Due to the close proximity of the Bay of Bengal and the freshwater inflow of Bhagirathi-Hooghly, Diamond Harbour appeared as an important coastal station of the Bhagirathi-Hooghly estuary. The spatial and temporal composition and abundance of microphytoplankton species was examined in relation to physical and chemical surface water variables (i.e.; salinity, nutrient, and temperature).The primary objective of the study was to observe the variations in phytoplankton species assemblages as a response to environmental variables. Hierarchical cluster analysis and non-metric multidimensional scaling were used to find out distinct seasonal groups based on the composition of phytoplankton. The results indicate that several key environmental factors like temperature, DIN content, and molar ratio of nutrients like DIN-DIP and DIN-DSi influenced seasonal phytoplankton assemblages within the estuary. The distribution of phytoplankton population showed two main groups where the blue-green and green algal populations favored the warmer conditions of summer and monsoon months, whereas the diatom population primarily flourished in the cooler months of autumn and winter. © 2010 Springer Science+Business Media B.V.