Groundwater quality determination and age estimation in a desert landscape of El Golea province situated in the south of Algeria has been investigated in the present research paper. For this regard, 57 water samples were collected from an aquifer composed of two superimposed systems; phreatic and deep continental intercalary (CI) aquifers which are a part of the Northern Sahara Aquifer System (NWSAS). Samples were analyzed to assess the age and water quality using descriptive, multivariate statistics (PCA and HCA) and stable isotopes. It is revealed that more than 71% of the IC points are characterized by a water type (Ca2+, Mg2+) (HCO3–)2 and more than 83% of the TC samples are defined by a water type (Ca2+, Na+) (HCO3–, SO42–) and very high salt ions contents due to the influence of surface water, evaporate leaching and irrigation water return. The isotopic composition of samples of phreatic and CI aquifers shows a clear difference between the two qualities of water. The phreatic aquifer is characterized by the δ18O range from –4.68 to –6.1, whereas δ2H from –47.25 to –59.48 and CI with values of the δ18O range from –5.96 to –7.6, and δ2H range between –53.7 and –65.78 isotopic signature. The unconfined aquifer above IC forms a special case of a mixture of ancient water from deep horizons and recent water strongly enriched from shallow horizon lands.