To supply necessary bacteria and available nutrients, a method of returning backwashing wastewater to the bio-filter for removal of iron and manganese was used. The ecological stability of bio-filter was investigated from 3 aspects: iron and manganese removal efficiency, micro-ecological characteristics and the quantity distribution of dominant bacteria. The results indicated that, the bio-filter held strong antishock loading capability, when the system was operated at high filtration rate (10-13.9 m/h) and high manganese concentration (3.5-4.5 mg/L), a removal rate more than 98.9% of iron and manganese was achieved. Iron and manganese oxidizing bacteria are the dominant microflora in biological filtering layer, they not only adhere on filter sand materials (4.3 x 10(6) MPN/mL) to form compact biofilm, but also exist among filter materials void (6.5 x 10(6) MPN/mL) to form suspended flocs, which is very important to complete removal of iron and manganese. In the past 5 years, the bio-filter realized a continuous and stable operation and kept a high removal efficiency of iron and manganese without adding any nutrients.