To efficiently remove nitrogen from the biofiltration system, the effect of different electron donors and C/N (dissolved organic carbon [DOC]/nitrate) on dissimilatory nitrate reduction to ammonium (DNRA), and denitrification was studied. Electron donor addition significantly increased the gene abundance (nirS and nrfA) and denitrification rate, resulting in higher NO3--N removal efficiency (over 70%) in refractory organic carbon (bagasse and rice straw) groups. Easily degradable organic carbon (sucrose) caused rapid DOC accumulation, fueling the DNRA process, and NH4+-N accumulation. Inorganic electron donors (ferrous sulfate and sodium sulfide) were unsuitable due to poor denitrification gene abundance, low rate, as well as low NO3--N removal efficiency. The decrease in C/N was beneficial to denitrification but restricted the occurrence of DNRA, finally reducing N retention capacity. Therefore, the regulation of C/N can play a significant contributory role in the switching of denitrification and DNRA process.