Over decades the River Elbe has been one of the worst polluted major rivers of Europe and polluted sediment was deposited spatially differently in its floodplains. The spatial variability of total As, Cd, Cu, Hg, Ni, Pb, and Zn concentrations and fractions of sequentially extracted Cd, Cu, Ni, and Zn were determined in soil samples taken at different length scales in the floodplain Schönberg meadow (stream km 436–440). Within a flood channel the low spatial variability of total As and heavy metal concentrations at depth of 0–10?cm (relative standard deviation (RSD) <30%) did not increase with expanding sampling distances from 1 to 28?m. The variation in the total As and heavy metal concentrations (RSD up to 130%) and in the NH4NO3-extracted heavy metals (RSD up to 320%) increased substantially in the floodplain at longer distances between points (30–3000?m). Close correlations between the concentration of metals in sequentially extracted fractions and basic soil properties (Corg, N, S, Fe, and Mn) within a topographic structure indicated their suitability to estimate the potential phytoremediation success and determined the "status quo" at the beginning of a phytoremediation experiment.