The chemical characterization of the Ghis-Nekor groundwater has become a concern of many researchers in Morocco. It is a crucial indicator for the environment situation and the socioeconomic development of this Moroccan region. Indeed, it helps decisionmakers carry out conscious and sustainable management. For this reason, 20 samples of the Ghis-Nekor aquifer were examined in terms of physicochemical parameters such as pH, temperature, electrical conductivity (EC), and total alkalinity (Alk), major cations–anions (Ca²⁺, Mg²⁺, Na⁺, K⁺, HCO₃⁻, Cl⁻, SO²⁻ 4^, NO⁻3^{, and TDS), isotopic elements (δ18} O, δ² H, and δ¹³ C), and concentrations of Br and Sr anions in 2020. Furthermore, spatial data analysis with a geographic information system (GIS) using the ArcGis software (Redlands, California, USA). Indeed, static maps show significant water quality information that helps characterize the groundwater of the study area. The spatial analysis by the GIS indicates that except the EC (from 2630 to 6950 mS/cm), all the physical parameters showed standard concentration values in most of the samples. A significant concentration above the Moroccan norm of groundwater quality for sodium (Na⁺ ) from 264.3 to 1500 mg/L, chlorides (Cl⁻ ) concentrations from 408.3 to 1510 mg/L, SO²⁻ 4 from 313.1 to 999.2 mg/L, and bicarbonate (HCO₃⁻ ) from 283.7 to 679.8 mg/L was observed, while all the points exceeded the recommended standards norm for SO²⁻ 4^. Most of the points met the potability standards for potassium (K⁺ ). In terms of the isotopic elements, the concentration values of δ¹⁸ O were from −3.92‰ to –5.60‰, while the δ² H concentration values varied between −28.67‰ and −39.99‰. The analysis revealed values of carbon isotope δ¹³ C ranging between −3.15‰ and −8.61‰, thus suggesting that the origin of the carbon is mineral, mainly deriving from calcite dissolution. The analysis of the bromide and strontium contents made it possible to discriminate the origin of the salinity anomalies. The Cl/Br, Br/Cl, and Sr/Ca molar ratios distinguished the areas of influence of geological setting (saliferous facies outcrops) or anthropogenic effect (wastewater). The results of the analysis shed light on factors of contamination, which are as follows: urban zones (Imzourene, Ait Youssef, and Souani) and agricultural activities. Therefore, the use of these waters could pose a risk to the health of humans and animals. Similarly, the GIS is a practical and effective tool for the Ghis-Nekor groundwater quality diagnostics and could help decisionmakers establish solutions.