The present study verified how hydrological regime affects the temporal variability of zooplankton communities in floodplains. Multidimensional methods were employed to characterise community variability, and the temporal trend of the community was also evaluated using a matrices comparison procedure. In connected ponds from the main river, the absence of floods (drought) modified the variability of the zooplankton community by increasing temporal dissimilarity of community. In these environments, the periodic input of water due to floods maintained a lower variability of environmental characteristics, sustaining a lower temporal variability of the community. This observation suggests that, in floodplains, flooding is a component of the system that assists with both the maintenance of ecological processes (temporal variability of the community) and the high biodiversity of these environments. This study therefore suggests that the temporal variability of communities in floodplains is increased by extended droughts, and emphasises the importance of flood dynamics to maintain temporal stability of zooplankton communities in river floodplain systems.