Surface and sub-surface currents along the ocean boundary of Western Australia were simulated using Regional Ocean Modelling System (ROMS) to examine the circulation within the Perth Canyon. Two major current systems influenced the circulation within the canyon: (1) The Leeuwin current interacted weakly with the canyon as the majority of the canyon was below the depth of the Leeuwin current and (2) Leeuwin undercurrent interacted strongly with the canyon, forming eddies within the canyon at depths of 400–800 m. The results indicated that within the canyon, the current patterns changed continuously although there were some repeated patterns. Recurrent eddies produced regions where upwelling or downwelling dominated during the model runs. Deep upwelling was stronger within the canyon than elsewhere on the shelf, but vertical transport in the upper ocean was strong everywhere when wind forcing was applied. Upwelling alone appeared to be insufficient to transport nutrients to the euphotic zone because the canyon rims were deep. Increased upwelling, combined with entrapment within eddies and strong upwelling-favourable winds, which could assist mixing, may account for the high productivity attributed to the canyon. The Leeuwin current is otherwise a strong barrier to the upwelling of nutrients.