In shallow coastal ecosystems where most of the seafloor typically lies within the photic zone, benthic autotrophs dominate primary production and mediate nutrient cycling and sediment stability. Because of their different structure and metabolic rates, the 2 functional groups of benthic macrophytes (seagrasses, macroalgae) have distinct influences on benthic−pelagic coupling. Most research to date in these soft-bottomed systems has focused on mature seagrass meadows where shoot densities are high and on dense macroalgal mats that accumulate in response to eutrophication. Relatively little is known about the influence of low-biomass stands of seagrass and macroalgae on nutrient fluxes and sediment suspension. Using an erosion microcosm with controlled forcing conditions, we tested the effects of the eelgrass Zostera marina L. and the invasive macroalga Gracilaria vermiculophylla on sediment suspension and nutrient fluxes under high-flow conditions. At low densities, G. vermiculophylla increased sediment suspension and increased the nutrient flux from the sediment to the water column. For macroalgae, increased sedi ment suspension is likely due to dislodgement of sediment particles by bedload transport of the algae. In this case, the increase in sediment transport was reflected in an increase in nutrient flux from the sediment, showing that modification of physical forcing by benthic primary producers can also affect nutrient flux. The presence or absence of Z. marina did not have a significant effect on nutrient flux. However, the results suggest that there may be a range of low shoot densities for which storm-like flows increase sediment suspension to values higher than those expected for a bare sediment bed.