A two-layer shallow-water equation model is applied to a flat-bottom ocean on the f plane to explore instability mechanisms in Western Boundary Current (WBC) that lead to the formation of strong cyclones in the deep ocean underneath. Findings reveal a tight coupling of surface meandering and deep cyclogenesis, in agreement with observational evidence. Barotropic cyclones develop in timescales of 5–10 days and attain swirl speeds of >50 cm/s (depends on initial strength of WBC) on a diameter of ∼100 km. Cyclogenesis is driven by advection of relative vorticity in the surface ocean and failure of the thermocline to respond rapidly enough to the associated sea level variations. Findings suggest that cyclogenesis and the associated strong abyssal flows (benthic storms) are ubiquitous features of WBCs and other frontal flows.