At low temperature, the treatment of raw water with high ammonia nitrogen and organic matter has always been one of the difficulties in the plant. The removal of ammonia nitrogen and CODMn by ceramide biofiltration was studied in pilot and the effects of assisted filtration and backwashing were analyzed. The results showed that the mean turbidity of the filtered water was stable below 0.3NTU if the particle size of the biofilter column was 2 mm to 4 mm. When ammonia nitrogen in raw water was lower than 2.5 mg/L, the mean value of ammonia nitrogen in filtered water could be stable below 0.3 mg/L and the maximum would be no more than 0.5 mg/L. The average removal rate was about 82%. When ammonia nitrogen in raw water was 2.5 mg/L to 3.0 mg/L, the removal rate of ammonia nitrogen was still higher than 50%, and the effluent would rise to 0.8 mg/L to 1.0 mg/L. The removal rate of CODMn by ceramic filter was 24% to 32%, and the effluent was stable below 3 mg/L. The average UV254 effluent was about 0.05 cm−1, and the removal rate was 20% to 30%. The filtration cycle would be up to 72 h in the low temperature period, and would be appropriately reduced in the high temperature period from 24 h to 36 h.