Impacts of deposits discharged from a municipal pipe on urban river sediment were investigated in the Hucang River in Tianjin, China. At the outlet of the pump station, the average concentrations of total nitrogen (TN), total phosphorus (TP), and total organic carbon (TOC) in the sediment increased sharply from 2390, 799, and 14,600 mg/kg to 6500, 3700, and 153,000 mg/kg, respectively, and remained stable at high level after the rainy season. A portion of pollutants would migrate along the river, and the concentration was usually in a negative relationship with the distance. The average Shannon-Wiener value on the upstream section was higher than those on the downstream sections. This revealed that the deposits discharged decreased the bacterial diversity in the sediment, and high concentrations of pollutants may markedly change the bacterial community structure in the sediment. To reduce the pollution of the urban river after rainy season, four kinds of microbial consortiums A (Zhangda), B (Aiersi), C (Qinghe), and D (Inpipe) were applied to bioremediate the polluted sediment in lab scale. Bioaugmentation with microbial consortium A showed good performance on the bioremediation of the polluted sediment. The average removal efficiency of TN, TP, and organic matter reached 35.5, 43.7, and 39.1%, respectively, after 22 days of treatment. Moreover, the bacterial evenness and diversity in the sediment markedly increased, indicating that the microbial environment was more favourable after bioaugmentation and sustainable development would be guaranteed. This study improves our understanding of the impacts of deposits discharged from a stormwater drain system on urban river sediment, and explores the effectiveness of bioaugmentation for the bioremediation of polluted sediment, which will provide the basis of sewer deposit pollution control.