Accurately assessing free ranging animals' patterns of surface activity and refuge use is critical, yet fundamentally challenging for biologists and wildlife managers. We evaluate the accuracy of an automated technique temperature based activity estimation (TBAE) in estimating surface activity and refuge use patterns of two sympatric reptiles, the western diamond backed rattlesnake (Crotalus atrox) and the Gila monster (Heloderma suspectum) in the Sonoran Desert. TBAE derived from a comparison of body temperature to shaded air temperature was effective in estimating the overall percent surface activity for both rattlesnakes (observed surface activity 51.8%, TBAE estimated surface activity 48.2%) and Gila monsters (observed 22.3%, TBAE 24.5%). There was, however, considerable interspecific difference in the effectiveness of TBAE in predicting surface activity at specific time points; TBAE was far more accurate for Gila monsters than for rattlesnakes (96% vs. 66% time point specific accuracy, respectively). We assert that, when validated, TBAE can be used to yield concurrent and accurate body temperatures and activity estimates for multiple free ranging animals, particularly in arid environments, which improves our understanding of animal biology and can be used to inform management decisions.