During a 9-day Lagrangian sampling campaign along the free-flowing section of the Elbe River in July 2005, water from the river as well as from major tributaries and sewage treatment plants was sampled to investigate major nitrogen transformation processes, focussing on denitrification and N-assimilation by phytoplankton. Samples were analysed for delta N-15 - NO3-, delta O-18 - NO3-, delta N-15 - NH4+, nutrient concentrations, chlorophyll a (Chl a), and particulate organic matter. A strong decrease in nitrate concentration accompanied by strong increases in Chl a, particulate organic carbon (POC) and delta N-15- and delta O-18 - NO3- values were measured along the river. The ratio of the increase in delta N-15 vs. delta O-18 of the river nitrate samples was 0.89:1. Together with the observed decrease in nitrate and the increase in Chl a and POC, this indicates a major role of nitrogen assimilation by phytoplankton. This finding is supported by budget calculations, while nitrate inputs from the sampled tributaries and from sewage treatment plants were of minor importance for the nitrogen budget of the Elbe River. The stable isotope analysis of nitrogen and oxygen in nitrate is shown to be a powerful tool for the identification of N transformation processes along large rivers, particularly if combined with Lagrangian measurements of algal biomass, and dissolved and particulate nutrient concentrations.