I run mine on the intake. THe original thought there was that if any bubbles got through, the impeller would chop them up. However, now that I have my reactor, I see that bubbles never make it all the way through it, so I doubt it would matter honestly. But, since the pump is working to push the water up against gravity, I suspect there's potential for even more impact to the flow rate of the canister if you put it on the exhaust of the canister.
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