Geochemical signatures of groundwater in the Pondicherry region, south India, were determined. The coastal aquifers are fragile and this situation becomes more intense in layered aquifer systems like that of the Pondicherry region. In this region, groundwater occurs in alluvium, Lower Cuddalore, Upper Cuddalore, Tertiary, Cretaceous and mixed aquifers. The geochemical signature of groundwater in these formations was studied by collecting 93 groundwater samples. The collected samples from specific formations were analysed for physical parameters, such as electrical conductivity (EC), pH and major ion concentrations, such as Ca, Mg, Na, K, Cl, HCO 3 , PO 4 and SO 4. The results of the analysis were interpreted with geology; the ionic concentrations in the groundwater vary spatially and temporally. The abundance of these ions are in the following order: Na [ Ca [ Mg [ K = Cl [ HCO 3 [ SO 4. Interpretation of analytical data shows that Ca-Na and Cl-SO 4-HCO 3 is the dominant facies in all the formations. Groundwater in the area is generally hard and fresh-brackish in most of the formations and brackish in nature in alluvium formation. The sodium absorption ratio shows that most of the samples are grouped under excellent category to good category in all the formations. The residual sodium carbonate also are in good category in all the formations. Chloro-alkaline indices reveal that the majority of samples show negative values in all the litho units indicating the exchange of Na and K in groundwater with Mg or Ca in rock. Scholler classification of water indicates that longer residence time of water with more prominent base exchange. High EC and TDS values in certain locations of alluvial, Upper Cuddalore and Cretaceous formations prove to be unsuitable for drinking and irrigation purposes.