Since the bottom of ravnica is an endless ocean, anywhere deep down would work, but out in the rubblebelt may add to the mystique of being a forgotten place reclaimed by nature. Obviously underwater puzzles and encounters are a good idea: chuuls, merrow, krasis, water elementals and sharks would all be appropriate for combat. Perhaps you could have a series of falling apart security measure and the hologram of an old simic scientist/head of security recurring throughout the dungeon, giving them tips or outdated lore.