I believe you're correct about distance being a factor. As best I recall this is related to accuracy issues in the occlusion system, determining which surface is "on top". If you can increase the difference between the water height and the underlying surface this should be solved. Alternatively you could just use a water shader on the terrain rather than a lake object; that should avoid those errors since the surface itself is water shaded, rather than being a plane over another differently colored surface. However I may be mistaken in how you're doing this.
Please do update us if you continue to experiment with this and get new results. This is something we will fix for the final version at least.
- Oshyan