Of the mechanisms that remove benthic algae during flood disturbances, relatively little is known about the effects of sediment scour. We investigated suspended sediment scour using naturally colonized benthic algal communities exposed to realistic velocities and suspended sediment concentrations in a laboratory flowtank. Increased velocity alone removed benthic algal biomass, and high suspended sediment concentrations further increased algal removal. Efficacy of biomass removal by velocity and suspended sediments was community-specific; communities with a tightly adherent cohesive mat physiognomy were resistant to removal, despite taxonomic similarity to easily disturbed communities. In addition, some taxa were more susceptible to removal by disturbance than others. The duration of scour and physical refugia on the substratum also influenced algal biomass removal. Our results indicate that suspended sediment scour may be an important mechanism for algal removal during flood events, and some variability in biomass removal among flood events may be the result of differences in suspended sediment load.