Railway induced vibrations on short-to-medium span simply-supported (SS) bridges is addressed in this contribution. Such structures may experience high levels of vertical acceleration at the platform, leading to adverse consequences such as a premature degradation of the ballast layer and passenger discomfort. In the present study, the evolution of the bridge dynamic response when soil-structure interaction (SSI) is taken into account is investigated. To this end a coupled three-dimensional (3D) Boundary Element-Finite Element model (BEM-FEM) formulated in the time domain is implemented to reproduce the soil and structural behaviour, respectively. First, a set of soil-bridge systems of interest is defined, covering a wide range of lengths and natural frequencies for the structures, and an interval of expectable elastic properties and damping levels for the soil. Then, different types of analyses are performed on the soil-bridge systems extracting conclusions regarding the effect of including SSI in numerical models for predicting the bridge behaviour under railway traffic. In particular natural frequencies and modal damping levels are identified, and the structure amplification after the passage of a moving load in free vibration is investigated. Conclusions regarding how resonance and cancellation conditions may be affected by soil properties are extracted. Finally, the dynamic response of a real bridge, belonging to the Spanish railway network, is evaluated under the circulation of trains that induce second and third resonances of the bridge fundamental mode. The effect of the soil flexibility, soil material damping and the bridge resonance order are evaluated. Conclusions regarding the appropriateness of the results provided by common models which do not include SSI effects are extracted.