How to Kill Blue Green Algae (Cyanobacteria) in Freshwater Aquarium

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Do you have a problem with blue green algae? In this article I will show you few methods on how you can get rid of the nasty blue green algae, also known as cyanobacteria. There are many types of cyanobacteria.

Blue green algae is actually not algae like the black-beard algae. This is a type of bacteria which is able to photosynthesize. It can reproduce really fast in freshwater aquariums. It usually grows on the substrate and at the front glass of your fish tank.

The cyanobacteria is very hard to kill, because it is a very primitive form of life, which can survive in very harsh environments.

Cyanobacteria is very easy to detect in aquariums. Blue green algae has a dark green color, it is very slimy, it grows and spreads over any surfaces and has a specific bad smell.

In large quantities, it can kill off your entire aquarium ecosystem. Cyanobacteria will produce toxins, which are harmful for fish, shrimp and plants.

Main Causes of Blue Green Algae

Algae in general is caused by excess nutrients and excess light. Blue green algae is mainly caused by excess light and ammonia. It grows extremely well in aquariums with low nitrate level. Dirty filter or substrate is usually the main reasons that cause blue green algae to grow and invade your aquarium.


Cyanobacteria will compete with the beneficial bacteria for ammonia. While beneficial bacteria will turn ammonia in to nitrites and nitrites to nitrates, the cyanobacteria will consume ammonia to produce other highly toxic compounds.

Blue green algae is very common in new aquariums, where the nitrogen cycle is not finished yet. However, it can also appear in already cycled tanks, with dirty filter or substrate.

To combat the blue green algae, first, you need to clean the filter and vacuum the substrate. Also try to remove as much of the slimy cyanobacteria as you can.

If a cleanup does not help kill off blue green algae, you will need to take extra measures.

In the following I will give you few tips that will help combat the blue green algae in your aquarium.

Black-Out Treatment

While cyanobacteria can grow really fast, it can die off fast too.

As I mentioned, cyanobacteria uses light to photosynthesize. In absence of light, the bacteria will die off in a few days.

So, to get rid of the blue-green algae, you can shot off your aquarium lights for 2-3 days. If your tank gets a lot of natural light, cover your entire aquarium for 3 days with a blanket.

You need to block all light in order to have great success.

If you have a planted tank, be careful with this method, because there are few plants that can suffer from not having light.

Most plants will be fine without light for a week.

After you are done with the “black-out” treatment, clean your filter and siphon the substrate. Do a 50% water change and remove as much dead algae as you can.

If you have plants, add fertilizer to help them grow and outcompete algae.

In most of the cases the “black-out” method works, but sometimes the infestation is so strong, that you need to use chemicals.


Hydrogen-peroxide is a very common household. It is a strong oxidizer, so you need to use it carefully.

You can purchase 3% hydrogen-peroxide on Amazon.

During the oxidation process, hydrogen-peroxide (H2O2) will break down into water (H2O) and pure oxygen (O2).

You can use 1.5 ml of 3% hydrogen-peroxide per 1 gallon (4 liter) aquarium water. Do not overdose, because it will kill of your entire livestock.

Hydrogen-peroxide will kill off beneficial bacteria too. So you need to be careful with your filtration.

The process of treating with hydrogen-peroxide is simple:

  • Stop the external or internal filter (if you have a sponge filter, remove it from your aquarium)
  • Add the recommended dose of hydrogen-peroxide into your aquarium
  • You can also use spot-treatment directly on the blue green algae if necessary
  • If the blue-green algae starts releasing tiny bubbles, it means, the hydrogen-peroxide is working (it is oxidizing)
  • Wait about 1 hour, before restarting your filter or placing back the sponge filter

The effects of hydrogen-peroxide are visible almost instantly. However, you will see significant improvement only after 1-2 days. When the cyanobacteria starts dying off, perform 50% water change and remove the dead algae.

After the treatment, clean your filter and help the beneficial bacteria recolonize quicker with the API Quick Start water conditioner from Amazon.

Chemi-Clean Treatment

If hydrogen-peroxide is not an option for you or you are not feeling comfortable using it, Chemi-Clean can also help kill blue-green algae.

Chemi-Clean is actually a product that is designed to treat red cyanobacteria in salt-water aquariums, but it is very effecting in getting rid of freshwater cyanobacteria too.

You can purchase Chemi-Clean from Amazon. Follow the dosing instructions on the label and do not overdose this product.

While treating your aquarium with Chemi-Clean, make sure your water is well-oxygenated. Use an air-stone or increase water surface agitation for good oxygen exchange.

After only 24 hours you will see significant improvement. Allow 2 days for the bacteria to die off, which after perform a 50% water change.

Also clean your filtration and remove all the dead blue-green algae that have been cough up in your filter.

In this video you can see how effective is Chemi-Clean for treating freshwater cyanobacteria:

Antibiotics Treatment

If the above mentioned tricks could not kill blue-green algae, the last thing you can do is to use antibiotics.

This is a very drastic method, because antibiotics will kill off all bacteria in your tank, including the beneficial bacteria.

Maracyn or Erythromycin is the antibiotics that will help cure blue-green algae. In some countries, antibiotics can be purchased only with a prescription.

If you live in the US, you can purchase this product from Amazon, which contains Maracyn 2, and works for both salt and freshwater aquariums.

Although I don’t recommend this method, I know that in some cases there is no other way to kill cyanobacteria, but with antibiotics.

After treating your fish tank with antibiotics, you need to keep great attention to ammonia levels and perform regular water changes.

You can help the re-cycling process with beneficial bacteria, using the API Quick Start.

Personally, I would remove all fish from the tank, while using antibiotics. Would only introduce fish again, when the nitrogen-cycle is done.


Cyanobacteria are nasty. It can be really hard to get rid of blue-green algae. However, with the use of above mentioned methods, you can clean your tank and remove all blue-green algae.

You can prevent blue-green algae, by doing regular water changes, regular filter maintenance and substrate vacuuming. Using fast growing aquarium plants will also help maintain the aquarium water clean.

I hope that this article has helped you figure out a way to get rid of blue green algae.

If you have any questions, or suggestions regarding blue-green algae, please get in touch using the contact form.

Author Image Fabian
I’m Fabian, aquarium fish breeder and founder of this website. I’ve been keeping fish, since I was a kid. On this blog, I share a lot of information about the aquarium hobby and various fish species that I like. Please leave a comment if you have any question.
Questions and Answers

… can the blue green algae in my tank cause respiratory issues for humans? i do regular water changes and siphoning as well as rinsing and changing my filters … i have a five gallon tank that gets more direct sunlight and keep it covered as long as possible while in direct light … im more concerned about the health to humans though … thanks

    I’m not a doctor so I can’t answer your question in a responsible way. I know from experience, that blue green algae smells bad. From research I found out that this smell comes from the toxins that are released. It is certain that in large quantity blue green algae can kill the fish. I don’t know if the toxins produced by blue green algae can affect humans; I guess that in very large quantities it can also affect human health.

Heather McNulty September 25, 2020 Reply

Hi, if using the dark method to kill the Cyanobacteria what do I do with the fish? Do they stay in the tank safely or have to be removed to another tank ? Thanks Heather

    The fish can stay in the tank, just make sure that you aerate the tank really well, so there is enough oxygen for them. Fish will be fine even with a week of darkness and no food.

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