Understanding the movement of water through thick vadose zones, especially on time scales encompassing long-term climate change, is increasingly important as societies utilize semi-arid environments for both water resources and sites viewed as favorable for long-term disposal or storage of hazardous waste. Hydrologic responses to Pleistocene climate change within a deep vadose zone in the eastern Mojave Desert at Yucca Mountain, Nevada, were evaluated by uranium-series dating of finely layered hyalitic opal using secondary ion mass spectrometry. Opal is present within cm-thick secondary hydrogenic mineral crusts coating floors of lithophysal cavities in fractured volcanic rocks at depths of 200 to 300 m below land surface. Uranium concentrations in opal fluctuate systematically between 5 and 550 μg/g. Age-calibrated profiles of uranium concentration correlate with regional climate records over the last 300,000 years and produce time-series spectral peaks that have distinct periodicities of 100- and 41-ka, consistent with planetary orbital parameters. These results indicate that the chemical compositions of percolating solutions varied in response to near-surface, climate-driven processes. However, slow (micrometers per thousand years), relatively uniform growth rates of secondary opal and calcite deposition spanning several glacial–interglacial climate cycles imply that water fluxes in the deep vadose zone remained low and generally buffered from the large fluctuations in available surface moisture during different climates.