Small-island coral reef ecosystems are usually closely coupled to the activities of human inhabitants. Ahus Island (Papua New Guinea) is an isolated Pacific island with a rapidly growing population, heavy reliance on marine resources and limited infrastructure. We hypothesized that untreated sewage was driving distinct benthic assemblages around Ahus and neighbouring uninhabited Onetah. At sites with varying proximities to beach toilets, fore-reef herbivorous fish biomass and benthic composition were measured alongside reef-flat sedimentary oxygen consumption (SOC); a high SOC rate reflects high organic input into coastal waters, thus serving as a potential indicator of sewage input. Fish biomass was low (17.1–20.1 g m–2), but consistent between sites. However, cyanobacteria dominated the fore-reef closest to toilets (62 ± 3%) with highest reef-flat SOC, whereas hard corals dominated furthest away (63 ± 1%), where SOC was lowest. To our knowledge, this is the first study that used SOC to detect local differences in sewage pollution. The results indicate that whilst corals can maintain their dominance on overfished reefs, additional sewage stress may drive pronounced benthic shifts, highlighting the urgency to improve small-island waste management.