Aquaria is an underwater 2d sidescrolling action-adventure game with a great emphasis on exploration and solving various puzzles. Players are invited to take the place of Naija, ocean dweller, resembling a human woman with fish-like features, which allow her to swim and breathe underwater. Naija has lost most of her memories and has to explore the world outside, and is up to players to guide her towards the center of the mystery of her origin, the creation of Aquaria and the world outside, wherein the centers of ruined civilizations ancient gods are resting.
The gameplay centers on the inability to directly interact with objects or items, but through the system of short musical tunes. In the default form, Naija can summon a circle, with eight positions to fill with differently colored notes. Surroundings will be affected by the notes of the corresponding color, and once players learn more complicated melodies after unlocking through the story will not only help to lift objects and to create a protective shield but change forms as well. A total of seven forms are available by the end of the game, some of which are used to go through the story barriers.