Phytoplanktons are free-floating microscopic plants in water and they are the primary producers providing food to aquatic organisms. However, water quality affects the species production and assemblage in terms of diversity, composition, and abundance. This study assessed the spatial and temporal diversity and abundance of phytoplanktons in the Gusii wastewater treatment plant. A total of 124 phytoplankton species were identified and belonged to six families: Euglenophyceae, Bacillariophyceae, Dinophyceae, Cyanophyceae, Chlorophyceae, and Zygnemophyceae. The phytoplankton biovolume was 385.24mm3/L, with the family Euglenophyceae contributing the largest percentage. The species diversity index (H’) was generally low (H’ = 1.759 and 0.7596) in the effluent and influent respectively, indicating a considerable increase in diversity as the wastewater undergoes treatment. The low diversity was attributed to changes in physical, chemical, and biological environmental conditions. The effluent was richer in species, with a value of 5.829, while the influent was the least with 3.409. The low phytoplankton diversity in the wastewater treatment plant was influenced by the physicochemical parameters. It is therefore recommended that the quality of the wastewater during treatment needs to be monitored continuously for quality as baseline information to guide stakeholders and to ensure sustainability for the Gusii wastewater lagoon ecosystem health.