Cyanobacteria, or Cyano for short, is not an algae like what many of you might think but is in fact a photosynthetic bacteria. It’s slimy and often grows in sheets that can be siphoned or blown off the rocks or substrate quite easily. It comes in different colors like red, green, or deep purple. 

A toxic "Red Tide" bloom off the Southern California coastline.  Photo Courtesy of SDfish.com user Baja_Traveler. A toxic "Red Tide" bloom off the Southern California coastline. Photo Courtesy of SDfish.com user Baja_Traveler.

In the ocean, there are species of Cyanobacteria that cause toxic “red tides” which can be detrimental to the entire ecosystem where they bloom.

In our aquariums, the cyanobacteria is not toxic per se, but can have some nasty side effects.  Not only is it ugly, Cyano will also shade and out-compete your corals for real estate, thus blocking light and stopping photosynthesis. If the conditions are right, Cyano grows quickly and can cover just about any surface in your tank.

Your aquarium can’t really “catch” Cyano from another tank because it is pretty much always around and in your tank.

Cyano outbreaks are caused primarily because of elevated nutrients and insufficient flow. These conditions then allow Cyano to grow rapidly and out-compete other beneficial bacteria and algae in your tank. Light spectrum and bacterial balance come into play as well, but in most situations, these are only secondary contributors.

Detritus in sump. Photo courtesy of reefcentral.com user FishyFishy69 Detritus in sump. Photo courtesy of reefcentral.com user FishyFishy69

Cyanobacteria feeds off the waste in your tank called detritus and will likely grow in areas where this waste accumulates. These areas are the sand bed, live rock or even in your filtration or sump compartments. Cyano also loves “dead spots” in the tank where water flow is very low. So make sure you have a high enough flow rate in your tank, and that all the corners of your tank have excellent water movement. This helps keep the detritus suspended for easy removal and prevents waste from building up in one particular area which is how 99% of cyanobacteria problems arise.

Dead Spot

Wavemakers like the EcoTech Vortech and Maxspect Gyre are awesome for achieving flow patterns that inhibit Cyano growth because they move large volumes of water. This voluminous type water flow helps to eliminate the dead spots throughout your entire aquarium without the need of multiple pumps.

Wide Flow Powerheads

You should siphon Cyano and detritus off your rocks and substrate immediately upon noticing it in your tank and then daily thereafter. If Cyano has a fuel source, it will grow back almost right away.

Siphon Cyanobacteria

Siphoning Cyano and detritus out of the tank daily will really help in your efforts to beat cyanobacteria. You will be removing the locked up nutrients the cyano has consumed. You will likely also be performing small water changes in the process, helping to dilute waste levels.

One clever trick for daily siphoning of cyano is to run the siphon through a filter sock and keep the water you remove.  The filter sock will trap the Cyano and allow clean water to pass through which can then be put back into your aquarium.  This avoids the need for daily replacing of saltwater when trying to combat a persistent Cyano problem.

Also be sure to change your filter media often and clean up any uneaten food within an hour of feeding.

Phosphate Test Kit

Test your nitrate and phosphate levels regularly because these parameters are a direct indication of the waste levels in your tank. Elevated phosphates and nitrates means your tank is not efficiently processing the nutrients that are going into the system.

You can reduce nitrate and phosphates in a variety of ways. The best option is a frequent and consistent water change schedule. Of course, proper biological filtration along with a protein skimmer and efficient mechanical filtration are also necessary.

In situations with a heavy bio-load, you might also consider using a media or chemical solution to target and remove phosphates and nitrates. GFO (Granular Ferric Oxide) such as AquaMaxx Phosphate Out Pro or RowaPhos are excellent at removing phosphate.

GFO Phosphate Remover

The use of the liquid chemical, lanthanum chloride, is also becoming a more popular way to remove phosphates rapidly but it should be noted that this stuff works instantly and will have adverse effects on your tank inhabitants if done too quickly or used incorrectly.

Blue Life Phosphate Rx

Bio-pellets are a popular solution for tanks with higher nitrate levels. This system actually utilizes bacteria to remove nitrates and is a great way to combat prolific Cyanobacteria problems.


Natural methods of nutrient control like refugiums or algae scrubbers will help reduce harmful nutrients as well. This natural method of nutrient control is becoming more and more prevalent in aquarium applications. It’s becoming more commonplace in many successful filtration systems.


After addressing your nutrients and flow inside the aquarium, 9 times out of 10 you can defeat cyano in a just a few weeks. However, sometimes the problem can be so bad that you need to kill it off completely and start fresh.

In these serious cases, you can consider a “black out” which means you turn off your lights and lay a blanket or tarp over the tank to block out ambient light for 72 hours.

Felicia's Mixed Reef Predator Reef Tank Felicia's Mixed Reef Predator Reef Tank

Cyanobacteria cannot survive without light for this long but your corals and fish will be fine. Just keep in mind that when the blackout is over, the cyano can bounce right back if you have not addressed elevated waste and water flow inside the tank as well.

You might also look at one of the easy chemical remedies such as the Ultralife Red Slime Remover or Boyd’s Chemi-clean to eradicate the cyanobacteria that is growing inside your tank.


Ultralife Red Slime Remover & Chemiclean Red Slime Cyanobacteria Remover are at the top of the list because they are safe for all fish, corals, invertebrates, desirable macro algae, and nitrifying bacteria in reef systems. They are simple to implement and fast acting.

A couple of things to note during a chemical treatment. Remove carbon or similar chemical filtration medias that could remove the medication from your tank water.

You will need to turn off your protein skimmer as well as your UV sterilizer and ozone generator if you have one.

It is best to also add an airstone to your system during treatment because oxygen levels can quickly get depleted and the airstone will ensure this does not happen. An airstone will also keep your pH stable during the treatment.  Always be prepared with extra saltwater on hand because you will need to perform a substantial water change 24-48 hours after treatment.

Although very rare, it is possible for Cyano to grow on living coral. In this case, you can dip the coral with a coral dip like Coral RX Coral Dip. Swish & shake the coral well in the dip to remove or dislodge any cyanobacteria that is present, then rinse in a separate container of saltwater before placing it back in your tank.

Dip your coral

Something to understand about cyanobacteria and many of the algae problems that will arise in similar situations is that an ounce of prevention is worth a pound of cure.

An ounce of prevention is worth a pound of cure.

Your aquarium husbandry techniques will drastically affect what happens in your tank so  unless you have a strange desire to battle any one of these aquarium ailments, don’t let waste levels become a problem in your tank to begin with.