A two-dimensional numerical model using the fifth-order weighted essentially nonoscillatory (WENO) scheme is presented in order to estimate topography change due to tsunami with high accuracy. In the model, the Cartesian coordinate system is adopted, and the fractional area/volume obstacle representation (FAVOR) method is introduced into the governing equations in consideration of applying the estimation to such as harbor shape with complex topography. In order to verify the validity and applicability of the model, it is applied to small-scale laboratory experiments and to large-scale actual topography change. Consequently, although the model cannot reproduce local scouring around breakwater where three-dimensional flow is developed, it is clarified that the model can reproduce the topography change well by contracted flow around a harbor.