The Ordesa and Monte Perdido National Park, located in the Southern Pyrenees, constitutes the highest karst system in Western Europe. No previous studies regarding its geochemical and isotopic groundwater characterization are available in this area. This work presents the results of field and sampling campaigns carried out between July 2007 and September 2013. The groundwater presents high calcium bicarbonate contents due to the occurrence of upper Cretaceous and lower Paleocene-Eocene carbonate materials in the studied area. Other relevant processes include dissolution of anhydrite and/or gypsum and incongruent dissolution of Mg-limestone and dolomite. The water stable isotopes (δ(18)O, δ(2)H) show that the oceanic fronts from the Atlantic Ocean are responsible for the high levels of precipitation. In autumn, winter, and spring, a deuterium excess is found in the recharge water, which could be related to local atmospheric transport of low-altitude snow sublimation vapour and its later condensation on the snow surface at higher altitude, where recharge is mostly produced. The recharge zones are mainly between 2500m and 3200ma.s.l. The tritium content of the water suggests short groundwater transit times. The isotopic composition of dissolved sulphate points to the existence of regional fluxes mixed with local discharge in some of the springs. This work highlights the major role played by the altitude difference between the recharge and discharge zones in controlling the chemistry and the vertical variability of the isotopic composition in high-altitude karst aquifers.