A pattern of increasing similarity among ecological communities in space or time is usually a consequence of anthropogenic pressures. However, natural causes such as flood pulse may also increase spatial similarity among lakes or temporal similarity within a lake. We assessed whether floods homogenize zooplankton and macrophyte assemblages in space and time using a 16 years data set obtained in six lakes in the Upper Paraná River floodplain. The spatial changes in beta diversity were tested by comparing assemblages in pairs of lakes located close to each other, while the temporal changes in beta diversity were tested by comparing assemblages of the same lake over time. We did not find lower spatial beta diversity for macrophytes or zooplankton during floods. In contrast, we found lower temporal beta diversity for aquatic macrophytes and littoral zooplankton among flood events. We did find the re-colonization of a similar set of species at each flood event as opposed to drought events for littoral species. On the other hand, for pelagic zooplankton, a diverse regional species pool and the arrival of zooplankton from littoral zones probably resulted in stochastic colonization in the different lakes, and thus less similar community composition during floods. We highlight the importance of explore simultaneously spatial and temporal beta diversities in complex and dynamic ecosystems such as floodplains, because the same event (i.e., flood or drought) may drive different community patterns across space or time.