The Nefza aquifer system in northern Tunisia has long been used for drinking water in its southern part. The decline in groundwater levels since the 1980s in the exploited area has prompted water management to concentrate on the depletion of the groundwater resource, despite limited understanding of the overall availability of the aquifer system. The objective of the current paper is to determine the amount of groundwater stored in the aquifer system, which has never been accurately assessed until now. The methodology involves the creation of a comprehensive database utilizing all available lithological and geophysical information, designing a 3D model of the aquifer system, and incorporating hydrodynamic parameters to estimate the groundwater storage. The model shows the spatial distribution of groundwater storage and enhances the mapping of the aquifer's geometry, as well as distinguishes the key aquifers and aquitards. Over 45 km(2) of the modeled area, the calculated groundwater storage in 2019 was around 3 x 10(9) m(3) with a highly variable spatial distribution. It was found that the area currently exploited for drinking water supply represents a poor groundwater storage range between 97 and 377 m(3)/voxel (voxel dimension = 1000 m x 1000 m x 5 m), while the non-exploited area had an excellent groundwater storage that can reach 798 m(3)/voxel. In addition, over the last 52 years (1976-2019), only 0.2% of the amount of groundwater stored in the aquifer has been depleted. The study suggests that water management should focus on accessing the non-exploited areas, even though the cost of development may be high. Further research into groundwater flow in the region is needed through multiple methods, such as geochemistry and hydrodynamic modeling.