This paper presents the assessment of the efficiency of the main biological nitrogen transformation processes in a shallow well-oxygenated river and conditions under which they are active and stabilise. The process dynamics was studied with the help of mathematical modelling of 2 years on-line data series measured in a reach of the Toess River, Switzerland. The algal nitrogen uptake was very stable and unaffected by most but frequent flood events. Daylight photosynthetic nitrogen uptake stabilised at 6 mgN m−2streambed h−1 (15 °C), dark uptake on storage products at rates of 0.5–2.5 mgN m−2streambed h−1. Nitrogen uptake by heterotrophic bacteria in the hyporheic zone was relatively constant at a level of 1.5–3.5 mgN m−2streambed h−1. Streambed nitrification could establish only during periods with average an daily concentration of at least 0.3 gNH4-N m−3 in river water for several weeks. The maximum nitrification rate was 35 mgN m−2streambed h−1 for 3 gNH4-N m−3. The effects of reduced nitrification in the WWTP and of river banks shading on a sudden ammonium peak were simulated. A river reach endangered by ammonium spills should be kept open to sun to favour ammonium uptake by algae. In-stream nitrification reduces ammonium peaks efficiently but leads to toxic nitrite concentrations.

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