The long-term operation of uranium sludge storages causes serious problems: it contaminates the neighboring aquifers with dangerous substances (uranium, nitrate, ammonium, and sulfate). To purify the aquifers can be costly and time-consuming; therefore, it is important to use the potential of in situ conditions, e.g., the aboriginal microflora and its ability to biologically remediate water reservoirs. In this work, we study the geological, geochemical, and microbiological characteristics of groundwater contaminated by uranium sludge storages resulting from the production cycles of four Russian chemical plants. All of the sites under consideration were extremely contaminated with nitrate (up to 15 g/L); in each case, we used denitrifying bacteria as a dominant group of microorganisms for purification. Our laboratory studies showed that microbial stimulation of water samples by milk whey promotes O2 and nitrate removal; this, in turn, started the cycle of anaerobic processes of authigenic precipitation caused by the reduction of iron and sulfate in the system. Thus, a mineral geochemical barrier preventing uranium immobilization formed. As a result, the uranium of the liquid phase decreased about 92–98% after 3–6 months (decomposition time depends on the nitrate concentration in the groundwater probe). The resulting amorphous biogenic phases contain sulfur, iron, phosphorus, and uranium.