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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) nearby the surface repository of radioactive waste (Russia, Tomsk region). Considered site has been operating for 50 years for disposal of nitrate containing radioactive waste and groundwater pollution has been going on for now, in addition to radionuclides, the current concentration of nitrate ions has reached 5000 mg/l. The presence of nitrate ions and a small amount of dissolved oxygen leads to high values of redox potential, which creates prerequisites for uranium and technetium high migration activity in higher oxidation states. In the samples from this aquifer we have found stable and rich microbial community with high cell number of denitrifying and sulfatereducing bacteria. Moreover, active microbial community capable of using nitrate, uranyl, pertechnetate ions for cell respiration was found five years ago [1], we made in situ biostimulation test by injection of sodium acetate and milk whey. And we managed to reduce nitrate concentration from 4.5 g/l to below the toxic level. But the general aspects of Uranium and Technetium behavior are still need to be clarified. In laboratory test with ground water and sediments samples, we have studied main biogeochemical aspects and main biological process rates: Eh decreasing, nitrate and sulfate-ions consumption, reduction of pertechnetate and uranyl ions. The process of sandy samples changes was studied after lab microbial stimulation test: rates and quantities of microbial biofilm formation on the surface, elements changing after microbial leaching and new biogenic phases with iron and carbonates. For radionuclides behavior modeling we also used Kd values from radionuclides sorption experiments. After that we have done aerobic and anaerobic sorption experiments. All this information was used for complex modeling of macro and microcomponent migration in water and in sediments by PHREEQC software. Computer geochemical modeling results 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.