Groundwater quality is strongly dependent on land use. Past and current anthropogenic activities can lead to the diffusion of contaminants in aquifers. This diffusion can threaten the resource exploitation for decades, thereby endangering the ecological health of groundwater dependent ecosystems. Thus, groundwater stakeholders need methods for long-term management which integrate groundwater vulnerability. This study was conducted on the shallow alluvial aquifer of the groundwater-dependent Biguglia lagoon on Corsica Island, France. The aquifer is exposed to anthropogenic contamination for many decades with nitrate contamination legacy linked to agricultural activities, uncontrolled urbanization and sewage leakages. In most cases, vulnerability mapping is done in the objective of comparing groundwater situation regarding an on-going contamination process. But the question is still pending for aquifers where contamination is inherited from past practices or contaminations and where anthropogenic influences have changed through time. To propose an effective and innovative method for territorial management in Mediterranean alluvial aquifers, four index-based groundwater vulnerability mapping methods were tested and compared: two intrinsic vulnerability mapping methods (DRASTIC and SINTACS) and two specific vulnerability mapping methods (Modified-DRASTIC and SI), the latter integrating land use in the accuracy of groundwater vulnerability. Novelty is coming from the comparison between vulnerability maps and their application and validation in a hydrosystem affected by nitrate legacy-type contamination. The specific vulnerability mapping methods are more likely to represent the current pressures to which groundwater are subject. Thus, specific vulnerability methods such as the SI one revealed here very relevant to assess groundwater quality and to react retrospectively. The comparison between groundwater nitrate legacy and intrinsic groundwater vulnerability methods appeared also useful to define priority protection areas in long-term territorial management planning (EU Water Framework Direction). In this sense, the SINTACS method seems to be the more appropriate in the Mediterranean and alluvial context of this study.