Underwater Ruins

Staple of Video Games and undersea movies, the Underwater Ruins are a city, temple, or similar place of majestic wonder submerged Under the Sea or a lake. Typically, the ruins will be Greco-Roman in appearance (lots of columns and arches) to evoke an Atlantis like catastrophe. Usually these ruins will be artfully decayed but remarkably well preserved. This setting is a Hailfire Peaks of Under the Sea and Temple of Doom.

You might see mer-people living in the ruins, or an actual domed city for air-breathers to live in nearby or hidden in the ruins. Expect to find areas with breathable air regardless for heroes to take a breather in.

Intrepid Travelers Beware! These ruins are sometimes subject to Down the Drain.

Anime and Manga

 * Agent Aika has modern underwater ruins from when the sea levels rose and flooded coastal cities.
 * Neon Genesis Evangelion has modern underwater ruins from when the sea levels rose and flooded coastal cities.
 * Appears in Transformers Armada. It's Atlantis, and was actually destroyed by a plot device.
 * Early in StrikerS Sound Stage X of the Lyrical Nanoha series, Subaru mentions an underwater ruin that was uncovered when the Marine Garden was being built. It could be seen from the Crystal Valley underwater tunnel. It's really romantic, the color's really blue and very beautiful,.
 * Blue Submarine No. 6 shows the flooded ruins of Tokyo at the beginning of the first episode and has even a underwater submarine battle around them in second one.
 * In the Lupin III film The Castle Of Cagliostro,

Film

 * AI Artificial Intelligence had underwater ruins of the submerged parts of New York City.
 * There was some of this in the James Bond film For Your Eyes Only. Not much, the "underwater" set wasn't particularly elaborate, but it was implied.
 * Kevin Costner's Waterworld had underwater ruins... which turn out to be the city of Denver.
 * In the Black Lake during the second task in Harry Potter, there's ruins of the underwater mermaid city.

Literature

 * In Jules Verne's Twenty Thousand Leagues Under the Sea, the ruins of Atlantis, making this trope Older Than Radio.
 * HP Lovecraft's "The Colour Out Of Space" takes place in a region of Massachusetts which is eventually flooded to create a reservoir. Several homesteads and small towns end up submerged, including the Colour-infested farm. (Minus the Colour, this is Truth in Television, as the Quabbin Reservoir was created in this manner.)
 * However, there are no ruins in the Quabbin -- well, except for the odd basement here and there -- they knocked down the buildings first.
 * Not to mention most of R'lyeh, where the titular Cthulhu lives.
 * Subverted in Terry Pratchett's Jingo, where it turns out that the ornate ruins on the ascended isle of Leshp.
 * Underwater Ruins were the source of the outbreak in World War Z. Patient Zero was a boy who had been diving for valuables with his father in the drowned township at the bottom of a Chinese reservoir. He returned to the surface with a bite wound and a death sentence for a large proportion of the human race, and his father never returned at all. It is implied by the authorities' reaction that the reservoir was created in the first place to attempt to cover up the (probably bioweapons) site.
 * Dinotopia by James Gurney has the ruins of Poseidos (read: Atlantis).
 * Lael Littke's short story Lucinda in Thirteen concerns the disappearance of the aforementioned Lucinda six years prior to the story's beginning. It's believed that Lucinda's body was hidden in the remains of what used to her hometown, Lake Isadora, after the buildings were moved and the remaining foundations flooded to create the new lake. The main character and her brother (Lucinda's ex-boyfriend) return to the lake after it had dried up.

Tabletop Games

 * A few blue-related Magic the Gathering cards feature these, including the Land card Academy Ruins, pictured above.

Video Games

 * Ace Combat 04 Shattered Skies provides a more modern example. Your enemy's capital city, Farbanti, has a submerged downtown full of scorched, tilted skyscrapers (and during the battle, submarines) due to an asteroid impact.
 * Blaster Master - The underwater world of Level 5 has some "Atlantis" like pillars for background.
 * In Banjo-Kazooie-Tooie, the Atlantis section of Jolly Roger's Lagoon.
 * Given the amount of damage it's suffered after a genocidal civil war, Rapture of Bioshock fame probably counts, even if it thankfully hasn't flooded yet.
 * In the sequel, as you're a Big Daddy in a self-contained suit, you supposedly can go outside and see what it's like from without.
 * Demons Crest had one level that was split into above-water ruins and underwater ruins. By playing through the above-water section, you could acquire the Crest of Water, which gave you a form that lacked Super Drowning Skills and let you complete the underwater section.
 * Donkey Kong Land
 * Ecco the Dolphin, played to the letter.
 * The Elder Scrolls III Morrowind had a secret Dwemer ruin some distance offshore, with a few interesting, entertaining or useful items inside it.
 * The Elder Scrolls IV Oblivion expansion Knights of the Nine'' adds an underwater Ayleid ruin where one of the artifacts was stored. For being underwater for so long, it still has a good amount of breathable air.
 * Endless Ocean has one as a bonus area.
 * The sequel has some as regular areas.
 * In Final Fantasy I, the Underwater Temple, home to one of the game's Cosmic Keystones. You can apparently breathe there, too, thanks to.
 * In Final Fantasy III, There's the Temple of Time near the continent of Saronia, underwater.
 * In Final Fantasy X, these crop up quite a bit. Able to be explored because three of the main characters seem to be able to hold their breath indefinitely (justified because two of them play underwater sports for a living and the latter is a thief).
 * The Lost Precursor City in Jak and Daxter The Precursor Legacy.
 * In La-Mulana, The Spring In The Sky, in which you had to swim through the water (thus, deliberately take damage) to get the underwater breathing item.
 * Metroid Prime features the ruins of the frigate from the beginning of the game about 3/4 submerged in water (accompanied by a beautiful piano song).
 * In the sequel, the lower part of Torvus - a ruined, sunken temple, with a remix of Red Brinstar from Super Metroid. Dark Aether's version doesn't have nearly as much water, but is MUCH creepier and even more derelict.
 * The Wrecked Ship in Super Metroid is similar to Prime's, except without the awesome music.
 * Ristar has ALL of Planet Undertow like this.
 * The Sonic the Hedgehog series seems fond of this:
 * Labyrinth Zone (Sonic the Hedgehog)
 * Aquatic Ruin (Sonic the Hedgehog 2, Genesis)
 * Aqua Lake (Sonic 2, Game Gear)
 * Aqua Planet (Sonic Chaos)
 * Hydrocity (Sonic 3 and Knuckles)
 * Tidal Tempest (Sonic CD)
 * Lost World (Sonic Adventure)
 * Aquatic Mine (Sonic Adventure 2)
 * Water Palace and Pirates' Island, the latter of which being built into a base. (Sonic Rush Series)
 * Sonic Generations features both Seaside Hill in the console version, which has been retooled to be partially underwater, unlike the original level, and the above Water Palace in the 3DS version, with a few added gimmicks for Act 1.
 * Star Fox 64's Aquas, which was a once-thriving planet before a bioweapon (the stage's boss) submerged the entire planet underwater. The ruins from the previous inhabitants are still present, though limited mostly to pillars that act as magnets to your torpedoes.
 * In World of Warcraft, the sheer number of elven ruins in Ashenvale and Azhara is staggering; there is nary a body of water in these zones without a downed column, sunken arch, or pockmarked pillar in it. Massive earthquakes are to blame for all those night elf ruins underwater. Though they seem remarkably resistant to pressure and the ravages of 10,000 years. There are also ruins of a sunken Troll city off the coast of Stranglethorn Vale and sunken Titan ruins in the waters between Arathi and Wetlands.
 * Another example from the Warcraft universe: the Tomb of Sargeras. Heck, the terrain type that was used to make these maps for The Frozen Throne is named 'Sunken Ruins' in the editor.
 * Should be pointed out that by the time we encounter any of the 'Sunken Ruins' locations in TFT, they've been raised from the ocean floor.
 * Cataclysm has the Sunken City of Vashj'ir and the town of Duskhaven in Gilneas, which gets flooded during the Worgen Starting zone because of the cataclysm.
 * Wario Land 2 had the very aptly named 'Ruins at the bottom of the sea' as a secret world/level.
 * In X-COM: Terror From The Deep, you shot down alien craft all over the world, then went to capture or kill them. This happened around underwater ruins an awful lot. The Atlateans must have had a global civilization.
 * A similar example from the same game. Occasionally, later in the game, the aliens will attempt to capture "Artefact Sites" in order to expand the range of their Molecular Control network. These sites are beneath ancient pyramid structures, and have a Used Future architecture.
 * In The Legend of Zelda the Wind Waker,.
 * zOMG! features ruins of Gambino's Tower as a major part of the Undersea Cliffs, and as a portion of the
 * Atlantis sank at the end of the campaign in Age of Mythology, but you end up having to go back in the expansion. It just hasn't sunk very far yet, so there are a lot of ruins that are just under the surface, and a lot of areas shallow enough to wade through.
 * In the Hunt has a stage like this where your submarine is chased upwards by a giant living statue.
 * Indiana Jones and The Fate of Atlantis, unsurprisingly enough.
 * The underwater indie game Aquaria naturally has a lot of these, mostly acting as dungeons.
 * Centaur Man's stage in Mega Man 6.
 * Slimy Spring Galaxy in Super Mario Galaxy 2.
 * Panzer Dragoon Saga has the ruins of Uru - you and your dragon fly over what few bits are tall enough to poke out of the water, then you wind up temporarily losing said dragon and explore a vast underwater laboratory.
 * American McGee's Alice has the Vale of Tears. It's an Under the Sea level with Underwater Ruins.
 * In Pokémon Black and White, there's the underwater Abyssal Ruins by Undella Bay.
 * Tales of Phantasia features Thor, a technologically advanced city that sunk into the sea 2 millennia ago when a meteor struck it. Being over 2000 years underwater hasn't stopped most of the technology thanks to the city being powered by Aska, who also keeps the city's dome under which the party can freely breath.

Western Animation

 * Futurama has the lost city of Atlanta, GA.
 * Little-known film Samson and Sally had brief references to Atlantis. Later in the film, Samson (a whale - most characters were marine animals) traveled to "the city man built" in order to find Moby Dick. This city is apparently a sunken New York.
 * In The Grim Adventures of Billy and Mandy Billy inadvertently destroys Atlantis.
 * Similarly, Cosmo of The Fairly Odd Parents sunk Atlantis… seven or eight times. Eventually the residents just gave up on living on the surface and evolved into mer-people. When Timmy wishes to visit Atlantis (to get cool pictures for a school history report or something), he ends up having to rescue Cosmo from their revenge/justice by proving they were actually better off safe and secluded under the ocean.
 * The sunken island of Quetso in Flipper And Lopaka.
 * The town of Moose Creek from "Scooby Doo Camp Scare" -- though it gets dried up by the bad guys.
 * In Atlantis the Lost Empire, the titular kingdom's capital is protected by a massive air bubble but the outskirts are exposed to the ocean and in ruins.

Real Life

 * In the UK, entire towns have been submerged over the years for various reasons.
 * Subversion: Venice. It's building dikes and other such anti-flooding devices, since the entire city is slowly sinking into the ocean because it's so heavy that the land underneath (formerly marsh, so that's understandable) can't hold up its weight.
 * As with the U.K. above, Italy has its share of submerged towns. One in particular is situated in a lake that gets drained periodically, allowing the interested to go visit.
 * A few have been found in real life, such as the Yonaguni Monument and temples of Mahabalipuram, but they are rarely more than a few sunken structures.
 * Similarly to the Quabbin Reservoir example (Literature), many towns along the Tennessee River were flooded by the construction of hydroelectric dams. Most of the buildings were demolished, but divers can still see the foundations of some.
 * The island of Thera was almost completely destroyed by a volcanic eruption. It is likely to be the origin of the Atlantis myth.
 * Many of the most ancient parts of Alexandria, in Egypt, have sunken.