Vertical catacombs
They go up, building up and then up and up and up and up. With lots of remains that become skeletons and zombies, etc.
I'm getting an image of dozens of mindless zombies and skeletons shuffling around carrying stretchers full of fresh corpses to be filed away in the catacombs, all directed by a very harried necromancer who complains that he didn't become a wizard to play file clerk... And maybe a swarm druid who controls beetles or maybe even fish to clean the bones...
Heh - the party is walking along on one of the walkways beside the canal, and suddenly it starts raining undead from five stories up because the corpses took a wrong turn, and a crumbly old balcony railing gave way... That'd be a hell of a variation on the old hit-with-the-contents-of-a-crap-bucket-thrown-from-a-second-story-window scenario, huh?
Feature a semi- or fully-aquatic race
That could be an elf, or merpeople, or titans, or even just halflings that travel on rafts and boats using poles and their friendly otters to move about.
My Dungeon23 project is a lost Dwarven settlement that just "resurfaced" (pun intended) out of a huge swamp after a recent earthquake partially drained it. Some of the larger landmasses within the swamp could have been vaguely considered small-scale ruined "canal cities" even
before the most recent earthquake, although the buildings mostly went
down instead of up...

(All but the very top of the settlement was originally built inside a small mountain that sank completely underground in a previous quake, and it's the very top floor of those uppermost buildings that are once again above the surface.)
Above the surface of the swamp, there's a clan of human swampfolk who run a joint smuggling operation with some pirates from further up the coast...Above and below the surface there's a tribe of relatively civilized lizard men as well as a green hag, and since the swamp becomes a salt marsh and then eventually open sea, there's also some interaction with the aquatic elves who live near an island just off the coast.
(On a more indirect note, the aquatic elves
may or may not be the long-lost surface elves who disappeared from the neighboring forest when an ancient magical cataclysm (original cause of the recurring earthquakes) turned it into the "Stonelands". Also, since the Dwarven settlement went from being a mountain to a swamp because the
Underdark cavern beneath it collapsed, I'm considering putting an aboleth way down in one of the lowest rooms.)
So there's at least as much going on
under the surface as there is above it.
