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Various numerical methods have been being extensively used to estimate the diffusion parameters of pertechnetate (⁹⁹TcO_4⁻) in compacted MX80 bentonite clay using through-diffusion (TD) techniques. In this study, an improved TD column test was applied, and the diffusion fluxes of tritium (HTO) as a non-reactive radionuclide, and ⁹⁹TcO_4⁻ with various dry densities, were compared under the same experimental conditions. Similar results were obtained for the apparent diffusion coefficients of HTO and ⁹⁹TcO_4⁻ using three estimation methods: a graphical method applying the asymptote calculation, an analytical solution using Lsqcurvefit installed in MATLAB, and the Marquardt–Levenberg optimization algorithm in the HYDRUS-1D inverse method. The statistical analysis showed that the densities using a one-way analysis of variance (ANOVA) for the three estimation methods ranged from 1200 to 2000 kg/m³, which indicated that there were no obvious differences between HTO and ⁹⁹TcO_4⁻. In general, the diffusion parameters of ⁹⁹TcO_4⁻ were lower than those for HTO due to anion exclusion effects and lower accessible porosity.