• We analyzed event C-Q hysteresis for a 43-yr dataset from a drained watershed. • Event-scale nitrate flushing patterns were controlled by antecedent conditions. • Most events had anti-clockwise hysteresis highlighting the role of near-drain zone. • Fertilization rates did not affect the direction of hysteresis patterns. • Intensive drainage may dampen N legacy in historically agricultural landscapes. Nitrate Concentration–discharge (C-Q) relationships have been used to infer nitrate sources, storage, reactions, and transport in watersheds, and to reveal key processes that control runoff chemistry. Yet, studies on long-term nitrate C-Q relationships are limited due to scarce high frequency (e.g., daily) concentration data. In this paper, using a long-term high-frequency dataset (1976–2019) comprising stream flow and nitrate concentrations, we quantitatively analyzed the long-term variations of event-scale hysteresis patterns (quantified by hysteresis index, HI, and flushing index, FI) to infer the leaching mechanisms of nitrate in an artificially drained agricultural watershed in Mid-western U.S. Our results revealed that most events exhibited anti-clockwise behaviors (HI < 0), regardless of whether nitrate was flushed or diluted during events. This means that water with high levels of nitrate-N reaches the stream network slower than water with lower nitrate concentrations. Long-term mean FI was close to zero but had strong seasonal patterns with dilution patterns observed during Winter and Summer, and flushing patterns during late Spring and Fall. The consistently negative HI values regardless of the FI value gave a strong indication of the preponderant role of the near-drain zone that usually exhibits accelerated leaching and less accumulation of nitrate in the soil profile in these drained agricultural watersheds. Both HI and FI depicted strong but opposite seasonality because of weather patterns and agricultural activities, particularly N fertilization. Overall, our findings suggest a little evidence of the role of deep groundwater and instead a strong evidence of the role of subsurface drainage as the primary pathway for nitrate transport in drained agricultural watersheds. Therefore, artificial drainage could dampen N legacy caused by the historically intensive N fertilization in drained agricultural landscapes.