Purpose <p>Some hydropower stations have encountered serious vibration problems, it is necessary to improve the dynamic prediction accuracy of key structures such as the runner and top cover.</p> Method <p>In this paper, a numerical model incorporating the runner, top cover, and gap water is established. The acoustic fluid-structure coupling method is used to simulate the mode of this model, and the interaction among the runner, water of leakage sealing gap and top cover is analyzed.</p> Results and Conclusions <p>The results show that the small deformation of the top cover has little effect on the mode of the runner, only changing the phase of the mode shape. The frequency of the nodal diameter (ND) mode shape of the top cover increases due to the influence of the runner. It is found that gap water has no effect on the nodal circle (NC) mode shape, while the frequency of the ND mode shape of the runner is improved with the increasing of the gap water thickness. Furthermore, it is also found that the gap water causes frequency hopping. The runner occurs frequency hopping at a thickness of 0.6δ, and the top cover occurs frequency hopping at thicknesses of 0.6δ, 0.8δ, and 1.0δ.</p>