The biological cycle in your filter: Ammonia, nitrite & nitrates explained

The biological cycle in your filter: Ammonia, nitrite & nitrates explained


In the wild fish are unlikely to live-in crystal-clear water, that is because they thrive in microorganism rich environments. When setting up a new tank for your fish, it is important to understand aquarium and nutrient cycling. If you have heard other hobbyists or aquarists talking about the biological cycle, they are referring to the cycling of waste inside the aquarium water. Imagine when going into a swimming pool, and everyone was to urinate in the water, a filtration system would need to be in place to remove this waste. You would not want to be swimming in strangers or even your friends waste, fish feel the same in an aquarium!

The filtration system in your aquarium is one of the most important functioning pieces of equipment in the water, it determines success or failure for your fish. Filters are designed to catch solid waste produced in the aquarium and convert them into harmless products. Basic filtration systems include mechanical and biological filters. Mechanical filters remove floating debris, but it is important to regularly remove and clean them. Biological filters allow bacteria in the aquarium to break down ammonia products and convert them into nitrites that are less toxic to the fish. You will still need to carry out partial water changes at least every month even with a fully functioning filtration system.

The placement and size of your filter depends on the size of the aquarium you have. External filters are placed on the outside and require a water pump, whereas internal filters are usually placed under the substrate or attached onto the side of the glass.

The nitrogen cycle is a big part of nature’s way to recycle nutrients in your aquarium. Your fish consume food and then produce waste from excretion, this comes in the form of ammonia. The healthy bacteria and live plants in the water absorb this lethal waste so your fish stay healthy. Nitrobacter will form when nitrite levels reach a certain stage. These nitrites are converted into nitrates and when levels of ammonia and nitrite read 0 ppm your tank has been successfully cycled and is safe for your fish.

Here is a simple way to understand the nitrogen cycle:

As the fish consume their food and turn it into waste, Ammonia is the first stage and if the tank is not cycled then you will have big problems, the ammonia will build up to toxic levels, the filter is lacking the bacteria to convert it to a less harmful version.

Remember, when first setting up a new aquarium, there will be no fish waste to cycle. You will not want to wait weeks or even months for these beneficial bacteria to grow, therefore you can start by only adding a few fish at the beginning. You will want fish that are ‘hardy’ and can cope with water changes.  Start by feeding only small amounts of food and increase this over time to allow beneficial bacteria to grow. If this is not your only aquarium, you can move some filter particulate matter into the new aquarium from another functioning tank you have to so speed up the process. Another method is purchasing live nitrifying bacteria from an aquatic retailer. As with any normal aquarium set-up, monitor the water quality closely before adding fish into the water.

If you are wanting to place live plants into the water, plant cycling is an easy and natural way to cycle the aquarium water. You will want enough light and fertilisers to help the plants thrive! Aquatic plants are just as effective as beneficial bacteria at consuming nitrogen waste that builds up. The larger the plants grow, the more ammonia they can consume, they also make your aquarium more colourful too.

When cleaning your filter, you want to ensure beneficial bacteria is not lost. When cleaning the filter sponge, siphon water from the aquarium and rinse in a bucket so the bacteria is preserved. Cleaning with tap water will remove them from the sponge and any chlorinated products added to tap water will kill the bacteria. If it is time to replace the sponge, only remove half of it. Cut it in half and place both the old and the new sponge in the filter so the bacteria is still present.

If you accidentally remove all the filter media, do not panic, you can quickly save your fish. Wait a few days to feed your fish and allow their ammonia waste to build up, test the ammonia levels and do a partial water change, add some ammonia remover and then add some beneficial bacteria into the aquarium.

Every time the filter is switched off the bacteria and live plants inside your aquarium will die due to an oxygen reduction. Sometimes we cannot prevent this, power cuts are common everywhere. The recovery of the tank depends on how long your electricity has been out.

Firstly, reduce the amount of food you feed your fish. Remove the filter sponge, give it a quick rinse in a bucket with aquarium water and place only the sponge directly into the tank. If the power has been out for more than 3 hours, it can cause serious problems for your fish. Constantly check the temperature and oxygen levels and leave the filter sponge submerged in the water. Try to raise the temperature of the water, but do not add hot water into the aquarium. Constantly watch your fish’s behaviour for oxygen deficiency (gasping at the surface or rapid breathing). If they start to show signs of this get a jar and put some aquarium water inside, shake it vigorously and pour back into the water. If you have a siphon, manually blow into the tube. This is not the most ideal method as we exhale high concentrations of carbon dioxide, however, if it is the last resort it is better than doing nothing. If you have a large aquarium, investing in a generator or purchasing battery-powered pumps will prevent any disruptions if a power cut were to happen.

Nitrite naturally enters the blood and gills of your fish. Once inside the body, it oxidises iron in the haemoglobin and is converted into methaemoglobin which is unable to transport oxygen in the blood leading to oxygen toxicity.

Ammonia is very toxic, at high levels fish will become lifeless and eventually die. Your poor fish will feel burning in the gills and damage their brain and organs. Nitrate is not as severe as ammonia and nitrite, but it can still kill your fish as elevated levels of nitrate makes fish more prone to diseases, affect their growth rate and make them unable to reproduce.

Initial biological aquarium cycling requires some time and effort, but the results are well worth the headache you may face if you skip this step. By making a healthy environment for your fish, maintaining water quality becomes easy and saves the life of your fish.

Author: FCA Marine biologist.