A modelling study was carried out to understand the effect of rock alteration on uranium radionuclide concentrations in rocks, in the vicinity of the Koongarra ore deposit, Australia. The one-dimensional, advection-dispersion-sorption model considers two important factors resulting from the process, mechanism and rate of chlorite weathering, one type of rock alteration that has occurred over a million-year period; (a) the changes in the distribution coefficients of uranium and thorium over time, and (b) that in rock porosity. The distribution coefficient and rock porosity at a given time, are expressed as average values of those of the coexisting minerals. By assuming a Darcy velocity of 0.9 m/y and an initial uranium concentration in the groundwater of 0.5 ppm, similar to present-day values, we were able to derive, from the finite-element modelling, uranium concentrations in the rock which are in good agreement with observed values. The calculated values of 230Th/234U activity ratios show a similar trend to those observed, although more experimental data are necessary to confirm the similarity. However, in the absence of the rock alteration, the calculated results did not agree with those observed. The present study suggests that rock alteration should be included in models used to predict uranium migration over long, geologic timescales.