In an underground rock characterization facility, the ONKALO tunnel in Finland, massive 5–10-mm thick biofilms were observed attached to tunnel walls where groundwater was seeping from bedrock fractures at a depth of 70m. In laboratory experiments performed in a flow cell with detached biofilms to study the effect of uranium on the biofilm, uranium was added to the circulating groundwater (CGW) obtained from the fracture feeding the biofilm. The final uranium concentration in the CGW was adjusted to 4.25×10−5M, in the range expected from a leaking spent nuclear fuel (SNF) canister in a future underground repository. The effects were investigated using microelectrodes to measure pH and Eh, time-resolved laser fluorescence spectroscopy (TRLFS), energy-filtered transmission electron microscopy (EF-TEM), and electron energy-loss spectroscopy (EELS) studies and thermodynamic calculations were utilized as well. The results indicated that the studied biofilms constituted their own microenvironments, which differed significantly from that of the CGW. A pH of 5.37 was recorded inside the biofilm, approximately 3.5units lower than the pH observed in the CGW, due to sulfide oxidation to sulfuric acid in the biofilm. Similarly, the Eh of +73mV inside the biofilm was approximately 420mV lower than the Eh measured in the CGW. Adding uranium increased the pH in the biofilm to 7.27 and reduced the Eh to −164mV. The changes of Eh and pH influenced the bioavailability of uranium, since microbial metabolic processes are sensitive to metals and their speciation. EF-TEM investigations indicated that uranium in the biofilm was immobilized intracellularly in microorganisms by the formation of metabolically mediated uranyl phosphate, similar to needle-shaped autunite (Ca[UO2]2[PO4]2·2–6H2O) or meta-autunite (Ca[UO2]2[PO4]2·10–12H2O). In contrast, TRLFS studies of the contaminated CGW identified aqueous uranium carbonate species, likely (Ca2UO2[CO3]3), formed due to the high concentration of carbonate in the CGW. The results agreed with thermodynamic calculations of the theoretically predominant field of uranium species, formed in the uranium-contaminated CGW at the measured geochemical parameters.This investigation clearly demonstrated that biological systems must be considered as a part of natural systems that can significantly influence radionuclide behavior. The results improve our understanding of the mechanisms of biofilm response to radionuclides in relation to safety assessments of SNF repositories.