We assessed short-term temporal and spatial variation of metal contents in the upper 100 cm sediment profile of intertidal marshes vegetated by common reed (Phragmites australis) along the Scheldt estuary in Belgium. The upper 0–100 cm sediment profile was sampled in three reedbeds at 56, 94, and 131 km from the river mouth. Sampling was repeated five times, at approximately two month intervals. Sediment properties such as texture and chloride, carbonate and organic matter content differed among locations. Metal accumulation, which is primarily due to association of metals with organic matter and clay in the surface sediment layer, seemed to be supplemented by an accumulation of sulphide precipitates deeper in the sediments. The depth at which sulphide precipitation significantly contributed to metal accumulation depended on the sampling location, and varied from less than 5 cm in clayey, organic sediments to more than 1 m in sandy sediments. Temporal variation of Cu, Cd, Pb, and Zn concentrations could only be linked to newly formed sulphides or sulphide oxidation at the sites with the lowest sulphide content. At sampling sites containing high sulphide amounts, variations should be primarily attributed to metal exchange and the presence of mobile metal complexes. Litter decomposition at the end of the growing season could hereby play a significant role.