The Capel River is located in the South West region of Western Australia, rising in the Darling Range east of Mullalyup and flowing approximately 32 kilometres in a north-westerly direction before emptying into Geographe Bay at Peppermint Grove Beach. With a catchment basin of 653 square kilometres, it is the largest river in the Geographe catchment. The river forms at the confluence of the Capel River North and Capel River South near Goodwood, and crosses the Bussell Highway near the town of Capel. An artificial river mouth was cut through the sand dunes adjacent to the Stirling Wetlands in 1880 to allow direct flow into Geographe Bay.

The most documented paddling route is a roughly 10-kilometre return trip graded at Grade I, accessed from Mallokup Road, Capel. This access point sits just upstream of a weir, which maintains water levels year-round and makes the route viable across seasons. The trip duration is approximately two hours. Paddling upstream from Mallokup Road, the first three kilometres pass through relatively open farmland, offering a pleasant winding paddle. At the three-kilometre mark the river forks; taking the right fork (when facing upstream) leads past the Capel Vale winery and continues approximately two kilometres to the Bussell Highway bridge. This upper section narrows and becomes fairly shallow, with a few minor logs to negotiate. Beyond the Bussell Highway bridge, extensive fallen trees and brush block further upstream progress, and the river becomes too shallow and narrow to paddle. The route requires no portages and no shuttle, as paddlers return downstream to the Mallokup Road put-in.

The river's aquatic habitat includes dense woody debris of various sizes, overhanging banks, submerged macrophytes including ribbon weed, and overhanging roots. Native fish species recorded in the river include nightfish, western pygmy perch, and freshwater cobbler, though introduced redfin perch are also present. The Capel River has also been used for organised paddling events, including a 15-kilometre descent combining river and open ocean paddling along Geographe Bay, first held in June 2009.