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Removing Cyanobacteria from the Aquarium

Updated on February 08, 2016
A close up of Cyanobacteria courtesy of the United States Geographic Survey - photo by Barry H. Rosen, USGS
A close up of Cyanobacteria courtesy of the United States Geographic Survey - photo by Barry H. Rosen, USGS

It looks as though the fish have been redecorating again, draping sheets of thin green algae over every surface and even hanging it from the sides of the tank for good measure. You’ve tried your trusty over the counter algae treatment, but it has failed, and every day the invasion gets worse. What is this menace and more importantly, how do you get rid of it?

Understanding the Menace

This menace is none other than Cyanobacteria, often referred to as blue-green algae in freshwater tanks or red slime algae in marine tanks. Cyanobacteria is one of the oldest living things on the planet with fossils dating to 3.5 billion years ago in the Achaean rocks of Western Australia. This is one resilient life form, but why has it been so successful? Simple, it makes use of the light waves that are discarded by higher plant life, lives in a wide range of temperatures, and subsists on organic waste materials including dissolved phosphates and nitrates. What do all of these things have in common? They are readily available in the artificially constructed environment of the home aquarium. Although it is not dangerous to the inhabitants of a freshwater or marine aquarium, Cyanobacteria can become an unsightly mess that can cover every surface of a tank in a matter of days.

One of the first questions aquarists ask when confronted with an outbreak of Cyanobacteria is, where did it come from? Unfortunately, there is no way to be sure. These bacteria can sit dormant for thousands of years until the right conditions arise and then it will bloom. So the initial colony could have hitched a ride on anything that wasn’t thoroughly bleached before entering the tank. This includes ornaments, aquarium hardware, substrate, live plants, live rock, and even the water from fish that have been introduced into the tank. The truth is, where it came from really isn’t the problem, why it proliferated is.

There is often no single cause that leads to a Cyanobacteria bloom, it is more likely that a combination of improper lighting, an abundance of freely available nutrients and a stagnant low-oxygen environment that hasten the bacterial growth. Tanks that exhibit this red slime, or blue-green algae, growth often have good water quality (low ammonia, nitrite and nitrate levels) and are otherwise unremarkable.

Instituting a clean-up crew in a marine aquarium can help reduce the slime but only treats the symptom of the problem, not the cause. The Red Scarlet Reef Hermit Crab is the best option for this method. It will readily devour any red slime algae in the tank. Unfortunately, there are no freshwater fish that graze on this “algae” and standard algae control additives fail to alleviate the situation. In a freshwater situation, removing it by hand is possible, but takes a significant amount of time and effort. There is, however, a procedure that can eliminate this particular bacterium from your aquarium, either marine or freshwater, in less than a week.

The method for completely removing Cyanobacteria involves a multi faceted approach including limiting or changing out lighting, modifying the tank feeding schedule, physical removal with a gravel cleaner, lowering tank temperature and adding additional aeration to the tank. Although this combination will eliminate the appearance of Cyanobacteria, there will still be minute pockets that survive, they will be so small that they won’t be visible, and you’ll still have to maintain an environment that won’t allow the reappearance of the bloom.

This is a tank with a severe cyanobacteria problem. Conditions like this can be seen in as little as four days from the initial sighting.
This is a tank with a severe cyanobacteria problem. Conditions like this can be seen in as little as four days from the initial sighting.

Addressing Tank Lighting

The photosynthetic nature of the bacteria means that it can produce its own nutrients or use the light energy from the tanks lighting array to help convert organic waste into a useable form of food. Cyanobacteria use wavelengths of light that are not used by higher order plants. This means that the lighting in your aquarium is the initial point of attack for removing these pests. Reducing or eliminating the wavelengths that they use will drastically reduce their ability to feed and propagate.

If the lighting in your tank is over a year old, it is probably not emitting light at the same wavelength that it was at the beginning of its lifetime. As a bulb ages, it emits a less powerful light, one of a lower wavelength. This is a common problem that most aquarists are unaware of. This light decay can cause a bulb that is rated as a 420 to 460 nanometer light source to cast light in the 560 to 620 nanometer range within one year. This 560 to 620 nanometer range is the one in which Cyanobacteria proliferates.

Replacing the bulbs in your current set-up with balanced light bulbs (6,400K to 14,000K) or actinic 50,000K bulbs will immediately reduce the amount of useable light for the infesting bacteria. Using an ultraviolet sterilizer to kill off free floating Cyanobacteria, while recommended, is not entirely necessary to eliminate the scourge in under a week. Replacing the bulbs in your aquarium every 9 to 12 months will help prevent a recurrence of Cyanobacteria.

Reducing Nutrient Availability

Changing the lighting in your aquarium is only the first step in eliminating a bacterial infestation. Reducing the free nutrients available to the colony will immediately reduce its ability to spread. The primary food source for Cyanobacteria is dissolved organic compounds in the aquarium water which consist of both phosphate (PO4) and nitrate (NO3). An overabundance of these materials can usually be tracked back to overfeeding or failure to remove dead plant materials from the tank. In marine invertebrate aquariums liquid and gelatin based foods are a likely source of these organics. It is also possible that phosphates have entered the aquarium environment through sea salt mixes, activated carbon filters, or through Kalkwasser precipitates in marine environments.

To eliminate the dissolved organic compounds, the first step is to complete a 30 percent water change. Follow this with a significantly reduced feeding schedule. Feed your tank about one-third of the normal amount. This will be enough to keep the fish happy without any leftovers for the bacteria to feast on. Ten percent water changes can be done every other day for the remainder of the week to bring the amount of PO4 and NO3 to acceptable levels. Once the tank environment is back to normal, feeding schedules should be adjusted to reduce the amount of waste food decay.

Removing Rogue Bacteria and Aerating the Aquarium

After the first day of new lighting and reduced nutrients, the bacterial blooms will begin to fall apart. Removing large clumps of bacteria by hand with a small net will significantly reduce the strain on the filtration system and prevent it from clogging. Remember to sterilize the net in a solution of 15-25 percent bleach when you are done so you don’t accidentally reintroduce Cyanobacteria to your tank at a later date. It is also advisable to clean the substrate with a gravel cleaner to remove any pockets of Cyanobacteria that may be lurking just below the surface.

Once the large clumps and sheets of Cyanobacteria have been removed, adding or increasing the amount of aeration in the tank is the next step. Cyanobacteria thrives in relatively still, poorly oxygenated water. Adding a bubbler or turning up the powerheads in a tank will remove stagnant areas from the tank and reduce the areas in which the bacteria can proliferate.

Lowering the temperature of the tank below 76 degrees Fahrenheit will also slow the growth of bacteria. This is only advisable if you are running a freshwater set-up as temperature changes in a marine environment can cause unnecessary stresses on the fish and corals in the environment.

In a marine aquarium, cyanobacteria often looks red or purple. It can be easily handled with the addition of a small group of crabs.
In a marine aquarium, cyanobacteria often looks red or purple. It can be easily handled with the addition of a small group of crabs.

Post Bacterial Environment

Using the above system of lighting, reduced feeding, manual cleaning, water changes and tank aeration your Cyanobacteria problem should be history in less than a week. There are some things to watch for in this post Cyanobacteria environment. The bacteria were consuming nitrates while in the aquarium so with it removed there may be a spike in nitrate levels while beneficial bacteria work to replace the Cyanobacteria in the ecosystem. These nitrate spikes are expected and may be minimal if you have been diligent in the water change schedule provided above. You may need to do additional ten percent water changes every other day for up to two weeks to bring the nitrate level back to a safe range below 10 ppm.

Why Not Just Use an Antibiotic or Chemical Treatment?

The number one question I get after recommending the above treatment is, “why don’t you just use an antibiotic like Erythromycin or some other chemical treatment to clear up the bacteria?” While there are several chemical controls advertised for Cyanobacteria removal, they all have the same potentially devastating effects. First, an antibiotic doesn’t discriminate and will destroy all of the nitrifying bacteria in the tank along with the Cyanobacteria. This will set an aquarium back to day one and result in exposure to ammonia, nitrite and nitrate spikes that can be disastrous to the tank. Second, although a chemical treatment may seem to work within moments of being introduced to the tank it does so at the cost of dissolving these bacteria into materials poisonous to fish in the environment. This can lead to a massive fish death and renewed optimal conditions for another Cyanobacteria bloom. It is best to avoid either of these options as tempting as the quick fix may seem.


T.N. & E.L. Taylor. 1993. The Biology and Evolution of Fossil Plants. Prentice Hall, New Jersey.


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    • Anonymous 16 months ago

      What should I do if I have a planted tank and I can't aerate it or else I'll kill the plants?

    • Lee Wood 13 months ago

      I had a planted tank with nitrate and Phosphate added for plant growth. Never saw any cyano till I disturbed the substrate. Everyone says cyano is caused by N and P levels too high, this is not true. It's caused by organic wast in the tank. Vacuum the substrate and change lots of water and it subsides(never goes away).

    • radddo 5 hours ago

      my problem is brown algae (diatomes i believe) had it for 3mts now.All remedies havebeen tried, less light coverover tank , done 50 30 and 20% water changes in one week to no effect. Has anyone any oyher remedies,would be greatly accepted.

      Thanks in advance

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