The pilot-and lab-scale reactor was constructed, respectively, to evaluate the influence of ammonia and nitrite on the performance of Fe and Mn removal. The results of pilot-scale filter indicated that the nitrite concentration of 0.1,0.2,0.3,0.7 mg／L, had no effects on Fe and Mn removal, as well the ammonia concentration of 1.2 and 2.2 mg／L. However, the ammonia concentration about 4.5 mg／L would inhibit the Mn removal, resulting in higher Mn in effluent than requirements; The lab-scale SBR experiments demonstrated that the activity of Mn oxidizing bacteria(MnOB) was enhanced by nitrite, but inhibited by ammonia, which showed the importance of nitrification in biological removal of Fe, Mn and ammonia process, especially in the period of start-up.