Abstract The instability of a surface-trapped jet over rough bottom topography is examined using a linearized quasigeostrophic model. The jet is laterally sheared and thus susceptible to both barotropic and baroclinic instability. The relative magnitude of the two depends on the jet width and on the spectral characteristics and amplitude of the bathymetry. The most unstable eddies in the upper layer are typically smaller over bathymetry than with a flat bottom. Topography also alters momentum flux convergence in the upper layer and causes the perturbations to resemble eddies in a 1.5-layer flow. But as long as the jet is wider than the deformation radius, baroclinic instability is present, yielding deep eddies that are phase-locked to those at the surface. In addition, topography facilitates scattering of energy at depth to other scales. So, instability over rough topography could be an efficient, and largely overlooked, means of transferring mesoscale energy to the dissipative scales. Significance Statement This study investigates the effects of bottom roughness on large-scale ocean currents and their associated eddies. Roughness affects the eddy size and speed and how they exchange energy with the mean flow. Roughness also facilitates energy transfer to smaller scales where it can be dissipated. Thus, instability over rough topography could be an important part of the oceanic energy balance.