Seawater intrusion is one of the most severe problems confronting coastal aquifers. These aquifers are often considered significant freshwater sources, particularly in arid regions. The water resources mobilized at the Al Hoceima (Northeastern Morocco) come from the Ghiss-Nekkor aquifer and the Abdelkarim El Khattabi dam. The degradation of groundwater quality of the aquifer and the probability of marine intrusion has become a severe concern for the communities. The current study provides multidisciplinary research using hydrogeochemical and statistical approaches to evaluate groundwater quality and determine the origin of salinity in this aquifer. Depending on the direction of the water flow, he results indicate that most wells have a total salinity exceeding 2 g/L. The dominant chemical facies encountered are Na–Cl–Na–SO4 resulting from rock-water interaction, meaning that the breakdown of halite was the predominant source of groundwater mineralization. However, septic waste, water irrigation inflows, and locally seawater intrusion seem to substantially influence groundwater quality in this area.