During small frequent spates (i.e. weekly), the river bed is stable, but flows are strong enough to transport large quantities of sand by a hopping motion called saltation. The effects of saltating sand on periphyton biomass are not well understood. Since small spates occur many times during the periphyton’s growth period, saltating sand could strongly influence the spatial distribution of periphyton biomass. We tested the hypothesis that a small spate-related refuge habitat exists between the edge of the varial zone and the deepest point of the channel, where high hydraulic stress and saltating sand reduce biomass. We studied an oligo-mesotrophic river in Quebec, documenting periphyton biomass across 15 riffles after three spates. Generalized linear models were used to examine cross riffle trends in post-spate periphyton biomass, spate related sand transport and shear stress, and velocity during growth. Our results indicate that sand transport limited the spatial distribution of periphyton biomass during a spate with an average recurrence interval of 7 days. As hypothesized, biomass increased away from the thalweg as sand transport rates decreased. However, biomass decreased again towards the edge of the channel where a small secondary peak in sand transport occurred, despite the decreasing flow strength.