Field data and the three-dimensional (3D) Estuary and Lake Computer Model (ELCOM) were used to investigate the impact of periodic forcing on the structure and dynamics of the benthic boundary layer (BBL) in Lake Kinneret, Israel, a large lake that experiences strong thermal stratification and wind forcing events. Microstructure data were used to derive the thickness of the BBL and to describe the mean turbulent properties within the BBL. Time series temperature data from thermistor chains were used to characterize the thermal structure of the lake and the basin-scale internal wave field in the lake that was shown to force the turbulent field in the BBL. A clear connection between the dynamics of the BBL and the large-scale features of the flow is presented. The time history of the thickness of the BBL, the mixing in the BBL and the resulting cross-shore flux were shown to vary with the phase of the basin-scale internal wave field. Detailed comparison of simulation results with field data revealed that the model captured well the lake hydrodynamics and the spatial and temporal evolution of energetics of the BBL. Together, field data and numerical modelling provided a clear characterization of the dynamics of the turbulent BBL and its central role in setting up a boundary layer mass flux up the slope from the lake bottom to the height of the metalimnion. Both the turbulent environment in the BBL and the mass flux are of great importance for the ecological processessing of material in a lake.