<p>Understanding phytoplankton beta diversity is crucial to maintaining ecosystem health and biodiversity in Niger State reservoirs, particularly in the face of increasing anthropogenic pressures. Despite its importance, the environmental factors influencing this diversity remain inadequately explored. This study therefore investigates the relationships between phytoplankton beta diversity and various environmental variables in ten reservoirs across Niger State, Nigeria. Sampling was conducted twice per hydrological cycle (once in wet and once in dry season) from June 2019 to March 2021, evaluating physical and chemical parameters alongside phytoplankton composition. A two-way ANOVA was used to assess the spatial and seasonal variation in environmental conditions, while Canonical Correspondence Analysis (CCA) was used to explore the relationships between phytoplankton assemblages and environmental variables. Physical and chemical analyses revealed significant differences across reservoirs, with conductivity, total dissolved solids, and pH showing notable seasonal fluctuations. A total of 226 phytoplankton taxa were identified, with Ochrophyta dominating. This study reveals that phytoplankton beta diversity in Niger State’s reservoirs is driven by environmental heterogeneity and hindered by spatial connectivity, exhibiting seasonal variations in alpha diversity and reservoir-specific differences in beta diversity. The complex interplay between environmental factors, nutrient fluctuations, and connectivity emphasizes the need for continuous monitoring and targeted management to conserve biodiversity and ensure ecosystem resilience in these critical freshwater ecosystems.</p>