The Swan River estuary flows through the city of Perth, in the south west of Western Australia. Its lower reaches are relatively wide and deep, with few constrictions, while the upper reaches are usually quite narrow and shallow.

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 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.