Abstract There have been few comparative studies of the fauna in the two major types of freshwater systems, lakes and streams, in the one locality. This study compared the faunal assemblages at two times of the year (summer and winter) on stones in three locations: the littoral zone of two shores in Lake Purrumbete (one wave-exposed and one sheltered) and riffles in the Curdies River, which flows out of the lake. The lake fauna was dominated by crustaceans, gastropods and planarians, whereas the stream fauna was dominated by insects. The most abundant lake taxa were also present, but much less abundant, in the stream. The total number of species and individuals and densities of some common species varied between the three locations and between seasons. However, no consistent pattern reflecting a difference between the two lake shores was evident. Interpretation of MDS ordinations of the lake fauna was dependent on the data standardizations applied, with increased separation of the season-location combinations when species were standardized to equal total abundances; the seasonal difference was always greatest for the exposed (cliff) shore. In contrast, MDS on the stream fauna showed seasonal differences under all standardizations. This was consistent with the high seasonal turnover of species in the stream compared with the lake. These results demonstrate that, even within a local area with similar geology and connected water bodies, lake and stream fauna from the same substratum (stones) can be markedly different. Taxa that occurred in both were more abundant in the lake, whereas seasonal differences in abundance were much greater in the stream.