Climate change and anthropogenic nutrient enrichment are driving rapid increases in ocean deoxygenation. These changes cause biodiversity loss and have severe consequences for marine ecosystem functioning and in turn the delivery of ecosystem services upon which humanity depends (e.g. fisheries). We seek to understand how such changes will impact seafloor functioning using biological traits analysis. Results from a sewage-sludge disposal site in the Firth of Clyde, UK spanning 26 years of monitoring showed that substantial changes in macrobenthic nutrient cycling and the provision of food for predators occurred, with elevated functioning on the margins 1–2 km from the centre of the disposal grounds. Thus, changes in food-web dynamics are expected, that weaken benthic pelagic coupling and lower secondary production (such as fisheries). Generally, functioning was conserved, but declined below a ~6% total organic carbon threshold. Similar to other severely deoxygenated systems, the recovery was slow and hysteresis was apparent.