Diverse bacterial communities colonize on the surfaces of aquatic macrophytes' roots and leaves and play important roles in promoting plant growth, nutrient uptake, and environmental fitness. These bacterial taxa also profoundly affect the biogeochemical cycles in aquatic ecosystems by co-evolving with their plant hosts as “holobiont”. However, the current understanding and application of the epiphytic bacterial community associated with aquatic macrophytes remains unclear. Understanding the composition and assembly mechanism of the epiphytic bacterial communities associated with aquatic macrophytes and elucidating the complex interactions between these bacterial taxa and their hosts will be helpful to reveal and regulate the ecological functions of aquatic macrophytes microbiome and maintain the health of aquatic ecosystems. In this review, we systematically summarized the diversity and composition characteristics of the epiphytic bacterial communities associated with aquatic macrophytes. We also summarized the driving factors that shape the bacterial community composition, from the perspective of host selection effects, environmental factor control, and bacterial interactions. Moreover, we discussed the ecological processes affecting the bacterial community assembly and further emphasized the impacts of macrophyte epiphytic bacterial communities on the carbon and nitrogen cycling in lake ecosystems. Finally, we proposed that future researches on epiphytic bacterial community associated with aquatic macrophytes should focus on microbial functional traits, core species, the application of synthetic bacterial communities, microbial response to global changes as well as technology aiming to increase pollutant removal and carbon sink via macrophytes and their associated microbes.