The distribution and abundance of biota in an aquatic environment is generally influenced by environmental parameters. This study was carried out to assess the relationship between environmental parameters and phytoplankton distribution in Lekki lagoon, Sub-Saharan Africa. Phytoplankton and environmental data were obtained from nine stations in three replicates each from January to December, 2016. The relationship between phytoplankton and environmental data was assessed through multivariate analysis using PRIMER v₆ Software. A total of thirty-seven (37) species from six (6) divisions were recorded which included Chlorophyta, Bacillariophyta, Cyanophyta, Charophyta, Ochrophyta and Euglenophyta. Chlorophyta appeared to be the most diverse division with 14 species, while Ochrophyta was represented by a single species. The highest number of individuals (25809 ind/ml) and species (21) was observed in Station 3, while Stations 8 and 1 ranked least in terms of number of individuals (10038 ind/ml) and species (14) respectively. The nine stations formed two non-significantly (p>0.05) different clusters based on the phytoplankton community and were strongly correlated with transparency, nitrate and total suspended solids combined. The model that best explained the pattern of distribution of phytoplankton among the stations included depth, conductivity, dissolved oxygen, biological oxygen demand, total dissolved solids and total suspended solids. The findings showed that distribution of phytoplankton is influenced by a complex of environmental parameters especially those related to light and nutrient availability.