When you have potion particles on you, or smoke is coming up from a fire or any other particle is in the air, if water is behind it you will see the water rendered on top instead. This has been in the game in every version I played since 1.4.7.

There are similar bug reports that are labelled fixed, but that is not the case.

Exceptions: torch smoke is not affected by this.

Proof: 

Image 1: smoke particles behind the water even if they are in front

Image 2: same effect as in image 1

Image 3: torch smoke is not affected

 

Image 4: beacon effect particles show behind far away water

Image 5: same effect as in image 4

Image 6: clouds doing very weird things, i don't know if is the same bug

Image 7: I think this is a different bug because it happens at chunk borders