Multi-layered coastal aquifers are complex aquifer systems with two or more aquifers divided by the impermeable or semi permeable layers. The objective is to assess the interaction between the aquifers using geochemical indicators in the urbanised multi-layered coastal aquifer of Sankaraparani river basin, India. Hydrogeologically, the coastal part of this region comprises of alluvium formation as upper aquifer and sandstone formation as lower aquifer. Groundwater samples were collected from 33 representative wells during June 2017 and January 2018. Electrical conductivity, pH, and alkalinity were measured in the field while the concentration of major ions was analysed in the laboratory. The groundwater level in the upper aquifer varies from 7.4 to 18 m msl. Na-Cl type groundwater is dominant in the upper aquifer whereas Ca-HCO3 and mixed Ca-Na-HCO3 type groundwater is dominant in lower aquifer. The processes that controls the groundwater chemistry are sulphate reduction, freshening ion exchange, calcite dissolution and conservative mixing of seawater and freshwater. Significantly different values of electrical conductivity, sodium and chloride ratio, base exchange index as well as the different geochemical facies between the upper and lower aquifer indicates the absence of interaction between the aquifers near to the coast. Whereas in the west, the similarity in these confirms the interaction and both the formation function as single aquifer. The groundwater in the upper aquifer is affected by seawater intrusion upto 2 km whereas the lower aquifer is not affected.