Uranium contamination of soils and water is a worldwide problem due to geology or anthropogenic release such as mining, or use of inorganic fertilizers. In situ remediation of low and moderately contaminated sites is a complicated procedure due to the complex chemistry of uranium. This study demonstrates that at pH 3.5, a fungal strain isolated from unprocessed uranium bearing shale creates hydrochemical conditions that immobilize 97% of a total of 10 mg L-1 dissolved uranium in a 0.20 μm pore system. The redistribution occurred within 10 minutes and remained for five weeks and just 12% of the inventory was retrieved in the biomass. Size exclusion chromatography of the dissolved phase identified organic substances in the range of more than 60 kD down to 100 D as a response to time of incubation. Geochemical modeling indicates formation of uranium-organic complexes where ligand size, coordination chemistry and their tendency to agglomerate determine the redistribution.