Recent efforts have been made to undergo a large revegetation project on Lady Elliot Island, a highly disturbed coral cay. However, there is currently little understanding of how island vegetation influences groundwater nutrient supply to adjacent reef systems. Here we combine stable isotope tracing, geophysical surveys, and satellite-based estimates to unravel the links between transpiration and the discharge of groundwater nitrate to the surrounding coral reef (from Leaf to Reef). We recorded a net loss of freshwater over the two-year study period. Transpiration was higher in forested areas which covered the leeward side of the island. This correlated with both increased salinity and nitrate concentration in groundwater discharge from that side of the island. We estimate that groundwater nitrate contributes at least 30% to the tissue content of reef flat reef primary producers and consumers. Interestingly, this discharge did not vary seasonally despite reduced rainfall and the absence of seabirds over the austral winter. We concluded that high rates of transpiration in forested areas alters aquifer dynamics and promotes continuous groundwater nitrate discharge to the reef systems surrounding tropical coral islands. This has significant implications for the management of vegetation in ecosystems that are sensitive to nutrient enrichment.