Natural disasters were not that much of a common thing back then. In these days, we have adapted mostly to them. We have flood protection technologies, emergency escape technologies and storm shelters and lots more! But, in the back days, the people didn't have these things, so, in a natural disaster, many villages could be destroyed in seconds.
Lets now see what type of natural disasters they had.
Floods, in the early civilizations, there were lots of floods, specially near rivers. But, instead of trying to build some flood protection technologies, farmers started using the area that used to get flooded and then use it for their crops. That way, other people didn't get their land used in crops, plus, the farmers got what they needed in a huge quantity, water...
Earthquakes, Earthquakes were a big problem for the early civilizations because they didn't have building stabilizers and technologies that would keep a building standing that well. Plus, depending on the time, their houses were also pretty different. They weren't made of bricks and cement, they were made of materials that could easily break. So that is why, Earthquakes were a big problem for the early civilizations.