Biogeochemical transformations and hydraulic processes in soil and groundwater can moderate nitrate loads in surface waters compared to nitrogen inputs to soil. A modelling approach was developed based on the loose coupling of a soil nitrogen model with a groundwater flow and a multi-species reactive groundwater-transport model. This approach combines transport time with availability of reaction partners and nitrate turnover. A case study was conducted in a small lowland catchment (Schaugraben, ∼20 km²) close to Osterburg in the north of Saxony-Anhalt, Germany, and demonstrated the spatial heterogeneity of nitrate loads and concentrations resulting from the spatial distribution of nitrate inputs, the arrangement of input areas to the channel network, and the consumption of reactive substances in the aquifer. An extension of this approach aims to describe turnover processes at the groundwater-surface water interface in order to close the gap between groundwater exfiltration and catchment outlet.