Dissolved oxygen is critical for proper operation of waterworks that utilize anaerobic groundwater and rely on biofilters to remove iron, manganese and ammonium. In these biofilters, planned or inadvertent oxygen deprivation may occur for a variety of reasons. The water quality effects of oxygen deprivation on the function of drinking water biofilters, however, have not previously been reported. In this study, a 5-day oxygen deprivation period in full-scale biofilters was found to affect iron, manganese and ammonium concentrations differently. During the oxygen deprivation period, iron continued to be removed, although a greater depth of filter media was required to carry out the removal. Manganese oxide in filter media was mobilized, causing manganese water concentrations to increase well above raw water levels. The ammonium in the raw water passed through the biofilters unchanged, indicating the dependence of nitrification microorganisms on oxygen as their sole electron acceptor. Stringent national drinking water criteria were exceeded during the deprivation period but were once again met within hours after oxygenation was recommenced. Manganese and nitrite recovery to pre-deprivation concentrations, however, required days. The results illustrate the interdependence of treatment parameters and provide valuable practical information to waterworks that experience or plan oxygen stoppage.