ObjectiveMicrobial contamination in drinking water distribution system is a critical factor affecting water supply safety, particularly in multi-source mixed water supply areas. Dynamic water quality variations and hydraulic fluctuations further complicate microbial community structures. This study aims to explore the effects of such fluctuations on microbial composition in blended supply zones.MethodsThis paper investigated blended water supply zones in Beijing, where water samples were collected from multiple locations to analyze the spatial variation of water quality parameters. In addition, high-throughput sequencing was applied to characterize the microbial community structures associated with planktonic and particle-attached fractions.ResultsResults indicated that electrical conductivity, residual chlorine, turbidity, and adenosine triphosphate (ATP) concentrations fluctuated across sampling points, highlighting the impact of blended water supply on water quality stability. Correlation analysis indicated that certain high-abundance microbial taxa were significantly associated with water quality parameters (p<0.05), with particle-associated microorganisms showing higher sensitivity to water quality fluctuations. Alpha diversity analysis showed that while the species richness of particle-associated communities was slightly higher than that of planktonic communities, the difference was not statistically significant (p>0.05), likely due to chlorine disinfection reducing the disparity between the two and the protective role of particulate matter in providing microbial refugia. Beta diversity analysis revealed that microbial community differentiation was primarily driven by water quality fluctuations associated with mixed water supply rather than by microbial phase states. Differences in microbial composition between planktonic and particle-associated communities were observed, with particulate matter enhancing the selective influence of water source variability and affecting the distribution of low-abundance microbial flora. The abnormal proliferation of Ralstonia spp. at specific sites intensified community divergence, while the high relative abundance of uncultured microbial flora suggested that unstable pipe network water quality could pose a potential risk for pathogen transmission.ConclusionThis paper provides insights into the spatial heterogeneity and potential risks of microbial communities in blended water supply systems, highlighting the need for enhanced dynamic monitoring of key water quality parameters and improved particulate control, thereby offering a scientific basis for water quality monitoring and management strategies in drinking water distribution system.