A biological process was adopted in a groundwater plant for iron and manganese removal. The process included low-level aeration and single stage biological filtration. The separated native iron and manganese oxidizing bacteria were inoculated to the filter bed alongside raw water containing high concentrations of iron and manganese after multiplication (Fe2 + 10–14 mg l−1, Mn2 +  0.65–1.1 mg l−1). The predominance of iron and manganese oxidizing bacteria were maintained in the filter by appropriately monitoring the operational parameters (filtration rate, backwash intensity, backwash duration and backwash period). Then the filter had a significant and stable ability for iron and manganese removal. The quality of the filtrate met the Chinese National Standard for Drinking Water with concentrations of 0.05–0.1 mg l−1 Total-Fe (T-Fe) and 0.05 mg l−1 Total-Mn (T-Mn) under the condition of the normal filtration rate (5–7 m h−1). The process reduced investment costs by 6 million yuans (¥) and power costs by 250 thousand yuans (¥) per year compared with the traditional process (chemistry-contact oxidation including two-stage aeration and two-stage filtration).