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Based on the analysis of dilution capacity and self-purification capacity of water body, the dilution, dispersion, entrapping and purification principles of pollutants in river system at river network area were discussed in this paper. Also, the one and two dimensional models of water quantity needed for improving water environment quality and pollutant concentrations were developed for rivers and lakes respectively. The calculation method for the quantity of water transfer was given and the forecasting evaluation of the effect of water transfer was carried out. It was took the project, water transfer from Yangtze River to improve the water quality of rivers in Zhangjiagang City, as an example, and changing principles of water quantity and quality were observed in rivers and lakes through site water transfer experiments. The theory of estimating parameters in inverse problem was used to determine parameters in water quantity and quality models. The water quantity and quality coupled models in river system were applied to calculate the minimal water transfer quantity. The theoretical and technical support for the improvement of water environmental quality in Zhangjiagang City and the project water transfer form Yangtze River to Taihu Lake were provided.