To gain biologically and chemically safe conditions in aquatic systems, as required by the EU Water Framework Directive, advanced oxidation processes are the only conceivable possibility to remove pharmaceuticals and their metabolites from waste water. Water treatment plants are not designed for the complete mineralization of these substances, so that oxidation by-products occur, whose chemical and toxicological properties are often unknown. In this study an UV-oxidation system with and without H2O2 was tested to optimize the elimination of pharmaceuticals, and replenished with toxicological investigations of untreated and oxidatively treated samples. The substances carbamazepine, metoprolol, amidotrizoic acid, diclofenac, and sulfamethoxazole were used as lead compounds. They were studied separately and as a substance mixture. The UV-system had a low-pressure lamp with an emission wavelength of 254 nm and a maximum UV output of 15 W. The sample volume was 1 L with a flow rate of 0.03 m³ h−1. Different matrices (waste water, ultrapure water) were used to detect possible matrix effects of real samples. The degradation rates of the substances were analyzed and quantified using LC-MS/MS with an API 3000 and a Q TRAP 3200. The comparison revealed that the additional use of H2O2 enhances the degradation significantly, especially in waste water samples. Cyto- and genotoxicity were tested with the MTT Assay and Alkaline Comet Assay, respectively, using Chinese Hamster Ovary cells. Generally, samples treated only with UV showed no toxic effects. Toxic results occurred only for samples with the substance mixture that were treated with UV+H2O2, indicating that combination effects might lead to the formation of toxic by-products.