Perfluorinated compounds (PFCs) are widespread environmental pollutants that pose risks to ecosystems. Our research in the Yellow River Delta watershed focused on two rivers, Shenxian Gou and Tiao He, representing the impacts of oil extraction and urban wastewater, respectively. The purpose of this study was to evaluate the effects of different concentrations of PFCs on the microbial community structure and to investigate the mechanisms of their degradation by microorganisms. The results suggested that the microbial communities were influenced by the combined effects of PFCs concentration and water quality (0.33), with a notable emphasis on the impact of PFCs (0.28). The 16S rDNA gene amplicon data revealed significant variations in both the structural composition and functional aspects of microbial communities across different concentrations of PFCs (p < 0.05). In particular, perfluorooctanoic acid (PFOA) was found to interfere with several microbial metabolic functions, including DNA functions, structural pathways, and the tricarboxylic acid cycle. Certain bacteria, such as Hydrogenophaga, Luteolibacter, and Pseudorhodobacter, were found to synergistically promote perfluorooctanoic acid degradation. The results improve our understanding of the mechanisms through which microbes adapt to and degrade PFCs in different environments and the complex effects PFCs have on ecosystems.