Using geochemical and pumping test data from 80 groundwater wells, the chemical, hydrologic, and hydraulic properties of the fractured Eocene carbonate aquifer located west of the Al-Minya district, the Western Desert, Egypt, have been characterized and determined to guarantee sustainable management of groundwater resources under large-scale desert reclamation projects. The hydrochemical data show that groundwater from the fractured Eocene carbonate aquifer has a high concentration of Na+ and Cl− and varies in salinity from 2176 to 2912 mg/L (brackish water). Water–rock interaction and ion exchange processes are the most dominant processes controlling groundwater composition. The carbonate aquifer exists under confined to semi-confined conditions, and the depth to groundwater increases eastward. From the potentiometric head data, deep-seated faults are the suggested pathways for gas-rich water ascending from the deep Nubian aquifer system into the overlying shallow carbonate aquifer. This mechanism enhances the dissolution and karstification of carbonate rocks, especially in the vicinity of faulted sites, and is supported by the significant loss of mud circulation during well drilling operations. The average estimated hydraulic parameters, based on the analysis of step-drawdown, long-duration pumping and recovery tests, indicate that the Eocene carbonate aquifer has a wide range of transmissivity (T) that is between 336.39 and 389,309.28 m2/d (average: 18,405.21 m2/d), hydraulic conductivity (K) between 1.31 and 1420.84 m/d (average: 70.29 m/d), and specific capacity (Sc) between 44.4 and 17,376.24 m2/d (average: 45.24 m2/d). On the other hand, the performance characteristics of drilled wells show that well efficiency ranges between 0.47 and 97.08%, and well losses range between 2.92 and 99.53%. In addition to variations in carbonate aquifer thickness and clay/shale content, the existence of strong karstification features, i.e., fissures, fractures or caverns, and solution cavities, in the Eocene carbonate aquifer are responsible for variability in the K and T values. The observed high well losses might be related to turbulent flow within and adjacent to the wells drilled in conductive fracture zones. The current approach can be further used to enhance local aquifer models and improve strategies for identifying the most productive zones in similar aquifer systems.