The presence of anthropogenic chemicals in the natural environment may impact both habitats and human use of natural resources. In particular the contamination of aquatic resources by organic compounds used as pharmaceuticals or household chemicals has become evident. The newly identified environmental pollutants, also known as micropollutants, often have i) unknown ecotoxicological impacts, ii) unknown partitioning mechanisms, e.g. sorption to sediments, and iii) limited regulation to control their emission. Furthermore, like any compound, micropollutants can be transformed while in the environmental matrix to unknown transformation products (TPs), which add to the number of unknown chemicals to consider and thus increase the complexity of risk management. Transformation is at the same time a natural mechanism for the removal of anthropogenic compounds, either by complete degradation (mineralisation) or to innocuous TPs. However, how transformation occurs in real-world conditions is still largely unknown. During the transport of micropollutants from household wastewater to surface water, a large amount of transformation can occur during wastewater treatment—specifically during biological nitrifying–denitrifying treatment processes. The thesis considers the systematic optimisation of laboratory investigative techniques, application of sensitive mass-spectrometry-based analysis techniques and the monitoring of full-scale wastewater treatment plants (WWTPs) to elucidate transformation processes of five known micropollutants. The first of the five compounds investigated was the antibiotic trimethoprim. Incubation experiments were conducted at different analyte spike concentrations and different sludge to wastewater ratios. Using high-resolution mass spectrometry, a total of six TPs were identified from trimethoprim. The types of TPs formed was clearly influenced by the spike concentration. To the best of our knowledge, such impacts have not been previously described in the literature. Beginning from the lower spike concentration, a relatively stable final TP was formed (2,4-diaminopyrimidine-5-carboxylic acid, DAPC), which could account for almost all of the transformed trimethoprim quantity. The results were compared to the process in a reference reactor. Both by the detection of TPs (e.g., DAPC) and by modelling the removal kinetics, it could be concluded that only experimental results at the low spike concentrations mirrored the real reactor. The limits of using elevated spike concentrations in incubation experiments could thus be shown. Three phenolic micropollutants, the antiseptic ortho-phenylphenol (OPP), the plastics additive bisphenol A (BPA) and the psychoactive drug dextrorphan were investigated with regard to the formation of potentially toxic, nitrophenolic TPs. Nitrite is an intermediate in the nitrification– denitrification process occurring in activated sludge and was found to cause nitration of these phenols. To elucidate the processes, incubation experiments were conducted in purified water in the presence of nitrite with OPP as the test substance. The reactive species HNO2, N2O3 and the radicals ·NO and ·NO2 were likely involved as indicated by scavenger experiments. In conditions found at WWTPs the wastewater is usually at neutral pH, and nitrite, being an intermediate, usually has a low concentration. By conducting incubation experiments inoculated with sludge from a conventional WWTP, it was found that the three phenolic micropollutants, OPP, BPA and dextrorphan were quickly transformed to biological TPs. Nitrophenolic TPs were only formed after artificial increase of the nitrite concentration or lowering of the pH. However, nitrophenolic-TPs can be formed as sample preparation artefacts through acidification or freezing for preservation, creating optimal conditions for the reaction to take place. The final micropollutant to be studied was the pain-reliever diclofenac, a micropollutant on the EU-watch list due to ecotoxicological effects on rainbow trout. The transformation was compared in two different treatment systems, one employing a reactor with suspended carriers as a biofilm growth surface, while the other system employed conventional activated sludge. In the biofilm-based system, the pathway was found to produce many TPs each at relatively low concentration, many of which were intermediate TPs that were further degraded to unknown tertiary TPs. In the conventional activated sludge system some of the same reactions took place but all at much slower rates. The main difference between the two systems was due to different reaction rates rather than different transformation pathways. The municipal WWTPs were monitored to verify these results. In the biofilm system, a 10-day monitoring campaign confirmed an 88% removal of diclofenac and the formation of the same TPs as those observed in the laboratory experiments. The proposed environmental quality standard of 0.05 μg/L might thus be met without the need for additional treatment processes such as activated carbon filtration or ozonation.