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 priority river reaches for environmental flow delivery in the Werribee system are the reach downstream of Lake Merrimu (reach 6), the reach within Werribee (reach 9) and the estuary. These support a diverse range of native fish species, waterbugs and platypus. Flows targeting the estuary are expected to provide some benefits to reach 8 and water may also be delivered for environmental objectives in this reach under suitable conditions. Environmental water released from Lake Merrimu can be reharvested in Melton Reservoir, minus en route losses. It can then be held and re-released from Melton at a later date to achieve environmental objectives in the lower Werribee River. Flows are measured downstream of Lake Merrimu (reach 6), downstream of Melton Reservoir (reach 8) and at the Werribee Diversion Weir for reach 9 and the estuary.