Denitrification and anaerobic ammonium oxidization (anammox) are considered the most important processes of removing reactive nitrogen from natural aquatic environments.We measured and compared in situ rates of the two processes across the sediment–water interface of Jinpu Bay using continuous-flow experiments combined with a 15NO3 − tracing technique to determine their relative importance in this hypereutrophic coastal ecosystem. Rates of denitrification and anammox ranged from 1.76 to 327.97 and 0.33 to 36.32 μmol N m−2 day−1, respectively.Both the denitrification and anammox processes were observed to be associated closely with the bioavailability of organic matter and concentrations of sulfide and iron oxides in sediments. Denitrification was the dominant pathway of eliminating reactive nitrogen and on average accounted for about 90 % of the total removed nitrogen. Totally, both the denitrification and anammox processes removed about 20 % of the externally derived inorganic nitrogen within the system. Most of the external nitrogen was still retained in the ecosystem,which may cause the severe eutrophication and algae blooms occurring at the study area.