Best Aquarium Filtration Methods for Fish Tank Water

best aquarium filters

Fish produce ammonia from their gills and in their waste.

Ammonia is also released through the decomposition of food and other organic compounds in the aquarium. Ammonia is toxic to fish. In sufficient concentrations, it can kill fish rapidly and in lower concentrations it will kill them if the condition is prolonged.

And. Even if the ammonia doesn’t kill directly by burning their gills, it will weaken the fish and they will succumb to opportunistic disease organisms that are constantly present in any aquarium.

When the pH of the water is in the acid range, much of the ammonia will be present as ammonium which is not toxic. However, if the pH rises into the alkaline range, the ammonium will convert back into ammonia and poison the fish.

What Is Aquarium Filtration?

You must neutralize the ammonia or remove it. It can be neutralized through chemically active agents such as Amquel or resins such as zeolyte clay which will lock the ammonia up.

However, this is a short term solution at best because the agents must continually be added or refreshed or the ammonia will build up. This would get very expensive. Also, because ammonia isn’t the only pollutant that builds up over time, this solution would also not address the problems presented by these other substances.

You could do daily water changes…but, as most of us are doing well to get them done on a weekly basis, that isn’t feasible for most of us.

So, the only viable solution for most of us is filtration.

3 Main Types of Aquarium Filtration

1. Biological Aquarium Filtration

Biological aquarium filters provide an oxygen-rich environment in which colonies of several types of beneficial bacteria can live. In a well-established aquarium, colonies of nitrifying bacteria grow on the surfaces of filter media, such as ceramic rings, bio-balls, or live rock. These tiny superheroes work tirelessly to break down ammonia, a waste product excreted by fish, into nitrite and then nitrate. This process, known as the nitrogen cycle, is essential for maintaining a healthy aquatic environment.

One group breaks ammonia down into nitrite. Nitrite, like ammonia, is toxic to fish so it would be a problem if it built up. Fortunately, another group of bacteria break nitrite down into nitrate, which is much less toxic than either of its precursors (although it is still toxic in sufficiently high concentrations and it inhibits fish growth).

The nitrates must be reduced, either through regular water changes or through addition of some denitrifying media to the aquarium. This may take several forms that will be discussed later.

Biological filtration systems often use porous materials like ceramic rings, bio-balls, or sintered glass to provide a large surface area for beneficial bacteria colonies to thrive. These media are designed to maximize water-to-surface contact, allowing efficient colonization and nutrient exchange.

To function as an effective biological filter, a filter must offer a surface on which bacteria can live and sources of ammonia and oxygen. Thus, the more surface area for bacteria colonization the better. Ditto for the rate at which oxygen-rich water moves through the media.

Without proper biological filtration, ammonia levels can quickly rise to dangerous levels, causing stress, disease, and even death in fish. By providing ample surface area for beneficial bacteria to thrive, biological filtration helps keep the delicate balance of the aquarium in check.

Benefits of Biological Filtration

  • Breaks down harmful ammonia and nitrites
  • Establishes a balanced nitrogen cycle
  • Supports a healthy ecosystem for fish and plants
  • Promotes water quality and clarity

2. Mechanical Aquarium Filtration

Mechanical aquarium filters can capture much of the solid fish waste, uneaten food, and organic particulates and, if the mechanical filtering media are changed or rinsed with regularity, these can be removed from the aquarium before they break down into ammonia.

Any media that is porous will work as a mechanical filter, but some media are better than others.

Choices include sponges, paper cartridges, polyester pads, or loose filter floss. If the pores are small, they will clog quickly. If they are too large, they will not capture the smaller particles.

The real key to effective mechanical filtration is the ease with which the media can be rinsed or changed. If it is a pain to rinse or change, most people will neglect to do it as often as it should be done and the trapped particles will break down into ammonia.

Benefits of Mechanical Filtration

  • Removes visible debris and particulate matter
  • Helps maintain water clarity
  • Prevents clogging of other filtration components
  • Easy to maintain and replace filter media

3. Chemical Aquarium Filtration

Chemical filtration involves the use of specialized media, such as activated carbon or zeolite, to adsorb dissolved pollutants, odors, and discoloration from the water. These media work like tiny sponges, attracting and binding unwanted substances, leaving your aquarium water crystal clear and free of harmful chemicals.

Chemically active filter media can be placed in the filter to capture or neutralize ammonia or other dissolved wastes and potentially toxic impurities. However, after the capacity of these media is filled, they may start to release toxins back into the aquarium. Thus, they may be more trouble than they are worth.

The most common chemical filtration agent is activated carbon. About half a cup per 20 gallons of water, changed monthly, is a good rule of thumb for using carbon.

Any filter that has a compartment in which such media can be placed will serve as a chemical filter. If you use such media, be sure to change them regularly.

One of the most common applications of chemical filtration is the removal of medications after treating sick fish.

The interplay between mechanical, chemical, and biological filtration creates a harmonious environment where aquatic life can flourish.

Benefits of Chemical Filtration

  • Removes dissolved organic compounds and impurities
  • Helps eliminate discoloration and odors
  • Removes medications and other chemical residues
  • Enhances water clarity and quality

Types of Aquarium Filters

Sponge Aquarium Filters

This is my preferred method of aquarium filtration. Air driven sponge filters provide an excellent, inexpensive, and highly portable biological filter bed. They can easily be moved from one aquarium to another and you can start new ones in advance of setting up a new tank by simply placing them in an existing cycled tank.

Sponge filters also serve as mechanical filters. However, that means they must be rinsed out every month or two to keep the water flowing through them at sufficient rates to provide adequate oxygen for the bacteria colony in the sponge.

The longer I have kept aquaria, the more I have dispensed with fancier filters and have gradually switched most of my tanks to sponge filters only.

The only exception is for tanks containing fish that are quite messy (e.g., large cichlids) as they tend to produce so many particulates that more mechanical filtration is useful.

Sponge filters have many advantages. They are inexpensive, portable, easily maintained, and easy to make for those inclined to “do-it-yourself.”

Their primary disadvantage is that they are somewhat unsightly, although they can be hidden behind plants, rocks, or driftwood fairly easily.

I like the Hydro Sponge line of filters, which come in sizes appropriate for a 10 gallon tank all the way up to pond sized units, However, other brands are also good (Tetra, Jungle, etc.)

Box Aquarium Filters

Box aquarium filters are an excellent adjunct to sponge filters as they provide more flexible mechanical filtration and also offer the possibility of using chemical filter media as well.

For example, it is common to stuff a corner box filter with filter floss and a layer of carbon.

Like sponge filters, they are portable, cheap, easily maintained, and, if anything, even easier to make yourself (just get a soda bottle, gravel, an airstone, and a little rigid plastic tubing.

Several companies make good box filters (e.g., Lustar) but most are fairly small. However, you can easily make larger ones yourself.

Undergravel Aquarium Filters

Undergravel aquarium filters consist of plastic plates placed under the gravel in a tank. Water is pulled down through the gravel and up a lift tube or, in reverse flow undergravel filters, water is pumped down the tube and flows up through the gravel.

The former has the disadvantage of pulling detritus down under the gravel where you cannot easily remove it. Reverse flow units push the detritus to the surface of the gravel so are easier to keep clean.

Such aquarium filters have the advantage of being out of sight and thus, are more aesthetically pleasing than sponge or box filters.

However, they are not portable and this can be a serious disadvantage when you need to use medications that may kill you biological filter bed.

The effectiveness of such filters may also be compromised by fish that move a lot of gravel. Since cichlids are about the only fish I keep and they generally dig a lot, I do not use undergravel filters.

Aquarium Power Filters

These filters hang on the back of the tank and serve as an excellent means of mechanical, chemical, and biological filtration.

They are particularly useful for fish that make a big mess. On tanks containing such fish, I generally run a power filter, often combined with a sponge filter for added biological filtration which is also handy for handling the bioload of big, messy cichlids.

Most power filters can be packed with media that permit mechanical filtration (e.g., sponges or polyester pads), biological filtration (the same sponge, pads, or bags of gravel, etc.), and chemical filtration (e.g., carbon or zeolyte).

I prefer power filters that have large media compartments that give me lots of flexibility with regard to what I put in it.

My preference is the Aquaclear line because they use a reusable sponge along with filter bags in which you can place carbon or other media.

On tanks in which I want alkaline pH and high carbonate hardness (e.g., rift lake cichlid tanks), I like to put coral gravel in a filter bag and put it in the filter for added buffering.

The gravel also provides an additional biological filter bed. I tend to dislike power filters that require me to buy replaceable filter bags as they tend to be expensive and I find that the bags bridge with detritus quickly and the water flow drops significantly in a short period of time.

I like the Aquaclear line of filters mainly because they have a very large media compartment and I have found them to be quite reliable. However, there are many other good ones.

Power filters have the advantage of allowing filtration of a lot of gallons per hour at fairly low cost. They are fairly easily cleaned generally reliable.

Their primary disadvantages are that they are often noisy and they can be unsightly. They also contribute to a lot of evaporation because of all the water moving through them.

Canister Aquarium Filters

A canister aquarium filter is simply a power filter that offers larger capacity, less chance for water to bypass the filter media, and generally doesn’t hang on the tank but rather can be placed out of sight in a cabinet below the tank.

(Actually, putting it above the tank would be better in the event that a hose splits because you won’t end up siphoning a lot of water onto the floor).

Canister aquarium filters are incredibly silent. I have a tank in my living room on which I’m running an Eheim 2213 and it is completely silent.

If I had to buy another canister filter, I’d almost certainly choose another Eheim because I’ve been very impressed with the reliability of the one I have. However, there are other good choices (e.g., the Fluval line).

In a typical Eheim or Fluval filter, you can put in a layer of course media on the bottom (where the water comes in) to trap large particles. I use the little ceramic donuts sold by Eheim as Efimech.

Above that you can put biological filter media (I use a bioballs), then a layer of filter floss. As for the floss, I recommend using the Eheim version because it doesn’t compress the way others do and the water flow stays at a good level.

When I’ve tried other brands, I’ve found they generally compress badly and quickly clog, slowing the water flow dramatically. Because the water can’t move through the filter without passing the filter media, such a filter is very efficient.

So, canister filters have many advantages: they are quiet, efficient, reliable, need servicing only every 3 months or so, highly flexible in terms of placement of intake and outflow tubes in the tank, and they are hidden out of sight.

However, they are not without disadvantages. They are expensive, difficult to tear down and clean, and, for that reason, too easy to neglect for too long so solid wastes build up in them and may contribute to higher nitrate levels than you might otherwise have if you got them out of the filter more often.

Fluidized Bed Aquarium Filters

These are a fairly new type of filter, at least in the aquarium hobby. They consist of a tube containing sand through which water is pumped. The water expands the bed of sand in the tube until it is “fluidized.” These floating sand grains provide a huge surface area for bacteria to colonize. Thus, these filters can generally handle very heavy biological loads – that is, lots of fish.

There are a number of models on the market now and the manufacturers seems to have worked out some of the early kinks. One problem in the past has been that the sand can solidify during power outages and not re-expand when the water starts flowing again. This spells disaster if it happens so be sure to get a unit that has built in safeguards against the problem.


As noted above, even if you have adequate filtration on a tank, over time, nitrates will build up in the tank. Although not nearly as toxic to fish as ammonia or nitrite, nitrates are still a problem at higher levels. They suppress growth and leave fish susceptible to disease and, in high enough concentrations, will poison the fish.

Some fish (e.g., cichlids from Lake Tanganyika) are particularly sensitive to nitrates. Thus, you need to find ways of reducing the nitrates in your tanks over time. There are a variety of old and new approaches to doing so.

Expanded bed filters

These are a just like a fluidized bed filter except that the water flow is much slower. This means that the sand bed expands much less. The water moves so slowly through the sand that the aerobic bacteria use up all the oxygen in the water before it has passed through all the sand. Thus, the upper layers of sand become a place for anaerobic bacteria to colonize.

This type of bacteria uses nitrate as a food source and break it down to nitrogen gas. This can be a great way to reduce nitrates, but it can be tricky.

You have to get the water flow just right or you can have serious problems. If too little water flows through the sand, then the anaerobic bacteria will consume all the nitrates before the water has passed all the way through the sand. This means that the anaerobic bacteria in the upper layers of sand will begin using other substances for food and produce toxic compounds as a waste product.

If this happens, the fish will be in serious trouble. To get things right requires careful testing of he nitrate levels in the discharge from the filter. But even once you have gotten it right, things can change if you add plants or do other things that reduce the nitrate level in your tank and you can end up with dead fish.

Coil denitrators

These use a long coil of tubing to accomplish the same thing as the expanded bed filter. The flow rate of water through the tube is quite slow, meaning that the bacteria at the start of the tube have an oxygen supply, but those in the more distant portions of the tube do not.

Thus, anaerobic bacteria thrive there and break down nitrates into nitrogen gas. The problems are the same as were described above for expanded bed filters. Specifically, if the tube is too long or the water flow too slow, the nitrate supply will be used up before the end of the tube and toxic waste products will be produced.

Aquarium Plants as denitrators

Aquarium plants have been used as denitrators for many years and they can be quite effective at the job. Many aquarists swear by the use of plants for this purpose.

There are a few problems, however.

First, growing plants is often not easy and requires good lights, which can be expensive.

Second, plants die and add to the biological load of the aquarium, producing ammonia as they decompose.

One solution to both problems that was described in a recent “Aquarium Fish Magazine” is to grow the plants outside of the aquarium. If the plants are grown in a separate container through which aquarium water is piped, they can remove the ammonia, nitrites and nitrates from the water without adding to the biological load.

Also, much less powerful lights are needed because the light doesn’t need to get through the aquarium water. In this article in AFM, Lee Newman described using an old wet-dry filter box in which he put Spathiphyllum plants, using no soil. The plants roots dangled in the aquarium water that was run through the box and reduced nitrates to unmeasurably low levels.

The cheapest and most reliable denitrator

Regular water changes. The most readily available approach to reducing nitrates is to do regular weekly water changes. Do them!

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