The Swan River drains the Avon and Swan Coastal catchments, which have a total area of about 121,000 km². The Avon River contributes the majority of its freshwater flow. The climate of the catchment is Mediterranean, with mild wet winters, hot dry summers, and the associated highly seasonal rainfall and flow regime.

The Avon River rises near Yealering (pronounced Yellering), 200km southeast of Perth: it meanders nor'nor'west to Toodyay (Toojay) about 90km northeast of Perth, then turns southwest: in the Walyunga National Park, at the confluence of the Woorooloo Brook, it becomes the Swan River.

The Canning River rises not far from North Bannister, 100km southeast of Perth and joins the Swan at Applecross, opening into Melville Water. The Swan and Canning rivers are salt water tidal rivers; Melville Water is their estuary which might have been purposely designed for sailing of almost every description. Blackwall Reach is narrow and deeper, leading the river through Fremantle Harbour to the sea.

The Noongar believe that the Darling Scarp is said to represent the body of a Wagyl - a snakelike being from Dreamtime that meandered over the land creating rivers, waterways and lakes. It is thought that the Waugal created the Swan River.

While the Swan River has not been dammed, two of its tributary rivers - the Helena River and the Canning River - have been dammed for collection of water supplies, at Mundaring Weir and Canning Dam.

The estuary is subject to a microtidal regime, with a maximum tidal amplitude of about one metre, although water levels are also subject to barometric pressure fluctuations.