Ozone has been shown to be effective in the transformation of several chemicals of emerging concern that escape the wastewater treatment process, but there is concern whether toxic transformation products are formed. Two parallel biofilter columns with granular activated carbon (GAC) and filter sand following a pilot-scale ozone unit to treat secondary treated municipal wastewater were studied. Results show reduced wastewater genotoxicity following ozonation and further reduction following biofiltration. The BAC biofilter outperformed the sand biofilter in terms of reduction in both organics and genotoxicity. Biofilter performance correlated with biological indicators (dissolved oxygen reduction and effluent E. coli counts) but not with ATP bioactivity measurements. Limited bacterial (E. coli) regrowth was observed in treated effluent from both biofilters.