The rainfall variability has been testified to be unprecedentedly remarkable in the context of climate change. Extreme storms and droughts have occurred throughout the globe and caused serious impacts on society and ecosystems. However, little has been done to explore the effect of rainfall variability on water quality. This study is aimed to investigate the effect of rainfall variability on Nitrogen (N) dynamics that impact water quality and aquatic ecosystems. The transport of flow and nitrate was simulated for a small agricultural catchment in central Germany, using the fully coupled surface-subsurface model HydroGeoSphere. Rainfall time-series with the designative parameter characteristics were generated using a stochastic rainfall generator. Three representative years (with high, normal, and low annual precipitations, respectively) were chosen from the past two decades in central Germany as target scenarios. Based on the scenario of low annual precipitation, a fourth scenario with reduced plant uptake was considered to represent the situation that vegetation is partially destroyed by extreme droughts. Simulation of each scenario was conducted to identify the impact of rainfall variability on N dynamics. The results suggest that higher annual precipitation can enhance the transformation and transport of nitrogen. Lower annual precipitation is conducive to the nitrogen retention capacity. Nonetheless, when vegetation suffers from drought stress, the capacity will decline significantly, suggesting that vegetation plays a vital role in N dynamics. The sensitivity analyses of selected parameters of the rainfall generator show that longer interstorm periods inhibit the transformation of N and prompt the accumulation of SON. However, alterative longer interstorm periods and storm durations enhance extensive transformation during a certain time. High mean rainfall intensities contribute to the transformation from SON to SIN in the season of vegetation growth and the season with high temperatures. Overall, the study clarifies the effect of rainfall variability on N dynamics in a small agricultural catchment, which provides theoretical support for us to protect aquatic ecosystems under climate change in the future.