The amphibian disease chytridiomycosis, caused by two fungal pathogens in the genus Batrachochytrium, has caused the greatest vertebrate biodiversity loss due to disease in recorded history. Both the pathogens and their amphibian hosts are impacted by biotic and abiotic conditions that are rapidly changing due to anthropogenic causes, challenging our understanding of how the host–pathogen relationship will shift in the future. By examining this problem through a physiological lens, we can elucidate the mechanisms driving increased susceptibility to disease. This chapter first examines the physiological tools that can be used by amphibian biologists to measure aspects of immune function, stress physiology, and energy expenditure, and the main environmental drivers of these physiological shifts. Then, we explore case studies that have linked environmental change, immune function, and shifts in disease susceptibility to inform amphibian conservation and management.