This is simple. I'm not sure if it is a bug or this is intended in Minecraft. When you fly into the water with an Elytra it seems to still be in "Fly Mode". When you swim up the water or go down it you are still in a vertical/horizontal position depending on which way you are looking, in the water.
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This ticket is invalid as it relates to a modified or 3rd party client, server, or launcher.
In addition this issue duplicates MC-97190.