If you've ever read Tom Sawyer, you'll remember the cave. It's a real cave that Sam Clemmens played in as a boy. Here's a map of it.
Notice anything? This is a natural limestone cave, carved by water seeping through cracks in the rocks over centuries. And there are chambers, passages, intersections, multiple ways around, and while the map doesn't show it, some elevation changes as well.
Now, I've heard before people bemoaning the fact that labyrinthine dungeons are unrealistic. "If dwarves or goblins or a wizard were really carving out rock, they wouldn't waste effort making long hallways between rooms," they say. Well, what if nature has already done a lot of the work for them? What if the dungeon started out as a natural cave system like this, and the dwarves or gnomes or orcs or whoever came along and just expanded and finished some of the already existing passages and chambers? Not so much work now, is it?