Estuary as a complex system receive shug equantity of dissolved chemical in put from a n umber of source sasrun of fsthrough the course of river. In addition, it is well known that human activities like in dustrialization, urbanization, tourism and domestic waste are affecting to the water quality. The pun naikayale stuary located with in the Thoothukudi district with Latitude 8o38’19.2” NLong 78o07’09.8” E. The parameters such as pH (7.97±0.32),Calcium (1440±36.44mg/l)and Magnesium (528±36.22mg/l)were revealed highest con cent rations during March, while salinity (22.56±0.57g/l) during January and TDS(37590±451.774 g/l) in February. No significant variations were observed at any of the sampling sites. In generals tuary water was good and maintains table and health yaquaticeco system. The mean values recor dedforall the parameters could support a quaticlife . This study helps to know the various factors influencing the see cosystems and there by conservation measures are in itiatedin collaboration with local NGO’s for protection of these mangroves wamps.