Biological aerated filter (BAF) was employed to remove iron, manganese and ammonia from groundwater. The filter was in continuous operation under hydraulic loading of 3m3/m2.h. The influence of air-water ratio, the removal effects of iron, manganese and ammonia respective, and the oxidation of the three pollutants, the change of dissolved oxygen along the filter depth were investigated in this research. And the results was obtained, that the optimal air-water ratio was determined by 3, which made the dissolved oxygen concentration in the filter central be 4.75mg/l, and the removal of iron, manganese and ammonia be above 90%, 99% and 87%, respectively. The efficient removal of manganese occurred in the central and lower parts of the filter. More iron was oxidated at the upper 0.75m of the filter, and the oxidation velocity of manganese and ammonia would be limited, when the inlet iron concentration was higher. Nitrification process consumed more dissolved oxygen, which made dissolved oxygen concentration decrease along the filter depth from 0 to 1.25m. The demand of filtration depth is 1.6m, for simultaneous removal.