Only the water passing through the lamp is irradiated, along with whatever is in the water passing through. With the proper flow rate, the water and the stuf in it is exposed long enough that it is killed or damaged sufficiently that it cannot reproduce. The effect is lasting on bacteria and algae that pass through the UV but the water itself is not changed.
I may be mistaken here (And I'm sure I'll be corrected if I am.), but I think that the reason that a UV filter doesn't hurt plants/fish/shrimp is that they don't get pumped through the UV filter and therefore are not exposed to the UV rays...
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