Abstract Both β diversity and metacommunity structure vary in time and space. It is necessary to examine different scales, especially in the face of extreme hydrological conditions. We investigated seasonal variation in β diversity and Elements of Metacommunity Structure [EMS] of zooplankton during four years (two years of prolonged drought and two years with extreme flood events) and at two spatial scales (sub‐basins and floodplain; smaller and larger spatial scale, respectively). We sampled 29 lakes quarterly during four years in the Upper Paraná River floodplain, Brazil. We estimated the replacement component of β diversity using the Jaccard dissimilarity index. We also used EMS to determine the metacommunity pattern of zooplankton distribution in each period and spatial scale. The flood peak observed in the snapshot sampling drove the homogenization of zooplanktonic assemblages. However, β diversity was not reduced in the two years with extreme flood events compared to the period of prolonged drought at either of the spatial scales (floodplain and sub‐basins), except for a single sub‐basin. This finding shows the importance of longer‐term ecological studies to better capture the dynamics of the zooplanktonic metacommunity. Regardless of the hydrological period and spatial scale zooplanktonic metacommunity structure remained practically constant throughout the four years, with a predominance of species range turnover (Clementsian). At the smallest spatial scale (sub‐basins), we found quasi‐structural patterns (quasi‐Clementsian and quasi‐Gleasonian). The predominance of the Clementsian pattern suggests that the associations of zooplankton species in the floodplain responded similarly to the environmental gradient and that the responses differed among species groups. Over time, the smaller spatial scale (sub‐basin) better represents the dynamics of β diversity than the larger spatial scale (floodplain), and better represents the structure of the zooplankton metacommunity. However, we emphasize the need for further studies to consider different biological groups and larger spatial scale over time to maximize the understanding of aquatic metacommunities dynamics.