Until 1906, the Green River flowed into the White in downtown Auburn. In 1906, however, the White River changed course above Auburn following a major flood and emptied into the Puyallup River as it does today. The lower portion of the historic White River—from historic confluence of the White and Green Rivers to the historic confluence with the Black River at Tukwila that forms the Duwamish—is now considered part of the Green River. Then, with the opening of the Lake Washington Ship Canal in 1916, the lake's level dropped nearly nine feet and the Black River dried up. From that time forward, the point of the name change from Green to Duwamish is no longer a confluence of rivers, though it has not changed location. Thus, the Green River now becomes the Duwamish River, flowing into the industrialized estuary known as the Duwamish Waterway and thence Elliott Bay in Seattle. By contrast, the White turns south at Auburn, and flows into the Puyallup River and later Commencement Bay in Tacoma.

Most of the river above and including Eagle Gorge Reservoir are part of the Green River Watershed, which is closed to public access, creating controversy among recreation proponents for some time. West of the Green River Watershed at Kanaskat, the river passes through the Green River Gorge with cliffs rising sharply as much as 300 feet from the riverbed. Flaming Geyser State Park, Nolte State Park, and Kanaskat-Palmer State Park are located in this area. The river is a popular tubing spot in the Summer. Downstream from the Green River Gorge is the half-mile wide Green River Valley, where farmland has been protected from development.  At Auburn, the Green River emerges from the Green River Valley and enters the much larger Auburn/Kent Valley, which was created by glacial action during the Pleistocene ice ages, then filled in by river sediments and lahars from Mount Rainier. After flowing generally west from its source, at Auburn the river turns north, entering a zone of light-industrial and retail development.