Abstract: Phytoplankton fluctuation analyzed at two sampling regions namely Buffalo Island (Hospital area) (A) and Koddamunai New Bridge area (B) according to seasonal variation in the year 2014. Sampling region B is a shallow area. The following Physiochemical parameters have to be taken for estimation; Water temperature, Conductivity, Salinity, pH, Nitrate and Phosphate were taken into the account. Samples were collected in dry (June) and rainy (November) seasons. During dry season (June) comparatively species diversity was higher than the rainy (November) season and the physiochemical parameters also highly reduced during rainy season. Moreover no algal bloom was recorded during the study period.