Water isn't affected by the "color fading" filter in beacon beams. This only affects water within a certain chunk distance for some reason. While this may not be a big issue, the problem causing this might be causing other water rendering issues with filters.
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However, this issue has been closed as Won't Fix.
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Confirmed on Windows 10 1.4.2.0.
Steps to reproduce:
Build a beacon (any power level) on land next to a dark ocean (the dark color makes the effect easier to see)..
Fly up a few blocks and look through the beam's edge at the water with viewing angles from near vertical to near horizontal.
Notice that as your view angle nears horizontal, the beam's effect has a discontinuity where it seems to fade out, then suddenly resumes stronger than anywhere else. Also notice that the boundary line seems to follow chunk boundaries.
Continue flying upward while observing the boundary.
Notice that the boundary remains at the same chunk boundaries.
Teleport to Y=126.0, at which point your eyes are at approximately Y=127.5. Notice that the effect persists.
Teleport to Y=126.5, at which point your eyes are at or above Y=128. Notice that the effect disappears.
I tried changing my render distance from 24 to 16 to see if it had any effect. It didn't appear to, but I'm not very certain of that.