A system for removing iron and manganese in groundwater, based on biofiltration technology, was developed at the Center of Sanitary Engineering of the National University of Rosario, Argentina. This process has been successfully applied in several new water treatment plants in Argentina. This paper describes the transformation of an existing plant for iron and manganese removal in groundwater from physicochemical to biofiltration processes. In the existing plant, iron and manganese removal was performed by a lime decarbonation process with the addition of four chemical products. A study was conducted to determine the feasibility of its transformation using biofiltration. The project included physicochemical and microbiological characterization of the water to be treated, a survey of existing facilities, pilot plant tests, and the design and construction of modifications. The operation of the transformed plant started in October 2011, and after the initial period of start-up, the concentrations of iron and manganese in treated water were below the values stated in the regulations. With the new scheme the use of chemicals was avoided, the operation was simplified and as a consequence the operating costs were reduced significantly.