Given the vital importance of water and energy in desert regions, we undertook a study dealing with the deep reservoirs in Gabes area, which is located in the southeastern part of Tunisia. Geothermal resources are taken from the Intercalary Continental [or Continental Intercalaire (CI)], known as the largest deep aquifer in Tunisia and are used in a number of applications, mainly in agriculture. Previous investigations performed on the thermal waters of this area focused on the genesis of the deep waters with regard to the thermal features of geothermal reservoirs. A more detailed investigation has been carried out, considering both deep and shallow waters. In order to estimate the potential temperatures of deep reservoir in the Gabes area, we developed a synthetic study including chemical geothermometers, multiple mineral equilibrium approach, and other approaches. Chemical types of the thermal waters and effects of mixing between shallow cold waters with deep thermal waters were also discussed. In fact, the application of Na–K–Mg diagram relative to deep geothermal reservoir capitulate estimated temperatures (about 90°C). In addition, the multiple mineral equilibrium approach submits a similar estimated temperature ranging between 65 and 70°C, showing a disequilibrium status which indicates a possibly mixing with surface water. Indeed, wells exploiting the CI aquifer in the south part of the studied area showed the same characteristics, corroborating the reliability of the applied methods.