Aircraft measurements of sensible and latent heat fluxes, surface and air temperature, mean wind and humidity were used to examine the boundary layer structure over the Great Lakes for two cases in late fall when the water was warmer than the air above. The sensible and latent vertical turbulent heat fluxes at the surface were in the range 5–10 mW em−2, and 6–15 mW em−3, respectively. Estimates of the mean vertical velocity at the interface between the mixed layer (where the equivalent potential temperature lapse rate was ∼1C km−1 and the mixing ratio was effectively constant) and the stable air above were obtained from the equations for the rate of change of sensible plus latent heat and of water vapor in the boundary layer. The values obtained by this method appear to be reasonable when compared with estimates obtained from the wind field. Using this mean vertical velocity, the vertical fluxes of latent and sensible heat and liquid water in the cloud layer just below the top of the mixed layer ... Abstract Aircraft measurements of sensible and latent heat fluxes, surface and air temperature, mean wind and humidity were used to examine the boundary layer structure over the Great Lakes for two cases in late fall when the water was warmer than the air above. The sensible and latent vertical turbulent heat fluxes at the surface were in the range 5–10 mW em−2, and 6–15 mW em−3, respectively. Estimates of the mean vertical velocity at the interface between the mixed layer (where the equivalent potential temperature lapse rate was ∼1C km−1 and the mixing ratio was effectively constant) and the stable air above were obtained from the equations for the rate of change of sensible plus latent heat and of water vapor in the boundary layer. The values obtained by this method appear to be reasonable when compared with estimates obtained from the wind field. Using this mean vertical velocity, the vertical fluxes of latent and sensible heat and liquid water in the cloud layer just below the top of the mixed layer ...