The Skagit system is comprised of the mainstem Skagit and tributaries as well as four secondary river basins: the Baker, the Cascade, the Sauk, and the Suiattle. It encompasses over 3,100 square miles (8,030 square kilometers) of watershed area and 80,728 acres (32,670 hectares) of delta connecting the river to Skagit Bay and Whidbey Basin. The Skagit drainage includes 2,989 identified streams totaling approximately 4,540 linear miles.

Anadromous forms of ten salmonid species, and several more sub-groups or stocks, exist within the Skagit Basin. These include six Chinook stocks (spring, summer, and fall); pink salmon; chum salmon; sockeye salmon; summer and winter run steelhead; sea run cutthroat trout; and Dolly Varden and bull trout.