Climate change and failure in the development project to control salinity intrusion adversely affects rice production and availability of reliable water in the Vembanad-Kol coastal agricultural wetland, a designated Ramsar site and a recognised globally important agricultural heritage system of India. Aquifers in the region has become saline. The wetland is surrounded by backwater, with most of the area lying one metre below sea level. Through generations, rice cultivation has been made possible by constructing dikes using local soil and pumping out water. The project to multiply crop production by preventing saline water intrusion results in large-scale salinity intrusion. Dispute developed between fishermen and farmers over the period of opening and closing of regulators during peak summer where there is no river runoff to displace saline water. Improper maintenance of the shutters permits leakage of saline water during high tide. Due to the failure in foreseeing the rising sea level and sand dune formation in the coast during monsoons, sea water enters the wetland through spillway. Rice production became half. Natural flushing is obstructed by the barrage and concentration of pollutants multiplied and the water resources became totally unsafe. Many native species of aquatic life and migratory birds have disappeared. Changing climate and rising sea level pose a new threat. Rainfall in the state is becoming highly seasonal, reducing the summer flow of rivers joining the wetland that is important in pushing away the saline water. Fall in rice production and deterioration of water quality leads to several socio-economic and health issues. A detailed investigation on the factors leading to increasing salinity in the wetland and a critical review of current strategies and policies for adaptation and mitigation has been made. Guidelines for an appropriate policy and strategy to save the wetlands agriculture from the salinity problem have been provided.