I don't have anything to show at the moment, but this is something on my future projects list.
My own idea's to recreate the Fallen London / Sunless Sea setting in a small scale. With various steampunk ships travelling an underground sea between various island settlements - as the sunken ruins of lost civilisations lie beneath the waves.
The way I was planning to do this was to have mostly rocky terrain for the above water location - lighthouses, and the like. With the odd Mythos like ruin and more historical like stuff poking through the waves. Done by just sculpting some waves about the top of a slightly askew building on a base.
In my case I wouldn't be looking for much of a pattern with the placement of the ruins or how they'd be angled on their bases. More upright buildings perhaps retaining their original foundations, and others having begun to topple over. Maybe mix up the heights of buildings - not necessarily going for taller ones capable of reaching from the sea floor or shelf to above the waves- to represent shallower waters.
I can imagine the suburbs of some island borne settlements reaching out beyond the rock they're built on. Standing on stilt platforms or built on the roofs of nearby ruins. Shanty town shacks sitting atop Cthulhu Mythos rocks (even having weird rocks on the islands towns are situated). Or perhaps up on the hulls of old ships (some anchored in place, others that were beached, but are the most stable foundation available for homes - if that's saying much). Maybe small house boats clustered around old bight buoys or even on the backs of giant dead sea animals.
With the watery bases it may be more of an undertaking than if you were just sticking your terrain in the dirt. At least if you're going for more complicated effects. You could get away with just some ripples about any objects touching the water (sculpted in clay) then maybe sculpt on some waves or undulating water - again with clay. Or start messing about with water effects. There's so many options for what to do with buildings. Like having them out in the open sea; built on old boats and flotsam -, or having them sitting atop a city - in which case just make the upper stories of buildings then add shacks to the upper most floors/ sides/ roofs. Personally I'd go for a mix of both styles. With shacks and walkways down at water level too as a place to access the buildings by boat.
If you're looking for inspiration then I'd say look at games like: Submerged, Flame in the Flood, The Sinking City and of course Sunless Sea. There's a game called Raft which is entirely set on a raft as you pick up junk floating in the ocean after the apocalypse. ...Not much other than the raft though.
Dishonoured had the whole "Flooded District" level, with the baddies hold up inside an office block (clearly made of sterner stuff in the style of 19th century granite buildings, as the newer buildings crumbled around it) - whilst outside the area was wooden walkways which deteriorated scum covered factory yards with rusting boats from the nearby river sitting between the buildings. As a setting Dishonoured could give you ideas - an island nation with a canning/ fuel industry having seen better days and dealing with a rat plague. As the authorities become more draconian criminals sprout up and plague victims turned zombies hide away in the Flood District where their corpses were dumped in their hundreds after police sweeps (perhaps these body piles could be used as dams in some macabre attempt to stem the water's encroachment?).
Jam by Yahtzee Crowshaw had a concept of a city filled with slowly rising man eating Jam. People walked through the jam in suits made of plastic bags (with air holes above their heads. I believe using poles to vault between buildings at one point. Things like cars and street furniture wound up strewn about some streets where waves of jam had passed, in others they were sitting in place - in case you want to go for more shallow water and have the roofs of cars poking out (or if the level's higher; double decker busses).
Oh and Brink was a game set on a flooded Earth - where survivors had fled to a luxury floating city. At first it was the plan for the best and brightest to live there, but as things grew worse on land many fled to the city on whatever seacraft they could find. Giving a contrast decades later between the original city areas - all futuristic and white, but breaking down and abused in places- and the slums outside these areas - made from shipping containers and boats. With one side taking the role of the city's security forces, and the other those standing up for the under class.
Unrelated, the novel Boneshaker had an evocative setting. In its case it was a city full of gas instead of flooded with water (or jam)- but still, people would build on roofs, create airtight buildings by digging down into them from above, use airships, tunnels and sealed vehicles to travel. The gas moves slowly so oiled cloth could stop its spread for a time. Though in areas where it was thicker it could break these down quickly (oh and turn people into zombies quicker too...).
Denver in the Fallout series similarly has people living on building's roofs as the streets are polluted and full of feral dogs - just as another concept which could give you transferable ideas for this sort of setting. 2000 AD's Rogue Trooper series had a city where the poisonous atmosphere congregated in a city's streets thicker than other areas (it was in a dust bowl from what I remember) so battles were fought between sky scrapers. Sides would attack each other using sealed tunnels telescoping out of the building's sides and use the lifts/ stairs to attack upper floors.
I'd say search "Hong Kong Rooftop Slums", "River Shanty" on Google too.