We investigate the effects of bottom roughness on bottom boundary-layer (BBL) instability beneath internal solitary waves (ISWs) of depression. Applying both two-dimensional (2-D) numerical simulations and linear stability theory, an extensive parametric study explores the effect of the Reynolds number, pressure gradient, roughness (periodic bump) height
$h_b$ and roughness wavelength
$\lambda _b$ on BBL instability. The simulations show that small
$h_b$, comparable to that of laboratory-flume materials (
$\sim$100 times less than the thickness of the viscous sublayer
$\delta _v$), can destabilize the BBL and trigger vortex shedding at critical Reynolds numbers much lower than what occurs for numerically smooth surfaces. We identify two mechanisms of vortex shedding, depending on
$h_b/\delta _v$. For
$h_b/\delta _v \gtrapprox 1$, vortices are forced directly by local flow separation in the lee of each bump. Conversely, for
$h_b/\delta _v \lessapprox 10^{-1}$ the roughness seeds perturbations in the BBL, which are amplified by the BBL flow. Roughness wavelengths close to those associated with the most unstable BBL mode, as predicted by linear instability theory, are preferentially amplified. This resonant amplification nature of the BBL flow, beneath ISWs, is consistent with what occurs in a BBL driven by surface solitary waves and by periodic monochromatic waves. Using the
$N$-factor method for Tollmien–Schlichting waves, we propose an analogy between the roughness height and seed noise required to trigger instability. Including surface roughness, or more generally an appropriate level of seed noise, reconciles the discrepancies between the vortex-shedding threshold observed in the laboratory versus that predicted by otherwise smooth-bottomed 2-D spectral simulations.