Water quality is crucial to the environmental system and thus its chemistry is important, and can be directly related to the water’s source, the climate, and the geology of the region. This study focuses on analyzing the hydrochemistry of specific locations within the Dakhla Oasis in Egypt. A total of thirty-nine groundwater samples representing the Nubian Sandstone Aquifer (NSSA) and seven surface water samples from wastewater lakes and canals were collected for analysis. Key parameters such as pH, electrical conductivity (EC), and total dissolved solids (TDS) were measured on-site, while major ions and trace elements (Fe+2 and Mn+2) were analyzed in the laboratory. The water quality index (WQI) method was employed to assess the overall water quality. Hydro-chemical facies were investigated using Piper’s, Scholler’s, and Stiff diagrams, revealing sodium as the dominant cation and chloride, followed by bicarbonate as the dominant anion. The hydro-chemical composition indicates that Na–Cl constitutes the primary water type in this study. This points to the dissolution of evaporates and salt enrichment due to intense evaporation resulting from the region’s hyper-aridity. In groundwater samples, the order of hydro-chemical facies is HCO3− > Cl− > SO4−2 > Na+ > Ca+2 > K+ > Mg+2, while in wastewater samples, it is Cl− > Na+ > SO4−2 > HCO3− > Ca+2 > Mg+2 > K+. When considering iron and manganese parameters, the water quality index (WQI) values suggest that most groundwater samples exhibit excellent to good quality but become poor or very poor when these elements are included. This study could prove valuable for water resource management in the Dakhla Oasis.