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High regulation of dams or sluices disturbs flow regimes and pollutant transformation process significantly in most basins over the world. The water quality and quantity simulation in highly regulated river basins is always a very complicated task. The Huai River Basin is a typical area in China with the highest density of water projects and serious pollution problems simultaneously. In this paper, a procedure based on Soil and Water Assessment Tool (SWAT) was proposed to carry out the water quantity and quality simulation of Huai River Basin by incorporating the operation rules of dams or sluices into the reservoir regulation module. The water quality module in SWAT is extended to suit the actual situation of river basin in China. The results show that: for runoff simulation, 28 of all the 38 stations (73.7%) have the acceptable performance, with the average correlation coefficient and efficiency coefficient of 0 …