The coastal aquifers system of Sfax Agareb Chaffar Mahres (Southern Sfax) located in the central east of Tunisia is well known for population growth and industrial development. These industrial and agricultural developments have led to the degradation of water quality. In this study, DRASTIC and GALDIT models were integrated with geographical information system (GIS) tools, in order to assess the aquifers vulnerability to pollution and the seawater intrusion risk. These methods use different parameters explaining the different results in the vulnerability degrees in the Aghereb–Chaffar–Mahres aquifer system. The vulnerability map to contamination as well as vulnerability to seawater intrusion showed three classes of vulnerability: low, moderate and high, depending on the intrinsic properties. In addition, the risk map showed three risk classes: low, moderate and high depending on hydrogeological characteristics, land use, distance from the coast and human impacts in the majority of the study area. GIS is used to manage, manipulate and analyze the necessary geographical data used in the different vulnerability methods. These maps could serve as a scientific basis for sustainable land use planning and groundwater management in Southern Sfax.