Bioremediation can be applied for the treatment of metal/metalloid and radionuclide bearing water streams in order to immobilize the targeted species. Interactions of microbial cells with soluble targeted species may occur during the microbial metabolism and result to the reduction of their mobility and toxicity. The most important metabolically mediated immobilization processes for metal/metalloid and radionuclide species are bioprecipitation and bioreduction. Bioprecipitation includes the transformation of soluble species to insoluble hydroxides, carbonates, phosphates and sulfides as a result of the microbial metabolism. In the case of biological reduction, the cells use the species as terminal electron acceptors in anoxic environments to produce energy and/or reduce the toxicity of the cells microenvironment. These processes can be the basis of technologies for the rehabilitation of contaminated sites both for surface and groundwater aquifers, soils and industrial water streams. Such technologies are recently developed and applied both in pilot and full scale, although the related mechanisms are complicated and not always fully understood.