Cleo and Rikki enter their final year of high school. They make friends with a new girl, Bella, and a new boy, Will. However, they encounter a new force on Mako Island that has the power to turn water against the girls.
With Will finding out about Mako Island, Bella tries to misdirect his search so that he will not discover the Moon Pool. However, Lewis and the girls find out that the Moon Pool is different.
At the marine park, Cleo seeks a job as a dolphin trainer. Meanwhile, until she and Bella reach an understanding, Rikki fires Nate's band, preventing them from playing in the cafe.
Cleo has to put off Lewis' romance plans in order to help Kim with her crazy love life. Meanwhile, Don meets up with a National Parks Manager, Samantha, and the two decide to date.
To get more interest in the cafe, Zane develops a dirt bike race. However, Rikki finds out that it is a scam. She and Bella decide to team up to teach him a lesson. Meanwhile, Lewis and Cleo find out something interesting about mixing the waters in the Moon Pool
Bella tries to get close to Will but when Bella goes to his place she sees him with another girl. Meanwhile Lewis tries to test the water from the moon pool but gets caught by his teacher.
Cleo's family and Sam go on a picnic to the beach, which leads to tension when Cleo refuses to go near the water. Kim abuses the fact that her father is happy in order to get lots of gifts. Will's sister Sophie competes with Bella to get the job Bella wanted at Rikki's Cafe.
During a full moon, the girls stay at Cleo's and Bella is attacked by the water creature. At the same time, Will decides to return to the moon pool after making the connection between his previous encounter with the moon pool waterfall and the timing of the full moon.
Cleo starts to experiment on the moon pool water without Lewis' knowledge, but things start going wrong when Cleo's fish Hector gets trapped in the bubble of floating water. Meanwhile, Lewis has to play golf with Cleo's father.
After Bella gives Will a shell-like fossil she found while swimming, Will becomes suspicious as the fossil is of a rare kind. Rikki realises how close Will is to finding out their mermaid secret and warns Bella to stay away from Will.
Bella helps Will with his free-diving training but when she realises he's more interested in her as a mermaid than a girl, she's hurt. Rikki and Cleo have to improvise when the cafe's first corporate function is actually a children‟s party.
Rikki receives counterfeit money at the cafe and is held captive by criminals on a boat. Bella and Cleo are forced to reveal the trio's secret to Will so they can rescue Rikki together.
Kim attempts to derail Don and Samantha's wedding. Lewis receives an opportunity to study in America. Cleo realises she's got to let Lewis live his own life and let him go overseas.
Will pushes himself too far when Zane challenges him to prove his skills as a free- diver. The girls discover a unique crystal in the rock from the Moon Pool.
Sophie uses Bella's idea for a fundraising concert and presents it as her own to Rikki to gain publicity for the cafe. Cleo's caught in the crossfire with Kim when Samantha moves in and puts her stamp on the Sertori home.
Rikki's frustrated by the water attacks and goes to Mako Island on a full moon to confront the strange force in the Moon Pool. With Cleo and Bella delayed, Will pursues her and discovers she's been affected by the experience.
Cleo's introduced to Ryan, a young geophysicist who's working for Samantha. Rikki doesn't react well to Cleo consulting Ryan about the Mako rock and a fracture begins to appear in the trio.
Rikki fears Ryan's explorations on Mako Island will uncover their secrets but Cleo and Bella discount her concern. She almost goes too far trying to stop Ryan from discovering the crystals in the Moon Pool.
Will competes in the Free-Diving Championships but afterward chooses to break from the sport and shrug off Sophie's influence on his life. Rikki sees Sophie kissing Zane at the event and breaks off their relationship.
Zane installs Sophie as head of staff at the cafe. Bella develops a sneezing allergy that also accidentally triggers her powers. Sophie seizes on the problem and looks to fire Bella and the band.
The girls discover the Mako crystals contain immense energy and need to mount a rescue mission when Zane jealously steals one in an effort to gain Rikki‟s attention.
The girls sit their final school exams and have to avoid a water attack in public when the full moon rises early. They confront the water force in the Moon Pool and are given a message about Mako Island.
Bella's eager to ask Will to the end of year party until she sees him asking Rikki. A big misunderstanding occurs which prompts Will to express his true feelings for Bella. Sophie tries to get Zane to change the name of the cafe.
Don gets a second job at the Marine Park on the Pirate ship and outshines Cleo, threatening the future of her Dolphin show. Bella and Will find difficulty trying to connect with each others' interests.
Cleo discovers a comet is causing fish to flee the waters around Mako Island. The girls find a way to restart the message in the Moon Pool and discover the comet will collide with earth. Sophie meets Ryan and with Zane's help they join forces to remove the crystals from the Moon Pool.
Sophie and Ryan damage the Moon Pool in their efforts to obtain the rare crystals. The girls improvise and use their own magic to prevent the impact of the comet and a planet wide catastrophe. Rikki, Cleo and Bella graduate with a surprise.
