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What Is Cyanobacteria?

It's the pits, the absolute worst feeling for an aquarist. Struggling with a nasty outbreak of algae or some other pest can be disheartening in a way that makes you second guess your commitment to the tank.  That said, many of these pests, including Cyanobacteria, can often be avoided altogether or at least reduced to a point at which control is very easy with just a few prevention measures.  

Often called "Red Slime Algae" or "Cyano", Cyanobacteria, is actually not a type of algae at all. Rather a photosynthetic bacteria that are opportunistic in our aquariums.  It exists in all aquariums and will only rear its nasty face when the conditions are right for it to grow prolifically.  In a balanced and healthy tank, cyanobacteria are out-competed for resources by beneficial bacteria and other micro-organisms within the tank.

The conversation around cyanobacteria in aquariums has certainly evolved over the years and the aquarium community is constantly learning as we gain more experience. Cyano is one of the most common ailments for hobbyists, both freshwater and saltwater. We get hundreds of calls and emails from hobbyists asking how to get rid of red slime. While there are some very effective removal techniques we will discuss, the best method of control is preventing the red slime altogether or at least ensuring your minimizing the opportunity. 

Cyanobacteria on sand bed

As mentioned above, it's a photosynthetic prokaryotic bacteria. It is one of the oldest living organisms in the fossil record too. There are incredibly diverse and exist in all environments on the planet, interestingly enough it is one of the few organisms that can exist in very extreme environments like deserts, polar regions, hypersaline water, and even around hot springs and thermal vents.

Cyano produces oxygen as a byproduct of photosynthesis (exactly why you often see little bubbles trapped in cyano mats) making it essential to life on planet earth!  It is thought to have been one of the first organisms to help oxygenate the planet and is responsible for producing much of the oxygen we breathe today.

When you read through the science of cyanobacteria, you are often conflicted as a hobbyist. While it is rather despised in an aquarium, Cyano is critical for the very existence of life on our planet!  Truth is, cyano comes in many forms and can be extremely dangerous but also very beneficial depending on the exact type and environment. 

For example, Cyanobacteria create great blooms in our world's oceans, primarily in areas of high pollution, and have been found extremely harmful to marine life. At the same time, oxygen-producing phytoplankton, the very basis of the marine food chain, also contains cyanobacteria.

Cyanobacteria In An Aquarium

In a saltwater aquarium, we most often encounter deep red, almost purple mats of slimy cyanobacteria covering just about any surface under the water. Sometimes it shows up as bright green or black too. In freshwater tanks, you most often see black or blue-green colored mats of cyanobacteria.

When left to grow out of control, the mats of cyanobacteria will cover and suffocate corals and live rock.  It looks terrible and can even throw off the bacteria balance in your tank, ultimately contributing to instability making it tougher to resolve the problem.

Effective Methods Of Controlling Cyanobacteria In An Aquarium

  • Balancing nutrients - NO3 and PO4
  • Chemical Treatments and Antibiotics
  • Bacterial Treatments
  • Physical removal

We will cover each of these in detail below but ultimately, the best method of control is prevention. If you understand why and how cyanobacteria will grow in your tank, you can avoid it altogether.  If it does show up, act quickly to eliminate the problem before it becomes detrimental.

Preventing Cyanobacteria Problems In An Aquarium

  • Remove cyanobacteria at the first site via siphon. Repeat as necessary.
  • Maintain balanced nutrients - Phosphate <0.10 ppm and Nitrate <5 ppm.
  • Maintain a healthy biofilter.
  • Keep a clean sand bed and remove detritus from the rocks regularly.
  • Maintenance of your filtration as needed - swap out filter socks and media, clean sponges, empty skimmer, etc.
  • Provide sufficient water flow - Ensures oxygenation, prevents detritus from stacking up, and promotes coral health.
  • Maintain proper water temperature - cyano growth accelerates in warm water
  • Keep stable water chemistry - Coral growth helps to outcompete cyano
  • Feed responsibly with high-quality foods.

We find cyanobacteria can grow in a range of aquarium conditions but if you focus on stability across the board, you are drastically reducing your chances. Cyanobacteria grow faster in warm water, it has been known to grow when alkalinity is low, it seems to grow in areas of low water flow and high detritus build-up. Lower-quality foods and additives along with excessive detritus can lead to collections of dissolved organic material, directly fueling cyanobacteria. There has been evidence, more so in the days of T5 fluorescent lighting, that an improper light spectrum could spark a cyano outbreak too. 

This advice might seem inherent to many of you because all of these things are required to keep your aquarium in optimal health for a variety of reasons, not just to prevent cyanobacteria.

Nitrate and Phosphate

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Nitrate, Phosphate, and Cyanobacteria

In days past, we always focused on nutrient reduction (nitrate/phosphate) and low water flow as being primary contributors to cyanobacteria outbreaks. In modern-day aquaria, we are realizing this is certainly part of the equation but not the entire picture. Cyano is capable of growing in very nutrient-poor environments as well as anaerobic (low oxygen) environments which, to an extent, contradicts the previous thought.

We can prove this anecdotally because we have seen cyanobacteria grow in reef tanks with 0 phosphate and 0 nitrate levels. 

With that in mind, you want to think about balancing your nutrients as opposed to simply eliminating them. We are finding just as much cyano growth in tanks with undetectable nitrates and phosphates as we see in tanks with elevated nutrient levels. The key is keeping both of these parameters within the ideal range, and not letting them fluctuate. Phosphate levels above zero but below 0.10 ppm and reasonable nitrates below 5 ppm.  This allows the "beneficial bacteria" that doesn't show up as nasty red mats, to thrive and outcompete the cyano for available resources.


Balanced nitrate and phosphate can also indicate a reasonable level of dissolved organic material in the tank. If too much food or rotting organic material and detritus are left to build up, nitrate and phosphate levels will rise. Cyanobacteria can directly use this excess dissolved organic material to grow. Rather than your beneficial bacteria getting it, cyanobacteria can now get it! This is the competition and you want to maintain the balance in favor of your beneficial bacteria.

What happens in a tank without enough nitrate and phosphate? The prevalence of beneficial bacteria begins to diminish allowing the ever-resilient cyanobacteria to take hold and outcompete nutrient-reducing bacteria for whatever resources are available in the aquarium.

Lowering Nutrients

If elevated nitrates and phosphates are the problems, lower them. Improve your filtration with something like a filter roller, algae scrubber, or refugium. Increase water changes or general maintenance on the tank.  Be sure you're cleaning the sand and rocks which will prevent the build-up of excess detritus and the resulting DOM-dissolved organic material that contains nitrogen and phosphorous.  

Felicia M.'s Soft Coral Tank

Raising Nutrients

If you're experiencing the dreaded double zero (0 nitrate and 0 phosphates) and cyanobacteria are present, raise those levels while also removing the cyano.  This is a much more common problem these days with advanced filtration techniques and carbon dosing additives. Increase your feeding or food input, reduce filtration, or simply dose with something like Brightwell Aquatics NeoPhos and NeoNitro.

The topic of nutrients in saltwater aquariums, specifically nitrate and phosphate, has been covered extensively and has most certainly evolved over the years. Ryan, the visionary behind BRStv, has produced an excellent video series that picks apart the various aspects, theories, and methods of controlling nutrients in modern aquaria.

Watch Entire Series: Master Nutrients: Nitrate, Phosphate and Reef Aquariums

Chemical Treatments

There are a variety of reef-safe chemical treatments or "antibiotics" available for aquarists. They are effective at killing the cyanobacteria that are growing in your aquarium without harming the beneficial bacteria in your tank.  These treatments do work but won't prevent the cyano from coming back after the treatment is over and the chemical has been removed.  It is important to perform the treatment exactly as directed by the manufacturer so as not to have adverse effects on your tank.  

These chemicals can lower oxygen levels in the aquarium and will call for an airstone because your protein skimmer must be turned off to prevent the removal of the medication. After treatment, be sure to remove the chemical using carbon and necessary water changes.  Repeat treatments are an option but we always recommend physically removing visible cyanobacteria via a siphon before and after treatments. This helps to reduce the general population of cyano, allowing for the growth of beneficial bacteria instead. 

Bacterial Treatments

More of a recent development, bacteria-based treatments have become available that work based on that bacterial competition we talked about.  Beneficial bacteria strains are added to the aquarium in order to slowly outcompete the cyanobacteria for resources.

Siphon cyanobacteria

Physical Removal - How To Remove Cyanobacteria From Your Aquarium

As a long-time hobbyist, I think this is the most important step you can take in overcoming a cyanobacteria outbreak. Siphon the scourge out of your tank, do it every day if you need to.  This involves using a siphon and/or gravel vacuum to pull the cyanobacteria mats off the rocks, sand, and other surfaces along with removing detritus. Yes, water does come out along with it so a water exchange needs to take place. If you are not keen on the idea of mixing up new saltwater that often, you can actually recycle the tank water by simply filtering it through a filter sock.

Just get yourself a drawstring filter sock and a large bucket or bin. Tie and/or clip the filter sock onto the end of your siphon tube. Drop it into the bucket. Once you start your siphon, the cyano and detritus will get caught in the sock and clean water will pass through. Then, just dump that filtered water back into your aquarium when you are done.

If you are persistent, doing this as soon as you see even the slightest amount of cyano begin to grow, you will drastically reduce the chances of having a detrimental outbreak of cyano.  In fact, it is best to physically remove cyanobacteria alongside all of the treatment methods we discussed.  Do it before a chemical treatment, do it alongside bacteria dosing, and most certainly do it alongside balancing your nutrients.