Riparian zones are important buffer zones for streams as they are hotspots of nitrate transformation and removal in agricultural catchments. However, mixing of water from different sources and various transformation processes can complicate the quantification of nitrate turnover in riparian zones. In this study, we analyzed nitrate concentration and isotope data in riparian groundwater along a 2-km stream section in central Germany. We developed a mathematical model combining end-member mixing and isotope modeling to account for mixing of river water and groundwater and quantify nitrate transformation in riparian groundwater. This enabled us to explicitly determine the extent of denitrification (as process leading to permanent nitrate removal from riparian groundwater) and transient nitrate removal by additional processes associated with negligible isotope fractionation (e.g., plant uptake and microbial assimilation) and to perform an extensive uncertainty analysis. Based on the nitrogen isotope data of nitrate, the simulations suggest a mean removal of up to 27% by additional processes and only about 12% by denitrification. Nitrate removal from riparian groundwater by additional processes exceeded denitrification particularly in winter and at larger distance from the river, underlining the role of the river as organic carbon source. This highlights that nitrate consumption by additional processes predominates at the field site, implying that a substantial fraction of agricultural nitrogen input is not permanently removed but rather retained in the riparian zone. Overall, our model represents a useful tool to better compare nitrogen retention to permanent nitrogen removal in riparian zones at various temporal and spatial scales.