The response of a coastal ocean model, simulating a typical eastern boundary system, to downwelling-favorable winds with and without the presence of a submarine canyon is studied. Three contrasting bathymetric configurations, considering shelves with different depths and slopes, are evaluated. Experiments without a submarine canyon represent the well-known downwelling circulation and cross-shore structure with a downwelling front and the development of frontal instabilities generating density anomalies in the bottom layer. The presence of the submarine canyon drives important changes in cross-shore flows, with opposing velocities on either side of the canyon. Onshore (offshore) and downward (upward) velocities develop in the upstream (downstream) side of the canyon in the time-dependent and advective phases. Instabilities develop and are modified principally downstream of the canyon. Overall, the net impact of the canyon is to enhance offshore and downward transport. However, particle tracking experiments reveal that particles can become trapped inside the canyon in an anticyclonic circulation when the particles pass the canyon over the continental slope or when particles inside the canyon are affected by downwelling conditions. Overall, similar to 20 %-23 % (similar to 15 %-18 %) of particles released directly upstream (in the canyon) at depths below the continental shelf become trapped inside the canyon until the end of the simulations (15 d).