Crystalline hard-rock aquifers, one of the most complex groundwater systems, are facing serious groundwater management issues due to their limited storage capacity and understanding of their complex hydrogeological characteristics. In this study, we have employed an operational decision support tool to calculate the groundwater budget under variable agro-climatic conditions for groundwater management in the crystalline hard rock aquifers of the Ankasandra watershed (${\sim}$380 km$^2$), southern India. The nature of fractures and the aquifer geometry are categorized based on a borehole camera logging and resistivity model derived from the airborne electromagnetic (AEM) survey. The water level and groundwater recharge, simulated at the seasonal time step for the three hydrological years from June 2015–May 2018, show a negative trend for all years with groundwater depletion of ${\sim}$19 m, indicating the status of the aquifer is overexploited. The futuristic simulations further predict that the depletion in water level would result in an increasing number of drying up of borewells and perhaps zero water days in coming years if no appropriate measure is taken. The model also suggests that changes in land use with a significant increase in artificial recharge in the coming years could rapidly transform the groundwater scenario and lead to a long-term sustainable management solution.