Every 5hrs 30mins Armageddon occurs and lasts three in game days. The flooding of the world is foreshadowed by rain which starts right before it floods and lasts till its over. The maximum height of the flood is determined by the lowest placed monolith, so a player settlement can never be drowned.
Hints:
The Armageddon is a nice feature. The flood comes and suddenly (if a dive tool is available) many places become accessible that have been inaccessible before.
Also the AI's drown and their bases are easy to plunder and destroy. Paradise for the submerged player!
But Armageddon can be prevented, too. The flood never drowns a settlement - so when you place a monolith just over the waterline the Armageddon can't raise the water and the flood is technically prevented.