We examine the dynamics of turbulence subgrid (or sub-filter) scales over a lake surface and the implications for large-eddy simulations (LES) of the atmospheric boundary layer. The analysis is based on measurements obtained during the Lake-Atmosphere Turbulent EXchange (LATEX) field campaign (August–October, 2006) over Lake Geneva, Switzerland. Wind velocity, temperature and humidity profiles were measured at 20Hz using a vertical array of four sonic anemometers and open-path gas analyzers. The results indicate that the observed subgrid-scale statistics are very similar to those observed over land surfaces, suggesting that the effect of the lake waves on surface-layer turbulence during LATEX is small. The measurements allowed, for the first time, the study of subgrid-scale turbulent transport of water vapour, which is found to be well correlated with the transport of heat, suggesting that the subgrid-scale modelling of the two scalars may be coupled to save computational resources during LES.transport of water vapour, and which is found to be well correlated with the transport of heat, suggesting that the subgrid-scale modelling of the two scalars may be coupled to save computational resources during LES.