Biodiversity loss and climate warming are occurring in concert, with potentially profound impacts on ecosystem functioning. We currently know very little about the combined effects of these changes on the links between the community structure, dynamics and the resulting in situ CO concentrations in freshwater ecosystems. Here we aimed to determine both individual and combined effects of temperature and non-resource diversity (species inedible for a given consumer) on CO concentration. Our analysis further aimed to establish both direct effects on CO concentrations and potential indirect effects that occur via changes to the phytoplankton and zooplankton biomasses. Our results showed that there were no interactive effects of changes in temperature and diversity on CO concentration in the water. Instead, independent increases in either temperature or non-resource diversity resulted in a substantial reduction in CO concentrations, particularly at the highest non-resource diversity. The effects of non-resource diversity and warming on CO were indirect, resulting largely from the positive impacts on total biomass of primary producers. Our study is the first to experimentally partition the impacts of temperature and diversity on the consumer-resource dynamics and associated changes to CO concentrations. It provides new mechanistic insights into the role of diverse plankton communities for ecosystem functioning and their importance in regulating CO dynamics under ongoing climate warming.