Floodplains remove nitrate from rivers through denitrification and thus improve water quality. The Danube River Basin (DRB) has been affected by elevated nitrate concentrations and a massive loss of intact floodplains and the ecosystem services they provide. Restoration measures intend to secure and improve these valuable ecosystem services, including nitrate removal. Our study provides the first large-scale estimate of the function of large active floodplains in the DRB to remove riverine nitrate and assesses the contribution of reconnection measures. We applied a nutrient emission model in 6 river systems and coupled it with denitrification and flooding models which we adapted to floodplains. The floodplains have the capacity to eliminate about 33,200 t nitrate-N annually, which corresponds to 6.5 % of the total nitrogen emissions in the DRB. More nitrate is removed in-stream at regular flow conditions than in floodplain soils during floods. However, increasing frequently inundated floodplain areas reveals greater potential for improvement than increasing the channel network. In total, we estimate that 14.5 % more nitrate can be removed in reconnected floodplains. The largest share of nitrogen emissions is retained in the Yantra and Tisza floodplains, where reconnections are expected to have the greatest impact on water quality. In absolute numbers, the floodplains of the lower Danube convert the greatest quantities of nitrate, driven by the high input loads. These estimates are subject to uncertainties due to the heterogeneity of the available input data. Still, our results are within the range of similar studies. Reconnections of large floodplains in the DRB can, thus, make a distinct contribution to improving water quality. A better representation of the spatial configuration of water quality functions and the effect of floodplain reconnections may support the strategic planning of such to achieve multiple benefits and environmental targets. Display omitted •A first estimate of the NO3 removal by large floodplains in the Danube River Basin.•We coupled a nutrient emission-, a denitrification-, and a flooding model.•Currently, active floodplains can remove ~33,200 t NO3-N (≙6.5 % of N emissions).•Reconnections could increase this by 9–32 %, besides other ecological improvements.•Assessing water quality functions supports the planning of floodplain restorations.