Blue-Green Algae in the Aquarium: Why It Is Not Algae, and What Actually Clears It

Blue-green algae is really cyanobacteria, a slimy bacterial film that smells musty and peels off in sheets. Here is how I tell it apart from true algae, the blackout that clears most of it, and why it keeps coming back until you fix the flow.

If you have a dark green, slightly slimy film creeping over your sand and sliding up the back glass, and it peels off in sheets rather than scrubbing away as spots, you are almost certainly looking at blue-green algae. The name is a lie. It is not an alga at all, it is a bacterium called cyanobacteria, and once you know that, the whole problem makes more sense and the usual algae tricks stop disappointing you. I have had it twice, once in a low-flow corner of a shellie tank and once across the front of a fry grow-out, and both times the fix was the same handful of steps rather than a bottle of anything.

This piece is specifically about the slimy sheet-forming stuff. If what you have is spot algae on the glass, hair algae on the plants or a stubborn black tuft on your hardscape, you want the broader aquarium algae guide or the dedicated piece on black beard algae instead. Those are true algae and they behave differently.

How to be sure it is cyanobacteria

Three tells, and if you have all three you can stop guessing.

The first is the smell. Cyanobacteria has a distinctive musty, earthy, slightly swampy odour. Rub a bit between your fingers out of the water and you will know it at once; it is nothing like the clean pondy smell of ordinary green algae. The second is the texture. It forms a continuous slimy film or mat, not individual spots or strands. You can slide a credit card or an old loyalty card under the edge and lift a whole sheet off the sand in one piece, which no true algae lets you do. The third is where it grows and how fast. It loves the low-flow spots, the dead corner behind a filter return, the front strip of sand where nothing much moves, the shaded base of the glass. And it spreads quickly, a clean patch of sand can be filmed over again in two or three days.

Colour is the least reliable sign. Most of mine has been a dark blue-green, but cyanobacteria can show up almost black, or a dull red, so do not rule it out just because it is not the postcard blue-green of the name.

Why it turned up in my tank

Here is the part the forums argue about, and I will give you my honest read from the two outbreaks I have cleared rather than a confident law.

The common thread in both of mine was poor water movement. Both patches started in a genuinely stagnant corner, and that matches what the better sources say: cyanobacteria exploits still, low-flow areas where true plants and algae are not competing hard for light and nutrients. Strong light over a tank with little healthy plant growth leaves energy on the table, and cyanobacteria is very good at mopping that up.

Nutrient balance is the other half, and it is counter-intuitive. A lot of keepers assume an outbreak means too much of everything, but cyanobacteria often takes hold when nitrate is very low while there is plenty of light and some phosphate about. That matters because if you are running a planted tank hard and your nitrate has bottomed out, starving the tank further can actually make things worse, not better. In my fish-heavy shellie tanks nitrate is rarely the issue; in the planted fry tank, letting nitrate sit closer to the floor was almost certainly part of what let it in. I am more careful now to not let a planted tank run completely empty of nitrate. If your own nitrate is climbing instead, that is a different conversation and the how to lower nitrate guide is the place for it.

So the honest summary: too little flow, strong light, and a nutrient imbalance, usually low nitrate, let it in. Fix those and it struggles to come back. Treat the symptom alone and it returns within a week.

The Hard Water Aquarium by Dan Mercer

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The Hard Water Aquarium

My practical guide to working with hard, alkaline tap water instead of fighting it: reading your water, choosing and setting up the tank, and keeping and breeding the fish that thrive in it, from livebearers to Rift Lake cichlids and shell-dwellers.

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The blackout, which does most of the work

Cyanobacteria needs light. Take the light away and it cannot hold on, while your fish and most plants shrug off a few dark days without complaint. This is the cheapest and most reliable thing I have done, and it has cleared early outbreaks on its own.

Here is the routine I use. First, do a decent water change and manually remove every sheet you can reach, siphoning it out rather than stirring it up; a turkey baster is handy for lifting film off sand without wrecking the layout. Then cover the tank completely. Not just lights off, actual darkness: I throw a couple of old towels or a bin liner over the whole thing so no room light gets in. Leave it blacked out for three full days, feeding lightly or not at all and keeping the lid on. Keep the filter and any airstone running the whole time, because oxygen matters when a lot of bacteria is dying back.

After three days, uncover, do another good water change, and remove whatever film has gone slimy and loose. Most of the time, that is it. If you have live plants, three days of dark is comfortably within what they tolerate; I have never lost a plant to a blackout, though a few stems sulked for a week.

A note on the air: a dying cyanobacteria mat consumes oxygen as it breaks down, so this is exactly when you want good surface movement or an air pump going. If you have ever wondered whether you need an air pump, a blackout is one of the few times I reach for one even on a tank that does not normally have one.

Fixing the flow so it stays gone

The blackout clears what is there. Flow is what keeps it from coming back, and this is the step people skip.

Walk the tank and find the dead spots. The easiest way is to drop a pinch of food or a few plant fragments in and watch where the water does not carry them. Those still corners are where it will return. I angle the filter return so the surface actually ripples and the far corners get some push, add a small powerhead or wavemaker if one side is genuinely dead, and trim back any plant or decor that is damming the flow. On a quiet shellie tank you do not want a washing machine, the fish like calm water, so it is a balance: enough movement to deny cyanobacteria its stagnant corner, not so much that your multies are swimming on the spot. If your filter is undersized for the tank, that is worth sorting on its own terms, and the choosing a filter guide covers sizing honestly.

While you are at it, check your light. If the tank gets strong light for long hours but has little plant growth to use it, dial the photoperiod back. I run most tanks on a timer at six to eight hours and the lighting hours piece explains why longer rarely helps and often feeds exactly this kind of problem.

When to reach for erythromycin, and why I treat it as a last resort

There is an antibiotic route. Erythromycin, sold in aquarium products for this purpose, kills cyanobacteria reliably because cyanobacteria is a bacterium. It works. I still treat it as the last option, and here is the honest reason.

Erythromycin does not only kill the cyanobacteria. It can knock back the beneficial bacteria in your filter, the ones doing your nitrogen cycle, which means you can trade a slime problem for an ammonia spike if you are not watching. If I ever use it I remove activated carbon from the filter first, because carbon strips the medication straight out, and I test ammonia and nitrite daily through the course and for a week after. Dosing is by water volume and varies by product, so follow the label for the one you have and work from your real tank volume, not the nominal size on the box; the volume calculator gives you the figure that actually matters for dosing. And none of it holds unless you also fix the flow and light. I have read enough accounts of cyanobacteria marching straight back after a successful antibiotic course to be sure of that.

For an early outbreak, blackout plus flow has never failed me and costs nothing. I would only consider antibiotics for a severe, entrenched mat that has already survived a proper blackout, and even then I would do the blackout again first.

The short version

Blue-green algae is cyanobacteria, a bacterium, which is why it smells musty, peels in sheets and favours your stillest, best-lit corners. Manually remove it, black the tank out completely for three days with the air running, then change water. Keep it gone by breaking up the dead spots with better flow and trimming the photoperiod, and do not let a planted tank starve of nitrate. Save the antibiotic for the rare mat that survives all that, and watch your filter closely if you use it. Mostly, though, this is a flow problem wearing a slimy green coat, and once you see it that way it is one of the more satisfying tank problems to beat. If you are working through a cluster of these at once, the maintenance schedule is how I keep the conditions that invite it from building up again.