I wish I read this before doing what I did.Here's how i clean my aqua clear filter media. I set aside about 2 gallons of the water from my tank as I'm doing a water change. I then turn off the filter, and then take out the media from the filter and rinse it off in the tank water i had set aside. You can shake the biomax around pretty good to get all the crap out of it. I also take the sponge and I squeeze it in and out several times to get all the crap out of it. You dont really have to be that gentle, just shake it around squeeze it out until it looks clean. There will be all kinds of brown stuff and debris floating in the water you cleaned it in. The main thing is you dont want to leave the media out of the water for too long. As soon as your done cleaning, put it all back in the filter and get the filter going again. You will have no problems with loss of bacteria. Be sure to fill the reservoir part of the filter with tank water before you start your filter back up so it doesnt burn out the impeller. Its not really as scary as youd think. Those bacteria are pretty tough.
Even if you did kill 90% of the bacteria it is still in the tank and will recolonize very quickly.
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THIS. Personally I use RODI water to rinse out my filters, but a little tap water won't kill off all the bacteria. The bacteria are more resilient than most people give them credit for, and a quick rinse in tap water won't kill them all.i rinse my canisters in room temp tap (chlorine and chloramine) everytime...a quick rinse may kill some, but it wont destroy your colony
Someone correct me if I am wrong but beneifitial bacteria is not in the water column.
^ +1for the most part no. but beneficial bacteria covers all the surfaces in the aquarium and can reproduce every 16-20 hours.. so once a decent amount is there. it doesn't take long to have a full level of BB