Reducing nutrient input in aquatic ecosystems has been widely recognized as a way to mitigate eutrophication. The paradigm of nutrient limitation by N and P is pervasively accepted, without considering the possibility of C limitation. However, our assumption that C might affect the aquatic biological composition, lacks fieldwork support. We tested the co-limitation of C/N/P on the growth of submerged macrophytes and phytoplankton in the Caohai Lake, a typical shallow karst lake in southwestern China. This study documented the seasonal variations in the concentration and comparative availability of nutrients C/N/P, in addition to physicochemical parameters, submerged macrophytes biomass, and phytoplankton composition in the lake. Our results show that dissolved inorganic carbon plays a substantial role in enhancing the primary production of phytoplankton and macrophytes, which suggests that primary production can be suppressed not only by P and/or N (as generally believed) but also by C, owing to the unique physicochemical characteristics that prevail in typical karst regions. Additionally, submerged macrophytes have been found to inhibit phytoplankton growth. Further analysis showed that the proportion of Cyanobacteria over Chlorophyta and Bacillariophyta throughout the year was reduced at dissolved carbon dioxide/total nitrogen (CO2/TN) ratios (>0.2) and dissolved carbon dioxide/total phosphorus (CO2/TP) ratios (>10) in this study. Isotopic evidence further indicated that the abundance of Cyanobacteria was reduced when CO2 >30 mu mol/L. In summary, the combined results suggest that when controlling N and P, CO2 fertilization may significantly affect both the growth and composition of phytoplankton communities/submerged macrophytes and carbon sequestration in karst surface water ecosystems. This implies a new "paradigm" in the mitigation of cyanobacteria blooms by adding more CO2 to aquatic ecosystems with low pCO2, during which carbon sequestration may also be enhanced.