The aim of this study was to provide a first-hand water quality assessment of the River Nyong estuary, Southern Atlantic coast of Cameroon. Environmental variables and phytoplankton communities were monitored at four surface stations in the estuary for 2 season cycles from 2014 to 2015. A total of 208 species of phytoplankton, belonging to five (5) groups of microalgae, were identified. The ShannonWeaver diversity index showed a qualitative seasonal difference in composition of the phytoplankton community. Dissolved nutrients (nitrogen and phosphorus) values showed seasonal fluctuations throughout the sampling period. A ratio appeared high (42.78) in the rainy season and low (5.89) in the dry season, two values corresponding to the change in specific richness (high and low respectively during the major rainy season and the small dry season). The Water Quality Index (WQI) showed that water quality fluctuates from good to bad, in conjunction with biological indicators (Shannon-Weaver, Abundance and Specific richness).