A detailed comparison of results from a numerical three-dimensional hydrostatic lake model with high-resolution observations of the vertical structure of the turbulent bottom boundary layer (BBL) in a medium-size lake (Lake Alpnach, Switzerland) is provided. The focus of this study is on the shear-induced generation and destruction of stratification in the BBL that may ultimately lead to unstable layers (convection). The model was shown to provide a reliable description of the internal seiching dynamics, as well as the local BBL properties, including the generation of shear-induced convection in two data sets from 2003 and 2007. Basin-scale mixing parameters, inferred from the simulations, are closely connected to the seiching motions, with the hypolimnetic mixing reacting almost immediately to the variable wind forcing and seiching activity. During upslope flow, the BBL becomes convectively turbulent, causing low mixing efficiency on a basin-scale, whereas during downslope flow, the BBL is restratifying and shear-induced turbulence is weak but leads to a higher mixing efficiency. The overall deep-water mixing efficiency varied in the range of 5 to 10% in this system dominated by turbulent boundary processes.