Rivers are often assumed to be the main source of nutrients triggering eutrophication in the Great Barrier Reef (GBR). However, existing nutrient budgets suggest a major missing source of nitrogen and phosphorus sustaining primary production. Here, we used radium isotopes to resolve submarine groundwater discharge (SGD)-derived, shelf-scale nutrient inputs to the GBR. The total SGD was ∼10-15 times greater than average river inputs, with nearshore groundwater discharge accounting for ∼30% of this. Total SGD accounted for >30% of all known dissolved inorganic N and >60% of inorganic P inputs and exceeded regional river inputs. However, SGD was only a small proportion of the nutrients necessary to sustain primary productivity, suggesting that internal recycling processes still dominate the nutrient budget. With millions of dollars spent managing surface water nutrient inputs to reef systems globally, we argue for a shift in the focus of management to safeguard reefs from the impacts of excess nutrients.