2-D Direct Numerical Simulations (DNS) have been performed to investigate the dynamics of the bottom boundary layer (b.b.l.) in the footprint of fully nonlinear internal waves (NLIWs) of depression propagating in a uniform-depth two-layer system. Use of a spectral multidomain penalty method enables an accurate and robust description of the wave-induced b.b.l. at values of Reynolds number (based on NLIW phase speed and wave-guide depth) as high as 100,000. Intermittent global b.b.l. instabilities and subsequent vortex shedding are found to occur when the wave amplitude surpasses a critical value which decreases with increasing Reynolds number, oncoming current strength and deeper thermocline. The structure of the numerically reproduced NLIW-induced b.b.l. shows strong similarities with its laboratory counterpart. Finally, our findings suggest that NLIWs propagating against a barotropic tidal current are highly likely to generate a powerful near-bed wake in the rear of the wave which can drive significant dissipation and particulate resuspension.