ABSTRACTShell shape varies markedly in freshwater mussels in the order Unionoida. Freshwater mussels belonging to the genus Velesunio (Family Hyriidae) are distributed widely in the rivers and wetlands of Australia, with recent molecular evidence suggesting at least three more species within the genus Velesunio than previously described using shell morphology. This study explored differences in shell morphology between and within two major Australian drainage basins: the Murray–Darling and Lake Eyre. Differences in shell shape among the species were difficult to detect with variability in morphology, showing the greatest difference between drainage basins. For all species, there were significant differences in morphology between rivers within basins; Shells from the Lake Eyre Basin, showed small differences in shell morphology among with greater species level differences in morphology at the site scale in the Murray–Darling Basin. Extreme flow variability of Lake Eyre Basin rivers means they spend considerable time as lentic waterholes. In contrast, the rivers of the Murray–Darling Basin, while still highly variable, spend a far greater time under flowing conditions. Thus, the variability in shell morphology among sites may reflect local hydraulic variability rather than large-scale flow variability.