The Kaluvelly watershed is a coastal area (Tamil Nadu, India) where water abstraction has resulted in a dramatic fall in the level of the water table and a piezometric depression in the most exploited aquifer, the Vanur aquifer. In addition, intensification/mechanization of agriculture may have affected the quality of recharge water. An initial hydrodynamic study showed that the Vanur aquifer is highly vulnerable to salinization due to potential seawater intrusion, and our aim was to determine the source of salinity recorded in the groundwater of this multilayered aquifer. Our approach involved the use of existing boreholes and of a moderate number of samples, with the aim of developing appropriate water resource management techniques. Major element, 18O/16O, 2H/1H and 87Sr/86Sr, ratios were measured in rainwater, surface water and groundwater collected during five sampling campaigns over a 2‐year period. Geochemical data indicate that the Vanur aquifer is recharged and that small mixings between aquifers fluctuate according to monsoon intensity. There was no evidence of seawater intrusion. The range of recorded salinity originated mainly from water–rock interaction but a disconnection of some deeper parts of the aquifer was apparent. Strontium isotopic ratios in the recharge area suggest an anthropogenic influence, possibly related to fertilizer use. A high SO 4 /Cl ratio was observed in the aquifer; in the deeper parts, the influence of a formation containing lignite is hypothesized, whereas near the surface, sulphate may partly originate from fertilizer use and fossil fuel combustion. Water isotopic data suggest that the origin of precipitation in this region has been unchanged for several hundreds or thousands of years. Copyright © 2011 John Wiley & Sons, Ltd.