Abstract: In order to provide a guidance for a coal preparation plant to make rational site selection of its emergency pond for guarding against pollution of surface water bodies by seepage of pollutants from the pond, a visualized three-dimensional groundwater seepage model and a pollutant migration model are developed using the MODFLOW and MT3D modules of GMS software to simulate the patter of migration of pollutants in groundwater. As revealed by study results, when the pond is set at the siteⅠ, the river and streams cannot be directly contaminated by pollutants even the effluents in the pond is temporarily kept in the pond for 30 days; in the case that the pond is set at site Ⅱ, the downstream rivers and ditches can get directly polluted; and the the siteⅠ, the effluents should not be kept in the pond for over 30 days for avoiding direct contamination of surface water bodies. It is demonstrated that with the use of the above mentioned two models established with the GMS software, a reliable intuitive basis can be provided for engineering construction and design.