Results from a case study of heat and moisture transport in the atmospheric boundary layer during the European Field Experiment in a Desertification-threatened Area (EFEDA) are presented. The experimental area is heterogeneous in respect of soil moisture and vegetation on scales of several tens of kilometres. An instrumented aircraft flew repeatedly at two different altitudes along two long flight tracks (legs) over regions with different surface properties. Vertical profiles of heat and moisture fluxes were calculated for these legs (west and south) for two flights, one at noon and the other in the late afternoon. Evaporation from the western surface seems to exceed that from the southern. The flux profiles over these terrains with different surface characteristics show significant differences throughout the mixed layer. Thermodynamic partitioning of sensible and latent heat fluxes explains these differences. The development of the mixed layer differs significantly from the ‘ideal’ case (a mixed layer of constant thickness existing throughout the afternoon); it reaches its full height only in the late afternoon. Reduced incoming solar radiation owing to cirrus cloud cover, as well as properties of the residual layer, seem to be responsible for this.