To understand the carbon and energy exchange between the lake surface and the atmosphere, direct measurements of latent, sensible heat, and CO 2 fluxes were taken using the eddy covariance (EC) technique in Western Lake Erie during October 2011 to September 2013. We found that the latent heat flux (LE) had a marked one-peak seasonal change in both years that differed from the diurnal course and lacked a sinusoidal dynamic common in terrestrial ecosystems. Daily mean LE was 4.8 ± 0.1 and 4.3 ± 0.2 MJ m À2 d À1 in Year 1 and Year 2, respectively. The sensible heat flux (H) remained much lower than the LE, with a daily mean of 0.9 ± 0.1 and 1.1 ± 0.1 MJ m À2 d À1 in Year 1 and Year 2, respectively. As a result, the Bowen ratio was <1 during most of the 2 year period, with the lowest summer value at 0.14. The vapor pressure deficit explained 35% of the variation in half hourly LE, while the temperature difference between the water surface and air explained 65% of the variation in half hourly H. Western Lake Erie acted as a small carbon sink holding À19.0 ± 5.4 and À40.2 ± 13.3 g C m À2 in the first and second summers (May-September) but as an annual source of 77.7 ± 18.6 and 49.5 ± 17.9 g C m À2 yr À1 in Year 1 and Year 2, respectively. The CO 2 flux (F CO2 ). Similar to LE, F CO2 had noticeable diurnal changes during the months that had high chlorophyll a months but not during other months. A significantly negative correlation (P < 0.05) was found between F CO2 and chlorophyll a on monthly fluxes. Three gap-filling methods, including marginal distribution sampling, mean diurnal variation, and monthly mean, were quantitatively assessed, yielding an uncertainty of 4%, 6%, and 10% in LE, H, and F CO2 , respectively.