With the increase of global carbon emissions since the industrial revolution, atmospheric CO₂ level is expected to be twice higher than the present level at the end of this century, reaching to 750 μL/L. As atmospheric CO₂ is the most important source of soluble CO₂ in water due to the deliberate CO₂ sequestration, global CO₂ elevation would significantly alter carbonate chemical environments of aquatic ecosystems. When atmospheric CO₂ concentration doubles at the end of century, it is predicted that pH value of surface oceans would drop approximately 0.3 units, the concentration of bicarbonate ion would increase by 6%, and carbonate ion concentration would decrease by 50%. Considering the smaller buffering capacity of freshwater ecosystems than that of oceans, carbonate chemical environments of freshwater lakes and rivers may change more notably after the increase of CO₂ level. The shift of carbonate chemistry would in turn have dramatic effects on aquatic ecosystems. Phytoplankton has been used widely as an indicator of changes of aquatic ecosystems because this relatively short-lived organism responds rapidly to subtle changes. Meanwhile, it contributes approximately 50% of the total global primary productivity, which plays a vital role in global carbon cycling. Therefore, the physiological and ecological responses of phytoplankton to global CO₂ elevation would have great significance on water ecosystems and biogeochemical cycle. Elevated carbon resource could enhance the photosynthetic activity of phytoplankton, particularly small phytoplankton or non-CCM (non-carbon concentration mechanism) phytoplankton. When CO₂ level increases, the cell size of phytoplankton would potentially decrease, and the elemental ratio of carbon to nitrogen in phytoplankton cell would increase up to more than 10%. Then, those changes in the individual phytoplankton cell would cause certain variations in the ecological level. Primary productivity would rise significantly as a result of enhanced photosynthetic activity of phytoplankton. The shift in assemblage composition of phytoplankton, and the variation of elemental ratio could affect the edibility of phytoplankton, which would alter the abundances and the community structure of zooplankton. Furthermore, the accumulating concentration of organic carbon in water would promote the growth and reproduction of heterotrophic bacterioplankton, which would strengthen the competition between bacterioplankton and phytoplankton for nutrients, such as nitrogen and phosphorus. More importantly, elevated CO₂ effects differ between oligotrophic and eutrophic water body. It is expected that effects on algal productivity in eutrophic aquatic ecosystems could be potentially larger, since in eutrophic water the input of nitrogen and phosphorus to the global biochemical cycle exceeds that of the carbon input by several orders of magnitude. Finally, we summarized the development of the methodology for studying the effect of enhanced CO₂ level on water ecosystems. Long-term in situ simulating experiment would be the best approach for studying the effect of enhanced CO₂ on natural phytoplankton community. In future research, picophytoplankton will attract more attention, since they are sensitive to the change of CO₂ level compared with large ones because of their high surface-area-to-volume ratio. In addition, more efforts should be exerted for freshwater ecosystems with respect to elevated CO₂ effects, as they are far less investigated than marine ecosystems even though they are closely linked to the survival of human being.