Some researchers have proposed the groundwater protection zone (GPZ) method as a methodological framework for defining safeguard zones of groundwater bodies. Its goal is to protect the quality of water intended for human consumption and to facilitate a common implementation of this method in all European Union member states. One of the criteria used to establish GPZs is to define contributing catchment areas (CCAs). This methodology has been applied to the Sierra de Cañete, a region comprising a carbonate aquifer in the province of Malaga, Spain. The tools used to define CCAs are hydro-chemical and isotopic characterizations, namely water isotopes (i.e., ²H, ¹⁸O and tritium) and the isotopes of dissolved sulfates (i.e., ³⁴S and ¹⁸O). Traditionally, the Sierra de Cañete aquifer has been divided into six sectors. Hydro-chemical and isotopic characterization differentiated between two large areas in the carbonate aquifer. The southern part presents younger water that is the result of faster recharge and that shows a high level of karstification, while the northern area has a slower flow, and recharge is produced over several years. In addition, the northern part is hydraulically connected to an alluvial aquifer (i.e., Llanos de Almargen) that borders the Sierra de Cañete to the north. This aquifer has high levels of pollution due to agricultural and livestock activities carried out in the Llanos de Almargen area. This pollution is transmitted to the carbonate aquifer when groundwater depletion occurs. Therefore, the Sierra de Cañete GPZ needs to be extended to include the Llanos de Almargen aquifer.