Clean and abundant water is essential for a healthy river. Threats to water quality and quantity include; diversion to supply hydroelectricity generation and irrigation; diversions for Canberra and the region; drought; possible climate change and pollution. Increased sediment load from the clearing of the Cooma‑Monaro plains is an ongoing issue. Water from urban areas may also affect water quality.

One of the goals of the project is to better understand flow requirements of species in the reach.