Sisterhood
Atlantia contains two significant sets of sisters: Maire and Oceana, and Rio and Bay. These two sets of sisters share very close relationships, but they also cause a great deal of sorrow and grief to each other. Despite (or perhaps because of) their closeness, sisters can also hurt each other more deeply than anyone else possibly could.
Freedom of Choice
Young people in Atlantia are given the choice to go to the Above or stay in the Below. However, once they make this choice, they must live with the consequences for the rest of their lives, and die without ever seeing the other side. Rio struggles with the fact that she was not able to exercise her choice freely because of a promise to her sister, who then betrayed her by going to the Above. Is this truly free choice, or does it only appear to be so?
Additionally, Rio learns to respect others' freedom of choice. Her siren voice allows her to force others to do her bidding, but she realizes that it is more valuable to convince people to make decisions out of their own free will than it is to coerce them into these actions.
Good and Bad
Related to the theme of sisterhood. Rio wonders if one sister is always good, and the other is always bad: for example, Maire is known as a sea witch while her sister Oceana is the beloved Minister of Atlantia. Rio wonders if she is the bad sister; even her mother said that thinking of the common good does not come naturally to her. Eventually, Rio discovers that good and bad are not so clearly defined: her beloved mother kept a number of secrets, and her aunt sacrifices a great deal to preserve Atlantia. Rio comes to realize that good and bad depend on a person's choices and actions; they are not inherent in one's personality.
Governmental Power
Minister Nevio is cunning and manipulative, and forces Rio from her position at the temple after Bay leaves for the Above. These actions are only a few of the dangerous abilities that his high position offers him. The government of Atlantia poses a curfew, takes siren children away from their families, cuts off transit between the Above and the Below, and keeps the citizens of Atlantia in the dark about the future of their civilization. Rio must find ways to circumvent the power of the government, and eventually change the political structure of Atlantia entirely.
Voice
Much of the action of the novel centers around the power of Rio's siren voice - she has the power to make others do her bidding, but revealing this ability means that the Council would take her from her family. Eventually, her pure siren voice allows her to intervene on behalf of Atlantia. However, the power of Rio's voice actually has little to do with her siren abilities. In addition to using her siren abilities, Rio must also learn to trust in herself and others and to express what she really feels. It is only by trusting in her own abilities and speaking out on behalf of Atlantia that she is able to save the city and herself.
Love
The relationship between True and Rio offers an inspiring model for young love. Rio, in keeping with her character, is much more slow to warm up to True, but he eventually becomes closer to her than anyone else in Atlantia. Likewise, Fen is willing to give up his comfortable life in Atlantia when Bay goes to the Above to keep Rio safe. The novel emphasizes that love means keeping a beloved's secrets and following one's beloved even into difficult circumstances.
The Environment
Though not a major theme in the novel, the whole conflict between the Above and the Below was caused by environmental destruction that rendered the water and air poisonous. Eventually, the pollution levels diminish and the air becomes breathable again, but the severe effects of this environmental degradation lead to social instability and personal conflict among the main characters.
