A system and method for removing fouling from a photoelectrocatalytic oxidation assembly is provided. The method includes resetting a first counter, increasing the first counter by a first channel increment value, and determining if the value in the first counter exceeds a value corresponding to the number of channels provided in the assembly. If the first counter does not exceed the number of channels, the polarity in a channel associated with the value in the first counter is reversed, and a first timer is reset. If an amount of time in the first timer does not exceed a first time period, the first timer is increased by a first time increment until the time remaining in the first timer exceeds the first time period and the polarity reversal is terminated, returning to the step of increasing the first counter by a first channel increment value.