Under higher atmospheric CO2 concentrations, increases in soil moisture and, hence in terrestrial-aquatic carbon transfer are probable. In a coupled terrestrial-aquatic experiment we examined the direct (e.g. through changes in the CO2 water concentration) and indirect (e.g. through changes in the quality and quantity of soil leachates) effects of elevated CO2 on a lake microbial community. The incubation of soils under elevated CO2 resulted in an increase in the volume of leachates and in both chromophoric dissolved organic matter (CDOM) absorption and fluorescence in leachate. When this leachate was added to lake water during a 3-day aquatic incubation, we observed negative direct effects of elevated CO2 on photosynthetic microorganism abundance and a positive, indirect effect on heterotrophic microbial community cell abundances. We also observed a strong, indirect impact on the functional structure of the community with higher metabolic capacities under elevated CO2 along with a significant direct effect on CDOM absorption. All of these changes point to a shift towards heterotrophic processes in the aquatic compartment under higher atmospheric CO2 concentrations.