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The Port del Comte Massif (SE, Pyrenees) contains one of the most important vulnerable and strategic karst aquifers for supplying freshwater to the city of Barcelona (Spain). It is a fragile system, whose possible environmental impact is highly conditioned by land use. To improve the hydrogeological knowledge of the system, between September 2013 and October 2015, a detailed fieldwork was carried out for the revision of the geological model, the inventory of water points, and the in situ physico-chemical characterization on major elements and isotopes of up to a total of 43 springs, as well as precipitation water. This paper focuses on the characterization of the geochemical processes that allow explanation of the observed chemical variability of groundwater drained by the pristine aquifer system to determine the origin of salinity. The results show that the main process is the dissolution of calcite and dolomite, followed by gypsum and halite, and a minor cation exchange-like process. Sulfur and oxygen isotopes from dissolved sulfate in the studied springs point out a geogenic origin related to the dissolution of gypsum from Triassic and Tertiary materials, and that the contribution from anthropogenic sources, like fertilizers, is lower. Nitrate in groundwater is not an important issue, with a few localized cases related with agricultural activities. The multidisciplinary approach has allowed the development of a consistent hydrogeological conceptual model of the functioning of the aquifer system, which can be replicated in other places to understand the geogenic character of the hydrogeochemistry.