspondingly large DO debt in bottom waters (Box 3). 

Schematic of exchange circulation in a 

fjord (cross-section)

Tidal Mixing

Entrance Sill

Main Basin Marine influence

(Salty, Dense)

Sharp Pycnocline

River Input

(Fresh, Light)

Outflow

Inflow/Reflux
25

Box 3. Dissolved Oxygen and Hood Canal 

Hypoxia (dissolved oxygen concentrations <2-3 mg/L), or even anoxia, in Hood Canal is 

not a new phenomenon, but considerable evidence suggests that this problem has 

increased in severity, persistence, and spatial extent (Curl and Paulson, 1991; Newton, et 

al., 1995; 2002). The most severe low DO conditions occur in the southern end of the 

canal, the point furthest from water exchange with the rest of Puget Sound. Comparing 

oxygen data from 1930-1960’s with data from 1990-2000’s analyzed using the same 

methods shows that in recent years the area of low dissolved oxygen is getting larger, 

spreading northwards, and that the periods of hypoxia last longer through the year 

(Collias et al., 1974; Newton et al., 2002) Inventories of deepwater oxygen in the 

southern main-stem of Hood Canal (Dabob Bay to Great Bend) for these time periods 

show that while variation is evident, in general the modern data are lower; levels 

measured during 2004 were at the historical low point for any recorded observations 

(Warner; http://www.hoodcanal.washington.edu/observations/historicalcomparison.jsp). 

Similar historical comparisons in lower Hood Canal (Sisters to Lynch Cove) show that 

while oxygen typically reached hypoxia or even anoxia during summer throughout the 

record, the recent data show that hypoxia is lasting longer, and of late, throughout the 

entire year. 

Although records of fish kills in Hood Canal date as far back as the 1920’s, repetitive fish 

kills during 2002, 2003, and 2004 indicate that the increasing hypoxia may be having 

biological consequences. Two fish kill events in Hood Canal during 2003 galvanized 

public awareness of the water quality challenges faced by this system. In 2003 the 

Washington Department of Fish and Wildlife closed Hood Canal to commercial and 

recreational fishing for all finfish except salmon and trout and for octopus and squid. 

This was the first time in Washington State's history that a fishery was closed due to a 

water quality issue such as low dissolved oxygen. The Washington Department of 

Natural Resources found that Hood Canal is only region in Puget Sound to have 

consecutive years of eelgrass losses since they started annual monitoring within the Puget 

Sound Ambient Monitoring Program in 2000. For this reason WDNR identified Hood 

Canal as an area of concern. Initial findings from 2005 suggest eelgrass declines are more 

severe in Hood Canal than previously seen, particularly in southern Hood Canal. 

A number of physical, chemical, and biological factors are thought to contribute to the 

low dissolved oxygen conditions in Hood Canal. These include: the circulation and 

flushing of the canal, which is affected by ocean and river waters; the degree of seawater 

stratification, which controls vertical mixing and is affected by river, ocean, and weather 

conditions; the productivity of algae, which is affected by sunlight and nutrient (nitrogen) 

availability, which can come from both natural and human sources; and other carbon 

loads from both natural and human sources. Like classic fjords, Hood Canal is prone to 

hypoxia because deep-water exchange with Puget Sound is limited by a shallow sill at the 

outlet of the canal and thus circulation in Hood Canal is slow relative to other Puget 

Sound basins (Warner et al., 2001). Vertical density stratification in the canal due to 

freshwater inputs or warm temperatures inhibits vertical mixing. In addition, the effect of 

ocean boundary conditions, specifically the seawater density, may play a large role in 
26

flushing of the canal, determining its residence time or “age” and thus its resultant 

oxygen content. Experimental evidence has demonstrated that Hood Canal, due to its 

persistent stratification, has phytoplankton growth limited by nitrogen (N) availability 

(Newton et al., 1995). Anthropogenic sources of N, such as septic system and hatchery 

discharges, fertilizers use, and salmon carcass disposal, may thus stimulate phytoplankton 

growth, increase microbial decomposition and subsequently decrease dissolved oxygen 

levels. Although overall human population density in Hood Canal basin is generally low, 

shoreline development is intensive in a number of regions of the canal and may influence 

oxygen conditions. 

At issue is that all of the mechanisms explained above are involved in determining the 

observed increase in hypoxia. The Hood Canal Dissolved Oxygen Program and its 

Integrated Assessment and Modeling study (HCDOP-IAM) arose out of the need to 

quantify what is driving the increasing hypoxia, to address whether human activities (and 

which ones) are major causes, and to evaluate the efficacy of potential corrective or 

mitigative actions. This need pairs scientists with the capability to make quantitative 

observations and modeling assessments with local, tribal, state, and federal decision 

makers through the HCDOP. The multi-year HCDOP-IAM study, begun in 2005, is 

primarily financed through federal funds secured by Congressman Norm Dicks. This 

study is administered by the Applied Physics Lab of the University of Washington, 

through a contract with the US Navy but involves scientists from federal, state, and local 

agencies, tribes, NGO’s, as well as UW and WWU. It is co-managed by APL-UW and 

the Hood Canal Salmon Enhancement Group. For more information on the HCDOPIAM study, check out www.hoodcanal.washington.edu. 

The effects of DO depletion are organism and habitat-specific. Benthic infauna--

particularly mollusks--are more resistant to hypoxia than are most fish species. 

Continuous or even intermittent low DO events may result in a shift in species 

composition due to mortality or reduced reproductive success of sedentary species, 

movement away from depleted areas by more mobile species, or greater susceptibility to 

disease. The species composition of a given area may also shift in response to changes in 

predator-prey relationships. The daily pattern of vertical migration exhibited by some 

zooplankton to avoid predation can be interrupted. Copepods have been found to remain 

in the pycnocline in an attempt to avoid a bottom layer of low-oxygenated water. In sum, 

the net effect of oxygen depletion in marine waters may be a shift in species composition, 

a decrease in population numbers and species diversity with a resulting decrease in 

amount and type of biomass, and a disruption of the usual predator-prey interactions. 

These combined effects can result in reduced availability and subsequent harvest of 

marine resources. 

Sources and sinks of nutrients can be from either natural processes or anthropogenic 

activities. Understanding the impact of human activities (e.g., sewage input, agricultural 

and domestic fertilizers, freshwater diversion, creation of impervious surfaces) on water 

quality is complex because the concentrations of important variables (e.g., DO and 

nutrients) in the water column are the net result of many dynamic input and uptake 
27

processes. Sources of nutrients in Puget Sound include dissolved and particulate matter 

carried by rivers, bacterial nutrient processing (e.g., nitrification), upwelled deep waters, 

treated and untreated waste from onsite sewage systems and sewage treatment plants, 

discharges from boaters and other recreational activities, agricultural and stormwater 

runoff, and wood waste. These nutrients reach the Sound through outfalls, groundwater, 

rivers, and from the ocean. Nutrient uptake processes include consumption by 

phytoplankton, bacterial uptake, and possibly the adsorption of nutrients to particulates 

that eventually settle out. 

Examples of oxygen sources are photosynthetic production, diffusion of oxygen from the 

atmosphere through the water column, and advection or mixing of highly oxygenated 

waters into lower saturated waters (e.g., downward mixing of surface waters). Examples 

of oxygen sinks are respiration (especially by bacteria which decay organic matter), 

chemical oxidation-reduction reactions such as the oxidation of metals (e.g., rusting of 

iron) or sulfides, and advection/mixing of deeper, oxygenated waters into shallower, 

saturated waters (e.g., upwelling of deep waters). 

Insert brief discussion of specific stratification, eutrophication/DO problems in Puget 

Sound; and how management can affect such processes (State of the Sound 2004) 

Tides and Currents

Tides in Puget Sound are of a mixed, semidiurnal (i.e., approximately once every 12 

hours) type with large tidal ranges and, in channels such as Deception Pass, impressively 

large currents. The shape of the Sound affects the tide as it moves through channels and 

inlets. Tides are characterized by rapid changes of amplitude and phases in the narrower, 

shallower reaches of the Sound and slowly changing amplitudes and phases in the deeper, 

broader regions. Daily tidal ranges of 2.6, 3.4, and 4.4 m occur at Port Townsend, 

Seattle, and Olympia, respectively (Mofjeld and Larsen, 1984). In the Strait of Juan de 

Fuca, a 2.2 meter tide at Cape Flattery will reach Port Townsend three hours and forty 

minutes later and will increase in magnitude to 2.4 meters. The tide will reach south 

Puget Sound one hour later and increase to 4.1 meters by the time the tide waters reach 

Olympia. Extreme high tides of 5.5 meters have been recorded in Olympia. 

Tidal currents dominate the circulation observed in Puget Sound—movement of water 

due to tides is about 5-10 times larger than the estuarine circulation seen throughout 

Puget Sound. As the tidal currents flow past points of land, the water forms eddies in the 

lee of the points. These tidal eddies provide a transport mechanism for offshore water to 

reach the shoreline, bringing nutrients and plankton to nearshore communities. Tidal 

currents in the main basin of Puget Sound, a region with depths of 200 m or more, 

typically are less than 0.25 m/s. In contrast, tidal currents in Admiralty Inlet and in The 

Narrows, regions with depths of 40-80 m, can be as large as 2.2 and 3.3 m/s, respectively 

(NOAA, 1984). 
28

Insert short paragraph linking processes to biological impacts....what food webs or 

habitat types are affected by tides? What human actions may have impaired circulation 

patterns? Is there any evidence of changes in circulation over time? 

Drift Cells and Sediment Transport

Puget Sound consists of over 4000 km (2500 miles) of shorelines, and this interface 

between terrestrial and aquatic environments plays an important role in the overall health 

of the Puget Sound ecosystem (see also Terrestrial and marine linkages). Fresh water, 

sediments, and nutrients are transported across the shoreline interface helping to create 

critical nearshore habitats. Nearshore habitat attributes, like the shoreline itself, vary 

tremendously across the Sound. Physical riverine, tidal and wave-driven processes, along 

with inherited topography and coastal geology (sediment type), determine the coastline 

habitat types observed in Puget Sound (see Habitat types). If sediment delivery and 

transport processes are disrupted, the habitat types we expect to see along Puget Sound 

shorelines and at greater depths (e.g., beaches, eelgrass meadows, mud flats) are more 

difficult to maintain. 

A useful way to organize the coastline is in terms of drift cells or littoral cells. Drift cells 

are landscape-scale units (10s – 1000s meters) that delineate the boundaries of beach 

sediment transport. Drift cell boundaries are most often defined by headlands, but they 

also can be embayments, rivers, or zones where alongshore drift is negligible. Waves 

breaking obliquely along the shoreline are the dominant marine-derived sediment 

transport process moving sediment within a drift cell. Alongshore sediment transport 

directions may shift on short time scales (i.e., over days, weeks, or months) as winds and 

wave directions change. Long-term net shore drift directions integrate over shifting wind 

and wave directions, and may be more relevant for management uses. 

Drift cells often are used to create a sediment budget for a stretch of coast, accounting for 

the sediment sources, transport pathways, and sediment sinks. Beach sediment within the 

Sound comes primarily from erosion of adjacent bluffs (Figure 6), with rivers adding 

smaller amounts (Shipman, 1995). Coastal bluffs are the most common shore type 

around the Sound and are generally carved into sequences of glacial and inter-glacial 

sediment consisting of fluvial sands and gravels, coarse outwash deposits, and glacial till. 

Shipman (1995) summarized erosion rates of coastal bluffs in the Sound and found rates 

ranged from 3-150 cm/yr at the sites studied. The volume of material added to beaches 

from bluff erosion is closely related to wave energy or fetch and ranges from less than 1 

m3

/m/yr to more than 10 m3/m/yr. Bluff failure, occurring either slowly or 

catastrophically, is an important process for replenishing beach sediments and 

maintaining nearshore habitats. 

Drift cell boundaries with net drift directions have been mapped for most of the Puget 

Sound shoreline (Department of Ecology, 1978; Schwartz et al., 1989; Schwartz et al., 

1991). The irregular and complex coastline of Puget Sound results in hundreds of drift 

cells. Several different estimates of the amount of sediment movement within drift cells 
29

have been made, and although the magnitudes are small compared to outer coast drift 

rates, they still result in significant potential for movement of sediment alongshore within 

the Sound (Finlayson and Shipman, 2003). Sediment availability—due to shoreline or 

riverine sources affects the rates of sediment transported. Along Hale Passage, a heavily 

armored stretch of coast in south Puget Sound, the drift rates are very low, from 30-50 

m3/yr, whereas for Vaughn Bay Spit, a stretch of coast with similar fetch, but fewer shore 

defense structures, the rates are much higher, 2000 m3

/yr. 

The extensive development of the coastal bluffs around the Sound has led to widespread 

use of engineering structures designed to protect the upland properties. Concrete 

bulkheads and rip-rap are the most common forms of shore protection used on Puget 

Sound shorelines (Canning and Shipman, 1995). The extent of shoreline armoring for 

Thurston County revealed that by 1993 56% of all shoreline parcels were armored. The 

extent of armoring in 1993 amounted to 29% of the total shoreline length in Thurston 

County, as compared to 14 % that was armored by 1977. With more people moving near 

the coast, the increasing trend has continued. More than half of the shoreline of the Main 

Basin and 79% of the eastern shoreline of the Central Basin has been modified by 

shoreline armoring (Puget Sound Action Team, 2000). 

Although shoreline armoring is often used to add some protection to upland structures 

such as buildings, there may be a negative impact in terms of a decrease in the supply of 

sediment to the beaches. In general, shoreline armoring can lead to a variety of impacts, 

direct effects such as impoundment or loss of sediment behind structures, and burial or 

loss of upper portions of a beach due to placement of the structure (Figure 7). Indirect 

impacts can include beach starvation, modification of groundwater hydraulics, increased 

wave energy and scour in front of or adjacent to a structure, beach lowering, changes in 

beach sediment grain size, and loss of organic debris. 

Impacts of Processes on Biological Resources

This section is fairly nearshore-centric: what more can reviewers suggest for marine basin 

processes and their impacts? 

Loss and modification of beach habitat due to shoreline armoring is having a deleterious 

effect on the ecosystem health of the Sound (Thom et al. 1994). The various structures 

that affect drift cells and nearshore physical processes also impact nearshore habitats and 

biological resources. 

There is substantial indirect evidence of serious harm to species and habitats due to 

shoreline armoring. Much of the concern centers around the critical importance of 

beaches for finfish spawning, foraging and rearing, and habitat for adult and juvenile 

invertebrates (Canning and Shipman, 1995). Negative impacts to finfish can arise from 

direct loss of spawning habitat, loss of shoreline vegetative cover, loss of organic debris, 

and modification of migratory corridors. Although not verified, the indirect impact that 

armoring can have on beach substrate could have significant effects on forage fish 
30

spawning. Similarly, changes in beach substrate could modify the habitat for shellfish. 

Armoring can also impair development of upland vegetation, groundwater flow, and the 

supply of sediment and nutrients to the upper beach. 

What about other impacts of impaired processes? E.g., how might have changes to 

timing and quantity of freshwater input to Sound, either due to water flow alteration or 

climate change—changed species, habitats, or ecosystem services such as nutrient 

cycling? Also, what about the possible threat to upwelling along outer Pacific coast due 

to future changes in large-scale atmospheric circulation and local winds as a result of 

climate change? 

Possibly include a section on another process--Recruitment of wood and shoreline 

riparian dynamics 

Key Gaps in our Scientific Understanding of Processes

The issues below are those gaps in our scientific understanding of processes that, if filled, 

will enhance the ability of decision-makers to make wise decisions about managing the 

Puget Sound ecosystem. As more information becomes available on the topics below, 

actions can be better targeted at protecting or restoring processes that underlie the 

ecosystem’s ability to provide species, habitat, and ecosystem service objectives for 

Puget Sound. 

This following section is fairly nearshore-centric—need to make sure we are considering 

deeper marine water processes, too. We also need to shorten the list of ‘key’ science 

gaps below. 

Comprehensive efforts to identify data and information gaps associated with nearshore 

processes, structures, and biological resources can be found in the State of the Nearshore 

Report (Williams et al. 2001) and in the research plan written for the Puget Sound 

Nearshore Ecosystem Restoration Program (PSNERP) (Gelfenbaum et al., in press). 

Both reports argue there is a paucity of scientific information with regard to nearshore 

ecosystem processes, structures, and biological resources. Without this understanding, 

we will not be able to develop action plans aimed at redressing underlying causes of 

habitat and species losses. 

Some of the pressing science gaps identified thus far are listed below. 

• Surface circulation in Puget Sound is not well described – important in transport 

of planktonic organisms, oil spills, etc. 

• Need improved predictions of the consequences of climate change: 

o E.g.-induced prevailing wind fields and coupling of surface currents, as 

well as actual tides vs. average tides. 

o Effect/Influence/Importance of advection of Pacific Ocean water – How 

much is Puget Sound water quality driven by advection of upwelled 

Pacific water? How important is this in predictions of nutrient dynamics 

and dissolved oxygen in the Sound? 
31

• Need trend analysis – our observations consist of snapshots of a dynamic system 

and do not provide enough data for comprehensive trend analysis. 

• Integrating and temporal/spatial scale issues—how do the processes interact to 

produce changes in ecosystem services in Puget Sound? A key science need is to 

be able to predict how processes such as changes in nutrient composition, 

production, consumption, and movement of sediments and water affect how 

marine communities and ecosystems function. Habitats important to species and 

food web function cannot be maintained without protecting or restoring the 

mechanisms (i.e., processes) that support those habitats. 

• What are the underlying causes of impaired ecosystem processes and how can we 

mitigate these? In particular, what land use, estuarine, and marine water activities 

impair ecosystem processes in the marine environment? For example, we 

understand relatively well how dams disrupt the delivery of gravels and finer 

sediments to river mouths, which can starve nearshore beaches of much-needed 

sands and cause significant erosion problems along coastlines (Box—Elwha). 

• What actions will enable the marine ecosystem to generate and maintain natural 

processes, which will in turn generate desirable ecosystem structures (e.g., 

eelgrass meadows, baitfish spawning gravels) and important functions (e.g., 

salmon and bivalve production, clean beaches and water)? 

Figure 6. Bluff failures contribute sediment to beaches 

(photo by Guy Gelfenbaum) 

Figure 7. Railroad grade along shoreline from Seattle to 

Everett (photo by Guy Gelfenbaum) 
32

Box 4. Ecosystem Response to the Elwha River Restoration Project 

The Elwha River, one of ten major rivers on Washington State’s Olympic Peninsula, has 83% 

of its watershed located within Olympic National Park. Over 90 years ago, dams were 

constructed 4.9 and 13 miles from the river mouth. Due to a lack of fish passage technology, the 

dams effectively blocked 10 runs of anadromous fish from returning to over 70 miles of spawning 

habitat in the upper Elwha River. Prior to dam construction, these fish numbered in the hundreds 

of thousands, making the Elwha River one of the most productive salmon rivers in the Pacific 

Northwest (Wunderlich et al. 1994). 

The Elwha River drains part of the high Olympic Mountains and delivers sediment to the Strait of Juan 

de Fuca. Two large dams that have been in place for over 90 years are slated for removal in 2009. [also 

include small photos of dams in this panel]

The ecological effects of the Elwha River dams on the river, estuary and nearshore 

environments were large and cumulative. Aside from the obvious impacts of changing the fish 

community and starving the upper river of marine-derived nutrients (provided via salmon 

carcasses), there also were cascading effects in the riparian and upland areas. At least 22 species 

of birds and mammals that utilized salmon carcasses were deprived of an important source of 

nutrients. The reservoirs created by the dams (Lakes Mills and Aldwell) have acted as sediment 

traps, storing 13.8 and 4.0 million cubic yards of fine-grained sediments. These reservoir traps 
33

have starved the lower river, the delta at the river mouth, and the nearshore and beach areas of 

these sediments, resulting in the transition of nearshore habitat from a predominantly sand into a 

cobble-dominated system. Impacts to the plant and animal species dependent on the river, 

estuary and nearshore habitats are only partly understood, but major changes in food web 

composition, habitat structure, and processes delivering sediment to Puget Sound have occurred. 

For example, the amount and quality of spawning habitat for salmon in the lower river has been 

greatly diminished, since it is dependent upon sediments and large woody debris supplied from 

the upper river.

The release of sediment from behind the dams when they are breached is hypothesized to alter nearshore 

and marine habitats as well as add to beach protection. 

Congress enacted the Elwha River Ecosystem and Fisheries Restoration Act of 1992 (PL102-

495) to address these problems. The stated goal of this legislation is, “...the full restoration of the 

Elwha River ecosystem and native anadromous fisheries.” The Elwha River Restoration Project

(ERRP) will begin with the removal of the two dams on the Elwha River, slated to begin in 

2008/2009. Ecological and physical responses to the restoration--such as the effects of restoring 

sediment delivery processes-- are expected to occur at multiple spatial and temporal scales. Dam 

removal is hypothesized to provide significant amounts of sediment to the lower river and 

nearshore marine environments. Sediment delivery will likely take years and is expected to 

preferentially add finer sediment (sand) to the existing coarse-grained river and nearshore marine 

habitats. The finer substrates are likely to have major impacts on habitat quality and species 

responses, and these unknown responses are the focal point of ongoing research. 
34

Terrestrial and Marine Linkages

Ecosystem structure, such as species and habitats, is affected by linkages between the 

freshwater/terrestrial and marine environments (Fig. 2). Freshwater and saltwater 

environments commonly are viewed as separate ecosystems, yet physical, chemical, and 

biological linkages between them are so strong that management actions in one 

dramatically affect the other. Examples include damming of rivers and reducing the flow 

of sediments to nearshore environments, urbanization and increased delivery of 

pollutants, and fishing pressures that reduce the number of spawning salmon returning to 

rivers. These interactions occur along two distinct interfaces between freshwater and 

saltwater environments: (1) nodes of high material transfer (both upstream and 

downstream) at river deltas, and (2) zones of lower material transfer along intervening 

shorelines Figure 8 -- Illustration of some processes for each zone here. In Puget Sound 

we have fundamentally altered these interactions by land management and fishing 

practices, resulting in reduced capacity and quality of nearshore habitats and food webs. 

To improve our ability to protect and restore the Puget Sound ecosystem, we need to 

understand how fluxes of water, sediment, nutrients, and pollutants between watersheds 

and Puget Sound alter ecosystem health and the goods and services it provides. 

Linkages and Human Impacts 

Nearshore, delta, and marine habitats in Puget Sound are in part shaped by the delivery of 

water, sediment, and wood debris from watersheds and shorelines to the marine 

environment. At Puget Sound river mouths, gravels and sand transported from 

watersheds build deltas and beaches, while fine silt and clay remain suspended in the 

water column far into saltwater. Sediments are also delivered to beaches from eroding 

bluffs, and wood transported downriver is deposited in deltas and along beaches where it 

reduces shoreline erosion. These processes create a variety of habitat types including 

freshwater and salt water marshes in deltas, beaches, and estuaries, as well as a variety of 

shoreline and beach habitats. Beach habitats provide spawning and rearing areas for 

forage fish and other species. Delta habitats are important to salmon, providing a critical 

rearing habitat as young salmon leave rivers and enter Puget Sound. 

Water and sediment quality in Puget Sound are substantially degraded by pollutants 

delivered from watershed and nearshore industrial activities. Pesticides are used widely 

across the landscape (including applications in forestry, urban, residential, agricultural, 

and industrial uses). More on industrial problems, kinds of pollutants. 

 Insert Box 5 – POLLUTION IN SOUND, toxics discussion. 

High input of organic and inorganic nutrients to Hood Canal also contribute to low 

dissolved oxygen levels (Box 3). 

Rivers and streams of Puget Sound transport organic matter and nutrients downstream 

where they support food webs in river deltas and nearshore environments. Along 

shorelines, riparian forests provide organic matter for food webs, and shade that helps 
35

stabilize environmental conditions in intertidal spawning areas used by forage fish. Trees 

that fall from eroding bluffs and are deposited in littoral areas are habitat for beach, 

intertidal, and marsh-inhabiting species. A number of fish species such as juvenile 

chinook and chum salmon consume insects that come from terrestrial and freshwater 

habitats. The upstream migration of salmon each year also delivers important marinederived nutrients to freshwater ecosystems 

Insert BOX 6 – SALMON NUTRIENTS 

Each of these linkages between terrestrial and marine ecosystems has been altered by 

human activities (Shared Strategy 2005). The most dramatic changes have occurred in 

urban landscapes where fresh and salt water marshes have been paved and converted to 

industrial uses but agricultural land uses have also eliminated vast delta habitats 

important to salmon and other species (Bortleson et al 1980, Collins and Sheikh 2005). 

(Figure 9 – Duwamish River). Reductions in supply of sediments from rivers by dams 

degrade nearshore habitats. Consequently, Puget Sound has seen declines in eelgrass and 

algal habitats for migrating salmon, forage fish and shellfish (Box 4). Fishing pressure 

reduces upstream transfer of nutrients. 

Insert discussion of key threats to the functioning of freshwater-terrestrial 

linkages—summarize information in sources such as the Shared Strategy recovery plan 

and Puget Sound Management Plan (PSAT) for land use, other human impacts. Use a 

table or Box to provide concrete examples. 

Key Gaps in our Scientific Understanding of Terrestrial-Marine Linkages

The issues below are those gaps in our scientific understanding of terrestrial-marine 

linkages that, if filled, will enhance the ability of decision-makers to make wise decisions 

about managing the Puget Sound ecosystem. As more information becomes available on 

the topics below, actions can be better targeted at protecting or restoring processes that 

underlie the ecosystem’s ability to provide species, habitat, and ecosystem service 

objectives for Puget Sound. 

This list of ‘key’ science gaps is incomplete and yet needs to be kept fairly short. 

3⁄4 Many land and water uses affect the quantity and timing of fresh water delivered 

to Puget Sound, including urban development (impervious cover), dams, water 

withdrawals, loss of wetlands, and channelization of rivers. However, we do not 

know the degree to which each factor contributes to altered stream flows and 

ecosystem degradation, or what percentage of each land use exceeds thresholds of 

degradation. 

3⁄4 The effects of water quality degradation on freshwater, estuarine and nearshore 

functions are not understood. While we are able to measure many aspects of water 

quality (including water temperature and concentrations of sediment, bacteria, and 

contaminants), we do not yet have a good understanding of the root causes of 

impaired freshwater quality (both ground water and stream flows), or how 
36

declining water quality affects freshwater, estuary, and nearshore ecosystem 

functions.

3⁄4 How does climate change effect the quantity, quality, and timing of the 

streamflow delivered to the coast? And how does that translate to changes in the 

Puget Sound ecosystem? 

3⁄4 We do not have good mechanistic linkages between human management actions 

(such as critical areas ordinances, shoreline master plans, zoning, restoration 

projects) and the functioning of processes that link terrestrial and marine 

environments. 

3⁄4 How declines in shoreline habitat quality are translated into effects on species up 

the food chain is not known. For example, if we understand how water quality in 

runoff from land and freshwater systems affects estuarine and nearshore habitat 

quality, quantity, and function, we can begin to develop mechanistic linkages 

between actions affecting water quality and ecosystem responses 

3⁄4 We know that biomass is transferred between freshwater and marine systems 

through organisms traversing the full range of habitats throughout their life cycle 

(e.g., anadromous salmon) or through passive and active transport of live and 

dead biota (e.g., freshwater algae washing downstream into estuaries; and 

seabirds, bears and other mammals carrying marine prey into terrestrial systems). 

There is virtually no information on how these fluxes of nutrients and organic 

matter affect the functioning of the Puget Sound ecosystem. Further, we do not 

know how human activities have altered the rates and magnitudes of such 

transfers, so encouraging recovery of the Puget Sound ecosystem is challenging. 

Puget Sound Food Web and Species Biology

Description of the Puget Sound Food Web 

Although a complete accounting of the plant and animal species of Puget Sound has not 

been accomplished, we know that this productive landscape supports at least 100 species 

of sea birds, 200 species of fish, 26 marine mammals, and thousands of different species 

of invertebrates. Although most are native species (including both full-time residents and 

seasonal residents), an increasing number of species are non-natives that have been 

intentionally or unintentionally introduced into the Puget Sound ecosystem. 

The species that occupy the Puget Sound contribute to some of its most obvious goods 

and services. This section describes the food web and interactions between species in the 

Puget Sound system (Figure 2). It is critical to consider the relationships between all 

species in the environment, including year-round resident, seasonally resident, and 

migratory species. At the core of this approach is the study and understanding of food 

web and predator-prey dynamics. By striving to understand these relationships, steps can 

be taken to manage and sustain the Puget Sound ecosystem. 

In what follows, major groups of organisms in the Puget Sound food web and 

anthropogenic threats that impact the biology of species and the number of species in the 
37

Puget Sound food web are described. Although the information presented here is not 

exhaustive, key organisms in major trophic levels are discussed to provide a better 

perspective on the organization of the Puget Sound food web and to identify population 

trends and anthropogenic threats for some representative species of concern in the Puget 

Sound Ecosystem. 

Phytoplankton

Phytoplankton in Puget Sound are highly productive. Daily productivity rates are among 

the highest of west coast estuaries (Emmett et al., 2000). The seasonal pattern of 

phytoplankton biomass is quite varied, both spatially and temporally, linked to the degree 

of stratification, sunlight availability, and in persistently stratified areas, nutrient 

limitation (Winter et al. 1975; Newton et al., 2002). 

The high level of productivity, combined with a wide range of aquatic habitats within the 

Sound, is what sustains the highly diverse population of marine organisms. Puget Sound 

has seasonally high phytoplankton standing stock; chlorophyll a bloom concentrations 

can range greater 60 mg m-3 (Bricker et al., 1999). The high primary production is 

important for food web dynamics of the commercially important fisheries. The timing of 

phytoplankton blooms is influenced by depth of the mixed water column layer relative to 

light availability. One study found that primary production in central Puget Sound is 

controlled by light availability during the winter (October to March), however, other 

factors, such as nutrient availability and stratification, controlled the amount of 

production during other months (Nakata and Newton, 2001). Studies throughout Puget 

Sound show variance in the control on primary production for Budd Inlet (Newton et al., 

1998), the Main Basin, Possession Sound (Newton and Van Voorhis, 2002) and Hood 

Canal (Newton et al., 1995). 

Phytoplankton populations in Puget Sound consist of mainly large-sized phytoplankton of 

two major groups: diatoms and dinoflagellates, with diatoms accounting for most of the 

biomass. The role of nano- and pico-phytoplankton has not been well addressed. Diatom 

species are dominant in the fall and winter months and typically dominate the 

composition of the spring bloom. Dinoflagellates become more abundant in the spring 

and summer. Subsequent blooms have been characterized as a series of intense blooms 

appearing during favorable physical conditions (Winter et al., 1975). Phytoplankton 

abundance is highly heterogeneous or “patchy” both spatially and temporally. Abundance 

can vary significantly on time scales of hours to days, possibly due to diatom life cycles 

and spatial heterogeneity (Dexter et al., 1981). 

The spatial abundance of phytoplankton has also been linked to upwelling, river runoff, 

stratification, and wind stress. Mixing and upwelling of water are important factors 

affecting phytoplankton distribution as they provide nutrients for population growth, seed 

populations, and affect residence time within a basin. Upwelling at locations such as the 

Tacoma Narrows provides a source of nutrients to the upper layers of the water column, 

supporting the high productivity of the Main Basin. Tidally-driven mixing at the Narrows 

contributes to spatial heterogeneity as surface water parcels originating on ebb tides are 
38

advected northward. The reflux of upper water layer into deeper waters due to mixing in 

Admiralty Inlet causes an increase in chlorophyll and a decrease in nutrients at depth 

(Boss et al., 1998). 

Zooplankton

The Puget Sound’s entrance sill alters the pattern of estuarine circulation by causing 

mixing and by restricting the exchange of water with adjacent basins (Strickland 1983), 

with apparent consequences for zooplankton assemblages. The plankton fauna of Puget 

Sound appears to differ from that of adjacent waters in the Strait of Juan de Fuca and the 

Pacific Ocean in a having a high proportion of shallow-water, coastal, and estuarine taxa 

such as the cyclopoid copepod Oithona similis, the calanoid copepods Acartia

(Acartiura) spp. and Paracalanus, and the cladocerans Podon and Evadne (Chester et al. 

1964, Dumbauld 1985, Giles and Cordell 1999, B. Frost unpublished data). In this 

respect, it is similar to other coastal marine embayments such as San Francisco and 

Tomales Bays (Ambler et al. 1985, Kimmerer 1993) and estuaries (Miller 1983). 

However, Puget Sound also has relatively deep basins with populations of deeper 

distributed species such as the calanoid copepod Calanus pacificus, the euphausiid 

Euphausia pacifica, the amphipod Themisto pacifica, and the chaetognath Sagitta 

elegans. Unfortunately the differences and similarities between Puget Sound and other 

coastal environments are poorly known, because quantitative studies of the zooplankton 

assemblage in the Puget Sound region are rare and quite limited in scope, consisting of 

several unpublished student theses (Dempster 1938, Hebard 1956, Damkaer 1964, 

Dumbauld 1985) and a few other studies. 

The habitats of zooplankton encompass all of Puget Sound and are best known from 

surveys and ecological studies of the food habits of regional biota. The zooplankton 

community is complex and diverse but represents one of the most critical components of 

the food web transforming matter derived from primary production into food for fish, 

birds, and mammals. Diatoms and phytoflagellates dominate spring blooms and are the 

major foods for suspension-feeding, dominant copepods such as Arcartia and Calanus. 

Secondary to the copepods are euphausiids, amphipods, and mysids (Strickland, 1983). 

The euphausiids are also suspension-feeders, feeding on the largest chains of diatoms and 

microzooplankton. Mysids are omnivorous and amphipods are carnivorous. There are 

may carnivorous zooplanktors at the third trophic level including predatory copepods, 

micronekton, an gelatinous species such as the chaetognaths, ctenophores, and medusae 

(Strickland, 1983). 

On the west coast of the United States, a number of estuaries and embayments have been 

invaded by planktonic copepods (Cordell and Morrison 1996, J. Cordell, unpublished 

data), but none so profoundly as San Francisco Bay. Eight Asian copepods have invaded 

this system (Orsi and Ohtsuka 1999), with apparent wholesale occupation of a variety of 

salinity zones and of both grazer and predator trophic levels (Orsi 1995). Findings from 

several recent sampling surveys (J. Cordell, unpublished data, Cohen et al. 1998, Cordell 

and Morrison 1996) indicate that reproducing populations of introduced planktonic 

copepods may not yet exist in Puget Sound. However, one species, Pseudodiaptomus 
39

inopinus, has established itself in the Columbia River and many other estuaries along the 

coasts of Oregon and Washington (Cordell and Morrison 1996). 

Benthic and Epibenthic Marine Invertebrates

There are more than 10 shrimp species, 30 crab species and 35 bivalve molluscs (e.g., 

oysters, clams, scallops, and mussels) in Puget Sound (Kozloff 1983). The benthic 

community, infauna, epifuana, and water column organisms, is incredibly diverse in 

terms of species and habitats, and thus our focus is limited to the status of listed priority 

species: Dungeness crab (Cancer magister), pandalid shrimp (Panadalus spp.), geoduck 

clam (Panopea abrupta), butter clam (Saxidomus giganteus), littleneck clam (Protothaca 

staminea), Japanese littleneck clam, (Tapes philippinarum), Olympia oyster (Ostrea 

lurida) and the Pacific oyster (Crassostrea gigas). Priority species require protective 

measures and/or management guidelines to ensure their perpetuation and must meet at 

least one of three criteria including 1) State listed and candidate ESA species; 2) 

vulnerable aggregations (i.e. shellfish beds); and 3) vulnerable species of recreational, 

commercial, and/or tribal significance (http://wdfw.wa.gov/hab/phspage.htm --Priority 

habitats and species; © 1997-1999 Washington Department of Fish and Wildlife). Not 

all priority species are native to Puget Sound and some, like the Pacific oyster, have 

impacted native populations within the benthic community. Recently, two exotic 

tunicates have been reported in Puget Sound and their invasions are predicted to impact 

regional bivalve populations. The blue mussel (Mytilus edulis) is widespread throughout 

Puget Sound and the West Coast shoreline and as such is an important integrator of 

coastal processes, such as bioaccumulation of contaminants, and is a prominent indicator 

species in the Nation’s benthic surveillance program. 

The Dungeness crab supports a valuable commercial and sport fishery in Puget Sound. 

Annual landings for the state commercial fishery from 1993 through 2001 averaged 2.3 

million pounds 

(http://wdfw.wa.gov/fish/shelfish/crabreg/comcrab/historiclandings.shtml). In 2001 the 

Dungeness sport fishery landings totaled 1,264,584 

(http://wdfw.wa.gov/fish/harvest/index.htm). Crab stocks are currently considered to be 

healthy even though there has been a continual increase in fishing pressure in recent years 

(http://www.dfo-mpo.gc.ca/zone/underwater_sous-marin/crab-crabe/crab-crabe_e.htm). 

Dungeness crab habitats are found from the intertidal to depths exceeding 180 meters. 

The species is widespread and occurs in bays and inlets, in estuaries, and across shelf 

waters. Although found on mud and gravel substrates, this crab is most abundant on 

sandy bottoms, and in shallow waters around eelgrass. Its larval form is planktonic 

(Pauley et al. 1989). Major prey include clams, other crustaceans, and small fish. Other 

crabs, Pacific halibut, dogfish, sculpins, octopus and sea otter feed on Dungeness crabs. 

Salmon and other finfish are predators of Dungeness larvae during the planktonic phase 

(Pauley et al. 1989). 

The geoduck is the largest bivalve found in Puget Sound. Populations are distributed 

subtidally, and regional stocks support important sport and commercial fisheries 

(Goodwin and Pease 1989). There are an estimated 109 million adult geoducks in Puget 
40

Sound (http://www.ecy.wa.gov/programs/sea/pugetsound/species/geoduck.html). 

Geoduck densities in Puget Sound bays and estuaries are the highest in the United States 

and the species is especially abundant in the South Sound. Geoducks are most abundant 

in sandy muds of the lower intertidal and subtidal zones at depths extending from 3 to 30 

meters below mean low tide. The species has planktonic larvae that are fed upon by fish, 

other plankton, and other suspension-feeding invertebrates. Post larvae stages are eaten 

by demersal and other finfish, worms, snails, starfish and crabs (Goodwin and Pease 

1989). 

Olympia oysters have an irregularly-shaped, fluted shell ranging in color from a chalkywhite to purplish-black (Couch and Hassler 1989). Once an important resource for tribal, 

commercial and recreational interests, this species has declined to levels below 

sustainability. The oyster has been commercially exploited since the 1850’s, and, in the 

South Sound, while fishing is not permitted, the population is threatened by pollution 

from motorboats, pulp mills and wastewater discharge, and increased siltation of shallow 

water beds. Some increases in local oyster populations have been associated with 

improved water quality in Puget Sound. Despite management efforts, Olympia oyster 

stocks have not returned to pre-exploitation levels and it is presently listed as a Federal 

Species of Concern and a Washington State candidate endangered species (Couch and 

Hassler 1989). Olympia oysters are found in estuaries, tidal channels; on the undersides 

of floats and on pilings. They are filter feeders and their primary prey is phytoplankton. 

Major predators include seaducks, various crabs, and two introduced species, the 

Japanese oyster drill (Ocenebra japonica) and a parasitic flatworm (Mytilicola 

orientalis). The larger and faster-growing Japanese and Pacific oysters and the slipper 

shell (Crepidula fornicate) are major competitors in Puget Sound habitats (Couch and 

Hassler 1989). 

There are hundreds of other benthic invertebrates in Puget Sound, yet their significance in 

food web structure and sustainability is poorly defined. Key species among them that are 

commercially fished are sea urchins and sea cucumbers. The 2001 commercial harvest 

was almost half a million pounds for each species 

(http://wdfw.wa.gov/fish/shelfish/divereg/). Pinto (Northern) abalone and the red sea 

urchin are listed as Washington State Priority species 

(http://wdfw.wa.gov/hab/phspage.htm). The red sea urchin (Strongylocentrotus 

franciscanus) is a "spiny-skinned" echinoderm with a spherical body encased in a hard 

shell completely covered by many sharp spines. Their color varies from a uniform red to 

a dark burgundy (http://seaurchin.org/Sea-Grant-Urchins.html#red). In Washington State, 

the commercial fishery grew rapidly from 1986 to 1988 and landings peaked at 8.1 

million pounds in 1989 prompting a first-ever emergency closure. Today, harvest quotas 

are limited to 215,000 pounds for commercial and tribal landings 

(http://wdfw.wa.gov/fish/shelfish/divereg/). Urchin habitats are located in the rocky 

subtidal from just below mean low tide line to 90 m. Larvae are planktonic. The urchins 

feed on seaweeds and kelp and are preyed upon by sea stars and crabs 

(http://seaurchin.org/Sea-Grant-Urchins.html#red). 
41

Pinto (Northern) abalone are marine gastropods that are closely-related to clams, oysters, 

mussels, and squids. The pinto abalone is one of the smallest species of abalone. It can 

grow to 6 inches in length, but its size is rarely larger than 5 1/2 inches 

(http://mehp.vetmed.ucdavis.edu/pdfs/browngaydos05.pdf). Very low population 

numbers have resulted in the Pinto abalone’s listing as a ‘Species of Concern’ under 

federal, and state endangered species provisions 

(http://mehp.vetmed.ucdavis.edu/pdfs/browngaydos05.pdf). Pinto abalone are found in 

coastal kelp beds and over sandy bottoms from low-low mean water to 10-15 meter 

depths. Larvae are planktonic. Pinto abalone feed on marine algae from minute particles 

to giant bull kelp. Its main predators include crabs, octopi, starfish, finfish, and marine 

snails (Harbo 1997). 

Squid

Several species of squid have been reported in Puget Sound; however, the most common 

is the market squid (Loligo opalescens). Stock structure among Pacific coast populations 

of L. opalescens is currently unknown (California Fish and Game 2005), but previous 

genetic research revealed little differentiation between stocks sampled from southern and 

central California (Reichow and Smith 2001; Gilly 2002). 

Market squid are likely an important component of the food web in Puget Sound as in 

California. As predators, squid feed on a variety of food items, including copepods and 

euphasiids, polychaete worms, squid (cannibalism), crustaceans, and some fishes 

(California Fish and Game 2005). As prey, they are important at several trophic levels 

and predators include killer whales (NOAA 2002), pinnipeds (NMML 1996), seabirds 

(Croxall and Prince 1996), Pacific salmon (Groot and Margolis 1991, California Fish and 

Game 2005), and many other marine species. Data on standing stocks in Puget Sound are 

scarce, but anecdotal information suggests that abundance varies annually and seasonally. 

Adults in significant numbers are present in central and south Puget Sound from 

September through February (WDFW, date unknown) and preliminary trawl data 

produced estimates of 0-1 g/m2 (T. Essington, University of Washington, personal 

communication). In general, habitat requirements of market squid in Puget Sound are not 

well documented but it is likely that a variety of habitats are utilized at various life stages. 

They are occasionally found in the nearshore habitat (C. Rice, NOAA, Northwest 

Fisheries Science Center, personal communication) and were captured during October in 

trawls at 20-80m (but not at 160 m; T. Essington, University of Washington, personal 

communication). In California, non-spawning squid are believed to be pelagic, migrating 

to the upper water column at night (California Fish and Game 2005) and preliminary data 

from acoustic tagging in the sound suggests some individuals travel a minimum of 10-12 

miles (John Payne, NOAA, Northwest Fisheries Science Center, personal 

communication). In Monterey Bay (California), offshore cohorts appear to move inshore 

for reproduction (Ish et al. 2004) and in Puget Sound spawning appears to occur on 

gently sloping bottoms, at depths of 15-60 feet with eggs found at almost all times of the 

year (WDFW, date unknown). Further research will be required to determine the status 

and importance of squid in Puget Sound. 
42

Demersal Fish (other than rock fish)

Demersal fishes are defined as those that spend most or all of their life histories 

associated with bottom or benthic habitats. Some fish species which have demersal egg 

or larval stages (e.g., herring and surf smelt) and species which spend some time feeding 

in benthic habitats (e.g., salmon) are not included here. Rockfish are also not included 

here as demersal fish. Most the fish that live in Puget Sound are demersal species which 

includes flatfish, surf perches, sculpins, gunnels, and gadids. While many demersal 

species change habitats within Puget Sound (e.g., moving from deep to shallow water in 

the summer), none of the demersal species migrates to and from Puget Sound. 

Other than several species which are commercially or recreationally harvested, such as 

some flatfish species and gadids, we have a poor understanding of the status and trends of 

this species group. This is primarily because we do not monitor abundance levels of most 

demersal species. One demersal species that has exhibited a dramatic decline in 

abundance is Pacific cod in central Puget Sound which was heavily overfished in the 

1970s and 1980s. 

Demersal species use the full range of shallow subtidal to deep benthic habitats. Major 

attributes of benthic habitat that affect composition of demersal species include depth, 

substrate type, and vegetation. For example, eelgrass beds have a diverse and abundant 

fauna comprised of perch, gunnels, and various sculpin species. In deeper benthic 

habitats, species that are commonly found include dogfish, ratfish, larger flatfish, larger 

sculpins, and gadids (e.g., tomcod). In general, there is a shift in fish size as a function of 

depth with smaller fish associated with shallower water and larger fish occupying deeper 

water. Several demersal species are tolerant of lower salinity and so can be found closely 

associated with major deltas. Many species undergo seasonal shifts in habitat use. 

Shiner perch are generally absent from inshore habitats in fall and winter but move from 

deeper water habitats. Postlarval flatfish settle on shallow intertidal mud and sand flats in 

late spring and summer (often in brackish areas) and then move progressively into deeper 

waters as fish size increases. 

Not surprisingly, most prey items eaten by demersal species are associated with benthic 

food webs. While information on food web relationships in nearshore areas have been 

well studied, diets in deeper benthic areas are still poorly understood. Major factors 

affecting prey eaten are fish species, fish size, season, and habitat where fish are foraging. 

In general, major invertebrate prey of demersal species include polychaetes, amphipods, 

mysids, bivalves (mostly siphons), and copepods (e.g., harpacticoids). While many 

demersal fishes eat similar prey (have high overlap) we do not know if and under what 

conditions food is limiting. Major predators within this species group include large size 

classes of several species such as halibut, cabezon, lingcod, and staghorn sculpin. Marine 

mammal species, probably sharks, as well as larger salmon often prey on demersal 

species. Great blue herons and several raptor species (Peregrine falcons) also prey on 

demersal species in nearshore areas. As with all Puget Sound found webs, there are a 

number of species that feed on the same types of prey as demersal species but spend little 

time in these habitats (e.g., juvenile salmon). 
43

Rockfish (section to be developed). 

Salmonids

There are five species of Pacific salmon that occupy the waters of Puget Sound. Each of 

the five species of Pacific salmon found in Puget Sound has the same basic anadromous 

life cycle, although several species also have life history types that spend their entire life 

cycles in freshwater (e.g., sockeye salmon). Within Puget Sound, a statewide inventory 

of anadromous salmon populations conducted in the state in 1992 and repeated in 2002 

identified 146 populations of all five species combined in Puget Sound. Abundance 

levels of a number of these stocks are low. As a group, Chinook salmon is in the worst 

condition and the federal government listed Puget Sound Chinook salmon as threatened 

in 1999. Chum salmon populations that spawn in Hood Canal and the eastern Strait of 

Juan de Fuca were also listed as Threatened. 

All species of salmon do not use Puget Sound habitats in the same way. Habitat use is a 

function of species, size, population, time of year, location within Puget Sound, and 

environmental conditions. Because salmon are migratory, they never are truly residents 

of any habitat once they leave freshwater. 

Salmon enter the waters of Puget Sound throughout most of the year. The first habitats 

these fish encounter are the deltas of natal spawning streams. The time spent in these 

systems and the habitats used are largely a function of fish size. For example, Chinook 

salmon fry that enter a delta in March can spend many months rearing in this system 

while coho salmon or Chinook salmon yearlings spend little time in the deltas. Channel 

networks in marshes provide high quality rearing habitat for salmon of all species. Once 

salmon enter Puget Sound, they first occupy shoreline or littoral areas. The time spent in 

these habitats depends primarily on fish size. Fish size and residence time in shoreline 

areas are inversely related. As fish grow, they progressively move from shoreline areas 

into more offshore areas. Eventually, by fall, most young salmon have moved into the 

deeper more offshore waters of Puget Sound as they are migrating towards the Pacific 

Ocean. Eventually, most salmon leave Puget Sound, although there is a component of 

each species that remains as residents in Puget Sound. 

Salmon are part of all food webs in Puget Sound and can occupy multiple levels of these 

food webs at the same time. They also perform an important function in freshwater 

ecosystems by transferring nutrients in the form of their tissues from marine systems into 

freshwater. Salmon of any species eat a progression of food that changes as the fish 

grows, as seasonal food web processes change, as the fish change location (e.g., between 

south Puget Sound and the Strait of Juan de Fuca. In general, fish size and species has a 

dramatic influence on what is eaten. Prey size tends to increase as the salmon get larger. 

For example, juvenile Chinook salmon shift from a diet of insects and amphipods to 

larger invertebrates such as amphipods, crab zoea, and polychaetes to a diet that is mostly 

fish by the time they occupy the offshore waters of Puget Sound. 
44

The organic matter and nutrients eventually utilized by juvenile salmon as food come 

from terrestrial (e.g., insects), benthic (e.g., amphipods and polychaetes), and pelagic 

food webs (e.g., copepods, crab larvae). The organic matter and nutrients that support 

each food web of course vary. One type of food web that is especially important to 

salmon is the detritus based food web. These nearshore food webs depend upon 

internally derived organic matter (e.g., from eelgrass). This organic material which is 

called detritus supports a grazing community of micro flora and fauna that in turn 

supports invertebrate prey such as copepods that are eaten by smaller size classes of 

juvenile Chinook salmon and chum salmon. 

Because salmon are associated with all types of food webs and occupy many different 

trophic levels they are eaten by many species of fish, birds, and mammal. As the salmon 

increase in size, the number of species that are predators declines as the salmon simply 

outgrow their predators (e.g., become too large for the predators to handle and eat). By 

the time salmon have reached subadult size, only mammals (including humans) are large 

enough to eat them. 

Within the marine waters of Puget Sound, there is no evidence that food is limiting, 

although such a possibility has not been rigorously tested. Many of the species salmon 

co-occur with have similar diets to salmon. And, often different species of salmon will 

have similar diets. There is evidence that food is limiting (i.e. resulting in density 

dependent processes) for Chinook salmon in natal deltas. 

 

Non-salmonid pelagic fishes

Non-salmonid pelagic fishes of Puget Sound include representatives from several 

families. Herring (Clupeidae), smelt (Osmeridae), sand lance (Ammodytidae), surfperch 

(Embiotocidae), tube snout (Aulorhynchidae), and anchovy (Engraulidae) are common, 

with rare occurrences of silversides (Atherinidae), pelagic sharks (Lamnidae), and 

armorheads (Pentacerotidae). However, the majority of biomass is concentrated in three 

key species; Pacific Herring (Clupea pallasii), Pacific sand lance (Ammodytes 

hexapterus), and surf smelt (Hypomesus pretiosus). This collective group of forage 

fishes represents a critical trophic link between primary / secondary producers (i.e. 

phytoplankton / zooplankton) and larger vertebrates, including endangered and other 

salmonids, seabirds, and marine mammals. Additionally, these three species transfer 

energy and nutrients from pelagic to nearshore regions during spawning (all three 

species) and nocturnal refuge (sand lance). They utilize surface, mid-column, epibenthic, 

and nearshore waters of Puget Sound. 

Pacific herring are a substantial component of several trophic levels of the Puget Sound 

food web. The estimated carbon contribution of herring spawning products to the Strait 

of Georgia during the spring spawning period is greater than maximum estimates of 

primary productivity during the same period (Hay and Fulton 1983). Herring eggs and 

larvae represent a primary food source for invertebrates including crabs, medusae, 

ctenophores, chaetognaths, and amphipods; fish including juvenile salmonids, sturgeon, 
45

smelt, and surfperches; and marine gulls and diving birds. Juvenile and adult herring 

serve as the primary prey for marine mammals including harbor seals, sea lions, and 

orcas (Schmitt et al 1995), and finfishes including endangered Chinook salmon, coho 

salmon, Pacific cod, Pacific hake, lingcod, and halibut (Lassuy 1989). 

Herring stocks in Puget Sound are defined by their spawning location; however, the 

extent to which these stocks are isolated and the residency of stocks in Puget Sound is 

still in question. Fish tagged in the Puget Sound have been recovered in the Strait of 

Georgia (British Columbia) and in the Pacific Ocean (Buchanan 1984, Trumble 1983). 

Cumulative spawning biomass estimates for herring in Puget Sound were 15,016 and 

12,007 tons for 2003 and 2004 respectively. These estimates are 85% and 68% of the 25 

yr mean (17,754 tons). Stocks in South-Central Puget Sound are relatively stable, while 

those in North Puget Sound are depressed primarily due to reduction in the Sound’s once 

largest stock at Cherry Point. The spawning biomass of herring at Cherry Point in 2004 

was only 43% of the 25 year mean (Stick 2005). 

Other forage species in Puget Sound, including sand lance and surf smelt, historically 

received less attention than herring, likely because of their perceived economic value. 

However, their ecological value as primary forage species should not be overlooked 

because they occupy similar niches with herring and represent important components of 

the diets of larger vertebrates. For example, sand lance often comprise a substantial part 

of the diet of Chinook and coho salmon (up to 70%; Groot and Margolis 1991) and sea 

birds (Abbokire and Piatt 2005). Surf smelt also can be important prey for salmon (Groot 

and Margolis 1991) and seabirds (e.g., Caspian terns in Commencement Bay; Thompson 

et al. 2002). Declines in abundance of forage fishes seemed to be an important 

contributor to declines in seabird populations in the Gulf of Alaska even though increased 

numbers of gadids and flatfish were available (Piatt and Anderson 1996). 

Sand lance and surf smelt deposit eggs in the intertidal zone of sand-gravel beaches. In 

Puget Sound 400 km and 320 km of beach have been identified as spawning habitat for 

surf smelt and sandlance respectively (Pentilla 1997, Pentilla pers. comm.). Because 

these beaches are scattered throughout Puget Sound and no apparent aggregations of 

adults occur, there is currently no practical methodology for monitoring the biomass of 

these species. Additionally, no data exist to suggest whether these species are resident or 

transient in Puget Sound (Pentilla pers. comm.). 

Marine Birds

The Puget Sound area supports several species of marine and terrestrial birds. Although 

many species of terrestrial birds, including eagles and other raptors, prey on fish and 

other marine organisms in the Sound, it is the group of more than 100 species of marine 

birds that almost exclusively rely on the marine food web for nutrition. Whether surface 

gleaners, plunge divers, or pursuit divers, the seabird diet consists of small coastal pelagic 

fish, young-of-the-year-predatory fish (e.g., salmonids and groundfish), macrozooplankton (large copepods and euphausiid crustaceans), and squids (Mills et al. 2005). 

As top predators in marine ecosystems, seabirds function as important indicators of 
46

ecological change because they are visible, abundant and relatively easy to study. In fact, 

seabird distribution and productivity have been linked to prey (forage fish and plankton) 

availability, nearshore habitat quality and oceanographic conditions (Piatt 2002, 

Speckman et al. 2005). 

Many species of marine birds come ashore only to breed, while the remainder of the year 

is spent on the ocean. Thus, nearly all species of marine birds are seasonal in their 

occurrence within the Puget Sound, a region that provides habitat for migrant, winter 

resident, and breeding marine birds (Manuwal et al. 1979). In the northern Puget Sound, 

the San Juan Islands and Protection Island are important areas for nesting marine birds 

(Manuwal et al. 1979, Mills et al. 2005). In fact, Protection Island (located at the 

southeast end of the Strait of Juan de Fuca) is one of the largest breeding colonies of 

seabirds in the Pacific Northwest (U.S. National Fish and Wildlife Service), including 

one of the largest Rhinoceros Auklet breeding colonies in the world and the largest 

Glaucous-winged Gull colony in Washington (Mills et al. 2005). For all seabirds, 

predation on eggs and chicks can be high at breeding colonies (Mills et al. 2005). 

Depending on the location of the colony, sources of predation on seabirds can include a 

large suite of predators; namely gulls, raptors, corvids, rodents, cats and other large 

introduced mammals (Mills et al. 2005). 

 

Recent studies in Puget Sound and surrounding waters have shown 50-95% declines in 

populations of many marine bird species during the past 20 years (Nysewander et al.

2001, Bower 2004). The species that have shown the most alarming declines (80-95%) 

are diving birds such as Common and Red-throated Loons, Western, Red-necked and 

Horned Grebes, and Marbled Murrelets, all of which specialize on schooling pelagic fish 

in their diets (Nysewander et al. 2001, Bower 2004). For example, Marbled Murrelets 

have declined by 83% in northern Puget Sound (Bower 2004) and have been identified as 

“highly imperiled” by the U.S. Fish and Wildlife Service (Seabird Conservation Plan 

2005). Marbled murrelets forage in nearshore marine waters, but nest far above-ground 

in complex, multi-storied forest stands in old growth forests (Bentivoglio et al. 2000, 

Meyer and Miller 2002). One source of mortality for these birds is entanglement by 

salmon gillnet fisheries in the Puget Sound region (Melvin 1997). 

Marked declines have also been observed in summer breeding populations of fish-eating 

seabirds. For example, Common Murres declined by 83% in the early 1980s, and 

numbers have never recovered (Manuwal et al. 2001). In large part because of these 

population trends, the U.S. Fish and Wildlife Service identified the Common Murre as 

species of “moderate conservation concern” (Seabird Conservation Plan 2005). These 

birds typically immigrate to the Strait of Juan de Fuca, Strait of Georgia, and Puget 

Sound following the breeding season in the late summer and fall where they mainly feed 

on Pacific herring and Pacific sand lance as well as some salmonids (Lance and 

Thompson 2005). One source of mortality for these birds is entanglement by salmon 

gillnet fisheries in the Puget Sound region (Melvin 1997, Lance and Thompson 2005). 

Another summer breeding population that has suffered a decline is the burrow nesting 

Rhinoceros Auklet (Mills et al. 2005). In fact, the Protection Island summer and spring 

breeding colony in the Strait of Juan de Fuca has declined steadily from a high of about 
47

17,000 pairs in 1975 to 12,000 pairs in 2000 , and as a consequence, the U.S. Fish and 

Wildlife Service identified the Rhinoceros Auklet as species of “high concern” (USFWS 

2005). When these birds forage in the Puget Sound, they prey primarily on Pacific 

herring, Pacific sand lance, and salmonids, but also consume considerable amounts of 

threespine stickleback (Lance and Thompson 2005). Sources of mortality include 

predation by Peregrine Falcons, Bald Eagles, and other avian predators at breeding 

colonies (Mills et al. 2005) and entanglement by salmon gillnet fisheries in the Puget 

Sound region (Melvin 1997, Lance and Thompson 2005). 

Moderate declines (50-60%) have also been observed in a variety of birds that are less 

dependent on pelagic forage fish because they can also subsist on benthic or demersal 

fishes (e.g., cormorants and guillemots) and sub-tidal or inter-tidal invertebrates (e.g., 

gulls and scoters). Specifically, the Pelagic Cormorant has been identified as species of 

“high concern” by the U.S. Fish and Wildlife Service (Seabird Conservation Plan 2005). 

These birds depend on steep, rocky cliffs above the ocean to nest during the spring and 

summer months (Mills et al. 2005), but also require year-round roosting habitat on dry 

land for drying their feathers because their plumage is not waterproof (Mills et al. 2005). 

Similarly, the Pigeon Guillemot forages on both dispersed demersal fishes and 

aggregated pelagic fishes (Litzow et al. 2004), and is currently listed as species of 

“moderate conservation concern” by the U.S. Fish and Wildlife Service (Seabird 

Conservation Plan 2005). Pigeon guillemots are nearshore-foraging seabirds that rely on 

the relatively inaccessible cliffs and headlands along the mainland coast and on larger 

islands for nesting sites (Mills et al. 2005). Like other seabirds in the Puget Sound 

region, salmon gillnet fisheries are a source of mortality for Pigeon guillemots (Melvin 

1997). 

Increasing our knowledge of the biology and ecology of some key marine bird species 

that were at one time very abundant but are now declining will provide us with a better 

understanding of how the Puget Sound ecosystem is changing. The causes of these 

dramatic declines are unknown in most instances, but possible explanations include 

natural variability in food supply or foraging habitats, and the negative effects of human 

development and fisheries on the marine environment and breeding habitat (John Piatt, 

pers. comm.; Manuwal et al. 1979; Mills et al. 2005). A better understanding of all of 

these factors will also help us to understand the Puget Sound ecosystem as a whole. 

Marine mammals

Eleven species of marine mammals that include six cetaceans (killer whale, gray whale, 

humpback whale, minke whales, harbor porpoise, and Dall’s porpoise) and five pinnipeds 

(harbor seals, California sea lions, Steller sea lions, northern elephant seals, and northern 

fur seals) are known to occur in the waters of Puget Sound, the Strait of Juan de Fuca, 

and Georgia Straits (i.e., the Salish Sea). Of these species, four of the cetacean species 

and two of the pinniped species can be considered key components of these systems due 

to their relatively large numbers or biomass or their potential influence on the abundance 

of their prey species. Key cetacean species include killer whales (piscivorous and 
48

mammal eating), harbor and Dall’s porpoises, and gray whales. Key pinniped species 

include harbor seals and California seal lions. 

Piscivorous and mammal eating killer whales are top predators that are distinct small 

populations of sympatric ecotypes (approximately 90 and 325, respectively (Caretta et al. 

2005, Angliss and Lodge 2002). The piscivorous population has been increasing since 

2001 following a 20% decline in the mid-1990s, but no trend data are available for the 

mammal eating population. Although both ecotypes occur throughout the Salish Sea 

year-round they have unique temporal and spatial habitat use patterns. There are seasonal 

peaks, with piscivorous whales being present most days during the summer and fall 

(Osborne 1999) and mammal eating being present sporadically in the fall (Baird and Dill 

1997). Piscivorous killer whales occur primarily in major channels surrounding the San 

Juan Islands in the summer and expand their movements into the Puget Sound in the fall 

(Osborne 1999). Habitat use includes the central parts of these main channels as well as 

particular nearshore areas with steep slopes. Mammal eating killer whales are found 

most frequently off southeastern Vancouver Island in narrow channels or close to shore 

(Baird and Dill 1997), and travel in relatively small groups (avg=3, Baird and Dill 1996). 

Mammal eating killer whales are also typically present for only a few days, although 

there have been two occurrences of extended residency periods in Hood Canal in recent 

years (London et al. 2003, 2005). The diet of piscivorous whales has been found to 

include a variety of fish species based on stomach contents (Ford et al., 1998) but more 

numerous samples from predation events have indicated that salmon, particularly chinook 

are important prey (Ford et al. 1998, 2005, Hanson et al. 2005). Mammal eating killer 

whales forge primarily on harbor seals although a few harbor porpoises and California 

seal ions are also taken (Baird and Dill 1997). There are no known predators of killer 

whales. Piscivorous killer whales may compete with humans for fish resources but 

mammal eating killer whales likely have no competitors. 

Each year very small fraction of the approximately 26,000 (Angliss and Lodge 2002) 

gray whales which migrate to Alaska from Baja California enter Puget Sound. The 

population has been steadily increasing since the first systematic counts were made in the 

late 1960s. They are observed periodically throughout the year but peak abundance of a 

few dozen individuals occurs in the spring. They occur throughout Puget sound, 

including the strait of Juan de Fuca and Hood Canal. Although they travel in the main 

channels it is not uncommon to observe them feeding in shallow waters areas with a 

sandy bottom . In particular, they are commonly observed in Port Susan and near the 

south end of Whidbey Island (Calambokidis et al. 1994) were they are known to feed on 

ghost shrimp (Weitkamp et al. 1992). Lower occurrence and residency time in Port 

Susan in subsequent years may indicate that the standing stock of ghost ship was 

temporarily depleted. Killer whales are known to prey on gray whale calves but this has 

not been observed in Washington State. 

Harbor porpoises are the most numerous cetacean in the Salish Sea, with an estimated 

population of 10,682 in 2002/2003 of the Washington inland water stock (NMML, 

unpublished data). The estimated population size has increased almost 3 fold since the 

since the first systematic surveys were done in the early 1990s (Calambokidis et al. 
49

1997). Despite their relative large numbers they are found almost exclusively in the 

Straits of Juan de Fuca and Georgia, with few sightings in Puget Sound. This situation 

contrasts with anecdotal observations from the 1940’s of harbor porpoise being extremely 

common in the lower Puget Sound (Scheffer and Slipp 1948). Seasonal survey data 

(PSAMP unpubl. data) indicated that these species are present year-round, and radio 

telemetry data suggests that seasonal movement patterns are limited to regions within the 

Salish Sea (Hanson 2005). Radio-telemetry data and genetic data also indicate that 

animals in the Juan de Fuca and Georgia Straits do not move between areas or inter-breed 

(Hanson 2005). Although harbor porpoise can be found in nearshore shallow water 

(Calambokidis et al. 1997, Hanson unpubl. data), most are found in the deeper central 

portion of the main channels (Hanson 2005). Their primary prey are small schooling 

fish, particularly herring. and squid (Walker et al. 1998, in prep.) but other species of 

importance include pollock, hake, smelt, midshipman, and sculpin. Their primary 

predator is mammal eating killer whales. They may compete with Dall’s porpoise for 

prey, (although generally, they appear to be spatially and temporally segregated), and 

harbor seals. 

Dall’s porpoise are a common small cetacean in the Salish Sea with an estimated 

population of approximately of 98,617 in the California/Oregon/Washington stock 

(Caretta et al. 2005). However, estimates for the inland Washington waters indicate 

about 3,500 porpoises are present (Calambokidis et al. 1997). There are no trend data 

available for this population. This species is found throughout the strait of Juan de Fuca 

and Puget Sound with primary concentrations in the Haro Strait area. Dall’s porpoise 

typically use the main channels and are associated with deep water locations where they 

are known to dive to near the bottom (Baird and Hanson unpubl data.). Based on 

telemetry studies, there is also some indication that seasonal habitat use patterns exist. 

Although sample size is limited, Haro Strait was used in the winter and spring followed 

by movement to areas just off the entrance of the strait of Juan de Fuca in the summer 

(Hanson 2005b). In the fall, the porpoises utilized the central Strait of Juan de Fuca. 

Like harbor porpoise, Dall’s porpoise prey on small schooling fish, but the diets of the 

two porpoise are somewhat different. Nearly half of the Dall’s porpoise diet is composed 

of pollock, but sculpin, herring, hake, squid and eulachon contribute to the other half of 

the diet (Walker et al. In prep.). Predators include killer whales, although no known 

predation event on this species has been documented in this region. Dall’s porpoise may 

compete with harbor porpoise, but it appears that these two species may be spatially and 

temporally separated. There may be some competition with harbor seals and California 

sea lions. 

 

Harbor seals are the most common pinniped in the Salish sea with a population in the late 

1990’s numbering close to 8,000 animals (Jeffries et al. 2003). This population had 

increased from only 3,000 seals in the late 1970’s (Jeffries et al. 2003), but appears to 

have plateaued in the early to mid-1990’s. These seals are year-round residents with high 

haul-out site fidelity and generally limited movements from these sites. Harbor seals are 

wide spread throughout all three basins and Hood Canal, but the majority of the 

population is in the San Juan Islands, the bays to the east of this area, and the Strait of 

Juan de Fuca. The seals are commonly found in the shallow waters near their numerous 
50

haul out sites but also venture into deeper portions of the main channels. Their diet is 

comprised primarily of fish, and although some seasonal and site specific variation does 

exist, hake and herring comprise 70% of their diet with 9 other fish and one squid species 

comprising the rest (Olesiuk 1993). (There may be some differences in prey in south 

sound – looking for this). Consequently, harbor seals may be in competition with harbor 

porpoises to a limited extent. Harbor seals are also a primary prey item of mammal 

eating killer whales. 

California sea lions were first observed in the mid 1970s and occur in relative small 

numbers throughout the Salish sea and Hood Canal. The number of sea lions in the area 

increases to over a thousand animals during the peak each spring. Recent counts number 

in the low hundreds despite the likely continued increase of this population (Caretta et al.

2005). These animals are comprised primarily of adult and subadult males that migrate 

north from the offshore islands in California during the post-breeding season. Although 

these sea lions are wide spread, they are known to concentrate in Shilshole Bay and in 

Port Gardner (Gearin et al 1999) . It is likely that the Shilshole Bay aggregation of sea 

lions formed because of the ease of foraging on concentrations of steelhead returning to 

Lake Washington watershed that are subject to increased vulnerability associated with 

the unnatural environment adjacent to the Government Locks. A relatively small number 

of California sea lions were responsible for nearly decimating this fish population (Gearin 

et al. 1988?). In Port Gardner the sea lions have been found to primarily prey on hake 

(80%), although 10 other fish species and one squid species make up the remainder of the 

diet (Gearin et al. 1999). Although hake was overfished prior to the arrival of sea lions in 

Port Gardner, the continued presence sea lions has been attributed to preventing this fish 

stock from recovering (Schmitt et al. 1995).

Threats to the Puget Sound Food Web 

The Puget Sound is an area that has been enormously altered by human activity. 

However, the specific anthropogenic threats that most impact the food web have not been 

identified. Similarly, the specific mechanisms that cause adverse effects are also 

unknown. Although several human activities impact the food web on many levels, this 

section will focus on anthropogenic threats that are either conducted through the food 

web or directly impact the food web structure. These activities result in removals or 

additions of species, impact predator and prey relationships, or affect the health of 

species in the food web. Examples of such anthropogenic activities, include vessel 

disturbance, fishing operations, introduction of toxic substances and pollution, and the 

introduction of non-native species. Catastrophic events such as oil spills and disease 

outbreaks are also concerns. Destruction of habitat also seriously impacts species in the 

food web, but those anthropogenic impacts are discussed elsewhere in the document (see 

habitat section). It is important to assess all anthropogenic threats in the Puget Sound 

ecosystem because these threats and other unidentified factors, such as climate change, 

may act either singly or in concert to affect reproductive success or survival of species in 

the ecosystem. 
51

Vessel Disturbance

Shipping, fishing, and recreational boating activities are high in the Puget Sound, and as a 

consequence, the mere presence of these vessels and the noise produced by them can 

negatively impact several species within the Sound. For example, cetaceans (e.g., killer 

whales and harbor and Dall’s porpoises) rely on their highly developed acoustic sensory 

system for navigating, locating prey, and communicating. Consequently the impacts of 

vessel disturbance and noise pollution on these species are of utmost concern. 

Specifically, the ESA-listed Southern Resident killer whale, a seasonal inhabitant of the 

Puget Sound region, is almost continuously surrounded by whale watching vessels during 

the summer months in the San Juan Islands. In fact, this group of whales have been 

exposed to a greater number of commercial and private vessels in recent years. The 

increase in the number of vessels in the vicinity of Southern Resident killer whales during 

the past decade is of concern because the Southern Resident killer whale population also 

suffered a 20% population decline from 1996 to 2001 (Krahn et al. 2002). As a result, 

vessel disturbance was identified as a potential risk factor to this group of killer whales. 

This is because the masking effects of noise produced by vessels and/or the behavioral 

changes in killer whales caused by vessel disturbance may inhibit these animals from 

foraging efficiently and/or increase daily energy expenditures. 

Seabirds are also impacted by vessel disturbance and noise pollution, particularly at 

colonies or roost sites. Human disturbance to seabird colonies can result from 

recreational and commercial boating activities, aircraft overflights, ecotourism, and 

investigator disturbance. Boats or aircraft that approach too closely to breeding seabirds 

on their nests may cause birds to flush, thereby leaving the eggs and/or chicks open to 

predation or overexposure to harsh elements (Mills et al. 2005). Like marine mammals, 

extra energy expended during disturbances or missed feeding opportunities by seabirds 

could act to reduce both reproductive success and survival, potentially having negative 

population-level consequences. 

Fishing Operations

The Puget Sound, as a highly productive marine ecosystem, has a high abundance of 

fishers. This has resulted in encounters and conflicts between certain fisheries and marine 

wildlife. Fishing operations can both directly and indirectly impact organisms in the 

Puget Sound. Direct disturbances by fisheries include boats disrupting feeding or 

injuring non-targeted animals, such as seabirds and mammals, either through direct 

collision or entanglement in fishing gear. In particular, seabirds; including Common 

Murres, Rhinoceros Auklets, Pigeon guillemots, Marbled Murrelets; have high incidences 

of mortality due to entanglement in the salmon gillnet fisheries in Puget Sound (Melvin 

1997). Incidental harvest of non-targeted fish is another important impact on several 

species of fish, including salmon, in the Puget Sound food web (National Science and 

Technology Council, Committee on Environment and Natural Resources 2002). 

Fisheries can also compete for the same fish or invertebrate species that are consumed by 

higher level organisms in the food web. For example, Southern Resident killer whales 

consume salmonid species which are also targeted by fisheries (Krahn et al. 2002). 
52

Finally, indirect human threats can involve reduction of prey as a result of competition 

with fisheries for shared prey resources and changes in the ecosystem structure produced 

by commercial fisheries activities due to biomass removal or habitat degradation (Mills et 

al. 2005). For instance, although the Pacific salmon stocks have declined I the Puget 

Sound, these stocks are still subject to substantial levels of harvest by commercial, sport, 

and subsistence fisheries (National Science and Technology Council, Committee on 

Environment and Natural Resources 2002).

Toxic Substances and Pollution

Due to human activities in the Puget Sound region, persistent toxic chemicals such as 

Organochlorines (OCs) and other pollutants contaminate the region. The effects of 

urbanization, such as pollution from waste water and sewage treatment plants, pesticides, 

excess nutrients and chemical waste are also cause for alarm (Puget Sound Action Team 

2005). Organochlorines comprise a diverse group of chemicals manufactured for 

industrial and agricultural purposes (including, polychlorinated biphenyls (PCBs), DDT, 

dioxins (PCDDs), and furans (PCDFs) that are highly toxic and remarkably persistent 

once released into the environment. These chemicals are initially introduced into the 

marine system from agricultural runoff and industrial effluents. Subsequently, as a result 

of biomagnification (substances become increasingly concentrated in organisms at higher 

trophic levels) through the food web, higher trophic level organisms in the Puget Sound, 

particularly marine birds (Ohlendorf and Fleming 1988) and mammals (O’Shea 1999) 

carry high levels of OCs. High levels of OCs are lethal to adult birds at high 

concentrations (Ohlendorf and Fleming 1988, Mills et al. 2005) and can cause immunodeficiency and inhibit reproduction in marine mammals (Ross et al. 1996a, Ross et al.

1996b). Because Southern Resident killer whales have high levels of PCBs, compared to 

other fish-eating killer whales, including the closely related Northern Resident killer 

whales (Ross et al. 2000) that also inhabit the Pacific Northwest, contaminants has been 

listed as a risk factor for the Southern Resident population (Krahn et al. 2002). 

A range of metals are present in trace quantities in the earth’s crust and thus throughout 

the marine environment, but at levels that are not toxic to marine organisms. However, at 

higher concentrations, all metals are toxic. Such elevated concentrations of metals can 

occur in the marine or onshore coastal environment from anthropogenic sources (Mills et 

al. 2005). Like OCs, metals are susceptible to bioamplification and accumulate at higher 

concentrations in higher trophic levels. In addition, concentrations of most metals tend to 

increase throughout an animal’s life. The primary metals of concern to marine mammals 

are lead, mercury, and cadmium (O’Shea 1999). These three metals, with the addition of 

selenium, are of concern to seabirds (Mills et al. 2005). With the exception of mercury, 

many marine mammal species are able to tolerate high amounts of metals or detoxify 

them (Reijnders and Aguilar 2002). In contrast, high levels of metals in bird birds can 

cause many adverse impacts, including reproductive failure (Mills et al. 2005). 

Because of the high level of shipping and ferry traffic, oil pollution is a great threat to the 

Puget Sound food web. Catastrophic oil spills can kill species from every trophic level of 

the food web. However, relatively minor oil spill can still impact several species. In 
53

particular, marine birds and mammals are particularly susceptible to oil spills. 

Interestingly, the Puget Sound area, with an extremely high density of seabirds, has been 

identified as one of the most susceptible areas to population-level impacts from oil spills 

(Mills et al. 2005). For marine birds, oil disrupts the waterproofing, and hence the 

insulation value, of birds’ feathers, often leading to hypothermia (Mills et al. 2005). 

Seabird mortality can also result from direct ingestion of oil, which occurs when birds 

preen oiled feathers (Mills et al. 2005). 

Exotic Species

Exotic species are organisms that are not native to the Puget Sound, but rather have 

arrived to the region as a result of human activities. In the Puget Sound there has been a 

fair amount of work done on exotic species (see Carlton 1979, Elston 1997, Cohen 

2004). The report from the Washington Department of Natural Resources (WDNR) 

Rapid Assessment Survey of exotic species in Puget Sound provided an updated and 

corrected list of 52 exotic species that were judged to be established in the Sound (Cohen 

et al. 1998). Most exotic species are detrimental to the food web because they either outcompete native species for prey or habitat, prey directly on native species, or alter habitat 

which impacts the survival of native species (for review see Cohen 2004). For example, 

non-native species that have been introduced to reservoirs, such as bass and walleye, prey 

on salmon and add to the mortality rates inflicted on young salmonids by native predators 

(National Science and Technology Council, Committee on Environment and Natural 

Resources 2002). Similarly, predation by rodents, cats and other large introduced 

mammals can impact breeding colonies of seabirds (Mills et al. 2005). 

Only a few of the many anthropogenic activities that impact the Puget Sound food web 

are described above. Once basic data on the impacts of human activity in Puget Sound 

are gathered, and the most important impacts are identified, further studies need to be 

conducted to assess how impacts on individual species have the potential to affect the 

status of their population and possibly the ecosystem. Multiple factors are undoubtedly 

responsible for changes in the populations of key species in the Puget Sound ecosystem. 

However, a thorough understanding of the anthropogenic threats in the Puget Sound will 

help us to reduce some of the uncertainty when modeling the viability of populations and 

assessing the relative risk of particular threats to the population. 

Eutrophication

Historically, Puget Sound has not been viewed as susceptible to eutrophication because 

of the typically high concentrations of nutrients incoming from the Pacific Ocean, as well 

as strong mixing in the Main Basin of Puget Sound, which limits exposure of 

phytoplankton to light and therefore reduces growth. These characteristics of central 

Puget Sound were responsible for the success of the diversion of sewage from Lake 

Washington to West Point (Puget Sound) in the late 1950’s (Edmondson, 1991). While 

nutrient loading to Lake Washington caused excessive algal growth, the same loading at 

West Point did not. Much of the current understanding of Puget Sound phytoplankton 

dynamics has been based on modeling and measurements of ambient productivity and 
54

nutrients at West Point (Winter et al. 1975). However, a much more complex picture is 

emerging, as a diversity of responses to nutrient addition is apparent both spatially and 

temporally within greater Puget Sound. 

Harrison et al. (1994) and Mackas and Harrison (1997) evaluated the issue of 

eutrophication in the Strait of Juan de Fuca, Strait of Georgia, and Puget Sound. They 

judged potential impacts from eutrophication of the Main Basin of Puget Sound to be 

relatively low. However, they reported that the more poorly flushed bays and inlets of 

Puget Sound, particularly in the southern end, showed depleted surface nitrate 

concentrations and very low oxygen concentrations at depth. They assessed that the 

“early warning signs of eutrophication” were already evident in these poorly flushed bays 

and inlets of southern Puget Sound. 

Bricker et al. (1999) reported the overall level of expression of eutrophic conditions to be 

moderate in (the Main Basin of) Puget Sound and Whidbey Basin and high in Hood 

Canal and South Puget Sound. The symptoms contributing to eutrophic conditions were 

chlorophyll a, macroalgae, toxic blooms, and, in Hood Canal, low dissolved oxygen. 

They predicted conditions to worsen, especially in Hood Canal and South Puget Sound, 

due to increasing population pressures. 

Studies utilizing nutrient addition experiments on phytoplankton productivity support this 

conclusion, as data from Budd Inlet (Newton et al., 1998) and Hood Canal (Newton et al., 

1995) show substantially increased rates of primary production upon nutrient addition. In 

a study on phytoplankton production in Puget Sound’s Central Basin and Possession 

Sound (Newton and Van Voorhis, 2002), considerable interannual variation in production 

was observed, potentially linked to differences in external physical forcings, and 

increased primary production due to experimental addition of nutrients was seen at times 

at all stations during spring and, more often, summer months but was most evident in 

Possession Sound. 

Harmful algal blooms

Harmful algal blooms (HAB) found in Puget Sound are those that can cause Paralytic 

Shellfish Poisoning (PSP) and Amnesic Shellfish Poisoning (ASP). PSP was first 

recorded in the region when in June 1793, four crewmen with Captain Vancouver’s 

expedition became sick and one died shortly after eating shellfish along the central coast 

of British Columbia. In Puget Sound, the causative agent for PSP is saxitoxim produced 

by the dinoflagellate Alexandrium catenella. 

There has been a documented spread in the occurrence of PSP throughout Puget Sound 

(Trainer et al., 2003). These authors present Washington Department of Health data 

documenting shellfish closures due to PSP beginning in the 1950’s, however these were 

constrained to sites just to the north of Puget Sound, outside of Admiralty Inlet (in 

Sequim Bay, Discovery Bay, San Juan Islands). The first closures within Puget Sound 

were reported during the 1970’s - specifically in 1978 where a large event followed a 

late-summer warm spell and heavy rains. PSP illness was reported from Saratoga Passage 
55

to Vashon Island. The “southward creep” of PSP closures continued, with increased 

incidents during the 1980’s and 1990’s. PSP went above the FDA action level in north 

Hood Canal for the first time during 1987 and similarly, in various inlets of South Sound 

during 1988, 1991, and 1997. In 2000, seven people were stricken with PSP from mussels 

collected in Carr Inlet, South Puget Sound; one man was severely stricken and spending 

several days in the hospital on a respirator. 

Diatoms in the genus Pseudo-nitzschia can produce the toxin domoic acid that can 

accumulate in shellfish and other organisms to levels dangerous to human and aquatic 

health causing ASP. In the fall of 1991, the WA Department of Health found domoic acid 

in razor clams along the Washington coast. Shellfish closures due to domoic acid levels 

are presently not uncommon and can be fairly chronic on the outer Washington coast. 

Prior to 2003, domoic acid had not been detected at closure levels within Puget Sound, 

though Pseudo-nitzschia and domoic acid had been documented in Hood Canal (Horner 

et al., 1996). In 2003, the first shellfish closure due to domoic acid was declared near Port 

Townsend, in the very north of Puget Sound. 

In 2005, elevated levels of domoic acid prompted closure of shellfish harvesting 

throughout Sequim Bay, Penn Cove, Saratoga Passage and Holmes Harbor. The factors 

prompting domoic acid production is a current topic of research, as the concentration of 

Pseudo-nitzschia is not correlated with the amount of domoic acid found in the shellfish 

(Trainer et al., 2000; 2002). 

Effects of Multiple Stressors

While much research has been performed on the direct effects of certain specific threats 

to the health of aquatic species (e.g. pollutants, pathogens), the effects of multiple, sublethal stressors on the health and population structure of aquatic animals are largely 

unstudied. Stressors could include, but are not limited to: infectious agents (e.g. viral, 

bacterial, protozoan or fungal pathogens), physical factors (e.g. abnormal temperatures, 

salinity, low dissolved oxygen, and contaminants including toxicants, pollutants, 

endocrine disrupters, pharmaceuticals and flame retardants), habitat alterations (e.g. 

quantity and quality) as well as various biological factors that are outside the normal 

range (density, competition, food availability, forage base). It is very likely that various 

species and life stages will respond differently to these threats. It is also likely that 

synergistic effects will be seen when sub-lethal levels of such stressors are combined, 

resulting in losses in affected populations. For example, we know that fish in the Puget 

Sound region are infected with erythrocytic necrosis virus and that such infections result 

in a severe anemia. While fish in normal habitats can often survive such infections, the 

combined effects of infection and other stressors (low dissolved oxygen, low salinity, 

other pathogens) can resulted in large mortality of some species (MacMillan & Mulcahy 

1979, Meyers et al 1986). 
56

Key Science Needs for Food Webs and Species 

Food Web Science Needs

The prey base that supports a large number of marine birds, marine mammals and 

predatory fish species in Puget Sound, Washington is largely understudied in terms of 

marine habitat requirements, life history, distribution and abundance. In Puget Sound, 

forage fish species including Pacific herring, surf smelt and Pacific sandlance provide an 

important link between lower trophic levels and marine predators like seabirds, marine 

mammals and predatory fish such as salmon (Puget Sound Action Team 2005). In Puget 

Sound, concerted efforts to describe the distribution and dynamics of most species of 

forage fishes occurring in the Puget Sound region are lacking— but major declines 

during the past 15 years in a large number of fish-feeding marine birds and changes in 

distribution of marine mammals (e.g. harbor porpoise) indicate that that forage fish 

populations in Puget Sound may no longer be adequate to support a wide variety of 

marine predators. 

Unfortunately, concerted efforts to describe the distribution and dynamics of most species 

of forage fishes occurring in the Puget Sound region have been limited, and there has 

been almost no effort to examine forage fish ecology and population trends with regard to 

oceanographic conditions or ocean climate change. Furthermore, seasonal and 

geographical variation in forage fish, salmon, marine bird and marine mammal 

abundance is undoubtedly linked to variability in plankton abundance (primary and 

secondary production), invertebrate abundance, oceanographic conditions (habitat 

parameters such as temperature, salinity, dissolved oxygen, and sediment load), 

bathymetry, and sediment type (or quality, including pollutants). While many studies 

have been conducted historically in Puget Sound that offer insight into some of these 

components individually, there has yet to be a study which attempts to examine covariation in marine predators, prey and habitats, or integrate these across differing 

temporal and spatial scales. 

Species Biology Science Needs

Many species in the Puget Sound have undergone a reduction in population number (e.g. 

salmon stocks and the Southern Resident killer whale population), a change in 

distribution patterns (e.g. harbor and Dall’s porpoises), or both. Although the basic 

biology of some key species are well known, basic biological information for other 

species in the ecosystem are lacking. Additional information could contribute greatly to a 

better understanding of the organisms in the Puget Sound and the ecosystem as a whole. 

Knowledge of the basic biology of individual species are essential to assessing the factors 

that may be contributing to their decline and/or change in distribution and to 

understanding the effects of anthropogenic inputs or other perturbations in their habitat. 

The biological information that is needed can be classified broadly in the following 

categories: genetic relationships, life history patterns, birth and death rates, factors 

affecting survival, body condition indices, reproductive physiology, nutritional 

requirements, and physiological responses to anthropogenic inputs, disturbance, and 
57

environmental change. Data on the genetic relationships of key species in the ecosystem 

will help us to understand the degree to which populations and subpopulations are 

evolutionarily isolated and demographically closed as well as provide accurate estimates 

of the time of divergence and rate of gene flow among groups. Consequently, we will be 

able to provide more accurate population definitions, determine gene flow rates, and 

assess the potential for inbreeding depression. Accurate data on the life history patterns 

(e.g. age at sexual maturity, age at functional sexual maturity, birthing interval, etc.), 

birth and death rates, factors affecting reproduction, and factors affecting survival of key 

species will help us to better assess the status of populations; and by continually 

monitoring these factors, we can better assess changes in the status of populations and 

how they respond to environmental perturbations. Physiological data on body condition, 

reproduction, nutritional requirements, and responses to anthropogenic inputs, 

disturbance, and environmental change are necessary to determine potential risk factors 

to organisms in the Puget Sound. Once additional data on these basic components are 

gathered, further studies need to be conducted to better determine how the biological 

characteristics of each species have the potential to affect the status of their population 

and possibly the ecosystem. Multiple factors are undoubtedly responsible for changes in 

the populations of key species in the Puget Sound ecosystem. However, a thorough 

understanding of the biology of key species within the Puget Sound will help us to reduce 

some of the uncertainty when modeling the viability of populations and assessing the 

relative risk of the threats to the population, and provide key information for management 

actions. 

Specifically Identified Science Needs for Species Groups 

Some Key Science Needs for Invertebrates

1. Despite the regional importance geoducks, reliable information about the species 

population dynamics, recruitment and genetics does not exist. 

2. It is important to point out that although some species are commercially or 

recreationally harvested, it is not clear what the impact of this is on lesser defined benthic 

organisms. 

3. The impacts of global climate change are already being visualized by increased Puget 

Sound water temperatures. It is probable that our changing environment will alter the 

dynamic impacts of marine harvests on lesser defined organisms and hence food web 

structure and sustainability, but how these things might change is unknown. 

Some Key Science Needs for Salmonids

1. Define the critical ecosystem features for the full life cycle of salmonid species and 

stocks. 

2. Quantitatively assess the risks (natural and anthropogenic) to salmon during upstream, 

downstream, and estuary/ocean life stages. 

Some Key Science Needs for Non-Salmonid Pelagic Fish
58

Aside from limited information regarding populations size and age structure of Pacific 

herring in Puget Sound, major information gaps exist in basic knowledge of forage fish 

stock abundances and roles in ecosystem function. Basic information necessary to 

effectively manage these stocks, including gross population sizes, relative abundances, 

bioenergetic values, and ecological selection pressures, is not available. 

Effective protection and management of forage fish, and threatened / endangered species 

that directly depend upon forage fish availability cannot occur until the following basic 

knowledge gaps are addressed: 

1. Total and relative size of forage fish populations in Puget Sound. 

2. Relative bioenergetic values of the primary forage species in Puget Sound. 

3. Seasonal residency and migration patterns of the primary forage species. 

4. Ecological factors influencing forage fish abundance, availability, and assemblages in 

Puget Sound. 

5. Significant species interactions among forage fishes and between them, their predators, 

and other competitors. 

Some Key Science Needs for Marine Birds

1. Investigate the predator and prey associations for each marine birds species, and assess 

the effect of prey abundance and distribution on the status of marine bird populations. 

2. Identify what factors cause disturbance or increase mortality of chicks at seabird 

colonies. 

3. What are the physiological effects and population effects of high contaminant loads in 

marine bird species in the Puget Sound? 

Some Key Science Needs for Marine Mammals

1. Assess how and if each of the key marine mammal species have the ability to switch 

prey versus moving geographically when prey resources change in abundance or 

distribution. 

2. Investigate the predator and prey associations for each marine mammal species, and 

specifically determine how and when the predators move relative to changes in prey 

abundance and distribution. 
59

3. Investigate the predator and prey associations for each marine mammal species, and 

assess the effect of prey abundance and distribution on the status of marine mammal 

populations. 

4. How are harbor porpoises able to remain resident to Puget Sound year round? Are 

they able to feed on same species all year or are there seasonal changes in prey 

availability and selection? 

5. Since harbor seals have now hit carrying capacity, what are the effects on prey and 

competitors? 

6. What are the physiological effects and population effects of high contaminant loads in 

marine mammal species in the Puget Sound? 

Humans and the Puget Sound Ecosystem

The Puget Sound region is home to more than 7 million people, with that number 

expected to grow to more than 9 million by 2020. The human population is a source of 

stress to the Puget Sound ecosystem but is also motivated to find ways to manage and 

relieve that stress. Our motivation partly lies in what are called ecosystem goods and 

services, which emanate from the structures and functions of the Puget Sound ecosystem 

(Figure 2). Sometimes these values are passively enjoyed, the proximity or even merely 

the existence of Puget Sound sufficient to generate them. In other cases, it is human 

actions like fishing or boating that generate these values. 

The same activities that generate these values, however, can also be sources of ecological 

stress if they exceed certain thresholds. Similarly, the presence of a growing population 

increases the passively enjoyed values of Puget Sound but also places more demands on 

the region’s resources and so increases the stress as well. Finding a balance arguably is a 

major goal of the effort to manage Puget Sound on an ecosystem scale. Identifying the 

goods and services generated by the Puget Sound ecosystem is therefore an important 

step in formulating management alternatives. 

While there is a growing literature on the identification, categorization, and nature of 

various ecosystem goods and services, empirical research directly related to Puget Sound 

is scarce. Because so much of the empirical research is indirect or only marginally 

relevant, this section concentrates on a conceptual framework for assessing ecosystem 

goods and services in Puget Sound. The key science need identified is to conduct basic 

empirical research relevant to a Puget Sound ecosystem-scale management effort. 

Ecosystem Goods and Services

Ecosystem goods and services are generated by the structure and function of natural 

systems, often in combination with other, “human-made” goods and services (Figure 2). 

The values of ecosystem goods and services come from direct consumption, through 

actions that enjoy but do not consume them, and through passive enjoyment or mere 
60

knowledge of their existence. The actions motivated by these values may produce effects 

that feedback and affect the ecosystem structure and functions. An evaluation of 

ecosystem goods and services, then, takes place in the context of this integrated, dynamic 

system (NRC 2004). 

Ecosystem goods and services are the “outputs” of ecosystems that benefit humans. In 

building a conceptual framework from this foundation, we note at the outset that the 

majority of values we attach to these goods and services are what are known as economic 

values. These are not just values that flow through markets, but any value that is rooted 

in the satisfaction of human wants. This admittedly anthropocentric view does not 

capture intrinsic values that stem from moral premises. Nonetheless, economic values 

are broadly defined to include not only the value derived from direct use of an ecosystem 

service (use value), but also nonuse values such as existence and bequest values. It thus 

includes the value of protection “for protection’s sake,” which is viewed as desirable by 

many humans. 

The Millennium Ecosystem Assessment, a recent global effort to catalog and assess 

ecosystem status and functions, offers a useful classification scheme (Box 7). Their 

classification includes four categories (MA, 2003). 

• Provisioning services are the products obtained from ecosystems, such as food 

and fresh water. These services are typically measured in terms of biophysical 

production, such as tons of salmon landings. 

• Regulating services are the benefits obtained from the regulation of ecosystem 

processes, such as erosion control and pollination. In the case of regulating 

services, as opposed to provisioning services, the level of “production” is 

generally not relevant. Instead, the condition of the service depends more on 

whether the ecosystem’s capability to regulate a particular service has been 

enhanced or diminished. 

• Cultural services are the nonmaterial benefits people obtain from ecosystems 

through spiritual enrichment, cognitive development, reflection, recreation, and 

aesthetic experiences. Recreation, ecotourism, spiritual and religious experiences, 

and a sense of place are all examples of this type of service. Perceptions of 

cultural services are more likely to differ among individuals and communities 

than, say, perceptions of the importance of food production, and so they are 

harder to measure. 

• Supporting services are those that are necessary for the production of all other 

ecosystem services. For example, humans do not consume low trophic level 

species like plankton, but these species support higher level species, some of 

which are consumed directly. Other examples of supporting services are primary 

production, production of atmospheric oxygen, soil formation and retention, 

nutrient cycling, water cycling, and provisioning of habitat. 

Ecosystem goods and services are potentially useful concepts for policy analysis because 

they can be used as performance measures for different management strategies. In a 

policy context, the evaluation of a management strategy is not concerned with 
61

quantifying the value of an entire ecosystem (unless the strategy under consideration 

would effectively destroy the entire ecosystem); rather, it is concerned with connecting 

physical changes in the ecosystem to a set of changes in ecosystem goods and services 

(NRC, 2004). Translating these resulting changes into a monetary value, as is commonly 

done in benefit-cost analysis, is another possible way of evaluating management 

alternatives, but not a necessary one. 

Forecasting changes in ecosystem goods and services across management scenarios is an 

exercise that involves a combination of modeling and expert judgment (MA, 2004, 

especially chapter 4). This approach is useful for revealing possible tradeoffs in 

particular goods and services (see next section of this report), but is less useful for 

addressing potential problems of ecological thresholds, extreme events, and irreversible 

changes. It is also an exercise that is inherently local in nature for the goods and services 

derived from ecological structures and functions that are less than global in scale. 

Assessing Ecosystem Goods and Services for Puget Sound

Marine and estuarine ecosystems like Puget Sound provide many of these goods and 

services (Peterson and Lubchenco, 1999). Puget Sound is home to commercial, 

recreational, and tribal ceremonial fisheries for salmon and other species, as well as clam, 

oyster, crab, and other shellfish harvests. It provides regulating services as global as the 

carbon cycle and as local as waste treatment through the uptake in estuaries of nutrients 

such as nitrogen and phosphorous. Puget Sound hosts myriad forms of recreation, 

including an active whale watching industry (Box 8). Underlying all of these are Puget 

Sound’s basic supporting services such as primary production and the provision of habitat 

for salmon, killer whales, and other species. A similar set of goods and services are 

provided by the freshwater ecosystems that are linked to Puget Sound (Postel and 

Carpenter, 1999). 

Quantifying this set of goods and services for Puget Sound is much more difficult. 

Assessing the quantities and values of ecosystem goods and services is a science in its 

infancy. This isn’t to say that economists and other social sciences have ignored the 

natural world, or that they have failed to develop models and conduct analyses that 

incorporate specific types of ecological structures and functions. Numerous studies and 

entire social science fields have done so over the past fifty years, but only recently has 

social science explicitly adopted the ecosystem as a unit of study. As a result, the 

overwhelming majority of this work cannot be used to link specific changes in ecological 

structures and functions to the resulting changes in the quantities and values of ecosystem 

goods and services (NRC, 2004). 

Among studies that are useful, relatively few cover marine or even aquatic ecosystems 

(NRC 2004), and only a handful have considered goods and services in the Puget Sound 

region. Leschine et al. (1997) estimates the economic value of wetland enhancement 

projects in two Puget Sound urban watersheds. They found annual values for these 

projects of between $2000 and $13,300 per hectare. In a study of Maury Island and its 

nearshore area, Herrera Environmental Consultants, Inc. et al. (2004) used existing 
62

empirical studies from other locations to estimate a comprehensive set of ecosystem 

goods and services. A second local study conducting a similar analysis was included in 

the development of the salmon recovery plan for the Green/Duwamish and Central Puget 

Sound watershed (WRIA 9) (Green/Duwamish and Central Puget Sound Watershed 

Water Resource Inventory Area 9 (WRIA 9) Steering Committee, 2005, Chapter 6, 

Ecological Economics Foundation). 

All of these studies have methodological and other limitations, however. Leschine et al. 

(1997) used a method known as the “cost of treatment” method, which equates the cost of 

a project (or sometimes the cost of replacing ecosystem goods and services) with its 

value. While this approach can be used as a “last resort” if certain conditions are met, its 

general use should be avoided (NRC, 2004). 

The other two studies used a method known as benefits transfer, which takes empirical 

results from studies undertaken in one location and “transfers” those values to another 

location. As NRC (2004) notes, studies that have investigated the validity of benefit 

transfers in valuing ecosystem services have found that this approach is not highly 

accurate. Natural systems exhibit considerable variability across space, scale, and even 

time in both their structure and functions. A small estuary in Puget Sound, for example, 

may have a far different structure and set of functions than a similarly sized one in the 

Gulf of Mexico, or than Puget Sound as a whole. As a result, transferring values from 

one ecosystem to another is an exercise fraught with peril. 

This conclusion points to the major science needs in this area: 

1. A better understanding of the links between the Puget Sound’s ecological 

structure and functions and specific ecological goods and services; 

2. Region-specific data on the magnitudes of these ecological goods and services; 

and 

3. A better understanding of the incremental effects of policy choices on ecological 

goods and services 

Meeting these science needs should proceed not by identifying abstract goods and 

services in a checklist, but by using actual ecological models such as those described in 

Section IV to link model components and relations to particular types of ecosystem goods 

and services. In this way, performance measures for ecosystem-scale management 

efforts could be identified and described in terms of ecosystem goods and services, while 

management strategies are devised that focus on the factors that stress the corresponding 

ecological components, structures, and functions. Alternative management strategies 

could then be evaluated using these measures grounded in an ecosystem goods and 

service framework. 
63

Box 7: Ecological Goods and Services 

Provisioning Services 

• Food and fiber. 

• Fuel. 

• Fresh water. 

• Genetic resources. 

• Biochemicals, natural 

medicines, and 

pharmaceuticals. 

• Ornamental 

resources. 

Regulating Services 

• Air quality 

maintenance. 

• Climate regulation. 

• Water regulation. 

• Erosion control. 

• Water purification 

and waste 

treatment. 

• Regulation of 

human diseases. 

• Biological control. 

• Pollination. 

• Storm protection. 

Cultural Services 

• Recreation and 

ecotourism. 

• Cultural diversity. 

• Spiritual and 

religious values. 

• Knowledge systems 

(traditional and 

formal). 

• Educational values. 

• Inspiration. 

• Aesthetic values. 

• Social relations. 

• Sense of place. 

• Cultural heritage 

values. 

Supporting Services: Necessary for the production of all other ecosystem services. 

Examples include soil formation, primary production, production of atmospheric oxygen, 

soil formation and retention, nutrient cycling, water cycling, and provisioning of habitat. 

Source: MA (2003) 
64

Box 8: Whale Watching in Puget Sound 

Whale watching is an increasingly important tourism industry in the Puget Sound region, 

with an estimated 52,000 participants in commercial boat-based tours during 1998. The 

current whale watching industry in Puget Sound is estimated to contribute approximately 

$18.4 million annually and 205 jobs to the 19 counties adjacent to Puget Sound through 

direct and indirect expenditures related to the industry (IE 2006). 

Whale watching would not be possible without the existence of the orca and other 

whales, and so it is tempting to ascribe the entire value of this activity to this ecological 

component. This ecosystem service, however, is the output of a combination of inputs, 

including human-made capital (boats) and fuel. Without any one of these components, 

this particular service would not be possible, making it problematic to ascribe the entire 

value of the service to any one input. 

Managing Puget Sound on an ecosystem basis is likely to change the value captured by 

whale watching, but how this value changes over time may be complicated. If the orca 

population increases through management efforts, whale watching opportunities may also 

increase, increasing the value of the service. At the same time, management may focus 

on the industry itself. Any restrictions deemed necessary to protect the population would 

effectively decrease the value of the service in the near term. 
65

Decision Frameworks for Ecosystem Approaches to Management in 

Puget Sound 

Effective management of a complex ecosystem like Puget Sound requires not only 

information about the individual components – the species and processes that constitute 

that ecosystem -- but also scientific and policy frameworks with which to evaluate efforts 

to restore and protect the ecosystem (Pew 2003, USCOP 2004). In previous sections, we 

have discussed individual components of the Puget Sound ecosystem; this section 

addresses the task of combining these components in a framework that supports 

management capable of achieving the dual goals of a robust natural system and thriving 

coastal communities in the Puget Sound region. 

A number of past and present efforts have addressed a variety of Puget Sound 

management issues. For that reason, this section discusses the development of an 

ecosystem-scale management framework for Puget Sound in general terms; the task of 

describing and developing the actual framework is one that this document is intended to 

support. We begin with a discussion of the potential use of a decision-support system – a 

framework for incorporating science into decision-making – to evaluate alternative sets 

of management strategies for the Puget Sound ecosystem. We then focus on an important 

component of such a system: conceptual and quantitative ecological and socioeconomic 

models. 

Decision-Support Systems for Ecosystem-scale Management 

The focus of ecosystem-scale management typically encompasses a wide variety of 

objectives, covering such issues as sustainable fisheries, endangered species, habitat 

structure, biodiversity, ecosystem integrity and resilience, as well as broader, regional 

economic and social objectives. Multiple ecosystem objectives such as these often arise 

from policies that describe a set of guidelines by which humans should exploit biological 

resources. The Puget Sound Partnership established by the Governor will set goals for 

Puget Sound “...to ensure that the Puget Sound forever will be a thriving natural system, 

with clean marine and fresh waters, healthy and abundant native species, natural 

shorelines and places for public enjoyment, and a vibrant economy that prospers in 

productive harmony with a healthy Sound.” As noted above, the choice of these 

objectives lies outside the purview of science; yet science can help policy makers 

illuminate the consequences of setting and pursuing multiple objectives such as these, 

and evaluate potential tradeoffs between strategies designed to pursue those objectives. 

For example, there is a clear potential for conflicts when policy embraces diverse 

objectives (Box 9). As a consequence, a useful support for ecosystem-scale management 

is a set of scientific tools that help policy makers identify potential conflicts and 

minimize their occurrence (Mangel 2000). We refer to this set of tools as a decisionsupport system. 

 

The complexity of managing an ecosystem requires a decision-support system that can 

relate the ecological and socioeconomic consequences of potential specific management 
66

actions to the broader policy goals (Sainsbury et al., 2000). They coined the phrase 

Management Strategy Evaluation (MSE) to describe a decision-support system that uses 

the following elements: 

1. Evaluate the status of the system being managed as a whole (not just isolated 

parts); 

2. Specify policy objectives and performance measures that are connected to those 

objectives; 

3. Relate alternative management strategies to predicted changes in the performance 

measures; 

4. Monitor the system; and 

5. Provide for iterative decision making that is based on data from the monitoring 

program. 

This approach recognizes and illustrates but does not resolve the conflicts among 

competing objectives. Instead, it relies on a number of candidate models that are put 

forward to evaluate multiple hypotheses. The choice of a “best” solution is then left to 

the policy makers (Box 9). The use of a formal framework, however, contributes to the 

transparency of the decision-making process. 

The approach outlined above is an example of a decision-support system that supports the 

evaluation of the managed system as a whole (Box 10). The ecological, socioeconomic, 

and management systems as well as the connections between them are modeled. The 

evaluation of alternative management strategies proceeds with a clear statement of 

management objectives and a choice of measures to gauge performance. Performance 

measures are best viewed as signals or surrogates, providing information on the status of 

the underlying systems, but should not be treated as policy ends in and of themselves 

(Van Cleve et al., 2004). Using performance measures implicitly embodies hypotheses 

about the relations between the measures chosen and higher level policy objectives such 

as ecological health, economic vitality, and social welfare. 

The framework described by Sainsbury et al. (2000) is intended for management that is 

adaptive (Walters 1986). If that approach is embraced by policy makers, each strategy to 

be evaluated should include a monitoring program; what measurements will be taken; 

how these data will be analyzed; and how they will be used in subsequent scientific 

assessments. A management strategy should also specify how the results of scientific 

analyses will be used in management decesions, and which instruments will be used to 

implement decisions. 

This formal adaptive-management approach can be used to investigate the consequences 

of a variety of scenarios evaluated across a range of models. Importantly, it can be 

transparent and collaborative if resource managers and stakeholders have input into 

candidate models and management scenarios. This approach encourages all participants 

to be clear about their goals, and the ground rules by which decisions are reached to be 

transparent. 
67

The decision-making process represented in a MSE approach is simplest if a single 

governance body controls the human activities that influence the ecological components 

of the system under consideration. For example, applying this approach to fisheries is 

often straightforward in cases where a single regulatory body is responsible for making 

harvest and gear decisions. Such a body has control over the full set of policy 

instruments and a limited set of objectives, which simplifies the analysis. 

This simple case does not apply to Puget Sound, however. The policy instruments 

needed to implement management at an ecosystem-level are distributed among dozens of 

government bodies. Local governments are responsible for traditional regulations zoning 

and the Washington State Growth Management Act; the Washington State Department 

of Ecology implements the Shoreline Management Act; the Department of Natural 

Resources manages the state’s aquatic lands; the Department of Fish and Wildlife sets 

fishing regulations in conjunction with tribal governments; NOAA Fisheries is 

responsible for the conservation of Puget Sound species listed under the Endangered 

Species Act and the Marine Mammal Protection Act; the Environmental Protection 

Agency sets water quality standards under the Clean Water Act; and so forth. Each of 

these government agencies effectively has jurisdiction over a part of the Puget Sound 

ecosystem, limited to a particular geographic subregion or to a subset of the ecosystem’s 

functions, or both. 

Given the diversity of governance bodies in Puget Sound, a major challenge for any 

decision-support system is accounting for interactions among the governance bodies 

themselves (Rosenberg and McLeod 2005). This problem can be partly addressed by 

identifying the particular set of management instruments each government agency 

effectively controls. In this way, management strategy evaluations can reveal important 

interactions among the individual agency objectives, as well as the advantages of 

pursuing a coordinated ecosystem-scale management effort. 

Additionally, a decentralized, uncoordinated management strategy can be established as a 

baseline against which to gauge the performance of other strategies, including ones that 

increase the coordination of the government agents or increasingly centralize their 

authority. By comparing performance measures across a range of possible strategies of 

these sorts, the incremental value of various degrees and forms of ecosystem-scale 

management can be estimated, at least in terms of the performance measures identified by 

the policy makers. 

Integrated Assessment Modeling 

Within Puget Sound, problems or causes of degradation are multiple and cumulative, and 

so management will also likely involve multiple and cumulative actions (Fresh et al., 

2004). For that reason, management must recognize the connectivity of marine, 

estuarine, nearshore, terrestrial, freshwater, and shoreline ecosystems with one another. 

It must also recognize the connectivity of these natural systems with the economic and 

social systems that use or simply enjoy them. 
68

Addressing these myriad connections within a decision-support system is often 

accomplished by using what is known as integrated assessment modeling (Millennium 

Ecosystem Assessment, 2005). Integrated assessment models usually include some 

description of the socioeconomic system and its interaction with the environmental 

system (regional water pollution, the climate system, land cover/land use, and so on). 

They can be qualitative (conceptual models) or quantitative (formal computer models), or 

include elements of both. 

A conceptual model for Puget Sound could illustrate how individual ecological and 

socioeconomic components are connected, as well as detail their inner workings (PSNP, 

2004b). It could also identify the directions and strengths of the connections and how 

stresses work their way through the system. It could thus help identify the types and 

locations of changes (i.e., resulting from restoration actions) needed to achieve a 

particular outcome (e.g., improved growth and survival of juvenile salmon); therefore, it 

can provide some insight into what actions might be most effective. 

These models can also illuminate possible unanticipated or unintended consequences. A 

narrow, single species management focus often overlooks effects that act through prey or 

predator species, some of which may have undesirable effects on yet other species. And 

the failure to consider human reactions to policy prescriptions often leaves management 

blind to possible effects that could counter the intended outcome. 

Generally, conceptual models are distinguished from quantitative models, which take the 

relations identified in a conceptual model and give them a dynamic, quantitative form. 

Obviously, the latter type of model is far more data intense, yet it is also capable of 

providing deeper insights into the workings of the ecosystem and therefore into the 

implications of particular policy choices. In some cases, for example, a conceptual model 

will identify multiple connections that act as opposing forces on a performance measure. 

A quantitative model is better able to address the relative strengths of these forces. 

Both conceptual and quantitative models of the Puget Sound ecosystem can play an 

important role in supporting ecosystem-based management. The models embody 

hypotheses about how each system is likely to respond to a given set of changes. If 

management decisions are focused on implementing such changes, the models can be 

integrated and incorporated as part of a decision-support system for ecosystem-scale 

management. 

Ecological models

Ecosystem-scale management for marine and related ecosystems is in part an outgrowth 

of the limitations of single species fishery models. These models have been criticized by 

some as inadequate for fisheries decision analysis because they consider only one 

possible effect of fisheries policy (Mangel and Levin, 2004). In contrast, management 

that focuses on an ecosystem needs to recognize and analyze a broader suite of system 

responses. For example, fishery management in an ecosystem context should explicitly 
69

recognize that fish stocks respond to underlying yet unpredictable ecosystem dynamics 

and that fishing itself can induce ecosystem changes. 

We presently have many (but not all) of the tools to identify potential ecosystem 

responses and behaviors. We have expanding knowledge, for example, of food web 

processes in marine ecosystems, building a strong conceptual framework of the types of 

food web relationships that are common, rare, and most importantly, potentially 

sensitivity to perturbation in the context of management focused on fisheries. In many 

systems, detailed site-specific information is available describing meso- and whole-basin 

scale oceanographic drivers of primary and secondary productivity. 

Existing analytical tools for ecosystem-scale management range from simple 

modifications of single species models to complex full ecosystem models. Single species 

models can be augmented with predator or prey abundance or environmental correlates. 

In these models, only the dynamics of single species are examined as a function of some 

aspects of the ecosystem. The utility of these models is limited because environmental 

feedback is unidirectional (from environment to target species), and indirect ecological 

interactions are ignored. A number of dynamic age- or size-structured multi-species 

models have been used in fisheries management. Such approaches often link fish survival 

to the abundance of predators and prey, and growth can be modeled as a function of food 

supply. These models are thus useful for examining trade-offs among different fishery 

sectors in the face of a variable environment. 

Models of entire ecosystems are even more complex than multi-species models. 

Ecosystem models are largely based on food web and bioenergetics. Typically, these 

models aggregate species at lower trophic levels into functional groups while target 

species may be examined individually. Among these models, Ecopath with Ecosim 

(EwE) is especially notable: More than 150 publications have used this approach 

(Christensen and Pauly 2004). EwE is essentially a biomass-dynamic model analogous 

to those commonly used in single species stock assessments. Unlike single species 

models in which ecological processes are implicitly represented through static functions 

(density-dependence, natural mortality rates, and so forth), EwE explicitly considers the 

ecological interactions that give rise to population dynamics. 

ATLANTIS, a modeling approach developed by CSIRO scientists in Australia, achieves 

the crucial goal of integrating physical, chemical, ecological, and fisheries dynamics in a 

three-dimensional, spatially explicit domain (Box 3). The ATLANTIS model has been 

used with great success in Australia, and versions of this model are currently being 

developed for the California Current and George’s Bank ecosystems (Fulton et al., 2003). 

Management for an ecosystem such as Puget Sound must encompass more than an 

individual species focus, however, as the objectives usually run the gamut of ecosystem 

goods and services. Developing conceptual and quantitative models for the Puget Sound 

ecosystem will be a major challenge. 
70

Socioeconomic models 

Like ecological modeling, socioeconomic modeling of marine and related ecosystems 

began with single species models applied to the problem of overfishing (Bjorndahl and 

Munro, 1999). These models typically utilize a simple stock-recruitment relationship and 

derive the optimal economic level of harvest for a fishery. Increasingly sophisticated 

models have refined numerous dimensions of the economic analysis of a fishery. For 

example, models have incorporated the effects of environmental stochasticity on optimal 

harvesting strategies and fisheries management; examined the use of transferable quotas 

and other rights-based management strategies; and addressed the problem of unintended 

bycatch for fisheries management. 

An important innovation in economic modeling that makes it more relevant to ecosystem 

management is the incorporation of spatial dimensions in fishery models (Wilen et al., 

2002). These models have been applied to the problem of creating marine reserves. As 

Wilen et al. (2002) show, a model that includes spatial location decisions as well as the 

choice to participate or not in the fishery can produce significantly different management 

recommendations than one that does not include these features. As they note, how 

fishery participants disperse spatially is just as important to the health and character of 

the ecosystem as is the biological dispersal process. 

Outside of the economics of fisheries, the social sciences have tended to model the 

human components of ecological systems at a highly aggregated level (Millennium 

Ecosystem Assessment, 2004). An exception is the growing field of multi-agent 

simulation (MAS) models (Bousquet and Page 2004). In this type of model, individual 

agents such as households, businesses, and land developers behave as if they are solving 

simple optimization problems given constraints imposed by market opportunities (e.g.

prices and budgets) and government policies (e.g., zoning and pollution regulation). 

Changing a government policy then changes the set of constraints, which in turn changes 

their predicted behavior. 

An example of a socioeconomic model being developed for Puget Sound is UrbanSim 

(Waddell, 2002; Box 4). The UrbanSim model operates at the level of individual land 

ownership parcels, which have GIS-based attributes such as land cover, land use, 

regulatory constraints, and so forth. Individual agents’ decisions cover location, travel, 

consumption, production, and so forth. The advantage of a model like UrbanSim is its 

ability to predict behavioral responses to policy changes rather than simple presume those 

responses are in lockstep with the policy. 

Integrating ecological and socioeconomic models

As Perrings (2001) notes, most environmental problem involve the interaction between 

social and ecological processes, and there are effects that provide feedback running in 

both directions. Integrating both ecological and economic models will therefore produce 

a more complete and possibly more accurate set of policy recommendations. 
71

Many ecological models have some economic components, and vice versa, but the 

components from the complementary system invariably have their levels set by the 

modeler rather than determined endogenously. Modeling a few components of the 

complementary system in this way vastly reduces the complexity and computational 

requirements of the model but may also provide inaccurate policy advice. A 

socioeconomic model with a limited set of ecological components is unable to capture the 

full range of potential ecosystem interactions, crippling its ability to consider issues such 

as resilience and stability. Conversely, an ecological model with a limited set of 

socioeconomic components is unable to discern whether restrictions on one set of 

socioeconomic components may induce human behavior that mitigates or even 

overwhelms the intended outcome (Wilen et al. 2002). Acknowledging these real world 

concerns can take forms ranging from simple methods of incorporating uncertainty into 

the effects of a management strategy to more complicated multiple-agent simulations in 

which individuals react to management instruments such as regulation and market 

incentives. 

In the context of Puget Sound ecosystem-scale management, an integrated model could 

combine an ecological model such as ATLANTIS with an economic model such as 

UrbanSim. Integrating the two types of models involves identifying links between 

human activity and the ecosystem’s natural components. For example, Section III above 

notes that activities such as shoreline development, habitat loss, water contaminants, and 

invasive species are among the sources of stress for Puget Sound species. By linking 

activity in the socioeconomic model to these sources, the two models can then be 

integrated and incorporated into a decision-support system for ecosystem-scale 

management. 

Conclusions 

Putting the pieces of Puget Sound ecosystem science together is not an easy task, of 

course, nor is it one that involves science alone. Developing a management framework in 

an ecosystem context involves more than just building models of the Puget Sound 

ecological and socioeconomic systems. The choice of policy objectives and goals is a 

primary task, of course, for it clarifies the areas where scientific information and analysis 

can best be used to illuminate the consequences of alternative policy choices. But 

incorporating science into the policy process is an iterative process, requiring ongoing 

scientific participation from the outset. 

This section has covered some of the key points involved in developing scientific support 

for the management of Puget Sound in an ecosystem context, including the following: 

• Building a decision-support system requires both scientific and policy inputs, with 

the two spheres interacting as the framework is developed and implemented; 

• A formal decision-support system can contribute to the transparency of making 

management decisions, encouraging a collaborative process that will strengthen 

the foundation of the process. 
72

• Formal modeling, conceptual and quantitative, of both the ecological and 

socioeconomic components of the Puget Sound ecosystem is an important 

element of a decision-support system. 
73

Box 9 – Tradeoff between Conservation and Economic Objective for the New Zealand Arrow Squid 

Fishery. 

0

0.02

0.04

0.06

0.08

0.1

0.12

0 0.2 0.4 0.6 0.8 1 1.2

Probability of Fishery Remaining Open

Increase in Probability of Recovery

A

B D

C

Maunder et al. (2000) considered the tradeoff between conservation and economic 

objectives for a New Zealand fishery (arrow squid) that impacted a sea lion population. 

They examined a policy of closing the fishery if the estimated fishery-related kill of sea 

lion exceeded a given threshold. Maunder et al. modeled the effects of this strategy on 

both the recovery of the sea lion population and the potential loss of yield for the fishery. 

They then derived feasible levels of each. 

This example illustrates the two roles of science and policy, as well as the iterative 

process of one informing the other. The identification of objectives such as the 

conservation of sea lions and the vitality of the arrow squid fishery are set by policy 

makers. Analyzing the tradeoffs between the two objectives, along with the sensitivity to 

other factors, the effects of uncertainty, and so forth, are scientific tasks. In the figure, 

science can identify points like A and B that produce the maximum possible level of one 

objective given a level for the other; it can also identify levels that are infeasible (C) or 

that do not take full advantage of the possible ways of increasing either objective without 

the diminishing the other (D). The choice between any point, however, is in the policy 

realm 
74

Box 10. Management Strategy Evaluation, from Sainsbury et al. 2000
75

Box 11. Components of ATLANTIS modeling framework 

ATLANTIS achieves the crucial goal of integrating physical, chemical, ecological, and 

fisheries dynamics in a three-dimensional, spatially explicit domain (Fulton et al. 2003). 

In ATLANTIS, marine ecosystem dynamics are represented by spatially-explicit submodels that simulate hydrographic processes (light- and temperature-driven fluxes of 

water and nutrients), biogeochemical factors driving primary production, food web 

relations among functional groups, and the model represents key exploited species at the 

level of detail necessary to evaluate direct effects of fishing. 

Climate and Oceanography

Biogeochemistry Hydrographic 

submodel 

Ecology 

submodel 

Habitat 

Fisheries 

submodel 
76

Box 12. Components of UrbanSim modeling framework 

The UrbanSim model (Waddell, 2002) operates at the level of individual land ownership 

parcels, which have GIS-based attributes such as land cover, land use, regulatory 

constraints, and so forth. Individual agents’ decisions cover location, travel, 

consumption, production, and so forth. Land use, land cover, and spatial location interact 

to produce flows that are linked to the ecosystem in which the urban system is embedded. 

The agents then make dynamic decisions about the use of their land. Changes in land use 

change the biophysical processes, habitat area, environmental emissions, and resource 

use. The urban behavior model is linked to four types of human-induced environmental 

change: land conversion, resource use, emissions, and habitat change. Each of these 

types of environmental change can be developed as a model that spans and therefore links 

the natural ecosystem models and the human system models. Currently, UrbanSim is a 

land-based effort but adapting and linking it to a marine ecosystem would be 

straightforward (if quite complex). 
77

Key Science Findings to Inform Near-Term Actions and Longer-Term 

Strategies for the Puget Sound Ecosystem 

In this section, we highlight briefly key findings from this document and summarize how 

they could inform development of goals, near-term actions, or longer-term strategies for 

achieving the 2020 vision for Puget Sound. 

The content of this section will be determined during the review process—if you have 

suggestions for which findings are critical and should be highlighted here, please provide 

those in your comments. 

Examples of the level of detail we could provide here (topics are meant to be illustrative 

only): 

3⁄4 Key finding: future climate impacts in the region will result in reduced summer 

freshwater flows and increased winter peak flows. 

Implications for Puget Sound action plan: 

o Actions aimed at improving storage, reducing use, or allowing re-use of 

fresh water could mitigate the potentially negative impacts of future 

climate on Puget Sound species, habitats and ecosystem services. 

o Strategies to reduce the magnitude of stormwater runoff events or the 

toxics and excess nutrients they deliver during winter high flows will help 

improve survival of commercially, recreationally and ecologically 

important species. 

3⁄4 Key finding: projected increases in human population growth in the Puget Sound 

region will place increasing pressure on goods and services in the region such as 

undeveloped shorelines, recreational and commercial fishing, and whalewatching. 

Implications for Puget Sound action plan: 

o Actions designed to allow shoreline development, fishing, or whale 

watching only in strategically chosen areas will allow ecosystem services 

such as beach nourishment, bank stabilization, maintenance of eelgrass 

and kelp habitats, or tourism to function in a way consistent with 

ecosystem goals. 

o Strategies that include incentives for fishers or whale watchers to manage 

the resources they consume in a sustainable way will increase the chances 

that an increasing human population can continue to benefit from the 

ecosystem. 

 

3⁄4 Key finding: the nature and strength of interactions among species in Puget 

Sound food webs is not well understood. 

Implications for Puget Sound action plan: 
78

o Management strategies designed to recover or re-build salmon, marine 

fish and Orcas should explicitly consider what happens as predators such 

as Orcas or salmon increase in number and potentially cause reductions in 

imperiled prey species such as salmon or herring. 

 
79

References 

Abookire, A.A., and J.F. Piatt. 2005. Oceanographic conditions structure forage fishes 

into lipid-rich and lipid-poor communities in lower Cook Inlet, Alaska, USA. 

Marine ecology progress series, 287:229-240. 

Ambler, J.W., J.E. Cloern, and A. Hutchinson. 1985. Seasonal cycles of zooplankton 

from San Francisco Bay. Hydrobiologia 129:177-197. 

Angliss and Lodge. 2002. Alaska Marine Mammal Stock Assessments, 2002. NOAA- 

 TM-NMFS-AFSC-133. 224pp. 

Baird and Dill 1995. Occurrence and behavior of transient killer whales: seasonal and 

 pod-specific variability, foraging behaviour and prey handling. Canadian Journal 

 of Zoology 73:1300-1311. 

Baird and Dill 1996. Ecological and social determinants of group size in transient killer 

 whales. Behavioral Ecology 7:408-416. 

Calambokidis et al. 1994. Gray whales of Washington State: natural history and 

 photographic catalog. Cascadia Research Collective, Olympia, Washington. 

Calambokidis et al.1997. Aerial surveys for marine mammals in Washington and British 

 Columbia inside waters. Final report to the National Marine Mammal 

Laboratory, Seattle, Washington. 

Carretta, J.V., K.A. Forney, M. M. Muto, J. Barlow, J. Baker, B. Hanson, and M. S. 

Lowry. 2005. U.S. Pacific Marine Mammal Stock Assessments: 2005. NOAATM-NMFS-SWFSC-375. 316pp. 

Ford et al, 1998. Dietary specialization in two sympatric populations of killer whales 

 (Orcinus orca) in coastal British Columbia and adjacent waters. Canadian 

 Journal of Zoology 76: 1456-1471. 

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. 

Beechie, T. J., P. Roni, E. A. Steel, E. Quimby. (Eds.) 2003. Ecosystem recovery 

planning for listed salmon: An integrated assessment approach for salmon habitat.

U.S. Dept. of Commerce, NOAA Tech. Memo., NMFS-NWFSC-58, 183 p. 

Bentivoglio, N., J. Baldwin, P.G.R. Jodice, D.E. Mack, T. Max, S. Miller, S.K. Nelson, 

K. Ostrom, C.J. Ralph, M. Raphael, C. Strong, C. Thompson, R. Wilk. 2000. 

Northwest Forest Plan Marbled Murrelet Effectiveness Monitoring 2000 Annual 

Report. U.S. Fish and Wildlife Service. 

Bjorndal, T., and G. Munro. 1999. The economics of fisheries management: A survey. 

In T. Tietenberg and H. Folmer (eds.), The International Yearbook of 

Environmental and Resource Economics 1998/1999. 

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. Prepared in cooperation with the U.S. Department of Justice and the 

Bureau of Indian Affairs, Renton, Washington. U.S. Geological Survey, 

Hydrologic Investigations Atlas HA-617, Washington, D.C. 

Boss, E., M.J. Perry, and M.C. Talbot, 1998. Observation of an Intense Deep-Water 

Intrusion in Puget Sound. In: Puget Sound Research ‘98 Proceedings. Puget 

Sound Action Team, Olympia, WA. 
80

Bousquet, F. et Le Page, C. 2004. Multi-agent simulations and ecosystem management: a 

review. Ecological Modeling 176 (3-4): 313-332 

Bower, J.L. 2004. Assessing Southern Strait of Georgia marine bird population changes 

since 1980: what we know and what we need to know. In T.W. Droscher and 

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

Research Conference. CD-ROM or Online. Available: [February 2004]. 

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. NOAA, National Ocean Service, Special Projects Office 

and the National Centers for Coastal Ocean Science. Silver Spring, MD: 71 pp. 

Buchanan, K.D. 1984. Tagging of Washington Herring, 1936-1984. Unpublished Data. 

Washington Department of Fish and Wildlife. P.O. Box 1100, La Conner, WA 

98257. 

Burns, R., 1985. The Shape and Form of Puget Sound. Puget Sound Books. 

Washington Sea Grant Publication. University of Washington Press. 

Canning, D., and Shipman, H., 1995, Coastal erosion management studies in Puget 

Sound, Washington: Executive Summary, Coastal Erosion Management Studies, 

Volume 1, Shorelands Program, Washington Dept. of Ecology, Olympia, DOE 

Report 94-74. 

Cannon, G.A., J.R. Holbrook, and D.J. Pashinski. 1990. Variations in the onset of 

bottom-water intrusions over the entrance sill of a fjord. Estuaries 13(1):31-42. 

Carlton, J.T. 1979. History, Biogeography, and Ecology of the Introduced Marine and 

Estuarine Invertebrates of the Pacific Coast of North America. Ph.D. thesis, 

University of California, Davis. 

Calambokidis et al.1997. Aerial surveys for marine mammals in Washington and British 

 Columbia inside waters. Final report to the National Marine Mammal 

Laboratory, Seattle, Washington. 

Calambokidis et al. 1994. Gray whales of Washington State: natural history and 

 photographic catalog. Cascadia Research Collective, Olympia, Washington. 

 Carretta, J.V., K.A. Forney, M. M. Muto, J. Barlow, J. Baker, B. Hanson, and M. S. 

Lowry. 2005. U.S. Pacific Marine Mammal Stock Assessments: 2005. NOAATM-NMFS-SWFSC-375. 316pp. 

California Fish and Game. 2005. Final Market Squid Fishery Management Plan 

(MSFMP) 

Chester, A.J., D.M. Damkaer, D.B. Day, G.A. Heron, and J.D. Larrance. 1980. Plankton 

of the Strait of Juan de Fuca, 1976-1977. Interagency Energy/Environment 

R&D Program Report, United States Environmental Protection Agency, Office of 

Environmental Engineering and Technology, Washington, D.C. EPA-600/7-80-

032. 

Christensen V., D. Pauly. 2004. Placing fisheries in their ecosystem context, an 

introduction. Ecological Modelling 172:103-107. 

Cohen, A.N., C.E. Mills, H. Berry, M.J. Wonham, B. Bingham, B. Bookheim, J.T. 

Carlton, J.W. Chapman, J.R. Cordell, L.H. Harris, T. Klinger, A. Kohn, C.C. 

Lambert, G. Lambert, K. Li, D. Secord and J. Toft. 1998. Report of the Puget 

Sound Expedition, September 8-16, 1998; A Rapid Assessment Survey of 

Nonindigenous Species in the Shallow Waters of Puget Sound. Washington State 
81

Department of Natural Resources, Olympia WA and United States Fish and 

Wildlife Service, Olympia WA. 

Cohen, A.N. 2004. An Exotic Species Detection Program for Puget Sound, Report 

prepared for the Puget Sound Action Team, Publication # OTH04-02. 

Collias, E.E., N. McGary, and C.A. Barnes. 1974. Atlas of Physical and Chemical 

Properties of Puget Sound and Approaches. Washington Sea Grant 74-1, Seattle, 

WA. 

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

change analysis of Puget Sound tidal marshes. Final project report to Washington 

Department of Natural Resources Aquatic Resources Division, Olympia, WA 

98504-7027. 

Cordell, J.R. and S.M. Morrison. 1996. The invasive Asian copepod Pseudodiaptomus 

inopinus in Oregon, Washington, and British Columbia estuaries. Estuaries 19 

(3):629-638. 

Couch, D., and T. J. Hassler. 1989. Species profiles: life histories and environmental 

requirements of coastal fishes and invertebrates (Pacific Northwest)--Olympia 

oyster. U.S. Fish Wildl. Serv. Biol. Rep. 82(11.124) U.S. Army Corps of 

Engineers, TR EL-82 4. 8 pp. 

Croxall, J.P. and P.A. Prince. 1996. Cephalopods as prey .1. Seabirds. Philosophical 

Transactions of the Royal Society of London Series B-Biological Sciences 351 

(1343): 1023-1043. 

Curl, H.C., Jr. and A.J. Paulson. 1991. "The biochemistry of oxygen and nutrients in 

Hood Canal." In: Puget Sound Research '91 Proceedings, Volume 1, T.W. 

Ransom (Ed.). Puget Sound Water Quality Authority, Olympia, WA, pp, 109-

115. 

Damkaer, D.M. 1964. Vertical distribution of Copepoda in Dabob Bay, December 1960. 

M.S. Thesis, University of Washington, Seattle, WA. 84 pp. 

Dempster, R.P. 1938. The seasonal distribution of plankton at the entrance to Hood 

Canal. M.S. Thesis, University of Washington, Seattle, WA. 

Department of Ecology, 1978, Coastal zone atlas of Washington, Jefferson County: WA 

Department of Ecology Shorelands Division, DOE Pub. No. 77-21-11. 

Dexter, R.N., D.E. Anderson, E.A. Quinlan, L.S. Goldstein, R.M. Strickland, S.P. Pavlou, 

J.R. Clayton, Jr., R.M. Kocan, and M. Landolt, 1981. A Summary of Knowledge 

of Puget Sound related to Chemical Contaminants. NOAA Technical 

Memorandum OMPA-13. National Oceanic and Atmospheric Administration, 

Boulder, CO. 435 pp. 

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

of Washington Press, Seattle, 126 p. 

Duffy, E.J. 2003. Early marine distribution and trophic interactions of juvenile salmon in 

Puget Sound. MS Thesis, University of Washington, Seattle, WA. 

Dumbauld, B.R. 1985. The distributional ecology of zooplankton in East Passage and 

the Main Basin of Puget Sound, Washington. M.S. Thesis, University of 

Washington, Seattle, WA. 211 pp. 

Edmondson, W.T. 1991. The Uses of Ecology: Lake Washington and Beyond. University 

of Washington Press. 329 p. 

Elston, R. 1997. Pathways and Management of Marine Non-indigenous Species in the 
82

Shared Waters of British Columbia and Washington. Puget Sound/Georgia Basin 

Environmental Report Series No. 5, Puget Sound Water Quality Action Team, 

Olympia, WA. 

Emmett R., R. Llansó, J. Newton, R. Thom, C. Morgan, C. Levings, A. Copping, and P. 

Fishman. 2000. Geographical Signatures of North American West Coast 

Estuaries. Estuaries 23(6): 765-792. 

Finlayson, D. and Shipman, H., 2003, Puget Sound littoral cells: the importance of waves 

and wave climate. Puget Sound Notes. Puget Sound Action Team: Olympia, WA, 

p. 1-4. 

Ford et al, 1998. Dietary specialization in two sympatric populations of killer whales 

 (Orcinus orca) in coastal British Columbia and adjacent waters. Canadian 

 Journal of Zoology 76: 1456-1471. 

Fresh, K., C. Simenstad, J. Brennan, M. Dethier, G. Gelfenbaum, F. Goetz, M. Logsdon, 

D. Myers, T. Mumford, J. Newton, H. Shipman, C. Tanner. 2004. Guidance for 

protection and restoration of the nearshore ecosystems of Puget Sound. Puget 

Sound Nearshore Partnership Report No. 2004-02. Published by Washington Sea 

Grant Program, University of Washington, Seattle, Washington. Available at 

http://pugetsoundnearshore.org. 

Fulton E. A., A. D. M. Smith, C. R. Johnson. 2003. Effect of Complexity on Marine 

Ecosystem Models. Marine Ecology-Progress Series 253:1-16. 

Gearin et al. 1999. Washington State Pinniped Diet Studies 1983-1998. Pp. 249-258, In: 

 A.L.Lopez and D.P. DeMaster (eds.) Marine Mammal Protection Act and 

 Endangered Species Act Implementation Program 1998. AFSC Processed Rept. 

 99-08. 305 pp. 

Gelfenbaum, G., Mumford, T., Brennan, J., Case, H., Dethier, M., Fresh, K., Goetz, F., 

van Heeswijk, M., Logston, M., Myers, D., Newton, J., Shipman, H., Simenstad, 

C., Tanner, C., and Woodson, D. 2006. Coastal Habitats in Puget Sound: A 

research plan in support of the Puget Sound Nearshore Ecosystem Restoration 

Program, in press. 

Giles, S.L. and J.R. Cordell. 1999. Zooplankton composition and abundance in Budd 

Inlet, Washington. Pp. 634-642 in: Puget Sound Research '98: From Basic 

Science to Resource Management, Puget Sound Water Quality Action Team, 

Olympia, Washington. 

Gilly, W.M. 2003. Population analysis of the California Market Squid, Loligo opalescens 

using DNA microsatellite analysis. Final report to the California Department of 

Fish and Game. Contract Number FG7334MR. 

Goodwin, C.L., and B. Pease. 1989. Species profiles: life histories and environmental 

requirements of coastal fishes and invertebrates (Pacific Northwest)--Pacific 

geoduck clam. U.S. Fish. Wildl. Serv.Biol. Rep. 82(11.120). U.S. Army Corps of 

Engineers, TR EL-82-4. 14 pp. 

Groot, G. and L. Margolis (editors). 1991. Pacific salmon life histories. University of 

British Columbia Press, Vancouver, British Columbia, Canada, 564 pp. 

Gross, M.R. 1987. Evolution of diadromy in fishes. American Fisheries Society 

Symposium 1: 14-25. 

Hanson, M.B., R.W. Baird, and G.S. Schorr. 2005. Focal behavioral observations and 

fish-eating killer whales: Improving our understanding of foraging behavior and 
83

prey selection. Abstract. Sixteenth, Biennial Conference on the Biology of 

Marine Mammals, December 12-16, 2005, San Diego, CA, 

Hanson, M.B. and R.L. DeLong. 2005. A tale of two porpoise species: Seasonal 

movements and habitat use of Dall's and harbor porpoise in the Salish Sea as 

determined by radio-telemetry. Abstract, 2005 Puget Sound Georgia Basin 

Research Conference 29-31 March 2005, Seattle, WA. 

Harbo, R.M. 1997. Shells & Shellfish of the Pacific Northwest, Harbour Publishing. 

Harrison, P.J, D.L. Mackas, B.W. Frost, R.W. Macdonald and E.A. Crecelius. 1994. An 

assessment of nutrients, plankton and some pollutants in the water column of Juan 

de Fuca Strait, Strait of Georgia and Puget Sound, and their transboundary 

transport. Canadian Technical Report of Fisheries and Aquatic Sciences, No. 

1948: 138-174. 

Hay, D.E. and J. Fulton. 1983. Potential secondary production from herring spawning in 

the Strait of Georgia. Canadian Journal of Fisheries and Aquatic Sciences, 

40(2):109-113. 

Hebard, J.F. 1956. The seasonal variation of zooplankton in Puget Sound. M.S. Thesis, 

University of Washington, Seattle, WA. 64 pp. 

Herrera Environmental Consultants, Inc. 2004. Ecological Economic Evaluation, Maury 

Island, King County, Washington, report prepared for King County, Department 

of Natural Resources and Parks, Water and Land Resources Division, Seattle, 

Washington. 

Horner, R.A., L. Hanson, C.L. Hatfield, and J.A. Newton. 1996. Domoic Acid in Hood 

Canal, Washington, USA. In: Harmful and Toxic Algal Blooms. Yasumoto T 

[Ed.], UNESCO. 

Hutchinson, I. 1988. The Biogeography of the Coastal Wetlands of the Puget Trough - 

Deltaic Form, Environment, and Marsh Community Structure. Journal of 

Biogeography 15:729-745. 

Ish, T., E.J. Dick, P.V. Switzer, and M. Mangel. 2004. Environment, krill and squid in the 

Monterey Bay: from fisheries to life histories and back again. Deep-sea research 

part II: topical studies in oceanography. 51(6-9):849-862. 

Jeffries et al. 2003. Trends and Status of Harbor Seals in Washington State: 1978-1999. 

 Journal of Wildlife Management 67(1):207-218. 

Kaczynski, V.W., R.J. Feller, and J. Clayton. 1973. Trophic analysis of juvenile pink and 

chum salmon (Oncorhynchus gobusha and O. keta) in Puget Sound. J. Fish. Res. 

Board Can. 30:1003-1008. 

Keeley, E.R., and J.W.A. Grant. 2001. Prey size of salmonid fishes in streams, lakes, and 

oceans. Can. J. Fish. Aquatic. Sci. 58:1122-1132. 

Kimmerer, W.J. 1993. Distribution patterns of zooplankton in Tomales Bay, California. 

 Estuaries 16:264-272. 

Kozloff, E. N., 1983. Seashore life of the northern Pacific coast, 2nd. Edition. University 

of Washington Press 

Komar, P.D., 1998, Beach processes and sedimentation, Englewood Cliffs NJ, PrenticeHall. 

Krahn, M.M., et al. 2002. Status Review of Southern Resident killer whales (Orcinus 

orca) under the Endangered Species Act U.S. Dept. Commer., NOAA Tech. 

Memo. NMFS-NWFSC-54, 133p. 
84

Kruckeberg, A. R. 1991. The natural history of Puget Sound country. University of 

Washington Press, Seattle. 

Lance, M.M., and C.W. Thompson. 2005. Overlap in diets and foraging of common 

murres (Uria aalge) and rhinoceros auklets (Cerorhinca monocerata) after the 

breeding season. The Auk 122:887-901. 

Lassuy. D.R. 1989. Pacific Herring. Species Profiles: Life Histories and Environmental 

Requirements of Coastal Fishes and Invertebrates (Pacific Northwest). U.S. 

Department of the Interior and U.S. Army corps of engineers. Biological report 

82 (11.126), 18 p. 

Leschine, T., Wellman, K. and Green, T. 1997. The Economic Value of Wetlands. 

Ecology Publication No. 97-100. Washington State Department of Ecology, 

Bellevue , Washington. 

Levings, C.D., and R.M. Thom. 1994. "Habitat Changes in Georgia Basin: Implications 

for Resource Management and Restoration." In: 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, 

January 13-14, 1994, Vancouver, British Columbia, Canada. 

Litzow, M.A., J.F. Piatt, A.A. Abookire, and M. Robards. 2004. Energy density and 

variability in abundance of pigeon guillemot prey: support for the qualityvariability tradeoff hypothesis. Journal of Animal Ecology 73: 1149-1156. 

Mackas, DL, Harrison, PJ. "Nitrogenous nutrient sources and sinks in the Juan de Fuca 

Strait of Georgia Puget Sound estuarine system: Assessing the potential for 

eutrophication." Estuar. Coast. Shelf Sci. 44: 1, 1997. 

MacMillian JR, Mulcahy D (1979) Artificial transmission to and susceptibility of Puget 

Sound fish to viral erythrocytic necrosis (VEN). J Fish Res Board Can 36:1097-

1101 

Mangel M. 2000. Trade-offs between fish habitat and fishing mortality and the role of 

reserves. Bulletin of Marine Science 66:663-674. 

Mangel M., and P. S. Levin. 2005. Regime shifts, phase shifts and paradigm shifts: 

Making community ecology the basic science for fisheries. Philosophic 

Transactions Royal Society of London 360:95-105. 

Manuwal, D.A., T.R. Wahl, and S.M. Speich. 1979. The seasonal distribution and 

abundance of marine bird populations in the Strait of Juan de Fuca and Northern 

Puget Sound in 1978. National Oceanic and Atmospheric Administration, 

Technical Memorandum ERL MESA-44. 

Manuwal, D. A., H. R. Carter, T. S. Zimmerman, and D. L. Orthmeyer, Editors. 2001. 

Biology and conservation of the common murre in California, Oregon, 

Washington, and British Columbia. Volume 1: Natural history and population 

trends. U.S. Geological Survey, Biological Resources Division, Information and 

Technology Report USGS/BRD/ITR–2000-0012, Washington, D.C. 132 pp. 

Maunder, M. N., Starr, P. J., and Hilborn, P. 2000. A Bayesian analysis to estimate loss 

in squid catch due to the implementation of a sea lion population management 

plan. Marine Mammal Science, 16: 413–426. 

Melvin, E.F., et. al., 1997. Seabird bycatch reduction: new tools for Puget Sound drift 

gillnet salmon fisheries: 1996 sockeye and 1995 chum non-treaty salmon test 

fisheries. Final report to the Washington Sea Grant Program, Seattle, WA. 
85

Meyer, C.B. and S.L. Miller. 2002. Use of fragmented landscapes by marbled murrelets 

for nesting in southern Oregon. Conservation Biology 16:755-766. 

Meyers TR, Hauck AK, Blackenbeckler WD, Minicucci T (1986) First report of viral 

erythrocytic necrosis in Alaska, USA, associated with epizootic mortality in 

Pacific herring, Clupea harengus pallasi (Valenciennes). J Fish Dis 9:479-491 

Millenium Ecosystem Assessment (MA). 2003. Ecosystems and Human Well-being: A 

Framework for Assessment. Island Press, Washington, D.C. 

Millenium Ecosystem Assessment (MA). 2004. Ecosystems and Human Well-being: 

Scenarios, Volume 2. Island Press, Washington, D.C. 

Miller, C.B. 1983. The zooplankton of estuaries. In : Ketchum, B.H. (ed.) Estuaries and 

 enclosed seas. Elsevier Science, Amsterdam, pp. 293-310. 

Mills, K. L., W.J. Sydeman, and P.J. Hodum (Eds.). 2005. The California Current Marine 

Bird Conservation Plan, v. 1, PRBO Conservation Science, Stinson Beach, CA. 

Mofjeld, H.O. and Larsen, L.H., 1984. Tides and tidal currents in the inland waters of 

Western Washington, NOAA Tech Memo ERL PMEL-56, Seattle, 52 pp. 

Morejohn, G. V., J. T. Harvey, and L. T. Krasnow. 1978. The importance of Loligo 

opalescens in the food web of marine vertebrates in Monterey Bay, California. In: 

C.W. Recksiek and H.W. Frey (Editors), Biological, oceanographic, and acoustic 

aspects of the market squid, Loligo opalescens Berry. California Department of 

Fish and Game, Fish Bulletin No. 169:67-98. 

Mote, P. W., A. F. Hamlet, M. P. Clark, and D. P. Lettenmaier. 2005. Declining 

mountain snowpack in western north America. Bulletin of the American 

Meteorological Society 86:39-+. 

Mundy, P. R., editor. 2005. The Gulf of Alaska; biology and oceanography. Alaska Sea 

Grant, University of Alaska, Fairbanks. 

Nakata, K. and J. Newton, 2001. Seasonal Patterns and Controlling Factors of Primary 

Production in Puget Sound’s Central Basin and Possession Sound. In Puget Sound 

Research 2001 Proceedings. Puget Sound Action Team, Olympia, WA 

National Oceanic and Atmospheric Administration (NOAA). 2002. Status review of 

southern resident killer whales (Orcinus orca) under the endangered species act. 

NOAA Technical Memorandum NMFS-NWFSC-54. 

National Marine Mammal Laboratory (NMML). 1996. Working paper: Biomass 

consumption estimates of California sea lions and harbor seals in Puget Sound, 13 

p. (Available from Alaska Fisheries Science Center, Natl. Mar. Fish. Serv., 

NOAA, 7600 Sand Point Way NE, Seattle, WA 98115.) 

National Research Council (NRC). 2004. Valuing Ecosystem Services: Toward Better 

Environmental Decision-Making. Committee on Assessing and Valuing the 

Services of Aquatic and Related Terrestrial Ecosystems, Washington, D.C. 

National Science and Technology Council, Committee on Environment and Natural 

Resources. 2002. From the Edge: Science to Support Restoration of Pacific 

Salmon, Washington, DC. 

Newton, J. and Van Voorhis, K. 2002. Seasonal Patterns and Controlling Factors of 

Primary Production in Puget Sound’s Central Basin and Possession Sound. 

Washington State Department of Ecology, Environmental Assessment Program, 

Publication #02-03-059. Olympia, WA. 
86

Newton, J.A., S.L. Albertson, K. Van Voorhis, C. Maloy, and E. Siegel. 2002. 

Washington State Marine Water Quality, 1998 through 2000. Washington State 

Department of Ecology, Environmental Assessment Program, Publication #02-03-

056, Olympia, WA. 

Newton, J.A., Siegel, E., and Albertson, S.L., 2003. Oceanographic Changes in Puget 

Sound and the Strait of Juan de Fuca during the 2000-01 Drought. Canadian 

Water Resources Journal., 28(4), 715-728. 

Newton, J.A., M. Edie, and J. Summers. 1998. Primary productivity in Budd Inlet: 

Seasonal patterns of variation and controlling factors. In Puget Sound Research 

‘98 Proceedings. Puget Sound Action Team, Olympia, WA, pp. 132-151. 

Newton, J.A., A.L. Thomson, L.B. Eisner, G.A. Hannach, and S.L. Albertson. 1995. 

“Dissolved oxygen concentrations in Hood Canal: Are conditions different than 

forty years ago?” In: Puget Sound Research ‘95 Proceedings. Puget Sound Water 

Quality Authority, Olympia, WA, pp. 1002-1008. 

NOAA, 1984. Tidal current tables, 1985, Pacific Coast of North America and Asia, U.S. 

Department of Commerce, Rockville, MD, 270 pp. 

PSAT, 1988. State of the Sound Report. 

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). 

Ohlendorf, H.M. and W.J. Fleming. 1988. Birds and environmental contaminants in San 

Francisco and Chesapeake Bays. Marine Pollution Bulletin. 19: 487-495. 

Olesiuk 1993. Annual Prey Consumption by Harbor Seals (Phoca vitulina) in the Strait 

 Of Georgia, British Columbia. Fishery Bulletin 91:491-515. 

Orsi, J. J. 1995. Radical changes in the estuary's zooplankton caused by introductions 

from ballast water. Interagency Ecological Studies Program for the SacramentoSan Joaquin Estuary, Newsletter, Summer 1995: 16-17. 

Orsi, J.J., and S. Ohtsuka. 1999. Introduction of the Asian copepods Acartiella sinensis, 

Tortanus dextrilobatus (Copepoda: Calanoida), and Limnoithona tetraspina 

(Copepoda: Cyclopoida) to the San Francisco estuary, California, USA. Plankton 

Biol. Ecol. 46(2):128-131. 

Osborne 1999. A historical ecology of Salish Sea “resident” killer whales (Orcinus orca): 

with implications for management. University of Victoria, Victoria, BC. 

O’Shea, T.J. 1999. Environmental contaminants and marine mammals. Pages 485-563 in 

J.E. Reynolds III and S.A. Rommel, eds. Biology of Marine Mammals. 

Smithsonian Institution Press, Washington, D.C. 

Pauley, G.B., DA Armstrong, R. Van Citter, and G.L. Thomas. 1989. Species profiles: 

life histories and environmental requirements of coastal fishes and invertebrates 

(Pacific Southwest)—Dungeness crab. U.S. Fish Wildl. Serv. Biol. Rep. 

82(11.121). U.S. Army Corps of Engineers, TR EL-82-4.20 PPPentilla, D.E. 1997. Investigations of intertidal spawning habitats of surf smelt and 

Pacific sand lance in Puget Sound, Washington. p. 395-407. In: Proceedings of 

the international symposium on the role of forage fishes in marine ecosystems, 

Lowell Wakefield Fisheries Symposium Univ. of Alaska Sea Grant College 

Program, Report No. 97-01. 
87

Pentilla, D.E. pers. comm. Washington Department of Fish and Wildlife. P.O. Box 

1100, La Conner, WA 98257. 

Perrings C. 2001. Modelling sustainable ecological-economic development, in H. Folmer 

and T. Tietenberg (eds) The International Yearbook of Environmental and 

Resource Economics 2001/2, Edward Elgar, Cheltenham. 

Peterson, C.H. ,and J. Lubchenco. 1997. “Marine Ecosystem Services,” in Nature’s 

Services: Societal Dependence on Natural Ecosystems, G.C. Daily, ed. Island 

Press, Washington, D.C. 

Pew Oceans Commission. 2003. America’s living oceans: charting a course for sea 

change. A Report to the nation., Arlington, Virginia. 

Piatt, J.F., and P.J. Anderson. 1996. Response of common murres to the Exxon Valdez 

oil spill and long-term changes in the Gulf of Alaska marine ecosystem. American 

Fisheries Society Symposium 18:720-737. 

Piatt, J.F., editor. 2002. Response of seabirds to fluctuations in forage fish density, Exxon 

Valdez Oil Spill Restoration Project Final Report (Restoration Project 01163M), 

and Minerals Management Service (Alaska OCS Study MMS 2002-068), Alaska 

Science Center, U.S. Geological Survey, Anchorage, Alaska. 

Postel, S., and S. Carpenter. 1997. “Freshwater Ecosystem Services,” in Nature’s 

Services: Societal Dependence on Natural Ecosystems, G.C. Daily, ed. Island 

Press, Washington, D.C. 

Puget Sound Action Team (PSAT). 2005. State of the Sound 2004. Office of the 

Governor (Washington State). www.psat.wa.gov Publication No. PSAT 05-01 

Puget Sound Water Quality Action Team, 2000, Puget Sound update: Seventh Report of 

the Puget Sound Ambient Monitoring Program. Olympia, Washington. 127 pp. 

Reichow, D. and M.J. Smith. 2001. Microsatellites reveal high levels of gene flow among 

populations of California squid, Loligo opalescens. Molecular Ecology. 10(5) 

1101-1109. 

Reijnders, P.J.H. and A. Aguilar. 2002. Pollution and marine mammals. Pages 948-957 

in W.F. Perrin, B. Würsig, and J.G.M. Thewissen, eds. Encyclopedia of marine 

mammals. Academic Press, San Diego, CA. 

Rosenberg, A.A., and K.L. McLeod. 2005. Implementing ecosystem-based approaches 

to management for the conservation of ecosystem services. Marine Ecology 

Progress Series 300: 241–296. 

Ross, P.S., R.L. de Swart, R.F. Addison, H. van Loveren, J.G. vos, and A.D.M.E. 

Osterhaus. 1996a. Contaminant-induced immunotoxicity in harbor seals: 

wildlife at risk? Toxicology 112:157-169. 

Ross, P.S., R.L. de Swart, H. van Loveren, A.D.M.E. Osterhaus, and J.G. vos, 1996b. 

The immunotoxicity of environmental contaminants to marine wildlife: a review. 

Annual Review of Fish Diseases 6:151-165. 

Ross, P.S., G.M. Ellis, M.G. Ikonomou, L.G. Barrett-Lennard, and R.F. Addison. 2000. 

High PCB concentrations in free-ranging Pacific killer whales, Orcinus orca: 

effects of age, sex, and dietary preferences. Marine Pollution Bulletin 40:504-

515. 

Sainsbury, K.J., A. E. Punt, and A. D. M. Smith. (2000) Design of operational 

management strategies for achieving fishery ecosystem objectives. ICES J. Mar. 

Sci. 57: 731-741. 
88

Scheffer and Slipp 1948.The whales and dolphins of Washington State with a key to the 

 cetaceans of the west coast of North America. American Naturalist 39(2):257- 

 337. 

Schmitt, C.C., S.J. Jeffries, and P.J. Gearin. 1995. Pinniped predation on marine fish in 

Puget Sound. p. 630-637. In E. Robichaud (Ed.) Puget Sound Research '95 

Proceedings, Bellevue, WA. Puget Sound Water Quality Authority. 2 Vols. 1038 

p. 

Shared Strategy 2005. Draft Puget Sound Salmon Recovery Plan. Shared Strategy, 

Seattle WA. Available at http://www.sharedsalmonstrategy.org/plan/index.htm 

Shipman, H., 2004, Coastal bluffs and sea cliffs on Puget Sound, Washington, In: M.A. 

Hampton and G.B. Griggs, eds., Formation, evolution, and stability of coastal 

cliffs-status and trends, 1693, US Department of the Interior, U.S. Geological 

Survey, Denver, CO., 123 p. 

Simenstad, C.A., W.J. Kinney, S.S. Parker, E.O. Salo, J.R. Cordell, and H. Buechner. 

1980. Prey community structure and trophic ecology of outmigrating juvenile 

chum and pink salmon in Hood Canal, Washington: a synthesis of three years’ 

studies, 1977-1979. Final Rep. Fish. Res. Inst., University of Washington, Seattle, 

WA. FRI-UW-8026. 113p. 

Simenstad, C.A., K.L. Fresh, and E.O. Salo. 1982. The role of Puget Sound and 

Washington coastal estuaries in the life history of Pacific Salmon: an 

unappreciated function. Pages 343-364 in V.S. Kennedy (Ed.), Estuarine 

Comparisons., Academic Press 

Smith, A. D. M., K. J. Sainsbury, and R. A. Stevens. 1999. Implementing effective 

fisheries-management systems–management strategy evaluation and the 

Australian partnership approach. ICES Journal of Marine Science, 56: 967–979. 

Snover, A.K., Mote, P.W., Whitely Binder, L., Hamlet, A.F., and Mantua, N.J., 2005. 

Uncertain Future: Climate Change and its Effects on Puget Sound. A report for 

the Puget Sound Action Team by the Climate Impacts Group (Center for Science 

in the Earth System, Joint Institute for the Study of the Atmosphere and Oceans, 

University of Washington, Seattle). 

Speckman, S., J.F. Piatt, C. Minte-Vera and J. Parrish. 2005. Parallel structure among 

environmental gradients and three trophic levels in a subarctic estuary. Progress in 

Oceanography 66: 25-65. 

Stick, K.C. 2005. 2004 Washington State Herring Stock Status Report. Washington 

Department of Fish and Wildlife Fish Program, Fish Management Division. P.O. 

Box 1100, La Conner, WA 98257. 

Strickland, R.M. 1983. The Fertile Fjord. University of Washington Press, Seattle, 145 

pp. 

Thom, R. M., Armstrong, J. W., C. P. Staude, K. K. Chew and Norris, R., 1976, A survey 

of the attached marine flora at five beaches in the Seattle, Washington area. 

Syesis 9:267-275. 

Thom, R.M., Shreffler, D.K, and Macdonald, K., 1994, Shoreline armoring effects on 

coastal ecology and biological resources in Puget Sound, Washington: Coastal 

Erosion Management Studies, Volume 7, Shorelands Program, Washington Dept. 

of Ecology, Olympia, DOE Report 94-80 
89

Thompson, C.W., E.R. Donelan, M.M. Lance, and A.E. Edwards. 2002. Diet of Caspian 

Terns in Commencement Bay, Washington. Waterbirds: Vol. 25(1):78–85. 

Trainer, V.L., N.G. Adams, B.D. Bill, C.M. Stehr, J.C. Wekell, P. Moeller, M. Busman, 

and D. Woodruff. 2000. Domoic acid production near California upwelling zones, 

June 1998. Limnol. Oceanogr., 45(8), 401-440. 

Trainer, V. L., B. M. Hickey, and R. A. Homer. 2002. Biological and physical dynamics 

of domoic acid production off the Washington coast. Limnology and 

Oceanography 47:1438-1446. 

Trainer, V. L., B. T. L. Eberhart, J. C. Wekell, N. G. Adams, L. Hanson, F. Cox, and J. 

Dowell. 2003. Paralytic shellfish toxins in Puget Sound, Washington State. 

Journal of Shellfish Research 22:213-223. 

Triangle Associates, Inc. 2004. Technical workshop on nearshore restoration in the 

central Strait of Juan de Fuca. Available from Olympic National Park, Port 

Angeles, Washington. 

Trumble, R.J. 1983. Management Plan for baitfish species in Washington State. State of 

Washington Department of Fisheries Progress Report No. 195. 106p. 

U.S. Commission on Ocean Policy (USCOP). 2004. An Ocean Blueprint for the 21st 

Century. Washington, D.C. 

U.S. Fish and Wildlife Service (USFWS). 2005. Regional Seabird Conservation Plan, 

Pacific Region. U.S. Fish and Wildlife Service. Migratory Birds and Habitat 

Programs, Pacific Region, Portland, Oregon. 

Van Cleve, F. B., C. Simenstad, F. Goetz, and T. Mumford, 2004. Application of “best 

available science” in ecosystem restoration: lessons learned from large-scale 

restoration efforts in the USA. Puget Sound Nearshore Partnership Report No. 

2004-01. Published by Washington Sea Grant Program, University of 

Washington, Seattle, Washington. Available at http://pugetsoundnearshore.org. 

Waddell, P. 2002. UrbanSim: Modeling Urban Development for Land Use, 

Transportation and Environmental Planning. Journal of the American Planning 

Association 68: 297-314. 

Walters, C.J, V. Christensen, S.J. Martell, and J.F. Kitchell. 2005. Possible ecosystem 

impacts of applying MSY policies from single-species assessment. ICES Journal 

of Marine Science 62: 558-568. 

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

Publishing. 

Warner, M.J., J.A. Newton, and M. Kawase. 2001. Recent studies of the overturning 

circulation in Hood Canal. In: Proceedings of the 2001Puget Sound Research 

Conference. Puget Sound Action Team, Olympia, WA, 9 pp. 

WDFW. Date unknown. The Tantalizing squid. Washington Department of Fisheries. 

Weitkamp, L.A., R.C. Wissman, C.A. Simenstad, K.L. Fresh, and J.G. Odell. 1992. Gray 

whale foraging on ghost shrimp (Callianassa californiensis) in littoral sand flats of 

Puget Sound, U.S.A. Canadian Journal of Zoology 70:2275-2280. 

Wilen, J.E., M.D. Smith, D. Lockwood, and L.W. Botsford. 2002. Avoiding Surprises: 

Incorporating Fisherman Behavior into Management Models. Bulletin of Marine 

Science70: 553-575. 

Williams, G.D., R. M. Thom, D. Woodruff, A. Borde, A. Skillman, M. Miller, R. 

Kropp, S. Blanton), Pentec Environmental (Jim Starkes, Jon Houghton), Striplin 
90

Environmental Associates, Shapiro Associates, King County DNR (Laura 

Blackmore, Jim Brennan). (2001).State of the Nearshore Ecosystem: Central 

Puget Sound including Vashon and Maury Islands (WRIAs 8and 9). Prepared for 

King County Department of Natural Resources, Seattle, Washington. 266 pp. 

Williams, G.D., R.M. Thom. M.C. Miller, D.L. Woodruff, N.R. Evans, and P. N. Best. 

2003. Bainbridge Island nearshore assessment: summary of best available science. 

PNWD-3233. Prepared for the City of Bainbridge Island, Bainbridge Island, WA, 

by Battelle Marine Sciences Laboratory, Sequim, WA. 

Winter, D.F., K. Banse, and G.C. Anderson. 1975. The dynamics of phytoplankton 

blooms in Puget Sound, a fjord in northwestern U.S. Marine Biology, 29: 139-

175. 

Wunderlich, R.C., B.D. Winter, and J.H. Meyer. 1994. Restoration of the Elwha River 

ecosystem. Fisheries 19(8):11-19. 
91

Figures, Tables and Boxes 

Overview and Introduction 

Figure 1. Map of Puget Sound, with five subbasins indicated. 

Table a. List of previously identified impacts to Puget Sound 

Box 1. Kelp-urchin-sea otter interaction story (with photos of urchin barrens/kelp 

forest) 

Box 2. List and description of ecosystem goods and services 

The Puget Sound Ecosystem 

Figure 2. Conceptual model of elements/components of Puget Sound ecosystem 

and their interactions 

Figure 3. Panel of photos showing variety of Puget Sound habitat types. 

Figure 4. Map of Puget Sound, showing drift cell locations and subbasins 

Figure 5. Fresh and salt water flow in Puget sound, pycnocline. 

Figure 6. Bluff failure 

Figure 7. Shoreline armoring 

Figure 8. Illustration of landscape processes in river deltas and shorelines 

Figure 9. Duwamish river 

Box 3. Dissolved oxygen in Hood Canal 

Box 4. Ecosystem response to Elwha Dam 

Box 5. Contaminants and toxics in Puget Sound (in development) 

Box 6. Nutrients and salmon carcasses (in development) 

Box 7. Ecosystem goods and services 

Box 8. Whale watching in Puget Sound 

Decision Frameworks for Ecosystem Approaches 

Box 9. Tradeoff between conservation and economic objective for a New 

Zealand fishery 

Box 10. General framework for Management Strategy Evaluation 

Box 11. Components of the ATLANTIS model 

Box 12. UrbanSim model.