|3D shell by Aki Inomata; crab by Evolution|
This city would move from the coast inland all the while flooding anything in its path and leaving brackish marsh in its wake. All the shell would be is a living reef of Kuo-toa singing mad hymns all the while. A tide pool from a briny hell. Maybe the crab would pick up chunks of cities, towers, and landscapes like decorator crab. Maybe it even has torn a piece of the night sky with it. Maybe this is actually the water elemental protecting itself from the eyes of other gods by disguising itself as a normal spiritual thing (See I have worshipers, cities, bits of land, factions, & sacrifice!). But really its just a crab that wants to eat everything.
The Kou-Toa themselves would be divided into two factions: THE TIDE (Kuo; pious majority) and THE DEEP (Toa; seditious and heretical minority).
Since the Kuo-Toa half the unique ability to make their own gods, I'd include rules that any extraordinary act, natural 20, or use of magic of a level equal to or greater than the observing Kuo-Toa's HD would result in them worshipping the PC. This would grant powers and abilities, but if left unchecked the PC would become a chaotic godling (and essentially dead). This would be the urging of the Toa who always seek to undermine the Kuo.
Maybe this would be a great dungeon idea or just become a wetter version of Broodmother Skyfortress. Maybe that is not so bad a thing. Maybe run it as a point-crawl with several small dungeons in it. Sorta like Legend of Zelda.