The giant ostracods Mytilocypris occupy temporary saline habitats in Australia and experience physical and chemical heterogeneity in association with evaporation. Three sympatric species, namely M. mytiloides, M. tasmanica chapmani, and M. minuta, show high genetic similarity and morphological boundaries that overlap. The large elongate, intermediate, and small blunt shells of the three species are associated with lakes of low, intermediate, and high salinity, respectively. The present study investigated whether all three phenotypes were produced through time in single habitats experiencing seasonal changes in physical and chemical properties. Three lakes at one site (Coorow) were temporally heterogeneous, showing a nearly 10-fold increase in salinity in a single season, whereas four lakes at a second site (Rottnest Island) were more or less permanent and showed less environmental variation. Successive generations in the lakes from Coorow became smaller and blunter in association with environmental changes, showing the range of phenotypes displayed in the three presumptive taxa. There was less phenotypic response in individuals from Rottnest Island, reflecting the relative homogeneity of the lakes. Possible mechanisms underlying the observed changes include phenotypic plasticity, genotype replacement, and strong selection.