Storage of fine-grained (<63 mu m) sediment and associated contaminants within river channels frequently represents an important component of a catchment's suspended sediment and geochemical budget. It has also been increasingly identified as a cause of degradation of aquatic habitats. Such problems are particularly evident in lowland permeable catchments in the UK, where the groundwater dominated hydrological regimes with a lack of high magnitude flows are conducive to sediment accumulation. In-channel storage of fine-grained sediment and a range of sediment-associated contaminants (C, Cd, Co, Cr, Cu, N, total P, Pb, Zn) has been documented for a total of 45 sampling sites using the findings of a regular bimonthly field sampling campaign in three contrasting lowland permeable catchments. The data demonstrate the spatial and temporal variability of both sediment storage and its contaminant content and provide a means of estimating the total storage of fine-grained sediment and associated contaminants within the main channel system of each study area.