The overarching aim of this field study was to examine causal links between in-situ exposure to complex mixtures of micropollutants from wastewater treatment plants and effects on freshwater microbial communities in the receiving streams. To reach this goal, we assessed the toxicity of serial dilutions of micropollutant mixtures, extracted from deployed passive samplers at the discharge sites of four Swiss wastewater treatment plants, to in situ periphyton from upstream and downstream of the effluents. On the one hand, comparison of the sensitivities of upstream and downstream periphyton to the micropollutant mixtures indicated that algal and bacterial communities composing the periphyton displayed higher tolerance towards these micropollutants downstream than upstream. On the other hand, molecular analyses of the algal and bacterial structure showed a clear separation between upstream and downstream periphyton across the sites. This finding provides an additional line of evidence that micropollutants from the wastewater discharges were directly responsible for the change in the community structure at the sampling sites by eliminating the micropollutant-sensitive species and favouring the tolerant ones. What is more, the fold increase of algal and bacterial tolerance from upstream to downstream locations was variable among sampling sites and was strongly correlated to the intensity of contamination by micropollutants at the respective sites. Overall, our study highlights the sensitivity of the proposed approach to disentangle effects of micropollutant mixtures from other environmental factors occurring in the field and, thus, establishing a causal link between exposure and the observed ecological effects on freshwater microbial communities.