The Macalister River flows from Mt Howitt in the Alpine National Park to join the Thomson River south of Maffra. It mostly flows through cleared floodplain that is used for dairy farming. Lake Glenmaggie is the single major storage and supplies water to the Macalister Irrigation District, with flows regulated at Maffra Weir. Environmental water is stored in Lake Glenmaggie.
Before Lake Glenmaggie was built, the Macalister River would regularly receive large floods in winter and spring. Although Lake Glenmaggie regularly spills, floods are now less common. A notable impact from irrigation and water harvesting is reversed seasonality of flows between Lake Glenmaggie and Maffra Weir, where higher-than-natural summer flows occur due to the delivery of irrigation water. In the same reach, flows are lower-than-natural in the water harvesting period in winter. Downstream of Maffra Weir most flows are diverted for irrigation in summer and autumn. The changed hydrology affects the migration of fish as well as the growth and dispersal of aquatic and riparian plants.
Maffra Weir prevents fish passage from upstream and downstream of the weir and the priority reach for fish migration flows is therefore reach 2 which is downstream of Maffra Weir to the confluence with the Thomson River. Non-fish objectives can be achieved in both reaches 1 and 2 (see below).