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In this paper, a two-dimensional numerical calculation algorithm for the water quality modeling in the Hengyang City section of the Xiangjiang River is researched considering the effect of the Dayuandu navigational key project. The research fiver is winding and has two branches resulted from an isle. The numerical calculation algorithm for the water quality modeling is set up on the basis of applying topographic map of the river course and the finite element method. The calculation result for the water quality modeling includes the concentration fields for various pollutants. The numerical calculation algorithm for the water quality modeling set up in this paper can be applied to shallow fiver with similar topographically complicated river course.