Through estuaries, large amounts of anthropogenic nitrogen (N) are delivered to the ocean where productivity is limited by N. To project how N may alter offshore ecology the knowledge of in-estuary N processes is critical. Ammonium and urea, two reduced forms of anthropogenic N commonly observed, are the preferred substrates for various microorganisms (e.g., uptake by phytoplankton or bacteria and oxidation by nitrifier), yet, how they are consumed remains underexplored in the estuary. In the winter of 2018, we applied 15N isotope tracer incubation techniques to determine the two main bio-consumption processes, i.e., uptake and oxidation, of ammonium and urea, in the dark for the Jiulong River Estuary, a eutrophic estuary in southeastern China. Results showed that light penetration depth ranged from 0.8-3.3 m leaving 76% of estuary water bodies experiencing dark situations even in the daytime. Accordingly, ammonia oxidation, though its light-sensitive, dominates the estuarine regenerated-N cycle, showing the rank: ammonia oxidation > ammonium uptake >> urea uptake ≈ urea oxidation. Urea uptake popped up downstream when ammonium was down to ~5 µM, suggesting microorganisms’ high preference for ammonium over urea. Such obstruct of urea utilization resulted in a much longer lifetime of urea (surface: 162 ± 88 days; bottom 148 ± 82 days) relative to ammonium (surface: 19 ± 9 days; bottom 12 ± 7 days). The relatively low ratio of urea oxidation to ammonia oxidation rates was accompanied by a low ratio of urea-N to ammonium concentrations based on the compilation of reported case studies in different aquatic environments further confirmed our conclusion. Such ammonium-inhibition in the estuary allows urea to be transported farther offshore to stimulate microorganisms capable of utilizing urea, which may have a significant impact on coastal ecology and has implications for the N cycle in other eutrophic aquatic systems.