In the companion to the present paper, the one-dimensional k-ε lake model SIMSTRAT is coupled to a single-column atmospheric model, nicknamed FIZC, and an application of the coupled model to the deep Lake Geneva, Switzerland, is described. In this paper, the response of Lake Geneva to global warming caused by an increase in atmospheric carbon dioxide concentration (i.e., 2 × CO2) is investigated. Coupling the models allowed for feedbacks between the lake surface and the atmosphere and produced changes in atmospheric moisture and cloud cover that further modified the downward radiation fluxes. The time evolution of atmospheric variables as well as those of the lake's thermal profile could be reproduced realistically by devising a set of adjustable parameters. In a “control” 1 × CO2 climate experiment, the coupled FIZC-SIMSTRAT model demonstrated genuine skills in reproducing epilimnetic and hypolimnetic temperatures, with annual mean errors and standard deviations of 0.25°C ± 0.25°C and 0.3°C ± 0.15°C, respectively. Doubling the CO2 concentration induced an atmospheric warming that impacted the lake's thermal structure, increasing the stability of the water column and extending the stratified period by 3 weeks. Epilimnetic temperatures were seen to increase by 2.6°C to 4.2°C, while hypolimnion temperatures increased by 2.2°C. Climate change modified components of the surface energy budget through changes mainly in air temperature, moisture, and cloud cover. During summer, reduced cloud cover resulted in an increase in the annual net solar radiation budget. A larger water vapor deficit at the air-water interface induced a cooling effect in the lake.