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
/particle endRod ~ ~-2 ~ 1 1 1 0 16000
Please let me know if you require my system information.