Abstract This study evaluated changes in the community of rotifers and microcrustaceans associated with the construction of a large and dendritic reservoir in Iguaçu River (Brazil), as the last reservoir of a sequence of five cascading systems. Differences were clear between pre-filling and post-filling phases for organisms and some of environmental variables. In the pre-filling phase, the community was more homogeneous along the downstream river gradient, and spatial compartmentalization in the new reservoir was common during the post-filling phase. From 140 identified taxa, 10 species occurred exclusively in the pre-filling phase and 32 in the post-filling phase. After completion of the fifth reservoir filling-up, opportunistic, pioneer and fast-developing species quickly dominated, and downstream of the fourth reservoir the pre-filling decreasing gradient of richness, diversity and evenness disappeared. Richness of rotifers and cladocerans, cladocerans diversity, and evenness of rotifers, cladocerans and copepods were generally higher in the post-filling phase. A non-metric multidimensional analysis based on a presence/absence matrix depicted a homogeneous and dense group of species associated to the pre-filling phase and a second, dispersed group related to the post-filling phase. Spearman correlations pointed out significant positive effects of transparency on rotifer species richness in the post-filling phase, and negative effects on the microcrustacean richness in the pre-filling phase. Dam construction caused disruption of the downstream lotic gradient along the series of dams, leading to the development of distinct species in lentic spatial compartments.