Willows (Salix spp.) were supposed to be suitable candidates for the phytoremediation of polluted floodplain soils, but it is unknown how willow growth alters concentrations and mobility of pollutants under the conditions of ongoing periodically flooding. Therefore, effects of willow cropping on total concentrations and mobility of As and heavy metals and soil microbial properties were determined after three and four growing seasons under willows in comparison to native grassland in a flood channel of a River Elbe floodplain (Central Germany). After 4 y of willow coppice, the heavy metal concentrations (mg kg–1) were increased not only in the grass control plots (final Cu 274, Pb 276, Zn 935) but also under the willows (final Cu 248, Pb 251, Zn 779) compared to the initial concentrations (initial Cu 170, Pb 156, Zn 579). This increase might likely be caused by the ongoing sedimentation by flood events. The smaller increase under willows compared to grass might be related to an initial net effect of phytoextraction. The concentrations of the mobile fractions of Cd, Cu, Ni, and Zn were significantly lower under willows than under grass. Higher β-glucosidase activities under willows than under grass might indicate a starting net decomposition of organic matter. Therefore, the study of long-term and large-scale effects are recommend before an appropriate evaluation of willow short-rotation coppice for phytoremediation of polluted floodplains will be established.