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Guess it depends on the type of filter unit were talking about here. Non-HOB canisters generally pass the water through the media before coming into contact w/ the impeller assembly. HOB's are the other way round, they pull water from the tank over the impeller assembly, then through the media. If you have HOB's, shorten your intake tube, and turn off the filters during maintainance. If you have a canister, no worries.
 
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