Due to inefficient removal of microplastics by drinking water treatment process, widely distributed microplastics in drinking water sources may pose risks to drinking water safety. To explore the factors influencing the colonization of bacteria on microplastics and biological risks posed by microplastics in drinking water sources, we exposed microplastics with different sizes and polymer types to water from Yangtze River and Jialing River for 21 days under controlled conditions. High-throughput sequencing and qPCR were conducted to qualitatively and quantitatively analyze the bacterial community on microplastics. The results showed that bacteria tended to adhere to the surfaces of microplastics, resulting in higher community richness and diversity and different community structure on microplastics compared with those in incubation water. The number of bacteria on microplastics increased with decreasing particle size. It was the nature of incubation water rather than microplastics determined the bacterial community structure on microplastics. Some potential pathogens were discovered on microplastics, especially Mycobacterium which accounted for a high proportion. Overall, this study provided an insight into microplastic biofilm and the challenges brought by them in drinking water sources.