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I have 2 Emperor 400's on my 120 gal tank. They seem to do a pretty good job. But, now they are not up to 100% and I think they are due for mainteneance.

What is the best way to clean these? I know I don't want to disturb the bacteria on the bio-wheels. And, I know I shouldn't use tap water to clean the filter. Will it hurt if I change the filter cartridges, or is there bacteria growing on these also? Will it help if I add activated carbon?

Last time I cleaned the filters I created a bacteria bloom that took weeks to clear up. I don't want to make that mistake again!

The nice thing about Hob’s is you can clean them at different times, like a week or two apart from each other. I don't run the Emperor 400's, and am not exactly sure of the filter media set up in them, I recall they have two separate chambers with media in each, etc. In general filters all have a couple components, first a media which catches and holds larger particles, this must be replaced at regular intervals, then it will have a second media, that may or not be used for chemical filtration, i.e. carbon. Then they will have a third media for biological filtration. i.e. a sponge or bio-wheels, etc etc. The biological filter, is the one you don't wish to disturb, the other two you can pretty much change and they will not cause to much of a disturbance in your tank's system. In yours, the bio-wheels become the repository, for the largest concentration of bacterial colonies. If there is also a sponge incorporated as well, then you may need to rinse this out, in clean tank water, to rid it of the finer particles that have accumulated in it, and are now slowing down the flow of water. Others here who run the 330's or 440's may have more detailed tips for you.

dito

Changing filter cart shouldn't be a problem becase you still have the 2 additional media trap and there are Bio Wheels which culture the bacteria. Just don't change all 4 things at the same time plus you still have the 2nd Emperor 400. I know if you don't change the filter pad for over 6 weeks the water flow decreases but then the filter carts are expensive. I started buying large filter pads and cut to size and replace the old filter and good carbons and just put a few rubberbands around to hold, therefore, the next time you need to change you don't need to rip it apart and glue it back. I change the pad every other time I change carbon and I change carbon every 3 weeks. I also have air bubble filter inside the tank which I change the carbon every month.

I've a 40gal tank with the Emperor 400 for about a year now and also started the Magnum 350 begining of the year because the water was so cloudy due to number of fishes that I constantly add.

Right now I have the following in the tank:
2 red oscars 8.5-9.5" ,1 albino oscar 8.5" (they were babies when I got them a year ago. 5 perrot fish ranging from 5-6.5", 3 flowerhorns 4.5-5.5", 3 Jack demseys 3.5-4.5", 1 baby Green Terror, 1 baby Jewel, and 1 baby Gold Severum or Midas(not sure which is which-it's kind of orange and white)? and 1 med and 1 large Pleco. To boot, 3 large sword plants, 1 med and 2 large driftwood, 2 pcs of small rocks.

And yes, they barely have enough space to swim around but they seem to have become one large family and of course the oscars have their moments especially the albino being the third wheel.

Back to your question, if you don't change everything at the same time you should be okay. Hope this help.