Suspended sediments (SS) pollution is one of the factors affecting the transfer from turbid water state to clear water state in shallow lakes. However, the interactions between suspended sediments and submerged plants are far from clear. In this study, we investigated the settlement laws of SS in overlying water and its impact on the epiphytic biofilm of Myriophyllum verticillatum and Vallisneria natans under water flow. At least 90% of turbidity can be removed from overlying water, and the decreasing trend of water turbidity fitted the logarithmic decay model in all treatments. The size distribution of SS fit the log-normal distribution model in the first 240 min after SS addition. It should be noted that the main peak particle sizes were lower in treatments with submerged macrophytes (8.71-13.18 μm) than without plants (15.14-19.95 μm). Water flow and SS addition significantly increased the thickness of biofilms attached to M. verticillatum (p < 0.05), but they together significantly reduced the biofilm thickness on V. natans (p < 0.05). SS increased the bacterial α-diversity but decreased eukaryotic one in epiphytic biofilms. However, water flow had a more significant impact on microbial communities (especially eukaryotes) than SS and plant species. The relative abundances of dominant phylum Proteobacteria, class Alphaproteobacteria and Betaproteobacteria, and class Verrucomicrobiae increased in epiphytic biofilms after SS addition. Co-occurrence networks reveal that photosynthetic microbes in epiphytic biofilms played an important role in microbial communities under water flow and SS, and many hub microbes were increased by SS addition but reduced by water flow. These data highlight that SS decline can be predicted by the logarithmic decay model and, SS and water flow can affect the epiphytic-biofilm on submerged macrophytes.