Set in the not-so-distant future, Atlantia is an underwater city populated with people who had to flee when the surface of the earth became too polluted to sustain healthy life. Some people still had to remain Above to farm the land and extract resources, but many lucky people went Below to Atlantia.
Years after this Divide, the young people of Atlantia must make a choice when they reach the age of sixteen - stay Below or go Above. Young Rio Conwy has always wanted to go Above, but her twin sister Bay has made her promise to remain Below, a promise that is especially poignant given the recent (and mysterious) death of their mother Oceana. During the ceremony, Rio is stunned when Bay decides to go above.
Rio is desperate to see her sister again, or at least to find an explanation for her sudden departure. Bay was also one of the only people who knew Rio's great secret - she is a siren, one of the miraculous creatures that appeared not long after the founding of Atlantia, who holds the power to influence people with her words. Her mother Oceana made her hide her abilities so that she would not be taken away by the Council to be raised with other sirens in the service of the state.
One day in the temple, Rio encounters True Beck, a boy her own age whose best friend Fen Cardiff also mysteriously departed for the Above. The two decide to figure out a way to get to the Above, and gradually the two fall in love.
Rio's attempts to make her way to the Above (a feat that no person has accomplished on her own before) lead her into a relationship with her mysterious and powerful aunt Maire, who had a complicated relationship with Rio's mother Oceana. Maire teaches Rio about a number of new and unusual siren powers, such as the ability to infuse her voice into a seashell and to control inanimate objects. Maire also reveals the secret history of the sirens: though originally believed to be miracles, they gradually came to be viewed as a liability after a public dispute between two siren sisters killed several people.
Rio tries to escape to the Above through the floodgates, but she is discovered and brought to the Minister Nevio, who is secretly a siren himself and has been controlling the people of Atlantia with his powers. She learns that the people of the Above have stopped sending resources to the Below, and Atlantia is running out of food and materials for repairing the walls. Rio is sent on a mission with the other sirens to convince the people of the Above to continue sending aid, despite the fact that the Above is now habitable and the people there hold a deep grudge towards the people of the Below. True accompanies her as well after he reveals that he has the special ability to discover when sirens are lying.
Instead of convincing the people of the Above to assist Atlantia, the sirens are massacred on the beach. Maire sacrifices herself to make sure that True and Rio escape; the two find their way to the temple of the Above, where they find Bay and Fen. Rio learns that Bay went above to protect her - sirens cannot live long in the Above, and only one sibling from each family in Atlantia is allowed to travel to the Above. Fen is struggling with a dangerous lung disease, but doctors in the Above will not treat people from the Below. They also meet Ciro, the minister of the Above, who explains how Nevio secured his own safety by delivering up the sirens of Atlantia. Nevio plans to let Atlantia crumble as long as he can keep himself alive.
The four young people decide they must do something. Bay goes to the Below to explain to the people of Atlantia that they must enter into a partnership with the people of the Above, and Rio does the same for the people of the Above. Rio uses her siren voice to force the people to listen to her, but rather than using her powers to force them to obey her, she convinces them to help the people of the Below through rational thought. She explains that Atlantia belongs to them as well, and they must help preserve it. The sisters' plan works, and the Above and Below are united once again.