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A study on the mathematical modeling of the two dimensional,time-dependent variation of bottom topography caused by the spur dikes of the deep water navigation channel project in the Yangtze estuary is reported. The hydrodynamic flows are computed using the DELFT3D which serves as the base of computation of sediment transport and bottom deformation. A model of fine sediment transport is developed and implemented in an orthogonal curvilinear coordinate system by the finite difference method. Using the observed water depth of the North Channel of Yangtze estuary from 2001 to 2002, the model is calibrated and validated to determine the parameters in the sediment model. The computational results of the changes of the bed in the North Channel induced by the spur dikes coincide with the measured data except the area near the structures.