Improving nitrogen (N) status in European water bodies is a pressing issue. N levels depend not only on current but also past N inputs to the landscape, that have accumulated through time in legacy stores (e.g. soil, groundwater). Catchment-scale N models, that are commonly used to investigate in-stream N levels, rarely examine the magnitude and dynamics of legacy components. This study aims to gain a better understanding of the long-term fate of the N inputs and its uncertainties, using a legacy-driven N model (ELEMeNT) in Germany’s largest national river basin (Weser; 38,450 km2) over the period 1960-2015. We estimate the nine model parameters based on a progressive constraining strategy, to assess the value of different observational datasets. We demonstrate that beyond in-stream N loading, soil N content and in-stream N concentration allow to reduce the equifinality in model parameterizations. We find that more than 50% of the N surplus denitrifies (1480-2210 kg ha-1) and the stream export amounts to around 18% (410-640 kg ha-1), leaving behind as much as around 230-780 kg ha-1 of N in the (soil) source zone and 10-105 kg ha-1 in the subsurface. A sensitivity analysis reveals the importance of different factors affecting the residual uncertainties in simulated N legacies, namely hydrologic travel time, denitrification rates, a coefficient characterising the protection of organic N in source zone and N surplus input. Our study calls for proper consideration of uncertainties in N legacy characterization, and discusses possible avenues to further reduce the equifinality in water quality modelling.