We conduct a high-resolution large-eddy simulation (LES) case study in order to investigate the effects of surface heterogeneity on the (local) structure parameters of potential temperature $C_T^2$ CT2 and specific humidity $C_q^2$ Cq2 in the convective boundary layer (CBL). The kilometre-scale heterogeneous land-use distribution as observed during the LITFASS-2003 experiment was prescribed at the surface of the LES model in order to simulate a realistic CBL development from the early morning until early afternoon. The surface patches are irregularly distributed and represent different land-use types that exhibit different roughness conditions as well as near-surface fluxes of sensible and latent heat. In the analysis, particular attention is given to the Monin–Obukhov similarity theory (MOST) relationships and local free convection (LFC) scaling for structure parameters in the surface layer, relating $C_T^2$ CT2 and $C_q^2$ Cq2 to the surface fluxes of sensible and latent heat, respectively. Moreover we study possible effects of surface heterogeneity on scintillometer measurements that are usually performed in the surface layer. The LES data show that the local structure parameters reflect the surface heterogeneity pattern up to heights of 100–200 m. The assumption of a blending height, i.e. the height above the surface where the surface heterogeneity pattern is no longer visible in the structure parameters, is studied by means of a two-dimensional correlation analysis. We show that no such blending height is found at typical heights of scintillometer measurements for the studied case. Moreover, $C_q^2$ Cq2 does not follow MOST, which is ascribed to the entrainment of dry air at the top of the boundary layer. The application of MOST and LFC scaling to elevated $C_T^2$ CT2 data still gives reliable estimates of the surface sensible heat flux. We show, however, that this flux, derived from scintillometer data, is only representative of the footprint area of the scintillometer, whose size depends strongly on the synoptic conditions.