Think about a completely dry sponge, shriveled and hard. If you hold it under a faucet, the water will run off the top of it for a few seconds before it starts absorbing water, and it will take quite a while before the sponge is able to soak up as much water as it can if it isn't pre-moistened.

The same thing happens with soil. Even just one inch of rain not getting absorbed by the ground equals millions and millions of gallons of water flowing over the land, collecting at low points and creating catastrophic floods.

As far as deserts go, it depends on the local geography, but plenty of them do have severe floods when they experience rain.