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The Ningxia Yellow River irrigation area, characterized by an arid climate and high leaching of NO3--N, exhibits complex and unique groundwater nitrate (NO3--N) pollution, with denitrification serving as the principal mechanism for NO3--N removal. The characteristics of N leaching from paddy fields and NO3--N removal by groundwater denitrification were investigated through a two-year field observation. The leaching losses of total nitrogen (TN) and NO3--N accounted for 10.81–27.34% and 7.59–12.74%, respectively, of the N input. The linear relationship between NO3--N leaching and N input indicated that the fertilizer-induced emission factor (EF) of NO3--N leaching in direct dry seeding and seedling-raising and transplanting paddy fields was 8.2% (2021, R2 = 0.992) and 6.7% (2022, R2 = 0.994), respectively. The study highlighted that the quadratic relationship between the NO3--N leaching loss and N input (R2 = 0.999) significantly outperformed the linear relationship. Groundwater denitrification capacity was characterized by monitoring the concentrations of dinitrogen (N2) and nitrous oxide (N2O). The results revealed substantial seasonal fluctuations in excess N2 and N2O concentrations in groundwater, particularly following fertilization and irrigation events. The removal efficiency of NO3--N via groundwater denitrification ranged from 42.70% to 74.38%, varying with depth. Groundwater denitrification capacity appeared to be linked to dissolved organic carbon (DOC) concentration, redox conditions, fertilization, irrigation, and soil texture. The anthropogenic-alluvial soil with limited water retention accelerated the leaching of NO3--N into groundwater during irrigation. This process enhances the groundwater recharge capacity and alters the redox conditions of groundwater, consequently impacting groundwater denitrification activity. The DOC concentration emerged as the primary constraint on the groundwater denitrification capacity in this region. Hence, increasing carbon source concentration and enhancing soil water retention capacity are vital for improving the groundwater denitrification capacity and NO3--N removal efficiency. This study provides practical insights for managing groundwater NO3--N pollution in agricultural areas, optimizing fertilization strategies and improving groundwater quality.
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•The leakage of TN and NO3--N increased with increasing N input and irrigation amount.•Controlled-release nitrogenous fertilizer delayed the release of NO3--N.•The leaching loss of NO3--N showed a quadratic relationship with N input.•The removal efficiency of NO3--N by groundwater denitrification was 42.70–74.38%.