This study developed a bioaggregate reactor by using Pseudomonas strain GF2. The response surface method indicated that the optimal parameters were pH 7, a hydraulic retention time (HRT) of 6 h, and an initial nitrate concentration of 25 mg L−1. Nitrate removal reached a maximum of 99.19 % at a C/N ratio of 2. Gas chromatographic detection revealed that nitrogen gas was the main product (98.46 %). 3D fluorescence spectroscopy showed that, with increasing HRT, the amounts of fulvic acid‐like, tryptophan, and protein‐like substances increased, which were consistent with the change in microbial community. Fourier transform infrared spectroscopy confirmed the existence of OH, CH, C=O, and C=C. High‐throughput sequencing showed that Pseudomonas and Azospira were the dominant genera.