Ive noticed a bug with the unity 3.2 pro water, now im not sure if everyone is getting this, ive tried re importing and everything, layers and stuff, what is happening is, in editor and in game at about the distance of 50m + the water goes through the trees as seen below, when i get closer than 50m its back to normal.
would imagine its a layer hierarchy problem, when it gets to the 50m far plane the trees render first then the water, try sticking the water on a separate layer or and this is a total guess, try taking the trees coping them and deleting the originals, should stick it above the water in the object hierarchy and thus the render hierarchy but just an idea, cant test it myself so…
The same has been reported here:
http://forum.unity3d.com/threads/77544-3.2-Water-over-billboard-trees