Because of anthropogenic activity and seawater intrusion, coastal aquifers worldwide frequently face a threat to their water supply due to salinization. This paper investigates the assessment of the groundwater quality in coastal aquifers of the Hauturivien aquifer in the Essaouira basin. In this study, 56 groundwater samples collected from the Hauturivian aquifer across four campaigns in 2017, 2018, 2019, and 2020 were subjected to multivariate analyses involving principal component analysis (PCA) and cluster analysis (CA) using SPSS software. Among the three main water types, the mixed Ca-Mg-Cl classification was predominant in the investigated aquifer. In addition to the natural processes (such as the water–rock interaction, ion exchange, dissolution/precipitation dynamics, and evaporation) that govern groundwater quality, current land use practices have increased salinization in this poorly drained semi-arid area. Based on assessments using Water Quality Index (WQI) and Irrigation Water Quality Index (IWQI), the water quality is suitable for human consumption, but its use for irrigation is limited to crops that can tolerate high salt levels. The stable isotopes (δ2H and δ18O) of groundwater demonstrated that local precipitation is the primary recharge source. Nonetheless, the evaporation process, influenced by various geological conditions, affects groundwater recharge, regardless of the topographical differences in the study area.