Abstract A flume study was made of bed skin friction and phytoplankton ( Thalassiosira weissf ogii) deposition about a sea scallop ( Placopecten magellanicus) mimic on a coarse (mean grain dia. =1200 μm), medium (615 μm) and fine (170 μm) quarry sand. Bed skin friction immediately upstream, and at one shell diameter downstream of the mimic was 1.2–2.4 times higher than ambient values (8.1 × 10 −2 Pa). Directly downstream of the mimic there was a region of near-zero skin friction. Bed diatom density was correlated with changes in skin friction; after 21 h, cell densities were 36–87% greater in the regions of high skin friction upstream and downstream of scallop than in control experiments. The pattern of bed diatom density about the scallop was similar in the coarse and medium sands, but deposition to the fine bed was not affected by the mimic. Diatom density was significantly correlated with grain diameter; deposition in the coarse bed was 2.3 times higher than in the medium sand, and 7.4 times higher than in the fine sand. A field experiment confirmed that the coarse sand was a greater sink of phytoplankton pigment than the fine sand. Previous studies and scaling arguments suggest that the differences in bed diatom density were controlled by the magnitude of interfacial solute fluxes. Regions of high skin friction about the mimic increased the porewater exchange, resulting in greater concentrations of diatoms retained within the bed. Similarly, the more permeable coarse sand would have a greater rate of porewater exchange than the fine sand, explaining the higher bed diatom density. Differences in the predicted volume of interstitial void space as a function of grain size closely matched the observed differences in bed diatom density. Results suggest that alteration of boundary layer flows by centimetre scale topography such as scallops, increases the flux of particulate organic matter toward the bed, but whether it is retained within the bed, and thus made available to the benthos is dependent on the sediment granularity.