GtaGamer222 has made a mod that does pretty much as advertised: it covers Los Santos in water, so much so that only the very highest parts of the city and surrounding countryside have escaped the deluge.
Here's a video by GtaGamer222 running around and piloting a sub:
While here's a good one by MkElite that's got a lot of first-person action, as well as a look at what happens when you change the weather conditions.
If this looks familiar, that's because a very similar mod was made for the console version of the game. Not sure that one could spawn giant whales in downtown, though.
Time to add this to the game's custom soundtrack: