Hydrogeochemical and water table behavior has been studied from March 2005 in the Weligama bay area, situated in the tsunami affected zone of the southern coast of Sri Lanka (Latitude 80.42; Longitude 5.97). Seventy affected shallow dug wells, situated in 8 km coastal strip, were selected for the study. The selected wells are sunk into the permeable quaternary sand deposits overlying Precambrian granite gneiss. The top quaternary sandy aquifer in the coastal margin of Weligama bay area is very permeable and hydro geological conditions are very favorable for salt-water intrusion. The study helped to prepare the hydro geological, and the hydro-geo-chemical maps of the area. Prior to the Tsunami wave of 26th December 2004, water in these wells was non saline and used by the people for drinking and other domestic purposes. The preliminary results of the study revealed that the Electrical conductivity of well water in all wells situated in the Tsunami affected Zone turned saline (EC in average increases from 300 μ Siemens per cm to around 1300 μ siemens /cm.). Total dissolved solids of the well waters are around 1000 mg/L. It could be concluded that the underground pressure wave may have disturbed the freshwater/saltwater equilibrium resulting in the mixing of fresh groundwater with saline water.