For effective coastal aquifers management, it is strongly required to effectively analyze seawater intrusion (SWI). This study used an integrated approach of hydrogeochemical, statistical, geological, and geospatial techniques to assess the extent of SWI in the Ghiss-Nekor aquifer by evaluating the physicochemical parameters of 52 groundwater samples. Two main groundwater facies were identified, Na-Cl (38%) and Ca-Mg-Cl-SO4 (62%). The correlation matrix and a principal component analysis (PCA) depicted that the high salinization in the study area is influenced by both geogenic and anthropogenic factors, including a potential mixing with seawater. A single indicator or a small number of techniques were insufficient to evaluate SWI owing to the multiple causes of salinization in the study area. As a result, we coupled various geochemical indicators with geospatial methods to assess this complicated phenomenon. Accordingly, several ionic ratios (Cl/HCO3, SO4/Cl, Na/Cl, and Mg/Mg + Ca) and SWI indices (GQIswi and SMI) were overlaid to generate the final map that highlights the regions prone to SWI. Most of the SWI spots were discovered within two kilometers or less from the coast. The saline water detected far from the coast was interpreted as the encroachment of seawater from the Souani area being trapped where the clay-marly substratum is deep. These results support the application of geospatial tools to manage groundwater resources in water-stressed areas with complex aquifer systems, by combining various ionic ratios and indices. These findings will assist decision-makers in the Al Hoceima region in developing suitable groundwater management plans and strategies.