This work proposes a comprehensive methodology for evaluating fissured hard-rock groundwater resources through an integrative approach based on fieldwork techniques, Geographic Information System (GIS)-based mapping, geospatial analysis and multiple-criteria decision analysis (MCDA). The study sites comprise distinct geological settings and geographic contexts, i.e. granitic rocks (NW Portugal) and metasedimentary rocks (SW Spain). A similar methodological approach was used in both areas to compare and assess the methodological approaches’ effectiveness. The cartographic, field, and laboratory data were analysed through GIS overlay and multi-criteria spatial analysis. This GIS-integrated analysis allowed the calculation of the Infiltration Potential Index (IPI) and groundwater vulnerability indexes: GOD-S, DRASTIC-Fm, SI and DISCO, as well as the development and improvement of the hydrogeological conceptual models. At the Entre-os-Rios site (NW Portugal), the IPI index showed that the most favourable areas for infiltration are the fractured granitic regions, where the slope has the lowest values, combined with forest areas. The recharge values are around 70 to 90 mm/year. Considering hydraulic connection with the borehole data, the DISCO index identified the geostructures with the most important trending to NNE-SSW, NE-SW and WNW-ESE in the area. The highest IPI values were identified in the regional aquifer quartzite unit at Herrera del Duque (SW Spain). The recharge values are around 60 to 80 mm/year. The DISCO index identified zones where discontinuities have a higher hydraulic connection to the borehole, mainly trending NW-SE and NE-SW. The models developed could be helpful for decision-making and sustainable water resources management regarding the planning of hydrogeological investigations, delineating potential contamination areas, and the definition of catchment protection areas.