Mechanistic models provide a powerful, minimally invasive tool for gaining a deeper understanding of the ecology of animals across geographic space and time. In this paper, we modified and validated the accuracy of the mechanistic model Niche Mapper for simulating heat exchanges of animals with counter-current heat exchange mechanisms in their legs and animals that wade in water. We then used Niche Mapper to explore the effects of wading and counter-current heat exchange on the energy expenditures of Whooping Cranes, a long-legged wading bird. We validated model accuracy against the energy expenditure of two captive Whooping Cranes measured using the doubly-labeled water method and time energy budgets. Energy expenditure values modeled by Niche Mapper were similar to values measured by the doubly-labeled water method and values estimated from time-energy budgets. Future studies will be able to use Niche Mapper as a non-invasive tool to explore energy-based limits to the fundamental niche of Whooping Cranes and apply this knowledge to management decisions. Basic questions about the importance of counter-current exchange and wading to animal physiological tolerances can also now be explored with the model.