Alot of areas have buggy water now. Some areas are transparent when underwater and some are tranparent from the surface.

You can either see straight to the bottom like there is no water or you can see forever while you are underwater.

I have no idea which patch did this though because, I have not been able to keep up with the game lately.

IS there any chance you can't see the spider webs,smoke,mountain mists and fire?Do you see the fire like heat?

I experience this bug sometimes when I tab out of the game and tab back in, but not always. Is the water always transparent for you, or just some times? Is it all water surfaces that have some kind of bug? Does exiting the game and restarting it fix it?

I've had this issue from day one, it seems pretty random, a reload usually fixes it.

If you are willing to mod your game I suggest this one: http://www.skyrimnexus.com/downloads/file.php?id=711 makes water look much better and so far I don't have any transparency bugs with it.

I have seen this bug in a cave and in Whiterun on Xbox 360 and PC since 1.3. Also I have seen the vanishing cloudy effect underwater (goes clear) since I first played the game on launch (also both platforms). That last bug is so random and horrible (and no I'm not talking about the water line surface bug, that has never been fixed since Oblivion).