Changes in water quality of a sand aquifer on the east coast of Sri Lanka due to the 26 December 2004 tsunami and subsequent remediation attempt by pumping were investigated. Two transects, disturbed (where pumping of groundwater took place) and undisturbed (where no pumping occurred), were monitored. In the undisturbed area, the average electrical conductivity (EC) in the wells affected by the tsunami showed a decrease from 3000 to 1200 μS/cm after the first full rainy season following the disaster; however, in the disturbed area the average EC stabilized around 1500 μS/cm. The observations were further analyzed by calculating hydrogeochemical mixing ratios, which showed that the seawater fraction was higher in the disturbed site than in the undisturbed site. The disturbance caused by physical cleaning by extensive pumping and subsequent disposal of the pumped water adjacent to the wells likely led to retention of salinity in the aquifer.