Carbon scarcity limits denitrification in micropolluted water, especially in drinking water reservoirs. Therefore, a Fe-activated carbon (AC) carrier was used in this study to enhance the nitrogen removal capacity of aboriginal denitrification in drinking water reservoirs under aerobic conditions. Following carrier addition, total nitrogen (TN) and permanganate index (CODMn) removal efficiencies reached 81.89% and 72.66%, respectively, and were enhanced by 40.45% and 39.65%. Nitrogen balance analysis indicated that 77.86% of the initial TN was converted into gaseous nitrogen. Biolog analysis suggested that the metabolic activity of denitrifying bacteria was substantially enhanced. 16S rRNA gene sequencing indicated that organic degradation bacteria, hydrogen-consuming, Fe-oxidizing, and Fe-reducing denitrifying bacteria (e.g., Arenimonas, Hydrogenophaga, Zoogloea, Methylibium, and Piscinibacter) evolved into the dominant species. Additionally, napA, nirS, nirK, and nosZ genes were enriched by 3.17, 6.68, 0.40, and 6.70 folds, respectively, which is conducive to complete denitrification. These results provide a novel pathway for the use of Fe-AC to promote aerobic denitrification in micropolluted drinking water reservoirs.