The Samish River is a small independent drainage entering Samish Bay at the northern boundary of the WRIA 3. The Samish watershed encompasses approximately 123 square miles of mostly lower elevation terrain. The lower Samish River occupies a portion of the larger post-glacial and presettlement Skagit River delta floodplain. The Samish Salmon Hatchery is located at river mile 1.3 on Friday Creek, the largest tributary of the Samish River.

The Samish River supports coho, chum, steelhead, and cutthroat and hatchery produced fall Chinook. About 1,100 acres of Samish Bay's tide flats are currently farmed for commercial production of shellfish: primarily Pacific oysters, Manila clams, mussels and geoduck