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Loot dots seem to appear in the water normally when you're walking on the shore, and then disappear as soon as you get in the water. Similar behavior with flying mounts - You can fly over the surface and see a loot dot appear but if you hop off the mount into the water to get it , the dot vanishes.
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I can attest to this.
I think it's a matter of how the game generates loot right now. I'll see what you're describing, but will then see another loot spawn somewhere else and I'll be able to get it.