Effects of anthropogenic inputs on corals are well documented in regard to the ecology of coral reefs. However, responses to anthropogenic changes by sponge assemblages, also a key component of coral reefs, have received less attention. This paper quantifies differences in abundance, size and distribution of the sponge Rhopaloeides odorabile across a cross-shelf reef system on the central Great Barrier Reef (GBR) from neritic to outer reef oligotrophic waters. Benthic surveys were conducted in reef habitats spatially separated across the continental shelf. The mean abundance of R. odorabile increased significantly with increasing distance from coastal habitats, with 3.5 times more individuals offshore than inshore. In contrast, the mean size (volume) of R. odorabile individuals did not differ significantly across the cross-shelf reef system. On inshore reefs, R. odorabile was restricted to depths <10 m, with a preference for shallower depths (5–6 m). On offshore reefs, R. odorabile was found as deep as 15 m and predominantly between 9 and 10 m. These demographic changes in R. odorabile populations, together with a general population size reduction from surveys made decades prior, suggest a response to anthropogenic impacts across the continental shelf of the central GBR.