The elevation of atmospheric CO 2 is an inevitable trend that would lead to significant impact on the interrelated carbon and nitrogen cycles through microbial activities in the aquatic ecosystem. Eutrophication has become a common trophic state of inland waters throughout the world, but how the elevated CO 2 affects N cycles in such eutrophic water with algal bloom, and how vegetative restoration helps to mitigate N 2 O emission remains unknown. We conducted the experiments to investigate the effects of ambient and elevated atmospheric CO 2 (a[CO 2 ], e[CO 2 ]; 400, 800 μmol﹒mol −1 ) with and without the floating aquatic plant, Eichhornia crassipes (Mart.) Solms, on N-transformation in eutrophic water using the 15 N tracer method. The nitrification could be slightly inhibited by e[CO 2 ], due mainly to the competition for dissolved inorganic carbon between algae and nitrifiers. The e[CO 2 ] promoted denitrification and N 2 O emissions from eutrophic water without growth of plants, leading to aggravation of greenhouse effect and forming a vicious cycle. However, growth of the aquatic plant, Eichhornia crassipes, slightly promoted nitrification, but reduced N 2 O emissions from eutrophic water under e[CO 2 ] conditions, thereby attenuating the negative effect of e[CO 2 ] on N 2 O emissions. In the experiment, the N transformation was influenced by many factors such as pH, DO and algae density, except e[CO 2 ] and plant presence. The pH could be regulated through diurnal photosynthesis and respiration of algae and mitigated the acidification of water caused by e[CO 2 ], leading to an appropriate pH range for both nitrifying and denitrifying microbes. Algal respiration at night could consume DO and enhance abundance of denitrifying functional genes (nirK, nosZ) in water, which was also supposed to be a critical factor affecting denitrification and N 2 O emissions. This study clarifies how the greenhouse effect caused by e[CO 2 ] mediates N biogeochemical cycle in the aquatic ecosystem, and how vegetative restoration mitigates greenhouse gas emission.