The Glenelg River is an integral part of the Wimmera-Mallee headworks system, which supplies towns and properties across the western region. Moora Moora Reservoir and Rocklands Reservoir, in the upper Glenelg catchment and three weirs on the upper Wannon River, are all used to divert water from the Glenelg system to the Wimmera catchment. Water for the environment is actively managed in the main stem of the Glenelg River between Moora Moora Reservoir and Rocklands Reservoir and below Rocklands Reservoir. Passing-flow rules are in place for the Glenelg River and upper Wannon River.
The priority reaches of the Glenelg River that can be targeted by environmental flow releases are Moora Moora Reservoir to Rocklands Reservoir (reach 0), Rocklands Reservoir to 5-Mile Outlet (reach 1a), 5-Mile Outlet to the confluence with the Chetwynd River (reach 1b), Chetwynd River to the Wannon River (reach 2) and Wannon River to the tidal extent just below the confluence with Crawford River (reach 3). Water for the environment in the Glenelg system is released from Rocklands Reservoir for reach 1a via the reservoir wall outlet and for reach 1b via the 5-Mile and 12-Mile outlets. Releases are made at these points to meet objectives in these reaches as well as reaches 2 and 3. The Glenelg River estuary benefits from releases of water for the environment to upstream reaches, but releases do not currently target the estuary.
The Glenelg River upstream of Rocklands Reservoir (reach 0) runs mostly through the Grampians National Park and retains significant environmental values. Flows through this reach are affected by the operation of Moora Moora Reservoir and work is continuing in 2019–20 to confirm its flow requirements. Work is also continuing to better understand how environmental releases from Rocklands Reservoir can influence the health of the Glenelg River estuary, which is listed as a heritage river reach and a site of international significance under the Ramsar Convention.