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Within phase I of the INTRAVAL project, the Koongarra uranium ore deposit which is located in the Alligator Rivers Region of the Northern Territory (Australia), was selected as a test case. This test case attributes to the understanding of the processes relevant for the modelling of long term radionuclide migration through the geosphere from a nuclear waste repository. The specific objective of this INTRAVAL test case is to develop a consistent picture of the processes that have controlled the transport of radionuclides in the weathered zone and the time scale over which they have operated. At the Koongarra site, the primary uranium ore consists of uraninite (UO2). The reaction path calculations modelling the alteration of uraninite and biotite, resulted in direct transformation of biotite to kaolinite. Precipitation of chlorite did not occur during the calculations, which is in agreement with the present hypothesis of hydrothermal alteration of biotite to chlorite at Koongarra. The modelling resulted in the precipitation of the uranyl silicate, soddyite. However, soddyite is not identified at Koongarra and hence, the formation of this uranyl silicate mineral during the modelling, can not explain the occurrence of the uranyl silicate zone at Koongarra. The formation of soddyite during the calculations is supposed to be caused by the use of inadequate thermodynamic data.