The Macalister River flows from Mt Howitt in the Alpine National Park to join the Thomson River south of Maffra. The river meanders in a south-easterly direction through predominantly forested, confined valleys and narrow floodplains upstream of Lake Glenmaggie to cleared, wide, alluvial floodplains downstream. The Macalister River is regulated by Lake Glenmaggie, the major water-harvesting storage and Maffra Weir, a small diversion weir located further downstream in the Maffra township. Both storages divert water for irrigation, urban and industrial purposes. Environmental water is stored in Lake Glenmaggie.
Before Lake Glenmaggie was built, the Macalister River would regularly receive high and medium flows in winter and spring. Although Lake Glenmaggie regularly spills, these flows are now less common as they are harvested by the storage. A notable impact of irrigation and water harvesting is reversed seasonality of flows between Lake Glenmaggie and Maffra Weir, where summer flows are higher than natural due to the delivery of irrigation water. Winter flows are lower-than-natural because a high proportion of the inflows are harvested. Downstream of Maffra Weir, most flows are diverted for irrigation in summer and autumn. The changed hydrology restricts fish migration, limits the growth and recruitment of in-stream and riparian plants and reduces the quality of in-stream habitat.
Maffra Weir is a major barrier to fish movement and environmental flows that target migratory fish objectives mainly focus on reach 2, which is downstream of the weir. All other objectives apply to both reaches 1 and 2.