We used the doubly labeled water method to measure the field metabolic rates (FMRs, in kJ kg-1 day-1) and water flux rates (WIRs, in ml H2O kg-1 day-1) of adult desert tortoises (Gopherus agassizii) in three parts of the Mojave Desert in California over a 3.5-year period, in order to develop insights into the physiological responses of this threatened species to climate variation among sites and years. FMR, WIR, and the water economy index (WEI, in ml H2O kJ-1, an indicator of drinking of free water) differed extensively among seasons, among study sites, between sexes, and among years. In high-rainfall years, males had higher FMRs than females. Average daily rates of energy and water use by desert tortoises were extraordinarily variable: 28-fold differences in FMR and 237-fold differences in WIR were measured. Some of this variation was due to seasonal conditions, with rates being low during cold winter months and higher in the warm seasons. However, much of the variation was due to responses to year-to-year variation in rainfall. Annual spring peaks in FMR and WIR were higher in wet years than in drought years. Site differences in seasonal patterns were apparently due to geographic differences in rainfall patterns (more summer rain at eastern Mojave sites). In spring 1992, during an El Nino (ENSO) event, the WEI was greater than the maximal value obtainable from consuming succulent vegetation, indicating copious drinking of rainwater at that time. The physiological and behavioral flexibility of desert tortoises, evident in individuals living at all three study sites, appears central to their ability to survive droughts and benefit from periods of resource abundance. The strong effects of the El Nino (ENSO) weather pattern on tortoise physiology, reproduction, and survival elucidated in this and other studies suggest that local manifestations of global climate events could have a long-term influence on the tortoise populations in the Mojave Desert.