Deterioration of water quality is of great concern, particularly in coastal aquifers where it has become difficult to meet water quality standards with appropriate salt content. As groundwater is the only alternative source of freshwater in the coastal plain of Ghiss-Nekor in northern Morocco, there is a need to assess its sustainability and suitability for drinking and irrigation purposes. For this purpose, data obtained from ABHL, corresponding to 13 monitoring wells existing in the downstream part of Ghiss-Nekor aquifer, were gathered and analyzed using a combination of statistical methods and GIS mapping tools. Various qualitative parameters namely; pH, turbidity, salinity, dissolved oxygen, conductivity, Chloride (Cl-), Sulphate (SO4) and some Nitrogen compounds were investigated and compared according to World Health Organization standards. These results suggest that groundwater samples are chemically dominated by chloride anions followed by sulphate anions; high levels of SO4 result from the mineral dissolving of evaporites in addition to the impact of seawater intrusion and the discharge of wastewater without adequate pre-treatment, while Cl- concentrations (408.3-1512.3 mg/L), strongly correlated with electrical conductivity, are related to the impact of seawater intrusion. A few samples along the Nekor River, considered as the aquifer’s recharge zone, showed the lowest salinity levels (<1.5 g/L) compared to the coastal samples which were classified as the most conductive and mineralized (EC greater than 3000 µS/cm) due to the combined impact of mixing with seawater and high evaporation rates. The outcome of this study reveals that the major dissolved anions assessed in the groundwater of the Ghiss-Nekor aquifer do not respect the stipulated criteria in terms of human consumption; therefore, all possible measures should be taken to protect and restore the water quality in this vulnerable coastal aquifer.