All Aquaponics keepers like to have a crystal clear water. Indeed, it allows to see the fish at any time. Mother Nature, on the other side allows the ecosystem to evolve with time. If the conditions are good for algae development, you will find your water turning green. Or the walls and bottom of your aquaponics fish tank will cover with algae. Again, this is not a problem for your fish even if the algae will make the oxygen concentration fluctuate. But, the algae will be in direct competition with your plants for nutrients. In this video/article, I will show you the easiest way to control algae in aquaponics. As a result, you will be able to keep a clear water. Some common techniques involve specific fish or snails. however, here we will see that we can fix this issue with simple actions.

What are algae?

Algae are aquatic creatures able to produce photosynthesis. In other words they are very close to aquatic plants. Unfortunately there is no easy definition of the difference between plants and algae. However, one clear point of difference is that algae don’t have a developed vascular system. We classify algae in the 2 following categories:


Mono-cellular algae are by definition composed of one unique cell. They are thus microscopic, you can’t see them with your naked eye. But, unlike most multi-cellular algae, the mono-cellular are generally “Pelagic algae”. That is to say that they are swimming on the column of water. Generally towards the surface to absorb the sunlight. If you can’t see a single cell with your naked eyes, a high density of micro-algae will color the water. The micro-algae color is generally green but depending on the species it can also be brown or red.


Several cells compose the multi-cellular algae. Hence, they are generally larger than mono-cellular algae. If they often remain at a reasonable size (less than 40 cm long), the largest of them (the Kelp) can measure up to 50 m long. Those algae, also called seaweeds, are generally fixed on the seafloor (or river/lake… floor). Therefore, we qualify then of “Benthic algae”. In a fish tank they will not color the water. They will grow on the tank bottom and walls. They are generally not a problem and some fish will be happy to eat them.

How are algae functioning?

Most algae function like plants. In other words, they consume CO2 + sunlight and produce energy + O2. We call this phenomenon “photosynthesis“. Algae are actually responsible for producing a large part of the oxygen we breath every day. However, they also breath (like plants). During the night, they don’t produce oxygen anymore but keep consuming it. Early morning is often a critical time for all aquatic creatures. This is the time where the oxygen level is at his lowest. If you have algae in your aquaponics tanks, you must keep this fact in mind.
Also, algae are consuming the same nutrients as the plants. So they sometimes compete for it. Especially if your aquaponics system is deficient in nitrate. Be reassured, it is rarely the case in aquaponics.

Where do they come from?

Algae can “contaminate” your aquaponics system via different methods. They generally come with the fish. They can also come with the wind, sometimes the rain, birds… As you understand, the factors are many. There is no point to fear the algae contamination. Algae will only multiply if they find good conditions. That is to say nutrients, the good temperature, and sunlight.
Algae have different ways of reproduction but most microalgae reproduce by cellular division. One cell divide in 2 cells. Some algae are able to reproduce in a short period of time. They can double the whole population every cycle. When a microalgae find the good conditions to grow at full potential, we call it a bloom. When a bloom occurs, the water can turn completely opaque. In those condition it is crucial to check the oxygen concentration during the night. Adding extra oxygen supply such as air pumps with air stones is very important.


Some algae have the possibility to produce toxins. However, such toxins are always observed in the natural environments. Never in aquaponics or even inland aquaculture.

Algae in the aquaponics grow-bed?

Algae can also grow on the surface of the media in the aquaponics grow-bed. However, it only happens when the rule of the 3cm is not respected. This rule state that you should set your bell siphon to preserve the top 3 cm of your grow-bed media dry.

How to regulate the algae population?

In aquaponics we have a simple technique to limit the algae growth.

The false “good idea”

First, please do not ask an aquarium shop! They will give you a product composed of coper to kill the algae. Yes it will work, you will kill the algae. As well as the bacteria of your aquaponics system… And even the plants and fish will not be happy. Please stay away from this very poor solution.

UV filters

Another solution is the Ultra Violet “UV Filtration”. It consist of using a strong UV light to kill the algae cells. This method works very well. Yet, it is also killing the bacteria in suspension into the water. UV need electricity. Also the light efficiency decrease with time. This system require maintenance, you will need to change the globes every 6 months. This solution is efficient but add complexity and cost.

The easy fix to regulate algae in aquaponics

Finally, the simple method recommended for aquaponics is to cover the fish tank. By covering the fish tank, you decrease the quantity of light available for the algae. Without light, the algae can’t grow. Please make sure to leave the tank open for few hours a day or to leave a section open to sunlight. Indeed you want to offer your fish the possibility to enjoy the sun as well.
In some cases, it is not possible to cover the tank. I am for instance thinking of fish ponds converted to aquaponics. In this case you can try to reduce the light with trees or shade on top of the tank. UV are still a possibility.
And you are you facing an algae challenge? Let me know in the comment section. 

You will probably be interested to discover Jonathan’s six steps to build and manage an Aquaponics system. Click here to access for free! Thanks and good reading 🙂