"A Lull in the Sea" is set in a world where humans once lived beneath the sea but later migrated to the surface, leaving behind a small group that chose to remain in the underwater village of Shioshishio. The story explores the cultural and emotional divide between the sea-dwelling "Sea People" and the land-dwelling "Land People." The narrative begins when the middle school in Shioshishio closes, forcing four childhood friends—Hikari Sakishima, Manaka Mukaido, Chisaki Hiradaira, and Kaname Isaki—to attend school on the surface. Their lives intertwine with Tsumugu Kihara, a surface-dwelling boy, and Miuna Shiodome, a younger girl who becomes deeply connected to their world.

Hikari, the protagonist, is impulsive and protective, often acting as the group's emotional anchor. Manaka, cheerful yet insecure, struggles with her feelings for Hikari and her growing connection to Tsumugu. Chisaki harbors unspoken affection for Hikari, while Kaname quietly supports the group, masking his own feelings for Chisaki. Tsumugu, a calm and observant surface dweller, bridges the gap between the two worlds, fostering understanding and conflict alike. Miuna, initially an outsider, becomes pivotal as the story progresses, her bond with Hikari deepening through shared experiences and loss.

The plot delves into themes of identity, belonging, and the tension between tradition and change. A key element is the "Ofunehiki," a ritual that symbolizes the connection between the sea and land, which becomes a focal point for both conflict and resolution. As the characters navigate their relationships, they face challenges such as prejudice, environmental threats, and the consequences of their ancestors' choices. The sea itself is a living entity, with the Sea God playing a central role in the narrative, particularly when Manaka loses her "Ena," the ability to breathe underwater, after an encounter with the deity.

The story escalates when the Sea God's power begins to wane, threatening the existence of Shioshishio. The characters must confront their fears and desires, making sacrifices to restore balance between the sea and land. Manaka's disappearance and subsequent return, altered by her time with the Sea God, further complicate the emotional dynamics. Miuna's journey, marked by her determination to protect those she loves, becomes a driving force in the latter half of the series.

"A Lull in the Sea" balances personal drama with broader societal themes, weaving a tale of love, loss, and reconciliation. The characters' growth is tied to their ability to bridge the divide between their worlds, ultimately finding common ground despite their differences. The narrative concludes with a sense of hope, as the characters forge new connections and honor the legacy of their shared history.