Emma and Cleo are suspicious of Rikki when they see her apparently out on a date with Zane. After her friends pester her about it, Rikki finally confesses that she and Zane are going out, and Emma and Cleo, fearing that Rikki will tell Zane their secret, tell her to dump him. Rikki refuses, and she and the others fall out; but when Zane's father unveils plans to turn Mako Island into a holiday resort, and Zane fails to stand up to him, Rikki begins to wonder whether she made the wrong choice.

In Mako: Island of Secrets, the crystals are encrusted in the Moon Rings used by the mermaids and the Trident as the magic sources of these objects.Also, they no longer are attracted to each other through magnetism. It is possible that they were enchanted to resist its magnetic pull for specific purposes. A full moon, in conjunction with a rare planetary alignment, calls the girls to the moon pool at Mako Island where their powers are greatly augmented and strengthened. The second series revolves around the arrival of a new girl, Charlotte Watsford ( Brittany Byrnes), who moves into the area and develops an instant attraction to Lewis. After Charlotte sees a film of her grandmother Gracie as a mermaid she meets Max Hamilton ( Martin Vaughan) who was once romantically involved with Gracie. Happy to have met his lover's granddaughter, he tells her about the previous mermaids—Louise, Julia, and Gracie—and of Mako Island. Charlotte travels to the moon pool during a full moon and becomes the fourth mermaid in possession of all the girls' powers. Believing herself superior, she and the girls become sworn enemies. This conflict results in a confrontation during an especially powerful full moon, which ends with Charlotte being permanently stripped of her mermaid form and abilities. Cleo and Kim's father Don takes them to the beach to get to know his new girlfriend, Sam. But while Cleo is willing to accept her for her father's sake, Kim hates her from the start, but uses the situation to get expensive gifts out of her father as bribes for her approval, much to Cleo's disgust. But Sam and Don get the wrong idea when Cleo refuses to go swimming with Sam, and think that Cleo is the one who has a problem with her. Meanwhile, Bella applies for a job at the cafe, and Rikki is keen to give it to her... except Zane wants to give the job to Will's ambitious sister, Sophie.

With the school's end of year dance approaching, Emma takes up the stressful job of heading up the dance committee. But, while the tough task of organising the dance is bad enough on her nerves, she is also flattened by the news that Byron, who she was hoping would ask her to the dance, is already going with Ice Queen Miriam. Cleo is also disappointed that Lewis is too caught up in his experiments to ask her to the dance, and, rather than go alone, she is forced to ask Nate. The only upside is that Lewis, after days of research and testing, has come up with a formula to make the girls' skin waterproof, and they no longer have to worry about getting wet. But, as the wise Miss Chatham declares, science and magic cannot mix, and Lewis' formula gives the girls an allergic reaction where their skin turns red, and they are forced to flee the dance. Things turn out well in the end, however, as Cleo finally admits to Lewis how she feels about him, and they become a couple. Also, the crystals create a magnetic pull between each other and the Comet Eva that regularly pulls it to the Earth. Like the Moon Rings, and the Trident, the crystals' magic is likely finite, and needed to be replenished by being exposed to the moonlight from any suitable source.Lewis gets a job as a lab assistant for Dr. Linda Denman, a beautiful marine biologist, and secretly plans to use her equipment to try to find out more about the girls' mermaid transformation. But he instead ends up putting their secret in danger, when he leaves a DNA sample from Cleo behind in the lab, and Dr. Denman discovers it. The girls realise that they are really in trouble when Cleo sneaks into Dr. Denman's lab, and discovers a scientific article on Dr. Denman's laptop about her unusual cell sample. With Lewis refusing to believe that Dr. Denman stole the cell sample from him (partly because he has a crush on her), Emma, Rikki and Cleo's secret could be about to be exposed to the world. Cleo counts down the days to her sixteenth birthday, not with excitement, but with dread. Emma and Rikki can't understand Cleo's mood, until Lewis tells them about Cleo's father's embarrassing birthday parties. Meanwhile, Zane is determined to find the "sea monster" that saved him from drowning, and recruits Lewis to help him. But Lewis has promised the girls that he will keep Zane as far away from Mako Island and them as possible. After seeing the work done at the marine park by the charity Dolphin Rescue, Bella comes up with an idea to hold a fundraising event for them at the cafe, but is deflated when Sophie overhears, and steals her idea, presenting it to Rikki and Zane as her own. What is more, as Sophie is organising the event, she spitefully refuses to let Bella and the band perform. But she gets into trouble with Rikki and Zane, when all of the bands she has booked instead of Bella's pull out, after hearing that Sophie has tried to make Dolphin Rescue pay a fee for the concert. Sophie is fired from the cafe, and Bella and the band perform to save the night. Meanwhile, Cleo, Sam, and Kim have difficulties sharing the bathroom, until Sam realizes what Kim is up to and finds a way to repay her for Cleo after Kim gets her in trouble. Lewis and the girls enter a short film contest held at the JuiceNet cafe, but Lewis, last year's champion, is fresh out of ideas. Rikki and Cleo are roped into doing a film about Emma's mother, but Rikki, thinking that the film is boring, sneaks off to shoot her own film, featuring some impressive underwater footage of sharks. Meanwhile, Zane, ineligible to compete himself, as his father is on the judging panel, recruits Lewis to shoot a film of him windsurfing around Mako Island, recreating (and hopefully beating), his father's windsurfing record of several years before. But things don't go to plan, when Zane falls off his windsurfer, right in the middle of Mako Island's shark breeding ground. When Lewis tells Cleo not to experiment with the floating water they collected from Mako, she cannot resist, and sends Lewis off for a day of golfing with her father, so that he won't discover her. But when Rikki accidentally gets the water in Cleo's fish tank, her goldfish, Hector, becomes imprisoned in a bubble of floating water! The girls' attempts to free Hector result in him going down the drain, and they must use their mermaid abilities to retrieve him from the canal. Also, the girls try to keep Will, who is in the house while looking for Bella with whom he has to do a project for school, from seeing Hector. Meanwhile, somewhere on the golf course, Lewis is pretending to lose to Cleo's father at golf, so that he can get into his good books.