The study area is located in the Debila and El-Oued regions in the northeast of the Algeria desert. The water samples were collected from the semi-confined Mio-Pliocene and Lower Pontian aquifers. Physicochemical parameters such as temperature, pH, EC, TDS, and major ions were measured and compared with WHO standards. There is significant water quality deterioration because of strong mineralization and anthropogenic activities. The hydrogeochemical evaluation of groundwater revealed that evaporation, dissolution of gypsum, and reverse ion exchange are the main controlling factors of the water composition in the study area. The two main hydro-chemical facies of the groundwater in the deep aquifers are Ca2+–Mg2+–Cl/SO42− and Na+–Cl−. The water quality index (WQI) was calculated by using the weighted arithmetic method to determine the suitability of water for drinking. The groundwater in Debila and El-Oued regions is not suitable for drinking. The groundwater is suitable for irrigation according to Sodium adsorption ratio (SAR), Na%, Magnesium risk (MR), Permeability Index (PI), and residual Sodium carbonate index (RSC). The values of the saturated index (SI) indicated that the groundwater is undersaturated with halite, anhydrite, and gypsum but saturated to oversaturated by calcite, aragonite, and dolomite.The groundwater in the Debila and El-Oued regions is classified as brackish water. Using brackish water for drinking and irrigation will have an adverse effect on human health and increase soil salinity and decrease plant production. There is no need for using fertilizers containing calcium where the SAR has a low to medium value and the soil will not be affected by sodification or decrease in the capacity of infiltration.