The exchange between the Humboldt and Patagonian large marine ecosystems, the largest marine ecosystems in the Southern Hemisphere, is investigated with numerical simulations. Most of the southern Patagonian Shelf waters originate from the South Pacific's upper layer. The exchange takes place mainly through the shelf break via the Cape Horn shelf. The interannual variability of shelf exchange is partly explained by the large-scale wind variability and associated with the Southern Annular Mode.