Municipal wastewater reclamation and reuse has been an effective way to solve problems of shrinkage and drying up of rivers and lakes. The residual pollutants in recycled water may pose a risk to groundwater. A field study on the spatial and temporal variations concentrations of nitrate, ammonia and chemical oxygen demand (COD) was conducted in Beijing, where recycled water is used to recharge dry rivers. And the effect of a riverbank filtration (RBF) on the nitrogen and organics removal from the Qingyang River was investigated. Water samples from recycled water, river water and groundwater were collected for nitrate, ammonia and COD measurement. The results indicated that river water quality was improved when recycled water was refilled to the river course. The concentration of nitrogen and total phosphorus decreased along the flow directions in the Qingyang River. Higher temperature in summer can promote nitrogen and COD removal in the river. The results indicate that about 63%, 89% and 41% of nitrate, ammonia and COD was removed from the river bank filtration. These results indicate that improving the removal of nitrogen and organics in recycled water and optimizing the management of recharging operation could reduce the risks of nitrogen and organics.