The Bunyip River rises below Mount Beenak, part of the southern portion of the Yarra Ranges within the Bunyip State Park, near Tomahawk Gap, and flows generally south by east then south, at times via an aqueduct, joined by four minor tributaries, before reaching its confluence with the Tarago River to form the Main Drain. From there the river used to flow into the Koo-Wee-Rup Swamp, the largest wetland in Victoria, covering an area of , before flowing into Western Port. The river descends approximately over its course.