The study addresses the nitrogen cycling in Elbe estuary. Observations of salinity, nutrients and oxygen from moored stations, ship casts and helicopter surveys are presented. Observations are complemented by simulations obtained from a coupled physical-biogeochemical 3D unstructured model, applied for the first time to the estuarine environment. Model simulations reproduce the temporal variability of nutrients and oxygen along the estuarine salinity gradient. Both, observations and model results, demonstrate mostly conservative mixing of nitrate and non-conservative behavior of ammonium. Model hind-casts of the years 2012 and 2013 provide a detailed reconstruction of nitrogen recycling with ammonium appearing as the key species of the remineralisation process. Estuarine turnover processes are fueled by inputs of diatoms and organic nitrogen at the tidal weir with intense primary production manifest in the shallow river section downstream of the weir. The harbor area is the hot spot of heterotrophic decay associated with growth of meso-zooplankton, sedimentation of degradable material, remineralisation, oxygen depletion, denitrification and ammonium production. In the harbor, biochemistry shows strong vertical gradients while hydrodynamics demonstrate connectivity between the main channel and the harbor. At the estuary bed nitrogen is deposited during spring and early summer. Resuspension leads to nearly closed budget by the end of the year. During the Elbe flood in June 2013, estuarine biogeochemistry is significantly disturbed with the harbor being deactivated as hot spot of heterotrophic decay. Plankton and organic matter are flushed towards the outer estuary which in consequence sees high abundance of grazers, oxygen depletion and elevated release of ammonium.