Summary Future moderate changes in evaporation and precipitation regimes could have pronounced effects on zooplankton populations in small and temporary aquatic habitats, by causing higher salinity and a shorter wet phase and by reducing passive dispersal via hydrological connections between pools and increasing it by exposing propagules to the wind. Using a hydrological model, we simulated various climate change scenarios in a natural cluster of temporary rock pools in South Africa. In our simulations, a shift towards a drier climate was associated with reduced permanence and increased conductivity, resulting in a lower percentage of inundations sufficient for the hatching, growth and reproduction of aquatic organisms (up to a 21% decline for a fairy shrimp). Connections between pools by overflowing occurred less frequently (by up to 28%). However, more frequent desiccation events (by up to 15%) led to increased exposure of dormant propagules to wind, possibly promoting dispersal within the pool cluster but also leading to losses from the propagule bank. Our results suggest that environmental change might not only affect local (within‐pool) selection pressures but also regional dynamics in rock pool metapopulations and communities.