Shell shape varies markedly in freshwater mussels in the order Unionoida, with shells of the Australian unionid family Hyriidae varying in size and shape, beak and surface sculpture, hinge dentition, growth lines, erosion of the periostracum and the colour and thickness of the nacre. Freshwater mussels belonging to the genus Velesunio (Family Hyriidae) are distributed widely in the rivers and wetlands of Australia. Molecular evidence suggests there are at least three more species within the genus Velesunio than previously described using shell morphologically. Morphological differences in shell shape between the species are difficult to detect and differences appear to differ between drainage basins. This study explored differences in shell morphology between and within two major drainage basins within Australia, the Murray-Darling Basin and the Lake Eyre Basin. For all species there were significant differences between basins and rivers within basins, however for shells from the Lake Eyre Basin differences in shell morphology between sites was low. In comparison greater species level differences in shell morphology were observed at the site scale in the Murray-Darling Basin. Although both drainages are essentially ‘dryland’ systems with highly variable flows, the 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 water conditions. Thus, the level of difference in shell morphology between sites may reflect local hydraulic variability rather than large scale flow variability