||— This study aims to assess seasonal and temporal changes in phytoplankton composition in Lake Ahémé. To achieve this, phytoplankton samples were collected in Lake Ahémé from September 2014 to September 2016. A total of 274 species were inventoried and the composition of algae includes Bacillariophyceae, Chlorophyceae, Cyanophyceae, Euglenophyceae, Conjugatophyceae, Trebouxiophyceae, Chrysophyceae, Dinophyceae, Xanthophyceae and Ulvophyceae. Bacillariophyceae were more abundant during the long wet season, the short dry season, and the long dry season, while Chlorophyceae dominated during the short wet season. The two-way analysis of variance (ANOVA) revealed significant seasonal variations in water physicochemical parameters such as conductivity, temperature, Total dissolved solids, pH, salinity, dissolved oxygen, turbidity, phosphates. Changes in phytoplankton structure were analyzed through similarity analysis (ANOSIM) and revealed that the heterogeneity observed in the spatial and seasonal distribution of phytoplankton of Lake Ahémé is linked with the dynamic of water inputs (freshwater, saltwater, nutrients). Redundancy analysis (RDA) revealed that phytoplankton community assemblages are mainly driven by two environmental gradients, one of anthropogenic origin, where the most influential factors were phosphates and DO. The second gradient is related to temperature, conductivity, and salinity.