Water flow management has significantly changed the natural dynamic of floods, which are responsible for the structure and dynamic of aquatic communities in river-floodplain systems. With the aim to elaborate a conceptual framework that describes the main ecological factors associated with zooplankton community structure in the Upper Paraná River, we investigated the mechanisms that regulate the communities structure and their response to inter-annual and hydro-sedimentological variations in the floodplain and the biological factors associated with species abundance in those communities. For this we conducted samplings every six months (potamophase in March and limnophase in September) to characterize intra and inter-annual variations in community structure between 2000 and 2008. The intra-annual differences on the species richness, abundance, Shannon diversity index, and evenness, were conducted using Bayesian procedures to show probabilistic predictions of the data fit to main variation sources. Non-metric multi-dimensional scaling (NMDS), multi-response permutation procedure (MRPP), and indicator species analysis (IndVal) were run to assess and characterize the seasonality of the community structure. During high water (potamophase), hydrologic connectivity favoured exchange and dispersal of species in some lakes, increasing local diversity; during low water (limnophase), higher local productivity favoured opportunistic taxa, increasing species dominance and decreasing local diversity. Food resources and density of small-size fish were biological factors associated with the seasonal dynamic of the zooplankton community; these factors were dependent on hydrosedimentological phase (potamophase or limnophase). Water levels and limnological modifications related to water flow management have promoted replacement and impoverishment of aquatic biota in affected lakes and have indicated the ecological importance of a natural dynamic flood, which displays regular flood pulses. The conceptual model presented encompassed interactions between diverse environmental variables to more understandable mechanisms of the main sources of community variation.
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