Clay mineralogy in the vadose zone at Los Alamos National Laboratory (LANL), situated on the Pajarito Plateau of northern New Mexico, differs significantly beneath wet and dry canyons. Drainage across LANL is generally from west to east and feeds into the Rio Grande along the eastern margin of the plateau. Canyons with headwaters in the Sierra de los Valles west of the plateau support more flow and are wetter than canyons with headwaters on the plateau. Los Alamos Canyon, one of the wetter canyons, has extensive clay alteration to depths >30 m in the subcanyon vadose zone. Mortandad Canyon, one of the drier canyons, has less clay alteration. Hydraulic property data for the Otowi Member of the Bandelier Tuff, one of the most widespread lithologies of the plateau, indicate that zones of high clay abundance have hydraulic transmissivities (Ksat) one to two orders of magnitude lower than less altered tuff (∼10−4 vs. 10−2 to 10−3 cm/s). Occurrences of halloysite, and perhaps kaolinite, indicate zones where the water/rock ratio is or has been high within the vadose zone. Gravimetric water content data collected at 110°C from vadose zone rocks with low to moderate clay content provide water abundance data for matrix flow calculations. These data may be in error by up to ∼5 to 16% because some of the water measured is actually held in clay interlayers rather than in pore spaces; such errors are minor but should be considered in the use of gravimetric moisture data. The use of electrical methods to explore for vadose wet zones is valid on the Pajarito Plateau as long as the results are treated broadly, with the understanding that some intervals of high conductivity are not entirely related to either movable water content or clay abundance.