AbstractTo understand the carbon and energy exchange between the lake surface and the atmosphere, direct measurements of latent, sensible heat, and CO2 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−2 d−1 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−2 d−1 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 −19.0 ± 5.4 and −40.2 ± 13.3 g C m−2 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−2 yr−1 in Year 1 and Year 2, respectively. The CO2 flux ( ) rate varied from −0.45 g C m−2 d−1 to 0.98 g C m−2 d−1. Similar to LE, 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 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 , respectively.