Investigations on geohydrological aspects of coastal aquifer are important in order to understand the mechanism of ground water salinisation. The present study describes the salinity variations of ground water in deep boreholes drilled in Charnockite rock formation of Kalpakkam, on the eastern coast of India. Water samples collected up to 600m depth were analyzed for salinity variation. It is noticed that in one of the boreholes, (borehole K1), the salinity level is found to be 74 parts per thousand (ppt) at 400 m depth. Influence of surface saline water bodies viz., sea (26-28.5 ppt), backwaters (27-30 pt) and Buckingham canal (27-32 ppt) as the possible sources of recharge of fresh waters through joint and fracture system of the rock are discussed in this paper. Studies would assist in understanding the geohydrological characteristics of deep geological formation.