This study evaluated the efficacy and environmental impact of two advanced oxidation processes, UV-C/sodium persulfate (SPS) and photo-Fenton, for the degradation of sulfaquinoxaline, a veterinary antibiotic. With the UV/SPS process, a significant reduction in antibiotic concentration was observed after 5 h of irradiation, reaching an elimination rate of 90%. In contrast, the photo-Fenton (UV/SPS/Fe(II)) process achieved complete degradation and mineralization (100%) in just 1 h of irradiation. Both processes followed pseudo-first-order degradation kinetics. In addition to treatment performance, the toxic effect of degradation by-products was also analyzed through their impact on phytotoxicity and ecotoxicity. These tests were carried out, respectively, on Sinapis alba (a plant species) and Daphnia magna (a planktonic crustacean). The results showed that the by-products generated by the photo-Fenton process were more toxic, affecting shoot and root growth to a greater extent. A similar trend was observed for ecotoxicity, with a particularly high immobilization rate of D. magna after photo-Fenton treatment. This increase in toxicity is attributed to the appearance of more harmful by-products with the Fenton process, despite its proven performance.