To limit the oxidation of waste rocks that originates from mining operations and the subsequent leaching of acidic solutions with high concentration of metal ions, a tailing–rock–clay triple layer capillary cover system was developed to prevent rainwater infiltration in humid climatic regions. The fine grained soil (FGS) layer consists of mine tailing and a hydrodesulfurization (HDS) clay from waste-water treatment with a 95:5 mass ratio. The coarse grained soil (CGS) layer consists of local waste rock granules with a size of 1–10 mm. Methyltrimethoxysilane (MTMS), an oxidation-inhibiting agent with strong hydrophobicity, was passivated on the rock grains to further reduce water infiltration and leaching of metal ions. Prototype-scale column tests were performed with matric suction and water content measurements under 680 min rainfall of 60 mm/h, the most severe annual precipitation case scenario for the Dexing Copper Mine (Jiangxi Province, China, 28.95° N, 117.57° E, humid climate). Both the uncoated and the coated covers exhibited zero leakage throughout the experiment. The passivation on rock granules in the coated cover increased the water entry value (WEV) of the CGS layer to −0.56 kPa. This led to a 15 mm water storage increment in the overlain FGS layer as compared to that in the uncoated cover, and induced lateral drainage (5% of the precipitation) in the FGS layer, which was not overserved in the uncoated cover. The concentrations of the leached Fe2+, Cu2+, Zn2+, Mn2+ and Mg2+ cations drained from the CGS layers of the uncoated cover were 0, 0.4, 0.8, 73.5, and 590.5 mg/L, which are all within the regulation limits of industrial discharge water standards. The concentrations of Cu2+, Mn2+ and Mg2+ cations drained from the coated CGS layer were reduced by 1–3 orders of magnitude. The abovementioned laboratory studies validated the water retention and leaching prevention abilities of the proposed three-layer capillary covers and the MTMS coating, which hold promises in engineering applications.