AbstractBenthic storms are episodes of intensified near‐bottom currents capable of sediment resuspension in the deep ocean. They typically occur under regions of high surface eddy kinetic energy (EKE), such as the Gulf Stream. Although they have long been observed, the mechanism(s) responsible for their formation and their relationships with salient features of the deep ocean, such as bottom mixed layers (BMLs) and benthic nepheloid layers (BNLs), remain poorly understood. Here we conduct idealized experiments with a primitive‐equation model to explore the impacts of the unforced instability of a surface‐intensified jet on near‐bottom flows of a deep zonal channel. Vertical resolution is increased near the bottom to represent the bottom boundary layer. We find that the unstable near‐surface jet develops meanders and evolves into alternating, deep‐reaching cyclones and anticyclones. Simultaneously, EKE increases near the bottom due to the convergence of vertical eddy pressure fluxes, leading to near‐bottom currents comparable to those observed during benthic storms. These currents in turn form BMLs with thickness of O(100 m) from enhanced velocity shears and turbulence production near the bottom. The deep cyclonic eddies transport fluid particles both laterally and vertically, from near the bottom through the entire BML and may contribute to the formation of the lower part of BNLs. A sloping bottom reduces both the intensity of the near‐bottom currents and the extent of vertical transport. Overall, our study highlights a significant response of the abyssal environment to near‐surface current instability, with potential implications for sediment transport in the deep ocean.