Underwater City

"It seemed a sure bet that by the early '70s we'd be flipping a coin as to whether we'd be spending our holidays on the Moon or at the Poseidon Hilton on the bottom of the Caribbean."

- Tales of Future Past

Not just Underwater Ruins or an Underwater Base, but an entire city of people living and "breathing" underwater. It's usually created with futuristic technology or powerful magic, and a popular depiction is to have a fully surviving Atlantis with domes and/or water breathing Fish People or Apparently Human Merfolk. Usually though it's a modern attempt at colonizing the ocean floor, or a villain's secret lair.

As might be expected, living in such a precarious location makes these cities inordinately prone to having something go Horribly Wrong. Be it sabotage causing the dome to break, an undersea volcano activating, or other disasters.

Anime and Manga

 * Daphne in The Brilliant Blue: The main cities of the aquatic New Eden were originally Underwater Cities created to escape the apocalypse.

Comics

 * In Scion, Ethan discovers an underwater city built by an aquatic sub-species of the Lesser Races who were able to escape their lives of slavery.
 * Both Marvel Comics and DC Comics have versions of Atlantis, although in both cases Atlantis is a big place with multiple cities.
 * There was an arc in Aquaman where half of San Diego slid into the sea following a massive earthquake... and those who survived it instantly adapted to underwater conditions.

Film

 * City Beneath The Sea (1971)
 * The City Under The Sea (1965), AKA War Gods of the Deep
 * The Underwater City (1962)
 * Otoh Gunga, home of the Gungans from the Star Wars prequels.

Literature

 * The Shadow Over Innsmouth by HP Lovecraft has Y'ha-nthlei, of the "titanic sunken porticos" and "labyrinths of weedy cyclopean walls." Located off the coast of Massachusetts and home to the Cthulhu-worshipping Deep Ones.
 * Isaac Asimov's Lucky Starr and the Oceans of Venus.
 * Michael Reaves and Steve Perry's novel Dome, which is set in a futuristic underwater lab complex.
 * Underwater colonies are a significant part of the backstory of "The Eve of RUMOKO" by Roger Zelazny.
 * A city of cray (lobster-centaurs) is featured in China Mieville's The Scar.
 * Attack from Atlantis by Lester Del Rey.
 * The great city of hi'Leyi'a on the planet Pacifica, in the Star Trek Novel Verse. First mentioned in Star Trek Titan, it finally appeared in Losing the Peace.
 * Handled as realistically as possible in "Ocean on Top" by Hal Clement. A colony of humans is established on the ocean floor, using geothermal power to provide light and a specially-made oxygen-carrying dive fluid in place of air. But since the humans are less dense than water, the humans have to wear weights if they want to stay on the bottom or even have neutral buoyancy. They sleep tied to the ceilings of their buildings.

Live Action TV

 * The Man From Atlantis episode "Crystal Water, Sudden Death".
 * In the first episodes of Stargate Atlantis, the city is underwater. In a subversion of the Gone Horribly Wrong situation mentioned above, when the shield fails, the city surfaces.
 * In a Double Subversion,.
 * ORCA in Ocean Girl is halfway between this and Underwater Base. The ORCA City project may be closer to this trope.
 * Sea Quest DSV is set in a world where the ocean floor has been so heavily colonized that there are whole underwater nations.

Tabletop Games

 * Dungeons and Dragons Known World/Mystara campaign setting. The Kingdom of Aquas, which was once part of the Empire of Alphatia.
 * Naturally, several D&D settings include undersea civilizations of merfolk, tritons, sahuagin or the like. Some of these use air-filled domes as housing for surface-dwelling visitors.
 * Aquilon's Reach has multiple underwater cities, as well as some atop glaciers. Unsurprisingly, they also boast the best navy in game.

Toys

 * Mahri Nui in Bionicle

Video Games

 * Rapture from Bio Shock ,which get extra points for being a steampunk and biopunk city as well.
 * Final Fantasy X has many of these.
 * The Crystal Dome from the last level of Heretic.
 * The Call To Power series has sea cities.

Web Comics

 * ...almost the entire world of Aquapunk. With Fish People and everything.
 * In Question Duck, he's been to an underwater city, really.

Western Animation

 * Futurama featured the Lost City of Atlanta.
 * Sealab 2020 and Sealab 2021...
 * ... not to mention the other Sealab featured on Centurions.
 * The Superjail episode "Superbar".
 * Jabberjaw.
 * The Real Adventures of Jonny Quest episode "Undersea Urgency".
 * Atlantica from The Little Mermaid.
 * They visited Atlantis on The Fairly Odd Parents. Also, Clevelantis.
 * The main premise of Atlantis the Lost Empire