The Werribee River flows south-east from the Wombat State Forest near Ballan before dropping through the Werribee Gorge to Bacchus Marsh and then flowing into Port Phillip Bay at Werribee. The Lerderderg River is a major tributary that joins the river at Bacchus Marsh. The main storages in the Werribee system are Pykes Creek Reservoir, Melton Reservoir and Merrimu Reservoir.
The Werribee River and its tributaries continue to be a place of significance for Traditional Owners and their Nations. The Registered Aboriginal Parties (RAPs) in the Werribee River area are the Wathaurung Aboriginal Corporation (on the western side of the Werribee River) and the Wurundjeri Land and Compensation Cultural Heritage Council Aboriginal Corporation (on the eastern side of the river in the upper catchment).