Energy fluxes across the surface of lakes regulate heat storage and affect the water balance. Sensible and latent heat fluxes are affected by atmospheric stability, especially for large lakes. We examined the effect of atmospheric stability on the heat fluxes on seasonal time scales at Lake Tanganyika, East Africa, by estimating hourly sensible and latent heat fluxes and net radiation using thermistor chains and meteorological stations. The atmosphere was almost always unstable, in contrast to the atmosphere above North American Great Lakes which is unstable in winter and stable in summer. Persistent atmospheric instability resulted in a 13% and 18% increase in the annual mean heat loss by latent and sensible heat fluxes, respectively, relative to conditions of neutral stability. The persistent unstable atmosphere is caused by a higher water surface temperature compared with air temperature, which we argue is the case in general in (sub)tropical lakes. Low humidity further enhanced the frequency of unstable conditions and enhanced the exchange of heat and vapor from the lake to the atmosphere. The estimated heat fluxes were sensitive to the temporal scale of data inputs and to the local values of parameters such as air density. To our knowledge this is the first paper that demonstrates and quantifies the effect of atmospheric stability on latent and sensible heat fluxes from a lake on an annual basis, using data collected from the lake surface.