Important freshwater systems found in arid areas range from springs to waterholes and rivers. Periods of extreme aridity in the Pleistocene, especially during the last glacial period, resulted in the drying of most freshwater systems apart from a few permanent water holes and artesian springs. The present composition of the freshwater molluscan fauna reflects this history and is a mix of recent recolonisers and relictual taxa. A database of 5,047 records of freshwater molluscs was compiled from museum records for continental Australia and interrogated for the purposes of examining distributional trends for inland arid and semi-arid Australia. Endemism and species richness were examined at species, genus and family level. Of the 125 species-group taxa included in the analysis, 42 (33.6%) are narrow-range endemics (occupying three or fewer 10 km² grid squares. Of these endemics, 33 (78.6% of the narrow range endemics and 26.4% of the remaining taxa are found only in artesian springs associated with the Great Artesian Basin. In addition to molluscs, these springs contain many other indigenous aquatic invertebrates and fishes and several rare or indigenous plants. A few large permanent waterholes also contain endemic taxa. Most molluscs found in intermittent waters adopt strategies to avoid desiccation or to facilitate dispersal and are generally widely distributed. The presence of molluscan and other (fishes, turtles) endemics in some large arid zone waterholes suggests that those habitats may have persisted through the last glacial. The continued existence of many of these habitats, and thus their inhabitants, is under threat from human activities relating to water use and modification of habitats.