The black-odor phenomenon has been widely reported worldwide and recognized as a global ecological risk for aquatic environments. However, driving factors for black-odor-related microorganisms and potential self-remediation strategies are still poorly understood. This study collected eight water samples (sites A–H) disturbed by different factors from the Jishan River located in Jinmen, Hubei Province, China. Black-odor-related environmental factors and functional bacterial structure were further measured based on the basic physicochemical parameters. The results indicated that different types of disturbed conditions shape the distribution of water quality and microbial community structures. Site B, which was disturbed by dams, had the worst water quality, the lowest abundance of functional microbes for Mn, Fe, and S biotransformation, and the highest abundance of functional microbes for fermentation. The natural wetlands surrounding the terminus of the river (site H) were keys to eliminating the black-odor phenomenon. Potential black-odor-forming microorganisms include Lactococcus, Veillonella, Clostridium sensu stricto, Trichococcus, Rhodoferax, Sulfurospirillum, Desulfobulbus, and Anaeromusa-Anaeroarcus. Potential black-odor-repairing microbes include Acinetobacter, Mycobacterium, and Acidovorax. pH and COD were paramount physiochemical factors contributing to blackening-odor-related microorganisms. This study deepens our understanding of driving factors for black-odor-related microorganisms and provides a theoretical basis for eradicating the black-odor phenomenon.