Crystalline aquifers are present in most parts of southern India with limited resources of groundwater. The groundwater storage map in the Maheshwaram watershed has been estimated from the product of specific yield (Sy) and saturate aquifer thickness as a system being an unconfined weathered–fractured combined aquifer. Land-use data has been used for the estimation of groundwater abstraction at a spatial scale. Storage and scarcity mapping demonstrate that the watershed is clearly vulnerable to drought in some areas because of significant pumping. Therefore, the result shows that on average, the availability of groundwater storage corresponds to 1.5 yr of the present groundwater abstraction rate with successive low monsoons (i.e., insignificant recharge). Additionally, 13% of the area shows no storage at present, 28% of the area has less than 1 yr, 40% area has less than 2 yr and 12% area has less than 3% of storage. Very few cells can sustain for more than 3 yr. Additionally, the Sy of the aquifer ranges from 0.2% to 5% with a mean value of 1.8%. A geo-statistical technique has been applied for the estimation of Sy at unknown cells where either the cell was dry or no pumping occurred. This estimated two-dimensional Sy value can also be used in classical groundwater numerical modelling for a better understanding of groundwater resource management.