The treatment plant was designed according to the theory of biological fixation and removal of manganese from water. The process included low level aeration followed by single stage filtration. The separated native iron and manganese oxidizing bacteria after multiplication were inoculated to the filtering medium alongside raw water. After 2–3 months of culturing, the filter exhibited strong manganese removal capability. Under the usual filtration rate conditions, the manganese concentration in the raw water was 0.575–3.05 mg l−1 and total iron (T-Fe) 0.01–0.5 mg l−1; the manganese concentration in the filtrate was 0.05 mg l−1 and T-Fe in trace, which was superior to the Chinese National Standard for drinking water (Fe<0.3 mg l−1, Mn<0.1 mg l−1). The product water was stable and of high quality that completely meets the above-mentioned standard. The process can reduce investment costs by 50 million yuans (Y=) and operation and maintenance cost by Y=12,000 per day compared with traditional processes.