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The paper presents data on the role of microbiological factors in behavior, uranium and technetium in the upper aquifers (10-15 m) near the surface repository of radioactive waste (Russia, Tomsk region). Pollution of groundwater has been going on for 50 years and now, in addition to radionuclides, concentration of nitrate ions reached to 5000 mg/l. The presence of nitrate ions and a small amount of dissolved oxygen leads to high values of the redox potential, which creates the prerequisites for uranium and technetium high migration activity in higher oxidation states. In the samples of ground water, an active microbial community capable of using nitrate, uranyl, pertechnetate ions for cell respiration was found. Laboratory modeling of the microbial stimulation process with organic substrates led to activation of microflora, consumption of nitrate ions to molecular nitrogen, reduction of pretechnetate and uranyl ions. The results of computer geochemical modeling have shown that the immobilization of technetium in the formation occurs mainly in the form of a tetravalent oxide and in a mixture with a biogenic sulphide. Uranium is immobilized in the form of biogenic uraninite, while biogenic sulfide ions can play the role of an antioxidant buffer in the event of ingress of new portions of the oxidant into the system. The process of polysaccharide microbial biofilms formation on rocks was studied. It was established that in a number of cases microbial biofilms on minerals surface could lead to in their sorption capacity increasing. The work was supported by the Russian Science Foundation, project No. 17-17-01212.