Filtration of planktonic algal cells from the water column into permeable sublittoral sediment and the fate of the cells in the shallow sands were studied during a red tide produced by the dinoflagellate Peridinella catenata at Hel Peninsula/Baltic in May 2004. Advective porewater flows associated with ripple topography of the bed caused rapid transport of algal cells down to 5 cm sediment depth. Sedimentary concentrations of algal cells mirrored algal concentrations in the overlying water column with increases and decreases within the upper 3 cm of the bed occurring within a few hours. Sedimentary algal uptake and release significantly differed between stations only 15 m laterally apart. Laboratory sediment-column experiments with 13C-labeled algal cells revealed algal decomposition at rates of up to 0.2% 13C h–1 in percolated sands originating from the study site. This was 2 orders of magnitude lower than observed decreases in sediment algal cell C abundance of up to 23% C h–1 after a drop in cell concentrations in the water column. Because bioturbation and ripple migration were negligible, we conclude that advective flushing of the uppermost sediment layer could rapidly remove cells from the sediment. Our results demonstrate close spatial and temporal coupling between algal cell concentrations in the boundary layer and those in the upper 6 cm of permeable sand sediment, and suggest that permeable beds can act as short-term storage buffer for phytoplankton. During passage through the sediment, planktonic algae may benefit from the higher nutrient concentrations available in the porewater.