The ultraviolet (UV)/free chlorine process is a very promising treatment technology to remove persistent organic contaminants (POCs, e.g., pharmaceutical and personal care products) from water. The radical chain reactions involved in the UV/free chlorine process are very complicated, and the reaction pathways for organic contaminants degradation are largely unknown. Therefore, we developed a computerized pathway generator that uses graph theory and experimentally determined reaction rules that were reported for the UV/free chlorine process. Our pathway generator predicts all possible intermediates, byproducts, and elementary reactions that are involved in the oxidation of organic contaminants. For example, the degradation of tricholoroethylene (TCE) produces 497 species (i.e., intermediates and byproducts) and 6608 elementary reactions. The predicted species from our pathway generator not only predict the major and stable byproducts that were observed in our experiments (e.g., CHCl2COOH, CHCl(OCl)COOH, etc.) but also include many other minor and toxic byproducts that were produced but not measured because they have a short lifetime. Overall, our pathway generator significantly improves our understanding of the reaction pathways that are involved in organic contaminant degradation in the UV/free chlorine process.