Sammy, a sea turtle, hatches on a deserted beach and tries to climb out of the hole where he hatched. Being caught by a seagull, he struggles for his life and manages to escape, as the seagull clashes in the air with another seagull, also carrying its prey, who turns out to be a female hatchling sea turtle, Shelly.
Sammy falls onto an old raft and gets carried into the open ocean, losing Shelly. In the ocean he meets another hatchling, Ray, who tells him the story of a "turtle paradise" on an island called "Lapagos", and they together start their voyage there. Later, the two get caught by trawls. Sammy is released back into the sea by the fishermen, but loses Ray.
Washed onto the shore in California, he is picked up by a hippie woman and lives as a pet in the hippie commune with Vera, another female sea turtle, who is older than Sammy, and Catoff, a cat, who claims to be French. On a Christmas evening the hippies draw a peace sign on his shell to sign him as the peace ambassador. When the hippies see that Sammy and Vera will not mate, they release Vera. The police evicts the hippie commune from the beach, and Sammy decides to return back to the sea.
There he meets Vera and a young female sea turtle who is attacked by a shark. Vera and Sammy save the turtle who turns out to be Shelly, his childhood friend. They decide to travel together to the paradise islands, but Shelly gets lost in the sea.
Vera tells Sammy to swim to the "cold waters". Sammy finds an old refrigerator drawn by the humans and uses it to travel to Antarctic. A gull he meets on his journey tells him that the paradise island can be only be reached through a "secret passage where the fresh waters run". In the Antarctic waters Sammy meets a fin whale who barely escapes a harpoon from a whaling ship.
The harpoon destroys the refrigerator, but Sammy is saved by the anti-whaling protesters and placed into the sea animal shelter where he finds Shelly, Catoff and people from the hippie commune (who now work in the shelter). The ex-hippie recognize the peace sign on Sammy's shell.
Shelly and Sammy are released into the ocean. They decide to find the secret passage and use it to travel to the paradise island. They manage to find the passage (which turns out to be Panama Canal) but get separated as they try to pass a lock. As he searches Shelly, Sammy encounters two sea turtles that urge him to help their friend who got trapped in an intermodal container. Sammy rescues the turtle, who turns out to be his old friend Ray. They swim together to a wrecked Spanish galleon where Roy lives with Rita, his girlfriend.
Being told about Shelly, Rita remembers her and advises Sammy to search for her in the galleon. Sammy finds Shelly being courted by another sea turtle. Disappointed and upset, Sammy returns to his friends only to find out that the turtle who courted Shelly is a playboy but has a strong relationship with another female. Together with Ray and Albert, a shark who lost his teeth, they set up a fake shark attack on Shelly to let Sammy save her again and win her heart. Shelly and Sammy then reunite and, along with Ray and Rita, return to the beach they hatched.
The closing scene of the movie shows Sammy helping one of his new-hatched grandsons to climb out of the hole.