The sudden and accidental water pollution response system (SAWPRS) for Yangtze River in central China required to develop a hydrodynamic and transport model, which is readily available and capable of simulating a large river system within GIS environment. This study facilitates such effort by developing a parallel computing method based on digital elevation model (DEM) using overlapping domain decomposition approach (ODDA) and message passing interface (MPI) protocol. The hydrodynamic and transport model was redesigned using finite volume method for hydrodynamic and transport model dispersion, the SIMPLEC method for solving the flow field, and the pressure weighted interpolating method for the flow field modification. This modelling approach was verified in two experiments using different sets of computer clusters. The model output was evaluated against the measured data collected for the year 1998 for Wanzhou, an upstream river segment of Yangtze River. The relative error was found to be less than 10%. The performance of parallel computation was found excellent as evident from the cost efficiency values greater than 0.81 in both experiments and increased computation speed while increasing the number of computer clusters. Overall, the parallel computing modelling system developed here was found to meet all requirements of SAWPRS. Copyright © 2010 John Wiley & Sons, Ltd.