Alligators breathe by inhaling air into their lungs. They do not have gills and cannot breathe underwater, though they can stay underwater for intervals of up to two hours, and it is believed they can hold their breath even longer if necessary.

Alligator lungs have unidirectional air flow, which means that air moving through the lungs is largely fresh air and has a high oxygen content. Bird lungs also have unidirectional air flow. The lungs of mammals have bidirectional air flow, meaning the air moves back and forth into and out of the lungs. Because of this, air coming into the lungs of a mammal is mixed with air that has been in the lungs for a while. This mixed air has less oxygen. In alligator lungs, more oxygen is available to diffuse into the blood.

Alligators primarily inhabit fresh water. They tend to submerge themselves underwater for between 10 and 15 minutes. When an alligator goes underwater, its nostrils, ears and throat are automatically closed off by a flap. These flaps prevent water from entering the lungs or stomach. Alligators slow their heart rate and close certain blood lines in their bodies, allowing more blood to get to the vital organs. The blood carries oxygen to these organs, delaying the need for the alligator to breathe.