The biosphere is undergoing an epidemic of human-caused extinctions. They greatly exceed background extinction rates, overstepping planetary boundaries for marine and terrestrial biodiversity loss. This destruction of wildlife abundance and reduction in range occupancy has been termed ‘the great thinning’. Multiple lines of evidence (e.g. numbers of threatened species on the IUCN Red List, the Living Planet Index) reveal that endangerment of freshwater biodiversity is greater than on land or in the sea: charismatic species such as the Yangtze River dolphin have become extinct; large fishes, amphibians and pearly mussels (Unionidae) are also at particular risk. Many Red List species classified as ‘Data Deficient’ may well be endangered. High levels of local endemism and species turn-over among freshwater bodies increases global biodiversity, but means they are not substitutable in terms of their species complements. Some fresh waters (e.g. ancient lakes such as Tanganyika) are hyper-diverse with many endemics. In in the case of Asian peatswamps, further degradation would result in species losses, a significant influence on the global carbon balance and on climatic warming.