How to loot sea monsters in The Witcher 3?

@Dallium seems to be correct in that critters that die underwater due to crossbow shots don't seem to drop loot. Unfortunately that doesn't seem to be what you're asking.

If you kill something over the water, (siren or other hybrid while on a boat) their body will drop to the surface of the water and float while their loot drops to the bottom. When the battle is over, dive in & swim down to collect your lovely, lovely loot. If you are over deep enough water, take a swig of Killer Whale before diving to extend your ability to hold your breath.

Of course, even on land, some of the critters you kill with your sword just don't drop any loot. This happens on boats too.

It seems to make a difference if you slay them "on the wing" vs. knocking them into the water & delivering the killing blow as they float next to your boat. I've not seen a stunned + floating + death blow opponent leave loot.

Edit

A recent patch seems to have reduced the vertical range at which loot is shown on the mini-map. It now seems as if you need to dive to detect loot if the water is more than a few fathoms deep.

I think you're asking how to loot the corpses of monsters who die in water. If that's what you're asking, you can't loot monsters who die in water.