Aircraft stacks were flown upwind and downwind of the First ISLSCP Field Experiment (FIFE) site in Kansas to measure the heat and moisture budgets of the boundary layer under fairly clear skies for four daytime periods. In this paper, we evaluate the terms in the conservation equation. The vertical flux divergence and advection do not account for the difference between surface and low-level aircraft flux estimates. Budget estimates of the surface fluxes using the aircraft data agree well with surface flux measurements, but extrapolation of the aircraft fluxes gives surface fluxes that are too low. With the 5 km cutoff filter used, the aircraft underestimate for sensible heat flux is about 40%, and for the latent heat flux about 30%. Part of the underestimation is attributable to long-wavelength contributions (longer than the 5 km filter), but more investigation is needed.