Microbial heavy metal retention was studied using seepage water sampled from a former uranium mining site in Eastern Thuringia, Germany. The seepage water has a low pH and contains high concentrations of metals, including uranium, rare earth elements (REE), and other heavy metals. Microbial influence on sorption and/or active uptake of heavy metals was studied using REE patterns. Incubation of seepage water with the bacterium Escherichia coli caused sorption of heavy metals to biomass. Incubation with the fungus Schizophyllum commune, however, had a much more pronounced effect, including significant fractionation of REE, pointing to the possibility of a specific active uptake mechanism. Extraction factors and fractionation coefficients are given to show the capacity of the presented bioextraction for future applications.