A novel approach that couples hydrological and thermochronological modelling is tested in a well-known hydrothermal system, the Inner Western Carpathians, providing insights of the yet-unexplained Apatite Fission Track (AFT) ages of the Podhale Basin. Our new model improves previous ones by incorporating the effects of fluid circulation, by considering compaction, smectite dehydration and meteoric water as sources of fluid. Rock properties such as thermal diffusivity, porosity and permeability, are dependent on lithology and the effective-stress state of the system, making our calculations depart from previous efforts on thermochronological modelling. Particularly, we examined young (around 12 Ma) apatite fission track ages from Oligocene strata of the Podhale wild flysch, which suggest the occurrence of either substantial burial or an elevated basal thermal paleogradient, even though none of the above have been documented in the area. Such problem is addressed on this contribution, since by reproducing previous numerical experiments but adding groundwater circulation this time, improved thermally-reset AFT ages of the Podhale Basin are obtained. Thermal, hydrological and mineralogical observations are successfully reproduced, putting forward the calibration and validity of the model here proposed. Furthermore, our findings not only unveil the linking between the hydrological and thermal phenomena present in the study region, but also, trigger new questions on the processes that should be taken into account when thermochronological calculations are concerned.