Surface waters can contain a range of micropollutants from point sources, such as wastewater effluent, and diffuse sources, such as agriculture. Characterizing the source of micropollutants is important for reducing their burden and thus mitigating adverse effects on aquatic ecosystems. In this study, chemical analysis and bioanalysis were applied to assess the micropollutant burden during low flow conditions upstream and downstream of three wastewater treatment plants (WWTPs) discharging into small streams in the Swiss Plateau. The upstream sites had no input of wastewater effluent, allowing a direct comparison of the observed effects with and without the contribution of wastewater. Four hundred and five chemicals were analyzed, while the applied bioassays included activation of the aryl hydrocarbon receptor, activation of the androgen receptor, activation of the estrogen receptor, photosystem II inhibition, acetylcholinesterase inhibition and adaptive stress responses for oxidative stress, genotoxicity and inflammation, as well as assays indicative of estrogenic activity and developmental toxicity in zebrafish embryos. Chemical analysis and bioanalysis showed higher chemical concentrations and effects for the effluent samples, with the lowest chemical concentrations and effects in most assays for the upstream sites. Mixture toxicity modeling was applied to assess the contribution of detected chemicals to the observed effect. For most bioassays, very little of the observed effects could be explained by the detected chemicals, with the exception of photosystem II inhibition, where herbicides explained the majority of the effect. This emphasizes the importance of combining bioanalysis with chemical analysis to provide a more complete picture of the micropollutant burden. While the wastewater effluents had a significant contribution to micropollutant burden downstream, both chemical analysis and bioanalysis showed a relevant contribution of diffuse sources from upstream during low flow conditions, suggesting that upgrading WWTPs will not completely reduce the micropollutant burden, but further source control measures will be required.