A novel transferable modelling approach was applied to reveal subsurface flow processes and thus complement, verify, and enhance the conceptual knowledge of the small (1.78 km2) mountainous experimental catchment Uhlířská in the northern part of the Czech Republic. We used the S1D model to simulate flow and tracer movement in the vadose zone. MODFLOW‐2000, MODPATH and MT3DS models were used to determine residence time and flow trajectories in the saturated zone. The isotopic tracers 3H and 3H/3He were used to calibrate the groundwater model in the deeper aquifer layers. The modelling approach was established to enhance our understanding and quantification of interactions between the hillslope (82% of the area) and wetland (18% of the area), as well as the aquifer beneath the catchment. Numerical methods corroborated the estimated groundwater residence times and provided a catchment water balance in support of process knowledge. The combined modelling yielded the following water balance for the period 1961–2014: 1220 mm annual precipitation amount, 456 mm of percolation through the soil matrix domain on hillslopes, 534 mm of water through the hillslope preferential domain, and 22 mm of water through the matrix of the riparian wetland. This partitioning resulted in an area‐weighted average annual groundwater recharge of 430 mm. The water residence time on the hillslopes did not exceed 1 year, and was about 10 years for the saturated zone, with 20% of water older than 100 years in the deepest part of the aquifer. The conceptual knowledge of subsurface hydrological processes combined with numerical modelling, computation of water balance and isotope‐supported calibration is considered innovative, particularly the 3H/3He method to determine water residence times of young groundwater in the saturated zone. Lessons learned and recommendations are presented to apply the knowledge from the Uhlířská in the broad context of small research catchments.