The aim of this study was to investigate the benthic bacterial communities in different depths of an urban river sediment accumulated with high concentrations of nutrients and metals. Vertical distributions of bacterial operational taxonomic units (OTUs) and chemical parameters (nutrients: , , dissolved organic carbon, and acid volatile sulfur; metals: Fe, Zn, and Cu) were characterized in 30 cm sediment cores. The bacterial OTUs were measured using the terminal restriction fragment length polymorphism analysis. Biodiversity indexes and multivariate statistical analyses were used to characterize the spatial distributions of microbial diversity in response to the environmental parameters. Results showed that concentrations of the nutrients and metals in this river sediment were higher than those in similar studies. Furthermore, high microbial richness and diversity appeared in the sediment. The diversity did not vary obviously in the whole sediment profile. The change of the diversity indexes and the affiliations of the OTUs showed that the top layer had different bacterial community structure from deeper layers due to the hydrological disturbance and redox change in the surface sediment. The dominant bacterial OTUs ubiquitously existed in the deeper sediment layers (5–27 cm) corresponding to the distributions of the nutrients and metals. With much higher diversity than the dominant OTUs, the minor bacterial assemblages varied with depths, which might be affected by the sedimentation process and the environmental competition pressure.