On the planet Aqua lies the watery city of Neo Venezia, a tourist hub in which people travel around in gondolas. Professional gondoliers known as Undines are well-revered as they act as tour guides for the people. Akari Mizunashi is a gondolier in training and also an employee of Aria Company. She gets to meet all sorts of people as she takes them on the gondola rides, from friendly mentors to special individuals, all this admidst the beautiful scenic backdrop of the entire city.
During their first practice after Carnevale, Alice speculates that Akari and Aika will take the Prima exam soon, but Akari is uncertain as she doubts her own skills after watching Alicia. Alicia receives a package of jam from satisfied Carnevale customers and invites Akira, Athena, Aika, and Alice to tea to share it. In a flashback, Akari tells the others how Alicia impressed the customers (and Akari) by accurately predicting when snow would start falling. In flashbacks, Aika describes how Akira saved a dancing customer from falling out of the gondola, and Alice how Athena stopped a toddler's tantrum by making funny faces. The three trainees admit they have a long way to go as undines, and their mentors tell them they themselves have more to learn, saying that if you're ever satisfied with your performance, you will never improve—the best thing to do is cherish the fact that there's more to learn and have fun along the way. On the balcony afterward, the trainees recall that this last was Grandma Akino's advice, and from inside their mentors watch them and conclude that their students will be wonderful undines, like none seen before in Neo-Venezia.
An older woman, Amarantha, requests a tour from Akari, who stays up late planning her route. At next morning's practice, Aika suggests the commission is suspicious, and Alice speculates it's an inspector from the Gondola Association. When Amarantha arrives, she requests Akari show her the Neo-Venezia that only she can. Aika and Alice follow them secretly. Akari takes Amarantha to a spot where a statue appears to cradle the floating climate-control island, and the woman shows her an even better vantage where two statues seem to hold it up together. Throughout the tour, Amarantha is shown knowing more about the city than Akari, and when Akari ends it by taking her to an abandoned monastery garden that ran wild after the water rose, Amarantha has Akari go through a door that leads to another flooded courtyard covered by a wisteria in bloom. Akari is disappointed to learn that Amarantha already knew everything she's been shown, but Amarantha thanks her for a tour that showed the Neo-Venezia she loves. Aika and Alice are discovered, and Alicia tells the trainees that Amarantha likes to test Singles, and once tested herself, Akira, and Athena as Singles.
During a study session, Akari learns that the interior decor of Caffè Florian was transported entire from Venice, and mentions she's never been inside despite knowing the owner. They visit during a break, and spot a candy-seller's cart in the Piazza San Marco. When a boy trips and drops his candy, the seller gives him a replacement bottle, but Akari still feels sorry for the chocolates spilled on the ground. Inside the cafe, Akari is impressed by the art. Some time later, Akari sees the candy-seller looking at the renovations to the Ca' d'Oro, and is disappointed he hasn't been selling since that first day. One morning Akari meets him outside the Piazza cafe, where he begins selling again, and he thanks her for her chance remark about the spilled chocolate, which reminded him of how he once wanted to give his customers joy, and says that after wandering the city's sights he figured out better packaging for his sweets. He treats her to a latte, and Akari realizes that Caffè Florian's art contains their creators' feelings, just like his chocolates, and the latter bring just as much beauty to the Neo-Venezia.
To get more gondola practice while Alicia is busy, Akari works on the traghetto ferry for the first time. One of the three Singles she's teamed with, Atora, gives her a candy to calm her nerves and says she can observe from the shore for a while. Another, Anzu, is gloomy and Atora tells Akari it's because she recently failed the Prima exam yet again. Anzu says that while she's depressed at the moment, she hasn't given up, and Akari tells her she thinks Alicia hasn't tested her yet because of her own lack of skill. When Akari takes a turn rowing, the other three realize she's actually very good, capable of balancing the traghetto with its standing passengers on her own. At the end of the day, they praise her rowing ability and tell her she'll be a Prima soon. Atora tells Anzu they all should be Primas and criticizes their examiner at Orange Planet as too strict. After talking about how discouraging it was to fail the exam six months ago, with the encouragement of the others, Atora agrees to take the exam again.
During practice, Aika sees Akari chat easily with many acquaintances and Alice row with her exceptional skill, then watches Athena's singing make passers-by stop to listen and Alicia gracefully catch a hat blown by the wind. Alice calls their mentors' talents the sorts one can only be born with, which disturbs Aika. While helping Akira clean her room, Aika finds a photo of Akira as a Single with Athena and Alicia as Primas, and demands to know how she could smile despite being promoted last. Akira says that of course it was hard having such talented friends, and tells a story, shown in a flashback: After Athena's promotion, while worrying about being left behind, Akira unsuccessfully searches a clover bed for a four-leaf clover with the help a child who turns out to be Aika. The child then says if there's nothing there, you have to make up for it your own way and adds a rose petal to a three-leaf clover to make four leaves, and Akira concludes she has to make up for her talent through hard work. In the present, Akira gives Aika the clover keepsake as a good-luck charm for becoming a Prima, and Aika returns to practice with renewed determination.
When Aika berates Akari for not taking practice seriously, saying at this rate Alicia will scold her, Akari says Alicia has never scolded her, nor even gotten angry. This startles Alice and to learn why she begins stalking Alicia—inventing lame excuses when she gets caught—but can't figure it out. After a week, Alice meets Alicia at a cafe and at Alicia's prompting asks her directly. In response, Alicia asks President Aria to give a candy to a girl at another table, and they watch him get distracted by sparrows and the waiter before finally succeeding, for which Alicia praises him. She then has him deliver another candy to another customer and praises him for being even faster. Alicia explains that criticizing people makes them fear making mistakes, and so she prefers encouragement over correction. She then says that if President Aria had continued making mistakes, she would have reflected on how she was instructing him wrong, and that teaching and being taught are very much alike.
On the anniversary of Aria Company's founding, Akari and Alicia visit one of its former Primas, Anna, on Neo-Burano Island. Alicia tells Akari how Anna fell in love with a fisherman named Alberto who was visiting the city. Anna admits she was lonely, the first few years on an island where she knew no one, but says eventually she met other women through lace-making. Grandma Akino arrives as a surprise visitor for dinner. After dinner, Grandma tells the story, shown in a flashback, of when she, then Himeya Company's undisputed top Prima for 14 years, first meets President Aria on a seawall staring out at the water. She tries talking to him several times, but doesn't find out what he is waiting for. On a rainy night, she finds him still sitting and shelters him with her umbrella through the night, and as the sun rises she realizes it had been the first time in a while she had spent time just sitting. After this, she founds Aria Company with him, in order to continue seeing the world through his eyes. In the present, Grandma and Alicia tell Akari they look forward to seeing "her" Aria Company starting soon.
Alice tells Akari and Aika she won't be at practice tomorrow because she invited Athena on a picnic. That night Alice makes elaborate preparations, but in the morning Athena leaves for work at dawn without speaking with her. When Athena finally returns, in her disappointment Alice snaps at her then accidentally rips the invitation, and in the ensuing fuss Athena slips and falls. Alice calls Akari and Alicia for help in a panic, and when they arrive, they learn that Athena has amnesia from hitting her head and cannot remember anyone around her. As they talk, her memories slowly come back, starting with President Aria and Alicia. To further jog her memories, they take her to familiar places, and by the end of the day she remembers everyone but Alice. When Athena asks what she was to Alice, the latter breaks down in tears, and Alicia makes Athena reveal she'd been faking amnesia to find out how Alice feels about her.
When Alice graduates from middle school, she's happy that she can now spend more time practicing with Aika and Akari. Athena invites Alice on a picnic on a canal through the countryside outside Neo-Venezia, and has Alice treat her as a customer. Athena praises Alice's skills as an undine, and Alice responds that she is training with an excellent mentor. As they pass through a lock, Alice is startled when an undine wishes her good luck. While waiting for the lock to fill, Alice tells Athena that she's confident in all of her undine skills except singing canzone, and Athena tells her conveying a love for singing is more important than any technical skill. When they reach the Hill of Hope, the destination of the Single promotion exam, Akari, Aika, the owners of Orange Planet, and a representative from the Gondola Association are waiting for them. After an exam on canzone, Athena takes off both of Alice's gloves, promoting her straight from Pair to Prima (the first undine ever to do so), and gives her the title Orange Princess.
Akari and Aika secretly observe Alice during her first day as a Prima, and when Alice asks how she was, Aika says she looked as stiff as a toy robot. To cheer Alice up, Akari invites her over for autumn moon-gazing. That night, Akari introduces her friends to Japanese Tsukimi customs, and Alice thanks her for helping her relax. When Al runs late, Alice teases Aika about inviting him, and Aika goes off flustered to find him. After they meet, Aika falls into a dry well, and when Al tries to pull her up he is pulled down instead, trapping them both. They are found by Maa, whom they send back to Alice for help. While waiting for rescue, they talk about Aqua's two moons, gravitation, and attraction, and it becomes apparent they are both attracted to each other. Akari and Alice eventually rescue them, and as they walk back to Aria Company, Al takes Aika's hand.
Two weeks after Alice's promotion to Prima, Akira hears some Himeya Singles gossip about how Aika, the heir to the company, is handling "losing" to a competitor. Akira worries over whether Aika is holding up, but has difficulty talking about it with her until Aika mentions she was present at Alice's promotion. Aika assures Akira she's been motivated by the competition and asks to be trained hard. Akira sets the date for Aika's Prima exam in a month, and says she won't forgive her if she, as the company's future queen, fails. Meanwhile, Alice is settling into her working life as an undine, but has little free time. She realizes it's been several days since she last saw Akari and Aika, at the moon-gazing, but can think of no excuse to call her friends, even though she misses them and is lonely. When Akari and Aika pay a surprise visit with a pizza, Akari tells Alice that being a friend is reason enough.
Akari tells Aika that practice has gotten lonely without Alice, and Aika apologizes that she can't practice either anymore: she's been promoted to Prima, with the title Rosen Queen, and will be managing a new Himeya Company branch office. When Akari tells Alicia, she wonders why Aika cried over this, and in response Alicia sets Akari's Prima exam for the next day. That night, Akari is too nervous to sleep and practices rowing until very late. In the morning it's raining, but Akari asks that the exam not be postponed, and by afternoon it has cleared enough to hold it. As Akari guides Alicia through the city, a number of friends greet her, and Akatsuki and Woody cheer her on from the Rialto Bridge. Alicia directs Akari down a very narrow, difficult channel, which she successfully negotiates, then gives Akari the choice of their final destination, which will determine what kind of Prima she'll be. Akari takes her to Aria Company, where Alicia thanks Akari for coming into her life and takes off Akari's glove, promoting her to Prima with the title Aquamarine, then says she has something important to tell her.
The next morning, Aika, Alice, and Akatsuki demand to know whether the news about Alicia is true, and Akari says yes, Alicia is retiring to get married and work for the Gondola Association. Alicia had delayed this until Akari became a Prima, and Akari blames herself for not becoming more reliable before now. Aika and Alice worry about Akari, but she says she'll be fine. The next several days are busy, as Alicia hands the running of Aria Company over to Akari. When Akari eventually breaks down crying, Alicia admits that Akari has long had the skills to be a Prima but she'd delayed the exam because she didn't want to leave Akari. Mr. Mailman, now retired himself, hires Akari for a tour, during which he offers to refer customers to her. At Alicia's retirement ceremony, all the undines of the city participate. The following morning, Akari sees Aria Company filled with memories of Alicia and her friends, then opens the reception-area shutter to let in her new beginning. In an afterword, Akari tells Ai what happens to the other characters—including Athena becoming an opera singer, leaving Akira the undisputed top Prima—ending with Ai's first morning as a new Pair for Aria Company.