Organic micropollutants, in particular those of anthropogenic origin, may have a toxic influence on water organisms. Photochemical oxidation processes are one of the most effective methods of decomposition of a wide range of those compounds. During the oxidation process a large number of different by-products are generated, which can still be biologically active. The development of analytical techniques, including the reduction of the detection limit to several fg/L, allows the identification of even trace concentrations of compounds. The paper presents the determination of pentachlorophenol and benzo(a)pyrene degradation pathways during the process of heterogeneous photocatalysis carried out in the presence of titanium dioxide. The gas chromatography–mass spectrometry (GC-MS) analysis of post-processing samples indicated the formation of different by-products of the parent micropollutants. Moreover, the toxicity assessment demonstrates for both tested micropollutants an increase in the toxicity within the whole time of the UV irradiation process run.