How about a dank temple complex that is slowly sinking into the muck. The players would need to know it was sinking and there would need to be something in the dungeon valuable enough that they would care. Maybe there are a series of big brass gates that take a long time to ratchet open, each revealing treasure. But the water level in the dungeon is rising each trip the party returns to open a few more gates. Until, finally, it becomes the Submerged Dungeon and the party knows there are several unopened gates still there, under the foul water.
The rate of sinking would need to be determined. I'd want it simple (as always), maybe half a foot a day. If the ceilings are ~8 feet tall that gives the party 16 days to explore before complete submergence. Although, those last couple feet might be just as bad as total submergence. I envision a whole new wandering monster table once you get about half way. It would be interesting to see the first inhabitants trying to get out during the submerging process, too: goblins on rafts, swimming ghouls, etc.