The removal of iron, manganese and ammonia from groundwater originating from four different locations in northern Croatia was studied. Four pilot plants, mainly differing in their aeration systems and operation pressures, have been used. Quartz sand, coated with a naturally formed layer of MnO2 and a biofilm containing micro-organisms, were used as filter media. The bacteria of the genus Siderocapsa, as well as the bacteria of the genus Nitrosomonas and Nitrobacter were identified as taking part in the removal of iron and manganese, and of ammonia, respectively. It was demonstrated that a well-established bio-filter mass from one water treatment plant is applicable in other plants. Removal of iron, manganese and ammonia from groundwater was achieved by single-step filtration, for which an adaptation period of 3-4 weeks was required. The filtration rates were as high as 22-24 m/h. Under optimal operating conditions, ammonium is oxidized biologically to nitrates and no nitrites appear in the effluent. The treatability factors k and n, which characterize the processes in packed bed bioreactors, were determined in this pilot plant study as well. They indicated that the simultaneous removal of iron, manganese and ammonium involves processes having different mechanisms and kinetics. (C) 2004 Elsevier Ltd. All rights reserved.