Abstract. Increased anthropogenic inputs of nitrogen (N) to the biosphere during the last decades have resulted in increased groundwater and surface water concentrations of N (primarily as nitrate) posing a global problem. Although measures have been implemented to reduce N-inputs especially from agricultural sources, they have not always led to decreasing riverine nitrate concentrations and loads. The limited response to the measures can either be caused by the accumulation of slowly mineralized organic N in the soils acting as a biogeochemical legacy or by long travel times (TTs) of inorganic N to the streams forming a hydrological legacy. Both types of legacy are hard to distinguish from the TTs and N budgets alone. Here we jointly analyze atmospheric and agricultural N inputs with long-term observations of nitrate concentrations and discharge in a mesoscale catchment in Central Germany. For three nested sub-catchments with increasing agricultural land use, we assess the catchment scale N budget, the effective TT of N. In combination with long-term trajectories of C-Q relationships we finally evaluate the potential for and the characteristics of an N-legacy. We show that in the 42-year-long observation period, the catchment received an N-input of 42 758 t, of which 97 % derived from agricultural sources. The riverine N-export sums up to 6 592 t indicating that the catchment retained 85 % of the N-input. Removal of N by denitrification could not fully explain this imbalance. Log-normal travel time distributions (TTD) for N that link the input history to the riverine export differed seasonally, with modes spanning 8–17 years. Under low-flow conditions, TTs were found to be systematically longer than during high discharges. Systematic shifts in the C-Q relationships could be attributed to significant changes in N-inputs resulting from agricultural intensification and the break-down of the East German agriculture after 1989 and to the longer travel times of nitrate during low flows compared to high flows. A chemostatic export regime of nitrate was only found after several years of stabilized N-inputs. We explain these observations by the vertical migration of the N-input and the seasonally changing contribution of subsurface flow paths with differing ages and thus differing N-loads. The changes in C-Q relationships suggest a dominance of hydrological N-legacy rather than a biogeochemical N-fixation in the soils, which should result in a stronger and even increasing dampening of riverine N-concentrations after sustained high N-inputs. Despite the strong N-legacy, a chemostatic nitrate export regime is not necessarily a persistent endpoint of intense agricultural land use, but rather depends on a steady replenishment of the mass of N propagating through the catchments subsurface. The input-output imbalance, the long time-lags and the lack of significant denitrification in the catchment let us conclude that catchment management needs to address both, a longer-term reduction of N-inputs and shorter-term mitigation of today’s high N-loads.