Rural areas lacking essential sewage treatment facilities and collection systems often experience eutrophication due to elevated nutrient loads. Understanding nitrogen (N) sources and transport mechanisms in rural catchments is crucial for improving water quality and mitigating downstream export loads, particularly during storm events. To further elucidate the sources, pathways, and transport mechanisms of N from a rural catchment with intensive agricultural activities during storm events, we conducted an analysis of 21 events through continuous sampling over two rainy seasons in a small rural catchment from the lower reaches of the Yangtze River. The results revealed that ammonia-N (NH4+-N) and nitrate-N (NO3−-N) exhibited distinct behaviors during rainstorm events, with NO3−-N accounting for the primary nitrogen loss, its load being approximately forty times greater than that of NH4+-N. Through examinations of the concentration-discharge (c-Q) relationships, the findings revealed that, particularly in prolonged rainstorms, NH4+-N exhibited source limited pattern (b = −0.13, P < 0.01), while NO3−-N displayed transport limited pattern (b = −0.21, P < 0.01). The figure-eight hysteresis pattern was prevalent for both NH4+-N and NO3−-N (38.1% and 52.0%, respectively), arising from intricate interactions among diverse sources and pathways. For NO3−-N, the hysteresis pattern shifted from clockwise under short-duration rainstorms to counter-clockwise under long-duration rainstorms, whereas hysteresis remained consistently clockwise for NH4+-N. The hysteresis analysis further suggests that the duration of rainstorms modifies hydrological connectivity, thereby influencing the transport processes of N. These insights provide valuable information for the development of targeted management strategies to reduce storm nutrient export in rural catchments.