AbstractAs the global climate is changing, average water temperatures and the supply of CO2 to water bodies are increasing. To determine how the effects of these changes on freshwater communities interact, we ran a month‐long factorial mesocosm experiment, in which we manipulated water temperature (heated, ambient) and pCO2 (preindustrial, ambient, future). We found that the total phytoplankton biomass responded positively to the pCO2 and temperature treatments but no interactive effects were detected. Green algae were positively affected by temperature and, over the course of the experiment, responded to pCO2 first positively, then negatively. Heterokonts, on the other hand, were unaffected by temperature but responded positively to pCO2. pCO2 enrichment also led to increases in seston C : N stoichiometry, although the experiment ended before we could observe any effects of pCO2 on the zooplankton community composition. Warming caused shifts in zooplankton community composition, primarily through higher abundances of the cladoceran Bosmina longirostris and the rotifer Conochilus unicornis, and lower abundances of the rotifer Polyarthra vulgaris. We found that, in contrast to the effects of temperature, which can be explained by temperature‐dependent plankton growth curves, the responses of algal groups to pCO2 enrichment were difficult to anticipate, despite the availability of priors from previous pCO2 enrichment experiments in the same lake mesocosms. We conclude that climate change‐induced increases in aquatic pCO2 and temperatures are likely to affect pelagic ecosystems, though further research in freshwater systems is needed before generalized claims regarding the simple and interactive effects of pCO2 can be made.