The solute transport model of groundwater is an important way to identify the contamination transfer rule and define the scope of pollution and the concentration distribution. It can provide the quantitative base for the reasonable exploitation of groundwater resources and the optimization design of groundwater exploitation program and the pollution remediation of groundwater. Based on the analysis of karst-fractured aquifer hydraulic properties and characteristics of pollutant migration in Mili river basin of Dehou reservoir,the paper used GMS software to establish the groundwater flow field and solute transport model. A numerical study for flow field and pollutants of karst-fractured water was made.It judged the distribution of pollution source and pollution plume extended range and analyzed the effect of pollutant migration on reservoir construction at arsenic factory.