Shallow aquifers in semi-arid hard rock regions serve as primary irrigation sources, yet the limited understanding of aquifer heterogeneity often results in unsuccessful or poor yielding boreholes and suboptimal irrigation efficiency. A comprehensive assessment of groundwater vulnerability is necessary to ensure judicious utilization, safeguarding long-term availability and resilience against over-abstraction and environmental stressors. This study assesses the spatial variability and dynamics of shallow and deep crystalline hard rock aquifers in the 368 km(2) Nagavali watershed (India), using an integrated approach combining geospatial, hydrogeophysical, and hydrochemical techniques. Analytic hierarchy process (AHP) modelling, electrical resistivity tomography (ERT), hydrograph analysis, and hydrochemical appraisal were used to decipher aquifer heterogeneity and vulnerability. Results demonstrate that AHP-derived groundwater potential zones (GWPZs) and ERT delineated a three-layer geological structure, effectively unravelling the heterogeneous nature of shallow aquifers. Pronounced groundwater level fluctuations (up to 5.6 m) observed in shallow aquifers (< 30 m depth) highlight their dynamic behaviour, driven by fragile geological structures and robust seasonal recharge-discharge dynamics. In contrast, deep wells (> 30 m depth) showed minimal fluctuations with R-2 = 0.82, reflecting the stable behaviour of deeper, confined aquifers. Further hydrochemical analysis revealed that shallow aquifers, reflecting dynamic flow conditions with frequent surface interaction, are dominated by carbonate weathering, whereas deeper, more static aquifers exhibit silicate weathering signatures indicative of longer residence times and limited surface influence. This study provides a comprehensive aquifer vulnerability map and proposes remedial measures to mitigate over-abstraction risks for sustainable management practices to ensure the long-term viability of shallow aquifers in hard rock regions.