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The Southern Ocean is undergoing rapid environmental change, which has impacted its ecosystems and food webs. There is need for ecosystem models that incorporate all levels of the biotic system and consider physical context. Using an end-to-end ecosystem model of the Prince Edward Islands (PEIs), we investigated the importance of the input of oceanic nutrients, oceanic plankton, and run-off of terrestrial ammonium to nearshore production. We compared ecosystem state as group production rates and as the relative scale of pelagic versus demersal food web pathways under alternate ocean current regimes, assumptions of macrozooplankton advection into shelf waters, and assumptions of plankton retention within the nearshore region. The major outcomes are: (1) oceanic plankton, more than oceanic nutrients or terrestrial nutrients, is the major driver of production for all groups within the nearshore ecosystem. Island run-off of ammonium is a minor driver of production but is most important among groups with higher reliance upon detrital food chains (benthic invertebrates, demersal fishes, Gentoo penguins); (2) groups most sensitive to changes in ocean current regime and assumptions of macrozooplankton advection into shelf waters are planktivores (southern rockhopper penguins, Macaroni penguins) and piscivores whose diets rely heavily upon planktivorous fishes; (3) zooplankton populations cannot support estimated levels of predation pressure within the nearshore ecosystem if they behave as purely passive drifters. Our findings suggest changes to physical processes, such as a postulated southward shift in the position of the sub-Antarctic front leading to intensification of currents approaching the islands, has already had and will continue to have significant impacts on the PEIs ecosystem.