Differences in the composition of ecological communities among rivers with contrasting flow regimes have been detected in many regions worldwide. However, we know little of how climatic variation alters these spatial patterns for constituent species with varying dispersal modes and strengths. We predicted that beta diversity (spatial variation in composition) of macroinvertebrate and fish assemblages among streams with near-perennial, mildly intermittent and highly intermittent flow regimes would be greater during prolonged drought than under wetter climate conditions. We hypothesised that changes in beta diversity between these climate phases would be greater for taxa with stronger dispersal ability. We tested these predictions with biomonitoring data from Australian subtropical rivers. Differences in average community composition among flow regimes were statistically significant for six groups of macroinvertebrates with differing dispersal (non-swimmers, weak swimmers, strong swimmers, non-fliers, weak fliers and strong fliers) and two groups of fish (potamodromous and diadromous), but not for locally dispersing fish. For each of these biotic groups, shifts in assemblage composition between supra-seasonal drought and a subsequent non-drought period were either statistically non-significant or of similar magnitude among flow regimes. Therefore, beta diversity among flow regimes did not change significantly with climate phase. Beta diversity within flow-regime classes was greater during the drought than afterwards or not significantly different between climate phases, depending on the flow regime and biotic group. Stronger powers of flight were associated with greater change in beta diversity between climate phases in near-perennial streams, but stronger powers of swimming were not. Within-regime beta diversity was driven more by replacement of taxa among samples than by nestedness, except for diadromous fish in near-perennial streams. Our findings are consistent with the hypothesis that decreasing hydrological connectivity and greater environmental heterogeneity during prolonged drought increase beta diversity of stream communities. However, changes in beta diversity between climate phases were not as pronounced as we expected. The communities may have been somewhat drought resistant because the magnitude and duration of the drought were within the range of historical variability and because surface water persisted at study sites during drought-imposed flow cessations. Our findings suggest that maintenance of refuge pools will be critical to lessening drought impacts on river biodiversity at landscape scales, particularly if drought duration and intensity increase in the future.