The importance of nitrogen within the Earth's biochemical cycle cannot be overstated. It is a vital component in numerous ecological processes, particularly crucial within river ecosystems. The hyporheic zone is the key channel for the interaction between river water and groundwater, and the migration of pollutants. There is frequent water exchange between river water and groundwater, driving the migration and transformation of substances as well as biochemical cycling in the hyporheic zone. The correct understand of the mechanism of the influence of different water exchanges on nitrogen migration and transformation processes is crucial to maintaining the health of river ecosystems and global water security. This study collected hyporheic sediments from the Weihe River Basin and conducted simulation experiments to investigate nitrogen migration and transformation processes within the hyporheic zone under various water exchange modes. The findings indicated that different water exchanges in the hyporheic zone of rivers led to differences in water flow morphology and dissolved oxygen (DO) concentration, which in turn affected factors such as Oxidation-reduction potential (Eh) and microbial community structure, thereby affecting the migration and transformation process of nitrogen in the hyporheic zone of rivers. During the process of surface water recharging groundwater, there was a noticeable increase in NO3--N and NO2--N content along the water migration path, while NH4+-N content decreased. Similarly, this trend persisted when groundwater replenished surface water, suggesting NO3--N migration during water exchange in the river's undercurrent zone. Denitrification and dissimilatory reduction to ammonium (DNRA) emerged as the primary pathways for NO3--N conversion during this exchange in the underflow zone of rivers. Proteobacteria dominated during the process of groundwater recharge to surface water, favoring denitrification over surface water recharge. Conversely, Firmicutes prevailed during the process of groundwater replenishing from surface water, enhancing DNRA. In both scenarios of surface water replenishing groundwater and groundwater replenishing surface water, the total interception rates of NO3--N in river underflow zone sediments were high, reaching 97.7% and 98.2%, respectively. Specifically, in the surface water replenishing groundwater mode, the NO3--N interception rates within the 0-15 cm, 15-30 cm, 30-45 cm, and 45-60 cm sedimentary layers were 34.8%, 24.5%, 23.5%, and 14.9%, respectively. Conversely, in the groundwater recharge surface water mode, the interception rates within the same sedimentary layers were 21.6%, 24.3%, 25.0%, and 27.3%, respectively. Despite exhibiting opposite trends, both models demonstrated highest NO3--Ninterception rates at the sediment-water interface. Consequently, water exchange within the river's hyporheic zone significantly influenced, the nitrogen migration and transformation process. This study held considerable importance for managing river nitrogen pollution and sustaining the health of the river ecosystem.