The protagonist of the game and the only playable character. Naija is an amnesiac Fish Girl who suddenly wakes up, "like in a dream", and journeys in order to find her origins and past.
- Action Girl: Averted at first, until she gets the Energy Form.
- Amnesiac Hero: Starts out as this. It's revealed later on her mother Mia wiped out her memories in order to prompt the events of the game and eventually cause her to kill The Creator.
- Determinator: Naija will do anything to discover who she is and her lost memories, to the point she slays a God, minor Gods, Mother Nature and many other beasts.
- Did You Just Punch Out Cthulhu?: In the course of her travels, Naija will kill or finish off at least 6, and up to 12, "lesser gods" of her world (including gods of battle energy, a personification of nature, the former god of a ruined city, a huge sun worm, and several "species bosses"), then top this off by slaying the creator of Aquaria. (But not her mother, the Creator's 13th creation, and the game's true puppetmaster. Too bad.)
- Hand Blast: In Energy Form, she can shoot energy bullets from her arms.
- The Heroine: She's the main character after all!
- He Who Fights Monsters: One of the things that worries Naija about the energy form is that she's starting to enjoy its destructive power, and fears she'll lose her sense of self if she succumbs completely to this. It's not just something she's saying, either; if you fire off a prolonged salvo (fighting something big and tough, like a leafy dragon, for example), she giggles.
- Hyperactive Metabolism: She's able to eat food to instantly heal, cure status ailments, or apply an assortment of buffs.
- Lady of Adventure: She becomes this. At the end of the game, she feels sorry for not being able of having any kind of adventure after starting a family.
- Last of Her Kind: What Naija fears. The loneliness that results from this is her motivation for venturing out into the world. Actually, she's the daughter of Mia, the first perfect creation of The Creator. In the final dungeon there are also mutants similar to her.
- Leotard of Power: Spots a nice one-piece with her exposed belly in most of her outfits (minus a few sets of armor).
- Magic Music: Naija sings (or the players can use hotkeys) to switch to different forms, pull certain objects, attract fish, etc.
- Mysterious Past: Naija doesn't remember anything about her past. During the course of her game, we can see glimpses of it.
- Quest for the Rest: Naija's starting motivation.
- Parental Abandonment: Implied to suffer this from Mia so that she would explore Aquaria due to her curiosity. She also inadvertently does this to her son Lucien and her husband Li, because of her mother's interference.
- Pink Girl, Blue Boy: Naija is pink in the Dual Form.
- Stripperiffic: Practically her entire wardrobe, considering both her alternate forms and the alternate costumes for her primary form, though some elements goofy helmets, or the claw-gloves of the Crab Armor could be considered Fetish Retardant. (Yes, there's a "nude mod" available.) Then there's the costume that Naija herself describes as "rather revealing". We'd call it a bikini. In the post-game scenes and stinger, she and Li, the spoiler of spoiler tags wear even less.... This isn't without some justification though, considering she is a humanoid who has always lived under water and the drag of flowing or porous excess cloth underwater makes swimming difficult.
- Swiss Army Hero: Naija has different forms she can switch from by singing.
- Talking to Herself: Naija shares her voice actress Jenna Sharpe with her mother, Mia.
- The Aloner: She's been this for a long time, but really begins to notice it when the game starts.
- The Power of Love: Her love for Li is what prevents her from succumbing to despair after The Creator kidnaps them.
- Underwater Kiss: Shares one with Li, partly because she doesn't understand the concept of scuba gear.
- Unscaled Merfolk
- You Gotta Have Blue Hair: She has white-pinkish hair, which makes sense since she's an underwater creature.
A researcher and explorer in the waters of Aquaria. He met Naija when she was still a kid and was exploring The Veil. Since that encounter with a strange fish girl, he started underwater explorations. Joins Naija in her quest after she kisses him and grants him the ability to breathe underwater.
- Apparently Human Merfolk: Naija makes him into one of these. At least while he's near her: Li puts his old diving helmet back on if Naija decides to leave him behind somewhere.
- Arm Cannon: He wears a bracelet that allows him to shoot blue projectiles.
- Distressed Dude: Twice. Towards the end of the game, both times because of The Creator.
- James Bondage: See above.
- Pink Girl, Blue Boy: Li is blue in the Dual Form.
- Satellite Character: Naija can leave him at either his home or hers, but there are a couple of places where he must be present to continue in the game.
- The Speechless: It's Naija who lets the player know what Li feels, sometimes.
- Non-Player Companion: He helps Naija with fighting and can help taking down enemies faster.
- A God Am I: He considers himself as this as he's Aquaria's creator.
- Chest Blaster: His final form.
- Cryforthe Devil: His tragic backstory and what lead him to become like this.
- I Just Want to Be Loved: He created the Gods in order to replicate the love his mother gave him. Upon realizing they would not love him unconditionally, he deemed all of them imperfect and destroyed them along with their creations.
- Love Makes You Evil: See above.
- Sequential Boss: He has five forms:
- The first of which is a humanoid figure on a white throne, who occasionally sprays fireballs from his hand.
- His second form is similar to his first, but loses his mask revealing a black void; and his legs, replaced by purple tentacles.
- His third form is insectile, but with the body of a human infant.
- His fourth form resembles a human child with Barbie Doll Anatomy and Li's hairstyle.
- His fifth form is a gargantuan humanoid figure with visible muscles, eyes and brain, as well as a stomach which opens up to reveal a baby's head which shoots a huge laser from its mouth for massive damage.
- The game's data files contain evidence of at least one more form that was Dummied Out.
Naija's mother and the one who wiped out her memories. She's been in the shadows for a long time, waiting for her daughter to be overcome with curiosity and explore the world of Aquaria.
- Batman Gambit: She removed Naija's memories, knowing her daughter's curiosity would push Naija to uncover her past and eventually defeat The Creator.
- Evil Matriarch: She wants to use her daughter's abilities to gain even more power.
- Meaningful Name: While her name is a variation of "Maria", it also coincides with the italian female possessive pronoun "mia" (mine).
- Parental Abandonment: She left Naija so that she could set her plan in motion.
- Talking to Herself: She shares her voice actress Jenna Sharpe with Naija.