Understanding the controlling factor of groundwater quality could certainly enhance the promotion of the sustainable development of groundwater resources. In fact, during the last decades, the coastal aquifer of Mahdia-Ksour Essef that belongs to the semi-arid region of Tunisia has been marked by an increase of groundwater extraction for irrigation and water for drinking. Moreover, the water quality shows deterioration due to the septic tanks and intensive agricultural activities especially in the coastal side of the aquifer. This study aimed to (1) assess the water quality using Piper Diagram, Box Plot, ions scatter diagrams, (2) understand the processes of mineralization acquisition in the aquifer, and (3) identify the chemical processes and their spatial distribution in the study area. To solve these objectives, the multivariate statistical analysis such as multiple correspondence analysis and hydrochemical analysis was performed. Accordingly, two types of groundwater are identified through the hydrochemical analysis as Na-Cl and Ca-SO4. According to multiple correspondence analysis, three water groups are determined (G1, G2, and G3). Indeed, the groundwater quality is controlled by the water-rock interactions and affected by the seawater intrusion and agricultural activities. The generated results would be helpful to provide a managing model highlighting the threatened locations. It could be considered as a basis for future monitoring programs that aspire to protect water resources.