The sources of groundwater pollution and the influence of Three Gorges Reservoir on the downstream of the Yangtze River is analyzed based on spatial and temporal distribution of flow rate, geological structures of the Three Gorges Reservoir area, and regional water balance. The analysis result shows that there are deep fault structures and underground river systems in Three Gorges Reservoir area, through which the reservoir leakage may be recharged to the downstream areas or other outside basins. Therefore, pollution sources of groundwater in the lower reaches of the Yangtze River include not only upstream pollution, mining industry pollution, agricultural pollution, domestic and industrial solid waste pollution, but also the recharge of upstream polluted water through deep channels. Upstream protection should be taken into priority for thd groundwater pollution control in lower reaches.