Unionid mussels are important constituents of aquatic systems that are affected by anthropogenic changes in hydrology and concomitant increases in suspended solids, yet little is known about the effects of flow on their suspension feeding. We examined the clearance rates (CR) of four species of freshwater mussels (Lampsilis siliquoidea, Lampsilis fasciola, Ligumia nasuta and Villosa iris) to determine whether they feed selectively on river seston and how this may vary with algal flux (concentration × velocity). The CR for the Lampsilis species was also determined using seston particle size, particle fluorescence, and algal taxon. The CR of all species increased linearly with flow chamber velocity, but exhibited saturation-like kinetics with increasing algal flux. The CR of Lampsilis species were higher for larger (>10 um) vs. smaller (<10 um) particles, the latter of which were numerically dominant in river seston. The CR of Lampsilis mussels on most of the algal taxa declined (linearly or non-linearly) with algal flux indicating that mussels have reduced ability to discriminate among algae at higher flux. This potential feeding limitation could affect mussel growth and survival and make unionids vulnerable to the aforementioned hydrological changes. Ecologically, differential use of algal taxa under different algal flux indicates selective feeding, which may be evidence of resource partitioning for mussel species that occupy the same rivers. The differential use of algal taxa under different algal flux within a mussel species indicates the complex nature of bivalve feeding, their habitat requirements, and their vulnerability to human impacts.