A depth-integrated two-dimensional numerical model of current, salinity and sediment transport was proposed and calibrated by the observation data in the Yangtze River Estuary. It was then applied to investigate the flow and sediment ratio of the navigation channel, i . e. the North Channel of the Yangtze River Estuary, before and after the first phase waterway project is implemented. Particularly, the influences of groin length and the orientation of the submerged dam on the flow ratio and sediment load discharging into the North Channel were discussed. The numerical results demonstrate that less sediment load discharges into the navigation channel, which unburdens the waterway dredging, but in the meantime the flow ratio is also decreased. The flow and sediment ratio can be adjusted by changing layout and dimensions of the hydro-structures, such as the groin length, the top height, etc. The effect of the orientation of the submerged dam is more obvious than the groin lengh.