BGA Battle Plan: Controlling Cyanobacteria in Saltwater Aquariums

Cyanobacteria, blue-green algae, on live rock

Cyanobacteria, blue-green algae, on live rock

You’re relaxing in front of your saltwater aquarium, enjoying the beautiful undersea vista you’ve created when you notice a few red, algae-like patches on your live rock that weren’t there before. You reach into the tank and give one of these growths a few taps with your finger and notice that it feels rather slimy to the touch. “Hmm, curious,” you think to yourself.

But your schedule gets busy, so you put this strange substance out of your mind for the time being. A few days later, however, there are more patches of the stuff, and you notice it’s spreading to the substrate.

Alarmed now, you grab an aquarium brush and fish net and go to work. Fortunately, the patches can be dislodged and netted out fairly easily. Within a matter of minutes, you’re able to remove almost all the patches of slimy gunk, and you stand back to observe your handiwork, heaving a big sigh of relief. Problem solved, right?

Not so fast! Several more days pass and your heart sinks when you discover that the stuff is back again in full force and possibly even worse this time. What in the world is going on in your aquarium?

You’ve got a cyanobacteria bloom on your hands! If left unchecked, this unsightly stuff can quickly spread to your whole system, carpeting the rocks and substrate and smothering sessile invertebrates.

What is it?

Despite its algae-like appearance, cyanobacteria—a.k.a. cyano, blue-green algae (BGA), or slime algae—is, as the name implies, a form of bacteria. It commonly forms slimy, loosely attached mats on the rockwork, substrate, and other surfaces in the aquarium (including corals). Bubbles may form within these mats and can eventually cause them to detach and rise up in the water column. In saltwater systems, cyano commonly appears in some shade of red, but it comes in a variety of other colors, as well, such as dark bluish green, purplish, and even black.

What causes it?

Cyano blooms occur when the levels of nitrate, phosphate, and dissolved organic compounds get too high. Several underlying factors can lead to excess dissolved nutrients, and thus a cyano outbreak, including:

  • Inadequate or nonexistent protein skimming
  • Overstocking and/or overfeeding
  • Inadequate water changes
  • The addition of live rock that has not been fully cured
  • Non-judicious use of aquarium additives
  • The use of source water that contains nitrate or phosphate

Note that cyano flourishes in areas with inadequate or slack water movement where detritus tends to accumulate, as well.

How can I get rid of it?

To eradicate cyanobacteria, it’s necessary to attack not just the symptom of the problem (the cyano itself), but also the underlying cause or causes. That means a multi-pronged attack is in order.

Your BGA Battle Plan should include the following eight strategies:


Use RO/DI source water
If your source water is coming right from the tap with no purification beyond the addition of dechlorinator/dechloraminator, you may be unwittingly adding nitrate, phosphate, and other dissolved nutrients with every water change or freshwater top-off. Consider investing in a good reverse-osmosis (RO) or reverse-osmosis/deionization (RO/DI) unit to remove those impurities from your tap water.


Step up your water change schedule
For example, if you’re doing a biweekly (as in once every other week) water change, step it up to once a week or maintain the same frequency but increase the volume of water that you change each time—again, using RO- or RO/DI-purified water.


Brush and vacuum
During each water change, brush as much of the BGA off the rocks and other surfaces as possible and promptly vacuum the dislodged bits out of the system.

A helpful technique is to tie-wrap a toothbrush to your aquarium siphon hose so the brush extends a few inches beyond the end of the vacuum attachment. With this contraption, you only need to use one hand and any cyano you liberate with the brush will be sucked immediately into the vacuum.


Assess your stocking and feeding rates
Sometimes it’s hard to be objective about whether your aquarium is overstocked and overfed or not. But if you want to bring a cyano bloom under control, it’s essential to assess both factors and make adjustments if appropriate.


Evaluate your protein skimmer
Make sure your protein skimmer is actually doing its job. Is it producing a copious amount of skimmate? If not, it needs to be adjusted to get the right air/water mixture. Also, make sure the neck of the skimmer is completely clean. A buildup of gunk lining the neck will interfere with proper foam production.

Sometimes a protein skimmer produces a decent amount of skimmate but is just too small to handle the dissolved organics produced in a given system. If you suspect that’s the case, consider replacing your current skimmer with a model rated for a larger aquarium. Of course, if you don’t have a protein skimmer at all, that should be your very next purchase.


Step up circulation
As mentioned, cyano favors areas of slack water movement and has a hard time gaining a foothold where circulation is brisk. Any “dead” areas in your aquarium (evidenced by the accumulation of detritus) should be eliminated through the addition or redirection of powerheads or other sources of water movement.


Hold the additives
If an additive or supplement is not absolutely essential to the health of your livestock (e.g., calcium or buffers for a reef tank stocked with stony corals and tridacnid clams), don’t put it in there—especially if it’s one of those proprietary “secret recipe” elixirs of dubious value.

Strategy #8

Practice patience!
Your cyanobacteria problem didn’t develop overnight, and it won’t be resolved that fast, either. In fact, it may take several months to turn the tide in your favor. So it’s important to be patient as you implement these strategies and take the battle to the BGA. Rest assured your persistence will ultimately pay off!


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About Jeff Kurtz

Jeff Kurtz is the Co-founder/Editor of Saltwater Smarts, former Senior Consulting Editor for Tropical Fish Hobbyist Magazine, and the aquarist formerly known as “The Salt Creep.” He has been an aquarium hobbyist for over 30 years and is an avid scuba diver.


  1. Lisa Foster says

    I have a 20g reef with no skimmer. I was having cyano issues, and then a greenwater explosion that simply would not go away no matter how much or often I changed water. On the recommendation of some reefkeeping friends, I bought a UV sterilizer and Dr. Tim’s Waste-away. Between those two, my greenwater went away and my cyano is gone. Turn the uv off for about 12 hours after each dose of waste-away.

    • Jeff Kurtz says

      Thanks for sharing your individualized battle plan, Lisa! Vigorous protein skimming will also help keep that BGA and free-floating algae at bay.

  2. I have these growths in my saltwater aquarium. They are fleshy Orange bodies with white or clear hair like bubble tipped arms or clumps of extensions from the centers or tops. My damsel got what looked like an injury outgrowth on the corner of his lips, then his face just fell off. He is alive and swimming well, but has no lips and can’t eat. Do you think that these are related ?

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