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The estimation of spatial patterns in surface fluxes from aircraft observations poses several challenges in the presence of heterogeneous land cover. In particular, the effects of turbulence on scalar transport and the different behaviour of passive (e.g. water vapour) versus active (e.g. temperature) scalars may lead to large uncertainties in the source area/flux- footprint estimation for sensible (H) and latent (LE) heat-flux fields. This study uses large- eddy simulation (LES) of the land–atmosphere interactions to investigate the atmospheric boundary-layer (ABL) processes that are likely to create differences in airborne-estimated H and LE footprints. We focus on 32 m altitude aircraft flux observations collected over a study site in central Oklahoma during the Southern Great Plains experiment in 1997 (SGP97). Comparison between the aircraft data and traditional model estimates provide evidence of a difference in source area for turbulent sensible and latent heat fluxes. The LES produces reasonable representations of the observed fluxes, and hence provides credible evidence and explanation of the observed differences in the H and LE footprints. Those differences can be quantified by analyzing the change in the sign of the spatial correlation of the H and LE fields provided by the LES model as a function of height. Dry patterns in relatively moist surroundings are able to generate strong, but localized, sensible heating. However, whereas H at the aircraft altitude is still in phase with the surface, LE presents a more complicated connection to the surface as the dry updrafts force a convergence of the surrounding moist air. Both the observational and LES model evidence support the concept that under strongly advective conditions, H and LE measured at the top of the surface layer (≈50 m) can be associated with very different upwind source areas, effectively contradicting surface-layer self-similarity theory for scalars. The results indicate that, under certain environmental con- ditions, footprint models will need to predict differing source area/footprint contributions between active (H) and passive (LE) scalar fluxes by considering land-surface heterogeneity and ABL dynamics.