The freshwater snail Potamopyrgus antipodarum has become a model system for studying invasion ecology, host–parasite coevolution, the maintenance of sexual reproduction and ecotoxicology. One understudied aspect of this snail is the variation in morphology within and among populations, which could provide insights into ecological differences across its native range. In this study of 17 New Zealand lake populations of P. antipodarum we used linear measurements and geometric morphometrics to compare several aspects of shell size and shape. We found that, except for those from Lake Te Anau, most lake populations of P. antipodarum differ slightly in shape, but differ significantly in size and in the presence of spines, where larger and spinier snails are found in deeper regions. These striking distinctions in size and shell armature, but not in shape, suggest that the various components of form are under different selective regimes. Snails from Lake Te Anau are different in both shape and size, implying that this population is diverging from the rest of the species in multiple ways, making it an interesting study population for further research.