Groundwaters of the coastal region are significant and serve as a fragile ecosystem in the sedimentary terrain. The Pondicherry region is characterized by different geological formations of distinct geological epochs Cretaceous, Tertiary and Quaternary. Ninety-three samples were collected from specific aquifers with respect to spatial distribution [Alluvium (31), Upper Cuddalore (13), Lower Cuddalore (13), Other Tertiary (7), Cretaceous (24) and Mixed—multiple completion aquifer (5)]. The collected samples were analyzed for major ions Ca2+,Mg2+,Na+,K+, HCO3-,Cl-,PO42-,SO42-, F and DOC. Stables isotopes of δ18O,δD and δ13C were also analyzed along with heavy metals like Al, Ba, Fe, Sr, Cd and Zn. The δ18O ranges between - 6.85 and - 2.15 %, and δD ranges between - 43.94 and - 19.41%. The distribution of these environmental isotopes in groundwater of this layered aquifer sequence was also attempted. A comparison of the isotopic data with the rainfall, Local Meteoric Water Line with a equation of δD = 7.398 * δ18O + 5.067, Indian Meteoric Water Line and Global Meteoric Water Line was performed. The δ13C values for groundwater ranges from - 5.3 to - 18.1 % . The result indicates that the groundwater in the study area is mainly meteoric in origin, and few samples show evidence of evaporation. The dissolved organic carbon (DOC) is a very important component in biogeochemical cycling of elements characterized by high susceptibility to leaching. The range of the DOC in the study area is 0–16 mg/L. Factor analysis was applied to classify the groundwater samples and to identify geochemical processes controlling groundwater geochemistry. The Alluvium aquifers show a complex hydrogeochemistry than the older aquifers. The major factor influencing the hydrogeochemistry of the region is rock–water interaction and anthropogenic processes. Hence, metal mobility of the groundwater shows the correlation of metal bonding and DOC. he relation between the DOC and heavy metal concentration in the aquifers was also identified.