Hal Gras had no experience with animals when he attended the museum's opening in 1952 with his wife Natie. Born in New Jersey in 1919, he had built a career in broadcasting after serving in World War II. Something about the museum captured him. He began hosting its television show Desert Trails, which first aired in 1953 and would run for 32 years with Gras presenting 1,551 episodes. As the museum's public relations director from 1955 to 1972, he started bringing live animals to his appearances at local clubs, schools, hospitals, and county fairs. The program grew into something called the Desert Ark, named for the car that transported the creatures. By his retirement in 1985, Gras had presented 5,382 Desert Ark programs. A street near the museum now bears his name.

The museum houses more than 230 animal species across exhibits designed to feel like natural encounters. At Cat Canyon, bobcats and ocelots prowl through naturalistic grotto settings. The Life Underground exhibit invites visitors into a tunnel where kit foxes, kangaroo rats, and ringtails reveal where desert creatures go when the sun bears down. The Desert Loop Trail uses fiber fencing designed to be nearly invisible, making the javelinas, coyotes, and lizards appear to roam free in open desert. The Mountain Woodland recreates Mexican pine-oak forest habitat with cougars, white-tailed deer, and brown bears. An artificial cave extends 75 feet, its chambers displaying fossils, gems, and cave formations lit from beneath pools.

The raptor free-flight demonstration defies everything visitors expect from a zoo show. From mid-October through mid-April, weather permitting, birds of prey fly completely untethered through the open desert while spectators stand directly in the flight path. No leg straps, usually no leg rings. Harris's hawks, peregrine falcons, barn owls, red-tailed hawks, and great horned owls pass so close that visitors feel feathers brush their skin. Harris's hawks feature prominently because they are the only raptor species in the world that hunts cooperatively as a family, using strategy like wolves. Morning and afternoon demonstrations showcase different species, making each experience unique.

The Sonoran Desert receives bi-seasonal rainfall, creating conditions for more than 2,000 plant species. The museum's gardens display 1,200 different species across 56,000 individual specimens, representing every biotic community found in the region. The Warden Aquarium, opened in January 2013, interprets the water that makes this lush desert possible: the Colorado River, the Gulf of California, and the monsoon moisture that sustains life. The museum's Hummingbird Propagation Program remains the only one of its kind in the world for North American hummingbirds, with four species nesting annually in the aviary. Scientists here study pollinators, seed dispersal, and climate change effects while collaborating on species survival projects for endangered creatures like the Tarahumara frog and Chiricahua leopard frog.

Approximately 500 volunteers support the museum's 120 paid staff, contributing about 130,000 hours annually. The Docent Program, established in 1972, requires each of its nearly 200 volunteers to complete a 15-week training course in natural history education. It is recognized as one of the finest docent corps in the industry. These trained naturalists staff stations throughout the grounds, offering presentations with live reptiles, birds, mammals, and fossil specimens. Since 1995, the museum's press has published more than 40 books including the 628-page 'bible' of the region, A Natural History of the Sonoran Desert. TripAdvisor has ranked it among the top 25 museums in the United States and the top ten in the world.