In Minecraft versions since 1.8, water "effects" start rendering when the player's view is still above water. This is extremely jarring when bobbing up and down in water. The attachment image with the glowstone in hand is from the latest snapshot. The attachment with the taiga biome in background (generated in an older version) was taken in 1.7.10 (notice the bug is not present). The third screenshot was taken in 1.8.9, with the bug present.
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This issue duplicates MC-95688.

So does that mean this bug is the result of a fix for a more serious bug? This problem hasn't existed in most versions of Minecraft and I didn't notice any other serious flickering issues.
I couldn't find another bug reported listed for this. This bug has really been bothering me because I thought it would have been caught and fixed already. It would be great to get it fixed for 'update aquatic'! Here's to hoping it and other water rendering bugs can be squashed once and for all.