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This paper presents a numerical method forsimulating the 2-D tidal flow and water quality with the or-thogonal curvilinear coordinates. In order to overcome thecomputational difficulties in natural rivers, such as the com-plicated boundary figures, the great disparity between lengthand width of computational domain, etc. , orthogonal bounda-ry-fitted grid was used. The irregular domain in physical planewas transformed into a rectangular domain in a transformedplane, and the depth-averaged momentum equations and massequation were given and discretized based on the altatingdirection implicit finite difference scheme in curvilinear coordi-nates. The application of the presented method was illustratedby an example of analyzing the Yangtze River in the vicinity ofNanjing city. A fair agreement between the measured data andcomputed results demonstrates the validity of the developedmethod.