Evaluating plant community response to atmospheric CO rise is critical to predicting ecosystem level change. Freshwater lakes offer a model system for examining CO effects as submersed macrophyte species differ greatly in their growth responses to CO enrichment, and free CO concentrations among these habitats show a wide range of natural, spatial variation. We determined free CO concentrations in the water column and sediment porewater in littoral zones with pH < 6.0 in Adirondack Mountain (New York, USA) lakes, and derived a community CO responsiveness index (CCRI) based on quantitative sampling of 15 submersed macrophyte communities coupled with greenhouse-derived growth responses to CO enrichment of constituent species to test two hypotheses: (1) CCRI, which is higher for communities dominated by species with greater growth responses to CO enrichment, is positively correlated to free [CO ] in the water column, and (2) in natural communities, the percent of sediment CO -using species, which are relatively unresponsive to CO enrichment, is negatively correlated to free [CO ]. A significant positive correlation (P = 0.003) between our physiologically based CCRI and the concentration of free CO in the water column supported our primary hypothesis that sites with higher levels of free CO are dominated by species with greater growth responses to CO enrichment. Our CCRI is also highly significantly correlated (P < 0.001) to the first axis scores for the same vegetation data from polar ordination. Finally, the relative importance of species that use sediment CO as a photosynthetic carbon source is significantly negatively correlated (P = 0.029) with the concentration of free CO in the water column. Our results indicate that natural variations in CO levels are important determinants of submersed macrophyte community composition. Further, we demonstrate the utility of a physiologically-based index of community composition, our CCRI, as an ecologically valid measure of community response to CO .