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Abstract Measuring the diffusion coefficient of clay-based liner materials is important in estimating and predicting long-term barrier performance in waste containment facilities. Various theoretical models, including the finite cylindrical model, have been commonly used to determine the diffusion properties of clay-based liner materials in leaching tests. However, the assumption of zero-concentration boundary conditions of the traditional finite cylindrical model contradicts the measured variation of concentration in real leaching tests, likely resulting in (1) underestimated and unconservative diffusion coefficient, or (2) requirement of a relatively large liquid-to-soil ratio and frequent leachate replacement in the experiment to maintain the zero-concentration boundary condition. In this study, a theoretical model was developed to evaluate the solute diffusion process within a soil specimen under arbitrary, time-dependent concentration boundary conditions. The proposed model, incorporating the time-dependent boundary conditions, provides efficient calculations of the concentration distribution and the cumulative fraction leached of solute across the soil specimen. The example application of the proposed model to experimental data demonstrates the capability of the proposed model to determine apparent diffusion coefficients of clay-based liner materials without introducing errors associated with the assumption of a zero concentration boundary condition. The proposed model provides a comprehensive method to investigate the dynamic transport behaviors of solutes through clay-based liner materials in future studies.