A coupled wave-current-sediment model is established and applied for muddy coasts. The model integrates the atmosphere model WRF, wave spectral model SWAN, 3D hydrodynamic model FVCOM, 3D suspended sediment model and 2D fluid mud transport model. To describe the properties of cohesive sediment motion under combined wave-current conditions, some key physical processes and their parameterizations are employed, including hindered settling, stratification effects, wave-enhanced sediment diffusivity, interactions between suspension layer and fluid mud layer, etc. A numerical simulation was carried out on the Lianyungang Harbor, China as a case study, validated against field observations during Typhoon Wipha. The storm-induced strong wind from NNW direction with speed higher than 15 m/s has lasted for a rise-and-ebb tidal cycle, turning the astronomical semidiurnal counter-clockwise rotary tidal current into quasi-unidirectional current with a constant direction of SE. The suspended sediment concentration presents to be higher in shallow water and the vertical distribution presents as the shape of “L” with high concentration accumulating near bottom but low concentration in middle and surface layers. The near-bottom maximum concentration is about 5–8 kg/m3 on the shoal and 3–6 kg/m3 in the channel and harbor entrance, whose occurrence lags behind the timing of the maximum wave height.