This study provides the first technique to investigate the turbulent fluxes over the Great Lakes from July 2001 to December 2014 using a combination of data from satellite remote sensing, reanalysis data sets, and direct measurements. Turbulent fluxes including latent heat flux (QE) and sensible heat flux (QH) were estimated using the bulk aerodynamic approach, then compared with the direct eddy covariance measurements from the rooftop of three lighthouses—Stannard Rock Lighthouse (SR) in Lake Superior, White Shoal Lighthouse (WS) in Lake Michigan, and Spectacle Reef Lighthouse (SP) in Lake Huron. The relationship between modeled and measured QE and QH were in a good statistical agreement, for QE, R2 varied from 0.41 (WS), 0.74 (SR), and 0.87 (SP) with RMSE of 5.68, 6.93, and 4.67 W·m−2, respectively, while QH, R2 ranged from 0.002 (WS), 0.8030 (SP) and 0.94 (SR) with RMSE of 6.97, 4.39 and 4.90 W·m−2 respectively. Both monthly mean QE and QH were highest in January for all lakes except Lake Ontario, which was highest in early December. The turbulent fluxes then sharply drop in March and are negligible during June and July. The evaporation processes continue again in August.