Desert-dwelling species may be especially impacted by climate change when historic environments already approach their thermal limits. In such cases, the availability of thermal refugia could determine species persistence. For example, increasing temperatures are thought to be a major extinction risk for blunt-nosed leopard lizards (Gambelia sila), an endangered species endemic to the San Joaquin Desert. Some populations of G. sila occur in habitats characterized by sparse shrubs whereas others occur in habitats without shrubs. We hypothesized that lizards in environments without shrubs are unable to maintain suitable body temperatures during the heat of the day and thus have fewer hours of activity. We used temperature-sensitive radio transmitters to measure the body temperatures of lizards from four sites, two with shrubs and two without, and used physical models to track body temperatures in each microhabitat. Throughout the season, we relocated each lizard two to three times per day and recorded their microhabitat use. Lizards co-occurring with shrubs displayed greater thermoregulatory accuracy and spent more hours active than those that did not occur with shrubs. These results demonstrate an important role of variable vegetation in determining habitats that are accessible to desert ectotherms as climates change.