The first stocktake of biodiversity in the river basin identified 473 native freshwater species including four mammals, 88 waterbirds, 126 freshwater associated birds, four reptiles, 20 amphibians, 40 fishes, 50 invertebrate species and 141 vascular plants.

At least 10 species – equivalent to 2% of total species – are on the International Union for Conservation of Nature list of threatened species. Three – the ningu, singida and Victoria tilapia – are “critically endangered”, threatened by the introduction of non-native fish such as the Nile perch.