In this paper, the performance of a single-span railway bridge with integrated retaining walls during high-speed train passage is investigated by considering different uncertainties originating from modeling assumptions and measurement processes. For this purpose, a single-span railway bridge is equipped with numerous accelerometers and is excited using a hydraulic actuator across different frequency ranges. A comprehensive 3D model of the bridge and the surrounding soils is created in Abaqus. Different sets of material properties for concrete and soil components are derived by converging the frequencies and damping ratios of the first three structural modes, using both the Error-Domain Model Falsification (EDMF) and Residual Minimization (RM) methods. These material properties are subsequently utilized in high-speed train passage analysis, and the results are compared.