Arlo Beauregard, a boy who is half-human and half-alligator, is placed in a sewage drain under New York City shortly after his birth, where he is taken by a stream of water into the ocean. Arriving in a swamp, Arlo is adopted and raised by a woman named Edmée. As a teenager, Arlo wishes to interact with other people but fears his alligator appearance will not be accepted by society. Edmée gives him his birth wristband on his fifteenth birthday and reveals to Arlo that he is from New York, and unaware that he was actually abandoned, Arlo decides to travel to the city to find his biological father, Ansel Beauregard.
While traveling, Arlo is spotted by a person who contacts two alligator hunters, Ruff and Stucky, to retrieve him using a creature known as "the Beast". After the hunters find him, Arlo is rescued by Bertie, who is also a teenager. At a wrestling club, the pair meet Furlecia, Teeny Tiny Tony, and Alia, who agree to drive Arlo and Bertie to NYC after they help rescue their friend Marcellus from an aquarium.
Arriving in NYC, the group spots Ansel Beauregard, an entrepreneur who announces his plan to rebuild part of the city near the seashore. Leaving his group after finding a way to talk to him, Arlo is told by Ansel that he is not his son, but Arlo disagrees. In an attempt to help, Ansel reveals his project to remodel the seashore environment of NYC into a large city, and tries to get Arlo to change his image, shocking him, and sends him away. Disappointed and alone, Arlo enters a sewage drain and is later found by the rest of his group at the same seashore site for Ansel's project, who then teach them that no matter how different he is, his flaws are what makes him who he is.
At the Met Gala that evening, Arlo and his friends break in but are secretly followed by Ruff, Stucky and the Beast. Soon after, Arlo interrupts the gala and Ansel tries to tell him the truth. However, Arlo is then captured by Ruff and Stucky. After Ansel manages to rescue Arlo, he reveals to an audience that he is, in fact, Arlo's father and also half-bird. He explains he only gave him up just to hide his half-animal identity and wants Arlo to forgive him to start over their kinship. Delighted, Arlo hugs his father and forgives him, but turns down living with him in favor of living with his friends instead, and accepts Bertie as a member of the group as well. Additionally, Ansel decides to let them move to and rebuild the seashore part of the city as it was in better condition, and Arlo officially accepts it as where he truly belongs.
In a mid-credits scene, Edmée receives a postcard and learns about Arlo's new life.
