Marine and Estuarine Protection and Restoration Strategies

This section focuses on the scientific basis for a suite of marine, nearshore, and estuarine protection and restoration strategies. The strategies addressed come from a number of sources including the Puget Sound Partnership Action Agenda (PSP 2009), the Puget Sound Nearshore Ecosystem Restoration Project (e.g., Clancy et al. 2009), and other existing state, federal, and tribal programs. The strategic topics addressed in this section are generally grouped by 1) Puget Sound water quality and 2) physical habitat protection, restoration, and management processes. Each strategy is evaluated on its scientifically demonstrated effectiveness, level of certainty, and/or gaps in science-based knowledge, based on thorough review of the literature. The strategies include ways to comprehensively manage/integrate all natural processes and human activities that involve salt and freshwater (infiltration, recharge, surface runoff, collection, storage, diversion, transport and use), effluent, wastewater treatment, point and non-point pollution, spills, and discharge at appropriate temporal and spatial scales, many of which are covered in Section 3. The ultimate goal is to replicate and maintain as much as possible the functional characteristics (quality, quantity, rates, connectivity) of the natural system at all appropriate scales, times, and places.

1. Background

There are two primary sources of water flowing into the Puget Sound: tidally driven marine water mixing in from the Pacific Ocean and freshwaters entering from rivers, streams, surface flow, and groundwater discharge. Rivers and streams at times deliver excessive nutrients, sediments, toxic contaminants, pathogens, and freshwater to Puget Sound. Watershed protection and restoration strategies are intended to result in improved water quality of freshwater rivers and streams entering Puget Sound estuaries and marine waters. These topics are covered in Section 3 and will not be repeated here. Therefore, water quality topics addressed in this section apply only to surface runoff, groundwater discharges, and effluents that drain directly into estuaries or marine waters along Puget Sound shorelines and to other water quality issues in Puget Sound proper, many of which are also covered in Section 3.

Nutrient Loading

WDOE High Nitrogen Study (WDOE 2008) summarizes the nitrogen input pattern for southern Puget Sound (see Chapter 2A and Section 3 of this Chapter).

Contaminant Loading

Some areas of Puget Sound have excessive contaminants in the water and sediments. The array of contaminants in Puget Sound includes heavy metals, PAHs, PDBEs, PCBs, dioxins, phthalates, pharmaceuticals, cosmetics, and other personal care products (Hart Crowser, Inc, et al. 2007). The primary sources of contaminants in Puget Sound are from surface runoff, atmospheric deposition, industrial and municipal waste waters, combined sewer overflows (CSOs), and direct spills (Hart Crowser, Inc., et al. 2007; see Chapters 2A and 3 of the PSSU).

Because of the challenges associated with reducing sediment contaminant loads in deep water, we focus on reducing the amount of contaminants delivered to Puget Sound. General strategies include reducing contaminants in treatment plant effluents, preventing contaminants spills, and cleaning up known sources of contamination.

One strategy that could help to reduce contaminant loading is to use a toxic loading inventory to guide loadings reduction strategies (e.g., Paulson et al. 1989, Hart Crowser, Inc. et al. 2007, EnviroScience Corp. et al. 2008). Many restoration strategies for reducing contaminant inflows are similar to those for reducing nutrient loads (e.g., wastewater treatment, reducing storm water, on-site treatment). Toxic spill prevention and cleanup are additional strategies that pertain to contaminants.

2. Improving Wastewater Treatment Plants that Drain Directly into Estuaries or Puget Sound

Wastewater treatment has a long history, based initially on common sense. The first treatment systems consisted primarily of flushing waste away from human population centers with water flow, often downstream to larger rivers and ultimately marine waters. We now know that when effluent is highly concentrated, not dispersed by tidal currents, and/or contains high concentrations of deleterious constituents, problems arise in the human and natural environment (e.g., Malins 1984, McCain et al. 1988). Effects of wastewaters on Puget Sound have been discussed in previous Puget Sound science update sections and the majority of wastewater treatment restoration strategies have been discussed in Section 3. In this section we discuss wastewater protection and restoration strategies that are either not covered in Section 3 or are particularly relevant to Puget Sound proper. They are: 1) Combined sewer overflows 2) Programs to address heavy nutrient loading of South Puget Sound and Hood Canal. 3) Reducing toxic loads in Puget Sound, 4) Preventing and reducing the effects of wastewater constituents that are not fully treated such as pharmaceuticals, cosmetics, cleaning products, industrial materials, etc. and 5) Water reuse as a restoration strategy.

Municipal and industrial wastewater treatment plants discharge effluent directly into Puget Sound in a number of locations, most notably West Point in Seattle, Snohomish Estuary and Port Gardner in Everett, and Budd Inlet in Olympia and others. These facilities receive much of the Puget Sound area municipal waste waters as well as permitted industrial effluent. Industrial facilities typically have systems customized to their waste products and sometimes discharge to municipal systems following pre-treatment. The treatment systems remove the majority of solids, biodegradable organics, and pathogens from the wastewater but they do not eliminate the high nitrogen loads from the effluent, nor do they fully remove many other toxics constituents such as heavy metals, pharmaceuticals, and PAHs, among many others (for details, see See Section 3 for a complete review of municipal wastewater restoration strategies.

Expanding and updating wastewater treatment facilities

The Puget Sound action agenda emphasizes need for expanding and updating wastewater treatment facilities (PSP 2009). The benefits from this restoration strategy have been described in Section 3. The essence of this restoration strategy is to implement wastewater technology that maximizes the concept of secondary and tertiary treatment, including removal of all constituents that occurred effluent greater than background levels. The action agenda has prioritized expansion and updating of wastewater treatment facility at the highest level (PSP 2009).

Advanced Wastewater Treatment Nutrient Reduction

Reduction of anthropogenic nitrogen loads in Puget Sound will depend on a combination of treatment approaches that include advanced wastewater treatment in plants that discharge into both rivers and Puget Sound proper. The details of advanced wastewater treatment are addressed in Section 3.

Contaminant Reduction

Heavy metals and other contaminants (e.g., PAHs, PDBEs, PCBs, dioxins, phthalates) are known to be accumulating in Puget Sound (Hart Crowser, Inc., et al. 2007, EnviroScience Corp. et al. 2008). Wastewater treatment only partially removes contaminants, depending on the process used and the target contaminant.

Some treatment processes remove heavy metals in varying degrees. The advanced treatment process of reverse osmosis system is effective in removing some metals, such as arsenic, cadmium, chromium, and mercury to safe levels (WEF 2006). New technologies hold promise for future improvements in heavy metal removal from effluents (e.g., Sayari et al. 2005), but the applications of these improvements in Puget Sound treatment plants is unclear1.

The relative treatment efficiencies for pharmaceuticals and personal care products (PPCPs) at five municipal wastewater treatment plants (WWTPs) in the Pacific Northwest were evaluated by Lubliner et al. (2010) and found to be mixed. Wastewater influent, secondary effluent, tertiary effluent, and biosolids were sampled. Four of the five WWTPs discharge within the Puget Sound watershed. Two of the plants provide secondary treatment, and three employ advanced (tertiary) treatment for nitrogen and phosphorus removal. Two of the plants produce tertiary-treated reclaimed water. Target analytes included 172 organic compounds (PPCPs, hormones, steroids, semi-volatile organics). Newly approved EPA methods were used to measure PPCPs, hormones, and steroids at low concentrations. Removal efficiencies were evaluated for each analyte at the five WWTPs. Secondary treatment alone achieved high removals for hormones and steroids. Approximately 21% of the 172 analytes were reduced to below reporting limits (i.e., 79% were not) by conventional secondary treatment, whereas 53% were reduced to below reporting limits by at least one advanced nutrient-removal technology. Roughly 20% of the 172 analytes (mainly polycyclic aromatic hydrocarbons) were found only in the biosolids and not the wastewater samples, so some analytes were clearly concentrating in the biosolids. Three PPCPs (carbamazepine, fluoxetine, and thiabendazole) were relatively untreated by the surveyed WWTP technologies. These three PPCPs may serve well as human-influence tracer compounds in the environment. Overall, the screening study indicates that (1) there are differences in PPCP removal between the WWTP processes and (2) advanced nutrient reduction and tertiary filtration may provide additional PPCP removal (Lubliner et al. 2010). A summary of the Department of Ecology program for control of toxic pollutants in Puget Sound is found at

Combined Sewer Overflows

Combined sewer overflows (CSOs) are a concern because untreated wastewater and stormwater may be discharged to Puget Sound during large storms posing risks to public health and the environment. Details on strategies for reducing CSOs can be found in Section 3.

Linking outlet quantities with nutrient and contaminant dispersal

One strategy for reducing the effects of wastewater effluents on receiving waters has been to relocate discharge pipes into areas that are more conducive to dispersal. When discharges enter shallow, closed embayments with low flushing rates there is a tendency for contaminants and nutrients to build up. There is substantial scientific and technical basis for the strategy of locating outfalls at locations and depths that maximize diffusion and therefore minimize physical and biological effects of high concentrations of nutrients and contaminants.

A further subcomponent of outfall relocation is to use the various permutations of diffusers and/or depth as techniques to increase dispersal of effluent. This is done by expanding mixing zones, and hence enabling increased total toxic pollutant load, through engineered changes to effluent outfalls (e.g., lengthening of discharge outfalls by adding diffuser ports). Outfalls have advanced from simple open-ended pipes not far from shore to long outfalls with large multiple-port diffusers discharging in deep water. An example of this in Puget Sound is the extreme dimensions of King County’s Brightwater project outfall: extending one mile offshore, at 600 feet deep, off of Point Wells in Puget Sound (see However, in other locations, outfalls have been constructed with much greater dimensions such as in Boston where one outfall is 9.4 miles long, 24.2 feet in diameter, including a 6,600 foot long diffuser section with 55 vertical risers, each with 8 discharges ports (NRC 1993).

The design of diffusion ports also has an important effect on the potential concentration of contaminants, especially in the sediments. Diffusers that lie on or near the bottom sediments will tend to concentrate certain contaminants more readily than diffusers that have vertical risers. The performance of a variety of diffuser configurations can be evaluated via a modeling environment (e.g., Roberts et al. 1989).

The optimal placement and configurations of effluent outfalls can be determined in concert with the interplay of ambient current patterns using models (e.g., Baumgartner et al. 1994, Frick 2003). In Puget Sound, such analyses could be conducted for both existing and proposed outfalls to determine the best locations and engineering design for either new outfalls or to retrofit existing outfalls.

Caution should be raised in terms of restoring water quality in Puget Sound through effluent relocation and redesign alone since this would likely result in simply expanding contamination into new areas of Puget Sound bays and estuaries. Restoration will therefore depend on a combination of reducing toxic constituents, nutrient loads, and total volume of effluent, as well as appropriate strategic placement and design of outfalls. The reduction of wastewater loading to Puget Sound is currently part of the Action Agenda (C3), but there is no specific reference to relocating or redesigning outfalls commensurate with state-of-the-art outfall design (PSP 2009).

On-site Wastewater Treatment

This topic has been covered extensively in Section 3 but it is important to note that on-site wastewater treatment is a critical restoration strategy for Puget Sound proper, especially in certain areas where high nutrient loads are contributing to nitrification such as southern Puget Sound and Hood Canal2.

Reclaimed water

An important emerging strategy relative to wastewater treatment that may be important for the health of Puget Sound and its watersheds is water reclamation1. The basic concept is to clean water sufficiently so that it can be used in municipal, agricultural, and industrial processes or infiltrated back into the natural system. One of the main benefits of reclaiming water is that ultimately less total water may be needed for human use, thereby freeing water that can remain in streams for fish and other aquatic life, as well as recreation.

3. Potential Effectiveness and Uncertainties in Wastewater Management

There has been extensive research on the effects of wastewaters on marine waters, and substantial review of the effectiveness of wastewater treatment on freshwaters (see Section 3), but less research has been conducted on the effectiveness of wastewater treatment in marine waters. From a marine ecosystem health perspective, the ultimate goal is to reduce nutrients and contaminants to safe levels. It may be technically possible to eliminate harmful constituents from wastewater; the few exceptions include processes for reducing some heavy metals and some pharmaceuticals and personal care products -- more research is clearly needed in this area3. Nevertheless, the key question is whether the return on the investment will be effective. The certainty that these activities will be technically effective is very high. The uncertainty comes from policy decisions, availability of funding, and fully functioning monitoring program that can determine if recovery goals are being met.

4. Programs to Reduce Stormwater Run-off Directly into Estuaries and Puget Sound

As discussed in Section 3, stormwater can deliver heavy loads of nutrients, pathogens, toxic contaminants, and sediment to Puget Sound bays and estuaries, adding significantly to the total loads from all sources. Mercury, PCBs, flame retardants, and other persistent chemicals are found throughout Puget Sound where they they can bioaccumulate and transfer through the food web (see Chapter 2A of the Puget Sound Science Update and Section 3 of Chapter 4).

5. Accidental or Long-term Contaminant Spills

Programs and regulations that prevent shoreline- and boat-based accidental contaminants spills

The most obvious strategy for protecting marine waters against contamination from accidental spills of toxic substances is through spill prevention. There are numerous specific spill prevention activities. Many have focused on preventing bulk oil spills but others pertain to hazardous chemicals in transit, industrial use, wastewater from system shutdown or storm overflow and fuel spills from marine accidents. Particularly insidious are small, gradual, chronic releases of contaminants from diverse sources.

In Puget Sound, the major spill prevention programs are coordinated by the Department of Ecology4. Critical aspects of the program are preparedness, pre-booming, a system for advanced notification of oil transfer, containment requirements, spill drills, and the Puget Sound Safety Plan. Each one of these components plays a role in prevention, but some of them, like preparedness and response, also comprise the system for responding to spills when they happen (and are therefore addressed below).

The Puget Sound Harbor Safety Plan includes guidance to avoid a variety of navigational risks and hazards including aids to navigation, advanced notice of arrival, automatic identification system, required charts, emergency response communications, fishing net conflicts resolution, naval vessel protection zones, avoidance of marine sanctuaries, pilotage, and small vessel and marine that management (Puget Sound Harbor Safety Committee 2008). The Plan also includes Standards of Care that, taken together, all lead to safer operational conditions that can prevent the likelihood of marine contaminant spills. The Plan addresses procedures for anchoring, operations near bridges, bunkering, equipment failures, heavy weather, hot work, lightering, propulsion loss prevention, restricted visibility, tanker escort operations, towing vessel operations, and under-keel clearance (Puget Sound Harbor Safety Committee 2008).

Enforcement of spill prevention regulations is an integral part of successful spill prevention. Another quasi-enforcement concept that probably lends itself to spill prevention is public recognition of corporations as good citizens (e.g., Konar and Cohen 1997). The Department of Ecology Spill Prevention Program also includes guidance to limit discharges of unwanted materials from cruise ships and guidelines for ballast water management to protect from invasive species.

Clean-Up of Contaminants

Cleanup ranges from major EPA Superfund sites to clean up of minor spills. In some cases hazardous materials have been on-site for decades and have been or will be cleaned up and sites remediated while contemporary spills are usually cleaned up immediately or soon after spills.

Effectiveness of cleanup generally depends on 1) the amount of product released, 2) the contaminants were released, 3) chemical composition of the hazardous materials, 4) the specific technology of cleanup for each contaminant, 5) effectiveness of the cleanup technology, 6) the area or extent of the spill, and 7) the dispersal modes and rates (e.g., Etkin 2009).

Depending on the contaminants toxins involved and who caused the spill and where it occurred, contemporary cleanup response is managed by a coordinated effort of federal, state, tribal, and/or local agencies and the private sector. Basic policies for this coordination are set forth in the National Incident Management System (NIMS) of FEMA5. Spills anywhere in the country can be reported through the National Response Center6. In Washington, the response system is stepped down to the Department of Ecology's Incident Command System (ICS)7.

Spill preparedness involves a continuous cycle of activities, capturing lessons learned and then incorporating them back into plans, policies and procedures. The cycle is necessary to promote coordination among a combination of the variety of entities involved, all using the ICS. Spill preparedness includes the following topics8:

  • Contingency Plans. The Washington Administration Code (WAC 173-182) requires certain oil handling facilities, pipelines, and vessels to have a state-approved oil spill Contingency Plan that ensures their ability to respond to major oil spills.
  • Oil spill drills enable response personnel to become knowledgeable and proficient in the strengths and weaknesses of plans, equipment and procedures. Oil spill drills are scheduled in advance on the area drill calendar. Ecology tracks drill progress over a three year cycle and has prepared a drill manual to assist in meeting the requirements of the drill program.
  • Primary Response Contractors (PRCs) are private companies or cooperatives that are in partnership with Plan holders to act as required response support teams. To be cited by a plan holder, the contractor must apply and be approved by the Department of Ecology. The PRCs have equipment and crews that are trained and equipped to mitigate leaks and spills when they occur. The need to respond as soon as possible, with trained operators and systems of equipment that are enhanced for maximum effectiveness, is critical to increase the opportunity for on-water recovery and reduce shoreline oiling.
  • Geographic Response Plans (GRPs) are site-specific response plans for oil spills to water. They include response strategies tailored to a specific beach, shore, or waterway and meant to minimize impact on sensitive areas threatened by the spill. Each GRP has two priorities, which are to: 1) Identify sensitive natural, cultural or significant economic resources; and 2) Describe and prioritize response strategies.
  • Incident Command System (ICS) is a standardized on-scene emergency management system specifically designed to allow its user(s) to adopt an integrated organizational structure equal to the complexity and demands of single or multiple incidents, without being hindered by jurisdictional boundaries.
  • PRC equipment maps depict the location of oil spill response equipment that is owned and operated by the state’s approved response contractors or oil spill contingency planners (industry). The maps include the locations of booms and skimmers and the capacity of each.
  • Trajectory Analysis Planner (TAP) is a computer-based tool that investigates the probabilities that spilled oil will move and spread in particular ways within a particular area. TAP does this by assessing hundreds of site-specific spill trajectories. The Puget Sound TAP Technical Document describes the TAP methodology and trajectory modeling behind TAP, as well as the accuracy and limitations of TAP.

Once a spill occurs, the progress of response and cleanup is tracked on the Department of Ecology's Spills website ( The scientific basis of contaminant cleanup is extensive, especially for spilled petroleum products; there is less extensive scientific guidance for cleaning up other contaminants. Several key books on the extensive science of oil’s effects on the environment, spill prevention and preparedness, and the techniques of cleanup are Lane (1995), Cormack (1999), and Ornitz and Champ (2002).

Clean-up of historic marine/estuarine industrial toxic waste sites

There are a wide variety of toxic cleanup sites that affect Puget Sound. Some include contaminants that were released years ago and the others are from more recent spills or chronic pollution problems. Because of the wide variation in on-site conditions and the contaminants that require cleanup, the cleanup process at each location is engineered case-by-case. In some locations, a bay-wide approach is taken to clean up, especially for toxins that were delivered from multiple sources but deposited in the sediments of the same area. Under the Puget Sound Initiative (PSI), the Department of Ecology has prioritized certain bays and organize cleanup in some locations by the bay-wide approach. The PSI includes all toxic waste sites within 1/2 mile of Puget Sound.

In the Puget Sound, the US EPA has the lead on federally-listed hazardous waste sites and Ecology has the lead on state clean up sites. There are many steps between discovery of a toxic site requiring cleanup and the final cleanup including initial investigation, site hazardous assessment, site ranking and listing, emergency actions if necessary, feasibility study, cleanup action plan, engineering design, cleanup construction, cleanup operation and maintenance, environmental covenants, periodic reviews, and finally, removal from hazardous sites list. The physical core of this restoration strategy is the construction phase (i.e., actions taken at a site to eliminate, render less toxic, stabilize, contain, immobilize, isolate, treat, destroy, or remove a hazardous substance). These generally include construction activities such as removal of contaminated soils or sediment for off-site treatment or disposal; pumping and treating of contaminated ground water; sealing off contaminated soils or sediment beneath a cap or barrier; the addition of chemicals or enhancement of the growth of microorganisms that break down contaminants in place9; etc. Specifics of each toxin remediation project can be found on the Department of Ecology’s website10.

Other critical considerations in toxic cleanup as a restoration strategy are the legal process and financial responsibility. The process for identifying responsible parties and coming to agreement on cleanup costs can be long and arduous. In addition to federal laws, basic legal vehicles for cleanup enforcement and associated Washington Administrative Code references are cited on the Department of Ecology website11.

Creating new habitat as part of hazardous waste cleanup is a restoration strategy that can add environmental and social benefit during recovery. One local example is at the Commencement Bay Asarco Superfund site where NOAA fisheries worked to include habitat features with the site remediation process. EPA supports the related Brownfields program that is designed to create new habitats and mediated sites pre-building development especially for community benefits12.

The scientific basis for toxic waste clean-up is extensive, but somewhat lacking in many technical areas. Several key books about scientific cleanup techniques and technologies are NRC (1995), Boulding (1996), Sellers (1998), and Lehr et al. (2001). NRC (1995) primarily evaluated current management practices and technologies for cleanup. They also cite, among the many technical challenges to be overcome in managing contaminated sediments, are an inadequate understanding of the natural processes governing sediment dispersion, the bioavailability of contaminants, and technical difficulties involved in sediment characterization, removal, containment, and treatment. Sellers (1998) is a comprehensive guide for numerous hazardous waste site cleanup procedures. Lehr et al. (2001) cover many of the techniques for cleanup of environmental hazards in marine waters and adjacent shorelands. EPA's Innovative Technologies section publications website contains references to a plethora of technical documents to guide remediation13.

Effectiveness of Spill Management

Effectiveness of remediating the legacy of toxic waste sites is often difficult to determine. In many cases when historically contaminated sites are remediated the process is only partially effective (NRC 2007). For example, depending on the on-site cleanup requirements and methods, some sites are "capped," the contaminants are left in place but the exposure pathway to environmental receptors is eliminated (e.g., Breems et al. 2009). However, in some cases a gradual leaching of contaminants into local groundwater (e.g., Wong et al. 1997) or surface water may occur that could result in releases local estuarine or marine waters.

The NRC Committee on Sediment Dredging at Superfund Megasites (2007) defined dredging effectiveness as the achievement of cleanup goals defined for each site, which take the form of remedial-action objectives, remediation goals, and cleanup levels. They also presented a framework to facilitate the evaluation of effectiveness of environmental-dredging projects at contaminated sediment sites. Their review found that evidence for dredging projects leading to achievement of long-term remedial action objectives, and within expected or projected time frames, is generally lacking (NRC 2007).The NRC Water Science and Technology Board (1988) also examined the criteria for achieving certain degrees of water quality in the areas of cleanup sites.

6. Physical Habitat Protection and Restoration Strategies

Protecting and restoring the physical integrity and ecological functionality of Puget Sound habitats provides the physical, chemical, and biological templates necessary for healthy fish and wildlife populations, as well as natural coastal ecosystems for human benefit. There are a variety of physical habitat protection and restoration strategies that can be applied to Puget Sound subtidal, intertidal, and shoreline marine and estuarine habitats. PSNERP has identified 21 management measures for implementing nearshore ecosystem restoration recognizing that (1) the measures can be capital projects, regulation,incentives, or education and outreach, and (2) the measures contribute to ecosystem recovery viaprotection, restoration, rehabilitation and substitution/creation (Clancy et al. 2009).These habitat measures can generally be divided into protection and restoration strategies.

Protection strategies

A key group of strategies includes the variety of regulatory and private activities that tend to protect habitats from degradation or to allow them to naturally recover their ecological function (Clancy et al. 2009). Although the initial costs of protection can be high, once the habitats are protected, the ongoing maintenance costs are often relatively low. Therefore, it is often preferable to protect currently functioning ecosystems or to protect somewhat degraded ecosystems from further degradation, allowing them recover. In some cases, it will be preferable to combine protection of the created habitats with restoration measures to speed recovery (Clancy et al. 2009).

Marine and estuarine shorelines and intertidal protection

There are a number of federal, state, tribal, local, and private programs designed to permanently protect estuarine and marine shoreline and intertidal habitats (subtidal marine protected areas are addressed below). These programs are increasingly being applied around the margins of Puget Sound. This strategy addresses PSNERP Management Measure 15, “Property Acquisition and Conservation” (Clancy et al. 2009). The PSP lists the protection of intact lands and resources as a strategic priority in the Action Agenda for Puget Sound (PSP 2008). The Puget Sound Salmon Recovery Plan (Shared Strategy 2007) highlights the importance of permanently protecting existing physical habitat as a key strategy for recovering Puget Sound Chinook (Clancy 2009).

The goal of marine and estuarine shorelines and intertidal protection is to preserve the ecological integrity of shoreline and intertidal habitats for the benefit of fish and wildlife species. It is likely that the highest functioning coastal and intertidal preserves will blend a variety of habitats, from upland forests through scrub or brush patches, beaches and/or rocky coastlines, and into the intertidal zone. At times, this transition distance may be relatively short when it occurs on steeper slopes or it may be much longer if the upland topography is relatively flat and/or the intertidal zone is broad. Clancy et al. (2009) review the variety of acquisition and protection processes as well as the various types of land and resource preservation. They also list the benefits and opportunities created by property acquisition and conservation.

Some of the metrics that could be used to decide what areas should be protected and, subsequently how well they are functioning as protected areas, include: the relative importance or critical nature of habitat types, reserve size, connectivity of migratory corridor, reducing threats to restored areas, andprotecting rare or sensitive species; Several specific property acquisition, protection, and conservation programs are explored further below.

National Estuary Program

The National Estuary Program (NEP), which was established by Congress in 1987 in amendments to the Clean Water Act. Its primary objective is to protect estuaries of national significance that are threatened by degradation caused by human activity. The program is administered by the US Environmental Protection Agency which provides funding and technical support to local NEPs. Local NEPs must be collaborative, locally driven entities that address the complex and competing issues facing the water body14 .

Puget Sound is one of 28 nationally recognized estuaries in the NEP. The PSP Action Agenda is recognized by the NEP as programmatically focused on the same goals for Puget Sound as the NEP is. This EPA program is an important vehicle for federal funding to implement the PSP Action Agenda.

Estuarine reserves

The National Estuarine Research Reserve (NERR) program is designed to provide some level of preservation and protection to local estuaries of significance. There is one NERR in Puget Sound at Padilla Bay in Skagit County, encompassing over 11,000 acres of tidelands and marshlands. The Padilla Bay NERR15 is managed cooperatively by the Washington Department of Ecology and NOAA. While most of the reserve is given sufficient protection to maintain ecological integrity, the NERR does not necessarily provide full protection and preservation, since many non-destructive uses are allowed, as governed by applicable state and federal laws. The various levels of protection are described in the Padilla Bay NERR management plan (Padilla Bay NERR 2008).

Beyond functionally protecting the designated estuary, Reserve staff work with local communities and regional groups to address natural resource management issues, such as non-point source pollution, habitat restoration and invasive species. Through integrated research and education, the reserves help communities develop strategies to deal successfully with these coastal resource issues.Guidance for the possible creation of additional NERRs16 in Puget Sound can be found in several references (e.g., Kennish 2004,).

Regulations for protecting biological integrity

Government agencies and jurisdictions have implemented a plethora of laws, regulations, and guidelines designed to protect natural habitats along Puget Sound shorelines and estuaries. These regulations are targeted at both public and private lands. On private lands the regulations are designed to control the overuse or abuse of natural habitats. They address bulkheads, dredging, filling, docks, and beaches17.

Programs for shoreline adoption, clean up, habitat enhancement and monitoring by citizen groups

Local and regional citizen volunteer groups have created programs for volunteers to help cleanup and maintain Puget Sound shorelines. For example, the Puget Soundkeepers Alliance regularly organizes clean-up days18.

Effectiveness and certainty of estuarine and shoreline protection

Programs and regulatory processes that preserve, protect, and limit access to natural coastal habitats are considered to be among the best possible protection and restoration strategies. This is because they protect the best habitat at what is perceived to be a lower-cost than what it would cost to restore habitat after its damaged (Clancy et al. 2009). However, there apparently is little specific research on the relative effectiveness of habitat protection as compared to restoration. This may be partly because the scientific community generally assumes that undisturbed ecosystems are automatically preferable to alter or restored habitats. Interestingly, there are many examples of species taking advantage of altered habitats such as the explosion of Caspian terns nesting on dredge spoil islands near the mouth of the Columbia River (e.g., USFWS 2005).

With the recent focus on ecosystem-based management of natural resources, there has been an upswing in research attempting to substantiate the connection between healthy critical habitats and species success. For example, several recent papers have explored the connection between the size and critical nature of habitat and the production of the species (e.g., Langton et al. 1996, Langton and Auster 1999).

Marine-protected subtidal areas

Marine protected areas (MPAs) have been applied in various settings around the world to either permanently protect critical and sensitive habitats or to temporarily allow habitat and faunal recovery from over-use. Implementation of MPAs has been viewed as a precautionary management strategy that protects functional attributes of marine ecosystems (Murray et al. 1999). Washington has 127 MPAs managed by eleven federal, state, and local agencies. These sites occur in Puget Sound and on the outer coast and cover approximately 644,000 acres and over six million feet of shoreline (Van Cleve et al. 2009). Twenty-six percent of the state’s marine waters and 27% of the state’s shorelines are included in the boundaries of MPAs (Van Cleve et al. 2009). The locations of many Puget Sound MPAs are shown at Interested parties can also access GIS coverage layers of MPAs at There are also many other de-facto MPAs, such as in marine state parks, Department of Natural Resources submerged aquatic lands, etc. See also, for helpful links to Washington MPAs.Other resources include:

Marine Protected Areas in Washington: Recommendations of the Marine Protected Areas Work Group to the Washington State Legislature

Marine Protected Areas in the Puget Sound Basin A tool for managing the ecosystem

MPAs are variously applied with a range of restrictions, from full protection in some MPAs, to limitations of certain activities in others. These protective measures have been demonstrated to provide excellent benefits by protecting natural areas from destructive overuse and for promoting recovery of damaged benthic habitats. They also support recovery of sessile demersal species or infauna, as well as benthic and demersal territorial fish species. For example, Halpern (2003) found in a review of 89 studies on MPAs that almost all biological metrics improved inside reserves, either compared to before reserve establishment or in comparison to similar areas outside the reserves. It must be noted, however, that whether perceived degradation of marine ecosystems can be reversed via establishment of an MPA may depend on the timescale of interest, and on whether fundamental new ecological processes have taken hold after a disturbance ends (Palumbi et al. 2008).

While improvements have been clearly observed within reserve boundaries (Halpern et al. 2003), the potential effects of reserves increasing dispersal of juveniles and adults to areas outside the reserves are less clear. Modeling results suggest that reserve networks may have the potential to enhance fishery yields under a surprisingly large number of circumstances (Gaylord et al. 2005). In at least one specific study, local dispersion and retention of molluscan shellfish larvae within and near a reserve network enhanced recruitment to local fisheries, although the effects were spatially explicit (Cudney-Bueno et al. 2009). In an Alaskan study of ling-cod, field results supported models indicating that populations increased within reserves and those populations supported increased recruitment to nearby fishing areas (Starr et al. 2004).

Scientific debate has ensued over whether MPAs, as a fishery management tool, result in improved fishery production compared to traditional methods. This is seen to depend largely on the interplay between the 1) target species, 2) nature of the larval, juvenile, and adult dispersal patterns, 3) the longevity and age at first spawning, 4) population abundance structure, 4) size of the reserve, 5) interactions between differentially affected taxa and 6) the length of time the reserve is imposed (Halpern et al. 2003, Botsford et al. 2003, Starr et al. 2004, Ruckelshaus et al. 2009).There are implications that traditional management techniques, such as size limits, seasons, and bag limits, are only partially effective at managing slow growing, late maturing, and territorial species such as rockfish and lingcod (Palsson 2001). Allison et al. (1998) concluded that MPAs were most effective when combined with other, more traditional management tools.

Application in Puget Sound

Several reviews have been done on the extent and implementation of MPAs in Puget Sound (Murray and Ferguson 1998, Palsson 2001, Van Cleve et al. 2009), but none of these are scientifically rigorous studies of their effectiveness. MPAs have been shown to be effective in certain other areas (e.g., Halpern et al 2003) and appear, at least preliminarily, to be effective in Puget Sound. The oldest Puget Sound MPA was established at Edmonds in 1970 and, as of 2001, had 15 times as many copper rockfish, as comparable nearby fished areas (Palsson 2001). Lingcod were also twice as abundant and were 50% bigger on average, than at nearby fished sites (Palsson 2001). Even if reserves are relatively small, they can still have benefits to areas outside of the reserve boundaries. For example, lingcod nests were 3 times as abundant in one Puget Sound MPA than in surrounding fished areas (Palsson 2001). The higher production of the MPA creates a dispersal mechanism to surrounding harvest areas.

Other needs for the best application of MPAs include the incorporation of fishing behavior, such as fishing just outside the reserve boundary (Kellner et al. 2007), into the management scheme that includes MPAs, as well as considerations of vertical zoning in application of MPAs (Grober-Dunsmore et al. 2008). Ultimately, the optimal management schemes, at least for fisheries management, will likely include some combination of MPAs and other management practices (Allison et al. 1998).

Potential Effectiveness of Marine Protected Areas

MPAs embrace the fundamentals of ecosystem-based management by protecting ecosystems or portions thereof (Ruckelshaus et al. 2008). There are numerous scientific analyses of MPA performance to generally support their use in habitat and species protection and restoration (e.g., Halpern et al. 2003), but specific selection, design, and implementation policies should be customized for each situation (Botsford et al. 2003, Roberts et al. 2003). If ecological, social, and economic criteria (Roberts et al. 2003) and potential resilience against climate change (McLeod et al. 2008) are carefully considered for selecting MPAs, they can be viewed as powerful tools among other marine protection and restoration strategies. A significant caveat is that much additional research is needed in both understanding the performance of specific MPAs, relative to their intended biological and/or management outcomes (e.g., White 2009), and in techniques to analyze and predict MPA performance (Pelletier et al. 2008).

Marine Spatial Planning

Marine spatial planning (MSP) is an emerging protection and restoration strategy in that it is a proactive approach for deciding which activities should have priority in certain areas and which activities are compatible or incompatible. Managing human activities to enhance compatible uses and reduce conflicts among uses, as well as to reduce conflicts between human activities and nature, are important outcomes of MSP (Ehler and Douvere 2009). It therefore encompasses decisions about the application of estuarine reserves and MPAs, described above, as well as other marine and estuarine protection, restoration, and development activities.

Well-conducted marine spatial planning can reduce conflicts between users and increase regulatory efficiency, facilitate the development of emerging industries such as wind and wave energy and aquaculture and help maintain ecological processes and the ecosystem services they support (such as fishing, marine tourism and recreation, and cultural uses of the ocean)19.

Coastal and Marine Spatial Planning (CMSP) is a hallmark of President Obama’s Executive Order on a U.S. Ocean Policy (CEQ 2010) and by a number of state, federal, and international marine planning organizations (e.g., Young et al. 2007, Ehler and Douvere 2009a,b, Commonwealth of Massachusetts 2009). The attractiveness of MSP is that it features place-based, integrated management of the full suite of human activities occurring in spatially demarcated areas identified through a procedure that takes into account biophysical, socioeconomic, and jurisdictional considerations (Young et al. 2007).

MSP Application in Puget Sound

MSP has not yet been fully applied in Puget Sound, although one of the action items in the Puget Sound Action Agenda is to “…conduct spatial (mapped) analyses to evaluate current ecosystem status and the primary threats and drivers affecting ecosystem health. Together with models and refined indicators, this work will highlight the location and relative importance of threats and drivers across the entire ecosystem, and help identify the features of Puget Sound that are most at risk” (PSP 2009). While this is not MSP in the fullest sense, this action item will establish a baseline for MSP in Puget Sound. So far, MSP in Puget Sound has occurred through site-by-site planning such as where to locate MPAs or the reservation of certain areas for industrial use or shipping lanes, etc. There is an apparent lack of a specific program aimed at implementing MSP in Puget Sound. There are a number of good models for administratively or legislatively directed MSP programs. For example, Massachusetts has been a leader in implementing a state Ocean Management Plan (Commonwealth of Massachusetts 2009). Another overarching MSP guidance source is the step-by-step guide for implementing MSP (see Intergovernmental Oceanographic Commission 2009).

MSP is a promising strategy for the future health of Puget Sound. Just as in land-use planning, a coordinated, concerted effort to assess and allocate marine and estuarine areas for their optimal use, while protecting the ecological attributes of the Sound. Many of the components and strategies that will support MSP in Puget Sound have been, or are being, organized, such as the Puget Sound Regional Synthesis Model (PRISM)20, the Puget Sound Ecosystem Portfolio Model (PSEPM)21 , and the for Puget Sound Marine Environmental Modeling (PSMEM)22 . While these tools have the potential to support MSP in Puget Sound, they are not yet specifically aimed at MSP.

In addition to the Puget Sound-specific spatial models mentioned above, many specific tools have been developed that can aid the MSP effort in Puget Sound.

MSP planning tools

MSP is an essential strategy for restoring and maintaining a healthy Puget Sound (Handbook item). There are a large number of MSP-specific planning tools already available23,24. There are also ecological, social, and economic criteria for selecting MPAs (Roberts et al. 2003) that can be incorporated into MSP.

Recently, more attention is being paid to the effects of vertical zoning in MPAs (Grober-Dunsmore et al. 2008), but little specific research has been accomplished on this topic. Connectivity is an important planning goal from an ecological perspective for MSP – see Australian CONNIE at Further, when planning for various uses, it is important to account for “edge” effects of users, such as the phenomenon of fishers “fishing the line” along marine reserve boundaries (Kellner et al. 2007).

Ecosystem analysis tools

A number of other ecosystem evaluation and planning tools could also be relevant as aids to MSP. See also

Integrated Ecosystem Assessment model (Levin et al. 2008)

Potential Effectiveness of Marine Spatial Planning

It will be somewhat difficult to asses the effectiveness or degree of uncertainty in the MSP process and, to date, there are no formal processes available for assessment of MSP uncertainty. Belfiore et al. (2006) and Ehler and Douvre (2009) outline a proposed processes for determining MSP effectiveness via establishing and monitoring indicators. Because MSP is a policy-oriented planning process, rather than a specific, physical protection or restoration strategy itself, it is less scientifically rigorous and does not easily lend itself to assessments of certainty in its outcomes. Nonetheless, MSP clearly should be included in any thorough review of marine and estuarine protection and restoration strategies. While the degree of certainty provided by MSP processes is presently undeterminable, the outcomes are clearly linked to correct regulatory decisions in the planning process and the variation in environmental conditions, enforcement of the resultant regulations, marine accidents and spills, etc. Ultimately, indicators are needed to monitor progress of MSP with respect to inputs, activities, outputs, and outcomes. Progress needs to be monitored at all levels of the system to provide feedback on areas of success, as well as areas where improvements may be needed (Belfiore et al. 2006, Ehler and Douvere 2009, Foley et al. 2010).

Ultimately, the evaluation of MSP effectiveness will be determined by whether the Puget Sound ecosystem recovers its basic dynamic ecological functionality, resiliency, and healthy fish and wildlife populations. Recovery potential and/or resistance can differ from place to place within the same marine or intertidal ecosystem (Palumbi et al. 2008). Determining effectiveness will depend on rigorous monitoring programs. Previous analyses of restoration programs have found, by studying such ecological features as species redundancy and complementarity, that recovery, resistance, and reversibility are key components of resilience (Palumbi et al. 2008). Monitoring effectiveness of marine planning has also revealed that the intended ecosystem effects of management plans are not always realized and, in fact, sometimes opposite outcomes are observed (e.g., Pine et al. 2009). There is also a critical lack of modeling tools for evaluating ecosystem-based policies (Pine et al 2009).

Marine and estuarine habitat restoration strategies

A large emphasis of Puget Sound protection and restoration strategies has been placed on physical habitat restoration. Here we discuss the variety of strategies for restoring the physical and ecological function of marine, estuarine, subtidal, intertidal, and shoreline function many of which can be expanded upon in future versions of the PSSU1. Much of the naturally occurring physical habitat in and around Puget Sound has been altered by the variety of human activities. These include diking, dredging, filling, water flow control, bulkheads, jetties, docks, bank hardening, loss of large and small estuaries, blockage of some coastal embayments, shoreline shortening, loss of natural sediment, increased unnatural sedimentation and cumulative effects of all these, as described in the chapter on threats. Shipman et al. (2008) illustrated the goal of some aspects of Puget Sound ecosystem functional restoration.

The goal of physical habitat restoration strategies is to restore connectivity and size of large river deltas, restore sediment input, transport and accretion, enhance shoreline complexity, and enhance habitat heterogeneity and connectivity. The strategies in this section speak strongly to the PSP priority B “Restore ecosystem processes, structures, and functions” and many of the Action Agenda items under that priority (PSP 2009).

Estuarine-specific habitat restoration

There are a number of documents designed to guide creation, restoration, and enhancement of coastal wetlands (e.g., Interagency Working Group on Wetlands, undated). See

Opening dikes and levees to recreate intertidal wetlands

This is Clancy et al. (2009) management measure 3, “Berm or Dike Removal or Modification”. The strategy applies to wetlands that have been closed off by levees, dikes, and channelization. It also is relevant to pocket wetlands along natural shorelines that have been closed off by modifications of beach structure, for habitat details see Shipman et al. 2008.

Eliminating migrational barriers: Hydraulic Modification

(Clancy et al. (2009) management measure 9. This strategy involves opening culverts, tide-gates, or breachways in existing dikes and levees. Hydraulic modification allows water to flow in and out of estuarine areas more naturally and creates opportunities to reduce migrational barriers.

Physical Exclusion

The purpose of physical exclusion is to close recovering natural habitats to human access to speed the recovery process. Physical exclusion applies to beach and shoreline restoration as well as estuarine restoration, but will only be described here.

Topography restoration

Applies to both estuarine and shoreline restoration.

Includes removing hard surfaces and restore natural features at the land/water interface.

Shoreline restoration strategies

This strategy is about restoring beach and coastline function from the effects of armoring, bulkheads, docks, uplands modification, light, noise, and other longshore migrational barriers.See articles in files at PS Gen/shorelines/. Also – from J Lombard 3-1-10: WDFW has posted a new science paper, Protection of Marine Riparian Functions in Puget Sound, Washington: This document was developed to provide shoreline planners and managers with a summary of current science and management recommendations to inform protection of ecological functions of marine riparian areas. It was prepared by Washington Sea Grant for WDFW, with Ecology’s participation and AHG review.)Clancy et al. (2009)also provide an excellent listing of the kinds of restoration activities that apply to shorelines and beaches. The strategies listed below, primarily from their list of restoration measures.

Armor Removal or Modification

  • Beach Nourishment
  • Debris Removal (MM 6)
  • Groin Removal and Modification
  • Overwater Structure Removal or Modification
  • Substrate Modification

Evaluating the effectiveness of physical restoration

Assessing the scientific basis for estuarine, shoreline, intertidal, and subtidal habitat restoration effectiveness is an emerging science. There are several key manuals and guides for "how to" conduct habitat restoration (e.g., Interagency Working Group on Wetlands, undated; NRC 2001, Clancy et al. 2009). However, because extensive habitat restoration has only recently been underway, there are a few long-term, rigorous scientific evaluations of estuarine and shoreline habitat restoration effectiveness.

Some recent scientific work has been targeted at evaluating cumulative ecosystem response to restoration projects (Diefenderfer, et al. 2004, 2009). Thom (2000) noted that it is very common for aquatic ecosystem restoration projects not to meet their goals. Other papers on evaluating restoration:

Thom et al. (2205) addressed uncertainty in coastal restoration projects. They found, for example, that all of the potential sources of error can be addressed to a certain degree through adaptive management.

Submergent restoration strategies

  • Eelgrass and forage fish spawning area restoration
  • Artificial underwater structures
  • Derelict fishing gear removal and recycling
  • Reducing the effects of boat and ship traffic, military activity, and other industrial activity on Puget Sound biota
  • Reducing underwater noise in the Puget Sound


1 Future versions of the PSSU can expand upon topics such as heavy metal sludge disposal, water reclamation, channel rehabilitation or creation, large wood replacement, physical exclusion, revegetation, species habitat enhancement, topography restoration, armor removal, beach nourishment, debris removal, groin removal or modification, overwater structure removal or modification, substrate modification, eelgrass and forage fish spawning area restoration, artifical underwater structures, derelict fishing gear removal and recycling and reducing the effects of boat and ship traffic, military activity and other industrial activity on Puget Sound biota.

2 see and for more information

3 See for more information

4 see and response actions are coordinated with the US Coast Guard (see

5 see


7 see for more details

8 from


















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