This paper demonstrates the additional benefit of the microbicidal efficacy of an ozonation plant implemented for micropollutant removal from tertiary effluent. Due to the low amount of viruses and protozoa in the tertiary effluent, bacteriophage MS2 and spores of Bacillus subtilis were dosed as surrogates. At specific ozone consumptions of 0.6 and 0.9 g O3/g dissolved organic carbon (DOC) a 2-log colony forming unit (CFU) reduction was achieved for indigenous Escherichia coli and enterococci, and the limits of the European bathing water directive for the excellent quality of inland waters were met. Higher removal was impeded by the shielding effect of suspended solids in the effluent, which implies the combination of ozonation with a preceding filtration step if higher microbicidal performances are required. The surrogate virus MS2 was reduced by 4–5 log while no significant inactivation was detected for B. subtilis spores. Additionally, the impact of ozonation on the biochemical oxygen demand (BOD) was studied. The BOD5 measurement was not adversely affected despite the reduced concentration of microorganisms after ozonation. The intrinsic increase in BOD5 averaged 15% at 0.6–0.7 g O3/g DOC. The impact of the projected increase on the surface water quality is generally not considered a problem but has to be assessed on a case-by-case approach.