Willows (Salix spp.) are considered to be effective for the phytoremediation of trace elements from contaminated soils, but their efficiency is limited in heavily polluted soils because of poor growth. Liming can be a desirable measure to decrease the plant availability of elements, resulting in improved plant development. Notably, large root area and maximum soil penetration are basic parameters that improve the efficiency of phytoremediation. The impact of soil chemical properties on willow root anatomy and the distribution of trace elements below-ground have rarely been studied. The effect of liming on root parameters, biomass allocation and trace element distribution in non-harvestable (coarse roots, fine roots, stumps) and harvestable plant parts (twigs and leaves) of Salix × smithiana was assessed at the end of a 4-year pot experiment with two trace element-polluted soils that differed in terms of soil pH. Stump biomass predominated in weakly acidic soil. In neutral soil, the majority of biomass was located in fine roots and stumps; the difference from other plant parts was minor. Trace elements were the most concentrated in fine roots. Translocation to above-ground biomass increased as follows: Pb < As < Zn~Cd. In contrast to Cd and Zn, great differences in As and Pb mobility in plants were recorded after measurements of individual below-ground biomass (stumps < coarse roots < fine roots). Lime application decreased the concentrations of mobile Cd and Zn and related levels in plants, improved biomass production and root parameters and increased the removal of all trace elements in weakly acidic soil. None or minimum differences in the monitored parameters were recorded for dolomite treatments in both soils. The dose and source of liming had crucial effects on root anatomy. Growing willows in limed trace element-polluted soils is a suitable measure for combination of two remediation strategies, i.e. phytoextraction of Cd and Zn and assisted phytostabilization of As and Pb.