The Kowmung River is located in the Hawkesbury–Nepean catchment. Most of the 80-kilometre stretch of the Kowmung River lies within Kanangra-Boyd National Park and the lower reaches of the river lie within the Blue Mountains National Park.
The river and its catchment have been the site of natural resource use and major mining and forestry proposals, but the protection of most of the catchment by the Kanangra-Boyd National Park has helped overcome these disturbances. Most of the river was considered to meet the criteria to be declared a wild river. The condition of its biology was very good and although modifications to the catchment and waterways by weed invasion and siltation from upstream had occurred they were considered in good health. It is expected the condition of the river and its catchment will continue to improve over time.