AbstractEstuaries act as an organic matter and nutrient filter in the transition between the land, rivers and the ocean. In the past, high nutrient and organic carbon load and low oxygen concentration made the Elbe River estuary (NW Europe) a sink for dissolved inorganic nitrogen. A recent reduction in loads and subsequent recovery of the estuary changed its biogeochemical function, so that nitrate is no longer removed on its transition towards the coastal North Sea. Nowadays in the estuary, nitrification appears to be a significant nitrate source. To quantify nitrification and determine actively nitrifying regions in the estuary, we measured the concentrations of ammonium, nitrite and nitrate, the dual stable isotopes of nitrate and net nitrification rates in the estuary on five cruises from August 2012 to August 2013. The nitrate concentration increased markedly downstream of the port of Hamburg in summer and spring, accompanied by a decrease of nitrate isotope values that was clearest in summer exactly at the location where nitrate concentration started to increase. Ammonium and nitrite peaked in the Hamburg port region (up to 18 and 8 μmol L−1, respectively), and nitrification rates in this region were up to 7 μmol L−1 day−1. Our data show that coupled re-mineralization and nitrification are significant internal nitrate sources that almost double the estuary’s summer nitrate concentration. Furthermore, we find that the port of Hamburg is a hot spot of nitrification, whereas the maximum turbidity zone (MTZ) only plays a subordinate role in turnover of nitrate.