Abstract: Scour around bridge and aqueduct piers is generally considered as a key factor that could probably bring devastating damage to river-crossing structures. Using numerical simulations, we can analyze and forecast the risks caused by such local scours during a flood. This paper describes a system of hydrodynamic and sediment transport models the authors developed, namely HydroCRS, which can be used for calculation of the flow field, sediment transport, and riverbed scour around underwater structures. This model system adopts integration of 1D and 2D models to improve computational efficiency, which also facilitates its connection to hydrological models. Associated with a hydrological model for real-time flood forecasting derived from the weather forecast data, it can achieve the prediction of dangerous scenarios of flows around a river-crossing structure. The model system is applied to simulations of the Shuangji River aqueduct of South-to-North Water Diversion Project, revealing the complicated characteristics of local scour around bridge piers and offering helpful results for the risk management of the aqueduct.