If you mean water clarity when the camera is above the water surface, go to data\shaders\water , and edit "watertransPS.fx" or "watertransp64PS.fx". can't remember which one. You can edit them with the notepad, search for DepthLength or MaxDist.
If you're talking about clarity for underwater view, open scene.dat with S3d
Node - sky -> EnvData -> EnvData -> Underwater -> Fog -> ZMax
I'm not sure how much is one unit of ZMax, though.
Hope that helps!
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