Two major structures regulate flow on the Thomson River: Thomson Reservoir — the largest water supply storage for metropolitan Melbourne — and Cowwarr Weir — a regulating structure which supplies irrigation water to parts of the Macalister Irrigation District.
Thomson Reservoir harvests most of the flow from the Thomson River upper catchment and has a significant effect on flow in all downstream reaches. Unregulated flows from the Aberfeldy River, which meets the Thomson River downstream of Thomson Reservoir, are essential for providing natural freshes and high flows in the Thomson River.
Water for the environment is held in the Thomson Reservoir and released into the river as required. 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, high-value native riparian vegetation, high-quality in-stream habitat and low abundance of exotic fish species.
At Cowwarr Weir, the Thomson River splits into the old Thomson River course (reach 4a) and Rainbow Creek (reach 4b) (see Figure 2.3.1). Passing flows throughout the year are split two-thirds down reach 4a and one-third down 4b to avoid impacts to irrigators located on Rainbow Creek. Water for the environment is primarily delivered to the old Thomson River course (reach 4a) to support fish migration, because Cowwarr Weir impedes fish movement through Rainbow Creek.