In the Precambrian granitic terrain, the occurrence of a multi-aquifer system is common. This study has examined the inter-communications between the shallow and deep aquifers using the hydrochemical and isotopic methods. The obtained results indicate distinct hydrochemical characters of the groundwater from shallow (~ 100 m) and deep (~ 400 m) wells, signifying their independent and unconnected nature initially. Hydrochemistry of deep groundwater is approximately constant (either Ca–Na–Cl or Ca–Na–Cl–SO4 type of water) from January 2015 to June 2016. Repeated measurements of the 14C activity in these deep groundwater samples during this period show 35.41 ± 0.48 to 85.01 ± 0.8 pMC (residence time of ~ 3 to 8 ky BP). However, as a result of excess rainfall during 2016, hydrochemical facies of the deep groundwater changed initially to Na–Ca–SO4–Cl. Subsequently, they stabilised at Ca–Na–HCO3–Cl type with a significant reduction in Cl− and increased HCO3− and NO3− concentrations, while the 14C activity changed to 100 pMC (modern age). These changes are attributed to the ingression of fresh water into the deep aquifer after paleo-groundwater in the deep aquifer is depleted due to the over-exploitation of the limited potential aquifer during the drought. The over-exploitation of deep aquifer possibly improved the migration potential of fresh water to the deep aquifer and led to enhancing the groundwater recharge during the excess rainfall years. It brings a new perspective to the hydrogeological dynamics between shallow and deep aquifers. Further, it also suggests that, under climate-driven drought conditions, deep aquifers could act as an emergent groundwater resource to meet the water demands. A conceptual model has been proposed to explain the observed phenomenon of deep and shallow aquifer communication.