First, thanks for the replies, they're much appreciated.
Second, I keep seeing comments about visibility entering the discussion. These are valid, and I think even in the Nightscale encounter, obscurement and cover are confused for one another- in the murky black waters of the lake, an all-black dragon would be hard to see clearly. But that's a different mechanic. Cover isn't about whether or not you can see the target, but how likely you are to hit an intervening obstacle that isn't your target- the "clear pane of glass" Sage question addresses this point.
That water can provide obscurement (a word that either doesn't exist or I apparently keep mispelling) is quite evident, even in relatively clear water, light is distorted by it.
I think, based on many of your comments, that water can provide cover in certain circumstances, it's just nailing down what those circumstances should be.