Filter Maintenance And Cleaning Tips

OB Guy

Staff member
NOTICE - This article is very important to new fish-keepers and for tanks that are less than six months old. It is during these early stages that learning proper filter maintenance is most critical since you are still growing a proper sized Nitrifying Bacteria (N-Bacteria) colony in your filter media and substrate.

This article is also very important and applicable for tanks over six months old that have limited filtration or overstocking issues or if you are having water quality issues, algae problems, sick fish, etc.

You should also have a Master Test Kit capable of testing ammonia, nitrites, nitrates and pH. Having GH and KH test kits are also encouraged in determining some basic water chemistry/quality issues. There are many other things going on in our tanks that we can not easily test for.


If your new tank has a small HOB (hang on back filter system) and you were told to buy and replace your filter cartridge once a month... or every other week, then that may be what is causing you so many problems. You are potentially putting your tank into a new mini-cycle everytime you "clean" the filters or change them out for a new one. NEVER clean the filters in the normal sense of the word "clean". If you cleaned the filter media by running the filter under tap water, the chlorine/chloramine in the water could have killed your GOOD nitrifying bacteria in the filter and you will have to "cycle" your filter media again. This will probably put your tank into a new mini-cycle which means testing for ammonia and nitrites and doing PWC's (partial water changes) to keep them at safe levels. This mini-cycle could take around two weeks but there is usually enough N-bacteria on other surface areas and in the gravel to keep major spikes in the ammonia or nitrites from happening but most of the N-Bacteria live in the filter sponges, pads, etc. so cleaning/maintaining them should be done carefully.

All you should do is once a week or every other week, when you do your 25% PWC (partial water change), take some of the tank water in a bucket and then you can take your filter cartridge or media out of the holder and swoosh it around in the tank water and squeeze it out to remove the big stuff off of it. Then put it back in the holder and back in your filter system. If it's really clogged up with detritus, you could also squeez it several times in the removed tank water bucket. This will possibly squeeze out some of the good N-Bacteria but will usually leave enough to keep your tank safe. The N-Bacteria are capable of doubling their colony size every 24 hours so as long as you leave enough, the colony will grow back shortly. This "swooshing or squeezing in removed tank water" method keeps the GOOD bacteria alive on the filter so you do not cause your tank to "cycle" again.

I know the filter companies and some pet store employees tell you to replace it once a month but they are just trying to sell filters. That is one of the leading cause of problems with new fish keepers ... changing out the filters because the "instructions" say to do it.

It is important to clean your filters regularly so you do not have excess detritus building up in them. Detritus in your filter media, when it starts breaking down, becomes a nitrate factory which goes into your water column as the tank water is filtered through it. Nitrates and phosphates feed algae blooms. Just like vacuuming your gravel to remove excess detritus before it breaks down, cleaning the filters often will also keep the nitrates much lower. I guess if you do frequent PWC's, that would substitute for keeping the filters cleaner but if you cleaned your filters before they become completely clogged, it would make the water quality even better between PWC's. Further, the bacteria that is consuming and breaking down the detritus use up a lot of O2 and KH and put out a lot of CO2. The higher CO2 further feeds algae growth and lowers your pH. The loss of KH can cause your pH to crash putting your fish into pH shock.

HOB's (Hang On Back Filter Systems - Power Filters and Bio-Wheel Systems) -

If you have a HOB filter system, you should really only clean the filter cartridge if the flow rate slows down or it's backing up back into the tank via the overflow outlet. But do NOT go more than a month between doing maintenance on any of your filters as they will build up a lot of detritus which will start to decay and possibly cause your nitrates to start climbing quickly. I just do the swoosh and/or squeeze method once a week with my 25% PWC and never have the problem. Don't worry.. most of us learned the hard way in the beginning.

Another thing if you have an HOB... is after you swoosh/squeeze the filter media/cartridge and have it ready to put back in the holder, dump the water out of the HOB reservoir as it will have some "big stuff" in there as well. Then put your filter back in the HOB, dip a few cups of water out of your tank to fill the HOB reservoir and then plug it back in.

If your HOB also has a Bio-Wheel, then you could technically change out the cartridge instead of using the swoosh/squeeze method since the actual Bio-Wheel would house sufficient numbers of N-Bacteria so that you would not cause a mini-cycle. The inventors of this system created it for that reason... so they could sell you lots of filter cartridges and encourage you to change them without causing harm to your fish. I still don't think it's necessary but if you find it simpler to change the cartridge every few weeks and don't mind the expense, then that is a choice that is available to you.

One last tip... if your "biobag" filters or filter cartridges have carbon in them, you can dump the carbon out after a few weeks since it has lost its effectiveness by then. This will also improve the flow rate through the "empty" biobag/cartridge as well. Some companies try to prevent you from emptying the carbon by sealing it inside of the plastic housing of the cartridge frame. I have been successful with doing "surgery" on the section holding the old carbon to open it up and dump the carbon while keeping the frame and floss/poly pad for reuse. The floss/poly pad or sponge material in the biobag/cartridge should last over a year but in the event you do decide you want to change your biobag/cartridge, put the new one in the reservoir for 2 weeks so it builds up a good bacteria colony. Then on your next PWC, you can trash the old one, swoosh the new one and then put in in the holder. It's not really necessary to change them very often... at least not until they look like they are about to fall apart. I have the same filter cartridges on my HOB's and they are all over a year old. (More about carbon below)


As far as a canister filter, I have four different phases of mixed mechanical/biological filtration in my canister filter system. I have a large sponge block with large pores, then a smaller sponge block with smaller pores, then even a smaller pore sponge and then a filter floss pad. I do maintenance on my canister twice a month or if I notice the flow rate slowing down. At the beginning of the month, I leave the sponges alone and clean the floss pad real good.. even running it under hot faucet water until it's white again. In the middle of the month, I squeeze the sponges to clean them and get the big stuff out of them but I don't run them under hot faucet water. This keeps a big portion of the nitrifying bacteria alive with each filter "cleaning" so I never have a problem with a mini-cycle. I also have two filters running on each of my tanks so I alternate the maintenance on them from week to week so I have at least one fully cycled filter running at all times.


Sponge filter cleaning should be treated similar to cleaning the sponges in canister filters but obviously on a much smaller scale. The safest thing to do would be to squeeze the sponge in some removed tank water to remove the detritus from the sponge but keeping the majority of the N-Bacteria alive on the cell walls of the sponge. Then replace it and you are good to go!


If you have more than one filter system on your tank, then you could do alternating filter cleaning or changing and more thoroughly cleaning the filters since the other one will still be fully cycled. I do this on my Goldfish/Pleco tank since they are such big waste producers. I alternate between the two filter systems and clean 1/2 the filter media every two weeks. This means that I am only doing a good cleaning on 1/4th of my overall filter media volume and one of the filter systems does not even get touched every other week.

UGF's (Under Gravel Filters) -

These systems are not as common any more but there is a reverse flow UGF that is making a comeback in the industry.

The purpose of the reverse flow UGF is to push water up through the gravel which raises the detritus into the water column to be sucked into the intake and filtered out of the water before the "clean" water is returned to the tank through the gravel. This could save time in gravel vacuuming since it would not have to be done very often with this type of system but it does not work for planted tanks where the plants with a normal substrate. It would work if the plants are containerized plants.

The main thing with a regular UGF, that sucks the water down through the gravel (so it's not good for a planted tank either), is to properly maintain them by vacuuming the gravel really good with the vacuum tube pushed down through the gravel to the UGF plate and make sure you suck up all of the detritus/mulm that gets caught between the gravel/plate/bottom.

As you may have noticed, I do not mention keeping carbon in my filter systems. Most experience freshwater fish keepers are not keeping activated carbon in their filters on a permanent basis any longer and rely on more frequent PWC's to keep the water quality in good condition. It's just another thing that the filter people are trying to sell you to keep revenue pouring in... pardon the pun. I haven't had any activated carbon in any of my four filter systems on two tanks for over two years and all of my fish are fine. I do keep some around in case of an emergency or if I need to filter some medicine out of one of my tanks but other than that, it sits in the closet. Of course, I am diligent about doing weekly 25% PWC's so I am removing any organic buildup that some people may rely on carbon to remove. Also, most carbon products available to consumers will leach phosphates into your tank, which can cause algae problems... and some carbon products have been reported to actually leech the chemicals they had previously absorbed which can cause other health problems.

If your filter cartridges have the activated carbon sealed up inside of a plastic housing, it might take some minor "surgery" to open the plastic housing up so you can dump out the carbon. I have done this to several different manufacturers cartridges so I think it's possible with any of them. This way, you still have the plastic frame and floss/sponge material that can be re-used many, many times using the swooshing method above. It's better for your fish and your wallet.

If you have juvenile fish in your tank(s), then running carbon or Purigen is encourage to help remove the hormone buildup which can lead to stunting and health issues. Remember carbon should probably be changed every two weeks. I am now using Purigen in my tanks since it is better than carbon and is rechargeable so it costs less.

I've been reading and researching more and more about a product from Seachem, called Purigen, which is a rechargeable granular additive that can be used in filter systems and from what I've been reading on forum threads, it does work as advertised. It's not like zeolite which can starve your N-bacteria colonies. This product is more like activated carbon but is advertised to work 500% better than activated carbon. Since it is rechargeable and actually filters organic compounds better and LASTS LONGER than carbon, I'm not opposed to using a product like this and may actually try it soon.

Purigen™ is a premium synthetic adsorbent that is unlike any other filtration product. It is not a mixture of ion exchangers or adsorbents, but a unique macro-porous synthetic polymer that removes soluble and insoluble impurities from water at a rate and capacity that exceeds all others by over 500%. Purigen™ controls ammonia, nitrites and nitrates by removing nitrogenous organic waste that would otherwise release these harmful compounds. Purigen’s™ impact on trace elements is minimal. It significantly raises redox. It polishes water to unparalleled clarity. Purigen™ darkens progressively as it exhausts, and is easily renewed by treating with bleach. Purigen™ is designed for both marine and freshwater use. This product is sold by volume. Cited weight is minimal weight.

Directions: Rinse before use. Use in a fine mesh filter bag. Each 1 L treats up to 4,000 L (1,000 gallons*) for up to six months. Exhaustion is indicated by a pronounced discoloration of the beads to dark brown or black.

Regeneration: Soak in a 1:1 bleach:water solution for 24 hours in a non-metalic container in a well ventilated area and away from children. Rinse well, then soak for 8 hours with a solution containing 2 tablespoons of ChlorGuard™, Prime™, or equivalent dechlorinator per cup of water. Rinse well. For freshwater use, soak for 4 hours with a solution containing 1 tablespoon of buffer per cup of water (Discus Buffer™, Neutral Regulator™, or Acid Buffer™). Original color and full activity should now be restored and Purigen™ is ready for reuse. Caution: some slime coat products may permanently foul Purigen™ and render regeneration difficult. Do not reuse if odor of chlorine is detectable. In case of doubt, soak beads in small quantity of water and test for residual chlorine with a chlorine test kit.


Zeolite is a white granular product that many consumers are often sold as a solution to ammonia issues in their tanks. While it does absorb ammonia, it gives you a false sense of security as it will "fill up" and then quit absorbing ammonia causing ammonia spikes in your tanks. If you did not use zeolite, you would have built up a proper sized N-Bacteria colony in your filter media which would have taken care of any potential ammonia issues. Further, when people get ammonia spikes, they are shortly followed by nitrite spikes. Then they are told to add salt to the tank to keep the fish from getting nitrite poisoning. The problem with this is that salt will cause zeolite to release ALL of the absorbed ammonia causing the ammonia level to spike even higher. Once again, it's a product that I keep on hand in case of emergencies... like when I went 15 days with no power after Hurricane Katrina, but it's not something I run in my filters on a normal basis.


I've been learning a lot more about hormone issues that happen in overstocked or undersized tanks. In various fishery related studies, it has been reported that your fish release a hormone into the water column and when this hormone level reaches a certain point, the fish begin to get stressed and stunting issues start to develop. Stress leads to immune system issues and fish start to get sick. The best way to solve this problem is to NOT overstock your tank or have fish that are supposed to get BIG in a small tank. If you are stuck with this problem, then doing frequent PWC's (sometimes daily, depending on your situation), will reduce these hormone levels. It is also reported that products like carbon and more advanced chemical filtration products like Purigen, will remove some or all of these hormones but this needs further research. The best and simplest solution to removing these hormone levels is through frequent PWC's.

In conclusion:

There's a saying... "Dilution is the solution to pollution"... which certainly holds true in the fish keeping hobby. Fresh, clean and frequent PWC's (partial water changes) will do more to keeping your fish healthy than anything else out there.