flood waters

Yes, it is correctly used, and no, "waters" is not redundant in that usage. It is an idiomatic usage, and there is some logic in that water might be present which was not produced by flooding, and so a reference to "flood waters" would be a reference to any water present which derived from the flood. Mostly, though, one uses the expression because it is a standard idiom.

Is the plural needed?

No, but it is commonly rendered as flood waters.

Yes, I agree. We say "monsoon rains". If it's rain that occurs every now and then, we say "rain".

"Look at the dark sky, the rain will come soon."

We drink water. If there is sudden high tide and the sea overflows its bank, causing widespread flood, we would say "The waters caused widespread destruction."

The waters has caused heavy flooding.

The waters have caused heavy flooding.

Should I use 'has' or 'have'?

Many thanks.