Background In reservoirs, zooplankton strongly interact with the physical and chemical characteristics of water, and this interaction is mainly influenced by climate variation and the different methods used to manage the dam water level. Therefore, the aim of this study was to evaluate how the distinct operating modes of two cascade reservoirs affected the richness, abundance, and composition of zooplankton, both spatially (intra and inter-reservoirs) and temporally (annual and seasonal). In this study, the upstream reservoir (Salto Santiago) operates using the storage method, with a water retention time (WRT) of 51 days, whereas the downstream reservoir (Salto Osório) operates using the run-of-river method, with a WRT of 16 days. Methods Zooplankton samples were collected for 16 consecutive years from the two reservoirs located on the Iguaçu River, Brazil. A total of 720 samples were collected. Four-way ANOVAs were used to determine the differences in richness and abundance of the zooplankton among years, periods, reservoirs, and environments. Multidimensional non-metric scaling (NMDS) and an analysis of similarities (ANOSIM) were used to describe similarity patterns in species composition. Finally, a canonical correspondence analysis (CCA) was used to select the environmental predictors that best explained the variation in zooplankton abundance data. Results We identified a total of 115 taxa in this study, and rotifers were the richest group. In contrast, the copepods were the most abundant. The four-way ANOVA results showed significant differences in the species richness and abundance of the zooplankton among years, periods, reservoirs, and environments. The NMDS ordination and ANOSIM test indicated that the largest differences in zooplankton species composition were annual and seasonal differences. Finally, the CCA showed that these differences were mainly associated with changes in water transparency, temperature, and the chlorophyll a, phosphorus, and total dissolved solids concentrations. Discussion Inter-annual changes in zooplankton species composition showed that over time, large filters-feeders (e.g., large daphinids and calanoid copepods) were replaced by small cladocerans (e.g., bosminids) and generalist rotifers. The highest species richness was associated with the fluvial environment, whereas the highest abundance was associated with the transitional and lacustrine reservoir environments. Variations in water temperature, nutrients, and food availability explained the annual and seasonal changes in community structure, whereas variations in the water flow characteristics of the environments explained the longitudinal changes in the richness and abundance of zooplankton in reservoirs. The differences in zooplankton structure between the two reservoirs can be explained by the functional differences between the two systems, such as their WRTs and morphometrics.

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