The river is 140 kilometres long and, along with the King River, drains into Oyster Harbour. The lower 9 km of the river take the form of a drowned river valley with steep hillsides of forest and farmland, and the occasional outcrop of granite . The river's source is west of the Stirling Ranges. It rises north-west of Kendenup and flows generally southwards until it reaches Oyster Harbour about 10 km north-east of Albany.

The River near Kamballup between the Porongurups and the Stirling Range
The lower section of the Kalgan River is tidal; a rockbar at the Upper Kalgan bridge separates the upper section from the tidal lower section. The tributaries of the Kalgan River include Napier Creek, Boonawarrup Creek, Young River, Stony Creek and Gaalgegup Creek. The river flows through two pools of note: Meriwarbelup Pool and Noorubup Pool.