A common reason, apparently, was fire. When a city was largely destroyed by fire, people would just level out the rubble and start building again on top. This also helped protect from floods.

We were still doing essentially this same thing in the U.S. even a hundred years ago. Philadelphia, for example, is a city built on originally swampy floodplain between two large rivers. Developers channeled streams into huge sewers in the valleys, cut off the tops of nearby hilltops, and filled in the valleys. This made a flat plain for development, as much as 30 feet above the original land surface in some cases, with sewers ready to go. The sewers were for both drainage and waste, in a time before flush toilets when people previously just tipped their chamber pots into the streets each morning. And remember that added to all that human waste was the waste of horses, the main form of transport. Then there were factories and slaughterhouses discharging all sorts of nasty things to those sewers and rivers. So there was a certain brutal logic to it at the time, but of course we don’t want to be doing this in new areas. It makes sense for people to use these areas where we have already sacrificed the environment more intensely, while greening them up with lots of trees and parks so they are actually nice places for people to live.

Interesting pictures and narrative on this process in Philadelphia are here and here.