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.