This study examined the impact of ozone (O3) and hydrogen peroxide+ozone (H2O2+O3) on organic matter and subsequent DOC and DBP precursor uptake across biofilters. Organic matter fractionation, using liquid chromatography – organic carbon detection (LC-OCD), confirmed that both O3 and H2O2+O3 oxidized high molecular weight fractions (biopolymers and humics) creating smaller, more easily biodegraded compounds (low molecular weight acids). O3 decreased trihalomethane (THM) and haloacetic acid (HAA) formation potential (FP) by 23% and 15% respectively; H2O2+O3 resulted in an increase of 52% and 41%.Biological activated carbon (BAC) removed 6% of DOC; removals increased to 15% and 23% when preceded by O3 or H2O2+O3, respectively. BAC without pre-oxidation reduced THM FP by 12%, compared to 38% and 14% removal with O3 and H2O2+O3, respectively. HAA FP decreased by 36% for O3+BAC and 20% for H2O2+O3+BAC; better performance by O3 was likely due to increased HAA precursor formation by the AOP. BAC was found to perform better than anthracite-based biofilters for all parameters. This study highlights the impact of pre-oxidation on organic composition, the benefits of biofiltration when used in combination with pre-oxidants such as ozone, and the importance of pilot-testing to assess alternative treatment processes.