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Anime and Manga
- In Yokohama Kaidashi Kikou, due to an environmental shift whose details are largely unrevealed, a great many coastal cities are completely covered by the ocean. At least one chapter revolves around exploring one such city, Yokosuka, whose street lights still come on even though the city is completely submerged.
- The namless ruined city in El-Hazard: The Magnificent World used to showcase the ancient destructive power of the demoness Ifurita.
- 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.
- 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.
- For a time, Aquaman was based in Sub Diego: a portion of San Diego that was submerged in an attempt to convert humans into subaquatic beings. The population consisted of a mix of these altered humans and Atlantian refugees.
- Tangent Comics: the city of New Atlantis was founded atop the ruins of Atlanta, Georgia, after the Florida peninsula was destroyed in Earth-9's version of the Cuban Missile Crisis.
- Buenos Aires in Conciencia y Voluntad, also with many other major coastal cities.
- The 1987 novel Drowning Towers (or The Sea and the Summer) by George Turner describes a future in which Melbourne was partially submerged in water. As the tops of sky scrapers are above the water level, they are still inhabited by the cities' poorer classes.
- In Dark Life, any city that is coastal in our time has become this.
- In The Lord of the Isles, it seems like you can't turn around without without running into a sunken city or island. They don't always stay sunken, either, what with all the wizards running around.
- In The Kill Order, Mark often flashes back to living in a skyscraper, because the city was flooded with scorching water after the solar flares melted the ice caps.
- H.P. 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.)
- Sunken City (possibly the Trope Namer) in The Legend of Zelda: Oracle of Seasons, flooded not by rising seawater (it's quite far from the ocean) but by melting snow from the mountains.
- Most of eastern New York State is at least half underwater in Superhero League of Hoboken. Global warming is to blame. A good part of the game is figuring out how to get to the flooded parts of the city, then to the open water, to reach new locations.
- The city of Thor in Tales of Phantasia sunk 2000 years prior to the events of the game due to a meteor crash. It's still, however, relatively dry and functional thanks to Aska's power. The protagonists actually get to rise it back to surface on the trip down there (and get elected as the new president to do this).
- In Dark Souls, the city of New Londo is half submerged in water, and mostly populated by homicidal ghosts. It turns out that the city was flooded by the Three Healers when the Darkwraiths (humans feeding on "Humanity" and becoming twisted by the Dark) began to get out of control and the Abyss began to take shape beneath New Londo: flooding the city sealed both of those up and put a stop to the spread of the Abyss.
- Dark Souls 2 has a couple: the realm of Heide is almost completely submerged by the sea, with only a couple of towers still habitable above the water. The Iron Keep is likewise sunken... in lava. The Old Iron King became too greedy, and built his castle too high; the castle (suggested to be pure iron) got really, really heavy and partially sank into the volcano the King had insisted it be built on.
- The Crystal Key has the Arkonian capital city of Suralon, which was almost completely submerged when the evil psychic Ozgar bombarded it with his gravity-altering satellites. Naturally, the people there evacuated the place while it was sinking.
- In Anno 2070, set after a massive global warming event, has city ruins occasionally located on underwater plateaus. They can be harvested for building materials.
- In Ace Combat 04: Shattered Skies, 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.
- 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 can go outside and see what it's like from without.
- Atlanta in Futurama, Played for Laughs of course. "The Lost City of Atlanta!"
- In an episode of Captain Planet, the characters go forward in time and see New York underwater. And yes, it was a Green Aesop about Global Warming.
- 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.
- In the UK, entire towns have been submerged over the years for various reasons.
- As with the U.K., 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.
- Venice 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.
- Many of the most ancient parts of Alexandria, in Egypt, have sunken along with the land under them.