Based on the characteristics of backflow, a two-dimensional mathematical model of sediment movement was established. The complexity of the watercourse boundary at the confluence of the main stream and the tributary was dealt with using a boundary-fitting orthogonal coordinate system. The basic equation of the two-dimensional total sediment load model, the numerical calculation format, and key problems associated with using the orthogonal curvilinear coordinate system were discussed. Water and sediment flow in the Chongqing reach of the Yangtze River were simulated. The calculated water level, flow velocity distribution, amount of silting and scouring, and alluvial distribution are found to be in agreement with the measured data, which indicates that the numerical model and calculation method are reasonable. The model can be used for calculation of flow in a relatively complicated river network