A long-term research project was conducted on Agassiz’s desert tortoises (Gopherus agassizii) at a 7.77 square kilometer plot at the Desert Tortoise Research Natural Area, Western Mojave Desert, California, USA. The plot included tortoise populations and habitat both inside and outside the protective fence at the Research Natural Area. Databases used in the research and publications from the research project are assembled here and include: census (survey) database used for the demographic analysis and Bayesian modeling of the desert tortoise population; shell-skeletal remains of desert tortoises; clinical signs of health, disease, and trauma in desert tortoises; perennial (shrubs, perennial grasses) and annual plant data from transects within the study area; potential avian predators of desert tortoises at the study area; evidence of mammalian carnivores at the study area; and evidence of anthropogenic impacts to desert tortoise and their habitats inside and outside the fenced Natural Area. These data support the following publications: 1) Berry, K.H., and Yee, J.L., 2021, Development of demographic models to analyze populations with multi-year data-Using Agassiz’s Desert Tortoise (Gopherus agassizii) as a case study: U.S. Geological Survey Open-File Report 2018-1094, 55 p., https://doi.org/10.3133/ofr20181094. 2) Berry, K.H., Yee, J.L., Shields, T.A., and Stockton, L. 2020. The catastrophic decline of tortoises at a fenced Natural Area. Wildlife Monographs 205:1-53. DOI:10.1002/wmon.1052