http://tvtropes.org/pmwiki/pmwiki.php/Main/UnderwaterCity

Complete with sea-floor highways!

Tales of Future Past "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."

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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.

See also City on the Water for cities atop the water instead of underneath.

Compare Underground City.

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Examples:

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Anime & Manga

Comic Books

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 Universe and The DCU 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.

Wonder Woman (1942): Venturia, an Atlantean outpost city once ruled by the cruel Wonder Woman villain Queen Clea, is an underwater city with a badly damaged infrastructure due to their former ruler's incompetence.

Fan Works

The Elements of Friendship gives us Lyonesse, the capital of Aquastria.

Pokédex: The Jellicent are the keepers of one beneath a massive, Jellicent-shaped dome, made out of shipwrecks and flotsam, lit and warmed by underwater vents and populated by sailors kidnapped en masse when their ships pass through the Jellicent's territory. The purpose for this seems to be so that the Jellicent can have access to human technology.

The Institute Saga has Sanctuary, a domed refuge which the Morlocks move into, followed by the Labrynth Clan.

A Diplomatic Visit: After being mentioned in the first story, the sequel Diplomat at Large has Twilight visiting Seaquestria in the eastern oceans, ruled by the seapony Queen Novo and home to a mix of seaponies and transformed hippogriffs, and Aquastria in the western oceans, ruled by merlion King Leo and inhabited by a mix of merlions, seaponies and mermares.

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Film — Animated

The Little Mermaid (1989): Atlantica, an underwater city or kingdom inhabited by mermaids and talking sea life.

My Little Pony: The Movie (2017) has an underwater city at Mt Aris. The hippogriffs fled the Storm King's forces and transformed themselves into seaponies to hide there.

Film — Live-Action

City Beneath The Sea a Made-for-TV Movie from the 70s about two futuristic divers discovering an underwater city that must be protected from alien forces. It was intended as a pilot for a TV series (produced by Irwin Allen) but never got picked up.

The City Under The Sea (1965), AKA War Gods of the Deep, a B-movie from The '60s features a Mad Scientist keeping a girl hostage in a city full of advanced humans with extended lifespans.

The Underwater City (1962) details a group of people testing out experimental underwater housing - and disaster strikes when the settlement caves in.

Captain Nemo and the Underwater City is a 1968 Steampunk film about a group of people encountering Captain Nemo, who had developed several advanced submarines aside from the Nautilus and had created an underwater city for his crewmen and their families.

Otoh Gunga, home of the Gungans from the Star Wars prequels, made out of a large number of sealed-off, interconnected domes at the bottom of a large lake.

The Abyss, in which the NTIs have a very large habitat on the ocean floor. (Whether it's a city or an enormous starship is never really made clear.)

Ultraman Cosmos 2: The Blue Planet: The Alien Gyashis, an underwater-based alien race who crashed on Earth decades ago after losing their planet to the Scorpiss horde, ends up living under the earth's oceans which can be accessed from a portal on the water's surface.

Literature

Live Action TV

Music

Jonas Brothers sung of this, where as a product of a time machine, everyone lives underwater; "I've been to the year 3000. Not much has changed but they lived under water."

Tabletop Games

Several Dungeons & Dragons settings include undersea civilizations of merfolk, tritons, sahuagin or the like; some of these use air-filled domes as housing for surface-dwelling visitors. The Known World/Mystara campaign setting has the Kingdom of Aquas, which was once part of the Empire of Alphatia.

Mechanical Dream: The Emovans are a fully aquatic species, and for the most part live in cities at the bottom of the world's subterranean oceans.

In New Horizon, Aquilon's Reach has multiple underwater cities, as well as some atop glaciers. Unsurprisingly, they also boast the best navy in game.

Shadowrun: In the 2nd Edition supplement Portfolio of a Dragon: Dunkelzhan's Secrets, the last will of the titular dragon left a bequest of five million nuyen to the first party to establish a self-sustaining community of at least 100 persons on the ocean floor. Yamatetsu Corporation eventually won the bequest with their SoaTome AquaDomes.

Transhuman Space has Elandra, an Australian-founded "free city" under the Pacific. It's more of a town than a city, really, but a respectably-sized one.

Underwater cities have cropped up occasionally in the lore of Warhammer 40,000.

Numenera: Several exist, some in fairly shallow parts of the sea and some in the blackest depths. Their inhabitants collectively refer to these places as oceia. Joria is a city built on the back of an enormous crustacean called a granthu, which moves in a roughly constant orbit around the ocean floor. The city is partly open to water, and inhabited by a species of amphibious humanoids called Jorians. The Jorians believe that there are other cities of their kind on the backs of other granthus, following their own orbits somewhere in the global ocean, and put in a great deal of time and effort in searching for them. The City of Rust is a large settlement on top of a massive slab resting on the ocean floor, which gets its name from the rust-red metal making up its buildings. It's mostly inhabited by a species of aquatic aliens called the skeane, and watched over by four massive and fickle AIs that its inhabitants worship as gods. Ahmas is a city in the darkest depths of the ocean, home to the descendants of humans who were transformed into monstrous Fish People by mysterious entities centuries in the past. Minifera, located even deeper than Ahmas, is lit by tiny, bioluminescent swimming creatures. It's home to the naiadans, an aquatic race whose individuals are made up of thousands of tiny creatures called dyremmi. Morenel is a city on the abyssal plain inexplicably inhabited by humans, who have been living there longer than any surface-based human civilization has been around. Onisteles is a colossal sea sponge that was colonized by an aquatic race called the glanae. The skin flakes the glanae shed feed the sponge, which in turn provides them with a home in a symbiotic relationship. What the glanae don't know is that Onisteles is in a similar relationship with a species of predatory animals called the ebons, where the predators protect the city from certain sponge-eating slugs... in exchange for Onisteles occasionally spitting out glanae to feed the ebons.

In the 20th Anniversary edition of Mage: The Awakening, the Avatar Storm cut off the Technocratic Union from bases maintained in Horizon Realms. In order to have bases of operation relatively secure from the prying eyes of the Sleepers as well as the Traditions, several of the Underwater Bases previously maintained solely by the Void Engineers have been converted (or are in the process of conversion) into full-on cities with representatives from all of the Union's Conventions.

Video Games

Web Comics

Web Original

In The Gamer's Alliance, Adlivun is a thriving underwater city populated by merfolk known as merrows.

Western Animation

Real Life