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Climate change poses a major threat to natural resources, especially water, leading to its recognition as a key priority in the 2030 Agenda’s Sustainable Development Goals. Mountain regions are particularly vulnerable due to shifting precipitation patterns, rising temperatures, and altered hydrological cycles. An integrated geological and geophysical approach is here proposed with the main goal to identify groundwater systems in complex, tectonically deformed mountain terrains. By combining 3D geological modelling with 3D airborne electromagnetic (AEM) surveys, this integrated approach enhances subsurface imaging and reveals the distribution of geological formations, fault networks, and karst features that control groundwater flow and storage. The method has been tested in the Aracena case study (South of Spain), where an AEM survey was carried out with the Xcite system by NRG. The geologically informed 3D AEM modelling of the area produces results that closely match known geological features and facilitate easier model interpretation. The integrated geological-geophysical approach developed in this study enhances the understanding of groundwater systems in mountain terrains and supports the evaluation of their potential for sustainable water resource management.