Deepwater Slough is a major distributary channel of the Skagit River system, the largest estuary in Puget Sound, and is well known for supporting all five native salmon species, a large wintering bald eagle population, and critical winter habitat for geese and swans. The slough is flanked by two islands that support approximately 450 acres of diked farmland and managed wetland. Freshwater and estuarine wetlands in this area experienced extensive ditching, diking, and filling associated with agricultural development in the late 1800s through the early 1900s. Previous restoration efforts have restored 200 acres of the historic estuary and the proposed restoration would completely remove all remaining dikes around each of the two islands. This action would allow unrestricted tidal freshwater flows and would create rearing habitat for salmon as they move through the Skagit River Estuary.

Phase 1 of the Deepwater Slough project was constructed in 1999 and 2000. The project restored tidal and riverine influence to 235 acres of previously isolated habitat. Funding for the project was obtained through the US Army Corps of Engineers Section 1135 program. Currently the Deepwater Slough Phase 1 project is being monitored for effectiveness of the restoration and fish use.

If recovery goals are still not being achieved after the ten-year time horizon the WDFW will come under increasing pressure to restore the remaining habitat at the Deepwater Slough site. This would likely involve the complete removal of levees around each of the two lobes left after the first Deepwater project.