Although sediment dredging is a widely employed water management and restoration technique for the removal of internal nitrogen (N), the long-term effects of dredging on N transformation in dredged rivers remain largely undetermined. In this study, we investigated the effects of dredging on N transformation processes spanning three years at ten sites in the purple-soil watershed within the middle reaches of the Fu River Basin. We combined isotopic and molecular techniques to provide novel insights into the interactions associated with microbial utilization capacities between sediment and river water before, during, and after dredging. Initially, dredging was found to significantly reduce the total nitrogen content by approximately 75 %, although over time, there was a slight increase in concentrations. Secondly, significant reductions in microbial richness and diversity were detected in both river water and sediment, with 39 classes reduced, 12 new classes emerging, and an increase in archaea, reshaping the microbial community. Lastly, dredging was found to promote a significant shift in functional contributions, with increases in the abundance of key enzyme activities (1.7.5.1 and 1.7.2.5) and denitrification genes (nirK, norB, and nosZ). This enhancement notably promoted denitrification and dissimilatory nitrate reduction to ammonium (DNRA), accompanied by significant environmental changes in sediment and river water. These changes facilitated the removal of nitrates in the Xiangshuitan watershed. Our study overcomes the limitations associated with watershed and microenvironment scales, providing insights into the mechanisms where by dredging activities influence the interplay between external and internal N transformations.