Phytoremediation on eutrophicated ecosystems has received growing research interest, and macrophytes and eutrophic gradients are considered as key influencing factors. This study used Vallisneria natans, Iris pseudacorus, and their mixed plantings in aquatic ecosystems (9 m × 2 m × 0.5 m, L × W × D) receiving increased eutrophic nitrogen and phosphorus gradients (4, 40, 80 mg/L of nitrogen and 0.4, 4, 8 mg/L of phosphorus), to unveil phytoremediation effects and corresponding microbial mechanisms. Different phytoremediations could effectively improve water quality with removal efficiencies of 57.4%–98.7% on ammonium, 45.7%–93.7% on total nitrogen, 46.7%–100% on available phosphorus, and 38.4%–95.2% on total phosphorus, respectively. Macrophytes and eutrophic gradients jointly affected diversities, compositions, structures, interactions, and functions of sedimental bacterial and archaeal communities. Microbial diversities increased with macrophytes presence and increased eutrophic gradients. Principal component analysis demonstrated that different macrophytes diverged microbial community structures, and increment of eutrophic gradients reduced structural dissimilarities. Dominant compositional communities, including Chloroflexi, Firmicutes, Proteobacteria, Anaerolineae, and Nitrososphaeria, were also keystone taxa of community co-occurrence networks in phytoremediations. Increased eutrophic gradients enhanced microbial cooperative interactions, whilst V. natans fostered bacterial interactions, and I. pseudacorus and mixed plantings strengthened archaeal interactions. Functional prediction indicated that bacterial “phosphate transferase” and archaeal “methanogenesis” were significantly reduced, whilst archaeal “nitrification”, “denitrification”, “comammox”, and “methane oxidation” were elevated by macrophytes and eutrophic gradients, indicating likely mechanisms for nutrient and GHGs metabolisms. This study extended our knowledge on microbial mechanisms of phytoremediations with different macrophytes treating eutrophicated waters of increased gradients, therefore providing references for further developing phytoremediation technologies.