I have to admit that I'm not sure what to think regarding the flood in the Genesis book. I've heard so many different theories that one can can easilly get lost in the details. My own opinion is that the Genesis book captures some terrible cataclysm in humanity's distant past.
But...
If the story is actually allegorical of something else, then I have to wonder if the reference to waters rising is actually symbolic of Gentiles rising up against the authors of the Scriptures. In other words, perhaps some kind of terrible war is being described in symbolic language which resulted in terrible calamities.
NIV writes:
The LORD saw how great man's wickedness on the earth had become, and that every inclination of the thoughts of his heart was only evil all the time. The LORD was grieved that he had made man on the earth, and his heart was filled with pain.
NIV writes:
Now the earth was corrupt in God's sight and was
full of violence. God saw how corrupt the earth had become, for all the people on earth had corrupted their ways. So God said to Noah, "I am going to put an end to all people, for the earth is
filled with violence because of them. I am surely going to destroy both them and the earth..."
I find it interesting that the only other place in the NIV where the phrase "filled with violence" appears is here...
Ezekiel 28:16 writes:
Through your widespread trade you were
filled with violence, and you sinned. So I drove you in disgrace from the mount of God, and I expelled you, O guardian cherub, from among the fiery stones.
I'll note the odd reference to the Nephilim prior to the cataclysm.
Some have suggested that the Book of the Apocalypse's mentioning that “there is no longer any sea” may be an indication that there is no longer a separation between Jews and Gentiles, erasing the exclusive relationship that God had with Israel. With the sea gone (the court of the Gentiles), all barriers have been removed, and the entire humanity can freely come to God.
In other words, some suggest that "sea" is a symbol of the rebellious masses of the Gentile nations in Revelations 17:15 for example. If so, perhaps the Genesis passages are using a similar theme.