Abstract: Phytoplankton fluctuation analyzed at two sampling regions namely Kalladi Bridge area (A) and Thannamunai area (B) according to seasonal variation in the year 2015. The main study focused on season rather that physio-chemical analysis. Samples were collected in dry (June) and rainy (November) seasons. The sampling region B is comparatively has low salinity due to the construction of two bridges (Koddaimunai Bridge & New Bridge) because the water flow is highly restricted. The sampling region A is brackish water. During study period sea water mixing doesn’t take place in dry season. During dry season species diversity was high rather than rainy season and during dry season high density of Diatoms were estimated at the sampling region B and high density of Cyanobacteria were estimated at the sampling region A. During rainy season high density of Cyanobacteria and Chlorophycean members were estimated both in the sampling regions A and B.