Maipura is a tropical mangrove estuary situated in the east coast of India. It is one of the largest sea turtle rookeries of the world and has a great ecological significance. The seasonal variations of different genera of planktonic algae were observed along with the physico-chemical parameters like DO, BOD, salinity and nutrients viz. nitrogen (nitrate, nitrite, ammonia), phosphorous and silicate of Maipura estuary during November 1998 and August 1999. The analysis of different community structure of these planktonic taxa revealed that the water of Maipura estuary is organically polluted, which may be due to the impact or organic litter of the adjacent mangrove forests. A total of 15 pollution tolerant genera were encountered during the study period belongs to the Classes Chlorophyceae, Bacillariophyceae, Cyanophyceae and Euglenophyceae. It has been observed that the estuarine stations were more organically polluted as compared to the coastal stations.