Abstract: The Modaomen Estuary has evolved from a runoff dominated to runoff-and-wave dominated estuary, since waves are now one of the important dynamic forces. However, the wave effects on the currents and floods in the Modaomen Estuary have not been studied well. A coupled wave-current model is developed in this study to consider the effects of waves on currents. The currents are simulated using a depth-averaged shallow water flow model that includes the wave radiation stresses varying with tidal level. The wave properties are calculated using the mild-slope equation, based on the water level and depth provided by the flow model. The numerical results show distinct wave induced currents and circulations in both ebb and flood tides in the Modaomen Estuary, especially around the shoals, under normal wave conditions. Because the wave propagates from the deep to the shallow water, the wave-induced currents block the ebb tide currents and the runoff. Thus, the seaward residual currents around the sand bars are reduced and the landward residual currents are increased. The wave effects cause the estuary adjustment and force the flow returning to the main channels, so that the seaward residual currents in the main channels are strengthened. The wave effects pose a threat of blocking the flood and altering the ratio of flood discharge in the main channels and floodplains. Because the annual average wave height is small, its effects are in the shallow water areas and the overall threat is limited.