The Mojave desert tortoise Gopherus agassizii experienced population declines during recent decades, which have persisted despite its designation as a federally protected species. A small number of populations were monitored with mark–recapture methods starting in the 1970s, but inconsistent sampling resulted in challenges estimating the range of factors influencing survival. Large amounts of tortoise telemetry data were collected in recent decades, providing an alternative source for survival estimation. Here we describe an integrated, spatially explicit analysis that combined mark–recapture (3923 tortoises, 35 sites, 1977–2022) and telemetry (2858 tortoises, 22 sites, 1988–2022) datasets to estimate variation in survival across tortoise populations. We produced robust estimates of annual survival conditioned on climate-related covariates and compared results to non-integrated known-fate and mark–recapture models. Integration allowed for estimation of effects on survival not recovered by non-integrated models, including higher survival of males than females, lower survival of juveniles and subadults than adults, and a positive effect of total precipitation from 2 prior winters and active seasons. The integrated analysis estimated permanent emigration rate as the difference between both true survival (via telemetry data) and apparent survival (via capture–recapture data). Annual emigration probability was ~5% in 1 km2 plots and decreased with increasing plot size. Our results demonstrate the strength of leveraging multiple data sources in describing historical demographic rates and identifying relationships with covariates that have delayed effects on survival. Our modeling framework could be used to examine the effects of additional factors on tortoise survival and resulting population dynamics.