Global loss and human-induced degradation of wetlands are presumed to impact waterbirds. To understand how human activities and habitat features drive waterbird species composition, there is need to understand beta-diversity and its components of turnover and nestedness. We identified and evaluated some potential drivers of waterbird beta-diversity across limnetic habitats domiciled within the catchment of the Warri River in southern Nigeria. First, we tested the prediction that beta-diversity would be driven by nestedness and turnover components. Second, we evaluated the impacts of habitat attributes on variations in waterbird beta-diversity. Linear models were used to assess the variation of waterbird abundance across season, pollution status and habitat types. We used Permutational Multivariate Analysis of Variance (PERMANOVA), redundancy analysis and variation partitioning to evaluate patterns of waterbird beta-diversity across season, pollution status and habitat types to see which factors influenced beta-diversity. A total of 2946 individuals belonging to 43 species of waterbirds were recorded, while the mean abundance of waterbirds across predictors showed significant variations (p < 0.05). Overall waterbird diversity was influenced by the turnover component of beta-diversity, while the nestedness component was negligible. PERMANOVA models associated with indices of turnover were very robust as they accounted for most variations in the configuration of waterbird community. Variations in seasonality, habitat type and pollution status generated species turnover within the habitat and as such increased spatial diversity. These predictors are important drivers of waterbird communities at this scale. Thus, management plans that integrate protection of wetland networks and aim at biodiversity conservation must be implemented.