When trying to spawn in 16000 particles like Dinnerbone did I noticed that I was able to see water through certain particles.

To recreate use the test world, or use the command while above water.

Particles: mobSpell, endRod, fireworksSpark, spell, mobSpellAmbient, witchMagic

Test World: https://www.dropbox.com/s/qggsekm6epeykx9/Test%20World.zip?dl=0

Command:
/particle endRod ~ ~-2 ~ 1 1 1 0 16000

Please let me know if you require my system information.