A six‐month pilot study was conducted to evaluate the use of fixed‐bed (FXB) bioreactors to treat perchlorate‐contaminated groundwater and to address some of the concerns associated with the full‐scale implementation of such a process. The pilot data illustrated that perchlorate‐reducing FXB bioreactors can be acclimated using organisms indigenous to the local aquifer; can achieve sustained perchlorate removal to below the analytical detection limit using reasonable contact times; can produce biologically stable effluent; do not foster the growth of pathogenic bacteria; and are robust with respect to system upsets. Based on this project, the California Department of Health Services conditionally approved FXB bioreactors for treating perchlorate‐contaminated drinking water, making it possible to consider the full‐scale design and implementation of FXB biological perchlorate treatment in California.