A storm surge is a complex phenomenon in which waves, tide and current interact. Even though wind is the predominant force driving the surge, waves and tidal phase are also important factors that influence the mass and momentum transport during the surge. Devastating storm surges often occur in the Bohai Sea, a semi-enclosed shallow sea in North China, due to extreme storms. However, the effects of waves on storm surges in the Bohai Sea have not been quantified and the mechanisms responsible for the higher surges that affect part of the Bohai Sea have not been thoroughly studied. In this study, we set up a storm surge model, considering coupled effects of tides and waves on the surges. Validation against measured data shows that the coupled model is capable of simulating storm surges in the Bohai Sea. The simulation results indicate that the longshore currents, which are induced by the large gradient of radiation stress due to wave deformation, are one of the main contributors to the higher surges occurring in some coastal regions. The gently varying bathymetry is another factor contributing to these surges. With such bathymetry, the wave force direction is nearly uniform, and pushes a large amount of water in that direction. Under these conditions, the water accumulates in some parts of the coast, leading to higher surges in nearby coastal regions such as the south coast of the Bohai Bay and the west and south coasts of the Laizhou Bay. Results analysis also shows that the tidal phase at which the surge occurs influences the wave–current interactions, and these interactions are more evident in shallow waters. Neglecting these interactions can lead to inaccurate predictions of the storm surges due to overestimation or underestimation of wave-induced set-up.