The first plantings were made by botanist and ornithologist Henry Nehrling in 1919; the gardens were neglected after his death in 1929.

In the 1950s, Julius Fleischmann added new plantings, created lakes and a pathway, introduced parrots and waterfowl, and opened as Caribbean Gardens in 1954.

The Naples Zoo began as a personal project of botanist Henry Nehrling, who purchased the land in 1919 to protect his plant collection, which had taken heavy damage during a 1917 freeze at his original garden in central Florida.

The Tetzlaffs began trying to get the county to purchase the land, and the Fleischmann family waited to allow the community to act.

Today, under the leadership of President and CEO Jack Mulvena, the zoo cares for a growing number of critically endangered species, supports conservation efforts in the wild, and reaches over 350,000 guests a year.

The Naples Zoo is laid out with one major loop about 1 mile long that winds through the botanical gardens past the main exhibits.

Nearby are critically endangered cotton-top tamarins, red-footed tortoises, Linnaeus's two-toed sloths.

There is glass viewing and a nearby educational display offers guests information on how their purchases of snacks, cosmetics, and other household items can help or hurt clouded leopards, orangutans, tigers, and more.

Visitors can see these islands can be viewed up close by taking the 15 to 20 minute Primate Expedition Cruise around the lake on one of the zoo's catamarans.

[17] After being nursed back to health he was brought to the zoo and put on exhibit in a recreation of what would be his local mostly wild habitat (mostly wetlands).

There are also other exhibits throughout the zoo for striped hyenas, Reeve's muntjac, yellow-backed duikers, honey badgers, cheetahs, coyotes and macaws.

On December 29, 2021, River Rosenquist, an employee with a third-party cleaning service working at the zoo was bitten by an 8-year-old Malayan tiger after he entered an unauthorized area and reached his arm into the animal's enclosure.