The data set contained herein were collected as part of a cooperative U.S. Geological Survey and U.S. Environmental Protection Agency (EPA) project entitled "Field Investigations to Help Support the Assessment of Background Concentrations for Uranium (U) at the Homestake Mining Company, Superfund Site near Milan, New Mexico, July 2016.” The site is underlain by alluvial and several consolidated rock units (Chinle and San Andreas aquifers) that contain in some cases elevated concentrations of U above the EPA MCL (maximum contaminant level). Borehole geophysical data were collected from six alluvial wells at the site. Borehole geophysical logs included: induction, fluid resistivity, natural gamma, spectral gamma, fluid temperature, caliper, casing collar locator, optical televiewer, and electromagnetic flow meter logging (ambient and stressed). Geophysical data collected from these wells were used to evaluate well construction, stratigraphy, distribution of potassium, uranium, and thorium, locations of passive sampler deployment and placement, and inflow and outflow intervals of a well under ambient and pumped conditions.