These data were compiled to evaluate the reproductive ecology of Agassiz's desert tortoises (Gopherus agassizzi) in the Sonoran Desert of California using two populations within Joshua Tree National Park, including five reproductive seasons that spanned 20 years (1997-1999, 2015-2016). Compared to their conspecifics inhabiting the Mojave Desert, the reproductive ecology of G. agassizii in the Sonoran Desert is understudied. Climatic variation between the two deserts can affect reproductive ecology, including fecundity and clutch phenology. Mature female tortoises (straight-line carapace length ≥ 20 cm) outfitted with radiotransmitters were located and X-radiographed approximately every 10-14 days during the reproductive season (April-July). The appearance of shelled eggs on X-radiographs allowed for the determination of clutch phenology (dates of appearance and disappearance of shelled clutches), as well as clutch size, clutch number, and X-ray egg width (XREW). XREW was measured at the widest portion of each egg, from the outermost point of each side of the shell, using dial calipers for film and K-PACS software for digital X-radiographs. XREW was determined from the first X-radiograph in which a clutch of eggs was clearly detectable. Data were also compiled on temperature and cumulative precipitation by wet and dry seasons using WestMap (https://cefa.dri.edu/Westmap/), and these data were used to reflect how temperature and precipitation potentially affect reproductive ecology. As a federally listed species, it is important to understand geographic variation in desert tortoise ecology for effective management of the species.