Anthropogenic nutrient discharge to coastal marine environments is commonly associated with excessive algal growth and ecosystem degradation. However in the world's largest coral reef ecosystem, the Great Barrier Reef (GBR), the response to enhanced terrestrial nutrient inputs since European settlement in the 1850's remains unclear. Here we use a 333 year old composite record (1680-2012) of 15N/14N in coral skeleton-bound organic matter to understand how nitrogen cycling in the coastal GBR has responded to increased anthropogenic nutrient inputs. Our major robust finding is that the coral record shows a long-term decline in skeletal 15N/14N towards the present. We argue that this decline is evidence for increased coastal nitrogen fixation rather than a direct reflection of anthropogenic nitrogen inputs. Reducing phosphorus discharge and availability would short-circuit the nitrogen fixation feedback loop and help avoid future acute and chronic eutrophication in the coastal GBR.