Thomson Reservoir harvests most of the flow from the Thomson River upper catchment and has a significant effect on flow in all downstream reaches. Natural flow from the Aberfeldy River, which meets the Thomson River below Thomson Reservoir, is 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 streamside 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 system map). 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.
The Heyfield wetlands is a cluster of several pools located between the Thomson River and the township of Heyfield. Due to the construction of levees and weirs along the Thomson River, natural wetting of river waters to the wetland rarely occurs; and while the largest pool receives stormwater from the Heyfield township, smaller ponds rely on rainfall or pumped water for the environment to maintain environmental values. These values include significant revegetation that has been done in recent years.