In two preceding papers, coherent structures of the atmospheric boundary layer (ABL), such as roll vortices or cells, were investigated through radar and aircraft observations collected during the TRAC-93 (Turbulence Radar Aircraft Cells) experiment held in France in June 1993. The analysis of this experimental data set provided information on the spatial characteristics of these organisations (length scale, orientation, type ... ), their temporal and vertical evolution, and their relation with the dynamic and thermodynamic conditions of the ABL. For the third paper in this series, a large eddy simulation model is used to examine the impact of the coherent structures on the ABL vertical fluxes. The analysis of the simulated horizontal fields is made with two-dimensional auto and cross-correlations applied on different pertinent ABL variables. The results emphasise a directional anisotropy of these organised fields throughout the ABL, much more pronounced in the heat flux fields, not only at the length scale of organisations but also at the turbulence scales. This finding has an important consequence for traditional ABL flux measurements based on the hypothesis of isotropic and homogeneous turbulence. It can explain part of the underestimation of the surface fluxes often mentioned in the literature. This approach makes it possible to modify the concept of diffusion time (in chemical modelling) and could also lead to revised ABL parameterisations in Range Scale models.