The mineral water of Vilajuïga village in Alt Empordà (NE Catalonia, Spain) owes its uniqueness to an emanation of geogenic CO₂ that modifies groundwater hydrochemistry to produce a differentiated HCO₃–Na- and CO₂-rich groundwater among the usual Ca–HCO₃ type found in this region. A hydrogeological conceptual model attributes its occurrence to the intersection of two faults: La Valleta and Garriguella-Roses. The former provides a thrust of metamorphic over igneous rocks, formed during the Paleozoic, over a layer of ampelitic shale that, from a hydrogeological perspective, acts as a confining layer. The Garriguella-Roses normal fault, which originated during the Neogene, permits the degassing of geogenic CO₂ that is attributed to volcanic activity occurring in the Neogene. Groundwater mixing from the metamorphic and igneous rock units plus the local occurrence of CO₂ creates a HCO₃–Na water that still holds free-CO₂ in solution. Interaction with the gas phase is restricted at the intersection of the two faults. Radiocarbon dating, after correcting for geogenic dead carbon, estimates an age of 8,000 years BP. The low tritium content (0.7 TU) indicates that Vilajuïga water is a mix of “older” groundwater recharged in the metamorphic rocks of the Albera range and “younger” groundwater from the igneous rocks of the Rodes range, over a recharge area of 45 km² and a maximum elevation of 600 m. Given its origin as rare groundwater in the southern slope of the Eastern Pyrenees, purposeful monitoring is necessary to evaluate the groundwater vulnerability and anticipate impacts from nearby wells and climate-change effects.