Groundwater aquifers in Morocco’s coastal regions are under serious threat as a result of climate change. This study was conducted to evaluate and map the quality of water resources, by evaluating the level of pollution of the groundwater in the Meskala-Ouazzi sub-basin, a coastal area of Essaouira based on the physico-chemical analysis of 58 samples using a geographic information system (GIS) technique, analytical analysis, nitrate pollution index (NPI), and groundwater pollution index (GPI). The diagram piper of the study area is dominated by Cl-Ca-Mg, Cl-Na, HCO₃-Ca-Mg, and SO₄-Ca types. The concentrations of nitrate ranged from 2 to 175 mg/L. It was discovered that 22% of the groundwater samples had nitrate amounts greater than the World Health Organization’s recommended maximum allowable level of 50 mg/L. The NPI ranged between − 0.9 and 7.8. According to the classification of NPI, 44.8% of the total groundwater samples represent clean water, indicating that the groundwater in the study area is suitable for irrigation. GPI values ranging from 0.6 to 3.7, with an average of 1.7, identifies 37.9% of all groundwater samples as low polluted. The inverse distance weighting (IDW) approach was used to generate a spatial distribution map, which indicates that appropriate groundwater is present in the sub-upstream basin’s part. Overall, the forte concentration in groundwater samples detected in western and central areas showed that the nitrate originated from large amounts of nitrogen fertilizer used by humans in agricultural activities during periods of irrigation. The low tritium (δ³H) content shows that the aquifer recharge is stale water and excessive use of fertilizers leads to groundwater pollution faster over time.