Global change has imposed multiple environment stresses on coastal waters. Rapid urbanization and increasing human perturbation resulted in severe nutrient loadings followed by eutrophication in coastal waters. Therefore source identification and tracking become critical for water quality management. Based on its feasibility,here we conducted a case study for Xiamen coastal river,in order to track possible nitrogen pollution sources. Water quality was measured in the whole river during dry season,in order to explore the biogeochemical processes of nitrogen. With dual isotopic techniques (delta15N and delta18 O) and statistical information of land uses,we identified the key source of nitrogen pollutants,and clarified the causes leading to ammonium levels of exceeding standards. Current results show that ammonium was the dominant form (>50%) of dissolved inorganic nitrogen at 63% sampling sites. Ammonium concentration increased along river downward and significantly correlated with the areal proportion of built /residence lands and aquaculture ponds in associate catchment. Soil organic nitrogen,manure and sewage,and synthetic fertilizer contribute 89% ~ 91% of nitrate sources. Therefore,we proposed that nitrogen emission abatement,ecological restoration and integrated sea-land management should be considered together for improving water quality management. This study provides an important reference for national water pollution control and management.