Sundarban Estuarine System is influenced by periodic tidal input and fresh water inflow. It is surrounded by world’s largest mangrove ecosystem and harbour naturally grown fishery. The total system is intersected by a network of many rivers and creeks. Bidyadhari is one of the major rivers of Sundarbans that is surrounded by human habitation on both banks. The dynamic condition of the river due to tidal inflow and fresh water input which is further increased many folds due to human interventions. In the present study, 26 zooplankton taxa have been recorded where 16 taxa were found perennial in all three seasons. 19 species showed its highest density in the monsoon season, 4 in post-monsoon and 3 in pre-monsoon season. Considering all seasons, Pseudodiaptomus serricaudatus was found to be the most abundant species in monsoon when there was a marked increase in temperature, nitrate, phosphate, silicate and a decrease in salinity, DO, TDS, EC and chlorophyll-a concentration. On the other hand, Acrocalanus longicornis was most abundant during the post-monsoon season when pH, EC, DO, chlorophyll-a were found to be highest and temperature was lowest of all seasons. Only 3 of the 26 taxa were found in highest concentration during pre-monsoon season when salinity was found in highest concentration. The Shannon-Weiner Diversity Index, Simpson 1_D Index and Margalef Richness Index of zooplankton diversity were found highest in station 3 (nearest to the sea) during all the three seasons. Pearson Correlation Analysis showed some significant correlation between different hydrological parameters and zooplankton diversity indices. The result of the study indicates the presence of organic pollutants and eutrophication in Bidyadhari river that demands regular monitoring of water quality for maintenance of long-term sustainability of one the largest naturally grown fisheries in the world.