<p>Microorganisms in sediments contribute to nutrient release and play crucial roles in nitrogen migration and transformation. However, the functional genes and bacterial communities in the sediments of the Danjiangkou Reservoir and the different forms of nitrogen affecting them remain poorly understood. In this study, high-throughput sequencing technology and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) analysis were employed to explore the profiles of functional genes and bacterial communities in surface sediments. The results revealed that the bacterial communities in the sediments of the reservoir were mainly composed of Proteobacteria, Acidobacteriota, Bacteroidota, Chloroflexi, Verrucomicrobiota, and Nitrospirota, which played roles in nitrogen migration and transformation within aquatic ecosystems. Mantel test analysis demonstrated significant correlations between bacterial communities at the phylum level and different forms of nitrogen (TN, NH₄⁺-N, NO₃⁻-N, DON, and urea), highlighting strong interactions between nitrogen and bacterial communities. PICRUSt analysis indicated that the surface sediment bacteria in the Danjiangkou Reservoir participate in various nitrogen transformation processes, including nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction (DNRA), assimilatory nitrate reduction (ANRA), the anammox process, and organic nitrogen metabolism. These processes involve 37 functional genes related to nitrogen transformation, such as nifD, nifK, nirS, norB, nirB, and nirA. By integrating bacterial community distribution, functional gene composition, and nitrogen speciation in surface sediments, this study provides insights into the nitrogen transformation functions of sediment bacteria. It also offers a theoretical foundation for understanding nitrogen transformation in canyon-type reservoir sediments and supporting water quality management.</p>