El Bahariya Oasis contains an extensive geothermal system with high potentialities of freshwater resources in the Nubian Sandstone Aquifer (NSA). The Nubian aquifer is formed mainly of three stratified sandstone layers (S1, S2, and S3) intercalated with shale and clay sheets, where groundwater occurs under confining conditions. The Nubian aquifer system is considered the sole source for human drinking and irrigation in such an arid climate. This study utilizes the geochemical, isotopic characteristics to investigate the NSA's subsurface groundwater flow and geothermal system. The studied groundwater is mostly fresh (Salinity < 1000 mg/l) to brackish (Salinity > 1000 mg/l) and be classified into five groundwater water types. Higher groundwater temperatures and lower salinity have been recorded at the deep horizon aquifer (Zone S1), while shallow groundwater (Zones S2 & S3) records a relatively higher salinity and lower temperature. The deeper groundwater in the NSA is depleted with the isotopic signatures of the delta O-18 and delta H-2 than the signature of the recent rainwater, indicating a paleo groundwater that has been recharged during the wet colder climate. The temperature shows a good relationship with the dissolved H-2 and CO2 gaseous in the groundwater; therefore, the Fourier model of heat conduction has been used to predict the shallow and deep groundwater temperature that has been well-calibrated with the measured temperature in the field sites. The mass transport groundwater modeling (NETPATH MODEL) has been calibrated using the value of the saturation indices (-ve means dissolution and + ve means precipitation) of each mineral. The model results show halite dissolution, precipitation of embedded carbonate minerals in the aquifer matrix (calcite, dolomite), precipitation of clay minerals (illite and montmorillonite), and evolved of CO2 gas because of subsurface pressure release due to the upward groundwater leakages. The multivariate statistical analysis suggested that three main factors could explain 91.64% of the total variance of 10 physicochemical parameters, indicating that the hydrogeochemical evolution of groundwater is mainly controlled by the evaporation, rock-water interaction, and dissolution process. The geochemical results coincide with the groundwater flow system and well describe the upward leakage from the deeper horizon.