I tried the "tiny" version of the Flood Mod (https://www.gta5-mods.com/misc/gta-v-flood-mod ), which just increases the sea level a few meters. This means Los Santos won't be underwater, but Vespucci Beach will be flooded. The only mission I know happens there is Repossession, so I tried it out with this mod.
The only problem is the objective motorbike gets destroyed. Maybe it gets underwater on some certain zone, and i couldn't reach it. But it was worth trying it!
Check the GTA V intro with Los Santos underwater: https://www.youtube.com/watch?v=d0rSLmHKRwY