Amazing work. The colors you managed in that piece are hyper-realistic; highly convincing.
I tried out the water shader issue and sure enough I reproduced it easily, but could not find a way to mitigate it. Well, by adding very small displacement to the land at the water's edge seemed to work, but that's certainly not practical or maybe even possible outside the lab, so to speak. It seems to be connected with the subsurface scattering settings.
There's post-processing. Sorta kills the animation thing.
I tried faking a water surface, but the default shader did not act like I felt it should. Maybe if you imported an OBJ the one attached to that would behave more predictably? That is, import an OBJ instead of using the Lake with water shader? Without subsurf you could maybe color the landscape beneath to obtain any effects your looking for...? I would test this out myself instead of shooting from the hip, but these people here seem to think they're paying me to work for them instead of just hang out with them... odd, I know.
Edit: [later than evening...] At home. Tried it. Failed completely. SO that's why there's a water shader....