Microbial communities in sediment are an important indicator linking to environmental pollution in urban river systems. However, how the diversity and structure of bacterial communities in sediments from an urban river network respond to different environmental factors has not been well studied. The goal of this study was to understand the patterns of bacterial communities in sediments from a highly dense urbanized river network in the lower Yangtze River Delta by Illumina MiSeq sequencing. The correlations between bacterial communities, the environmental gradient and geographical distance were analyzed by redundancy analysis (RDA) and network methods. The diversity and richness of bacterial community in sediments increased from upstream to downstream consistently with the accumulation of nutrient in the urban river network. Bacterial community composition and structure showed obvious spatial changes, leading to two distinct groups, which were significantly related to the characteristics of nutrient and heavy metal in sediments. Humic substance, available nitrogen, available phosphorus, Zn, Cu, Hg and As were selected as the key environmental factors shaping the bacterial community in sediments based on RDA. The co-occurrence patterns of bacterial networks showed that positive interaction between bacterial communities increased but the connectivity among bacterial genera and stability of sediment ecosystem reduced under a higher content of nutrient and heavy metal in average. The sensitive and ubiquitous taxa with an overproportional response to key environmental factors were detected as indicator species, which provided a novel method for the prediction of the pollution risk of sediment in an urban river network.