It rises at the edge of the Darling Scarp and flows in a north-westerly direction across the northern part of the Blackwood plateau to the confluence of the Capel River North and Capel River South, near Goodwood.

The original inhabitants of the Capel basin were the Noongar Aboriginal people of the Wardandi dialect group.

The lower reaches of the Capel were of cultural importance for the Wardandi because they buried their dead there.

An artificial river mouth was cut through the sand dunes adjacent to the Stirling Wetlands in 1880 to allow it to flow directly into Geographe Bay.

The inaugural 2009 Ranger Outdoors Capel Descent[9] was held in June 2009, consisting of a 15-kilometre (9 mi) part down river, part open ocean paddle along the Capel River and Geographe Bay.