Fundamental knowledge gaps on the bioaccumulation, trophic transfer and effects of nanoplastics in fresh waters limit the estimation of their ecological risks. In the present study, we investigated these unexplored aspects in a simplified stream food chain. Specifically, we used stream periphyton, which drives crucial ecosystem processes and forms the basis of the food web, and an aquatic snail feeding on periphyton as a primary producer and a primary consumer. Importantly, we used metal-doped polystyrene nanoplastics (nominal concentrations of 0.5, 5 and 50 mg plastics L−1), which allowed quantitative assessment of nanoplastics exposure across this complex biological system. Despite the ecological importance of periphyton in fresh waters, we are yet to understand whether microbial diversity and functions in periphyton, as well as grazer populations, are respectively impacted by accumulation of nanoplastics and dietary exposure. We demonstrated that periphyton efficiently accumulates and retains nanoplastics, which are consequently transferred to the grazers through dietary exposure although this did not lead to notable impacts on periphyton communities. Conversely, combined nanoplastics exposure and grazing pressure shifted community composition. Moreover, dietary exposure resulted in inhibited reproduction and reduced growth of the primary consumer, potentially leading to severe consequences for population dynamics due to trophic interactions in streams.