Modeling of wastewater transport and degradation in soil aquifer is a problem of concern with regard to the optimization of design and operation of the wastewater soil treatment system.To solve this problem, three-dimensional groundwater flow and wastewater transport and degradation model was developed using MODFLOW and MT3DMS modeling.The developed model was calibrated using the Soil Infiltration Treatment System (SITS) in the Chongming island of China after considering the river-groundwater interaction and the regional geological and hydrological conditions.Using the calibrated model, the following problems with regard to the design and operation of SITS were discussed: (1) Allowable hydraulic load.The hydraulic load increases with the drop in the water level of the adjoining river, the increase in the actual soil area under operation, and the increase in the distance among the individual operation units of SITS.(2) Optimized layout of the groundwater monitoring wells.The concentration contour of the simulated contaminants is very useful to depict the typical areas that are most severely polluted and very sensitive to the peripheral environment,, thus lesser number of monitoring wells can be set up based on the model, and the goal of the accurate assessment of the influence of soil-infiltrated wastewater on groundwater can be achieved.