Vegetation in natural river interacts with river flow and sediment transport. This paper proposes a two-layer theoretical model based on diffusion theory for predicting the vertical distribution of suspended sediment concentration in a flow with submerged vegetation. The suspended sediment concentration distribution formula is derived based on the sediment and momentum diffusion coefficients through the inverse of turbulent Schmidt number (S c t) or the parameter η which is defined by the ratio of sediment diffusion coefficient to momentum diffusion coefficient. The predicted profile of suspended sediment concentration moderately agrees with the experimental data. Sensitivity analyses are performed to elucidate how the vertical distribution profile responds to different canopy densities, hydraulic conditions and turbulent Schmidt number. Dense vegetation renders the vertical distribution profile uneven and captures sediment particles into the vegetation layer. For a given canopy density, the vertical distribution profile is affected by the Rouse number, which determines the uniformity of the sediment on the vertical line. A high Rouse number corresponds to an uneven vertical distribution profile.