[Objective] The middle route of the South-to-North Water Diversion Project faces risks of sudden water pollution due to hazardous material transport over cross-canal bridges and inflow of external floodwaters during the flood season. To support the treatment of water pollution emergencies, a unified hydrodynamic and water quality model for the canal system, including structures such as control gates, offtakes, inverted siphons, and escape gates, was developed. [Methods] The St. Venant equations were solved to simulate hydrodynamic characteristics of the water flow. Based on a cross-sectional control volume, a one-dimensional water quality model was established, with the continuity equation representing the pollutant mass conservation equation. The model was developed using FORTRAN90, enabling online pre-simulation of sudden water pollution diffusion and multi-gate joint control operations. [Results and Conclusion] Simulation results show that closing the diversion and increasing the discharge of the water discharge gate can significantly improve the pollutant emission efficiency, while the closing speed of control gates determines the pollution control effectiveness. This study provides technical support for the prevention and control of sudden water pollution incidents in the middle route of the South-to-North Water Diversion Project.