Summary1. Hydroregime (duration, frequency and predictability of the aquatic phase) is a key feature of temporary aquatic habitats that not only moulds community structure and diversity (species sorting) but also life history characteristics of the inhabitants (natural selection). However, since hydroregime is a complex multidimensional entity that cannot be estimated from short term observations, morphometric variables are commonly used as proxies for hydroregime, making it impossible to separate effects of habitat size and hydroregime on biota.2. We have used a simple hydrological model, validated with recent (average r2 = 96%) and historic water level observations (average r2 = 81%), to accurately reconstruct hydroregime based on historical rainfall and evaporation data in a cluster of 36 temporary rock pools in central South Africa.3. Using the model output, we demonstrated that both hydroregime and habitat size had unique and shared effects on temporary pool biota and that these effects depended on the dispersal modes of the taxa. Model-generated hydrological data explained more variation in community patterns than short-term observations of hydroperiod. Hydroregime was more important for passive dispersers than for active dispersers that can migrate when pools dry up. Basin morphometry was a relatively poor predictor of pool hydroregime. We concluded that simple modelling may greatly improve the resolution of studies linking hydroregime to biological variables.4. An accurate account of hydrological variation provides a firm foundation to understand community and population structure and dynamics in temporary aquatic habitats. Since many of these habitats have been destroyed or degraded in recent decades, our findings and tools may contribute to the development of reliable conservation guidelines.