Abstract:The Miocene limestone bedrock of the Jaffna Peninsula of Sri Lanka extends below the sea level and is an into the soil and forms a layer of freshwater in the limestone above the seawater. This freshwater is in the form of a convex lens, which thins out towards the coast and the lower part of the lens is a transitional zone where the freshwater becomes increasingly brackish with depth. The thickness of the lens freshwater in the lens is able to sustain irrigation and domestic usage till the end of the dry season. The groundwater has an abundance of calcium and bicarbonate ions, the varying concentrations of which affects the pH, causing it to vary from neutral to slightly alkaline. The concentrations of chloride ions increase with the depth of the transition zone as well as towards the coast. The nitrate contents of the well water are higher in the urban areas due to contamination from septic tanks and also in intensively cultivated farm areas where high amounts of nitrogen fertilizers are used. In some wells, both the chloride and nitrate concentrations do exceed the WHO standards for safe drinking water. Thus, the quality of well water is site transition zone and the surrounding environment.