The 2004 great Sunda-Andaman earthquake (Mw- 9.3) accompanied with unprecedented catastrophic tsunami caused significant crustal deformation or vertical land level changes in its rupture zone manifested by broad uplift and subsidence, that severely affected the groundwater regimes in the South Andaman Island. In the regions of principle coseismic subsidence such as in the western and eastern coast of South Andaman, tsunami wave trains with run up height of ~ ≤ 10 m inundated most of the land surface and contaminated the aquifer system by direct infiltration during the first flooding waves and later percolation of ponded seawater. Corollary to this significant changes in physiography and hydrology of the subsided areas were observed and most parts remain permanently inundated owing to flow of sea water into fresh water facilitated by interlinked fracture zones. Consequently, a systematic geophysical survey was conducted using Schlumberger configuration encompassing 12 vertical electric soundings (VES) and profiling at four potential coats of South Andaman to map the vertical and lateral resistivity contrast of the fresh and contaminated aquifer zones respectively. Besides groundwater samples are taken at VES locations during dry and monsoon season from dug and bore wells according to the standard procedures to ascertain the periodic analysis geochemistry of groundwater.The integrated analysis is compared with island lithostratigraphy, borehole data and nearby well inventory for precise interpretation of the subsurface fresh/saline aquifer geometry. The integrated analysis shows that low-lying coasts are found more vulnerable to seawater intrusion than east coast owing to its gentle topography, macro porosity of the upper soil formation and highly brecciated bedrock formation which interlinks the existing extensional and shear fractures and greatly facilitates the movement of seawater into freshwater formation.