We characterized the functional and taxonomic composition of the active and dormant communities from perennial lagoons and temporary ponds in a coastal plain. We sought to determine the degree of coherence between the egg bank and the active community within the same type of environment (temporary or perennial) and between environments subject to different hydrological cycles. We sampled the zooplankton community and environmental variables in six temporary ponds and five perennial lagoons in the dry and the wet periods of the hydrological cycle. Temporary ponds and perennial lagoons differed in abiotic conditions, with higher values of dissolved carbon in temporary ponds and higher values of salinity in perennial lagoons. The taxonomic coherence between active and dormant communities in temporary environments was greater than in perennial environments. In functional terms, we observed a high coherence between active and dormant communities for both types of environments. Our results highlight the need to conserve both temporary and perennial environments to assure the maintenance of zooplankton diversity. Although these environments are subject to the same set of climatic variables and pool of species, their idiosyncrasies are important forces promoting and sustaining biological diversity.