Vulnerability analyses of coastal or inland bridges in terms of flood actions and structural and fluid flow characteristics are carried out. In particular, a numerical model based on a two-phase fluid flow is implemented for the multiphase fluid system, whereas a three-dimensional formulation based on shell/volume finite elements is adopted for the structure. The governing equations can simulate the interaction between fluids and the structures, by using the Arbitrary Lagrangian–Eulerian (ALE) strategy. The results of the hydrodynamic forces, bridge displacements and dynamic amplification factors (DAFs) show that the existing formulas, available in the literature or in structural design codes, do not accurately predict the maximum design effects. For the investigated cases, the DAFs may vary from 1 to 4.5. The worst scenarios are observed for the upload vertical direction. Finally, the performance of the protection fairing system is investigated. The results show that such devices are able to efficiently reduce the effects of the wave load in terms of the applied hydraulic forces on the structure and bridge deformability, in particular, with 40% more accuracy than the unprotected configuration.