It has been hypothesized that the energy balance closure problem of single-tower eddy-covariance measurements is linked to large-scale turbulent transport. In order to shed light on this problem, we investigate the functional dependence of the normalized residual for the potential temperature and humidity conservation equations, i.e. the imbalance ratio for the fluxes of latent and sensible heat. We set up a suite of simulations consisting of cases with different stability and surface Bowen ratio. We employ a nesting approach in the lower part of the atmospheric boundary-layer to achieve higher spatial resolution near the surface. Our simulations reproduce earlier simulation results for the mixed layer and also mimic the saw-blade pattern of real flux measurements. Focusing on homogeneous terrain, we derive a parameterization for the spatially averaged flux imbalance ratios of latent and sensible heat in the surface layer. We also investigate how the remaining imbalance for a given point measurement is related to the local turbulence, by deriving a statistical model based on turbulence characteristics that are related to large-scale turbulence. The average imbalance ratio scales well with friction velocity, especially for sensible heat. For the latent heat flux, our results show that the Bowen ratio also influences the underestimation. Furthermore, in the surface layer the residual has a linear dependence on the absolute height divided by the boundary-layer height. Our parameterization allows us to deduce an expression for the residual in the energy budget for a particular measurement half hour, based on the measurement height and stability.