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Carbonate aquifers constitute a water reserve of essential importance for human supply. For this, it is necessary to establish suitable protection measures in order to achieve the good status of groundwater bodies intended for human supply according to the requirements of the Water Framework Directive. The objective of this paper is to present a methodology to define safeguard zones for the protection of carbonate groundwater bodies intended for human consumption. To do this, firstly the risk of groundwater contamination is evaluated through a combination of characterising pressures and the evaluation of the intrinsic vulnerability to contamination. Secondly, the existing water abstraction points are identified and their zones of contribution are delineated in order to establish priorities when defining protective measures in the region. Finally, the existing wellhead protection areas and those defined according to the proposed methodology must be integrated into the delineated safeguard zones. The results obtained in a carbonate groundwater body in southern Spain are consistent with the existing quality data and they show the percentage of land that must be protected to preserve the quality of water intended for human consumption, thus facilitating their future integration into adequate land use planning tools.