Evidence shows the important role biota play in the carbon cycle, and strategic management of plant and animal populations could enhance CO 2 uptake in aquatic ecosystems. However, it is currently unknown how management-driven changes to community structure may interact with climate warming and other anthropogenic perturbations to alter CO 2 fluxes. Here we showed that under ambient water temperatures, predators (three-spined stickleback) and nutrient enrichment synergistically increased primary producer biomass, resulting in increased CO 2 uptake by mesocosms in early dawn. However, a 3°C increase in water temperatures counteracted positive effects of predators and nutrients, leading to reduced primary producer biomass and a switch from CO 2 influx to efflux. This confounding effect of temperature demonstrates that climate scenarios must be accounted for when undertaking ecosystem management actions to increase biosequestration.