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Clouds are transparent when you are above/in them but not when you're underneath them.

Lava and water are completely transparent at certain height levels

Having high leveled Respiration enchantment makes it hard to see underwater

can't see other player in bed

you can see a stained glass pain clearer through stained glass

trapdoor dubble inside texture

Vignette effect's visibility is not being updated according to light level when GUI is hidden

Visibility option has a tick box

Water Breathing visibility underwater

Respiration visibility underwater

Can't see rails through glass underwater

Light levels/render distance being affected in well-lit covered structures

In splitscreen multiplayer mode on Consoles, only the first player can see through water appropriately. All other players have opaque water and minimal visibility underwater

Foxes can't see mobs that are in fenced areas or behind glass blocks