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 20 Hz 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.