Abstract. Numerous studies have shown the importance of riparian zones to reduce nitrate (NO3−) contamination coming from adjacent agricultural land. Much less is known about nitrogen (N) transformations and nitrate fluxes in riparian soils with short hydroperiods (1–3 days of inundation) and there is no study that could show whether these soils are a N sink or source. Within a restored section of the Thur River in NE Switzerland, we measured nitrate concentrations in soil solutions as an indicator of the net nitrate production. Samples were collected along a quasi-successional gradient from frequently inundated gravel bars to an alluvial forest, at three different depths (10, 50 and 100 cm) over a one-year period. Along this gradient we quantified N input (atmospheric deposition and sedimentation) and N output (leaching) to create a nitrogen balance and assess the risk of nitrate leaching from the unsaturated soil to the groundwater. Overall, the main factor explaining the differences in nitrate concentrations was the field capacity (FC). In subsoils with high FCs and VWC near FC, high nitrate concentrations were observed, often exceeding the Swiss and EU groundwater quality criterions of 400 and 800 μmol L−1, respectively. High sedimentation rates of river-derived nitrogen led to apparent N retention up to 200 kg N ha−1 yr−1 in the frequently inundated zones. By contrast, in the mature alluvial forest, nitrate leaching exceeded total N input most of the time. As a result of the large soil N pools, high amounts of nitrate were produced by nitrification and up to 94 kg N-NO3− ha−1 yr−1 were leached into the groundwater. Thus, during flooding when water fluxes are high, nitrate from soils can contribute up to 11% to the total nitrate load in groundwater.