Water sediment contaminated with heavy metals is a problem worldwide. The presented ecological conditioning and bioleaching process was demonstrated on a practical scale with the aim to improve material properties and to reduce the heavy metal content so that the sediment can be reused. The bioleaching part of the process was performed in two trials, resulting in the removal of zinc and cadmium. After the treatment the sediment was suitable to be reused for recultivation of mining dumps, while the precipitation sludge may possibly be used as a source for strategic elements.