The Karnali River Basin, well-known for intense monsoon rainfall and unstable, steep slopes, experiences high rates of soil erosion, landslides and sediment loads in rivers and tributaries. This river basin has the lowest mean annual rainfall among major five river basins. The West Seti River and the Bheri River are the main tributaries of the Karnali River. Minor tributaries include the Kawari River and the Tila River. Natural disasters, such as flooding, seriously disrupt local livelihoods by damaging agricultural production and destroying infrastructure, and other assets. The Government of Nepal has been supporting a number of different projects in the Karnali River Basin, including the Nepal Flood Resilience Program, irrigation schemes (e.g., Rani Jamara Kulariya Irrigation Scheme), Karnali River Corridor Management Project, Upper Karnali Storage Dam Project, and Karnali Chisapani Multipurpose Project, among others.
The Karnali River Basin's lakes, wetlands and tributaries provide habitats for 197 fish species belonging to 32 families and 92 genera. Five endemic species can be found in Karnali River Basin, including the critically-endangered Schizothorax nepalensis and Schizothorax raraensis, which were located in Rara Lake (2,990 masl). The basin also provides habitat for 50 migratory species and 24 species currently on the IUCN Red List for conservation