Water shortages have become an increasingly serious problem in Pondicherry region. Groundwater has become the major source of water supply for domestic, industrial and agricultural sectors in this region. This coastal aquifer shares with the continental aquifers many hydrogeological characteristics and there is a risk of water quality deterioration. Pondicherry region is the sequential sedimentary terrain composed of Sandstone, Sand and Clay along with occurrences of Lignite in formations of Mio-Pliocene period, which indicate the presence of the organic carbon in these aquifers. Cuddalore formation is also witnessed to be in reducing environment due to the presence of Marcasite, peat and also lignite. The Late Cretaceous formation consist of limestones, sandy clays and sandstone deposited in marine environment and they serve as the natural sources of organic carbon which is later leached from sediment to the groundwater. The anthropogenic sources are mainly represented by agrochemicals, industrial effluents, Land fill leachate and Agricultural practices.