Under the Ocean of the Source (spoilers)

[Nalien]

For some reason I seem to remember some ARR lore hinting at the Sahagin Queen residing in some ancient ruins, but I cannot for the life of me remember where I recall that from... Certainly had me going "Wait a minute..." when I got to the Ondo in Tempest, though... Maybe it was a line somewhere in the Sahagin daily quests...

[Enkidoh]

It's on the main FFXIV promotional website in the description of the Sahagin, in that they live in an city deep under the ocean, but I never took that to mean they were merely inhabiting underwater ruins and more that they built that city themselves (probably with lots of coral):

This aquatic race of beastmen reside in a city built at the bottom of the Indigo Deep.

Looking at it, it can come across as ambigious now, but I still think it just refers to a city the sahagin themselves built and nothing more than that, and to think otherwise is perhaps overthinking things a little too much.

[Sathona]

If im not wrong Yshtola mentioned due to the many calamities most of these ruins will be destroyed by now,so it will be difficult to find one~

[Iscah]

The Sahagin living underwater with their queen is also brought up in their beast tribe quests. It sounds like their culture is the same as the Ondo.