Cyanobacteria (Blue-Green Algae): Causes & Removal

What Is Cyanobacteria?

Despite the common name 'blue-green algae', cyanobacteria isn't a true algae -- it's a photosynthetic bacteria. It forms thin, slimy sheets in shades of blue-green, dark green, or occasionally red/purple, and it's easily identified by two traits true algae don't share: it peels off the substrate or glass in intact sheets rather than scraping off in flecks, and it has a distinctive musty, swampy smell.

Why It Grows

Cyanobacteria thrives in tanks with poor water circulation (dead spots where debris settles), high organic waste, and often low nitrate combined with available light -- which is counterintuitive, since most algae problems are linked to excess nutrients rather than a deficiency. Old, undisturbed substrate and light leaking into the tank outside the normal photoperiod (from room lighting) are also common contributors.

Step-by-Step Removal

Manually siphon it out during water changes -- lift it gently rather than disturbing it aggressively, since bursting the sheets can spread spores through the water column.
Improve water flow throughout the tank, paying particular attention to corners and low-flow zones where it tends to establish first.
Do a 3-day blackout combined with reduced feeding if manual removal and improved flow aren't enough -- cyanobacteria generally can't sustain itself without light.
Consider a UV sterilizer for persistent cases, which helps control it in the water column.

Prevention

Consistent gravel vacuuming to prevent organic buildup, improved circulation (an additional powerhead in dead zones), and checking for stray light entering the tank outside your set photoperiod are the most effective long-term preventions. If nitrate is consistently near zero, allowing it to rise slightly (via feeding or a nitrate-containing fertilizer) can sometimes help outcompete cyanobacteria's advantage.

A Note on Antibiotic Treatment

Some hobbyists use erythromycin to treat severe cyanobacteria outbreaks. This is an antibiotic and carries real downsides -- it can disrupt your biological filter and shouldn't be used routinely. Manual removal, improved flow, and a blackout period are the safer first-line approach for most cases.

Frequently Asked Questions

Is cyanobacteria dangerous to my fish?

Most fish avoid eating it and it's not typically dangerous in small amounts, but some strains can produce toxins, and large outbreaks can affect water quality. It's best treated promptly rather than left to spread.

Why does cyanobacteria smell bad?

The musty, swampy smell is one of its defining traits and a reliable way to distinguish it from true algae, which generally doesn't have a strong odor.

Will a UV sterilizer get rid of cyanobacteria?

A UV sterilizer helps control free-floating stages in the water column but won't clear established sheets on surfaces -- it works best combined with manual removal and improved flow, not as a standalone fix.

Should I turn off my filter to avoid spreading it?

No -- poor flow is actually a cause of cyanobacteria, not a solution. Improving circulation is part of the fix. Just be gentle when manually removing sheets so you don't burst them and spread spores.

Can I use erythromycin to treat cyanobacteria?

It can work, but it's an antibiotic that can also harm your beneficial bacteria colony, so it's generally considered a last resort after manual removal, improved flow, and a blackout period haven't resolved the outbreak.