We investigate the impact of observed surface heterogeneities during the LITFASS-2003 experiment on the convective boundary layer (CBL). Large-eddy simulations (LES), driven by observed near-surface sensible and latent heat fluxes, were performed for the diurnal cycle and compare well with observations. As in former studies of idealized one- and two-dimensional heterogeneities, secondary circulations developed that are superimposed on the turbulent field and that partly take over the vertical transport of heat and moisture. The secondary circulation patterns vary between local and roll-like structures, depending on the background wind conditions. For higher background wind speeds, the flow feels an effective surface heat-flux pattern that derives from the original pattern by streamwise averaging. This effective pattern generates a roll-like secondary circulation with roll axes along the mean boundary-layer wind direction. Mainly the upstream surface conditions control the secondary circulation pattern, where the fetch increases with increasing background wind speed. Unlike the entrainment flux that appears to be slightly decreased compared to the homogeneously-heated CBL, the vertical flux of sensible heat appears not to be modified in the mixed layer, while the vertical flux of latent heat shows different responses to secondary circulations. The study illustrates that sufficient time averaging and ensemble averaging is required to separate the heterogeneity-induced signals from the raw LES turbulence data. This might be an important reason why experiments over heterogeneous terrain in the past did not give any clear evidence of heterogeneity-induced effects.