Haruka Nanase has a love for water and a passion for swimming. In elementary school, he competed in and won a relay race with his three friends Rin Matsuoka, Nagisa Hazuki, and Makoto Tachibana. After claiming victory at the tournament, the four friends went their separate ways. Years later, they reunite as high school students; however, Rin couldn't care less about returning to the way things used to be. Not only does he attend a different school, but the sole thing important to him is proving that he is a better swimmer than Haruka. After the bitter reunion, Haruka, Nagisa, and Makoto decide to form the Iwatobi High School Swim Club, but they will need a fourth member if they hope to take part in the upcoming tournament. Enter Rei Ryuugazaki, a former member of the track team whom Nagisa recruits. As the time to compete draws near, the four develop a close bond while training intensely to come out on top and settle things between Haruka and Rin once and for all.

Even though it has been a year since the Iwatobi High School Swim Club has been created, new members have yet to join the club. Now that Haruka Nanase and Makoto Tachibana are senior students, along with their younger friends Nagisa Hazuki and Rei Ryuugazaki, they have to find a way to attract new members. If not, the club will be forced to close the following year due to a lack of membership. Meanwhile, with impending graduation, it is also time for the seniors to decide their plans for the future. Unlike their friend Rin Matsuoka, the new captain of Samezuka Academy Swim Club who is determined to fulfill his dream of being a professional swimmer, Haruka and Makoto are unsure about what career path they want to take. Further problems arise when an old friend of Rin's, Sousuke Yamazaki, comes to the city to study at Samezuka Academy; the recently scouted swimmer's arrival causes tension in the relationship among him, Rin, and Haruka.

With the seniors having graduated from high school, the determined swimmers eagerly take on their futures with a dream to fulfill. Now attending Hidaka University in Tokyo, Haruka Nanase unexpectedly runs into Shiina Asahi, an old teammate and friend from his middle school days. Consequently, the troubling memories regarding his middle school swim team resurface, as it was a time when Haruka's views on swimming became negative and led him to quit the team. Haruka later reconnects with his other middle school classmates; all except for Ikuya Kirishima, who still resents Haruka for quitting the team, resulting in its disbandment. Aware of the issues between them, Haruka resolves to improve his friendship with Ikuya. However, he quickly realizes that making amends with an old friend isn't his only obstacle. Facing the reality and challenges of encountering higher calibre swimmers, Haruka must work hard to establish himself if he dreams of competing on an international level.

Haruka Nanase has reconciled with his rival Rin Matsuoka, and they have re-established their friendship, determined to race each other again. Now Haruka, along with Makoto Tachibana, Rei Ryuugazaki, and Nagisa Hazuki, prepare for their upcoming tournaments, determined to compete wholeheartedly and achieve victory as a team. At Samezuka Academy, Rin resolves to do the same. Further, the seniors near graduation, and Rin has decided his future plans. However, Haruka and Makoto remain uncertain, and they begin to feel the pressure of having to choose their own paths.