Dr. Pam Blondell (Colleen Flynn) a naval officer, relocated to the Florida Keys to join Dr. Ricks at the institute to perform dolphin research.
Mike is unhappy about the move until he meets Maya Graham (Jessica Alba), a free-spirited 14-year-old girl who has a special connection with Flipper and the ocean.
Next door to the institute, a new substation for Air Sea Rescue opens, introducing Deputies Tom Hampton (Whip Hubley) and Quinn Garnett (Wren T. Brown).
In season 3, Dr. Daulton and Maya are written out of the series by leaving Bal Harbour to perform research in the Red Sea and San Diego.
Hampton and Parker, along with her two kids, Chris (Craig Marriott) and Jackie (Laura Donaldson), set up housekeeping, and the series begins to focus more on their family.
Chris was unhappy about the move to the Florida Keys at first but slowly became accustomed to his new home and Jackie forms an unbreakable bond with Flipper.
In season 4, Tom's niece Courtney Gordon (Skye Patch), moves in with the Hampton/Parker family after being unhappy living with her mother in Washington, DC.
The series ends on an initially tragic note as Flipper accidentally becomes beached on a sand dune and is unable to free himself.
Upon learning what has happened, the entire cast rushes to the scene, but arrives too late; Flipper's heart stops as they are trying to save him.
Seasons three and four regular cast member Darrin Klimek also appeared briefly as a different character in the season-one episode "Treasure Hunt".
Between seasons one and two, the Air Sea Rescue Substation was built next door to the research institute when the series began focusing less on ocean- and dolphin research-based plots.
A fourth location, just east of Conch Key adjacent to Overseas Highway 1, was used when Maya meets Keith in a Jeep to inform him Mike is in trouble.
After filming on Flipper wrapped, the building was demolished to accommodate Sea World's Imagine Dolphin Show attraction located nearby.
Although the area is unrecognizable today, an aerial shot in the season-one episode "F. Scott" shows the original configuration of the building at Sea World.