In this paper, a numerical model that can simulate the flow in a storm sewer system with merging and dividing pipes is developed. The model is based on the de Saint-Venant equations and the four-point implicit finite difference scheme is used. The boundary condition at the dividing junction can be treated using one of the following three methods: weir flow equation, regression equation obtained from experimental data, and side-weir flow equation. In actual applications, the suitable equation can be chosen according to the type of the dividing structure. The upstream boundary condition can be either discharge or stage hydrographs. The downstream boundary condition can be chosen from the following: the water stage hydrograph, the discharge hydrograph, the rating curve, or their combination. Actual applications show that the simulated results are in good agreement with the observed data.