beta-Diversity can be driven by different factors, and it is necessary to understand how the characteristics of communities contribute to biodiversity. We investigated composition patterns and taxonomic and functional beta-diversity, in addition to determining the possible processes driving the beta-diversity of zooplankton in 42 lakes, distributed in two regions with distinct rainfall patterns, a semiarid and a humid region both in the Brazilian Northeast. Environmental heterogeneity was higher in the semiarid region. The species composition was different; however, taxonomic and functional beta-diversity did not differ between regions. These data sets showed that although the composition was distinct, the change in species and traits occurred similarly. Taxonomic and functional beta-diversity were driven by environmental factors. They showed a predominance of niche assembly and the importance of abiotic variables in the selection of species and traits. In our case, the dispersion limitation did not influence beta-diversity. Species are deterministically filtered, and each region imposes a distinct environmental filter that selects them. Due to the limited studies on the partition of functional beta-diversity and the uncertainty of ecological patterns for intermittent environments, more scientific research is required that considers this approach for dry regions and over longer time periods.