I use it and have never seen the water black. It's actually has more color and transparency to it.
When you say black, even in the daytime? Could be a mix of mods or as Webster said a file in the wrong place. I'll assume you've updated all drivers and stuff like that.
One thing I learned when playing with mods is to have a clean backup of the games data files in a seperate folder. My water didn't go black, but once went purple. I had somehow placed a file from one mod into another.
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