The early reaction of the plankton communities to environmental changes makes it a useful tool for monitoring the pollution of aquatic environments. Lake Azili is a small water body, the majority of which is strongly influenced by river Ouémé during the floods time. Its ecosystem is one of the most important for the country, due to its rich biodiversity, especially that of halieutics. By following the evolution of its health, due to the strong anthropological pressure, this study aims to estimate the structure and the dynamics of its planktonic biodiversity and to assess its current state. It was carried out for seven months between May to November, 2012, according to the hydrological seasons of Benin. Plankton samplings were monthly, taken in a vertical sense from the lake, from all depths, using plankton net. The diversity indices were calculated for the compartment of zooplankton, that of phytoplankton being a preliminary evaluation. A total of 51 species of phytoplankton and 36 zooplankton species were inventoried. Instability is observed in the seasonal structure of both communities, especially for the period of transition between the floods and the floods recession. Due to the specific composition and the diversity, the ecosystem of Lake Azili is perturbed.