Toxic microcystins (MCs) produced by freshwater cyanobacteria such as Microcystis aeruginosa are of concern because of their negative health and economic impacts globally. An advanced oxidation process using UV/TiO₂ offers a promising treatment option for hazardous organic pollutants such as microcystins. The following work details the successful degradation of MC-LA, MC-LR, and MC-RR using a porous titanium–titanium dioxide (PTT) membrane under UV-LED light. Microcystin quantitation was achieved by sample concentration and subsequent LC–MS/MS analysis. The PTT membrane offers a treatment option that eliminates the need for the additional filtration or separation steps required for traditional catalysts. Controlled periodic illumination was successfully used to decrease the total light exposure time and improve the photonic efficiency for a more cost-effective treatment system. Individual degradation rates were influenced by electrostatic forces between the catalyst and differently charged microcystins, which can potentially be adjusted by modifying the solution pH and the catalyst’s isoelectric point.