The next challenge of wastewater treatment is to reliably remove micro-pollutants at the microgram per litre range in order to meet reuse applications and contribute to reach the good status of the water bodies. A hundred of priority and relevant emerging substances were measured to evaluate at full-scale the removal efficiencies of 7 advanced treatment lines (1 membrane bioreactor process and 6 tertiary treatment lines) that were designed for reuse applications. To reliably compare the processes, specific procedures for micro-pollutants were applied for sampling, analysis and calculation of removal efficiencies. The membrane bioreactor process allowed to upgrade the removal efficiencies of about 20% of the substances measured, especially those that were partially degraded during conventional processes. Conventional tertiary processes like high rate clarification, sand filtration and polishing pond achieved significant removal for some micro-pollutants, especially for adsorbable substances. Advanced tertiary processes, like ozonation, activated carbon and reverse osmosis were all very efficient to complete the removal of polar pesticides and pharmaceuticals; metals and less polar substances were better retained by reverse osmosis.