The emission fluxes of CH4 and CO2 at the water-air interface of two large reservoirs were evaluated using two methods: (1) static chambers (STAT) and (2) the boundary layer equation (BLE). Such a comparison was rendered necessary In order to verify the information yielded by various automated measurement devices recently developed and based on BLE flux measurement principles. Our study shows that the BLE method underestimates the actual fluxes of CO2 and CH4. The variation observed between the two measurement techniques may be explained by different errors or biases inherent in the methods and therefore not a reflection of the true emissions. Variability observed in both data sets impose cautiousness on any drastic conclusion about this comparison, but it appears that the BLE method underestimates the CO2 and CH4 emission fluxes from large water bodies. Additionally, compared to the STAT technique, the BLE method overestimates the wind effect in deep areas. For shallow zones, however, the use of the BLE underestimates emissions when winds are light. Our data set support that gas exchange across the airwater interface is largely independent of low wind speeds. Finally, our results suggest that the thin boundary layer equation, which enables high resolution observations by means of automated devices, cannot he used, without considerable caution, for estimating global greenhouse budgets from large water bodies.