How to Get Rid of Cyanobacteria in a Tank

Cyanobacteria can appear as green, blue, or red slime on the surface of water.
Cyanobacteria can appear as green, blue, or red slime on the surface of water. (Image: Thinkstock Images/Comstock/Getty Images)

Cyanobacteria can appear as a blueish, green or sometimes red slime in both freshwater and saltwater aquariums. It can be difficult to tell the difference between algae and cyanobacteria, but generally cyanobacteria will appear as blue or red slime. The process for removing algae and cyanobacteria is nearly identical, except for the chemical treatment. Although it looks like algae, it is actually bacteria that uses photosynthesis to create energy, similar to algae. Cyanobacteria can be difficult to remove and the first step is to identify all causes. Sudden blooms of the bacteria is a sign that the aquarium water system is not balanced and some chemicals (usually phosphate) are excessive. The key to removing the bacteria is to identify and remove its food sources.

Things You'll Need

  • Turkey baster
  • Siphon tube
  • Powerhead
  • Protein skimmer
  • Chemical phosphate remover
  • Chemical cyanobacteria remover

Remove the bacteria by sucking it out of the aquarium with a siphon or turkey baster. Take out as much of it as you can as this will give you a head start with the next several steps.

Change 20% of the total water volume once every 4 days using clean source water. Tap water contains phosphates and sometimes nitrates that cyanobacteria thrives on. The presence of the bacteria is an indication that these nutrients are excessive and need to be reduced. Reverse osmosis deionized (RODI) water is best for both saltwater and freshwater aquariums as nearly all the phosphate is removed in the filtration process.

Reduce the light in the aquarium. Cyanobacteria use photosynthesis to create energy so reducing the light will slow their growth. When you are first battling the bacteria, dimming or turning off the lights while you conduct your water changes will help prevent the bacteria from rapidly coming back. A longer term solution is to shorten the total time the lights are on (the photoperiod) by turning the lights off a little earlier.

For saltwater aquariums, install a protein skimmer. Protein skimmers remove organic compounds from the water before they can break down into nitrate. Nitrate feeds the cyanobacteria and other forms of nuisance algae. Removing material before it becomes nitrate will help slow and prevent cyanobacteria growth.

Increase the water flow in the aquarium. Cyanobacteria lives in areas of low water flow (sometimes called "dead zones"), and increasing the movement of water in these areas can clear up the bacteria. Powerheads accomplish this as they can be pointed in nearly any direction.

Use a chemical phosphate remover. If the previous steps do not remove the cyanobacteria, there may still be too much phosphate in the water, often introduced by fish food. In this case, using a chemical phosphate remover can help eliminate the excess phosphates. These chemicals are available at most fish hobby stores and online. The best way to use them is through a phosphate reactor, but these can be expensive and too large for small aquariums. Avoid phosphate removers that use aluminum since the heavy metal can poison fish.

Use a chemical cyanobacteria remover. There are several products that are specifically designed to remove cyanobacteria, such as Chemiclean and Dr Tim’s Re-Fresh and Waste-Away. If the previous steps do not solve the problem, one of these products may be needed. Confirm that the cyanobacteria is completely removed or it will likely return or be replaced by other nuisance algae.

Tips & Warnings

  • If you test your water for phosphates and nitrates with a cyanobacteria problem, the tests will likely read 0. This is because the cyanobacteria are consuming the phosphates and nitrates before they are measurable in the water. The presence of the bacteria is an indication that one or both of the chemicals are elevated.
  • Battle cyanobacteria as soon as it appears. It grows quickly and can easily get out of control.

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