The partial pressure of carbon dioxide (pCO2) in lake ecosystems varies over four orders of magnitude and is affected by local and global environmental perturbations associated with both natural and anthropogenic processes. Little is known, however, about how changes in pCO2 extend into the function and structure of food webs in freshwater ecosystems. To fill this gap, we performed laboratory experiments using the ecologically important planktonic herbivore Daphnia and its algal prey under a natural range of pCO2 with low light and phosphorus supplies. The experiment showed that increased pCO2 stimulated algal growth but reduced algal P : C ratio. When feeding on algae grown under high pCO2, herbivore growth decreased regardless of algal abundance. Thus, high CO2-raised algae were poor food for Daphnia. Short-term experimental supplementation of PO4 raised the P content of the high CO2-raised algae and improved Daphnia growth, indicating that low Daphnia growth rates under high pCO2 conditions were due to lowered P content in the algal food. These results suggest that, in freshwater ecosystems with low nutrient supplies, natural processes as well as anthropogenic perturbations resulting in increased pCO2 enhance algal production but reduce energy and mass transfer efficiency to herbivores by decreasing algal nutritional quality.