Seasonal distribution of both phytoplankton and zooplankton of Agniar Estuary was studied from January to December, 1985. The study indicated that the distribution of plankton is controlled by the flood and salinity. The salinity of the estuary varied from 0.1 %, to 36%,. The marine oriented phytoplankton with a major peak during July, a period of moderate salinity (15 %o) and fresh water oriented phytoplankton with a minor peak during November, a period of freshwater dominance were recorded. Among zooplankton, copepods constituted the major portion (96%) during the period of neritic water dominance and less abundant (6.9 %) during the period of freshwater dominance. Among copepods Oithona sp., was the most common and found throughout the year except during November. Copepod nauplii occurred throughout the year and the peak of copepod nauplii succeeded the peak of diatoms suggesting the herbivorous trophic level of estuarine ecosystem. The rotifers and daphnids were present only in the period of freshwater dominance. The veliger larvae were abundant during July which coincided with the peak of diatoms. Tintinnids were present throughout the year with a peak during summer. The paper discusses with reference to the salinity and water discharge in the Agniar River.