This study systematically elucidates the mechanisms of hydraulic performance of geosynthetic clay liners (GCLs) by using tailings leachates from two representative mines, Xikuangshan and Shizhuyuan, in Hunan Province. A series of physical parameter tests, including fluid loss, free swell index, and liquid limit, together with microstructural characterization using X-ray diffraction (XRD), X-ray fluorescence (XRF), and scanning electron microscopy (SEM), were conducted to clarify the governing processes underlying the degradation of GCL performance in the presence of tailings leachates. The results demonstrate that the Xikuangshan tailings leachate markedly diminishes the hydraulic barrier performance of the bentonite component of the GCLs. This reduction primarily results from the exchange reactions between the high-valence cations in the leachate and the interlayer cations of bentonite. Such cation exchange compresses the diffuse double layer, reduces the swelling potential, and consequently manifests macroscopically as a pronounced increase in fluid loss and decreases in both the free swell index and the liquid limit. Microstructural observations further reveal that although the dominant mineralogical composition of the bentonite remains unchanged, its pore structure undergoes notable alteration: the hydraulic radius increases, the clay fabrics (crystallites) become looser and more dispersed, and the permeant pathways become more conductive. In addition, the hydraulic conductivity of GCLs permeated by different test solutions was estimated based on the measured fluid loss. The calculated values were slightly higher than the measured permeabilities, indicating that the proposed method can provide conservative estimates for rapid evaluation of GCL hydraulic performance.