And it all has to do with boundaries.
Without a Sanhedrin and Torah-mandated executions (which hardly ever happened), Hashem executes by strangulation those who deserve it – and one of those ways is by drowning.
So here are why the Generation of the Flood suffered torrents of water:
1) First of all, strangulation is the halachic execution for those who indulge in relations with a married woman. The Generation of the Flood was really into this particular sin. Such a sin is an invasion of the boundaries of marriage & family. It also affects the children's lineage, since people can't know who is the child's real father, which was also a huge problem during Dor HaMabul.
2) Secondly, the sin of theft is another invasion of boundaries. So middah k'neged middah, the water overrides its boundaries into flooding (or into lungs, invading the air that is supposed to be there instead). The Generation of the Flood was hopelessly steeped in theft and all kinds of deception – "deception" is referred to as geneivat hadaat (theft of mind/knowledge) in Hebrew.
3) Third, avodah zarah is another breach of boundaries. Everything originates from One Creator. There is only ever One God. Scattering one's prayers among other entities is a terrible breach. So even though the official execution for avodah zarah is stoning for an individual and the sword for an entire city of idolaters, Hashem sent a flood instead.
Furthermore, Yirmeyahu 2:13 mentions the people who forsook Hashem, "the source of fresh water," and who instead dug "cisterns for themselves, broken cisterns that can hold no water." Radak interprets this as abandoning Hashem to worship idols. So that's another aspect of this theme of water.
Furthermore, because Dor HaMabul worshiped the luminaries & constellations, Hashem spread an opaque density of clouds to block out all sight & light of the astronomical bodies.
(Note: Rabbi Elihu Levine's English-rendering of the Kli Yakar proved invaluable to understanding the above points.)
The Kli Yakar & Hurricanes
In addition, Netivot Shalom explains that the Rosh Hashanah idea of everything passing in judgement before Hashem is actually metaphor for Hashem's scrutiny of every living creature to see whether its existence is necessary for the coming year.
I couldn't help thinking that Hashem decided that certain islands in the Caribbean are no longer necessary, and that He decided so for the reasons stated above – all based on how they were mostly wiped out by the flooding of ferocious hurricanes.
If you know anything about that part of the world, the above breaches are part & parcel of those societies.
May we all merit to remain joyfully entrenched within our Torah boundaries.