The origin and salinization of groundwater in multi layered coastal aquifer of Sankaraparani river basin, India was studied using isotopes and geochemical signatures. Groundwater in this region occurs in shallow unconfined and deep confined aquifers. The shallow aquifer comprises of Quaternary Alluvium whereas the deeper aquifer comprises of Tertiary sandstone. Groundwater sampling from different aquifers was carried out once in three months since June 2017. Parameters such as pH, electrical conductivity, oxidation reduction potential and temperature are measured in the field whereas the concentration of major ions (Ca, Mg, Na, K, Cl, SO4, HCO3) and stable isotopes (δ18O and δD) are measured in the laboratory. Geochemical signatures such as electrical conductivity, sodium chloride ratio, base exchange index and seawater mixing index indicate that upper aquifer is affected by seawater intrusion whereas the lower aquifer contains fresh groundwater. The isotopic composition of groundwater shows that in the upper aquifer δ18O ranges from -6.8‰ to -1.3‰ and δD ranges from -43.1‰ to -13.8‰ whereas in lower aquifer, δ18O and δD ranges from -5.96‰ to -3.59‰ and -39.29‰ to -23.07‰. Enriched δ18O and δD is observed in few regions near the coast. d-excess in the groundwater of upper and lower aquifer ranges from -3.7‰ to 10.9‰ and -1.03‰ to 20.13‰. Higher d-excess and depleted δ18O shows that evaporation process dominant in this region. The relationship between δ18O and δD compared with the local meteoric water line shows that the groundwater in this region is the meteoric origin. Groundwater samples near the coast with a higher concentration of chloride and enriched δ18O indicate seawater intrusion. The origin of groundwater in the upper and lower aquifers is from rainfall recharge and the groundwater in the upper aquifer has a high concentration of ions due to seawater intrusion.