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.