Investigations were carried out on spatial and seasonal composition, distribution and abundance of phytoplankton in Adjin lagoon located in south-eastern of Côte d'Ivoire. Samples were collected at six stations during the four seasons in 2013 year. Freshwater inflow from Bété, Djibi and Mé Rivers influenced the variability of nutrients concentration in this lagoon. From a seasonal point of view, the parameters studied are significantly affected by freshwater inputs during the rainy season. This period is characterized by high values of turbidity, suspended solids and nutrients in the water. Overall, 66 taxa from six phyla were recorded. The Chlorophyta had the highest species diversity and Cyanobacteria had the highest relative abundance throughout the year. The temporal distribution of phytoplankton showed that the highest values of density were recorded in the long rainy season and the lowest values in the long dry season. Spatially, the highest abundance (297,927 × 10 3 cells•L −1 ) of phytoplankton was found in station 3 and the lowest (74,222 × 10 3 cells•L −1 ) in the station 5.