Aerobic denitrifiers coupled with a denitrification agent were applied in the sediment of an urban river for the bioremediation of nitrogen pollution. The results revealed that 14.7% of the total nitrogen in the sediment was removed after 115 days of treatment and the nitrate nitrogen concentration removal rate was enhanced in the overlying water. Compared with the control, the total transferable nitrogen in the sediment increased from 0.097 to 0.166 mg/g, indicating that more nitrogen is likely to be involved in the biogeochemical cycling of nitrogen. Increased urease activity indicated the possible further potential of nitrogen biodegradation, while the decreased protease pointed to the low concentration of protein remaining in the sediment. Sequencing revealed that the bacterial community diversity in the sediment increased significantly after 43 days of treatment and that the effect persisted. Compared with other microcosms, the dominant phyla in the sediment after 43 days were Firmicutes, Elusimicrobia, Spirochaetae and Fibrobacteres; whereas, after 115 of treatment, the dominant bacteria were Nitrospirae, Deferribacteres and Chloroflexi. The dominant bacteria in the sediment are mainly associated with nitrogen cycling and thus contributed considerably to nitrogen removal in the sediment. Overall, the direction of species succession was similar to natural succession; namely, there were no undesirable ecological risks involved. This study highlights the possible benefits and feasibility of using bioaugmentation technology coupled with biostimulation to remediate nitrogen-polluted sediments.