A large-eddy simulation (LES) study is presented that investigates the spatial variability of temporal eddy covariance fluxes and the systematic underestimation of representative fluxes linked to them. It extends a prior numerical study by performing high resolution simulations that allow for virtual measurements down to 20 m in a convective boundary layer, so that conditions for small tower measurement sites can be analysed. It accounts for different convective regimes as the wind speed and the near-surface heat flux are varied. Moreover, it is the first LES imbalance study that extends to the stable boundary layer. It reveals shortcomings of single site measurements and the necessity of using horizontally-distributed observation networks. The imbalances in the convective case are attributed to a locally non-vanishing mean vertical advection due to turbulent organised structures (TOS). The strength of the TOS and thus the imbalance magnitude depends on height, the horizontal mean wind and the convection type. Contrary to the results of a prior study, TOS cannot generally be responsible for large energy imbalances: at low observation heights (corresponding to small towers and near-surface energy balance stations) the TOS related imbalances are generally about one order of magnitude smaller than those in field experiments. However, TOS may cause large imbalances at large towers not only in the case of cellular convection and low wind speeds, as found in the previous study, but also in the case of roll convection at large wind speeds.
In the stably stratified boundary layer for all observation heights neither TOS nor significant imbalances are observed.
Attempting to reduce imbalances in convective situations by applying the conventional linear detrending method increases the systematic flux underestimation. Thus, a new filter method is proposed.