Resource subsidies can influence the structure and dynamics of recipient food webs in a wide range of ecosystems through direct and indirect effects. On the sub-Antarctic Prince Edward Islands (PEIs), large populations of top predators import substantial amounts of nutrients from the oceans to the islands. Guano runoff from the islands increases the availability of nutrients in the nearshore marine environment, supporting phytoplankton blooms. We apply food web models to the PEIs marine ecosystem to investigate food web responses to variability in resource subsidies. Modelled scenarios of island-associated blooms indicated small effects on the ecosystem under both normal bloom conditions and when the input of blooms was removed entirely. Benthic communities benefited most strongly from blooms and a fivefold increase in bloom production had broadly positive impacts throughout the entire food web, including the pelagic food web. Land-based predators were shown to contribute significantly to nearshore ecosystem production via their contributions to ammonia runoff. Transfers of material across the land–sea interface were estimated to contribute 0.73 t N km−2 y−1 to the nearshore ammonium pool. The effects of removing terrestrial nutrient input were very small when 100% of nutrient runoff was converted to island-associated bloom phytoplankton while the macrophyte production rate was held constant. If, however, macrophyte production was also supported in part or wholly by terrestrial nutrient runoff, the ecosystem-level effects of runoff variability were much greater and more broadly distributed throughout the food web. Given the potential of habitat linkages to alter or structure communities, populations, and environments, it is important to incorporate land–sea linkages into ecological models.