The Barham River rises as the West Branch of the river in the Otway Ranges near Marriner Ridge and flows generally south then east before reaching its confluence with the East Branch of the river near the locality of Paradise.

From there, it flows directly east to its mouth at the town of Apollo Bay and empties into Bass Strait, north of Cape Otway.

From its highest point, the river descends 481 metres (1,578 ft) over its 16-kilometre (9.9 mi) course.

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