Some nonlinear aspects due to the coupling of a single column atmospheric model (SCM) with both a land-surface model (LSM) and a lake model has lately been published by Goyette in 2017. In this previous study, the surface type abruptly changed from land to an open water surface. This article further investigates the potential of this SCM to explore the nonlinear effects through the analysis of the impacts of fractional land and open water surfaces on the surface fluxes and variables, as well as on the atmospheric air temperature,specific humidity, and wind speed vertical profiles, with an application to deep Lake Geneva, Switzerland. It is shown that the coupling methodology depending on the surface type produced realistic and coherent results and indicated that the mean fluxes and other relevant quantities may not be simply averaged on the basis of the fractional area of the land and that of the openwater. If Lake Geneva relative surface area is prescribed to its observed value with respect to the model grid-mesh size, the remaining being land surface,results showed maximum seasonal mean differences of 7.5 and 5.4 W m−2for the latent and sensible heat flux in Autumn respectively, 1.6 deg C, 0.8 gkg−1 for the screen-level air temperature and specific humidity in Autumn respectively,and 0.6 ms−1for the anemometer-level windspeed in Winter with respect to the original land surface, owing to the different behaviour of the vertical turbulent transfer of heat, moisture and momentum but also to the different thermal and radiative characteristics of land and water surfaces.