The change in the dynamic response of shallow soils as caught by two geophysical test campaigns is exploited to numerically predict the variation in the ground borne vibrations induced by the passage of underground trains. Multiple causes may lead to a variation in the perception of vibrations over time: from an increase in the train load to the roughness of the railway track, from the increase of the train speed to the modification of the dynamic response of the surrounding soil. In the present study, special attention is devoted to the effect of the hydrological regime on the latter. Two scenarios were calibrated on the results of repeated geodynamic tests on the same site in Milano but at two different times. The two investigations revealed differences in the dynamic response of above-ground soils which can be related to different saturation profiles. The passage of a typical convoy is simulated in the time domain. Differences between the two scenarios are highlighted together with the role played by the static axle load of the train. Furthermore, comparisons with recorded accelerations are provided to validate the model.