The basis for the proper functioning of the freshwater aquarium is to create a stable ecosystem in it, in which living organisms that make up the biocenosis (animals, aquatic plants, and microorganisms) and the elements of the biotope (water, substrate, elements of decor) maintain a dynamic balance. This equilibrium is achieved when the chemical parameters of water, such as hardness, pH, and concentration of nitrogen compounds – remain at a constant and appropriate level, animals and plants develop and grow healthy, and algae remain in an amount that does not threaten other living organisms. Symptoms that indicate the lack or disturbance of the biological balance may be: the smell of rot or hydrogen sulfide in the aquarium, unusual behavior, diseases or even fish dying, poor growth or death of plants, an excessive amount of algae, or rapid bloom of protozoa.

Although many aquarium hobbyists don’t like articles about the science present in every planted aquarium, understanding the basics is essential to have a low-maintenance aquarium which is the main goal of many. A self-sustaining fish tank is not possible but with help of common knowledge in this topic combined with specialized equipment- there won’t be much to do if some basic rules were followed.

General tips to set up a healthy and balanced ecosystem

The chosen fish species must have the same requirements regarding:

  • water temperature- this is obvious, but must be mentioned. Tropical fish will certainly need higher temperature that cold water species. It’s worth using an aquarium heater with suitable controller to maintain the stable temperature.
  • water pH- some fish species live in nature in water where the pH is higher because of rock or stones present in the substrate, e.g. African cichlids, while some gasp for air in the same conditions.
  • water quality- there are species that live in black waters in nature while some occur only in crystal clear water. This must be taken into consideration.
  • substrate- some fish like catfish love digging and some may not like it at all. In case of fish which prefer digging in the substrate, well-rooted plants are the best choice.
  • behavior- some fish are territorial and may not be a good option for a community tank. Look for compatible species while choosing the stock.
  • space- every fish needs enough space to swim. Overstocking is one the worst mistakes that aquarists make. The amount of the fish must be always compared to the tank size and again- behavior of the fish. Some species are more lively than other fish so even if the herd is small, the larger tanks are recommended. For smaller tanks fish like neon tetra or rasbora will be a great choice.
  • arrangement- there are fish or shrimp that like hiding places more than others. Add some to your arrangement to reduce stress in your aquarium friends. Moreover hiding places are important for spawning and baby fish.

The aquarium as an ecosystem

In order to achieve biological equilibrium in an aquarium, the right proportions between individual elements of the ecosystem, and in particular its living part, the biocenosis, are needed. Or, simply put – the right amount of aquarium plants, fish and microorganisms. Each of these groups of organisms plays an appropriate role in the planted aquariums and influences other groups. And so, to put it simply:

  • Aquarium plants – take up carbon dioxide and inorganic compounds such as phosphorus, potassium and nitrogen. In return, they provide oxygen and biomass, which is food for animals, and when they die – a medium for bacteria (and also for some animals). Aquarium plants and activated carbon are considered as two best chemical filter media.
  • Animals – they take oxygen from the water and give back the carbon dioxide needed by aquatic plants. In addition, they excrete metabolic products, which are broken down by appropriate bacteria into inorganic compounds needed by plants.
  • Microorganisms, including bacteria, convert dead organic matter into inorganic compounds, and also play an important role in the nitrogen cycle and nitrification processes.

Both the excess and the shortage of representatives of each group have specific and usually unpleasant consequences. Sometimes they can be easily eliminated by providing supplements or taking specific actions. Sometimes it is very difficult. The lack of plants in the aquarium results, among other things, in an increased content of carbon dioxide and oxygen deficiency, and the accumulation of inorganic substances. This situation can be ‘rectified’ by the use of efficient filtration, aeration and regular partial water changes. On the other hand, a large number of aquarium plants, with the absence or a small number of animals (as is the case in a plant aquarium), necessitates the supplementation of carbon dioxide and inorganic substances (by fertilization), which would otherwise be supplied by the metabolic products of animals. The most difficult thing in the aquarium ecosystem to replace are microorganisms. Especially, if we want to keep fish in the tank, we should take care of the presence of “good” bacteria, without which it is impossible to provide them with stable living conditions.

Nitrogen cycle in the aquarium

Time is needed to achieve biological balance in the aquarium. This is commonly referred to as nitrogen cycle. This is the period in which, inter alia, the nitrification processes as well as the nitrogen cycle stabilize. The process usually takes 4 to 6 weeks.

There are no or only minimal amounts of nitrifying bacteria in the new set up. If you let fish into such a tank, and they start to eat and excrete, the ammonia content would rise very quickly to the values ​​at which we would observe mass deaths. Therefore, animals should never be introduced into the aquarium for the first few weeks until the appropriate bacteria have multiplied in it.

In order for them to multiply – they need organic matter that gives off ammonia or ammonium ions. For this purpose, it is best to deliver something rotting to the tank – it can be dead plant parts or a small amount of fish food. Some sources also propose the introduction of 1-2 “very resistant” fish – but for animal welfare reasons, we do not recommend this method. The matter delivered to the tank during rotting releases ammonia into the water, the level of which rises and causes the bacteria of the genus Nitrosomonas to multiply and begin to convert ammonia into nitrite. Initially, there are few bacteria, and although they are working hard to process ammonia, its level continues to rise. Don’t be concerned about this – this is a perfectly normal step in the process. After a week or so, they will multiply to such an amount that the ammonia level will slowly decrease and the nitrite level will increase. After about two to three weeks, the ammonia level should be practically zero and the nitrite level very high, which means that all ammonia has been converted to nitrite. In this situation, bacteria of the genus Nitrosospira begin to multiply in the aquarium, converting nitrites into the least harmful nitrates for fish. Within the next week or two, there should be enough Nitrosospira bacteria to deal with all the nitrites. At this point, neither ammonia nor nitrite should be detectable in the water anymore, but it will contain nitrates. Before introducing fish, it is best to check their levels with tests. If there is a lot of them, the most common practice is to change the water, but another type of bacteria can help us, namely denitrifying bacteria from the genera Pseudomonas, Escherichia, Bacillus, Thiobacillus, Micrococcus or Paracoccus. They convert nitrates into nitrogen, which is released as a gas from the water into the air.

Maturing of the aquarium always takes time. However, in order to obtain more reliable results and shorten the whole process a bit, you can use aquarium preparations containing bacteria as a start. Such preparations can also be used during water changes, after using antibiotic treatments, and in any situation where there is a suspicion that the bacteria may have become extinct.

How to care for good bacteria?

Like all living things, bacteria also need the right conditions for them to live and reproduce. Theoretically, nitrifying and denitrifying bacteria are everywhere in the tank, but most of them are in the substrate. For this reason, the type of substrate is significant. The best are medium granulation gravel and stoneware made of natural aggregate – quartz or basalt, and volcanic lava. The porous structure of these materials is an excellent habitat for bacteria, and the appropriate granulation ensures oxygen access to all layers of the substrate.

In most reservoirs, the amount of bacteria inhabiting the substrate and elements of the reservoir decoration is not enough for the nitrification processes to run efficiently enough. For this reason, biological filters are used, filled with highly porous beds, which can be a “house” for large numbers of bacteria. Nitrifying bacteria are aerobic bacteria, which means they need oxygen exchange to live. This will be partially ensured by the plants in the tank (if any) as well as proper filtration and regular water changes. It’s worth placing the medium with beneficial bacteria somewhere in the aquarium where the water passes throughly. Then the bacteria absorbs the oxygen from the water, ridding it of ammonia and nitrites. Without the right amount of oxygen, our beneficial bacteria will begin to die. These microorganisms are quite sensitive to UV rays, especially in the initial phase of multiplication – therefore it is better not to expose the “maturing” tank too much to the natural sunlight. It is obvious, although it is not always remembered about it – all substances with a bactericidal effect, such as antibiotics, preparations containing chlorine, copper ions, methyl blue, formalin or alcohol are lethal to bacteria. Using them in the aquarium causes that not only pathogenic bacteria die, but also those responsible for nitrification. Therefore, if possible – medical treatments on fish with the use of the above substances are better to be performed in a specially designed hospital tank. In the event that it is impossible, after completing the treatment, it is worth using a preparation containing bacteria to rebuild the bacterial flora.

What can disturb the biological balance in the tank?

While the role of bacteria is crucial to maintaining the biological balance in your tank, some basic rules should be followed:

1. Be careful with overstocking

We do not introduce too many fish, especially fish that are “voracious” and thus produce large amounts of fish waste products. Their excess may cause bacteria not to keep up with converting ammonia into nitrites and nitrates, which can quickly poison the entire community.

2. Be careful with feeding

We do not allow uneaten foods to remain on the bottom (or drift on the surface). We give the fish only as much as they can eat in a short time for best fish development – the rest should be caught. Otherwise we can wait for high ammonia levels or snail invasion with open arms.

3. Be careful with dead organisms

We do not allow plant and animal remains. We remove dead fish or dead plant debris. If you have a dense plant life in your freshwater aquarium, huge tank volume and tiny fish inside- count them from time to time to avoid extended ammonia levels in case of the fish’s death.

4. Be careful with filters

We monitor the work of the filtration system. Its inefficiency or insufficient work will result in the accumulation of harmful substances in the water. If the filter is clogged, it should be pushed as soon as possible, preferably by rinsing with water from the aquarium (not with the untreated tap water), so as to prevent the extinction of the bacteria inhabiting there. It’s good to introduce some cleaning species to support the filtration system work. Then we can say about almost self sustaining fish tank.

5. Provide regular water changes

We regularly change part of the water in the tank, because even in a stabilized tank, nitrates accumulate in it, which are harmful to fish in large amounts. Most often it is recommended to change up to 25% of the water every two weeks – although it depends on the fish species and the size of the tank. For replacements, use only standing fresh water, preferably treated water, free from chlorine and heavy metals. Sometimes it turns out that the tap water is soft and can be poured into the tank without treatment.

6. Be careful with the substrate

We do not rummage in the ground that is the habitat of beneficial bacteria for no reason. We only desludge what is on the surface.

7. Be careful with cleaning

We do not exaggerate with cleaning – regular “polishing” of decorative elements, litter or technical devices (especially with the use of chemical cleaning agents) kills the colonies of bacteria that are on them. It’s good to have some animals in the cleaning crew such us otos or Amano shrimp. These ones will help you to have a crystal clear glass and eat algae from almost every corner of the tank. A well- chosen crew may help you to have an almost self cleaning fish tank. Look into our article HERE to get closer to this topic!

8. Use a hospital tank if needed

If possible – all medical treatments on fish are performed in a special hospital tank, and the individuals after therapeutic baths before they enter the aquarium – thoroughly wash them with aquarium water.

9. Perform aquarium tests regularly

Whenever “something is happening”, it is worth using the aquarium test kit and determine the cause before dramatic situations occur.

10. Maintain stable water parameters

Most fish can handle slight water parameters swings such as water temperature or pH while other fish are very sensitive to any changes. A very useful tool to control the pH level is the drop checker. This method allows to see the pH level with a naked eye as the pre made mixture changes the color from dark blue to yellow depending on the CO2 level in the water. Look into our ARTICLE about drop checker method to read more.

11. Be careful with intense lighting

To understand the functioning of the aquatic life, we need to understand the impact of lighting on the functioning of the tank. The light is necessary for live plants to perform the photosynthesis. To put is simple, the more the light, the more carbon dioxide the plants absorb because they are able to produce more sugar which is food for them. For low tech setups it’s recommended to stay in low light zone because to intense lighting will for sure cause excess algae growth. On the other hand, the plant growth is stuned and it’s more likely that the plants will grow unhealthy. That’s why injecting CO2 is beneficial for aquarium live plants. Look into our offer to buy the most reliable CO2 System in the world!

Of course, carbon dioxide must be injected only during the day because during the night the plants don’t perform the photosynthesis and consequences may be lethal to fish. This is why you have to follow the day and night cycle as it happens in natural environment. Moreover, the natural light is not enough to maintain a healthy and well-functioning aquarium so artificial lighting will be needed. Read more about lighting in our article.


As you can see, our home aquarium can be a true reflection of the nature if all rules are being followed. Everything that happens in the aquarium has an impact on the water parameters and in consequence- surrounding organisms- fish and live plants. Understanding the functioning of the natural ecosystem will allow you to maintain the healthier environment and avoid unnecessary problems which are very unwelcome in aquarium hobby.

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