How did people control the flooding in Mesopotamia and ancient Egypt?

Answer 1

it was because of the rain it did not stop so they just let it flood

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Just like in modern times, the ancients used canals to divert water and levees to hold back water. These were pretty straightforward to make, and with the help of slave labor these efforts could be realized relatively quickly. Cities always had the option of building on higher ground, as well.

Answer 2

They didn't, they used it or took advantage of it. When the Nile, Tigris and Euphrates rivers flooded, the waters deposited fertile silt in the fields that helped recondition the soil and helped crops grow.