Our previous report based on a batch reactor system for the Advanced Fenton Process (AFP) showed that pH, hydrogen peroxide and the organic substances treated are among the most important factors affecting the oxidation efficiency. As an extended study towards its commercialisation, this paper reports the effects of the main process parameters including those relating to a new AFP flow-through system. In order to systemise and correlate the results, the Taguchi experimental design method was used. Total organic carbon (TOC) removal was utilised as the measure of the oxidation efficiency and it was found that the removal of phenol from aqueous solution at pH 2.0 and 2.5 was very similar but hydrogen peroxide supply significantly affected the TOC removal with the change of flow rate from 14.4 mL/hr to 60 mL/hr. Also, the initial concentration of phenol was a highly significant factor, with higher concentrations resulting in a lower TOC removal rate. The temperature effects in the range of 14 °C to 42 °C were investigated and it was found that there was accelerated oxidation of phenol in the early stages but after 90 minutes there was no significant difference between the results. Sonication with a bath type sonicator resulted in relatively small enhancements of TOC removal but further studies with cup-horn and probe type sonicators showed that TOC removal increased with higher intensity of sonication on additional input of hydrogen peroxide.