In this research, we develop a numerical fluid simulator coupled with a structural analysis. The purpose of this system is to efficiently calculate all stages of a tsunami from source to runup, including structural deformation. We also investigate the stability of breakwaters at Kamaishi port. The numerical results are compared with physical experiments, revealing good agreement. The system is applied to the local conditions at Kamaishi port to verify its applicability. Most of the breakwaters are washed away, which is similar to the actual reported damage, indicating that the proposed system can effectively reproduce tsunami structural damage.