Unionid mussels are among the most threatened group of freshwater organisms globally. They are known for their ability to filter food particles from flowing and standing waters. However, invasive bivalve species, such as the Asian clam (Corbicula fluminea) in North America, have the potential to overlap in feeding and potentially out-compete the native species. Yet, the feeding preferences of unionid mussels and C. fluminea are incompletely understood. We hypothesized that Elliptio crassidens (native) and C. fluminea (invasive) would select for specific organic components present within seston. We examined changes in seston (dry mass and ash-free dry mass) resulting from bivalve feeding activity for three size classes of material that were isolated using gravimetric filtration. The treatments were also sub-sampled for flow cytometry (FC) which separated the suspended materials in the stream water into five categories: detritus, heterotrophic bacteria, picoautotrophs, nanoautotrophs, and heterotrophic nanoeukaryotes. Our results indicated that both species of bivalve showed preferences for organic and living materials. E. crassidens preferentially filtered nanoeukaryotes, whose decreases were associated with an increase in bacteria. In contrast, C. fluminea preferred smaller materials through selective filtration of picoautotrophs. In addition, both species increased the concentration of large materials toward the end of the experiment because of the suspension of their pseudofeces biodeposits. To our knowledge, this study is the first to examine grazing by bivalve species on natural stream particulate matter using FC. Our results suggest that native and non-native mussels have different functional roles, which has important implications for organic matter processing and food webs in streams.