AbstractThe thermocline of Lake Ontario is in constant motion, and as it washes back and forth along the sloping lakebed there is a striking asymmetry in near‐bed stratification and benthic turbulence between its rise and fall. Detailed field observations of the stratification and water currents from the summers of 2012 and 2013 showed that the thermocline motions had large amplitudes (as high as 15 m) and a dominant period between 16 and 17.5 h, corresponding to a near‐inertial internal Poincaré wave. During the falling phase, the warmer down‐slope flow was strongly stratified with near‐bed water temperature gradients of 1°C m−1. In contrast during the rising phase of colder up‐slope flow, there was an unstable stratification in near‐bed water and large temperature overturns due to the differential advection of stratified waters, i.e., the shear‐driven convective mechanism. Using a Thorpe‐scale analysis of overturns, the inferred turbulent diffusivity during the up‐slope flow was Kz =5 × 10−4 m2 s−1. In striking contrast during the down‐slope flow, the strong stratification had lower turbulent diffusivities of Kz =10−6 m2 s−1. The near bottom region of Lake Ontario within the thermocline swash‐zone has intense biological activity and the highest concentrations of invasive dreissenid mussels. We discuss the potential biological implications of the striking variability in benthic mixing and near‐bed stratification for nutrient cycling in the Lake Ontario nearshore.