"Kandagawa Jet Girls" is set in a futuristic world where jet ski racing, known as "Jet Racing," has become a popular competitive sport. The sport involves teams of two: a "Rider," who pilots the jet ski, and a "Shooter," who uses water-based weapons to disrupt opponents and protect their own team. The story centers on Rin Namiki, a skilled Rider who moves to Kandagawa City to pursue her dream of becoming a top Jet Racer. Rin's mother was a legendary Rider, and Rin aspires to follow in her footsteps.

Upon arriving in Kandagawa City, Rin meets Misa Aoi, a talented but inexperienced Shooter. The two form a team, with Rin as the Rider and Misa as the Shooter, and begin competing in Jet Racing tournaments. Their partnership is initially rocky due to their contrasting personalities and lack of coordination, but they gradually develop a strong bond and improve their teamwork. The series follows their journey as they face various rival teams, each with unique skills and strategies, while striving to climb the ranks of the Jet Racing world.

The narrative explores themes of friendship, perseverance, and teamwork, as Rin and Misa navigate the challenges of competitive racing. Along the way, they encounter other teams, such as the confident and experienced duo of Jenna Morrison and Emma Green, and the mysterious and skilled pair of Kaguya Jinguji and Pan Ziyu. These rivalries push Rin and Misa to refine their abilities and deepen their understanding of the sport.

As the story progresses, Rin and Misa uncover secrets about the history of Jet Racing and its connection to Rin's family. The series balances action-packed racing sequences with character-driven moments, highlighting the growth of the protagonists and their relationships with other characters. The competitive nature of Jet Racing serves as a backdrop for the personal journeys of the racers, emphasizing the importance of trust and determination in achieving their goals.