Ecosystems generally are not stable over long periods of time and are subject to disturbances of different frequencies and intensities. As a result, natural communities usually are not in equilibrium, and temporal snapshots can show different stages of community assembly. Nonequilibrium is especially common in temporary aquatic systems where desiccation continuously resets the development of communities and hydroperiod is an important determinant of species richness and community structure. We investigated effects of disturbance regime on community assembly of aquatic invertebrates in a cluster of 36 temporary rock pools in central South Africa. Pools were assigned to 4 categories based on their long-term disturbance regime and were sampled 4 times during 1 inundation. Disturbance modulated the relative importance of deterministic and stochastic processes driving community assembly and reduced both α and β diversity. Premature desiccation truncated community development. Initial communities were dominated by resident large branchiopods (fairy shrimp and clam shrimp). Arrival of flying colonists, including many predators, caused a drastic change in community composition and initiated a new successional phase dominated by cladocerans. For residents, the link between local environment and community structure was strongest early during inundation and decreased during community assembly. For flying colonists, variation in arrival time and habitat selection led to a better match between communities and environment later during inundation. We conclude that the combination of colonization–extinction dynamics and niche partitioning in space and time determines metacommunity structure in this extreme type of aquatic habitat.