Thanks Oshyan
I agree that the water is bit too blue. The tone is similar to unmasked water so I'll try dropping the saturation first and compare it to unmasked water.
I was toying with the possibility of doing some extra surfacing with the water mask to simulate some subsurface colours, but this would only work for a high camera position. There is some subsurface detail in the Landsat image I could start with, mostly in the shallow end of Lake Jackson. The other possibility may be to use an internal drop shadow (0 offset) in Photoshop on the water mask image to use on a child layer of the water surface. I'll apply that to my next high camera render and see how it goes.
Update: Render's in progress. I've set up a demo mask for changing the water colour using an image mask on the colour function of the water shader. This shows some merit given a better mask image.
The other fix was getting rid of the fake stones from everywhere to just the lake beds and surrounds. Even though the fake stone shaders were child layers of a base "lake bed" layer they still extended across the entire terrain screwing up grass and snow in the process.
I plugged in the mask for the parent layer into the blending shader for each fake stone layer (and set blend by shader) and everything was fixed
. I had found some other interesting rocky areas up on the mountains while exploring this file so I'll probably have to put some stones back in this area. Given this behaviour of fake stones, it's probably pointless having them as child layers. This is not an entirely bad thing as I can now combine extra masks to place the same stones in other areas of the terrain as well without having to duplicate them to another surface layer.