Understanding the mechanisms that generate organism distribution patterns from the beta diversity perspective can assist in environmental monitoring strategies. In this study, we emphasized the limnic zooplankton due to the ability of these organisms to respond quickly to environmental variations. Therefore, we evaluated the following questions: (i) Do different regions of the same lake have the same importance in contributing to beta diversity? (ii) Do beta diversity and its components vary over the hydrological cycle? (iii) What is the importance of local and spatial predictors in beta diversity and its components? (iv) Do beta diversity and its components show a consistent pattern throughout the hydrological cycle? We found that the contribution of different sites to diversity was more associated with regions with low abundance and richness of organisms values, such as the littoral and igarapes, which shows the relevance of these areas for biological monitoring and for the delimitation of priority areas for the zooplankton diversity conservation. Despite the peculiarities of each hydrological period and regarding beta diversity components, we verified a species substitution and differences in abundance pattern in the lake. We also found low concordance patterns between the periods and low environmental and spatial variables prediction on beta diversity patterns.