Observations from the Eel River shelf, northern California show that during times of significant sediment supply and energetic waves, sediment flux is dominated by down-slope, gravitationally driven transport within a near-bed turbid layer. These fluid muds are supported by wave-induced turbulence. Their thickness scales with the height of the wave boundary layer, and therefore thins offshore. Flux within these layers is not resolved by conventional three-dimensional hydrodynamic and sediment transport models. To represent this transport mechanism we therefore modified an existing three-dimensional sigma-coordinate model to include a near-bed turbid layer by adding a wave-boundary layer grid cell beneath the conventional sigma grid. Sediment concentrations within the wave boundary layer represent a mass balance between erosion and deposition from the seafloor, entrainment into the overlying water column, sediment settling, and flux divergence in the across- and along-shelf directions. The transport velocity within the wave boundary layer is estimated by a balance between frictional drag and the negative buoyancy of the turbid layer. The modified three-dimensional transport model replicates water-column and sea-bed observations of sediment dispersal and deposition on the Eel Shelf. Concentrations within the layer and depositional footprints of flood events proved to be sensitive to the settling and turbulence properties of the turbid layer. Development of a module for sigma coordinate models that includes this transport mechanism provides a means of comparing relative contributions of gravitationally-driven transport to conventional dilute resuspension, for studying other energetic, sediment-laden environments, and for comparing parameterizations of wave-supported fluid muds.