Surface water and groundwater always behave in a coupled manner and are major components of hydrologic cycle. However, surface water simulation models and groundwater simulation models are run separately most of the time. Few models focus on the impact of hydraulic changes in the surface water flows on the groundwater, or specifically, the impact of a water transfer project to fill a seasonally dry channel. In this study, a linked surface water and groundwater simulation model was developed to assess the impact of a trans-basin water diversion project on the groundwater. A typical plain area east of Beijing was selected as a case study, representing Beijing’s main source of groundwater used for drinking water. A surface water quality model of the Chaobai River was developed based on the Water Quality Analysis Simulation Program (WASP), and a groundwater model was developed based on the Modular Finite-Difference Groundwater Flow Model (MODFLOW) and the Modular 3-D transport model (MT3D). The results of the surface water simulation were used as input for the groundwater simulation. Water levels and four contaminants (NH -N, COD , F, As) were simulated. With the same initial and boundary conditions, scenario analyses were performed to quantify the impact of different quantities of diversion water on the groundwater environment. The results showed the water quality of the groundwater sources was not significantly affected.