Natural analogues provide an approach to characterize and test the long‐term modelling of a repository performance. This article presents geochemical information about the alteration conditions of the Nopal I uranium deposit, Mexico, an analogue for the proposed Yucca Mountain radioactive waste repository. Mineralization and hydrothermal alteration of volcanic tuffs are contemporaneous, according to petrographic observations. Trace element geochemistry (U, Th, REE) provides evidence for local mobilization of uranium under oxidizing conditions and further precipitation under reducing conditions. O‐ and H‐isotope geochemistry of kaolinite, smectite, opal and calcite suggests that argillic alteration proceeded at shallow depth with meteoric water at 25–75 °C, a low‐temperature context, unusual for volcanic‐hosted uranium deposits. This temperature range is compatible with some post‐closure evolution models of the proposed Yucca Mountain repository.