While the intricate frustules of diatoms have been well described, understanding of function lags behind that of form. Here, we show that in the presence and absence of tangential flows of up to 800 pm s(-1), diatom surface microtopographies control the diffusion and advection of submicrometre particles across their surfaces. With no flow, particles were localised on the solid areas of diatom frustules and had reduced diffusion compared to diffusion over flat glass. The magnitude of the effect was dependent on the ratio of the bead radius to the areolae radius (a/R-0). Under flow, particles were deflected from the direction of flow by up to 170 degrees, with over 60 % of particles shifted more than 20 degrees from the direction of flow. These results suggests that diatom frustules act as particle sorting structures, determining which particles reach the cell membrane and its receptors. This effect has important implications for nutrient uptake and fouling of cells by colloids and particulates, particularly when the particles are much smaller than the areolae. Variations in the hydrodynamic effects of different frustule microstructures on the diffusion and advection of Brownian particles may help explain the diverse range of frustule morphologies observed amongst diatoms.