So You Want a Fish Tank: Filtration

The reason I am writing this series of articles is because it turns out that one of the things I get asked about most is keeping fish. Sure, I could talk about what biogeography tells us about the evolution of Siluriformes, but people seem to want to know why their guppies are dying. So here’s a series of articles on setting up and maintaining a fish tank and the science behind it. If you want a quick, simple, here’s-how-to-own-some-fish guide this isn’t for you. This is a science blog, so I’m going to tell you not just what to do but why. That way if you can’t use my favored approach you’ll be able to make an appropriate substitute, or at least you’ll know why your guppies are dying (and then hopefully stop buying more and condemning them to death).

This article series is also aimed primarily at people who want relatively unfussy tanks. This is partly a demand issue, where there are far more people who want a low-maintenance tank with some pretty fish in the living room than people who want to breed rare Central American fish in a basement fishroom. This is also partly an issue of knowledge: people running their own complicated set-ups are likely to already know this stuff, and I am also less knowledgeable about complicated set-ups. I have a lot of fish tanks in my teaching and research labs but most of them are deliberately set up so that if I miss a water change during finals week nothing bad happens.

Our first article is about filtration because filtration is how you are most likely to kill your fish. If you are saying, “I don’t have a filtration issue because my water looks clean,” then this is you for sure.

The short take-home, for people who really wanted a different sort of article, is:

  1. Filtration is mostly about getting rid of invisible fish waste.
  2. Biological filtration is where it’s at.
  3. Biological filtration requires you to cycle your tank BEFORE you add fish.
  4. Ultimately, filtration can only save your fish for so long, so you’ll need to change the water periodically as well.

Fish are Toxic Waste Machines

Fish are little toxic waste machines. Filtration is generally divided into three different varieties (mechanical, chemical, and biological) but the first and most important thing to understand about filtration is that a perfectly healthy fish in perfectly clean water will, as a direct product of its metabolism, produce toxic waste which needs to be filtered out. Time and time again I see people asking for help on fish-keeping forums who are sure that their fish caught a disease and need medicine when their fish have merely, but largely literally, peed until their water became toxic. And, instead of changing the water to remove this dangerous waste, these people often spend money buying treatments that, at best, treat the wrong problem and at worst kill the very organisms that will help them solve that problem.

The central issue here is that a fish tank is not a closed ecosystem. Fish tanks are not closed ecosystems because, most importantly, you feed the fish. While there are lots of things fish may eat all fish eat products that were once alive (other animals, plants, or single-celled organisms). What is most important here is that all living things contain at least trace amounts of protein. Even plant food, which is generally considered to be protein-poor, has small amounts of plant enzymes in it, and those enzymes are proteins. Moreover, many fish eat relatively protein-rich animal food, and all fish need to eat protein to build their own protein-rich bodies. The problem with this is that protein contains nitrogen, and lots of it. When protein is used to build more protein (i.e., a fish eats a worm and converts some worm-proteins into fish-proteins) that isn’t an issue. However, when protein is used for energy, which is also very common (and impossible to prevent, before you ask if you can feed a special diet that will stop this), the nitrogen in the protein just becomes waste. What it becomes as part of the metabolic process is ammonia (NH3).

This sealed ecosystem requires no filtration because: 1) it’s sealed, with no added food 2) it supports nothing larger than the tiny dots swimming in the water. (And it does have the biological elements of biological filtration, just no pump driving water through.)

This is where the problem starts. If you’ve ever used ammonia as a cleaning product you are probably familiar with its toxicity (and with the fact that it looks just like water). Even smelling ammonia can make your nose and eyes burn. Ammonia is so toxic that in land vertebrates energy is expended to transform ammonia into something less toxic (either urea or uric acid, depending on what sort of land vertebrate you are1). Fish2 have the luxury of being surrounded by water and so instead of storing urea or uric acid for later excretion they simply dump the ammonia into the water. This actually happens largely through the gills. While fish do urinate like land vertebrates they also have a large area in the gills where blood is a thin membrane away from the surrounding water (if this weren’t true they wouldn’t be able to extract oxygen from the water) and ammonia simply diffuses out of the bloodstream. In the wild this ammonia would be dispersed across gallons and gallons of water. In a fish tank the ammonia can’t go anywhere and so it can rapidly accumulate to dangerous levels.

Fish waste isn’t the only source of ammonia in a fish tank. Dead animals also produce ammonia as they decay, since bacteria causing a body to rot are just eating it, and dead animals are full of protein. These dead animals may be a fish that died while you were gone for the weekend, or a snail that you didn’t realize came in on a plant and which has now died, or the bits of dead animals in the food your fish didn’t eat.


Filtration is commonly divided into three categories, and so I’ll go through them under the normal titles.

Mechanical Filtration Mechanical filtration is what people who just got their first fish tank tend to worry about most. Mechanical filtration is about removing the “bits” that make the water look dirty. It normally involves some sort of pad or grating that catches these bits and has to be cleaned off or changed out on a regular basis.  Two important things to note about mechanical filtration are:

1) The fish mostly don’t care. Sure, getting rid of bits that will rot reduces ammonia, and that’s good, but fish live in water that is muddy, full of sticks, or stained with tannins all the time. Some fish do like or maybe even need crystal-clear water but other fish actually prefer water that is hard to see through. I have some fish in my lab that live in water the color of weak coffee. Originally their tank was clear water, but after some reading I discovered that these were fish from blackwater environments where tannins leaching from dead plants turn the water brown or black. I added these chemicals and the fish are much more active now. Mechnical filtration is largely something you do to make your fish tank look nice to you.

2) You should be doing water changes, and when you do this you should be using a siphon. It’s a lot easier to get rid of visible fish feces and old food by siphoning it out than it is to rely on a filter to do this. With a siphon you can also stir up your gravel to get out things that have become trapped between the pieces. (If you have a sand bottom everything will collect on the top.) I have largely abandoned mechanical filtration except for this siphoning in my tanks.

Chemical Filtration

Sometimes you have weird chemicals in your tank. Chemical filtration deals with these. These can come from a variety of sources – something you put in the tank as a decoration, something your water treatment company put into the water, or some off-kilter biological process. The most common chemical filtration you will see is activated carbon (charcoal) filtration. These filters use either loose activated carbon or bags of activated carbon to remove harmful chemicals from the water. This is exactly what most drinking water filters for home use use. A few important notes about chemical filtration:

This is loose activated carbon. It is often sold in a white cloth bag instead.
  1. The most worrisome chemical, unless you (or your child) throw random things into the fish tank, is the chlorine or chloramine your water treatment company probably adds to your water. This stuff kills bacteria quite nicely, which is a problem in your tank (biological filtration depends on a colony of beneficial bacteria to work) and also burns fish gills. I have a friend who changed water in their tank and didn’t remove the chlorine first. Within two hours all of her fish had died of suffocation. You can trickle water through activated carbon to remove this but a better strategy is to get a bottle of water conditioner and add some to the water you are about to put in the fish tank. The only time I have ever run chemical filtration on a tank was when I once had a problem with wood staining the water in a tank that was supposed to stay clear. I added some activated carbon to the filter and within a week the problem was solved.
  2. All chemical filtration runs out over time and has to be changed. Activated carbon filters eventually stop working and may even begin to shed previously-trapped toxins back into the water. Unlike biological filtration, which tends to improve over time, chemical filtration works best straight out of the box and gets worse over time.

I have an ambivalent relationship with chemical filtration. One thing I see far too much of is tiny plastic tanks sold with a “filter” that isn’t anything more than a way to suck water through a bag of activated carbon. These probably do save some fish from owners who dump water into the tank straight out of the tap without adding a dechlorinator or (shudder) use cleaning products to clean out the tank and leave chemicals behind. They also probably make a killing for the companies that make them, since the carbon bag will be regularly replaced, and my guess is that a lot of fish will also be getting replaced. On the other hand, a bit of activated carbon in a filter can save you from all sorts of chemical weirdness. I always keep some in lab for the day when someone knocks a strange chemical over into a fish tank. It hasn’t happened yet, but when it does I’ll be dumping that carbon in the filter.

This extremely tiny all-in-one tank was sold for betta fish (it’s suitable for shrimp). The filter consisted of nothing but a bag of activated carbon and a pump to pump water across it. I’ve helped this tank out by adding plants and putting a sponge over the filter intake (which serves as a place for biological filtration bacteria to colonize).

Biological Filtration

Biological filtration is your right-hand man, your best weapon, in the fight against ammonia. Far too often it seems that people go to a pet store and say that their fish are doing poorly. The store may ask to test the tank water (most places that sell pet fish will test your water for you, which is good to know) and they determine that the person in question has too much ammonia in their tank. So they sell them something like AmmoLock and the person goes home, treats the tank, and in a few weeks their fish are dead. I’m not saying that short-term ammonia-detoxifiers aren’t any good. However, they are short-term solutions. When you realize that you’ve got 2 ppm of ammonia (which is REALLY bad) something like AmmoLock will save your fish now. But what keeps you from having that 2 ppm next week again? Biological filtration.

I’m sitting about six feet from a fish tank that I built all the filtration for myself. It has no chemical filtration. It has mechanical filtration only by accident. What it does have is about 100 times as much biological filtration as a “normal” store-bought filter for a tank that size would have. (It also has live plants, which serve as backup biological filtration.) Biological filtration is filtration3 and everything else is making the tank look pretty.

The concept behind biological filtration is to make ammonia less toxic. One way to remove ammonia would just be to change the water in the tank constantly. In fact, some large aquariums “filter” their tanks exactly like that, pumping water out of the ocean constantly and sending the old water back. (It’s one reason so many aquariums are right on the waterfront.) However, if you can’t do that maybe you can make the ammonia less toxic so that it doesn’t cause a problem until the water does get changed. This involves converting ammonia into less-toxic nitrite and then converting nitrite into less-toxic nitrate. I said above that 2 ppm of ammonia would be very bad. 2 ppm of nitrate is nothing. I’ve had fish survive short periods in which the nitrates spiked above 100 ppm.

So how do you convert ammonia to nitrate? Several different kinds of bacteria do this4 to get energy. So, in effect, all you need to do is provide these bacteria with somewhere to live and then send them water with ammonia to “eat”. These bacteria also need oxygen. Hopefully, your water has enough of this, but a wet/dry filter design (which is a design in which the biological filter stays wet but isn’t submerged) really maximizes this.

This sump tank serves as the main filter for a 110-gallon salt water tank on the stand just above it. Water pours in through the hoses at the top, trickles through the filter media visible inside, and is pumped back to the tank. By trickling the water through the media in a shower-head fashion the media is exposed to both water and high levels of oxygen, increasing its effectiveness.

CYCLE YOUR TANK. Biological filtration depends on an entire mini-ecosystem in which fish produce ammonia which some bacteria use for food, producing nitrites, which another group of bacteria use for food and produce nitrates. There are no “out of the box” mini-ecosystems. You have to grow one in your filter before you can safely add fish. There are a few ways to do this.

  1. There are directions for fishless cycling online. That’s what it will be called. It involves adding ammonia directly to a tank with no fish and monitoring the levels of nitrites and nitrates. Once the ammonia is reliably converted to nitrates in a timely fashion the tank is cycled.
  2. You can feed the tank like there were fish in it. The rotting food will produce ammonia just like it would going through a fish. This doesn’t always work perfectly, since you may get the amount wrong, but it’s worked well for me. Mind you, I also follow all the extreme safety tips I give later about adding fish.
  3. If you’ve got a large enough tank you can cycle it with some hardy fish (or invertebrates). Guppies work well for freshwater. The idea is simple: a 55-gallon tank can hold far more than a few guppies. If you add a few guppies the sheer volume of water will keep the ammonia concentrations low for a while and give the bacteria in the filter time to start growing. Once that seems to be working well you can (slowly) add other fish.

Cycling takes time. A lot of fish stores (that admit that you need to cycle tanks – some will pretend that you can just plug the filter in and go, probably because that way you’ll be back to buy more fish really soon) will say that it takes a week to cycle a tank. Cycling isn’t binary. A tank can be more or less cycled, and cycling probably continues for months or years, as ecological communities become more complex and shift in composition. I generally cycle for several weeks, and in one case a rather-accidental four months.

So can you cut down on the time to cycle a tank? Yes! And no.

  1. You can buy a lot of products that claim to do this. I’ve heard that there is one refrigerated bacterial infusion that may or may not be available in the US that works well. However, most of these are just ways to pay money for something that is free. There are no products that can instantly cycle a tank and you don’t need to buy any products to cycle a tank. One of the major barriers here is that you need live bacteria of the right sort, and keeping bacteria alive in storage with no ammonia for food is hard. Another barrier is that I’m not sure we really know exactly what bacteria are involved in cycling a tank. Nitrosomonas and Nitrobacter are obviously important but there’s reason to suspect that this is a complicated story with a lot of ancillary characters.
  2. However, you may know people who have live, complete bacterial communities available. These are people with working fish tanks. People such as myself, who have more than enough biological filtration, can often pull a sponge or some media out of a working filter and either drop it in your filter (or tank) or squeeze it out into the tank. This will look like someone just squeezed disgustingly dirty water in a nice clean tank but that “dirt” is the bacteria you need. This can cut cycling time by a lot. You do want to match water type as much as possible. Putting filter material from a saltwater tank into a freshwater tank is probably unhelpful. If your tank is tropical you will probably get better results from a tropical tank, and so on (but any freshwater tank should help some with any other freshwater tank).
  3. It is possible to start a tank already cycled. It’s the filter that cycles, not the tank (mostly), so if you take a filter off a working tank and put it on a new tank it’s already cycled. This is most useful if you are moving small fish to a larger tank where they will grow larger. Imagine that you have a 10 gallon tank and just realized that the fish you bought will grow a lot larger than the fish store told you. You want to switch them to your new 40 gallon tank now before they grow larger and let them grow up in that tank. However, you don’t have a cycled 40 gallon filter. No problem! You only have 10 gallons worth of fish right now, so you can move the filter for the 10 gallon tank to the 40 gallon tank and start both filters. In a month both filters will be full of bacteria (the small filter will “seed” the big one) and the small filter will have carried you through the danger period. You can take the small filter off.
This homemade sponge filter is effectively filtering the water in a shrimp breeding tank. It does extremely poor mechanical filtration (despite some people claiming that sponge filters are mechanical-only) which saves the lives of the small shrimp, who can’t get sucked in anywhere. It does excellent biological filtration as water is drawn into the chunks of filter foam and expelled at the top. My sponge filters are uglier than many commercial ones, but also have a lot more sponge, which is probably why mine seem to work better. I could also easily pull one sponge block off and transfer it to a new tank to kick-start the cycle.

As always, a few more important notes about biological filtration:

  1. Biological filters get better over time. “Cleaning” a biological filter makes it worse. You’re cleaning off the bacteria that do the work. Yes, they look like sludge (“biofilm” is what a bacterial sludge layer is termed by experts) but they are what makes this all work. Now, sometimes you do need to clean the biological filter because it’s jammed up and water doesn’t move through it but try to do two things. First, clean it in tank water, not chlorinated water. Remember, as far as aquatic organisms are concerned, chlorine is murder. Second, if at all possible clean only part of the filter so the bacteria from the other part can rapidly re-colonize the post-apocalyptic landscape of the cleaned filter. I like filters that have things like two different sponges in the biological filtration section so you can clean one and leave the other alone. (Admittedly, custom filtration is easy when you build your own filters.) I sometimes see people on fish forums say they think their tank has a fish disease when it has ammonia poisoning and so they clean everything really well to kill the germs. This just kills their fish faster.
  2. Biological filters are alive. Things like fish medicines can kill parts of them. The wrong temperature or the wrong pH can kill them. If you have a filter go bad that can make a bad day a lethal day for a fish, so if things seem to be going crazy consider that maybe the first problem (temperature, pH, medicine) caused a filter problem.
  3. The key to a biological filter is the conversion of ammonia to nitrite and nitrite to nitrate. You can buy a test kit for these chemicals at most fish supply stores. This can help you troubleshoot a lot. If, for instance, you see an ammonia spike but no nitrite or nitrate spike the biological filtration isn’t working because lots of ammonia should rapidly become lots of nitrite and so on. If you see a nitrate spike but the other numbers are staying low something bad may have happened but the biological filtration isn’t the problem. The day I wrote this I found a dead fish in a tank in lab. It had probably actually died the day before and been rotting the whole day. I had a bad nitrate spike but the biological filter (homemade out of two pieces of PVC and some high-grade filtration sponge from SwissTropicals) had converted a deadly ammonia spike into an unpleasant nitrate spike.

Change Your Water

All this filtration is great, but even with the best biological filtration in the world your nitrate levels will gradually creep up. There’s no way around that, and the very expensive devices you can buy to hold back the inevitable are not worth it. What is easy is to change the water regularly. Back when I first wrote this I aimed for changing 50% of the water every week. However, that has now changed to something more like 20% of the water per week. I sometimes don’t manage this, but I also test my tanks for ammonia, nitrite, and nitrate, and so I know exactly which tanks need water changes. Changing the water is simple: turn off the filter and heaters if they will get dry during this process. Dry filters tend to burn their motors out and dry heaters can sometimes explode. Remove 20% of the water (don’t remove all the water). Dechlorinate more water. Let it sit for a bit to get to room temperature. Add it into the tank. Turn the filter and heaters back on.


Your tank plus your water changes plus your biological filtration define your maximum bioload. Bioload is the “load” your animals place on the system. Above a certain amount of living animal tissue5 in a tank (be it fish, shrimp, snails, or whatever) and the level of nitrates in the tank will get too high before you change the water. More water dilutes the nitrate, more biological filtration prevents ammonia from staying as ammonia, and more water changes gets rid of all the fish waste faster. I advise you (if you are a beginner) to under-load your tank.

Imagine that your tank can hold 2 pounds of live fish without going toxic. (I’ll discuss how to determine what load you can support in another article.) The temptation is to put 2 lbs of fish in it and have the tank look “alive” with lots of fish, or maybe a really large centerpiece fish. The problem with this it that you have no room for error. I mentioned earlier that I found a dead fish in a tank today. I probably missed that fish yesterday (it had been looking poorly two days ago and yesterday was crazy). That fish went from producing ammonia like a live fish to producing much, much more ammonia as it rotted. If I had that tank stocked at 100% bioload I would have gone over 100% and I probably would have killed all the fish in the tank. Instead, I have that tank understocked. I might be at 40-50% bioload. When a single zebra danio died in the tank that might have temporarily pushed me up closer to 100%, but it didn’t push me over. I did a big water change today and it’s all taken care of.

A lot of my lab tanks do not get optimal maintenance. I under-load them and I don’t ever have issues with them. Meanwhile, I know lots of fish hobbyists who always pack their tanks and have to stay on top of everything. It’s possible to do (I know people who do it) but if you want a casual, low maintenance fish tank avoid the temptation to cram it chock full of fish.

I Wish I’d Known That, But Now It’s an Emergency

So, what if you didn’t read any of this until after you put fish in your tank? You didn’t cycle the tank, you maybe don’t have any kind of filter, and now the fish are acting funny.

  1. Get a filter. The right sort, which means one that has biological filtration (it may say this, or it may have a “biowheel”, or it may have sponges that water go through, or it may have media bags that look like broken pottery).
  2. When in doubt, water change. Just make sure to dechlorinate.
  3. If you need to use an emergency anti-ammonia product go ahead.
  4. If you can get filter-gunk from someone with a working tank do it. This will kick-start your cycle.
  5. Start testing the water, or getting it tested. What you want to see is the ammonia levels drop and the nitrate levels rise. Once your ammonia is getting converted into nitrates reliably you have a working biological filter and your tank is cycled. This can take a while, especially since you’ll need to be removing ammonia from the tank to keep the fish alive rather than leaving it in to feed the bacteria.

In the next article I’ll discuss choosing tanks, for those who haven’t already committed themselves.

  1. Since I have a pretty good guess at what sort of land vertebrate you personally are the answer is “mostly urea, with a little bit of uric acid”
  2. With some notable exceptions, like lungfish
  3. Except that it doesn’t actual work by filtering under some of the definitions of that word
  4. Some of these “bacteria” are actually archaea, which I should note because this is a science blog, but which doesn’t matter to a fish-keeper at all
  5. Plants do not count towards bioload, and in many ways help deal with animal waste

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