what's the render mode?
are you sure that it isn't a light_spot that is in your map? If it is then it will mess with the water.
What texture are you using? Default blue water, a Xen texture? Certain textures don't interact with water quite correctly, perhaps the texture is messing with the light.
Other than this it may be that there is something blocking the water's light filter, try backing up your file and taking out the water, see if it's still dark where the water would of been.