Alarming amounts of microplastics have recently been shown to accumulate in the environment. Recent focus has been on synthetic material contaminating the marine environment, while effects on freshwater habitats and organisms have received less attention. We here confirm and analyse occurrence of microplastics in the duck mussel, Anodonta anatina, in a Swedish river. All analysed mussels contained microplastics, and the number of microplastic debris found in the mussels increased with mussel size. In addition, we demonstrate higher concentrations of microplastics downstream urban areas with wastewater treatment plants compared to a rural upstream location. Both fibres and particles were found in the mussels, indicating that the emissions of these pollutants may have varying origin. Our study indicates that microplastics can be suspended in the water column in streams and that concentrations are higher downstream anthropogenic activity. We discuss our results in light of potential pathways in rural versus surrounding arable land, and highlight a number of required research directions in the aquatic system.