Filters, For Dummies

Your tanks have too many fish in them. My tanks have too many fish in them. Everyone who keeps fish has tanks with too many fish in them. “But,” you say, “I only have one inch of fish per gallon, like you told me to have”. Very good. You therefore have a low enough fish density that it is possible to maintain a healthy tank, but you are still going to have to maintain it. It will not take of itself…there are just too many fish in it for that. How many lakes do you suppose have one inch of fish per gallon in them? Answer: none. The same goes for the rivers and the oceans. Let’s face it, fish densities in our aquaria are much, much higher than in nature. Our aquaria therefore require regular maintenance in the form of feeding, water changing, and cleaning. You can not eliminate these chores, you can just reduce their urgency by keeping your tanks’ fish densities as low as is practical.

So, you are stuck with doing (at least some) tank maintenance. Ho hum. But all is not lost, since there is a very simple way to reduce the workload, a method that is so universally employed that it is often thought of as involving a mandatory piece of equipment. The filter.

All filters have one thing in common: they move water through a porous material. This material is called “filter media” in the aquarists’ parlance. All filters also require some form of pumping mechanism, and these come in two basic types: air lift and power. The air lift filter makes use of air bubbles rising up a vertical tube to move water. These are relatively low capacity devices that require an external air pump. Power filters have a small electrically powered water pump incorporated within them and do not rely on an external air pump. These can move water at a much greater flow rate than can an air-lift filter of comparable cost, power consumption, or physical size.

Filters will do a number of things for you. Most obviously, they will strain suspended junk out of the water (mostly fish poo and uneaten food). This makes the water clearer. Filters may also have a biological action, where living organisms remove dissolved fish wastes. This makes the water purer. Another way to make water purer is through chemical filtration, in which dissolved chemicals are taken out of the water by a chemical filter medium. Various kinds of filters are used to produce one or more of these three types of filtration – mechanical, biological, and chemical. So I will discuss each of these three in turn.


Most easily supplied, but alas, also the least important, is mechanical filtration. The reason it is the least important is simple, fish really don’t care (within limits) if their water is clear or not. Not many lakes and rivers are as clear as the typical aquarium (or certainly, at least, not as clear all the time) so fish can handle a modest amount of suspended solids without trouble.

But everyone uses mechanical filters anyway. It looks nicer. All mechanical filters pass water though a filter media that serves as a mechanical strainer. Because the filter media traps the solid material, it will eventually clog up, thus rendering the filter ineffective. Mechanical filters therefore require regular maintenance. The more you clean a mechanical filter the better, because the gunk they trap will decompose and add pollution to the water.

In the distant past the filter media of choice was “glass wool” – horrible stuff that cut fingers and looked like it would give you asbestosis. Then polyfiber filter material came on the market in the late 60’s – a vast improvement. This is the same stuff sold to stuff pillows, but it is repackaged and sold in pet stores for a comparatively exorbitant price. Nowadays, however, the most popular filter medium is open-celled foam rubber, for the simple reason that it can be rinsed and reused. They can also be cut to fit any filter box. A useful trick if you want to cut foam (and own a table saw) is to freeze the foam in an ice block, then cut the ice on the table saw.

Not only do you need a filter medium, you also need a filter box to put it in. The first of the mechanical filters to be widely used in aquaria were submersible box filters. These are operated via an airlift. Box filters are cheap, but they have low capacities and are consequently only recommended for tanks smaller than 40 liters.

Hanging power filters were introduced in the 60’s and were a great step forward in performance. There are two basic types of hanging power filter. The earlier filters all used the siphon design, where filtered water is pumped out of the filter box and is replaced by tank water that flows into the filter box through a siphon. This design relied on the siphon being maintained or they would run dry. It is (and always will be) a real pain to get all the air out of these filters’ siphons. But with a hacksaw you can modify those filters with the “motor on top” so that they at least do not rely on a finicky siphon. Cut a notch in the top off the filter on the side opposite the hanging lip, and then hang the filter inside the aquarium. The tank water then simply overflows into the filter box through the notch, and no siphon tubes are required. Some hanging filters perform much better after this modification is done. The hideously over-powered Superking model comes to mind, since water just cannot flow through the siphon tubes fast enough to keep this monster’s motor satisfied.

Most modern hanging filters are nowadays of the “overflow” design. In this design the pump is connected to the tank water directly through an inlet pipe, and the pump pushes water into the bottom of the filter box. The water then flows up through the filter material and overflows into the aquarium as a small waterfall. The advantages of this design are that they are quieter (never blowing air) and self-priming (you don’t have to get the air out of a siphon tube). Their disadvantage is that you can not direct the return water, it just falls straight down. They therefore tend to refilter the same water over and over again. You can solve this problem by attaching a length of hose to the inlet pipe, so water is drawn in from the other side of the tank rather than from below the waterfall.

Another design of power filter is the canister filter. This design uses a sealed filter sitting on the floor and connected to the aquarium by lengths of siphon hose. Thankfully, the siphons on canisters are a lot easier to get going than the ones on hanging filters because canisters are placed much lower than the aquarium. Canisters tend to be somewhat more expensive and also pump much less water (per dollar) than hanging filters. They may leak as well, so should sit in a bucket on the floor. And they are also much more difficult to clean than hanging filters, as they must be partially disassembled before cleaning. They do however hold much more filter media than hanging filters and so serve as reasonably efficient bacterial filters (see below). They also have the potentially tremendous advantage that they do not require that the tank be completely full of water to operate.


Although I have a low opinion on the usefulness of mechanical filtration, there is one application in which a mechanical filter is very useful: as a pre-filter for a biological filter. Biological filtration removes dissolved pollution, and so it is the most important kind of filtration, and the only kind of filtration that a fresh water aquarium actually needs. But if you use a mechanical filter to strain the solid gunk out of the water before it reaches the biological filter, the biological filter can be left alone to do its job for longer periods of time.

The most important role that biological filtration has is the elimination of ammonia, which is quite toxic to fish. You can get rid of ammonia in two ways: let plants eat it or let bacteria eat it. In practice, of course, both types of filtration will occur in any planted aquarium, regardless of what you do. Filter bacteria will grow on the plant roots and stems, and the plants will take up ammonia as they grow. By including an additional biological filter you are only promoting a natural process so that it can occur quickly enough to rid the tank of the ammonia produced by the number of fish in that tank.


Aquarists often think that bacterial filters are the only kind of biological filters there are. This is not so, but it is true that most biological filters in use are bacterial filters. In these filters bacteria eat the ammonia, thus creating nitrate as the final waste product. The ammonia is consumed in a two-stage process. First Nitrosococcus bacteria convert ammonia to nitrite, and then Nitrospira bacteria convert nitrite to nitrate (by the way, these two bacterial genera are almost always misidentified as Nitrosomonas and Nitrobacter, respectively). Both of these conversions consume oxygen, and so they are called “aerobic”. And both of these conversions require some time to get going, because the bacteria involved are slow growers. The ammonia-to-nitrite conversion is usually well underway within two weeks of setting up a new filter, but the nitrite-to-nitrate conversion generally takes longer, usually four to six weeks. A bacterial filter is not “mature” until it successfully converts ammonia all the way to nitrate. The process of maturing a bacterial filter is called “cycling”. Filters that are not fully cycled can lead to “New Tank Syndrome”, which is the loss of fish from ammonia and/or nitrite poisoning. This is the reason that it is recommended that new aquaria be left with only a couple of fish for six weeks before the remainder of the fish population is added.

Various commercial products are sold to help you cycle a tank faster by providing packaged bacteria. A lot of discussion has been around about their relative merits, and manufacturers have made lots of claims backed by “scientific” research (that for some reason never gets properly published) on how good their product is, but all this stuff is just so much crap. Don’t buy any of it. They will just add organic pollution to your tank – they are basically just sewage anyway. If you want to speed up the process then seed a new filter with some filter media from an established one. If you don’t have an established filter handy, just be patient. Your filter will cycle by itself.

The first bacterial filter to gain wide use is the undergravel filter, which became popular in the 70’s. These are inexpensive and effective bacterial filters, and so are still in wide use. In undergravel filters, water is pulled down though the gravel by an airlift or water pump that draws water from below a slotted false bottom beneath the gravel. The flow of oxygenated water allows the bacteria to grow on the gravel grains, and so ammonia is consumed while passing through the gravel.

The problems with undergravel filters become quickly apparent. First of all, they don’t do plants any favors. People can and do grow plants with undergravel filters, but growing plants is a lot easier without them. More importantly however, because UG filters draw water and fish poo down into the gravel, these filters are very hard to keep clean and they soon clog up. All the solid matter gets broken down by other bacteria which creates free phosphate and even more ammonia, and hence even more nitrate. Nitrate and phosphate levels increase rapidly, and so algae grow with abandon. Keeping the gravel clean enough to prevent this only results in the removal of most of your desirable bacteria along with the gunk. Undergravel filters cause far too many long-term maintenance problems (especially in moderately to heavily stocked tanks) to be recommended.

An improvement over undergravel filters is the reverse-flow undergravel filter. In these devices, water is pumped down through the “uplift” tubes and then rises up through the gravel. The water is mechanically pre-filtered before it is pumped so that the poo is not trapped in the gravel. By keeping the mechanical pre-filter clean you prevent the solid waste from breaking down and adding to the nutrient load of the aquarium. This allows the bacteria in the gravel to grow undisturbed for much longer periods of time. So with proper maintenance, reverse flow UG filters result in a cleaner and less algae-ridden tank. A regularly cleaned mechanical prefilter is now regarded as a very important part of any high-capacity biological filter. Biological filters that lack a mechanical prefilter should only be used in very lightly stocked tanks.

Reverse-flow undergravel filters do however have their disadvantages as well. Plants suffer from reverse-flow undergravel filters just as they do from downward-flow UG filters. Tanks with these filters also require supplemental aeration, since oxygen is removed from the water as it passes up through the gravel, and the filter does not create any surface agitation or bubbles to replenish it.

The next advancement in bacterial filters was the wet/dry trickle filter, popular by the mid-80’s. This filter is essentially a small aquarium underneath the main one. Water flows into the filter after exiting the main aquarium through an overflow pipe. The water is mechanically pre-filtered and then passed over the filter media, which is kept otherwise emersed (“dry”) and thus fully exposed to air. Once the water passes over the filter media, it collects in a (“wet”) sump, and from there a powerful water pump lifts the water back up to the main aquarium. By passing water over an emersed surface these filters actually saturate the water with oxygen rather than deplete it. Also, because an overflow is used, this filter has the benefit of “surface skimming”, which removes the film that builds up on the water’s surface.

The filter media used in wet/dry filters is several liters of any one of a wide variety of little plastic thingies. Various manufacturers of the thingies tell of all sorts of unpublished “scientific” results proving that theirs’ are the best. But the thingies of choice are still those plastic pot scrubbers sold at Safeway (or available in bulk at CostCo). They cost less than half of what the imported German ones do, and they work just as well.

Unfortunately, wet/dry trickle filters are large devices, and they take up pretty much all of the room under the aquarium. They also require a powerful pump that is expensive to both buy and to operate. A wet/dry filter is really a second aquarium under the “real” one, so there are obvious additional costs involved with building and connecting two aquaria where one was used before. One wet/dry filter can however service many aquaria, and so these filters are the most popular choice in “central” filter systems.

Also available are “fluidized bed filters’. These filters are more compact than wet/dry filters. In these filters water is pumped up through graded filter sand, which is suspended by the up-flow. Since sand grains are so small, a tremendous biological filter area is available in a small volume. Unfortunately, they are tricky to design since it is necessary to keep the sand suspended but not have it flow out of the top. The small sand grains also pack tightly and go anaerobic very quickly if there is a power outage.

Much less expensive and complicated are the new combination mechanical/biological hanging filters. These are highly recommended for medium-sized to larger tanks. These devices are essentially hanging power filters with some kind of biological filter module downstream of the mechanical filter. The biological filter can be a drip plate or a turning water wheel. The wheels are also sold separately so they can be retrofitted to an existing canister filter (a very nice idea). These devices are new on the market but they are now widely available.

The final kind of bacterial filter is the sponge filter. These are simple airlift devices that have a relatively low capacity. Essentially they are just foam rubber blocks with airlifts attached. The foam rubber sits on the tank bottom and water is drawn through it and up the airlift tubes. Because these filters lack a mechanical prefilter, they trap the solid material that really should be removed, just as undergravel filters do. Rinsing the filter clean removes most of the bacteria it was intended to grow, thus disrupting its biological activity. These filters do however have the tremendous advantage that they can not trap even very small fishes, and are therefore often used in fry tanks.

Another very good use for a sponge filter is to use it as a mechanical prefilter for a canister filter. As previously mentioned, canister filters require disassembly to clean, and cleaning the filter removes the bacteria they are intended to grow. But by sticking a sponge filter over the inlet of a canister, we prevent gunk from entering the canister, thus allowing it to act as a purely biological filter that would almost never need to be disassembled for cleaning.


The second kind of biological filter is the photosynthetic plant filter. Plant filters are a major improvement in biological filtration over bacterial filters in several ways. Plants take up ammonia and incorporate it into its tissues directly, and so there is no build up of nitrate. They also take up metals and phosphates and so purify the water much better than do bacteria. They therefore help combat the problem of algae growing in the aquarium, rather than contribute to it. And of course, plants are net producers of oxygen, rather than consumers.

The plants are grown in trays through which the water flows.

The temple plant (Nomophila stricta) is a very good choice as a filter for fresh water since it is incredibly fast growing and has a correspondingly high uptake of ammonia and other nutrients. Temple plants can be grown fully submerged, but they grow faster, and therefore filter better, when they are allowed to grow up out of the water. They do not need to be grown in gravel. Instead, it is possible to grow temple plants “hydroponically”. Simply stick cuttings through the holes of an egg crate held just above the water surface. Make sure that the bottom of the cutting is in the water. The cutting will start to take root almost immediately. I have also had great success growing temple plants in an illuminated wet/dry trickle filter that uses Perlite® potting soil additive as a filter medium. The plant roots grew throughout the Perlite.

Salt water, on the other hand, is filtered best with a (fully submerged) higher alga like Caulerpa, or a salt-tolerant vascular plant like the mangrove. Caulerpa must attach itself to a solid surface (such as coral rock) to grow, while mangroves can be grown hydroponically.

The difficulties of plant filters are twofold. First of all, a plant generally requires more care than a bacterium; and secondly, plant filters are physically quite large and expensive. The typical plant filter design is similar to the under-the-tank wet/dry trickle filter (discussed above) but with the additional cost and complexity that comes with the requisite bright illumination.

The only plant filters offered for sale are called “algal turf scrubbers” which are designed for growing submerged algae in salt water. If you want to grow emersed plants in a filter you will have to build the filter yourself.


The third form of filtration is chemical filtration. Most often this is done with activated carbon. Activated carbon will adsorb dissolved organic molecules and metals, thus purifying the water. Adsorption (with a “d”) differs from absorption (with a “b”) in that adsorption is a process in which the pollutant sticks to a solid surface by an electro-chemical bond, while absorption is the purely mechanical process of “sopping it up”.

Carbon filtration requires the regular purchase of fresh filter media because the old carbon must be discarded when it is exhausted (carbon can not be economically reactivated at home). There are a large number of brands of activated carbons available. These carbons come from a variety of different sources, including wood, coal, and coconut shells. Most commonly used are bituminous and lignite coal.

Tests reveal that the most expensive carbon is not necessarily the best at removing organic matter from aquarium water. Surprisingly, the inexpensive Aquarium Pharmaceuticals Super Activated Carbon brand scored best of those brands commonly sold in local stores (Harker, 1998).

Carbon filtration is quite important in salt-water aquaria because marine fishes are very sensitive to pollution, and because of the expensive sea salt they require. It is therefore very expensive to make the massive water changes required to keep pollution levels low enough for salt-water fish. So it is in everyone’s best interest to purify the old water through carbon filtration. A lot of debate goes on as to how much carbon is needed, but current thinking is that you should use only a little carbon but change it often. Harker recommends about 1mL carbon per 4 liters of water (3 tablespoons per 50 gallons), and to use the carbon only intermittently, about 12 hours per week, using fresh carbon each week. Put the carbon in the filter so water flows through it, but only slowly.

Also recommended for marine aquaria is chemical filtration with a foam fractionator, also known as a protein skimmer. A large protein skimmer is now generally considered to be mandatory equipment for all salt-water tanks.

Skimmers work like this: fine air bubbles are injected into a downward flowing column of water. Hydrophobic molecules like lipids and most proteins adhere to the bubbles and rise with them to form a froth at the surface of the water column. This froth is pushed upward through an outlet by more froth that continues to collect below it. The froth then flows into a collecting cup for removal. By removing the organic molecules before they break down, the skimmer helps maintain a much higher water quality than can be easily maintained without one.

Skimmers inject air into the water by one of two ways. Air can be injected conventionally with an air pump and a fine air diffuser. This design tends to be used in lower capacity skimmers suitable for tanks smaller than 400 liters. But larger aquaria and reef aquaria usually employ venturi skimmers. These have powerful water pumps that force water through a narrowed opening into which an air inlet leads. This opening is called a venturi. The water must speed up to go through the narrowed opening of the venturi, and the faster a fluid travels the lower its pressure is. So air is drawn through the inlet to the inside of the venturi.

But alas, only very large, powerful, and expensive skimmers work in fresh water. This is because fresh water has a higher surface tension than salt water and so the air bubbles are larger – too large to cause the water to froth. Very energetic pumps are consequently required to froth fresh water, making a fresh water skimmer economically unviable. They consequently are not used in fresh water aquaria, but they are used in sewage treatment plants where pollution levels are much higher and frothing is more easily achieved.

So how do you chemically filter a fresh water aquarium? If a fresh water aquarium is full of very inexpensive tap water then the simple answer is…you don’t. Why bother? Tap water is cheap and so why not just change the water with fresh instead of trying to purify the old stuff? The nitrates, phosphates, and organic matter dissolved in your tank are great fertilizers, and since you have to water your lawn and houseplants anyway, just water them with old tank water and give your fish new water. While you are at it, rinse your mechanical filter foam in the wastewater before giving it to the plants so they get some solid fertilizer too. Nothing beats organic!


So, that should be about all you need to know about the various kinds of filters used in both fresh and salt water tanks. But for your first fresh water aquarium, I would recommend a hanging biological power filter and a lot of plants in the tank. For a fish room, I would recommend a central filter system using a combination wet/dry trickle filter and plant filter. For marine fish tanks, the same recommendations apply except that you should also add a carbon filter and a large protein skimmer. Marine coral reef tanks (which receive very little feeding) are better off with only a large skimmer and carbon filtration (no wet-dry filter), along with a large quantity of porous “live” rock that serves as an in-tank biological filter. But the filtration of coral reef tanks is a specialized topic beyond the scope of this article, so I would recommend you do some further reading before you attempt it.


Hovanec, T. A. and E. F. DeLong. 1996. Comparative analysis of nitrifying bacteria associated with freshwater and marine aquaria. Appl Environ Microbiol 62:2888-2896

Harker, R. 1998. Granular Activated Carbon In The Reef Tank: Fact, Folklore, And Its Effectiveness In Removing Gelbstoff — Part One Aquarium Frontiers on Line May & June 1998?


Diatomaceous Earth Filtration

Also used as a mechanical filter medium is something called “diatomaceous earth”. This is made of the hard silica exoskeletons of single-celled marine organisms called diatoms. These skeletons are not only very small, they are festooned with a baffling assortment of spikes, holes, hooks, and assorted appendages that trap suspended particles very well. Anything larger than a bacterium gets trapped by these filters, so they make the water very clear. That’s why they are often used in swimming pools.

Diatomaceous earth requires its own specially designed filter unit. These filters are tricky to set up because you have to suck up free-floating diatoms so that they coat the inside of a nylon filter bag before filtering your tank. You then run tank water through the bag until it clogs up. The bag is then rinsed out, discarding the diatoms along with the trapped gunk. The process is then repeated with a fresh coating of diatoms. Fresh diatoms must be purchased separately.

Because DE is so effective at filtering out anything and everything, these filters clog up in no time. And because of their short running time between cleanings, diatomaceous earth filters are only good for intermittent use. The idea is that you would only filter a tank for ½ an hour or so once a week, rather than running the filter continuously.

These filters were once very popular – aquarium magazines from the 60’s and 70’s were full of their ads – but nowadays, few people bother to use them because quite frankly they are more trouble than they are worth. Water clarity is more easily achieved through conventional filters and proper tank maintenance.



For a short time in the early to mid 90’s there were advertised a lot of different kinds of denitriying filters. But you don’t see them much anymore because they don’t work. That sort of put a damper on their sales.

Anyway, this is how they are supposed to work. Nitrate can be used by anaerobic bacteria as an oxidizer instead of oxygen. In effect, the bacteria breathe nitrate instead of oxygen. So if you create a region where there is no oxygen, but lots of nitrate, and a food source for the bacteria in the form of a carbohydrate, then the bacteria will consume the nitrate. The end result is nitrous oxide or nitrogen gas, which diffuses out of the water into air.

In denitrifying filters water is very slowly passed through a submerged filter medium. A small amount of a sugar (bacteria-food) is added. Aerobic bacteria consume all the oxygen in the outer layers of the filter medium, and so bacteria in the inner filter consume the nitrate in order to metabolize the remaining sugar. By the time the water passes through the filter, it has had all of the sugar and oxygen consumed, as well as at least some of the nitrate. The water is then aerated to replace the lost oxygen and get rid of the excess nitrogen gas. It is then returned to the tank.

So, why don’t they work? Well, in practice, they are just too touchy. Too much organic matter in the water and you get poisonous hydrogen sulfide being produced. Pass the water through too quickly and ammonia is produced. Etc., etc. And even if you do get them set right, you must pass the water through them so slowly that they do not produce enough nitrate-free water to make any real difference to your tank, unless you get a very big denitrification filter. That means big bucks. ?