The spatiotemporal surface heat flux (SurHF) distribution over Lake Geneva, the largest lake in Western Europe, was estimated for a 7‐year period (2008–2014). Data sources included hourly maps of over‐the‐lake assimilated meteorological data from a validated numerical weather model and lake surface water temperature (LSWT) from satellite imagery. A set of bulk algorithms, previously optimized and calibrated at two locations in Lake Geneva, was used. Results indicate a systematic long‐term average spatial range of >40 Wm‐2 between different parts of the lake and little year‐to‐year variability. This variability is mainly due to topographically induced wind sheltering over parts of the lake, which in turn produces spatial variability in the sensible and latent heat fluxes. These results are supported by a systematic spatial heat content variability obtained from long‐term temperature profile measurements in the lake. During spring, a lower SurHF spatial range was evident. Unlike other seasons, the spring spatial variability of air‐water temperature differences and, to a lesser extent, the global radiation variability resulting from sheltering by the mountainous topography were the main drivers of the SurHF spatial variability. Analysis of the atmospheric thermal boundary layer showed stable conditions from March to early June and unstable conditions for the rest of the year. This regime change can explain the low SurHF spatial variability observed during spring. The results emphasize that spatial variability in meteorological and LSWT patterns, and consequently in the spatiotemporal SurHF data, should be considered when assessing the time evolution of the heat budget of large lakes.