Abstract: Phytoplankton are the major source of primary production in water bodies. But, due to increased anthropogenic pressures in the coastal waters, there is a gradual decrease in the population of this biological resource. In the present study, multivariate statistical methods including principal component and cluster analysis were applied to surface water quality data sets obtained from Vellar Estuary, Parangipettai, Southeast coast of India. Studies on physicochemical and biological parameters were made during August 2008 to July 2009. Totally 45 species representing different classes namely Bacillariophyceae (36); Dinophyceae (6); Chlorophyceae (1) and Cyanophyceae (2) were recorded. Among the four classes, Bacillariophyceae appeared as the dominant group in terms of total species and cell numbers. The multivariate statistical analysis revealed that the surface water quality and phytoplankton density of the Parangipettai waters and its tributaries is being affected by increased aquaculture practices, agriculture discharges and high level of organic load. These data on the phytoplankton distribution and abundance with reference to hydrography will be of immense help for further ecological assessment in Parangipettai waters.