Two parallel pilot-scale biological filters which used manganese sand and silica sand as media respectively were tested for the removal of iron and manganese from drilled well water in Harbin. Iron and manganese oxidizing bacteria were isolated and used as inoculums for filter start-up. Manganese sand filter and silica sand filter can remove 3-6 mg/L of ferrous iron 0.9 mg/L and 0.6 mg/L of manganese respectively under the operation conditions of DO (5 mg/L), pH 7.2, and flow rate 3.9 m/h. The kinetics analysis indicated that the iron removal versus flow rate followed the first-order reaction. This kinetics model also demonstrated that a manganese sand filter had higher removal efficiency than a silica sand filter. Gallionella sp. was found in the backwashing water after 6 months of operation.