The Macalister River flows from Mt Howitt in the Alpine National Park and joins the Thomson River south of Maffra. The river winds its way in a south-easterly direction through mostly forested, confined valleys and narrow floodplains upstream of Lake Glenmaggie. The downstream reaches flow through wide alluvial floodplains that have been cleared for agriculture. The Wellington River and Glenmaggie Creek are the main tributaries of the Macalister River.
Lake Glenmaggie is the major water-harvesting storage regulating the Macalister River, and the Maffra Weir is a small diversion weir located further downstream in Maffra.
The Macalister River and its tributaries continue to be an important place for Traditional Owners and their Nations. The Registered Aboriginal Party (RAP) in the region is the Gunaikurnai Land and Waters Aboriginal Corporation. The West Gippsland CMA engaged with representatives from the RAP during the preparation of the Macalister River seasonal watering proposal.