Food webs of many ecosystems are sustained by organic matter from other habitats. Human activities and climatic change are increasingly modifying the quality and supply of these resources, yet for most ecosystems it is unknown how the taxonomic composition of organic matter influences community composition. Along the coastline of Sydney, Australia, the once abundant habitat-forming macroalga, Phyllospora comosa, is now locally extinct. Shallow reefs are now primarily occupied by Sargassum sp. and, to a lesser extent, the kelp Ecklonia radiata. We experimentally manipulated the supply of P. comosa, Sargassum sp. and E. radiata to estuarine sediments to assess responses by macroinvertebrate communities to: (1) changing the identity of the dominant detrital resource; and (2) varying the ratio of input of different macrophytes. Estuarine sediments dosed with P. comosa supported greater abundances of macroinvertebrates than sediments receiving Sargassum sp. or the kelp E. radiata. Whereas plots receiving Sargassum sp. or E. radiata had fewer macroinvertebrates than controls, plots receiving a moderate (120 g dry weight per m2) loading of P. comosa had more. Mixtures of detritus dominated by P. comosa supported similar macroinvertebrate communities to monocultures of the alga. Communities in sediments receiving detritus comprised of less than one-third P. comosa were, however, distinctly different. Our study provides evidence that the ecological ramifications of species decline can extend to spatially removed ecosystems, subsidised by allochthonous materials. Even prior to extinction of detrital sources, small changes in their provision of organic matter may alter the structure of subsidised communities.