The next challenge of wastewater treatment is to reliably remove micropollutants at the microgram per litre range in order to reduce the discharge for priority substances and to meet the environmental quality standards set by the European Water Framework Directive. The present work assessed the occurrence of 60 organic substances (priority substances and other relevant pollutants) in municipal wastewater and sludge. Their fate in the treatment processes and their removal efficiencies were quantified. Thorough on-site mass balances were carried out at 8 municipal wastewater treatment plants chosen among conventional and advanced secondary processes. It was found that 70% of the substances were quantified in raw wastewater and 50% in effluent, with a transfer without a limited degradation for most of them. Low loaded activated sludge (AS) process reduced the emission of more than half of micropollutants. At low sludge retention time (AS under high load), lower removal efficiencies were measured compared to low loaded AS. No influence of temperature of the biological reactor was shown. The membrane bioreactor process increased the removal efficiencies for one third of the substances that were partially removed with AS. Still, five substances were measured at concentrations exceeding the environmental quality standards at the outlet of the studied plants. In addition to efforts for source-reduction, complementary treatments need to be set-up.