A number of years ago I wrote some well received articles for a Goldfish forum that I was a member of, and I recently discovered that the forum, sadly, no longer exists. I was able to retrieve my articles, using an online “wayback machine” and would like to post them here to access for anyone who might be interested.

Both articles, this one and the “Guide to Cycling an Aquarium”, are relevant not only to fancy goldfish enthusiasts, but to all freshwater fish keepers and ponders alike.

Guide to Cleaning Aquarium Filters

by Ci Shepard

I would like to clear up some misunderstandings about cleaning filters, why, how and when. I have used all kinds of filters on indoor tanks and ponds, for many years, and have a good understanding of how they work, how to use them successfully, how to maintain them, even how to build them.

To understand how various filters work, you need to know a bit about the nitrification cycle in addition to understanding what you want your filter to accomplish.

To simplify:
Fish produce ammonia as a waste product. If they are alive, they are excreting ammonia, even when not being fed (as in pond fish during a winter fast). They also produce solid feces, and if left in the tank, these feces break down and produce more ammonia, as do decaying plants, uneaten food, undiscovered dead fish and infertile eggs left in the tank.

In any fish tank or pond, even one without filtration, bacteria that consume ammonia grow naturally. In other words, you do not have to add them, they just exist - the come in from the air, the water, the fish, plants. They cling to all surfaces in the tank and will grow a colony large enough to consume all the ammonia produced as long as there is enough surface area for them to live on.

If more ammonia is introduced, as in adding fish, fish growing larger and/or feed increased, the colony will expand. If less ammonia is produced, some bacteria will die off. They regulate themselves this way, and in an established tank the changes are virtually imperceptible by us.

These ammonia eating bacteria create nitrite as a by-product. Once nitrite starts appearing in the tank another type of bacteria start growing (again, appearing out of nowhere and clinging to all surfaces) which consume nitrites and convert them to nitrates. They form a colony as well which co-exist with the other bacteria.

There are no bacteria that grow naturally in a home aquarium or pond that consume nitrate ... for our purposes, nitrate needs to be controlled by either water changes or perhaps using enough live plants that they take up the excess nitrate. Water changes are important for other reasons, so usually controlling nitrate is not an issue.

Back to the filters:

Basically, there are mechanical filters, biological filters, combinations of these (most of those available for home aquaria are combinations) and another category might be fines filters.

Mechanical filters are used to trap and filter out solid waste and debris. Biological filters contain media that provides large amounts of surface area for bacterial colonies to grow on. Fines filters give a final polish to the water before sending it back to the main body of the tank.

So let's look at some common filters:

HOB (hang on back) filter:

This filter is a device that hangs over the rim of the tank on the outside. It sucks water through an intake tube usually from somewhere in the bottom half of the tank and sends it through either a foam block, possibly some media in the chamber and/or a cartridge that holds dense fibres and sometimes a layer of charcoal.

This is primarily a mechanical filter, although with a sponge or other media in the chamber it provides some biological filtration as well. It is meant to suck up solid waste, trap it in the sponge or cartridge and send clean water back to the tank.

If you don't clean the resulting mulm (dirt, sludge, muck, debris) out of the filter chamber, sponge or cartridge regularly, what happens to it? It decomposes, as it is sitting there, and creates more ammonia. I am going to emphasize this - there is no point in sucking it up and trapping it in the filter if you are not going to then remove it. It is still in the water column and still polluting the tank, just as much as if you had left it on the bottom. In fact, with swiftly moving water constantly pushing against it in the filter, it decomposes even quicker, and crates small particles that get through the sponge or cartridge and back into the tank.

Cleaning your HOB depends on how it is set up and it's intended use. Due to its size, it clearly does not provide an abundance of biological conversion, but if you have sponges or media in it, it does provide some, and if you have a large tank (lots of surface area on the glass), low stocking levels, a shallow layer of gravel or stones on the bottom (more surface area), and even plastic plants and ornaments, you may not need more from your filter. You may also have additional biological filters to take up the slack, leaving the HOB to be purely mechanical.

So - if there is a sponge to trap solids - rinse it regularly to remove those solids. The more often the better.

If your tap water is treated (chlorine or chloramines as opposed to, say, well water) use dechlorinated water or fish tank water from your water change. Running water or squeezing and swishing both work.

If there is biological media in the chamber (little plastic balls or tubes, ceramic or stone-like bits, things like that) rinse them - they will work better if not covered with mulm.

If all you have is a "disposable" cartridge, you can do several things. One is rinse it over and over till it falls apart, then replace it, another is to take it apart and put something more durable in the frame, like a thin sponge, or, to get the most out of your HOB, fit in some biological media or a sponge into the chamber before the cartridge and consider the cartridge the final "fines" filter, and replace it when necessary.

Before I move on to other types of filters, I want to make an important point, one that causes the most confusion, and causes people to advise NOT to rinse your filters often. Beneficial bacteria do not live free swimming in the water and they do not live in mulm. They live on hard surfaces (including the plastic that a sponge is made of) and, in fact, cling tenaciously to these surfaces. They cannot be rinsed off with normal tap pressure, even vigorous scrubbing will not make a serious dent in their numbers.

As proof, I offer the concept of the moving bed filter, common in high end koi ponds. A barrel is filled with "Kaldness" media, which is a small plastic tubular media, each piece having ridges and wings providing a lot of surface area. Pond water passes through the barrel, and the media is kept in a constant rolling boil with large air pumps. The scrubbing action is enormous, and in fact, the claim is that old, dead bacteria are rubbed off this way, making room for fresh, new microorganisms to grow on the media. This is considered one of the best and most efficient biological filters for ponds that are dealing with fish 2-3 feet long and feed measured in pounds per day. There are huge amounts of ammonia to process in these ponds and, believe me, these filters harbour the bacteria perfectly well, despite the banging and constant rinsing they are subject to.

I have always rinsed my filters once to twice a week, and have never experienced an ammonia or nitrite spike afterwards. As long as you are not killing your bacteria with chlorine, they will survive any amount of rinse offs just fine. If you are still worried, just gently swish all of your filter components in a bucket of tank water - the mulm and debris will fall off, the bacteria will stay.

Sponge filters, sponge walls and Matten filters:

Sponges are dual purpose. They are usually set up to suck water through them using powerheads or air bubbles, trapping solids on their outer surfaces, while also providing a great amount of surface area per square inch for bacterial colonies. However, the more clogged a sponge gets with mulm, the less clean surface is available for bacteria, and their numbers can be reduced by essentially being oxygen starved.

Sponges should be squeezed out frequently - the solids will be removed from the water column and the bacterial colonies will work more efficiently.

Canister filters:

These usually have different layers inside that provide mechanical (layers of different density sponges), biological (some kind of specialized media in baskets) and fines (a final piece of fine sponge or filter floss pad). It amazes me that people leave their canisters for months at a time before cleaning. And then describe them as disgusting when they do. Again, if you don't take them apart and rinse the components, it is as if the solid waste were still in the tank!

Canisters are very efficient, and have a lot of room in them for biological activity - a much greater volume of media can be had compared to most all-in-one filters, and, depending on how many fish you have, how much water, etc, they can probably easily handle the extra ammonia produced by decaying fecal matter and debris trapped inside for weeks on end.

But, and here is my whole point, keeping filters rinsed properly reduces the total ammonia levels in the tank (by removing solids before they decay further) and creates a more efficient environment for beneficial bacteria to grow and consume pollutants in our tanks. This is good insurance for fish health, allows higher stocking levels if you so desire, reduces odours and unsightliness around the tank area and is simply good husbandry.

Undergravel filters

These filters don't seem to be as popular as they were in the recent past, but are still included in a lot of "starter kits", so I'll address them here. Now that we've covered the how's and why's of keeping filters clean, you can see how an undergravel filter might be problematic.

This type of filter consists of raised slotted plates that sit on the bottom of the tank with riser tubes in one or more of the corners, and it is covered with a layer of aquarium gravel. Either an airstone is put down the tubes or a powerhead is attached to the top, which pulls water up from underneath the plates. This results in water and debris being pulled down through the gravel, and circulated under and back up. The process can be reversed with water being pushed down through the riser tubes and up through the gravel instead.
The benefits are that you have fresh, oxygenated water running through a bed of media (the gravel) which provides a lot of surface area for biological filtration and keeps it aerobic, which beneficial bacteria need to survive. The top of the gravel acts as a mechanical filter, trapping solids and debris.

But the downfall is the amount of work it takes to effectively remove that debris, get it out of the water column and prevent channeling of the water through the gravel bed. The only reasonable means is to syphon the gravel thoroughly and regularly, short of emptying the tank and rinsing everything. It is a chore that often gets put off, or done incompletely, and ultimately build up occurs and compounds. Fine mulm also accumulates under the plates, which can't be reached with a syphon.

It's too bad, because it is actually a fantastic filter combining more media space than any other type with the look of gravel a lot of people like in a tank, and not a lot of expense. If an easier method of upkeep were found, or if you were willing to do the work necessary to keep it as clean as possible, it could be the best of all possible worlds.


Some might feel that taking proper measures to avoid introducing pathogens to the tank will suffice. Quarantining new livestock, not sharing equipment across tanks (nets, hoses, etc.), and washing your hands between working in tanks, will keep your fish healthy so that their immune systems can fight off pathogens.
 However, it is impossible to keep a sterile environment in a habitat containing living things. Just as beneficial bacteria simply "happen" to populate a filter, so can harmful bacteria. There is no need to over tax the filters with added ammonia, when some simple weekly maintenance will allow for increased stocking level and guarantee of a clean environment. Personally, I consider filter maintenance to be one of the hallmarks of "keeping your fish healthy". For a newcomer to the hobby, this is certainly the best habit to aspire to.

Regarding Mulm build up in an aquarium or pond filter, there are a few things to consider.

First of all, the accumulation of mulm clogs the pores and surfaces of bio media intended for aerobic conversion of ammonia and nitrite. As the layer thickens it creates anaerobic conditions from which colonies of beneficial bacteria will retreat and shrink, thus the filter becomes less efficient at conversion, while at the same time, the additional ammonia produced by the decaying material requires extra conversion. While it is true that sometimes the bacteria in anaerobic bed, usually in the substrate, can process nitrate, the management of such a bed, especially with goldfish who like to dig and disturb gravel and sand, is a risky endeavour. Far easier and beneficial to the fish to control nitrate with regular water changes. Allowing mulm to build up in the filter is not the same thing as creating a purposeful anaerobic bed.

Leaving mulm to build up in any type of filter also causes "channeling". Water will take the path of least resistance and bypass the blockages. This creates pockets in the media where fresh, ammonia laden water is not penetrating and so the bacteria that live there die off. These pockets can be anaerobic and large build ups of mulm can also harbour the types of bacteria that are present in internal infections and external ulcers in our fish.
Decaying material in the aquarium is not a harmless 'inert' substance - the process of decay not only contributes extra ammonia, but also can release unwanted minerals, metals, proteins, carbohydrates, skatols, phenols, albumen etc. into the water column. Also, bacteria need large amounts of oxygen to decompose this material, reducing the total oxygen concentration of the system.

These dissolved organic and inorganic substances contribute to poor water quality above and beyond what we routinely test for, and is the number one reason for stress and immune system breakdowns in fish.

Anaerobic bacteria utilize fish feces and decaying matter as a food source and produce hydrogen sulfide and methane gas as a byproduct, which can be deadly to goldfish. Aeromonas and psuedomonas can weaken fish and cause ulcers. Mycobacteria can live in mulm and causes all kinds of health problems in fish including organ failure (of which dropsy is a symptom), blood, brain and bone infections, deformities of the spine and ulcers. Mycobacteriosis is potentially infectious to people and can enter through cuts in the skin.
These types of bacteria cannot be barricaded out of a system. They come in on healthy fish, with no outward symptoms, sometimes living inside the body and organs, and shed into the environment on feces and slimecoat. They can be airborne and might even exist in the foods we feed (salmonella, e.coli, molds and fungus). Like beneficial bacteria and algal spores, they just 'happen' no matter how long you quarantine your fish and how sterile your equipment was to start with, and a buildup of anaerobic deritus is of great benefit to these microbes.

Some ciliated protazoans like trichodina can thrive in mulm, and the best preventative is to keep the tank and filters clean. There are many links between poor water quality and outbreaks of chilodonella and costia, and the stress of living in poor water subjects fish to invasions of all the more visible parasites as well (which are often present on fish and in their environment but cause no harm to a healthy fish). It is not a solution to treat a fish or tank with chemicals to eradicate every possible parasite as a preventative. This in itself would severely compromise a fish, opening it up to any pathogen that you've missed.

Just as a captive mammal, bird or reptile would eventually sicken and die when kept in a relatively small environment where it's feces were never removed, so it is with fish. You can say that you've pushed the waste to one side (as into a filter) and that it is inert now because it has composted (the mulm is no longer producing ammonia) and that the animals are healthy because they get fresh air (or fresh water) but that is never the whole story . It behooves us to provide fresh drinking water, a proper diet, unpolluted air or water to live in, enough room to be comfortable and to remove the animals waste products from it's environment, at the very least, for any species of pet in our care.

The connection between keeping an environment clean for captive animals to remain healthy is well understood by zoologists, biologists, and advanced hobbyists.

It is common sense. It is good husbandry.