Reservoir sediment is one of the most stressful environments for microorganisms due to periodically oxygen minimum conditions. In this study, the abundance and composition of bacteria associated with sediments from three drinking water reservoirs (Zhoucun, ZCR; Shibianyu, SBYR; and Jinpen, JPR) were investigated by quantitative polymerase chain reaction and 16S rRNA-based 454 pyrosequencing. The results of physico-chemical analysis of sediments showed that the organic matter and total nitrogen were significantly higher in ZCR as compared to JPR (P < 0.01). The bacterial abundance was 9.13 × 10(6), 1.14 × 10(7), and 6.35 × 10(6) copies/ng DNA in sediments of SBYR, ZCR, and JPR, respectively (P < 0.01). The pyrosequencing revealed a total of 9,673 operational taxonomic units, which were affiliated with 17 phyla. The dominant phylum was Firmicutes (56.83%) in JPR; whereas, the dominance of Proteobacteria was observed in SBYR with 40.38% and ZCR with 39.56%. The Shannon-Wiener diversity (H') was high in ZCR; whereas, Chao 1 richness was high in SBYR. The dominant genera were Clostridium with 42.15% and Bacillus with 20.44% in JPR. Meanwhile, Dechloromonas with 14.80% and Smithella with 7.20% were dominated in ZCR, and Bacillus with 45.45% and Acinetobacter with 5.15% in SBYR. The heat map profiles and redundancy analysis indicated substantial differences in sediment bacterial community composition among three reservoirs. Moreover, it appears from the results that physico-chemical variables of sediments including pH, organic matter, total nitrogen, and available phosphorous played key roles in shaping the bacterial community diversity. The results obtained from this study will broaden our understanding on the bacterial community structure of sediments in oxygen minimum and stressful freshwater environments.