India is second largest sugarcane producing nation with water foot prints ~ 104 BCM/year of which 80% met from groundwater of deep-wells. The large-scale groundwater management practices were found mostly untenable affecting the sugarcane agrarian and associated sectors. We developed a cell-level (2km x 2km) decision support tool (DST) employing the integrated hydro-geophysical investigations in sugarcane agro-watershed (399 sq.km) beset over granitic aquifer systems of Tattihalla River watershed, Southern India. The refined hydrogeological conceptual model derived from electrical resistivity tomography (ERT) and groundwater level (head) has been accounted into the numerical modelling. The model was run on transient mode for four stress periods during 2015–2017 and validated with calculated and observed heads. The normalized RMS error 7.57% of the validated model conveys its robustness and estimates groundwater budget at the demarcated 77 cells. The theoretical scenarios for water level projections against the increased groundwater pumping rates of 10%, 25% and 50% were generated. It showed declining trend of water level for projected 10 years period with varied magnitude and vulnerability for drought conditions. The different time periods of water level touching the basement (i.e. dry borewell), infers a distinct hydrogeological property of an individual cell advocating to adapt a cell level management plan. In this article, we explained two cells (Nos. 12 & 60) in detail to show the varying characteristic of aquifer against the different pumping rates.