The development of megalopolises in coastal areas is often linked with severe eutrophication, requiring mitigation of anthropogenic dissolved inorganic nitrogen (DIN) pollution. Yet, identifying the DIN-sources responsible for eutrophication is challenging, hampering mitigation efforts. Here, we utilize the stable nitrogen isotope ratio of endosymbiotic dinoflagellate Symbiodinium spp. (δ15Nsym) associated with the hard coral Porites to trace DIN sources in one of the most urbanized areas of the planet: the Pearl River Delta (PRD). The mean δ15Nsym value found in the coastal waters of Hong Kong (HK), located on the eastern edge of the PRD, (7.4‰ ± 1.2‰) was +2.7‰ higher than at Dongsha Atoll, a reference site unaffected by anthropogenic-DIN (4.7‰ ± 0.4‰). The isotopic enrichment suggested a consistent dominance of DIN deriving from local and regional sewage discharges on the eastern edge of HK. Furthermore, the strong depletion of the summer δ15Nsym value (-1.6‰) observed in southern HK revealed that the Pearl River plume strongly modulates the coastal DIN pool. Our results revealed the value of benthic marine organisms' δ15N for deciphering the complex dynamics of coastal eutrophication and highlighted the pivotal role of transboundary coordination in DIN-pollution mitigation.