Abstract. In oceans, estuaries, and rivers, nitrification is an important nitrate source, and stable isotopes of nitrate are often used to investigate recycling processes (e.g. remineralisation, nitrification) in the water column. Nitrification is a twostep process, where ammonia is oxidised via nitrite to nitrate. Nitrite usually does not accumulate in natural environments, which makes it difficult to study the single isotope effect of ammonia oxidation or nitrite oxidation in natural systems.However, during an exceptional flood in the Elbe River in June 2013, we found a unique co-occurrence of ammonium, nitrite, and nitrate in the water column, returning towards normal summer conditions within 1 week. Over the course of the flood, we analysed the evolution of δ 15 N-NH During the flood event, > 97 % of total reactive nitrogen was nitrate, which was leached from the catchment area and appeared to be subject to assimilation. Ammonium and nitrite concentrations increased to 3.4 and 4.4 µmol L −1 , respectively, likely due to remineralisation, nitrification, and denitrification in the water column. δ 15 N-NH + 4 values increased up to 12 ‰, and δ 15 N-NO − 2 ranged from −8.0 to −14.2 ‰. Based on this, we calculated an apparent isotope effect 15 ε of −10.0 ± 0.1 ‰ during net nitrite consumption, as well as an isotope effect 15 ε of −4.0 ± 0.1 ‰ and 18 ε of −5.3 ± 0.1 ‰ during net nitrate consumption. On the basis of the observed nitrite isotope changes, we evaluated different nitrite uptake processes in a simple box model. We found that a regime of combined riparian denitrification and 22 to 36 % nitrification fits best with measured data for the nitrite concentration decrease and isotope increase.