In this study, the rates of denitrification and anammox, as well as their contributions to nitrogen removal, were quantified using the ¹⁵N isotope labeling technique in the riparian zones and sediments of different sampling sections within the 3rd Drainage Ditch in Ningxia's saline-alkali region. By integrating metagenomic sequencing and quantitative PCR (qPCR) analysis of functional genes, the influences of physicochemical properties, functional gene abundances, and microbial community structures on nitrogen removal processes in these two matrixes were systematically investigated. The results revealed that denitrification rates (1.22~3.75μmol N₂/(kg·h) were significantly higher than anammox rates (0.16~0.48μmol N₂/(kg·h) in both riparian zones and sediments (P<0.05), contributing 83.91%~92.95% and 7.05%~16.09% to total nitrogen removal, respectively. This indicates that denitrification is the dominant nitrogen removal pathway in the studied drainage ditch system. Sediments exhibited significantly higher denitrification rates than riparian zones (P<0.05), while no significant difference in anammox rates was observed between the two zones (P>0.05). Regarding functional genes, the abundance of the denitrification gene nirK was significantly higher in riparian zones than in sediments (P<0.05), whereas the opposite trend was found for nirS. Notably, the combined abundances of denitrification genes (nirK + nirS) were significantly greater than those of anammox-related genes in both matrixes (P<0.05). Microbial community analysis showed that Nitrososphaera was the most dominant genus among nirK-type denitrifiers in riparian zones, while Dechloromonas dominated the nirS-type denitrifier community in sediments. Environmental factors regulated microbial activity by influencing the abundance and expression of functional genes, thereby driving nitrogen removal processes. Higher total organic carbon (TOC) content, more anaerobic micro-environments, and greater functional gene abundances in sediments were identified as core driving factors contributing to their significantly enhanced denitrification capacity compared to riparian zones.