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The influence of backwashing on biological perchlorate reduction was evaluated in two laboratory scale fixed bed biofilm reactors using 1- or 3-mm glass beads as support media. Influent perchlorate concentrations were 50 μg/L and acetate was added as the electron donor at a concentration of 2 mg C/L. Perchlorate removal was evaluated at various influent dissolved oxygen (DO) concentrations. Complete perchlorate removal was achieved with an influent DO concentration of 1 mg/L resulting in bulk phase DO concentrations below the detection limit of 0.01 mg/L. The influence of increasing influent DO concentrations for 12 h periods was evaluated before and after individual backwash events. Partial perchlorate removal was achieved with an influent DO concentration of 3.5 mg/L before a strong backwash (bulk phase DO concentrations of approximately 0.2 mg/L), while no perchlorate removal was observed after the strong backwash at the same influent DO level (bulk phase DO concentrations of approximately 0.8 mg/L). The immediate effect of backwashing depended on influent DO concentrations. With influent DO concentrations of 1 mg/L, strong backwashing resulted in a brief (<12 h) increase of effluent perchlorate concentrations up to 20 μg/L; more pronounced effects were observed with influent DO concentrations of 3 mg/L. Daily weak backwashing had a small and, over time, decreasing negative influence on perchlorate reduction, while daily strong backwashing ultimately resulted in the breakdown of perchlorate removal with influent DO concentrations of 3 mg/L.