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The aquifer of the semi-arid Kairouan plain has been exploited for decades to supply the growing irrigated agriculture and the need of drinking water. In parallel, the major hydraulic works drastically changed the natural groundwater recharge processes. The continuous groundwater level drop observed since the 1970s naturally raises the question of groundwater storage sustainability. To date, hydrogeological studies focused on groundwater fluxes, but the total amount of groundwater stored in the aquifer system has never been fully estimated. This is the purpose of the present paper. A complete database of all available geological, hydrogeological and geophysical data was created to build a 3D lithology model. Then, the lithological units were combined with the hydraulic properties to estimate the groundwater storage. Over the 700 km(2) of the modelled area, the estimated storage in 2013 was around 18 x 10(9) m(3) (equivalent to 80 times the annual consumption of 2010) with a highly variable spatial distribution. In 45 years (1968-2013), 12% of the amount of groundwater stored in the aquifer has been depleted. According to these results, individual farms will face strong regional disparities for their access to groundwater in the near future.