1. Please make certain MSAA is turned off on the main camera, as they rely on the depth buffer.
2. Please make certain Cast Shadows are off on the water Mesh render Materials.
3. Deferred Rendering Mode
shaders require deferred rendering for the depth fade functions to work correctly as use with Unity's default depth buffer.
4. Linear Color Space should be active
The above 4 items are the most common reasons for the issues in setting up and water shaders, if you verify all 4 are correct and the issues still remains please contact us for further support!