Akari Mizunashi continues her training to become a Prima Undine (a professional tour guide gondolier) along with her friends Aika and Alice in the peaceful city of Neo Venezia. Despite the fact that these three girls are from competing companies, they are constantly together, learning more about how to become better tour guides and more about the mysteries of Neo Venezia. As the group continues to meet interesting and unforgettable people through their daily routines, they will also come closer to the secrets that make the enigmatic and ever beautiful city of Neo Venezia so warm and alive. Welcome back to Neo Venezia: the city where miracles can be created by hand.

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.

There was a rumour among the young people in Harajuku, Tokyo. There is a place called Ura-Harajuku somewhere in Harajuku, and it seems that there is a shop run by a witch. The witch's name is Nina. A young witch with a chameleon and a pig fulfills the secret wishes of her guests. Her method is to invite her to a mysterious space and look into the "real feelings" deep inside her heart. Customers are sometimes excited, sometimes hurt, and make their own choices to fulfill their wishes.