A total of 11 sediment samples were collected from the sites along Haihe River-Bohai Bay, with site 1 at the beginning of Haihe River and site 11 in Bohai Bay, about 150 km away from site 1. Quinone profiles were used for the analysis of microbial community as influenced by pollutants in water and sediments, such as heavy metals, and other environmental factors. Nineteen species of quinones were found at site 1 while only six species at sites 10 and 11. Both the diversity of quinone species (DQ) and the number of quinones were higher in the sediments from Haihe River and the near-sea area of Bohai Bay than in those from the deep-sea area. The β diversity values were significantly higher, while Jaccard indexes of similarity were much lower among non-contiguous pairs of sites as compared with the contiguous ones. Cluster analysis indicated that quinone profiles may be grouped into two main clusters (sites 1-7 and sites 8-11), and there were higher similarities within the groups than between groups. Quinone species composition varied at different sites. Ubiquinones such as UQ-8, UQ-9, and UQ-10 and menaquinones such as MK-6, MK-7, MK-8 were isolated from all the sites and accounted for the largest proportions. Pearson correlation analysis revealed that both the number of quinone species and DQ correlated positively with total organic carbon contents in water and sediments, but negatively correlated with salinity and electroconductivity and did not correlate significantly with heavy metal contents in water.