Phytoplankton diversity, their abundance based on flow cytometric (FCM) analysis and seasonal nutrient dynamics were investigated from a waste water fed wetland of Eastern India (88° 24.641′E and 22° 33.115′N). The primary objective of the study was to correlate the seasonal fluctuations in phytoplankton abundance to the environmental variables. Total chlorophyll content and FCM based cell counts were used to characterize and quantify the phytoplankton population. Multivariate statistical methods were employed in predicting the possible relationships between biotic and abiotic variables. Distinct seasonal variations characterized by high abundance during the pre-summer period compared to other seasons were detected. The results indicated that environmental factors like water temperature and nutrients, such as various forms of nitrogen and phosphate, influenced the seasonal phytoplankton accumulation. Cluster analysis and non-metric multidimensional scaling helped analyze the seasonal distribution of phytoplankton based on their composition. The dominant genera among the entire phytoplankton community were Scenedesmus spp. of Chlorophyta, followed by Merismopedia spp. of Cyanoprokaryota. Around 3.7 × 105 phytoplankton mL−1 were recorded during the study period. Due to the very high count of individual species in the community, FCM based counting was applied for determination of Species Diversity Index. The entire population was divided into 13 subpopulations based on the cell sorting method and the seasonal abundance in each sub-population was illustrated.