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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 …