In general, water is used as an uncountable noun, which means that it does not change to a plural form. Listen to these:
Put plenty of water in the bath!
Put plenty of peas in the soup!
Fill the bowls with water.
Fill the bowls with stones.
Now, peas and stones are countable nouns, so they can take both singular and plural forms, but as water is an uncountable noun it doesn’t alter, so we have one glass of water or two glasses of water. And this is probably the usage that you’re most used to hearing.
But in your example, you seem to be referring to a flood situation, and waters is used to mean a specific body of water – that is, a lake, a river or a sea. And the situation seems to describe a river that’s burst its banks, or an area of land that’s been flooded by heavy rainfall. So in this case, waters refers to the presence of a large body of water, rather than the running water that we use from the tap. This is a topical example, because many areas of the world have suffered extreme floods this year.
As well as the example you give, we could also talk about UK fishing waters, which means an area of sea belonging to the UK, where it’s possible for UK boats to go fishing. And we also refer to fresh waters, meaning rivers, as opposed to salt or saline waters, which means the sea.