The heat budget of a lake is a fundamental component of physical limnology, and is strongly dependent on the surface heat flux. However, the surface energy exchange depends on several factors, making it difficult to estimate. In this study we employed several bulk formulas to estimate Lake Geneva’s surface heat flux. Combination of different surface heat flux terms leads to a surface heat exchange model which requires various data. Different data sources were used in the heat flux estimates. Meteorological data were taken from an operational numerical weather prediction model, namely COSMO-2 (run by the Swiss meteorological service), while satellite imagery was used for the lake surface water temperature (LSWT). In order to find the best combination of the bulk formulas and to calibrate the model, the temporal evolution of the heat budget was estimated using long-term time series of vertical temperature profiles. Vertical temperature profiles at two points (one in the Lake Geneva’s large basin and one in its small basin) were used. A sensitivity analysis was performed to find the key parameters, and more significantly the optimal combination of different heat flux terms. Finally, the spatio-temporal surface heat flux variation was calculated according to the proposed model. In addition, the relationship between variability of the surface heat flux and meteorological forcing was assessed. The different models, which are of differing complexity, gave reasonably consistent results, with differences attributed to simplifications inherent in them. The modeling results revealed that the LSWT and wind forcing are dominant factors underlying Lake Geneva surface heat flux spatial variation, while its temporal variability is mainly due to the global radiation and air temperature changes. In conclusion, the bulk heat balance approach is a useful tool to estimate various heat flux terms as well as their monthly or seasonally contributions. But, in large lakes where the LSWT is highly variable, the variable surface heat flux would be unavoidable.