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Zooplankton exhibit several trends of variation in space and time, and these trends can be more evident in natural environments without anthropic perturbations. Examples of anthropic factors are climate change, eutrophication and construction of reservoirs. This study evaluated the influence of three factors – seasonality, type of environment and the presence of aquatic macrophytes – on various ecological attributes of rotifers in a river-lake system located in the Paraná River floodplain. Monthly samplings were conducted during 1993 and 1994. The mean species richness per sample was 60 species. The seasonality and the type of environment influenced the ecological attributes of rotifer assemblages, while the presence or absence of aquatic macrophytes did not. Species richness was highest in the lake system and during the months when water levels were low. Multivariate analysis indicates a small group of species associated with the low water-level phase. In contrast, many species were associated with high water levels or increasing water levels. The seasonal variation of hydrological cycle and the type of environment are the most important factors for rotifer structure in natural conditions.