I love this concept! Really looking forward to seeing what you do with it.
Here's an idea that popped into my head: What if there were a couple (or more) baby turtles with small fishing/gathering communities on their backs, that periodically return to the "mother" to offload their sea harvest? Ropes could be thrown (or swimmers could pull them across) to secure the babies to the mother while everything is offloaded (either by small boats/canoes, or by pulling a rope bridge across). These smaller communities could be like "villages" with fixed families, or they could be made up of temporary workers who are swapped out each time the babies "pull into port".
And here's some top-down images that might be useful for reference, and some artwork for inspiration.
Saltwater Turtles
Sea Turtle by Autodesk Premium
Green Sea Turtle 06 by wolverine041269
green sea turtle 1 by meihua-stock
turtle stock 21 by hatestock
turtles 2 by fa-stock
Loggerhead Sea Turtle (Caretta caretta) by NOAA, Jack Javech
Black Turtle HD Wallpapers
Green Sea Turtle (Chelonia mydas) by NOAA, Jack Javech
Freshwater Turtles
Turtle by Touchy-Stock
Turtle.2_Mind-Matter by Mind-Matter
Turtle by MACN3XU5
Turtle - 1 by ElaineSeleneStock
Turtle 01 by aussiegal17
Turtle by lindowyn-stock
Turtle Stock 7 by Squirt-Stock
oh noes more turtle :: 004 by Linkch-stock
turtles 3.2 by meihua-stock
TemocStock243-turtle- by temoc-stock
Yellow-Blotched Map Turtle by Tennessee Aquarium
Turtle Top View Wallpapers
Land Turtles
franklin agian by DeadlyStryker
Alligator Snapping Turtles (excellent species for "mountains" reference)
Alligator snapping turtle by Gobius
Alligator Snapper
Alligator Snapping Turtle Shell by Bone Clones
Alligator snapping turtle - Macrochelys temminckii
Alligator Snapping Turtle by Dr. Andre Mursch
City Layout Idea
Pattern 4 - Turtle Shell by PoppyLady
Artwork Inspiration
Turtle City by nydwyngreendragon
Turtle City by manillalu
The Moving City by my-wishful-thinking
Turtle Island by KenHuys
A Very Big Tortoise by R-Tan
turtle city by nclclaudiu
Slow Motion by DarkAngelPandora
Cast Away by pranjal22
Collapse by KaiserFlames
The Underwater City by ti-DESIGN
Tortuga voladora by Pintoro
Scrap by Pintoro
Untitled by Pintoro
Negotia by CoolCurry
Lepus: Page 03 by JoeWierenga
Maybe the city could generate a magical domed shield in times of danger, protecting everyone and everything inside while the turtle is submerged? (think: Stargate Atlantis) Or, maybe this happens periodically anyway, when the turtle feeds. It gorges itself for a period of time (a few days, a week, maybe more?) and its body stores the food so that it doesn't need to feed again for a few months?
Underwater City by TracyGiza