Punnakayal is a mangrove ecosystem located in the south east coast of India where Thamirabarani River joins the Arabian Sea. Mangroves especially Avicennia sp. are abundant and domestic waste, fish waste, human and animal excreta are disposed in this region. The present investigation was carried out to find out the changes in physicochemical including heavy-metal concentration in the Punnakayal estuary of Tuticorin coast. Among the various parameters, salinity and electrical conductivity are low; turbidity was high during monsoon due to the river run off. Nutrients and heavy metal are found to be well within limits of nominal coastal ecosystems.