Micropollutants from municipal wastewater generally influence the water quality of rivers with a high amount of municipal wastewater. They might also affect water bodies that have an important function as drinking water resources. For micropollutants from municipal wastewater, we distinguish four different input pathways into surface waters: (1) Input with treated wastewater through wastewater treatment plants; (2) input with untreated wastewater through sewer overflows if the capacity of the sewer system or the wastewater treatment plant is exceeded; (3) input through leaks in the sewer network or wrongly connected sewers; and (4) input of polluted rainwater from roofs and sealed areas through rainwater channels. Because many micropollutants are not considerably degraded in conventional wastewater treatment plants, the major part of them enters the surface waters with the treated wastewater effluents of wastewater treatment plants.Using a prioritization procedure, 47 Swiss-specific micropollutants were identified out of 250 candidate substances. The selected Swiss-specific micropollutants are representative for the contamination caused through micropollutants from municipal wastewater. Beside the Swiss-specific micropollutants, locally appearing chemicals from commerce and industry might be of importance. This has to be considered depending on the particular situation. For the ascertainment of micropollutants in surface waters, we suggest a procedure in two steps: (1.) Identification of potentially contaminated waterbodies; and (2.) detailed assessment of the potentially contaminated waterbodies. In the first step, mainly estimations are used, such as the estimation of the wastewater fraction in the waterbodies. In the second step, for a more detailed assessment, different sampling strategies and a selection of the Swiss-specific micropollutants for chemical analysis is suggested. The proposed sampling strategies focus mainly on the determination of the basic contamnation through continuously through municipal wastewater entering substances. For the evaluation of the water quality, the measured data are compared to ecotoxicologically based quality criteria. Therefore, based on the technical guidance document for environmental quality standards of the EU, quality criteria were derived. For the assessment of the water quality, predicted environmental concentrations (PEC) are compared to annual average environmental quality standards (AA-EQS). Based on the Modular Stepwise Procedure (MSK) of the federal office for environment (FOEN), the water quality is divided into five classes: excellent / good / moderate / unsatisfying / poor. Based on the presented assessment concept, further investigations can be prioritized, and reduction strategies and measures for the reduction of micropollutants from municipal wastewater can be evaluated.