The Skagit River is the largest tributary to Puget Sound and is home to ten salmonid species, including Chinook salmon that were listed as threatened under the Endangered Species Act in 1999. Chinook smolts rely on estuaries for food and protection as they transition from fresh water to salt water. The Skagit delta has lost approximately 85 percent of the historic estuary; in 2005 the Skagit River Chinook Recovery Plan identified estuary habitat as an important limiting factor for recovery.

A key challenge with estuary restoration in the Skagit delta is that the areas most important for Chinook are also some of the most agriculturally productive farmland in the world. Local farms can support up to 80 different crops varieties and are a major worldwide producer of vegetable seeds. However, much of the farmland is sub-tidal and reliant on a complex system of dikes and drainage infrastructure.