Hi MrMcintosh,
I've been doing a fair amount of work on the rendering engine until a few months back when I had to interrupt for a number of real-life reasons. I hope to get back on track in a few months when a number of things have fallen into place. I seem to remember what you'd like to deal with is shader-based and I barely scratched the surface there, so I can't be of much help at this stage. I imagine you already found that WorldRendererImpl is the entry point for all things rendering, in particular its render() method. If you dig enough from there you should find what you are looking for. I warn you, it might not be pretty. Much of that code is not particularly well documented, something I've been trying to address elsewhere, so far only in high-level rendering code and there still is plenty of work to be done in that direction.
If you do manage to find your way around down there in shaderland, would you mind checking if you can use the biome's tint to give a proper color to the water? I.e. the landscape underwater seen from above water should have a distinct turquoise tint in a life-like biome. Also, I don't remember if tint is a 3 or 4 components vector, but either way it should be possible to interpret that information also in regard of the opacity of the water, i.e. to render some water as very transparent or very murky. I'm not saying you have to do it, but you might just stumble on the piece of code that would allow this with little tweaking.
Again, sorry I can't be of more help at this stage.
