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The dynamics associated with the propagation of unstable waves along a density front and their interaction with submarine canyons are simulated and analyzed with a fine-resolution three-dimensional primitive equation coastal ocean model. Simulations consider flow in an alongshore density front over two bottom topographies: an idealized straight shelf and a shelf incised by a canyon. The stationary circulation over the idealized shelf exhibits a geostrophic balance that is perturbed when the canyon topography is introduced. Enhanced cross-shore and vertical motions are produced as a result of the front-canyon interaction. A second set of simulations consider the effect of a small perturbation superimposed on the frontal circulation which develops growing meanders. In this case, the perturbation over the shelf grows rapidly by baroclinic instability into a steepened backward breaking wave characterized by significant cross-shore and vertical motions. The canyon topography accelerates or slows the development of the perturbation depending on the relative position of the unstable waves and the canyon. Finally, we use model results to determine the shelf-slope exchanges based on two methodologies. The first method computes the water transported across the shelf break while the second accounts for cross-shore displacements of water. The application of both approaches reveals that not all water transported across the shelf break is effectively exchanged between the shelf and the open ocean. However, cross-shore and vertical motions are enhanced by the unstable front and the submarine canyon leading to a large exchange between shelf and open ocean waters.