One possibility is that the phrase means no more than “the flood waters in the time of Noah”.
Another view is that in some sense they are Noah’s waters, implying that Noah is at least partly to blame for them.
If he had been a better leader of his generation, the argument runs, they might have been more faithful to God, and the flood might not have been necessary.
But Noah did try to teach his contemporaries, and it is not entirely his fault that they did not respond. Thus it is not fair to blame him for a wayward generation.
The Midrash Tanchuma declares that God believed that when the people of the time saw Noah building an ark they would ask what he was doing and Noah would have warned that if they did not repent there would be a flood… but things did not work out as God expected, and the people took no notice.
Yes, there is a rabbinic belief that had Abraham been the leader of that generation and not Noah, things might have been different, but another rabbinic principle is that you cannot transpose leaders between generations.
All that you have is “the judge that shall be in those days” (Deut. 17:9), even if that judge is inferior to a judge of a previous (or a later) generation.
It sounds attractive to imagine how much better things would be if, for example, the Rambam were alive in the 21st century, but it’s only a dream, and the reality is that Noah was the best leader they had in his generation, and our leaders are the ones we have in our own days.