A non-hydrostatic model in cross sectional form with idealized topography representing a sill and forced by a barotropic tidal flow is used to examine the role of a hydraulic transition and internal lee waves in determining mixing in the sill region. Calculations using smooth topography show that unsteady lee waves are generated on the sill slope during flood tide. These waves propagate toward the sill when the tide reverses leading to enhanced mixing in the sill region. The addition of small scale topography on the leeside of the sill changes the lee wave distribution with an associated increase in mixing depending upon wavelength and amplitude of topography. Calculations show the importance of the hydraulic transition, lee waves and small scale topography in determining mixing in sill regions compared to smooth large scale topography.