Aspiring Orange Company Undine Anya Dostoyevskaya feels dejected upon learning that her gondolier mentor, Alice Carroll, is not spending much time with her own mentor, Athena Glory. Athena—the Undine-turned-opera singer—has been attempting to arrange a meeting with Alice, but the latter seems to be avoiding her for unknown reasons. To try and resolve this predicament, Anya calls upon her fellow Undines Ai Aino and Azusa B. McLaren. As the trio works to bring Alice and Athena together, Anya gains a deeper insight into her seniors' feelings, which might just be the key to untangling the uncertainties between them.

Akari Mizunashi dreams of life after attaining her goal of becoming a Prima Undine, but upon waking realizes that she might not actually have the confidence to run Aria Company on her own. Wary of the future, she seeks advice from her mentor Alicia Florence—one of the three great Water Fairies of Neo-Venezia. Much to Akari's surprise, Alicia reveals her own struggles of the past, but also shares the steps she took in overcoming her self-doubt of running the company and taking on an apprentice. Finding solace in her teacher's words, Akari prepares to embrace whatever trials she must overcome on her path toward achieving her dreams.

In the 24th century on the planet Aqua, three girls—Akari Mizunashi, Alice Carroll, and Aika S. Granzchesta—continue to work hard toward achieving their goal of becoming Prima Undines: professional tour guide gondoliers. Luckily, the girls have the guidance of the three best Prima Undines in Neo-Venezia—Alicia Florence, Athena Glory, and Akira E. Ferrari—who are known as the Water Fairies in honor of their skill. With their help, the young apprentices train hard and work to overcome any situations that they find themselves in. Aria The Origination follows the hardships and daily lives of these three young girls, who are doing their best to improve as tour gondoliers in Neo-Venezia, a terraformed replica of Venice.

Drift peacefully into Neo Venezia, a city on the planet Aqua (formerly known as Mars). By the 24th century, humans have found a way to colonize the previously uninhabitable planet. As futuristic as that sounds, Neo Venezia is still teeming with rustic beauty; gondolas on wide canals and waterways are the main mode of transportation. The city itself is a faithful replication of Manhome's (the planet formerly known as Earth) Venice. To make sure that residents and tourists alike get the most from Neo Venezia's many wonders, companies offering guided tours via gondola were formed, one of which is named Aria Company. This is the workplace of Akari Mizunashi, a free spirited teenager from Manhome who is now a novice Undine (the title given to tour guides). Join Akari as she becomes intimately acquainted with other Undine, tourists, Neo Venezia's residents, and even the city itself, learning many valuable life lessons along the way, such as the wonderful truth that there are such things as manmade miracles.