How to Kill Cyanobacteria – Is the Natural or Chemical Way Best?

Remember that beautiful planted tank I designed for my betta? Well, it ain’t paradise any more because we've got cyanobacteria, baby! Keep reading as I talk about what causes it, the natural versus chemical methods I used to treat it, and which one worked the best!

All I want is a super easy, low tech, low maintenance aquarium to just sit back and enjoy when I’m stressed at work. Unfortunately, my office tank had a reoccurring issue with, well, multiple types of algae, and one of them was blue-green algae, or more accurately, cyanobacteria. No longer was I calm and relaxed when gazing at my betta fish Soundwave. Instead, his home was an eyesore and constant source of stress… (Why oh why don’t you look like the aquascapes on my Instagram feed?)

Cyanobacteria outbreak while on vacation (source: Keudn from Reddit)

Causes of Cyanobacteria

There have been lots of studies done on what causes cyanobacteria in aquariums, but nothing is concrete because the bacteria is so genetically diverse and can rapidly spread through practically any ecosystem - freshwater, saltwater, or on land. Potential causes reported on aquarium articles include:

• Dirty tanks with an excess ammonia (hmm, my ammonia measured 0 ppm)
• Anaerobic areas from lack of flow (hmm, my algae started right under the filter output)
• Excess light (hmm, my timer’s only on for 5 to 6 hours per day)
• Very low nitrates... or very high nitrates according to other sources

Ok, so clearly there’s a lot of conflicting info out there on causes of cyanobacteria. What about the remedies? Most people say it’s a pain to get rid of and spreads like wildfire. I did find that when I rubbed off some slime from a bucephalandra plant up high, it landed somewhere down below and started conquering my staurogyne repens.

Natural Treatment for Cyanobacteria

The natural remedy I followed came from a blog called AQUAdesign with the following instructions:

1. Manually scrub off the algae from all surfaces (which shouldn’t be difficult because it just flakes off in sheets) and then gravel vacuum up as much of it as possible, removing up to 50% of the water.
2. If you have low nitrates, use fertilizers to dose it up to 20 ppm.
3. Turn off any CO₂ and use an air stone (with air pump and airline tubing of course) to increase oxygenation.
4. Cover your tank with a black trash bag and tape, keep the aquarium light off, and do a blackout for three to four days. Don’t worry, your fish will be fine during this brief fasting period.
5. After the blackout, do a large water change to remove all the dead algae, redoes your fertilizers back to 20 ppm nitrates, turn on the light and CO2, and increase flow to avoid dead spots.

And what do you know? The blue-green algae was gone! I didn’t have to use any expensive meds and the treatment was relatively painless… until the cyanobacteria came back again 6 weeks later. Ok, no more Mr. Nice Guy. I’m going in with guns a-blazing!

Chemical Treatment for Cyanobacteria

The chemical method I heard was from Aquarium Co-Op, and it goes something like this:

1. Manually remove all algae and gravel vacuum just like before.
2. Clean your filter – including intake sponges, sponge filters, foam inserts, etc.
3. Nuke your tank with one full dose of erythromycin per the manufacturer’s instructions and let it sit for seven days. (In the United States, it is sold by brands like Fritz Aquatics and API.) If you have an extra tank lying around, you can remove any animals, but this antibiotic is safe for fish, invertebrates like shrimp and snails, and plants.
4. After seven days, do a large water change to remove all dead algae. You can continue to do more water changes and even use activated carbon to remove the remaining medication.
5. If it’s a really bad case, you may have to follow up with a treatment or two. Thankfully, erythromycin will not harm your beneficial bacteria, according to Aquarium Co-Op and in my own experiences.

And voila! It’s been four months since the chemical treatment, and I haven’t seen any hint of that evil blue-green slime. Soundwave the betta is no worse for wear, and I can finally breathe a sigh of relief and get back to enjoying his tank!

Question of the Day

Have you ever dealt with cyanobacteria, and if so, how’d you get rid of it? Comment below to share your experiences because I’d love to hear them. Take time to enjoy your aquariums and I’ll see you next time!

---

Subscribe to my YouTube Channel for practical fish care tips for busy aquarists and follow me on Instagram for more updates! 🎮❤️🐟