In order to clarify the effect of mineral alteration on nuclide migration, we examined the processes, mechanisms, and kinetics of chlorite weathering, and the uranium concentrations in minerals and rocks at Koongarra, Australia. The observed concentrations of uranium in rocks were compared to those calculated. The sequence of chlorite weathering may be simply expressed as a chlorite → vermiculite → kaolinite conversion. These minerals occur as a function of depth, which corresponds well to uranium concentrations on the meter scale. Iron minerals, closely related to the uranium redistribution, are released during the weathering. The first-order kinetic model of the weathering process suggests that the weathering rate is not constant but time-dependent. The uranium concentrations are qualitatively proportional to the extent of the weathering; the weathered part having higher uranium concentration. Uranium mainly occurs with iron minerals, and sub micron sized saléeite, a uranyl phosphate, is one of the most probable uranyl phases associated with the iron minerals. The uranium fixation mechanisms are probably saléeite microcrystal coprecipitation and sorption to the iron minerals. Our model, which describes uranium concentrations in rocks as a function of time, shows that the transition zone (a vermiculite dominant area) plays an important role in the uranium migration. We have established that weathering of chlorite has affected the redistribution of uranium for more than one million years. The present study demonstrates the significance of mineral alteration when we estimate nuclide migration for geologic time.