Treat Cyanobacteria (Blue-Green Algae) in Your Planted Tank

If you have a stroke of bad luck, you may wind up with cyanobacteria in your planted tank. You may have heard of this microorganism under the names Blue-Green Algae or Blue-Green Slime.

how to treat cyanobacteria in your freshwater planted tank

Despite some of the common names, cyanobacteria are not a type of algae, but rather are photosynthetic bacteria that draw energy from sunlight and carbon dioxide much like plants.

They appear as an ugly, dark, slimy blue to blue-green substance that covers and chokes plants.

In some cases, they are confined to growing near the shoot tip of stem plants, but other times they spread across the surface. While the ones found in aquarium tanks are mostly harmless to fish, shrimp, and other stock, they can quickly cover plants and kill them.

Cyanobacteria are typically ignored by algae-eating fish and other fish that may nip on actual algae. They reproduce rapidly and can become a serious issue, so knowing how to face them can be a lifesaver. Here we’ll examine various ways to deal with them.

cyanobacteria microscope

Cyanobacteria-covered Staurogyne. This microscope image was taken with a camera through the eyepiece under 400x magnification.


Your first step should be to siphon off what you can find in your tank. Simply put, the less there are, the less you have to fight. Cyanobacteria typically grow in flat sheets that only adhere very loosely to plants or hardscape, so as a result it’s relatively easy to siphon them off sheet by sheet.

A narrow siphon too small to suck up the plants is especially useful as it will be unable to remove anything you want to keep. A 5 ml syringe will fit on the end of 1/2” (12/16 mm) tubing, or a 20 ml syringe on 5/8” (16/22 mm) tubing. Using a narrow siphon also works well against longer hair algae.

Causal Treatment​

The best way to fix the problem by treating the cause. Besides being introduced to the tank from outside sources, the bacteria also occupy an ecological niche in your tank. Eliminate that niche and they can once again be outcompeted by plants. In plant-less tanks, you can make their life a bit harder by shifting to unfavorable conditions.

1. Lighting​

Reducing the intensity and/or duration of lighting often helps. You have to test what works for your situation. Both cyanobacteria and plants rely on photosynthesis to survive. Thus, shifting the lighting conditions to a level that favors plants over bacteria isn't trivial.

But experience shows that going to the lower end of adequate lighting may help. Generally, brighter-lit tanks should be lit for a shorter duration. The typical duration range runs between six and 12 hours. Wait at least two weeks to see the effects of changed lighting.

2. Flow rate and oxygen levels

Optimal water flow rate is at least twice the tank volume per hour, and no more than 10 times the volume per hour. Check if the filter/circulation pumps are operating correctly and aren't clogged, and check that they generate sufficient circulation.

Cyanobacteria have a big advantage over plants: unlike plants which must get their nitrogen from urea, ammonia, or nitrate, cyanobacteria can use atmospheric nitrogen (N2). But the presence of oxygen interferes with their shortcut.

Thus, more oxygen and/or a better distribution of oxygenated water can remove the niche that your cyanobacteria have exploited.

3. Nitrate levels

At a minimum, nitrates should be kept in the low single-digit parts per million (ppm). The plant’s capacity to keep cyanobacteria at bay relies on their health, and a lack of nitrogen in particular can hamper their ability. Nitrogen-deficiency symptoms in plants include pale growth and large transparent spots in older leaves. In severe cases the newest growth may also be stunted and deformed.

Weaken the cyanobacteria

The weaker they are, the better the chances your plant can suppress them.

1. Blackout

Cyanobacteria are photosynthetic organisms, so a blackout will kill them. Three days without light usually weakens them far more than most plants, so your plants should be able to take over again. This is not recommended, however, when the spread of the cyanobacteria is very advanced, and the plants are already severely weakened.

It should be noted that cyanobacteria are pretty resistant to low-light conditions, so just leaving the lights off is usually not dark enough - you need cover the tank too.

2. Salicylic Acid

This is one of the substances some plants naturally produce to protect themselves. White willows, for example, are well-known producers. It may be enough to add some white willow branches or bark to the tank directly, but it’s hard to achieve consistent results that way.

Certain additives (e.g. Easy Life Blue Exit) contain a more consistent dosage of salicylic acid. A typical dosage would be between 0.25 mg/l and 0.4 mg/l once a day for five days.

Killing them directly

It’s possible to kill cyanobacteria outright. They can't reproduce when they are all dead. Afterwards you must practice good tank hygiene to prevent reintroduction.

1. Nuke them with erythromycin

Erythromycin is an antibiotic intended for this use. Maintaining 2.5 ppm for a week will do the job. Antibiotics will work too, but they can be harder to come by and are more a final measure than a first response. Also, be careful not to end the treatment to early and create resistant cyano.

2. Kill them by chemical means

Treating selected spots or a whole tank with a biocide works too. Hydrogen peroxide (H2O2) or glutaraldehyde are two common choices. To perform a spot-treatment, turn off everything that generates flow within the tank, carefully spread the biocide in the desired area with a syringe, wait 15 min, then turn the flow on again. To treat an area of 10 x 10 cm (4 x 4 inches), spread 80 mg (for mild treatment) to 400 mg (for aggressive treatment) of H2O2 in the area no more than once a day. You may dilute the biocide to a volume that ensures even coverage of the treatment area.

For glutaraldehyde (Seachem Excel, various 'Liquid CO2' products) you may use between half and twice the recommended dose for the whole tank. Repeated mild treatments are better than one severe one. A whole-tank treatment is much more aggressive: dose between 25 mg/l and 40 mg/l H2O2 and turn your flow up as high as possible for 15 min, then perform a 100% water change. It’s possible for plants and/or stock to die in this process, so this shouldn’t be done lightly.

For an even more aggressive treatment, you may follow up the water change with a triple dose of the manufacturer’s recommendation of glutaraldehyde-containing product.

Change their behavior

As it turns out, you can prevent cyanobacteria from spreading and choking plants to death.

1. Increase your potassium (K) significantly

A spike of over 30 ppm K+ in the water will cause the cyano to clump together in smaller granules rather than forming choking blankets. This makes them very easy to siphon off. There are also reports that this weakens the cyanobacteria.

A 30-ppm spike in K+ in the water is generally unproblematic for fish or shrimp. That said, changing the Ca:Mg:K ratio of your water may cause issues in a handful very demanding plants.

Manipulate your microflora

It turns out you can recruit allies in your fight against cyanobacteria. The basic idea here is to introduce competition in the form of other bacteria. This is generally a fairly safe method, though you may need to be cautious if you have stock that has extremely weak (e.g. discus cichlids) or primitive immune systems (e.g. Taiwan Bee shrimp) or if your stock has been severely weakened for other reasons.

1. Help from outside – soil-based method

Fill a sealable bottle with some soil or compost, add water, shake it and let it settle a bit. Then add the resulting fluid (not the soil itself) to your tank water. In doing this, you’re introducing bacteria that can compete with the cyano. Add just enough that you see a very slight turbidity. Wait a day, and if the water isn't still slightly turbid, add more.

This method can work because soil is rich in nitrifying bacteria, among others, so the soil shake adds more competition. In place of a soil shake you may also use bacteria starter products that are usually made to help cycle tanks.

2. Boost your own microflora

Add vinegar to the tank. About 8 ppm increases bacterial growth without creating a full bloom, and helps fight the cyano. 16 ppm will, however, cause a bloom, so be careful. The vinegar is simply an easily-accessible carbon source from which bacteria can grow.

In the marine hobby, vodka or ethanol is occasionally used in a similar way to make small bacteria blooms, albeit usually to feed filter feeders. Growing bacteria do consume oxygen in the water, so please ensure that your tank has an oxygenation source like a filter or airstone.

3. Help from outside – lactic acid bacteria

Dose yogurt. Yes, the one you eat. The lactic acid bacteria used to make yogurt will also help drive the cyano away. However, yogurt bacteria are not aquatic and will die relatively quickly, so they must be redosed every few days to keep up the effect.

It is also important to use plain yogurt - fruit pieces and excess sugar may lead to an unwanted bacterial bloom. 50 mg/l worth of plain yogurt is a good dose. Their inability to survive permanently submersed makes yogurt bacteria a good apply-and-forget method for dealing with small amounts of cyanobacteria.

Unknown means

Some additives don't disclose their active ingredients, yet some people report success with them.

  1. Chemiclean: This is an additive from the saltwater side of the hobby. Quite a few people report good success with it.

  2. Various local products that can't be all covered due to their large numbers.

Whatever approach you plan to use, the best way to start is to clean your tank first.

Eliminating the cause of the cyano bloom is most ideal since it offers a permanent solution; if they have no niche, the problem takes care of itself. Even if you introduce some more to the tank, they won’t be able to take hold.

In my experience, when searching for causes, lighting is a good place to focus if the tank is brightly lit, while flow rate is a better focus on dimmer, low-tech tanks.

If causal treatment isn't possible, eradication or near eradication is the next-best option. Here lay the widest array of options, so the path isn't clear.

A good standard of practice is to try and inflict as little collateral damage as possible. Thus, the slower and milder options are a good way to start: try to manipulate your microflora to your advantage to start with, and possibly combine that with the K spike.

If these don't work well for you, salicylic acid, a blackout, and spot or whole-tank treatments with biocides may be used. Erythromycin is a last resort that will almost surely work.

Not everyone has the patience or time for slow options, or they may simply not care much about the plants. For such cases, starting with more aggressive options is one way to go.

Addendum – Units, math help, and examples

Units of volume are liter (l) and gallon (gal). A liter is the volume that fits in a cube with 10 cm (about 4”) sides, while a gallon is equal to 3.7 litres. A millilitre (ml) is a thousandth of a litre. The unit of mass used is the milligram (mg), or one thousandth of a gram (g). Units of concentration are milligram per litre (mg/l) as well as parts per million (ppm). in this case, ppm is based on mass, so mg/l and ppm are equivalent amounts. Percentage by mass (%) is also commonly used.

It is good to know that almost all watery (aqueous) solutions have a density of close to 1 g/ml, especially when they are dilute. Hydrogen peroxide (H2O2) is typically sold by mass-percent concentration.

Example 1

Dosing 80 mg for a spot treatment using a 3% solution: One milliliter of 3% solution has a mass of approximately 1 g (1000 mg), and 3% of that is the active substance, so 30 mg per ml. Since we want to dose 80 mg, we need 80 mg ÷ 30 mg/ml = 2.666 ml of 3% solution.

Example 2

Dosing 50 mg/l yogurt to a 20-gallon tank: 20 gallons is approximately 74 litres, so we need to dose 74 litres x 50 mg/l = 3400 mg = 3.4 g ~ 3.4 ml.

Example 3

Dosing 30 mg/l K+ from K2SO4 to a 55-gallon tank. 55 gallons = 204 litres. 30 mg/l x 204 litres is 6100 mg = 6.1 g of K+. However, we have K2SO4, which is only partly K. The ratio of K in K2SO4 is calculated by looking at the molar masses. K weighs 39 g/mol while K2SO4 weighs 174 g/mol. K2SO4 contains 2 K, so the ratio is 2*39 g/mol ÷ 174 g/mol = 0.45. Thus, we need to dose not 6.1 g, but 6.1 g ÷ 0.45 = 13.5 g of K2SO4.

Further Reading:

“The 'One Two Punch' Whole Tank Algae Treatment” by DarkCobra on