How to Properly Cycle a Freshwater Filter

by Esteban Parreno January 30, 2019 10 min read

How to Properly Cycle a Freshwater Filter

In order to maintain a healthy aquarium ecosystem — and by extension, healthy, good looking fish — maintaining good water quality is key. Arguably the most important aspect of achieving this is by correctly cycling your tank/filter, which will ensure the system is well balanced, before adding fish to the tank.

What is cycling a tank/filter?

Cycling a tank is essentially allowing the system to evolve through the various stages of the nitrogen cycle so that beneficial bacteria (which break down toxic fish waste) can colonize the filter before you go ahead and populate the tank with a large number of fish.

Having a clearer understanding of the various stages of the nitrogen cycle will help you better understand the chemistry of your evolving system and how this will affect fish and other living organisms inhabiting your tank. So let's break it down…

Nitrogen Cycle Explained

The nitrogen cycle is a three-stage process during which beneficial bacteria convert toxic ammonia into nitrite (also harmful to fish) and finally into non-toxic nitrate as follows:

Stage 1: Ammonia — Any fish living in your tank will excrete waste, which is high in ammonia. Uneaten food can also contribute to a buildup of ammonia within the tank. Ammonia levels will continue to rise until nitrifying bacteria that feed on ammonia begin to colonize the filter/tank, at which point the water in your tank may become murky. Ammonia levels will eventually max out before they start to drop, signaling the start of stage 2 — the nitrite phase.

Stage 2: Nitrites — As ammonia levels start to decline, you will notice that nitrite levels will start to rise. This is because nitrifying bacteria known as Nitrosomonas consume the ammonia, converting it into nitrite, which is extremely harmful to fish. As with stage one, nitrite levels will continue to build up in your tank until a new group of nitrifying bacteria (Nitrospira) that feed on the nitrites starts to colonize your filter/tank, at which point nitrite levels will start to decline.

Stage 3: Nitrates — The Nitrospira bacteria consume the nitrites, converting it into nitrate. Once ammonia and nitrite levels in your tank have been reduced to 0 parts per million (ppm), you will know that your mini freshwater ecosystem has completed the nitrogen cycle and your tank has been successfully cycled.

The nitrates that are produced by the nitrifying bacteria during the final stage of the nitrogen cycle are harmless to fish at low levels and beneficial to aquatic plants. However, high concentrations (>20ppm) of nitrates can be harmful to your fish and can also promote algae blooms. It is therefore important to monitor nitrate levels regularly so that you can take appropriate measures to keep nitrate levels in check should they start to rise. To prevent nitrate concentrations from rising to harmful levels, you should perform weekly/monthly partial water changes, depending on your stocking rates, replacing 20-50% of the water in the tank. You can also add aquarium plants that will absorb some of the nitrates — a plant nutrient that promotes growth.

fish waste nitrogen cycle

Why you should cycle a tank

Fish excrete waste (urea) contains high levels of ammonia, which if not removed can build up in the water column and kill fish. This is particularly problematic in the closed environment of an aquarium, which unlike a natural freshwater system doesn't have a fresh flow of water flowing into the system or dirty waste-filled water flowing out. Consequently, unless it is removed, organic waste from fish excretions, dead and decaying plant matter, and uneaten fish food will remain within the confines of the tank, where it will accumulate, eventually causing the water to become toxic to your fish.

The smaller your tank, the more critical it is to keep ammonia levels low through moderate stocking rates and adequate filtration. A larger tank holds more water, which in effect dilutes the ammonia, reducing its toxicity to fish. A larger filter has a larger surface area, providing more real estate for beneficial bacteria to colonize and go about their business of breaking down ammonia and nitrites.

It is also important to note that while snails and other invertebrates can assist in breaking down and removing the organic material that accumulates on the floor of the tank, essentially helping to keep the tank aesthetically clean, they do not remove ammonia or nitrites. Instead, they too excrete waste that further contributes to the ammonia load in the system. Wastes can only be removed through biological filtration, where nitrifying bacterial communities living on the filter media convert ammonia into nitrite, and finally into nitrate, as the water passes through the filter and comes in contact with the bacteria. However, it takes a while for these communities to establish themselves in sufficient enough numbers for them to be an effective mechanism for keeping the system in balance, which is why it is so important to cycle your tank before adding your fish. It allows bacterial communities that will support your fish to multiply so that they can effectively tackle the vital task of breaking down the toxic ammonia excreted by the fish, thereby making the tank habitable for your fish.

how to cycling your aquarium filter

Different Ways to Cycle your Filter

There are several different ways to cycle a tank to establish a healthy colony of beneficial bacteria in your filter. Essentially, the cycling process involves adding ammonia to the water in the tank to get the nitrogen cycle up and running, and the associated bacterial communities established. Ammonia can be added to the water from various sources, for example by waste produced by fish living in the tank (fish-in cycling) or by fishless methods where ammonia, fish food, or fertilizer is added to the water. No matter which method you opt for, you will need a water test kit that is capable of measuring ammonia, nitrite, and nitrate. This will allow you to monitor these vital water parameters and will give you some indication as to how the cycling process is progressing.

But before you proceed, you will need to ensure that the water in the tank (as well as any water that is added when performing water changes) has been dechlorinated and is free of chlorine or chloramines, which are toxic to the bacteria and will, therefore, derail the cycling process if they are present.

Cycling a tank with Fish

When using live fish to cycle your tank, you will need to add a few hardy fish species (for example, White Cloud Minnows) that you intend to keep in the tank in the future. These fish will provide the ammonia that the bacterial communities need to survive and thrive. It is very important that you do not overstock the tank before the bacterial communities have had a chance to colonize and establish themselves within the system. Overstocking the tank can result in a buildup of ammonia that can kill the fish, which will no doubt already be stressed due to high ammonia levels. Likewise, be careful not to overfeed the fish, as decaying food waste can contribute excessive amounts of ammonia to the system. You can perform a water change every couple of days, changing between 10-15% of the water to reduce ammonia levels, but be careful not to change too much water, otherwise, you run the risk of removing the ammonia and nitrates needed to sustain the colonies of nitrifying bacteria you are trying to establish.

Because being forced to live in a tank with spiking ammonia levels is not very kind to fish, fishless cycling is now considered a more acceptable way to cycle a tank.

Fishless Cycling with Ammonia

Instead of using fish to add ammonia to the system via their waste, a few drops of household ammonia (a dosage of between 2-4ppm, or ~2-4ml per liter, is recommended) can be added instead. There are online ammonia calculators that can help you with this task. The day after you have added the ammonia, use an ammonia test kit to measure ammonia levels in the water. If they have dropped to below 3ppm, add small amounts of ammonia to ensure there is still sufficient ammonia present in the water to sustain the bacterial communities you are trying to cultivate. Repeat this process every day for about a week, then start testing for nitrites. When nitrites are detected, it indicates that the first stage of the cycle is in full swing and the bacteria are happily doing their thing. Continue monitoring ammonia levels daily, and nitrite levels every second day. You will soon notice nitrite levels starting to rise (stage 2), before they start to drop off again a few weeks later, indicating the initiation of stage 3, when nitrate levels will rise. Once ammonia and nitrite levels have dropped back down to 0ppm, the nitrogen cycle is completed and it is now safe to add fish.

Fishless Cycling using Fish Food

For this method, rather than adding household ammonia to the water in the tank, you will add a few flakes of fish food instead. The decaying food releases the ammonia needed to start the cycle into the water. As with the ammonia method above, test the water for ammonia daily, and should this drop below 3ppm add a few more flakes of fish food into the tank. Start testing for nitrite the following week. Continue monitoring ammonia and nitrite levels every second day, adding a few more flakes if ammonia levels drop below 3ppm. After a few weeks, nitrite levels will start to decline and nitrate levels should start to rise, indicating the system has reached stage 3 of the cycling process. The cycle is complete once ammonia and nitrite levels have dropped down to 0ppm, and you can now add fish to the tank.

How we Recommend Cycling your Filter

An often overlooked, yet extremely simple and effective way to cycle a tank naturally is by establishing a healthy community of plants and algae prior to adding any fish.

The cycling process in a planted aquarium works slightly differently to all the above methods as the plants play a large role in physically removing ammonia produced by fish from the water, essentially serving as a giant natural filtration system. This is a method commonly used by wastewater treatment facilities to clean wastewater before discharging the treated effluent water back into the environment (river/lake/other freshwater bodies). Live plants do an excellent job of cycling a tank. So, rather than simply trying to establish bacterial colonies in your filter, we recommend that you focus on establishing a living ecosystem by cultivating life (i.e. a system that consists of a diverse range of life forms including plants, algae, and bacteria).

Living plants absorb ammonia, nitrites, and nitrates, as well as other potential contaminants from the system and use these as the building blocks for growth. Another advantage of adding live plants to your aquarium is that they usually come in a bag containing some water from the original tank they where housed in, and are often also potted in a rockwool growing media, both of which will contain an established colony of beneficial bacteria that will help inoculate your tank with nitrifying bacteria.

However, because the system will have no ammonia inputs before the fish are added, you will need to feed the plants and bacteria by adding a nitrogen-based liquid fertilizer that promotes plant/algae growth. One of the major benefits of establishing a living ecosystem consisting of plants is that when you introduce your fish to the aquarium, the established plants (that are now used to processing those nutrients) will simply consume the ammonia, nitrites, and nitrates produced by the fish, enabling them to grow faster and thrive.

Which begs the question: When is the best time to add the fish? The answer to that is of course when the tank has been cycled. However, when it comes to testing whether your tank is adequately cycled, things work slightly differently in a planted aquarium. When testing the progress of the cycling process, one would normally use an ammonia test kit to monitor nitrate levels to see whether bacteria have converted the ammonia to nitrates. In a conventional cycling method, you would initially notice an ammonia spike (stage 1), followed by a nitrite spike (stage 2), followed by a nitrate spike (stage 3) before nitrate levels taper off and ammonia and nitrite levels stabilize at 0ppm, indicating the tank has been successfully cycled.

If your tank contains a lot of living plants, this reading may not give a true reflection of the cycling process as plants absorb these nutrients, converting them into growth. So instead of seeing the successive spikes in ammonia, nitrites, and nitrates across the various stages of the nitrogen cycle, in a planted aquarium you are more likely to see an initial spike in ammonia then nothing. Because this doesn't follow the conventional pattern, it can be a tad confusing, but the reason for the lack of nitrites and nitrates is simply because the plants are absorbing them. So if you are seeing algal or plant growth in your tank, it indicates that your mini freshwater ecosystem is alive and ready to receive fish, though we would recommend waiting about 1-2 weeks before adding fish. If you are not getting any new algal or plant growth then your system is not ready to receive fish just yet.

Introducing Fish

Ultimately, the goal is to maintain water quality so that fish can live happily in the tank and that waste produced by the fish doesn't accumulate in the water to the extent that it kills the fish. As we can see, there are several ways of achieving this, including performing regular water changes to remove ammonia, cultivating a colony of nitrifying bacteria that will break down the waste into less toxic forms that allows us to get away with doing less frequent (weekly/monthly rather than daily) water changes, or establishing a living community of plants that will physically remove ammonia from the water.

Because it takes a while for beneficial bacteria to colonize the tank in sufficient numbers to be effective at processing the waste produced by the fish, you will initially have to either physically remove this waste by performing more regular water changes, or you can simplify your life and let plants take care of that job for you. The same applies to algae — leaving the back and sides of your tank covered in algae can help reduce the need for regular water changes during the initial stages and can be removed at a late stage once an ecological balance is reached within the system.

Slow and Steady Wins the Race

Regardless of which method you decide to use to cycle your tank, don't be tempted to speed things up by adding chemicals that reduce ammonia levels. This would be counterproductive as the beneficial bacteria and/or plants you are trying to cultivate require this to survive and thrive. Cycling a new aquarium is a slow and steady process that can take anywhere from 4-6 weeks, sometimes even longer, and therefore requires a fair degree of patience. However, having said that, you can speed things up naturally if you have access to another aquarium that has an established colony of bacteria. Simply add some gravel, potted plants or filter media from the existing tank to help kickstart the process and shorten the cycling time. Work in harmony with nature and let the biotic communities develop naturally and you will be blessed with a stable system in the long run.

If you would like more information, check out our video on cycling your filter. Happy fish keeping!