With Cleo's parents now divorced, Cleo is ordered by her father to take more care of Kim, starting with taking her to a concert. But on the night, Cleo, Rikki and Emma all accidentally see the full moon, and take off to Mako Island, with Lewis in hot pursuit. Once there, the girls undergo another magical transformation in the Moon Pool, as a rare planetary alignment intensifies the power of the full moon – Emma's power is enhanced so that she can produce snow and frost, Rikki can conjure lightning, and Cleo can now control wind as well as water. After the moonstruck girls nearly harm Lewis, they realise that they must work to control their new powers, before anyone else gets hurt.
A new girl, Charlotte Watsford, moves to the Gold Coast, and it is evident that she is developing a crush on Cleo's boyfriend, Lewis. But Charlotte may soon have her chance, as Cleo is getting fed up with Lewis' constant, smothering concern for her, and is considering breaking up with him. Meanwhile, the girls are still trying to learn how to control their powers, and Emma in particular is put to the test when she sees Elliot being bullied by a member of his soccer team. Furious when she sees the boy (Nate's little brother), shove Elliot in the middle of a game, Emma then executes total control of her newfound powers... by making the boy slip on a sheet of ice. But elsewhere, Cleo makes the tough decision to break up with Lewis.
Rikki is bothered by Zane's reappearance on the Gold Coast, as she realises she still likes him. With Zane thinking that Rikki gave up her mermaid powers at the lunar eclipse during the war with Dr. Denman, can she manage to keep her secret from him for a second time? Meanwhile, Cleo grows jealous when she sees that Lewis and Charlotte are becoming close friends, and, in a mad rage, she steals Charlotte's diary... and discovers that she apparently already has a boyfriend named RJ. The episode ends with Zane rediscovering that Rikki is a mermaid, when Nate blasts her with water, but he promises not to tell anyone, and they rekindle their relationship. Cleo ends up embarrassing herself when she confronts Charlotte about her secret other boyfriend, and learns that the dates in the diary are meetings for Charlotte's theatre group (RJ stands for Romeo and Juliet).
When Emma's parents head off to a crystal-wear convention, she is left in charge of the house, and invites Cleo to stay... but instead ends up with the messy and rebellious Rikki. However, when Rikki criticises Emma for being a control-freak, Emma sets out to prove that she can have fun too, and throws a wild party at her house. But she starts to regret her decision when the party gets out of hand. Meanwhile, Nate convinces Lewis that Cleo broke up with him because he wasn't manly enough, and offers to teach him judo. But the lessons are actually a ploy to keep Lewis away from Cleo, so that Nate can flirt with her.
Emma convinces Wilfred to shoot a TV commercial for the steadily failing JuiceNet cafe, but is taken aback when he asks her to star in it. Meanwhile, Lewis digs up an old book on mermaid magic, and with it, an alleged wish-granting potion. He and the girls brew up the potion in a storage room at the JuiceNet, but when it apparently doesn't work, a smug Rikki overheats the potion, causing it to grow into a foul fungus that begins to engulf the cafe. However, when Cleo takes home an untouched sample of the potion in order to make her father wish her mother return, she discovers that it does indeed work, but only when it is used by a mermaid.
Cleo and Kim are concerned when it seems that their father has found a new girlfriend. With no desire for a step-mother, the girls are horrified when their father invites the woman over for dinner; but Cleo is even more horrified to discover that she is Charlotte's mother! Feeling that desperate times call for desperate measures, Cleo invites Rikki and Emma round, and persuades them to use their powers to ruin her father's dinner. Only afterwards do the girls realise their mistake; Charlotte's mother was a business associate of Cleo's father, interested in buying some of his catch.
Cleo is fired from her job at the marine park for feeding Ronnie the dolphin the wrong food, but Emma and Rikki tell her not to worry, and that her boss will soon call her back. Unfortunately, Lewis, needing the money for a new computer, unknowingly takes Cleo's job, and she vows never to speak to him again. In an attempt to get Cleo her job back, Emma and Rikki use their powers to make Lewis' job ten times harder, but he soon finds them out, and sends them off. But, on their way out, the girls leave the marine park's underwater gate open, and Ronnie the dolphin escapes. When Lewis gets the blame, and his boss threatens to have him arrested, Emma and Rikki are forced to confess to Cleo, and the three of them search the ocean for Ronnie.
While dirt biking through a caravan park, Zane and Nate spot a rundown Harley-Davidson motorcycle, and Nate steals the badge. A guilty Zane, however, tries to return the badge, but is caught by the owner, who thinks he is the thief. Zane has an argument with the man, and insults him... not realising that he is girlfriend Rikki's father, and that the caravan park is where Rikki lives; but she has been too embarrassed to admit it. When Zane finds out, he tells Rikki that he doesn't care where she comes from or how much money she has, but her father doesn't approve of Zane, and keeps them apart. Meanwhile, Cleo begins to suspect that Charlotte and Lewis are secretly going out.
When Emma's mother makes her take her brother Elliot for riding lessons, she ends up getting into a competitive conflict with the riding instructor, Ash (who Rikki and Cleo are convinced she has a crush on). However, Emma's stubbornness towards Ash lands her in trouble, when she ignores a warning from him, and accidentally lets his horse, Rebel, eat some poisonous weeds. Meanwhile, Lewis wins an award for young inventors, and asks Cleo to accompany him to the awards ceremony, but she declines, saying that they are just friends now. Lewis instead decides to take Charlotte as his date, but then Cleo changes her mind, and accepts Lewis' invitation, not realising that Charlotte is going in her place.
Cleo is devastated when she fails a biology exam, and realises that it was all because she did not have Lewis to tutor her. Cleo's father then schedules Cleo a re-sit for the exam, and also finds her a new tutor... Charlotte. Determined to keep Cleo and Lewis apart, Charlotte sets Cleo a whole weekend of studying, and then takes Lewis to paint with her... on Mako Island. The girls try to stop Lewis from taking her there, but he refuses, thinking they are being paranoid. Cleo sneaks off from studying to go with Emma and Rikki to Mako, and try to keep Charlotte from discovering too much. But she ends up with her heart broken when she falls into a stream, and looks up to see Lewis kissing Charlotte (not realising that he only did it to stop Charlotte from seeing her as a mermaid).
Zane comes to Rikki with an offer to find a priceless Tibetan statue lost at the bottom of the ocean. The owners of the statue are offering a large reward for its return, but Rikki refuses, thinking that Zane is being greedy. But then she discovers that her father is in serious financial trouble, and when he tells her that they might have to leave the Gold Coast, Rikki agrees to find the statue with Zane, and persuades the others to help (without telling them that there is a reward involved). But when Emma and Cleo discover that the recovery of the statue was all about making money, they take off, leaving Rikki and Zane to find the statue on their own. Rikki overworks herself, and ends up being struck on the head by the statue crate, and is knocked unconscious. Emma and Cleo rush back to help, but Lewis is held back by Charlotte, who switches his phone off to ensure that no one interrupts their time together.
While out swimming, Emma collects a beautiful piece of coral for Cleo's new fish tank, but accidentally cuts herself on it. Soon after the coral is placed in the tank, however, Cleo's goldfish, Hector, starts behaving very strangely, and his scales begin to turn white. Stranger still, Emma seems to be suffering from the same illness, as she begins ravenously devouring fish, and her mermaid scales also turn white. Cleo and the others soon make the connection between Emma and Hector and the piece of coral (which turns out to be toxic), and Lewis takes Hector to the marine park to get an antidote (blowing off a date with Charlotte, who is convinced that Cleo wants to ruin her and Lewis' date). But things get complicated when an eerily changed Emma disappears into the pools of the marine park. Even worse, Emma sneaks to her house and eats the lobster while her parents are celebrating their wedding anniversary. However, her parents hear her inside, forcing the girls and Lewis to try to find a cure before Emma's parents discover the situation.
When Cleo's father revives the tradition of the Sertori family camping trip, two problems arise. Firstly, the trip is on Mako Island; secondly, it is a full moon. Emma, Rikki and Lewis tag along to help Cleo, and Charlotte annoyingly follows Lewis. Once on the island, the girls try to scare the campers off of it by telling Kim and Charlotte stories of monsters, and using their powers to freak them out. But when a nervous Kim climbs into the moonlight-proof tent Lewis has constructed for the girls, Cleo glimpses the full moon's reflection outside, and wanders off. When Emma and Rikki discover that Cleo is missing, they decide to face the power of the moon, and go out looking for her. Meanwhile, a moonstruck Cleo bumps into Charlotte out walking, who torments her, thinking that she is jealous of her new relationship with Lewis. But when Emma and Rikki (now also under the full moon's spell), see this, they frighten Charlotte away with their powers. Unfortunately, Charlotte runs straight into the cave where the moon pool is... just as the full moon passes over it. She sees the full moon's strange effect on the pool and is intrigued, but luckily Emma is able to stop her from touching the water by freezing the moon pool's surface, preventing Charlotte from becoming a mermaid.
Cleo begins to realise that she misses spending time with Lewis, and asks her friends for advice. Rikki tells Cleo to re-establish her friendship with him, and use her unique mermaid abilities to her advantage – after all, Charlotte is just an ordinary girl, but Cleo is not. But Charlotte soon realises what Cleo is doing, and uses her bond with Lewis to make her rival jealous. Meanwhile, Wilfred leaves the Gold Coast, and Emma thinks that he has left the JuiceNet cafe to her, until the new manager shows up... and it is Ash, the cute riding instructor. Ash makes several quick changes to the cafe, which annoys Emma. But just as Emma is starting to accept Ash, some food gets stored in the wrong place and spoiled, and Ash, believing that it must have been Emma because she was the only one protesting about the changes, fires her. But he later finds out that it was another member of staff who simply got confused because of the quick changes, and gives Emma her job back. He also asks her out on a date which she accepts.
Zane reads a myth about mermaids being attracted to ambergris (a substance found in whale droppings), and purchases a bottle of it from the internet. Lewis is not too keen on the idea (even though he realise it could be a chance to get back with Cleo), but he offers to look at the ambergris with Zane. The two are disgusted by the liquid's foul smell, and abandon the bottle on a table outside the JuiceNet cafe... where it is unfortunately found by the odious Nate, who apparently likes the smell, and sprays some on himself. But while everyone else retreats from Nate's smell, Emma, Rikki and Cleo seem drawn to him, and it doesn't take Lewis and Zane long to realise that Nate's popularity with the girls is due to the ambergris. Under its influence, the girls travel down to the beach with Nate, putting their secret in danger.
Lewis is being troubled by recurring nightmares of Cleo being exposed as a mermaid, and it is clear that he still has feelings for her. Meanwhile, Elliot surprises everyone by asking Kim out on a date, and Lewis and Cleo act as chaperones when they go to the marine park. However, Lewis' nightmare comes true when Cleo falls into the water, and someone spots her. Elsewhere, Emma grows suspicious when she discovers that Rikki has been having secret meetings with Ash... but it turns out the two of them were only planning to give her an award.
Unable to convince Emma to tell Ash the truth about herself, Rikki and Cleo encourage Ash to make a bold, romantic gesture to her. But he musters his courage at exactly the wrong time, when he cooks Emma a surprise dinner at her home on the night of a full moon. By leaving the front door open, he doesn't realise the chaos he is about to cause, when Cleo accidentally looks up at the moon. The mischievous, moonstruck Cleo then forces Rikki to see the full moon, and the two of them plot to get Emma wet, so that Ash can see her in mermaid form.
With the arrival of the girls' one year anniversary as mermaids, Cleo organises a party at Mako Island to celebrate. But when Zane accidentally spills some drinks on Emma at the cafe, he is forced to have an argument with Ash to stop him from seeing her as a mermaid. Overhearing Zane calling her a ‘clumsy waitress', Emma doesn't realise he is only trying to help her, and gives him the cold shoulder. This leads to Emma and Zane's girlfriend Rikki becoming enemies, and it looks like there will be no party at Mako Island, which upsets Cleo. Meanwhile, Lewis feels guilty when he realises he hasn't been spending much time with Charlotte.
While doing some research on Mako Island, Lewis uncovers the work of Max Hamilton, who, fifty years before, was also investigating the place. Realising that his findings could be the key to finding out more about the Moon Pool and the girls' transformation, Lewis tries to befriend the old man, but finds him unwilling to talk... until, that is, he sees Cleo talking to Lewis, and recognises the locket around her neck. Max follows Lewis and Cleo to Mako Island, splashes some water on Cleo, and discovers that she is a mermaid as well. He is not shocked, however, because Max was a friend of Miss Chatham's when she was a mermaid along with Gracie and Julia Dove in the 1950s, and was romantically involved with Gracie. Max promises to keep Cleo's secret, and hands his research on Mako Island to Lewis.
Sifting through Max's research on Mako Island, the girls discover an old reel of film, and a photograph of his beloved Gracie. But elsewhere, Charlotte wants answers as to why Lewis is spending so much of his time with Cleo, Emma and Rikki, and storms over to Cleo's house. Whilst there, she sees the photo of Gracie in amongst Max's papers, and the girls are all stunned when Charlotte reveals that she is Gracie's granddaughter. Lewis is then given the task of finding out just how much Charlotte knows about her grandmother, but his questions only make her more suspicious, and, thinking that Lewis and the girls are hiding something from her, she goes back to Cleo's house, and steals the old reel of film in amongst the research. After getting the film transferred on to a DVD, Charlotte watches it, and finds that it is a home movie of her grandmother, Gracie, as a mermaid. Meanwhile, Ash makes a well-intentioned attempt to help Emma overcome her apparent fear of water, which leads to him almost discovering her secret.
Charlotte is determined to find out whether or not her grandmother was truly a mermaid, and follows Lewis to Max when he goes to give the research back. Max is delighted to meet the granddaughter of his beloved Gracie, and, not realising that Charlotte is a threat to Emma, Rikki and Cleo, tells her everything. With the girls unaware that Charlotte now knows about them, and also preoccupied with the arrival of the full moon, they are unable to stop her from travelling back to Mako Island and diving into the moon pool just as the full moon passes. The next day, she tells Lewis that she has become a mermaid.
Lewis tells the girls that Charlotte is a mermaid. Although they are unhappy that Charlotte has become the fourth mermaid of Mako Island, they decide to welcome her into their group and befriend her. The perfect opportunity comes when the four of them are placed on the school's beach volleyball team to stop them from failing gym class (as they have been avoiding swimming lessons). But, although the girls do form a bond, Emma, Rikki and Cleo still have reservations about Charlotte, when it is revealed that she possesses all three of their mermaid powers, and declares herself a "super mermaid".
When the girls offer to help Charlotte learn how to control her new-found powers, she rejects them, thinking that they are trying to cut her off from her full potential. Charlotte's powers soon go to her head, as she declares herself the only "real" mermaid, and recklessly uses her powers in public. After almost killing Ronnie the dolphin in a fit of panic, she then tries to get revenge on Nate when he attacks Lewis, and it takes all the girls' effort to stop her. Will Charlotte's lack of control mean the exposure of the mermaids' secret?
Charlotte takes control of the planning for Lewis' birthday party, and refuses to let any of the other girls help. Rikki, fed up with Charlotte's intrusion into what was once their close-knit group, decides to exclude herself, and leaves to spend more time with Zane. Meanwhile, at the boring birthday party that Charlotte has organised for Lewis, Charlotte jealously locks Cleo and Emma in a flooded storage room, where they are left trapped as mermaids. Their secret is threatened when Ash hears them in the storage room and tries to unlock the door, only for Zane and Rikki to arrive in time to help. Zane leads Ash away whilst Rikki uses her powers to dry the girls. Realising what Charlotte has done, the girls then organise a party boat to come and take Lewis from Charlotte's terrible party, and then tell Charlotte that she is not one of them any more.
Charlotte's short-lived friendship with Emma, Rikki and Cleo is over, and she forbids Lewis to talk to them. When Cleo shows concern for him, Charlotte lies to her, saying that Lewis willingly gives Cleo the cold shoulder because he doesn't care about her any more. A fight leads to Charlotte taking Cleo's locket, and when Lewis does nothing (believing that Cleo gave the locket to Charlotte, because it was her grandmother's), an upset Cleo is convinced that Lewis is on Charlotte's side, and leaves a phone message for him (which he doesn't hear, as Charlotte has stolen his phone), about how he has abandoned her and wants nothing to do with her, before running away from home. When Lewis eventually hears Cleo's message, he breaks up with the venomous Charlotte, and races after Cleo. Meanwhile, Cleo is being hunted by a pack of sharks, who can sense that she is weak. Lewis arrives just in time to save her, and the two of them get back together.
A rare full moon with the power to strip away the girls' powers permanently is approaching. The girls attempt to forewarn Charlotte, but Charlotte instead uses her powers against them out of spite. She releases her hold on them once Ash comes out; Emma attempts to make Ash forget what he saw, but not giving up, he visits her that night to try to get an explanation. Charlotte, still bitter, controls the water in Emma's house from the outside, and the girls cannot fight back unless they end up revealing their secret to Ash. When Cleo follows Lewis and Charlotte to Mako Island, Rikki and Emma join her as well. Cleo, Rikki and Emma have a power battle with Charlotte, in which Charlotte loses both the battle and her powers. The following morning, Lewis retrieves the locket from Charlotte, Emma tells her secret to Ash, and the season closes with the girls running into the ocean while their boyfriends look on.