Availability of essential food resources is one of the most important drivers of survival and to persist in environments where critical resource abundance is changing, animals must either relocate or adapt in place. Testing an animal’s ability to respond to alternative conditions can reveal differences in physiological responses. We used flow-through respirometry to characterize metabolic phenotypes of the desert-adapted cactus mouse (Peromyscus eremicus) under diurnally variable environmental conditions that mimic the Sonoran Desert and treated mice with two different diets; a standard diet and a low-fat diet. We found significant diet-specific differences in the rate of water loss and serum electrolyte values. Mice fed the low-fat diet lost more water relative to those eating the standard diet and patterns of de novo lipogenesis are not limited by dietary composition. Our results are consistent with the hypothesis that diet contributes to water homeostasis. Compared to other desert animals, rodents have limited capacity to dissipate heat using evaporative cooling, limiting thermoregulatory performance at higher temperatures. We predict that a mismatch in physiological requirements and environmental conditions could significantly impact small mammal survival in desert environments if optimal foods become less abundant, as may be the case given climate change.