For the design and the assessment of river restoration projects, it is important to know to what extent the elimination of reactive nitrogen (N) can be improved in the riparian groundwater. We investigated the effectiveness of different riparian zones, characterized by a riparian vegetation succession, for nitrate (NO-3) removal from infiltrating river water in a restored and a still channelized section of the river Thur, Switzerland. Functional genes of denitrification (nir S and nosZ) were relatively abundant in groundwater from willow bush and mixed forest dominated zones, where oxygen concentrations remained low compared to the main channel and other riparian zones. After flood events, a substantial decline in NO3− concentration (> 50%) was observed in the willow bush zone but not in the other riparian zones closer to the river. In addition, the characteristic enrichment of 15N and 18O in the residual NO-3pool (by up to 22‰ for δ15N and up to 12‰ for δ18O) provides qualitative evidence that the willow bush and forest zones were sites of active denitrification and, to a lesser extent, NO-3 removal by plant uptake. Particularly in the willow bush zone during a period of water table elevation after a flooding event, substantial input of organic carbon into the groundwater occurred, thereby fostering post-flood denitrification activity that reduced NO-3 concentration with a rate of ∼21 N-1 d-1. Nitrogen removal in the forest zone was not sensitive to flood pulses, and overall NO-3 removal rates were lower (∼6 μmol l-1 d -1). Hence, discharge-modulated vegetation-soil-groundwater coupling was found to be a key driver for riparian NO-3 removal. We estimated that, despite higher rates in the fairly constrained willow bush hot spot, total NO-3 removal from the groundwater is lower than in the extended forest area. Overall, the aquifer in the restored section was more effective and removed ∼20% more NO-3 than the channelized section. © 2012 Author(s).