Even with the conduit effect which allows underwater breathing, the "bed is obstructed" message appears when trying to sleep on it.
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We're actually already tracking this issue at MCPE-87848, so I will resolve and link this ticket as a duplicate.
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If the waterlogged bed is at the water surface, you can sleep in it only when you have water breathing or conduit power effect.
Otherwise it's just obstructed by water.