Porter receives a radio distress call from Bill Darmon, the victim of a shark attack. Darmon is far out to sea and in need of an immediate blood transfusion. Porter radios Miami for blood then sets off to locate Darmon's boat. When the plasma arrives at Darmon's boat, a mishap causes the container to tumble to the bottom of the sea in waters too deep for human diving. Flipper is brought in via helicopter and retrieves the plasma just in time to save Darmon's life.
Bud and Sandy discover a bullet-riddled car at the bottom of the bay. Johnny, the barge operator who dumped the car, knows it's evidence of a murder but says nothing to the boys. Johnny's partner-in-crime Dick decides the car should be dynamited. Johnny dives to plant the charge but drops it when the Ricks boys swim into view. He locks the boys in the submerged car then flees. Flipper grabs the dynamite and carries it to Porter who disposes of it far out to sea. Flipper leads Porter to the trapped boys and the two are freed. The police apprehend Johnny and Dick.
Porter receives orders from Washington to close the park. He then learns from visiting ichthyotoxicologist Dr. Rockwell that the preserve has been invaded by poisonous scorpion fish. Dr. Rockwell descends in a two-man submarine to investigate. Leaving the sub for closer examination of the sea floor, Rockwell is stung by one of the fish. He regains the sub but sinks into unconsciousness. Flipper leads Porter to the sub and Rockwell is rescued.
Bud thinks his father wants to marry.
A troubled teen from New York City causes concern for Porter.
A dishonest fisherman lures Flipper away from the preserve.
Porter discovers lobster traps on the preserve.
Flipper is believed to have eaten a valuable research specimen.
A ventriloquist wants to use Flipper in a circus act.
An elderly sponge diver poaches on the preserve.
A paralyzed young woman finds herself in the path of a hurricane.
A congresswoman arrives at the park to conduct an inspection.
Congresswoman Browning takes a tour of the preserve.
A man with heavy gambling debts concocts a dangerous scheme.
Boats are robbed at the park.
A Spanish doubloon sparks an under water treasure hunt.
An oceanographer wants to test Flipper's lifesaving abilities.
Porter discovers sharks on the preserve.
Sandy helps a floating zoo operator search for her lost seal.
Bud unknowingly spends counterfeit money.
Flipper and Bud find a Spanish wreck.
A fortune hunter wants to trap a rare white dolphin.
The Coral Key Park swim race is ruined by toxic chemicals.
Flipper helps rescue the sinking survivors of a floating zoo.
The boys join a scheme to save the floating zoo.
Flipper and the boys stage an aquatic show.
Bud and a runaway set sail on a raft.
An investigator is bitten by a sea snake and cannot sail his yawl.
A researcher uses dolphin sound recordings to attract Flipper.
An under water monster movie is filmed on the preserve.