Nagi no Asukara unfolds in a world where humanity was once divided by the sea. Long ago, all people lived beneath the water, but some chose life on the surface and permanently abandoned the ocean, losing the god-given protection called "Ena" that allows them to breathe below the waves. As the centuries passed, the divide between the sea village of Shioshishio and the people of the land only deepened, even though contact between the two worlds never fully disappeared.
When their school closes, Hikari Sakishima and Manaka Mukaido are forced to leave the sea and attend Mihama Middle School on the surface alongside their childhood friends Chisaki Hiradaira and Kaname Isaki. There they meet Tsumugu Kihara, a quiet classmate and fisherman who loves the sea, and their lives begin to shift in ways none of them can control. As old prejudice and discrimination collide with changing feelings within the group, their circle widens to include Miuna Shiodome and Sayu Hisanuma, while an approaching tempest threatens everyone living on the surface. Caught between land and sea, Hikari and his friends must find a way through a fragile world shaped by tradition, separation, and growing up.