Temporary ponds are unpredictable habitats that exhibit inundation periods of variable duration (hydroperiods). We hypothesised that changes in microcrustacean assemblages, namely among ponds (spatial variation) and within ponds at a monthly scale (intra-annual variation), would differ according to hydroperiod length. We found that the microcrustacean assemblages of the study ponds demonstrated distinctive individual patterns that were dependent on monthly variation. During pond filling, species turnover was particularly high in short-hydroperiod ponds, probably due to the fast hatching of the initial pool of species, which seemed to determine subsequent species succession. Some of the long-hydroperiod ponds were able to hold water during the summer, which meant that they could harbour adult microcrustaceans in the early autumn, in contrast to the recently filled ponds; species turnover could thus increase at the onset of the inundation cycle. In the summer, species turnover decreased (while the contribution of nestedness to b-diversity increased) because only a few tolerant species were able to withstand the poor water quality found in drying ponds. We suggest that preserving the broader hydroperiod gradient, by protecting ponds with different environmental conditions within each hydroperiod category, would safeguard the ecological dynamics of the microcrustacean assemblages found in temporary ponds.