Near shore surface water (0.5 m) of an estuarine station along eastern Indian coast was studied for the first time to understand the seasonal composition, distribution and assemblage patterns of micro phytoplankton in relation to different environmental variables. Regular samplings at bi weekly intervals for micro phytoplankton and water samples were carried out for a period of 2 years (July 2007-June 2009). Implementation of multivariate procedures like principal component analysis and multi dimensional scaling allowed us to enumerate the regulatory role of environmental variables in seasonal micro phytoplankton succession. The habitat water was slightly alkaline with variations in salinity from 4 to 17 psu. 25 micro phytoplankton taxa were recorded during the study period, with green algal dominance in summer and diatom dominance in winter. Seasonal changes in abundance and the diversity of micro phytoplankton population differed significantly, showing maximum diversity in autumn and minimum in winter. Species richness ranged from 7 to 16 with low inter annual variations. The study area represented a habitat where nutrients were optimally present with low micro phytoplankton cell counts. Distinct seasonal succession pattern was prevalent in the study area where nutrient concentrations, temperature and salinity played deterministic roles in regulating seasonal micro phytoplankton assemblages. © 2013 The National Academy of Sciences, India.