In the year 2301, Akari Mizunashi travels by spaceship from Tokyo on Manhome (formerly Earth) to Neo-Venezia on the planet Aqua (formerly Mars). Through emails to a friend, Akari writes of her trip to the watery planet, describing some of its history and development. Upon her arrival, she meets a Martian cat who becomes affectionate toward her. Akari and the cat wind up in the boat of the local postman, where she explains to him how she had been waiting for someone to pick her up and take her to Aria Company to begin her apprenticeship toward becoming an Undine, a gondolier who ferries sightseers around the city. When he asks her to demonstrate her rowing skills, she displays a natural talent honed from practicing alone with a virtual simulator. Later, she awakens in the boat and finds that she has reached Aria Company, where Alicia, the chief Undine, greets her and informs her that the cat she met earlier is actually the president and namesake of the company, and that he had been the one whom she had been expecting to pick her up.
NAVIGATION 02: THE GUIDE ON THE WATER
At the start of her first day, Akari awakens to find that President Aria has brought her the uniform that she'll be wearing. After breakfast, she demonstrates in uniform her rowing skills for Alicia, who praises her technique but informs her that she is actually rowing backwards. But when Akari tries rowing forward, she does not do as well and bumps into another gondola being rowed by Aika, an apprentice from Himeya, a sister company. While Alicia attends to some guests and Akari and Aika are distracted, President Aria jumps into Akari's gondola and is swept away by the current. The two girls pursue but are unable to catch up. It is Alicia in her own gondola who manages to rescue President Aria.
NAVIGATION 03: THE CITY SUBMERGED
Aqua Alta is a high tide that occurs annually, flooding the streets and shutting down most city functions, including gondola travel. So Alicia declares Aria Company closed for the duration of it and leaves for the day to attend a meeting. Akari discovers that President Aria's food has been ruined by the flood waters, so she sets out with him to buy some more. But a rain storm strands them at Himeya Company where they must spend the night with Aika and Hime, a female cat who is the company president and the love interest of President Aria.
NAVIGATION 04: THE KINGDOM OF CATS
Once a month, President Aria takes his own electric-powered gondola and disappears for the day. Alicia tells Akari that she believes he is attending an assembly of cats called by the King of cats, Cait Sith. Akari talks Aika into going with her to follow President Aria, and they both wind up getting lost in an old section of the city. President Aria shows up and stirs them in the right direction back to Aria Company. Later, he himself returns just in time for the evening meal.
NAVIGATION 05: THE HILL OF HOPE
Aika shows Akari that she now wears only one glove, indicating her graduation from apprentice, or Pair, to journeyman, or Single. She explains that, to become a full-fledged Undine, or Prima, one must be able to row with no gloves at all. Alicia later invites Akari on a picnic, and the two set out in Akari's gondola with the eager apprentice at the helm. They first pass through a narrow channel that proves difficult to navigate; then, in order to continue upstream, they must ride the aquatic elevator, a water lock that takes about 30 minutes to fill. Finally, they reach the Hill of Hope, a place dotted with several large windmills. Here, Alicia removes one of Akari's gloves and informs her that she has just passed her test to become a Single.