Estuaries are the mixing zones between fresh and salt waters. Tidal mouths of streams and rivers are estuaries, but so is the larger Puget Sound. Estuaries are characterized by smaller sediments that are carried in from terrestrial runoff and subsequently carried out by tidal influences, often creating large mud flats or surrounded by sandy beaches. Estuaries in their natural states are highly productive ecosystems and are characterized by highly diverse plant and animal communities since they are the transition zones not only from fresh to salt water environments but also from terrestrial to aquatic habitats too. These are vital habitat zones for migrating salmon as they serve as nurseries for very young fish, the gateways to and from the sea, and the place where the fish physiologically change to adapt to and from fresh/saltwater both as juvenile fish migrating out to sea and again when they return as adults to spawn in the rivers/streams.

Historically, some estuaries have been altered to decrease tidal influence by creating dikes, sea walls or tide gates and by filling upper intertidal areas with landfill. This was usually done to allow these lands to be utilized for agricultural or residential purposes. Many of these efforts resulted in creating only marginal working or living landscapes, areas that may be better served over the long run to be returned to their natural states.

Estuary restoration projects seek to restore natural function to estuaries. Often this entails removal or setback of dikes and fill materials to restore tidal influence. These projects are designed to enhance or restore salt marshes, tidal channels and other features that are highly valuable for out-migrating salmonids as well as other aquatic and terrestrial organisms.
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This large-scale initiative seeks to restore and enhance habitat forming freshwater and marine processes to the critical estuary reach of one of Hood Canal's most productive and diverse salmon producing watersheds. This reach includes the freshwater channel, floodplain, and estuary downstream of SR101 (with some analyses listed here also assessing upstream reaches). Actions include multiple Level 3 projects such as reach analyses, levee setbacks, riprap removal, woody debris placement, riparian enhancements, and saltwater dike removal. The majority of these actions occur in partnership with Washington State Parks within the Dosewallips State Park.

Historically, the salt marsh complexes around the mainstem and distributary channels of the Dosewallips River were large, complex, and interconnected, though anthropogenic impacts have served to fragment these complexes and diminish their ability to support salmonids.

A series of projects in the Dosewallips Esturine Salt Marsh will seek to restore fish access to a major blind tidal channel known as Sylopash Slough while restoring its ability to maintain quality fish habitat. Up to 1000 feet of a levee system will be removed on the salt marsh face to restore tidal prism and native salt marsh vegetation.

Wolcott Slough Restoration initiative seeks to restore tidal inundation to a large estuarine complex in the Dosewallips Estuary. Fish habitat and fish access are currently diminished by a series of anthropogenic impacts resulting from landfill, undersized culverts, concrete spillways in the antiquated USFWS fish trap, and decreased riparian habitats. Function in the western lobes of Wolcott Slough would be improved with enlargement of the culverts under Highway 101.