Hi All
This may be due to the different height of the water. The further the water is from the terrain, the darker the effect will be between the water surface and the terrain.
If you are mixing classic water, and water effect layers, then there will definitely be a difference in look as the water effect layers are generated in a different way to classic water. Classic water uses the 'water colour' box in the environment settings to set the colour, whilst water effect layers use the top skybox colour to set the water colour (or more, the water reflects the top sky colour).
Regards