The water inflow into a tunnel has been studied in a granite massif in Jizera Mountains, Czech Republic. The dominant inflow occurs in the shallow parts of the system and in few fault zones in the deeper part. A combination of 2D discrete fractures (planar representation of vertical conductive faults) and 3D equivalent continuum are used to model the flow around the tunnel in a kilometre-scale domain with Flow123D. The geometry is based on the digital terrain model and the positions of faults determined by geophysical methods. The meshing is difficult due to the small scale of the tunnel and intersections with the fault planes. The inflow is measured as a flow rate in a collecting canal either by either weirs or by the tracer dilution method in five segments of the tunnel. The hydraulic conductivities of upper weathered zone, lower compact massif, and the vertical faults were calibrated by fitting the inflow from these subdomains, using the inverse solver UCODE. The model is verified against a 2D vertical plane solution with a finer mesh. The fitted hydraulic parameters are consistent with data for other sites in the Bohemian massif.