Defining effective measures to reduce nitrate pollution in heterogeneous mesoscale catchments remains challenging if based on concentration measurements at the outlet only. One reason is our limited understanding of the sub-catchment contributions to nitrate export and their importance at different time scales. While upstream sub-catchments often disproportionally contribute to runoff generation and in turn to nutrient export, agricultural areas, which are typically found in downstream lowlands, are known to be a major source for nitrate pollution. To disentangle the interplay of these contrasting drivers of nitrate export, we analyzed seasonal long-term trends and event dynamics of nitrate concentrations, loads and the concentration-discharge relationship in three nested catchments within the Selke catchment (456 km²), Germany. The upstream sub-catchments (40.4 % of total catchment area, 34.5 % of N input) had short transit times and dynamic concentration-discharge relationships with elevated nitrate concentrations during wet seasons and events. Consequently, the upstream sub-catchments dominated nitrate export during high flow and disproportionally contributed to overall annual nitrate loads at the outlet (64 %). The downstream sub-catchment was characterized by higher N input, longer transit times and relatively constant nitrate concentrations between seasons, dominating nitrate export during low flow periods. Neglecting the disproportional role of upstream sub-catchments for temporally elevated nitrate concentrations and net annual loads can lead to an overestimation of the role of agricultural lowlands. Nonetheless, in agricultural lowlands, constantly high concentrations from nitrate legacies pose a long-term threat to water quality. This knowledge is crucial for an effective and site-specific water quality management.