This study deals with numerical modelling of hydraulic and transport phenomena in granite of the Bohemian massif in Bedrichov, Czechia (Czech Republic). Natural tracers represented by stable isotopes δ¹⁸O and δ²H were collected at the tunnel outflow points and nearby catchment and their concentrations were monitored for seven years. The study compared transport simulations by a two-dimensional (2D) physically based model (advection-dispersion) developed in Flow123d software and a simpler lumped-parameter model, calculated with FLOWPC. Both variants were calibrated with UCODE software, either fitting the concentration data alone, or including the tunnel inflow rates in the case of the 2D model calibration (either in separate steps or within a single optimization problem). Since each of the models describes the tracer transport with different parameters, the models were compared based on the mean transit time as a postprocessed quantity. Besides this, two different options for processing the recharge data (input for both models) were evaluated. Calibration and data interpretation were possible for three of the four observed places in the tunnel, thus determining the depth limit of applicability of the stable isotopes. The estimates for discharge sampling at 25–35 m depth based on inverse modelling provide reasonable values of mean transit time (20–40 months) for the lumped parameter models, little revising the results of previous studies at the site. The resulting transport parameters of the advection-dispersion model (porosity and dispersivity) are in accordance with the hydrogeological structures present at the sampling sites.