Parameters of waves in water area of the projected port are normally obtained using physical and numerical modelling. Physical modelling allows defininig structural details of the port’s facilities and provides with information for the appropriate selection of a numerical model. The problems created by this approach are shown in the case study of the projected port in Vostok (East) Bay, the Sea of Japan. The experimental study of waves propagation in the port water area was carried out in the wave basin. The port area was reproduced at a scale of 1:50, and the modelling was conducted under the Froude number similarity. Experimental results are provided for the study of wave propagation in the port model from the effects of the waves of 5 % exceedance probability. To confirm the results of the laboratory experiments, four relevant mathematical models were used, one of them is the ARTEMIS model which is based on gentle slopes equations. The heights of numerically modeled waves in the control points were compared with the waves measured with sensors-wave gauges. The calculated values at the control point and minimum and maximum values in a circular neighborhood with the radius of 30 m (1/4 of the average wavelength of 120 m) were compared with the results of the experiments. The proposed approach allows comparing the results of physical modelling with the results of numerical modelling and selecting the appropriate numerical model based on the results of the comparison.