Sandy Ricks is sent off for the summer to stay with his Uncle Porter Ricks in the seaside town of Coral Key. At first, the teen is not thrilled about the change, joking that he would rather be at a Red Hot Chili Peppers concert. His mood hardly improves after meeting Cathy, a local shopkeeper with whom his uncle flirts, and Kim Parker — a girl his own age.
On Porter's fishing trawler, they encounter the source of much of the town's tension: Dirk Moran, Porter’s rival who openly hates most other fish-eating animals. A pod of bottlenose dolphins frolic nearby, a sight Moran disregards as he fires at them and kills a dolphin. Sandy forms a quick bond with another dolphin he names Flipper, a moment that plants the seed of an unlikely friendship that will steer the summer’s events.
That night, Sheriff Buck Cowan visits to explain that the dolphin cannot be kept in captivity. The next day, Kim heads out with Sandy in a dinghy in a bid to find Flipper, though they don’t succeed. They do witness barrels dumped into the ocean from Moran’s boat, a troubling clue that hints at broader trouble. The following morning, Cathy arrives and, with the help of her son, follows Porter's pet brown pelican Pete, who leads them to Flipper, who lies beached and sick. The group manages to nurse the dolphin back to health.
Cathy concludes that Flipper has been poisoned by toxic waste poisoning the water and fisheries around Coral Key. The team uses Flipper’s echolocation and a small camera strapped to his head to locate the barrels, uncovering a leak of toxic waste that threatens the local ecosystem. Flipper finds and reunites with his pod, though he drops the camera in the process. Porter races to alert the sheriff and the town to the danger, while Sandy—driven by concern for Flipper—decides to search for the animal in a dinghy, keeping his plans mostly to himself.
Sandy’s risky journey nearly ends in disaster when Moran’s boat dismantles the dinghy. He misreads a dorsal fin, thinking it belongs to Flipper, but it is Scar, a notorious great hammerhead rumored to have sunk a tourist boat. Sandy swims toward Moran’s boat as Scar closes in, but Flipper unexpectedly appears and begins nose-butting Scar in the gills. The tide of danger turns as Flipper’s dolphin pod arrives just in time to drive Scar away. Moran is ultimately arrested for illegally dumping toxic waste and for attempted harm to Sandy, brought to justice by the local sheriff.
The morning after these harrowing events, Martha Ricks arrives with Sandy’s younger sister to pick him up, and Flipper surfaces to bid him farewell, a quiet and hopeful end to a season that tested the bonds between family, friendship, and the sea.
