A numerical investigation on the effectiveness of open and in-filled trenches in reducing the building vibrations due to passing trains is presented. Particularly, a two-dimensional soil-structure system containing the cross section of a railway embankment, the underlying soil, a trench barrier and a nearby six-storey building is considered. For the analysis, a time domain coupled boundary element-finite element algorithm is employed. Unlike most of the previous formulations, this model completely considers the soil-structure interaction effects and directly determines the effect of the wave barrier on the structural response. The effects of geometrical and material properties of the trench and its backfill material on the structural response are investigated. The results point out that using a trench barrier, a reduction level up to 80% of the building vibrations and internal forces can be achieved. Increasing the depth or the width of a trench may improve its reduction effect and a softer backfill material results in a better isolation eff