Objective: This study was to assess the influence of interaction of combination of immobilized nitrogen cycling bacteria (INCB) with aquatic macrophytes on nitrogen removal from the eutrophic waterbody, and to get insight into different mechanisms involved in nitrogen removal. Methods: The aquatic macrophytes used include Eichhornia crassipes (summer-autumn floating macrophyte), Elodea nuttallii (winter-growing submerged macrophyte), and nitrogen cycling bacteria including ammonifying, nitrosating, nitrifying and denitrifying bacteria isolated from Taihu Lake. The immobilization carriers materials were made from hydrophilic monomers 2-hydroxyethyl acrylate (HEA) and hydrophobic 2-hydroxyethyl methylacrylate (HEMA). Two experiments were conducted to evaluate the roles of macrophytes combined with INCB on nitrogen removal from eutrophic water during different seasons. Results: Eichhornia crassipes and Elodea nuttallii had different potentials in purification of eutrophic water. Floating macrophyte+bacteria (INCB) performed best in improving water quality (during the first experiment)and decreased total nitrogen (TN) by 70.2%, nitrite and ammonium by 92.2% and 50.9%, respectively, during the experimental period, when water transparency increased from 0.5 m to 1.8 m. When INCB was inoculated into the floating macrophyte system,the populations of nitrosating, nitrifying, and denitrifying bacteria increased by 1 to 2 orders of magnitude compared to the un-inoculated treatments, but ammonifying bacteria showed no obvious difference between different treatments. Lower values of chlorophyll a, CODMn, and pH were found in the microbial-plant integrated system, as compared to the control. Highest reduction in N was noted during the treatment with submerged macrophyte+INCB, being 26.1% for TN, 85.2% for nitrite, and 85.2% for ammonium at the end of 2nd experiment. And in the treatment, the populations of ammonifying, nitrosating, nitrifying, and denitrifying bacteria increased by 1 to 3 orders of magnitude, as compared to the un-inoculated treatments. Similar to the first experiment, higher water transparency and lower values of chlorophyll a, CODMn and pH were observed in the plant+ INCB integrated system, as compared to other treatments. These results indicated that plant-microbe interaction showed beneficial effects on N removal from the eutrophic waterbody.