The effect of the addition of an organic monolayer to the surface of a clay mineral on the speciation of metal ions intercalated into the clay interlayer is probed by X-ray absorption spectroscopy. The presence of the monolayer changes the surface of the clay from hydrophilic to hydrophobic. It inhibits the interlayer ions from exchanging freely into environmental water and reduces the leach rate of cations out of the clay by approximately a factor of 20. Significant changes are observed when these coated samples are treated under hydrothermal and thermal conditions. Reductions of uranium(VI), in the form of uranyl, and copper(II) ions occur. In addition, the uranium aggregates, forming small particles that appear similar to UO2. Comparable conglomeration occurs with lead cations and with the reduced copper species.