The patchy spatial distribution of benthic algae (periphyton) on gravel-bed rivers might be caused by physical disturbances during small frequent flow spates. During such spates, the gravel–cobble river bed is stable, but flows are often strong enough to transport large quantities of sand by a hopping motion called saltation. We tested the hypothesis that a spate-related refuge habitat exists in a transition zone (TZ) between the edge of the varial zone and the thalweg of the river channel where high hydraulic stress and saltating sand reduce biomass. We documented physical disturbance and periphyton biomass across 15 riffles after 3 summer spate periods in an oligomesotrophic river in Quebec. Periphyton perturbation thresholds were identified for near-bed water velocity during prespate growth (0.25 m/s) and for sand transport (64–180 g m⁻¹event⁻¹) and flow shear stress (15 Pa) during spates. Generalized linear models were used to examine cross-riffle trends in these 3 disturbance variables and in postspate periphyton biomass. The highest biomass occurred in the TZ. Periphyton increased away from the thalweg as sand transport rates decreased. Biomass continued to increase toward the edge of this zone unless disturbed by high rates of sand transport that were associated with a small, near-shore secondary peak in sand transport rate. Of the 3 disturbance variables, sand transport patterns controlled the spatial distribution of periphyton biomass after small spates with an average recurrence interval of 7 d. No cross-riffle refuge was found after a higher-magnitude spate (3× mean annual discharge) when disturbance thresholds were typically exceeded across the entire riffle. The intensity and distribution of physical disturbance, particularly sand abrasion, over the streambed dictated size and arrangement of periphyton refuge zones. These zones are crucial to promote stream system resilience to landuse change.