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Yes mate, most people run them on the return pipe so they don't clog as quickly but a few on here run them on the intake side of the filter to keep the mist out of the display, even with an in tank diffuser a certain amount of co2 will end up passing through the filter.
I have run in tank diffusers into my intake for the last year. Just get a bit of burping. There is a thread discussing this on here some where but I couldn't find it on my phone sorry
I think i read somewhere that running co2 through the filter media can kill or harm the media. Not sure though. ATM, I am running my co2 with the glass diffuser attached through the internal filter chamber of a Juwel Bio3 between the media and the inlet of the pump. The diffuser breaks down the gas to a mist as we know and the co2 is then more easily distributed into the tank without the "burping".
The bacteria needs oxygen to survive and co2 will not limit ghd amount of oxygen in the water passing through. Worst that will happen is your o ring/seals will corrode a little faster
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