The next challenge of wastewater treatment is to reliably remove micro-pollutants at the microgram per litre range in order to meet the environmental quality standards set by new regulations like the Water Framework Directive. The present work assessed the efficiency of different types of primary, secondary and tertiary processes for the removal of more than 100 priority substances and other relevant emerging pollutants through on-site mass balances over 19 municipal wastewater treatment lines. Secondary biological processes proved to be in average 30% more efficient than primary settling processes. The activated sludge (AS) process led to a significant reduction of pollution loads (more than 50% removal for 70% of the substances detected). Biofilm processes led to equivalent removal efficiencies compared to AS, except for some pharmaceuticals. The membrane bioreactor (MBR) process allowed to upgrade removal efficiencies of some substances only partially degraded during conventional AS processes. Preliminary tertiary processes like tertiary settling and sand filtration could achieve significant removal for adsorbable substances. Advanced tertiary processes, like ozonation, activated carbon and reverse osmosis were all very efficient (close to 100%) to complete the removal of polar pesticides and pharmaceuticals; less polar substances being better retained by reverse osmosis.