Fluid inclusion, isotopic, and geochronological studies of secondary calcite and silica at Yucca Mountain indicate a long history of deposition in the 500- to 700-meter-thick unsaturated zone. The minerals form coatings in fractures and cavities of the 12.7-million-year-old tuffs that compose Yucca Mountain, a potential site for the development of a high-level radioactive waste repository. Depositional temperatures gradually decreased from as high as 85°C for the older deposits of secondary calcite and opal to 35°C or less in the younger deposits. Oxygen-isotope compositions of the calcite are consistent with protracted cooling of the rock mass at the level of the potential repository. This thermal history reflects slow cooling of the Timber Mountain caldera a few kilometers north of Yucca Mountain following cessation of volcanic activity about 11 million years ago. Petrographic studies show that the latest calcite is easily recognized by its clear and sparry appearance, overgrowth habit, and growth banding. This latest calcite started to form at least 1.9 million years ago and contains no fluid-inclusion or oxygen-isotope evidence of temperatures higher than modern values. The elevated depositional temperatures have been used as evidence for hydrothermal fluids upwelling into the unsaturated zone (Dublyansky et al., 2001, Chemical Geology, p.125-149). However, the restriction of coatings to the footwalls of fractures and the floors of cavities, and the heterogeneous and sparse distribution in less than 10 percent of potential depositional sites, are inconsistent with an origin from upwelling fluids. Although the older secondary calcite and opal formed at slightly elevated temperatures, they are consistent with an origin from water that was heated as it moved downward through the unsaturated zone.