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Water resources in high mountain karst aquifers are usually characterized by high rainfall, recharge and discharge that lead to the sustainability of the downstream ecosystems. Nevertheless, these hydrological systems are vulnerable to the global change impact. The mean transit time (MTT) is a key parameter to describe the behavior of these hydrologic systems and also to assess their vulnerability. This work is focused on estimating MTT by using environmental tracers in the framework of high-mountain karst systems with a very thick unsaturated zone (USZ). To this end, it is adapted to alpine zones a methodology that combines a semi-distributed rainfall-runoff model to estimate recharge time series, and a lumped-parameter model to obtain MTT. The methodology has been applied to the Port del Comte Massif (PCM) hydrological system (Southeastern Pyrenees, NE Spain), a karst aquifer system with an overlying 1000 m thick USZ. Six catchment areas corresponding to most important springs of the system are considered. The obtained results show that hydrologically the behavior of the system can be described by an exponential flow model (EM), with MTT ranging between 1.9 and 2.9 years. These MTT values are shorter than those obtained by considering a constant recharge rate along time, which is the easiest and most applied aquifer recharge hypothesis when estimating MTT through lumped-parameter models. (C) 2018 Elsevier B.V. All rights reserved.