I've experienced this recently and if it's a bug then here you go:
This doesn't happen with the default resource pack. When this error happens, I am using a 128px resource pack.
When I move away from water (say about 10-20 blocks) it simply disappears. The shadow is still there so I can see where the water would be, but the water is not actually rendered.
If I move back towards the water, it will reappear.
When this glitch occurs, it affects all visible water, there seems to be a limit on how close you have to be to water before it renders, and if you are outside this range, it all disappears at once.