Naturally present aquatic microorganisms play an important role in water purification systems, such as the self-purification of surface waters. In this study, two water sources representing polluted surface water (Olympic Green; OG) and unpolluted surface water (Jingmi river; JM), were used to explore the self-purification of surface water by bacteria under different environmental conditions. The dominant bacterial community of OG and JM waters (both are Firmicutes and Proteobacteria) were isolated, cultured, and then used to carry out flocculation tests. Results showed that the flocculation ability of the dominant bacteria and extracellular polymeric substances (EPS) obtained from OG isolation was significantly greater than that from JM. Further examination illustrated that the main components of EPS were polysaccharides, which played an important role in improving the flocculation ability of bacteria. EPS from dominant cultural bacteria strains (OG1 and JM3) isolated from the two different sources lacked hydrophilic groups (e.g. COOH) and had a networked structure which are the main reasons to enhance the flocculation ability. The bacterial diversity and redundancy analysis (RDA) results also showed that microbial community composition is determined by water quality (SS, TOC, and NH4+), and different Bacteroidetes, Actinobacteria and Proteobacteria community structures can improve the water body's ability to remove environmental pollutants (such as SS, humic acid and fulvic acid). These findings provide new information showing how bacterial communities change with environmental factors while maintaining the purity of surface water.