Abstract: Impact of industrial pollution on water quality and phytoplankton population was done for a period of one year in Uppanar estuary at three location (Ia, Ib and Ic) and open sea. Water quality and phytoplankton diversity and distribution patterns indicated that, the water quality of this environment was highly polluted. Higher levels of nutrients, heavy metals, primary productivity, chlorophyll a and total carotenoid content in station Ia indicated a possibility for eutrophication, which also confirmed by the dominance of phytoplankton Asterionella japonica and Thalassiothrix frauenfeldii. In addition to that the species diversity was also very low when compared to open sea.