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This research investigated the effects of surface functional groups on both rates of organic compound oxidation (phenol, p-nitrophenol, benzoquinone, and oxalic acid) and perchlorate (ClO 4 − ) formation at boron-doped diamond (BDD) film anodes at 20 °C. X-ray photoelectron spectroscopy measurements determined that various oxygenated functional groups (e.g., C-OH, C=O, COOH) were incorporated on the BDD surface by applying an anodic ageing process, and fluorine functional groups (e.g., C-F, -C n F 2n+1 ) were incorporated by electrochemical oxidation of aqueous perfluorooctanoic acid solutions. Batch oxidation experiments revealed that ClO 4 − formation via the oxidation of ClO 3 − was highly variable during anodic ageing, which was attributed to changes in oxygenated functional groups, while organic compound oxidation rates were not significantly affected. The fluorinated electrode showed a lower ClO 4 − formation rate (19 ± 4 μmoles m −2 min −1 ) compared to the oxygenated electrode (436 ± 26 μmoles m −2 min −1 ) indicating the fluorinated surface limits ClO 4 − production. Measurement of the electrode response to the Fe(CN) 6 3−/4− redox couple using cyclic voltammetry and electrochemical impedance spectroscopy indicated that lower ClO 4 − formation on the fluorinated electrode was likely a result of dipole-dipole interactions between the negatively charged F atoms and ClO 3 − and steric hindrance caused by the perfluorocarbon chains. This effect along with the hydrophobicity of the fluorinated electrode resulted in significantly lower ClO 4 − formation (96% decrease) while slightly enhancing measured oxidation rates of hydrophobic organic compounds. The use of benzoquinone as OH probe confirmed that the fluorination process did not inhibit OH production. The rate of benzoquinone oxidation was 2212 ± 183 μmoles m −2 min −1 on the oxygenated electrode and 2926 ± 201 μmoles m −2 min −1 on the fluorinated electrode. Density functional theory calculations indicated that the fluorination of the BDD surface by both F atoms and perfluorinated carbon radicals ( C n F 2n+1 ) of varying chain lengths (n = 1 to 7) was feasible, and that the fluorinated edge sites (=C-C n F 2n+1 ) were more electrochemically stable than fluorinated planar sites (≡C-C n F 2n+1 ). [ABSTRACT FROM AUTHOR]