An aquatic city was a city that existed primarily or entirely on and/or under the surface of a large body of water such as an ocean.
The Aquans, water-breathing inhabitants of the planet Argo, lived in an aquatic city, notably called the Aqua-City. (TAS: "The Ambergris Element")
New Martim Vaz was an aquatic city in the Atlantic Ocean on Earth in the 24th century. (TNG: "The Survivors")
Though not specifically mentioned in the episode, The Waters from VOY: "Thirty Days" was also seen to have what seemed to be several large aquatic cities.