Steps to reproduce:

1) Download attached project "New Unity Project2.zip" and open in Unity 5.3.x version.
2) In Project tab, click on Standart Assets >> Environment >> Water(Basic) >> Prefabs >> WaterBasicDaytime.
3) Drop this prefab in Hierarchy tab/Scene and you will notice that water is lost his shader(pink color of water)(see image attached "pink.png")
4) Open project in 5.4.0b22, drop same prefab in to Hierarchy tab/scene and shaders will be fine(see image attached "fine.png").

Reproduced with: 5.2.1f4, 5.3.4f1, 5.3.5p5

Not reproduced with: 5.4.0b22.