In the multilayered aquifer of Kaluvelly (India), comprising various sedimentary layers overlying a charnockitic basement, concentrations of trace elements were measured in aquifer formations and in groundwaters to identify geochemical tracers for water bodies. The two main sandstones (Cuddalore and Vanur) originate from the charnockites and the Cuddalore sandstone has experienced lateritization. In the studied area, two charnockite end-members were identified: a dioritic and a granitic one. Mineralogical composition and whole-rock Ti concentrations confirmed the charnockite which displayed the granitic composition as the parent rock of the two sandstones. Titanium distribution indicates that the Cuddalore sandstone originates from a more intense weathering of the parent material than the Vanur sandstone. Despite extensive differences in trace element contents recorded in aquifer formations, only a few trace elements were suitable to distinguish the water bodies. Among soluble elements, Li (in the Vanur aquifer) and Ba (in the charnockite and carbonaceous aquifers) can be used as tracers. As the input of these elements in solution is mainly regulated by the available stock, for a given mineralogical origin there is a direct link between the aquifer formation composition and water signature. With the exception of As, concentrations of redox-sensitive elements were not preserved during pumping because of oxidation, preventing their use as tracers. Low-mobility elements such as La, Ce, Th, Zr, Nb, Hf, or Ta were too insoluble to be detected in waters and/or to record the aquifer formation signature. Their input in solution was not regulated by the available stock but by the dissolution rate of rock-forming minerals. Only Ti can be used to distinguish between two out of the three aquifers (charnockite and Vanur). The specific behavior of Ti recorded in these waters may be linked to rutile inclusions within plagioclases and to the influence of climate on Ti solubility.