How to Get Rid of Cyanobacteria in Aquarium (Blue-Green Algae)

Cyanobacteria, or blue-green algae, is one of the most common aquarium pests. 

Blue-green algae can spread in saltwater or freshwater tanks, and it impacts the health of your fish and coral. 

It rapidly reproduces and can survive harsh environments, making it difficult to kill.

By following these steps, you can eliminate cyanobacteria and prevent its spread in your aquarium

Causes of Cyanobacteria in Aquarium

Cyanobacterial blooms can arise from various chemical and physical factors, such as:

  • Altering the water flow
  • Changes in the pH
  • Nitrate and phosphate nutrient loading, but especially phosphate
  • Too much light
  • Vertical mixing
  • Temperature
  • Presence of trace metals
  • Excessive dissolved waste
  • Anaerobic conditions

Usually, a combination of these factors results in a more serious outbreak of cyanobacteria. 

The availability of organic matter, light attenuation, nitrogen to phosphorus ratio, and temperature significantly impact the number of cyanobacteria each season.

Cyanobacteria can cause your aquarium to develop an odor and toxins that could poison the fish. 

Cyanobacteria drive up maintenance costs and lead to animal deaths. Also, they can harm the fish from ingestion or dropping oxygen levels.

How to Get Rid of Cyanobacteria in an Aquarium

Whether you have a freshwater or saltwater aquarium, you can experiment with these steps to eliminate cyanobacteria from your tank.

Decrease the Lighting

Cyanobacteria grow when you have excess light because they are photosynthetic. The light energy helps them convert your fish’s organic waste into food.

However, they do not use all wavelengths of light.

As lightbulbs age, they emit lower wavelength light that higher-order plants do not use for photosynthesis. Cyanobacteria proliferate in 560-620 nanometer photons.

To get rid of cyanobacteria, you should shut off the lights and cover your aquarium with a blanket for three days.

Keep in mind that many plants will not survive this technique, so be wary if you have real plants in your tank. You will want to add fertilizer once you finish the blackout.

Once you remove the blanket, you can clean the filter to siphon the substrate. Then, replace about half of the water.

Make sure you replace the lights with ones with higher wavelengths to prevent the issue from occurring again. Try to change them each year.

Maintain the Water

Changes in water flow and composition can create an unhealthy environment for your marine life by building up organic wastes. 

Excess organic matter encourages cyanobacteria growth, and you may get other pests like red and bubble algae.

Look for a nitrate and phosphate test kit to determine the nutrient levels in your tank. These chemicals can enter from unfiltered water, food, plants, or aquarium products.

Be careful when using gelatin or liquid foods, activated carbon filters, sea salt mixes, and Kalkwasser precipitate.

If you have confirmed the levels are too high, you should perform a 30% water change. Then, reduce the feeding schedule by two-thirds.

For the rest of the week, change the water by 10% every other day. Finish off with a test to confirm everything is safe before increasing the feeding schedule.

Ensure you have a functioning and clean reverse osmosis and deionization filter. Also, use high-quality salts if you have a saltwater tank.

Try to quarantine any new rocks or plants in a separate tank before introducing them to your aquarium. They could add cyanobacteria if you are not careful.

Remove Clumps of Cyanobacteria By Hand

Cyanobacterial blooms usually start deteriorating once you have changed the lighting and nutrient situation.

Using a small net, scoop out any loose chunks of cyanobacteria to prevent clogs in your filter.

Sterilize your net using a 15-25% bleach after using it to kill any cyanobacteria without harming your fish. Also, use a gravel cleaner on your substrate to eliminate more blue-green algae.

Increase the Aeration

Cyanobacteria prefer still water because of its higher carbon dioxide content, so adding aeration will boost the water flow in stagnant areas to prevent proliferation.

Try to maintain a medium or strong flow in the aquarium using a powerhead, wavemaker, or another surge device. These also boost the filter’s efficiency.

Decrease the Temperature

If you have a freshwater aquarium, you can lower the temperature to below 76 degrees Fahrenheit to slow cyanobacterial growth.

Low temperatures in a saltwater tank can cause stress on the corals and fish, so skip this step for a marine aquarium.

Get a Hermit Crab

Hermit crabs will help your saltwater tank by feeding on algae in your tank. They also clean organic matter from the substrate and any hard-to-reach cracks.

Some of the best hermit crabs to remove cyanobacteria are:

  • Dwarf Yellow-Tip
  • Dwarf Red-Tip
  • Dwarf Blue-Tip

These crabs can exchange shells with each other, making them an entertaining addition to your tank. They target red and hair algae as well.

Make sure to introduce the hermit crab to a clean tank after completing the above steps.

Consider Harsher Treatments

If you have a stubborn cyanobacteria problem and the other steps did not help, consider a harsher treatment.


Fluconazole is an algaecide that will kill any algae in your aquarium. While it gets rid of the visible blooms, it does not eliminate the root cause.

If your tank has aggressive algae, give it a fluconazole blast. This treatment takes time to work, but it will remove algae from filters, rocks, and corals.

After using fluconazole, you should completely clean and replace the water in your tank within ten weeks.

Hydrogen Peroxide

Hydrogen peroxide is a household product with strong oxidizing capabilities. Look for a 3% one to use on your tank.

This chemical breaks into water and oxygen when oxidizing. Aim to use 1.5 milliliters per gallon of aquarium water.

Keep in mind that hydrogen peroxide will kill the good and bad bacteria in your tank. You may need to reintroduce some beneficial bacteria after the treatment.

You can complete the hydrogen peroxide treatment by following these steps:

  • Stop or remove your filtration system from your aquarium
  • Add 1.5 mL of hydrogen peroxide per gallon of water
  • Use a clean sponge to spot-treat any stubborn cyanobacteria spots
  • Wait an hour before restarting the filter or putting it back in

The hydrogen peroxide should oxidize in the water and cause the cyanobacteria to release bubbles. Full results are visible within a couple of days.

Once the cyanobacteria die, complete a 50% water change and scoop out any loose blooms. Then, clean your filter and use a water conditioner to replenish healthy bacteria.


An extreme method that kills all the bacteria in your tank is antibiotic treatment. You can use erythromycin or maracyn to get rid of cyanobacteria.

In the United States, you can buy maracyn online. Maracyn works for saltwater and freshwater.

Try to reserve this method if all other options fail due to its drastic effect on your aquarium’s biome.

You will need to remove the fish from your tank before using the antibiotics. Quarantine them in a separate, clean tank until you complete the treatment.

Follow the steps provided on the prescription. Then, monitor the ammonia levels and change the water regularly. 

Keep observing and testing the tank for the next few days, returning your fish after finishing the nitrogen cycle. 

You can accelerate the process using a nitrifying bacteria product water conditioner.


Chemi-Clean is a product designed to get rid of red cyanobacteria. While made for saltwater aquariums, it should eliminate freshwater cyanobacteria as well.

To use Chemi-Clean, follow these steps:

  • Increase the aeration in your tank to boost oxygen levels
  • Turn off the ozonizer and UV sterilizer
  • Remove any carbon products
  • Continue to use your protein skimmer, ensuring there is no overflow
  • Use pumps and powerheads to maintain a healthy flow rate
  • Dissolve one level scoop of Chemi-Clean in one cup of aquarium water for every ten gallons of your tank
  • Pour the Chemi-Clean into the aquarium and disperse it evenly
  • Wait 48 hours before performing a 20% water change
  • Turn the ozonizer and UV sterilizer back on
  • Replace the carbon products you removed
  • Repeat as necessary until all cyanobacteria are gone

Make sure you monitor your filter to remove any algae that it catches. It should eliminate most of your blue-green or red algae.

Chemi-Clean is more powerful than hydrogen peroxide, but not as strong as antibiotics.

Nevertheless, try not to use it until you have exhausted the non-chemical treatments.

Monitor Your Results

The above steps should destroy any cyanobacteria within the week. However, you must monitor the environment to ensure you maintain the results.

Your tank will likely see more nitrate levels once you get rid of the cyanobacteria. These pests eat nitrates, and the beneficial bacteria may try to replenish cyanobacteria.

Test your aquarium’s nitrate levels daily and perform 10% water changes every other day until the end. Keep these tasks up until the nitrates are below ten ppm.


Getting rid of cyanobacteria in your aquarium can drastically improve your marine life’s appearance and health.

Try to stick to the gentle treatments, only resorting to the harsh ones if nothing else works. The initial steps should eliminate most, if not all, of the problem when performed correctly.

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