The rapid release of nutrients by aquatic macrophyte decomposition directly results in the degradation of water quality and the deterioration of aquatic ecosystems. However, decaying macrophytes have indirect negative effects, mediated by bacteria in aquatic ecosystems, which may have long been underestimated. In this study, 16S rRNA sequencing was used to investigate the structural succession, possible metabolic function shifts, and specific environmental drivers of the bacterial community during the decomposition of four typical aquatic macrophytes over 188 days. Results indicate that nutrients released by macrophyte residues alter the physiochemical properties of overlaying water and have dual concentration effects of low promotion and high inhibition on α- and β-diversity of bacteria, driving their succession in different directions. High nutrient concentrations not only resulted in more substantial changes in the abundance of dominant bacteria at various taxonomic levels, but also inhibited carbon and nitrogen metabolic functions while promoting the phosphorus and sulfur metabolic functions of the bacterial community, which was in contrast to the effects of low nutrient concentrations. These effects persisted for a long time, potentially leading to a decrease in redundant genes and the loss of rare functional genes. This, in turn, indirectly reducing the structural stability of aquatic ecosystems and their resilience to external disturbances. Our findings indicate that the indirect and persistent negative impacts of macrophyte decomposition on aquatic ecosystems should not be ignored and that macrophyte residues should be harvested and properly treated before they undergoing explosive nutrient release.