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Lakes impact atmosphere boundary layer processes and are thus important for catchment scale climate modeling and regional water and heat budgets. To explore the differences in lake-atmosphere interaction parameters, meteorological variables and turbulent heat fluxes in small and large water bodies, we collected eddy covariance observations and meteorological data during ice-free periods of the Lake small Nam-Co ("small lake") in 2012-2013 and Lake Nam-Co ("large lake") in 2015-2016 on the Tibetan Plateau. Significant differences exist in their lake-atmosphere interaction processes due to differences in their inherent attributes and environmental backgrounds. Relative to the "small lake", the maximum surface temperature of the "large lake" in summer is approximately 3 degrees C lower; "large lake" also has a larger wind speed, a higher monthly average air temperature and delayed peaks of the seasonal variation of water and air temperature. The typical values of the roughness length and standard bulk transfer coefficient for momentum are approximately 80% and 21% higher, respectively, for the "large lake". The typical values of the roughness lengths for heat and water are one order of magnitude lower in the "large lake" while the corresponding standard bulk transfer coefficients are only 7% lower. The latent and sensible heat fluxes of the two lakes have quite different seasonal variations, with evaporation peaking in November for the "large lake" and in June for the "small lake". The estimated evaporation during the ice-free season of the "large lake" (approximately 981 +/- 18 mm) is also higher than that (812 mm) of the "small lake" and this is mainly related to the observed lower Bowen ratio in the "large lake".