Clay–cement slurry, as a widely used anti-seepage material, is prone to calcium leaching and deterioration when exposed to environmental water. The influence of microstructural and mineralogical evolution on the transport properties of clay–cement samples under leaching conditions remains to be investigated. In this paper, accelerated calcium leaching tests were conducted on clay–cement pastes. A variety of techniques, including XRD, SEM, and NMR, were used to characterize the microstructural and mineralogical changes in the leached samples. The effect of accelerated leaching on transport behavior was studied by measuring changes in the water permeability and calculating diffusivity. XRD and SEM analyses show that after 28 days, the characteristic peaks of portlandite and ettringite almost disappear, while C-S-H gel undergoes decalcification and decomposition, leading to an increase in pore number and a notable rise in pore size (up to 1.90 μm). NMR results indicate that total porosity and peak pore size increase significantly, with the proportion of gel pores decreasing and that of small capillary pores (10–50 nm) rising from 10% to 22.1%. Moreover, the surface layer porosity (0–5 mm) increases from 31.33% to 50.65%, while the middle and lower layers show less degradation, indicating a progressive deterioration pattern. Regarding transport properties, the hydraulic conductivity increases from 4.7 × 10⁻¹⁰ cm/s to 2.14 × 10⁻⁸ cm/s (a two-order-of-magnitude increase), and the diffusion coefficient rises from 1.6 × 10⁻¹¹ m²/s to 8.6 × 10⁻¹¹ m²/s (a 5.3-fold increase). Both the diffusion coefficient and its increase factor gradually decrease from the surface to the interior, consistent with the evolution of porosity.