Periphytic algae are a rich food resource that sustains the upper trophic levels of stream ecosystems. These algae are susceptible to loss through hydraulic shear and abrasion by mobile sediments, but there are few documented linkages between periphyton biomass and sediment transport regimes. In this study, we use both a large set of field observations and an in situ experiment to document the relationship between periphyton biomass and sand transport rate. The in situ experimental design investigates the response of diatom-dominated periphyton biomass to abrasion from fine and coarse sand in transport over low-lying and higher protruding host rocks. Our results showed that periphyton biomass decreased with increasing transport rates in a threshold-type response (transport rates > 0·04–1·8 g m−1 s−1) quantified using classification and regression trees. The in situ experiment revealed that low-lying rocks lost more biomass for a given transport rate than the higher, protruding ones. Saltating coarse sand abraded surfaces more effectively than fine sand travelling primarily in suspension. The observed pattern of biomass loss was similar to that reported in flume studies of the effects of suspended sediment on periphyton. The negative relationship between sand transport rate and post-flow event biomass was nearly identical to that found on the Skona River, Norway, for larger flow events. Sand constitutes a large percentage of the bedload of gravel-bed rivers and is susceptible to transport during frequent flow events. Even small increases in sand loadings to the gravel-cobble river bed can cause large increases in streambed abrasion. Copyright © 2012 John Wiley & Sons, Ltd.