Nitrate pollution is a significant environmental issue closely related to human activities, complicated hydrological interactions and nitrate fate in the valley watershed strongly affects nitrate load in hydrological systems. In this study, a nitrate reactive transport model by coupling SWAT-MODFLOW-RT3D between surface water and groundwater interactions at the watershed scale was developed, which was used to reproduce the interaction between surface water and groundwater in the basin from 2016 to 2019 and to reveal the nitrogen transformation process and the evolving trend of nitrate load within the hydrological system of the valley watershed. The results showed that the basin exhibited groundwater recharge to surface water in 2016-2019, particularly in the northwestern and northeastern mountainous regions of the valley watershed and the southern Beishan Reservoir vicinity. Groundwater recharge to surface water declined by 20.17% from 2016 to 2019 due to precipitation. Nitrate loads in the hydrologic system of the watershed are primarily derived from human activities (including fertilizer application from agricultural activities and residential wastewater discharges) and the nitrogen cycle. Nitrate loads in surface water declined 16.05% from 2016 to 2019. Nitrate levels are higher in agricultural farming and residential areas on the eastern and northern sides of the watershed. Additionally, hydrological interactions are usually accompanied by material accumulation and environmental changes. Nitrate levels tend to rise with converging water flows, a process that becomes more pronounced during precipitation events and cropping seasons in agriculturally intensive valley watersheds. However, environmental changes alter nitrogen transformation processes. Nitrogen fixation, nitrification, and ammonification intensify nitrogen inputs during river pooling, enhancing nitrogen cycling fluxes and elevating nitrate loads. These processes are further enhanced during groundwater recharge to surface water, leading to evaluated nitrate load. Enhanced denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anaerobic ammonia oxidation, and assimilation promote the nitrogen export from the system and reduce the nitrate load during surface water recharge to groundwater.
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