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Puget Sound is a deep inlet of the Pacific Ocean in Washington, extending south from the Strait of Juan de Fuca through Admiralty Inlet. It was explored and named by Captain George Vancouver for his aide, Peter Puget, in 1792. The ninth Puget Sound Update, from the Puget Sound Action Team reports that:

"the Puget Sound has biological resources which include all of the living organisms which inhabit the marine waters and shorelines. These biological resources are plankton, invertebrates, fish, birds, mammals, and aquatic vegetation, including species that are either residential or migratory." The abundance of creatures and foliage allowed for the native peoples of the area to thrive and prosper by harvesting it. Many of the problems of the Puget Sound originated from explorers and trappers hunting and killing the indigenous species off of which the natives thrived and prospered. In the past 30 years there has been a large recession in the populations of the species which inhabit the Puget Sound. The decrease has been seen in the populations of: forage fish, salmonids, bottom fish, marine birds, harbor porpoise and orcas. This decline is attributed to environmental issues in Puget Sound. Because of this population decline, there have been changes to the fishery practices, and an increase in petitioning to add species to the Endangered Species Act (ESA). There has also been an increase in recovery and management plans for many different area species.

Puget Sound, Washington is a body of water lying east of Admiralty Inlet, through which ocean waters reach inland some 50 mile (80 km) from the Pacific Coast to complex and intricate system of channels, inlets, estuaries, embayments and islands. Industries in this area include aerospace, military, biotechnology, fishing, electronics, computers, forest products, marine industries, telecommunications, transportation and other commerce industries. Due to improper storage methods for dangerous chemicals, such as arsenic, areas of soil and aquatic land in Puget Sound are being managed under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). Standards for the storage and discharge of industry chemicals have improved, and Puget Sound remains vital to the industries that depend upon it, such as shipping ports. Ports in Washington are diverse. Governed as municipalities, the ports operate shipping terminals, marinas, docks, and associated infrastructure, such as roads, railroads and parks. The fastest growing part of Washington ports is industrial development.

The Puget Sound region has been rapidly growing. According to the Puget Sound Regional Council (PSRC), a board that plans for growth in the four central counties of the area (Kitsap, Pierce, Snohomish and King counties), the combined population of these counties was nearly 3.4 million residents in 2003. Times have changed since the 1970s, when a billboard in Seattle read "the last person to leave Seattle please turn out the lights". Between 1970 and 2000, the Puget Sound region's population increased by 1.3 million people. The 12 county Puget Sound region, including Seattle and Tacoma, has quadrupled to four million people since the 1950s, and the state predicts one million more residents by 2025. The PSRC predicts that between 2000 and 2020 the region will increase by 1.7 million people. Another change the region faces involves the demographics of its population. The segment of its population ages 65 and older is projected to increase by 150 percent, making up 17 percent of the total population by 2040. Under the Growth Management Act (GMA), local governments plan, coordinate and manage for growth in Washington, while protecting natural resources and public interests. The GMA requires local governments to develop long term comprehensive plans for land uses in their jurisdictions. Plans must be coordinated with surrounding counties and be approved by a regional board. Finally, as part of the GMA, local governments must address sensitive fish and wildlife areas through Critical Area Ordinances (CAOs).

Hood Canal is a fjord off the Puget Sound. Hypoxia is a low oxygen condition occurring in Hood Canal. One overriding factor of this is the underwater topography of the canal. While the shallowest part of the canal is its entrance, where the ledge, or sill, of the canal measures only 150 feet (46 m) deep, the deepest parts of the canal are more than 600 feet (180 m) deep. The Hood Canal Dissolved Oxygen Program (HCDOP) and the United States Geological Service (USGS) are studying Hood Canal circulation, trying to model the tidal circulations and salinity distribution patterns between the canal and Admiralty Inlet. Other factors that, when combined with the constrictive shape, could also influence hypoxia in Hood Canal are:

Pacific Ocean marine water may be entering with a lower oxygen content than historically received. Marine water may be entering at a density lighter than needed to flush out Hood Canal quickly or effectively. Riverine freshwater input has changed—increased or decreased—altering the stratification (water) of Hood Canal marine life. Organic material input may have increased. Light input may have increased (algae growth increases with light, as well as organic nutrient input). Wind currents may have altered water column circulation (Atmospheric circulation). The picture surrounding hypoxia in Hood Canal is complex; research models point to more than one contributing factor: Nutrient level. Nutrient level is a large issue due to the human impact. The supply of nutrients, primarily nitrates, to the euphotic zone is thought to impact levels of dissolved oxygen. Nutrients feed algae, which under the right conditions, "bloom" and then die and decompose; the entire process requires a large amount of oxygen. This decreases the oxygen in the water column, lowering the dissolved oxygen level. This is a threat to the biodiversity of marine wildlife as it degrades/damages the marine habitat. Due to high amounts of excess nutrients and water disturbance, there are fewer number of benthic invertebrate species found near CSO outfalls. One of the nutrients found in excess amounts is Nitrogen, which can cause low oxygen level. Many fishes and shellfish can be affected by some pathogens that are naturally found in the Puget Sound. High turbidity can decrease light penetration which can decrease food sources for fishes. If the turbidity is high enough it can kill fishes and/or affect reproduction and growth. For example, heavy metal buildup can cause physiological and reproductive harm. For example, lead in river otters and spotted sandpiper affect their reproduction. Furthermore, build up in pollutants has been found to affect fish growth.

King County, Washington, US, has two plans to help improve CSO impacts on the environment: CSO Long term Control Plan and the Integrated Plan Alternative. The purpose of the plan is to reduce pollutants entering the water. It has suggested three methods: (1) increasing the number of streets that are swept; (2) build a water quality facility in South Park to remove pollutants; and (3) maintaining existing rain gardens and/or natural drainage systems. Changes in the oceans kelp have direct effect on other species. This is particularly due to the unique three dimensional habitats that the plants provide for invertebrates, fish, birds, and mammals. Widespread loss of kelp throughout Puget Sound would have repercussions for the marine ecosystem as a whole. Research has shown that eelgrass beds in Puget Sound can be found in two different habitats: flats, which can be described as either large, shallow bays or small "pocket" beaches, and fringe beds along steep shorelines. During low tide, eelgrass beds shelters other small animals from extreme temperatures, and in tideflats the beds act as a sponge for moisture. In eleven embayments there was almost of eelgrass lost between 1995 and 2004.

60% of the ground fish populations are currently considered, by the areas scientific community, to be in acceptable or good conditions. The populations which are in decline are: middle trophic level predators such as rockfish, spiny dogfish, Pacific cod, and hake.

There was a spawning decline for copper and quillback rockfish of close to 75% between 1970 and 1999; more recent data shows a continued decline. Many rockfish species which are popular to harvest in the area are showing large population decreases, while less popular species are showing signs of increased population.

There are over 100 species of marine bird which rely on the Puget Sound as habitat. A survey completed by the Western Washington University (WWU) reports that the total number of marine birds in the Puget Sound is decreasing. The cause of this decrease in population is not clear, although researchers suspect likely causes such as pollution, non native species, and collisions with man made structures, abandoned or lost fishing gear, some fishing practices, unavailable food sources, and loss of habitat. One of the factors that contribute to declining salmon runs in Puget Sound, and the Pacific Northwest in general, is the lack of logjams in rivers. Logjams are essential to the survival of healthy salmon populations. Logjam and river current interaction carve deep pools into riverbeds, providing salmon and their young, also known as fry, with hiding places from predators. Logjams also force some of the water from the main river to spill out over the adjacent Floodplain, forming Tributaries along the river, which supply ideal habitat for maturing salmon. The natural processes of spawning and reaching maturity become much more difficult for salmon without the services logjams provide. Also, as the organisms that salmon feed on begin to dwindle due to factors including overfishing and invasive species, salmon are further threatened as their food sources become precarious, as is the case with herring populations around Puget Sound (Puget Sound Action Team). For more information see Salmon conservation. The increased urbanization around streams connected to the Puget Sound has led to the annual increase in premature (adult salmon who have not yet spawned) spawner mortality rates. The exposure to metals and petroleum hydrocarbons which originate from motor powered vehicles in the urban area, have led to the recurring fish kills. Salmon that transition from saltwater to freshwater are vulnerable to the toxic substances found in the urban streams.

"Nearshore" is most commonly defined as the backshore, intertidal and shallow subtidal areas of shoreline. In Washington, for example, the Shoreline Management Act defines the upland edge of this area to be 200 feet (61 m) behind the shoreline. Many groups also consider the nearshore to go fairly deep beyond the intertidal zone. More than 10,000 streams and rivers drain into Puget Sound. Approximately 1800 mile (2897 km) of shoreline surround the estuary, which is a mosaic of beaches, bluffs, deltas, mudflats and wetlands. A number of factors have been listed as potentially contributing to continued degradation of the nearshore environment. These include changing the nearshore by adding artificial structures, such as Tide gates and bulkheads increased pollution from various sources, such as failing septic systems; and various impacts from agricultural and industrial activities. One third of more than of Puget Sound shoreline has been modified by some form of human development, including Armoring, Dredging, filling and construction of overwater structures.

Aquatic nuisance species are non native plants or animals that threaten the diversity or abundance of native species; the Ecological stability of infested waters; or the commercial, agricultural or recreational activities that depend on such waters. In recent years, the Puget Sound has seen an increase of invasive species, specifically from Japan, as early as 1971. Invasive species have come to the Puget Sound via several factors, including aquaculture, importation of live seafood, shipping (attached to ship hulls and through ballast water), research and academic institutions, deliberate introductions, pet stores and public aquaria, and natural dispersal. The Japanese wire weed Sargassum muticum and the marine grass Spartina are currently two of the most damaging species. In response to such trends, ocean species have migrated to places they shouldn't. The Puget Sound has the most introduced invasive species. Nationwide, about 400 of the 958 (42 percent) species listed as threatened or endangered under the ESA are considered to be at risk, primarily due to competition with and predation by non native species. The WDFW is now attempting to combat its exotic species problem with the Washington State Aquatic Nuisance Species Management Plan. Under this plan, Washington State Patrol Commercial Vehicle Inspectors search incoming vessels for harmful invasive species, such as the zebra mussel, and decontaminate the vessels before they can spread the organism. The city of Olympia, Washington has worked with the United States Environmental Protection Agency to use the shells of invasive water snail which has started to decrease the numbers of the endemic Olympia Oyster. The invasive arched slipper limpet (Crepidula fornicata) shell is taken and, packed into the sidewalk. With doing so, the shells of the said invasive species of water snail will slow down the runoff and will reduce the flow of stormwater which will in turn reduce flooding and potential environmental damage. Walker says that "The scoop shaped shell of the snail could help slow storm water. Currently the city uses rock and gravel beneath sidewalks to stabilize the concrete. City officials want to try using snail shells instead." The millions of snail shells could act as micro reservoirs slowing the flow of stormwater and reducing the chances of city streams, brooks, and waterways. Emmett Dobey, the program manager at Olympia’s Department of Public Works says, "The process also seemed to reduce the amount of pollutants that typically come along for the ride".

Since 1989, there have been 225 oil spills in Puget Sound. Nearly every day Puget Sound imports 550,000 barrels of unrefined oil, thus making Puget Sound one of the country's primary centers for refining petroleum. One such spill on October 14, 2004 in Dalco Passage leaked nearly 1,000 gallons over Vashon and Maury Islands.

The Washington state government has adapted the federal government's Marine Protected Area (MPA) system into designated Aquatic Reserves, defined as "aquatic lands of special educational or scientific interest or lands of special environmental importance that are threatened by degradation". Aquatic Reserves are meant to serve as aquatic versions of national parks or sanctuaries. Through the Aquatic Reserve Program, the DNR hopes to control these areas in an effort to restore, preserve or enhance habitats and species that directly tie into the aquatic ecosystem. The first Aquatic Reserve created under the program was at Maury Island in November 2004. Further candidate sites under review include Cherry Point, Fidalgo Bay and Cypress Island.

Pollution advisories are posted for some of the beach areas on the Puget Sound. These advisories warn the public of health concerns due to contact with sand and water of the posted areas. Showering after contact with material from these areas is advised. It is also advised to avoid eating fish and shell fish from these areas.