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. Plain Language Summary Nitrogen is an important nutrient for agricultural crops. However, excessive nitrogen input into surface water in the form of nitrate can lead to algae blooms and lack of oxygen. The riparian zones of rivers are important buffer zones where groundwater is connected to soils, which are rich in soil organisms and organic matter pools fueling reaction processes. Hence, plants and bacteria can remove nitrate from riparian groundwater before it reaches the river. Bacterial consumption of nitrate (denitrification) leads to complete removal of nitrogen via release of nitrogen gas into the atmosphere. In contrast, other biogeochemical processes such as nitrate uptake by plants merely result in nitrogen retention within riparian zones. To quantify the role of denitrification relative to other processes, we developed a novel model combining concentration and isotope data of nitrate and applied it to a groundwater study site in Central Germany. We found that nitrate removal from riparian groundwater by additional processes largely exceeded denitrification. Hence, a major fraction of nitrogen inputs was retained in the riparian zone and may eventually end up in the river. Such information is highly relevant for many river ecosystems at risk of eutrophication because of high nitrogen inputs from agriculture. Key Points We present a model using concentration and isotope data to distinguish riparian denitrification from additional nitrate removal processes The model was applied to concentration and dual‐element isotope data of nitrate from riparian groundwater wells Nitrate removal by additional processes greatly exceeded denitrification, particularly at larger distance from the river and in winter