The Thomson River flows from the slopes of Mt Whitelaw on the Baw Baw Plateau to join the Latrobe River south of Sale. The major tributaries of the Thomson River are the Aberfeldy, Jordan and Macalister rivers, with most unregulated flows originating from the Aberfeldy River.
Environmental water in the Thomson system is held in Thomson Reservoir. Reach 3 of the Thomson River (from the Aberfeldy River confluence to Cowwarr Weir) is the priority for environmental watering due to its heritage river status, relatively intact native riparian vegetation, high-quality in-stream habitat and low abundance of exotic fish species.
At Cowwarr Weir, the Thomson River splits in two and water can move down the old Thomson River course (reach 4a) and Rainbow Creek (reach 4b). The preference is to pass environmental water down the old Thomson course to enable fish migration, as Cowwarr Weir prevents migration through Rainbow Creek.