The Thomson River flows from the slopes of the mountains of 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. A new environmental entitlement in the Thomson system which will provide an additional 3.9 percent of Thomson Reservoir inflows per year will become available for the first time in 2017–18. This extra environmental water will help meet more of the environmental flow objectives for the Thomson River and will provide benefits to native fish including Australian grayling, tupong and Australian bass.
Reach 3 of the Thomson River (from the Aberfeldy River confluence to Cowwarr Weir) is the highest priority for environmental watering due to its heritage river status, relatively intact native riparian vegetation, high-quality instream 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 River course to enable fish migration, as Cowwarr Weir prevents migration through Rainbow Creek. The passing flows are split two-thirds down reach 4a and one-third down 4b throughout the year to avoid impacts on Rainbow Creek irrigation customers.