Just tried a nvidia 670 on the same levels were I was seeing artifacts on water surfaces with the 290 but dropped the details from very high to high so it would match the framerate and lo and behold it does the same thing with the nvidia card.
So either this is a Crysis 3 bug just on water in some levels that some don't notice or there is something else on my system that is causing it.
Probably a game bug, just ignore it.
