A general lack of energy balance closure indicates that tower-based eddycovariance (EC) measurements underestimate turbulent heat fluxes, which calls for robust correction schemes. Two parametrization approaches that can be found in the literature were tested using data from the Canadian Twin Otter research aircraft and from tower-based measurements of the German Terrestrial Environmental Observatories (TERENO) programme. Our analysis shows that the approach of Huang et al. (Boundary-Layer Meteorol 127:273– 292, 2008), based on large-eddy simulation, is not applicable to typical near-surface flux measurements because it was developed for heights above the surface layer and over homogeneous terrain. The biggest shortcoming of this parametrization is that the grid resolution of themodel was too coarse so that the surface layer, where ECmeasurements are usually made, is not properly resolved. The empirical approach of Panin and Bernhofer (Izvestiya Atmos Oceanic Phys 44:701–716, 2008) considers landscape-level roughness heterogeneities that induce secondary circulations and at least gives a qualitative estimate of the energy balance closure. However, it does not consider any feature of landscape-scale heterogeneity other than surface roughness, such as surface temperature, surface moisture or topography. The failures of both approaches might indicate that the influence of mesoscale structures is not a sufficient explanation for the energy balance closure problem. However, our analysis of different wind-direction sectors shows that the upwind landscape-scale heterogeneity indeed influences the energy balance closure determined from tower flux data. We also analyzed the aircraft measurements with respect to the partitioning of the “missing energy” between sensible and latent heat fluxes and we could confirm the assumption of scalar similarity only for Bowen ratios ≈1.