A coupled single-column atmosphere-lake model, along with the Stein–Alpert factor separation methodology, is used to explore some of the non-linear interactions in the vertical dimension between the lower atmosphere and the deep-Lake Geneva, Switzerland, during three selected periods in 1990. The first from the end of April to the end of May when Lake Geneva was building its stratification, the second from mid-August to mid-September during stable stratification, and the third from the end of November to the end of December during destratification. It is recognized that the large thermal inertia of Lake Geneva reduces the surface annual and diurnal temperature variations for neighbouring regions. However, the question of how the open water and the overlying atmosphere interact and which of these “factors” has the most influence needs much attention. The sole presence of the lake is shown to be a major feature with regard to the surface energy budget components whose contributions counteract those of the lower atmosphere, thus supporting the fact that Lake Geneva acts as a damping factor to the regional climate system. It is also shown that not only did the presence of the lake and the overlying atmosphere independently modulate the surface energy budget, but also the synergistic nonlinear interaction among them, either positive or negative, was often found non-negligible. Moreover, some processes may turn out to be important on short time scales while being negligible on the long term.