"Mizukano: Water Girls in Sparkle" centers on a group of high school girls who discover a hidden connection to a mystical underwater world. The protagonist, Aoi Mizukano, is an ordinary student with a deep fascination for the ocean. Her life takes an unexpected turn when she encounters a mysterious pendant that grants her the ability to transform into a "Water Guardian," a protector of the aquatic realm. Alongside her friends, Haruka, Sora, and Yuna, Aoi learns that their school sits atop an ancient gateway to an underwater civilization threatened by dark forces.

The narrative unfolds as the girls balance their daily lives with their newfound responsibilities as Water Guardians. Each girl possesses a unique elemental power tied to water, such as controlling tides, summoning rain, or manipulating ice. Together, they must defend the gateway from malevolent entities known as the Abyssal Shadows, which seek to corrupt both the underwater world and the surface. The story explores themes of friendship, environmental stewardship, and the balance between humanity and nature.

As the series progresses, the girls uncover the history of the underwater civilization, revealing its ties to their own lineage. They face increasingly complex challenges, including internal conflicts, moral dilemmas, and the growing threat of the Abyssal Shadows. The plot intertwines action-packed battles with moments of introspection, as the characters grapple with their dual identities and the weight of their responsibilities. The series concludes with a climactic confrontation that tests their unity and resolve, ultimately determining the fate of both worlds.