The remediation of heavy metal-polluted sediment by solid-bed bioleaching, using the percolation principle, requires a material well permeable to air and water. Freshly dredged sediment is nearly impermeable, unsuitable for solid-bed leaching, and therefore needs preliminary conditioning. During conditioning, the sediment underwent physicochemical changes such as oxidation and acidification, which were significantly accelerated by the presence of reed canary grass (Phalaris arundinacea L.) in comparison to the processes taking place in sediment without plant cover. P. arundinacea transpired large amounts of water followed by the formation of cavities in the sediment package which were then penetrated by atmospheric oxygen. Furthermore, P. arundinacea actively transported oxygen into the sediment via the roots. Oxygen and root exudates stimulated the growth of microbes, which together with hair roots made mineral sediment particles stick together, forming larger aggregates and changing the sediment structure from muddy-pasty to crumbly and soil-like. The structural changes markedly improved the permeability of the sediment to water by a factor of 5,000. Sediment conditioned with P. arundinacea consisted of larger and more stable particles and therefore it was twice as permeable as unplanted sediment. Comparative solid-bed bioleaching experiments on a pilot scale demonstrated that the removal of heavy metal occurred at nearly the same rate and efficiency with conditioned (for six months with P. arundinacea) and spontaneously ripened (stored for six years in the open) sediment.