Abstract: A complete plant structure-foundation-water body coupling FEM model have been developed to study the effects of water bodies in the flow passages and reservoir on the dynamic characteristics and seismic responses of a run-of-river hydropower house. This model adopts potential-flow fluid elements to simulate these water bodies, and a viscous-spring boundary for considering the radiation damping of the foundation. The results show that the water bodies have a significant effect on the vibration frequencies and seismic responses of the powerhouse and that neglecting the effects of water body may be unfavorable to the structural design of powerhouse. Simulation errors could be produced by simplification in those methods that simulate the water body in the reservoir only, such as the added mass model or potential fluid model, because the water bodies in the flow passages have a significant effect. Thus, the effect of water bodies in the flow passages must be considered for more accurate simulations.