A single column atmospheric model (SCM) coupled to a one-dimensional lake model devised for climate simulations is described in this paper. As a test case, this coupled model is applied to the deepest section of Lake Geneva in Switzerland. Both atmospheric and lake models require a minimal set of adjustable parameters to reproduce the local observations of temperature, moisture, and wind as well as those of the lake thermal profiles. A number of simulations have been performed to produce a sorted set of optimal model parameters that reproduces the mean and the variability of the seasonal evolution of the thermal profiles in the lake as well as those of the mean and the variability of the surface air temperature, moisture, and winds. The lake water temperature is reproduced realistically using the optimal calibration parameter values with a seasonal- and depth-averaged error of 0.41°C in summer, −0.15°C in autumn, 0.01°C in winter, and 0.27°C in spring when compared to the lake observations. Also, the errors of the seasonally averaged simulated anemometer-level wind speed, screen-level air temperature, and specific humidity to the station-derived values are 0.04 m s−1, 1.04°C, and 0.74 g kg−1, respectively. Results of this study contribute to the understanding of the air-lake interactions present over the deep Lake Geneva. In addition, the sensitivity experiments carried out in this paper serve as the basis for experiments aiming at studying the thermal response of the deep Swiss Lake Geneva under future global climate change conditions reported in a companion paper.