Mitch Bucannon, on leave in Oahu, Hawaii while he sorts out his thoughts during a mid-life crisis (his failed romance with Neely, his mother's recent death, and Hobie living on the East Coast), decides to form an international team of lifeguards in Hawaii called 'Baywatch Hawaii' for saving lives after a rescue of a family on a remote beach in which a little girl is put in a coma after being submerged.
During the first week of training for the new lifeguard team of Baywatch Hawaii, competition between Jessie and Kekoa, as well as Jason and J.D. threaten to turn the tryouts into an all-out war. Jason, at Kekoa's advice, visits an old Hawaiian native to look into his true Hawaiian roots, and Allie takes a job as a helicopter tour pilot to make some extra money for herself.
Dawn Masterson, a lifeguard from Florida and a travelling archaeologist, joins the team and proves almost irresistible to the male lifeguards while she squares off against Sean who tries to find her weakness, while also Dawn seeks her own personal agenda with J.D. whom she used to know.
Mitch takes Tanner on an overnight camping trip to a small island where a dream encounter with a ghostly Hawaiian drives Tanner to deal with his inner conflicts from his troubled life back in Los Angeles.
Sean and the rest of the team risk their lives when they help with the local Coast Guard in a daring rescue to save six kaiakers who have gotten stranded on Kauai's Pina Nova coast. After saving four of the kaiakers, including two in an enclosed lagoon, night falls and the search for the remaining two is called off.
The abrasive Sean tries to get the team, on a week-long holiday in Kauai, from giving into the island's sun-and-fun atmosphere and concentrate on a return to training.
After Jason risks his life in a rash attempt to save two scuba divers trapped on a reef, Sean threatens to throw Jason off the team if he doesn't change the way he thinks about the risks and lives of people in need of a rescue in which Jason is confined to a beach for the whole day to learn what the people that are there are confronted, with Sean keeping a close eye on him.
Mitch struggles to prevent Hobie from marrying his new girlfriend, Sarah, at a local hotel during a visit, while Mitch also deals with Sarah's overbearing and obnoxious parents seeking to create the perfect wedding.
Sean, Allie, J.D., Jason and the rest of the team race to help Jessie as she faces the challenge of her career when she rashly attempts to track down a pair of shark hunters who are decimating the animals in the Hawaiian area.
During a girls swim out in the ocean, Allie discovers a rare gold coin dating back to a ship that was lost in 1941 during World War II which allegedly contains un-circulated gold coins and rare artifacts somewhere off the Hawaiian coast.
Allie's relationship with Nick begins to heat up, especially after he suggests a commitment between them. Then things take a turn when Allie, Nick and the rest of the team must cooperate with the Coast Guard to rescue two people trapped on a disabled submarine 200 feet on the ocean floor.
A secret from Dawn's past could jeopardise her position on the team when she gets served with a civil suit from the spouse of a diseased lifeguard from when she was involved in a failed rescue while working as a lifeguard years ago in Florida with J.D.
After a rescue of a man who survived after more than 20 minutes underwater, Dawn and Sean are drawn to the strange and spiritual power of the mind over matter theory which she tries to prove the theory of the mind controlling the body after its other functions have shut down to sustain life.
Sean has his hands full in dealing with Jenna Avid, the new head of the Oahu North Shore lifeguards, who issues some stern recommendations to the team, which is overshadowed later that day when a group of nudist activists, lead by a certain Leesa Strickler, choose the beach near the Baywatch Hawaii headquarters as their place of protest against the establishment which Sean, Jason, Allie, and Dawn have also deal with the media circus that arrives too.
Sean faces a personal conflict where he tries to resist Kekola's flirting advances which leads her, Dawn and Allie to re-examine their own femininity in themselves.
Another long day begins with Sean, Jessie, and Kekola trying to save a woman trapped in an air pocket beneath a coral reef and trying to escape from the dangerous sulphur fumes within the cave. After a rescue of three skydivers whose parachutes open late, Dawn find a number of similarities between one named Jerome, and her ex boyfriend Ryan whom she discovers that they are both the same person.
Sean sends Jason to the big island of Hawaii to meets with Kulu Puno, an elderly Hawaiian and his beautiful young granddaughter where Jason is given a task of building an old fashion Hawaiian canoe as part of a path he must see to redeem himself from his arrogant, immature nature.
During a long day when Sean takes Jenna out on a Scarab motorboat when after a rescue of a injured young boy from a offshore reef, Sean reveals a secret to Jenna that could threaten his position when he tells her about his own son, that no one knows about, who drowned years ago which ruined his life and paved his way to becoming a lifeguard.
Jessie tries to overcome her physical condition, and Sean's objections, to compete in a Maui triathlon with Dawn as her personal coach while Allie suspects an agenda behind Dawn's motives to train Jessie.
Sean tries to keep his blossoming relationship with Jenna a secret to avoid upset and criticism from the rest of the team when he attends a lifeguard conference on Maui to speak about the dangers of drowning where Jenna, Allie, Kekoa, Dawn, and Jason are in attendance.
Mitch helps Jessie try to prevent her World War II veteran grandfather from committing suicide who was a survivor from the USS Utah at Pearl Harbour and who harbours a guilt over surviving when many of his friends didn't on December 7, 1941.
Mitch is asked by a government agent to investigate a certain Zack Martin, a former Navy SEAL who may be part of an environmental terrorist group called "Green Scorpion" who are planing to blow up an unknown target.
