Beiyun River Basin is holistically suffering a water shortage and relatively concentrated flood risk. The current operation (level-control) of dams and floodgates, which is in passive defense mode, cannot meet the demands of both flood control and storm water resources. An integrated flood forecasting and management system is developed by the connecting of the hydrological model and hydrodynamic model and coupling of the hydrodynamic model and hydraulic model for dams and floodgates. Based upon the forecasted runoff processes, a discharge-control operation mode of dams and floodgates is proposed to be utilized in order to well regulate the flood routing in channels. The simulated water level, discharge, and water storage volume under different design conditions of rainfall return periods and floodgates operation modes are compared. The results show that: (1) for small floods, current operation modes can satisfy the objectives, but discharge-control operation can do better; (2) for medium size floods, since pre-storing of the floods affects the discharge of follow-up floods by floodgates, the requirement of flood control cannot be satisfied under current operations, but the discharge-control operation can; (3) for large floods, neither operation can meet the requirement because of the limited storage of these dams. Then, the gravel pits, wetlands, ecological lakes and flood detention basins around the river must be used for excess flood waters. Using the flood forecasting and management system can change passive defense to active defense mode, solving the water resources problem of Beijing city and Beiyun River Basin to a certain extent.