The river and groundwater are contaminated by pollution source of a waste landfill and others near river. The contaminant transport and response of aquifer parameters are studied in the aquifer affected by variation of river stage. First, the equation for component of variation velocity with river stage is developed by using the analytical solution of groundwater governing equation. The numerical model which considered component of variation velocity is constructed for the transport of mass by advection and dispersion. In order to verify a numerical scheme, the analytical solution is used. The numerical solution is coincided with the analytical one. Aquifer parameters of Nanjido are used as the data for numerical experiment. Second, the range of aquifer parameters is established in order to reponse contaminant transport in aquifer with river stage. The result of numerical experiment shows that the range of the storage coefficient except hydraulic conductivity and effective porosity is relatively sensitive to the contaminant transport. When the storage coefficient is the order of 10$^$－2/, the response is very sensitive to the variation of river stage.