The Rapid River originates at , at Grouse Lake and at on the west slopes of Jove Peak on the crest of the Cascades, east of the Beckler River. The latter source flows through Lake Janus—at —before meeting the Grouse Lake source creek, whereafter the river continues southwest. An early tributary comes from high Dow Lake, southwest of Union Pass and Union Peak, also on the Cascade crest. The Pacific Crest Trail follows the crest and parts of the high Rapid River basin. Both Jove and Union peaks are on the high crest of the Cascade Range, separating the Rapid River's drainage basin from the Little Wenatchee River drainage to the east. While the waters of the Rapid River ultimately empty into Puget Sound those of the Little Wenatchee enter the Columbia River via the Wenatchee River.