The Green-Duwamish River basin has been modified significantly since settlement of the area. Urbanization in the lower basin has influenced water quality and diversions for municipal and industrial water supply have altered the stream flow of the Green-Duwamish River. Groundwater has been developed for consumptive use within the basin. The White River originally had a confluence with the Green River near Auburn but since 1906 it has been diverted into the Puyallup River. A dam on the Black River near Tukwila prevents water from the Green River from flowing into Lake Washington during periods of high flow. In 1913 the city of Tacoma commenced diversions for municipal and industrial uses. Since 1962 the Green-Duwamish River has been influenced by the operation of the Howard A. Hanson Dam, a Corps of Engineers flood control project with authorization to provide instream flow maintenance of at least 110 cfs for fisheries conservation purposes. The operation has also considered drinking water quality requirements of the city of Tacoma.

The Green-Duwamish River basin is a natural rearing and spawning area primarily for steelhead trout and chinook, coho and chum salmon. Fish hatcheries are located on tributary streams and these contribute to total numbers of fish produced by the river system. The river itself and the shoreline also offer easily accessible recreational opportunities.