Micropollutants (MP) from municipal wastewater are frequently detected in surface waters and occur in ecotoxicological relevant concentrations. Therefore a broadly accepted method for the assessment of MP is needed. Here, we propose a procedure for the assessment of MP from municipal wastewater. The suggested method comprises (1) a substance list with relevant MP, (2) toxicologically based quality criteria, (3) an approach for the identification of potentially polluted sites, (4) a sampling strategy that considers the input-dynamics of chemicals and (5) a scheme to rate the water quality concerning MP. In the proposed concept the assessment of continuous entering substances is focused.