What Causes Cyanobacteria in a Reef Tank?

A dark red-brown mat is usually a sign that something is building up faster than your tank is exporting it — not a sign that you need to kill something.

Written for reef keepers who test their own water. Corrections and questions

The short answer

Cyanobacteria is a group of photosynthetic bacteria, not an algae — which is why the fixes aimed at algae often miss it. What keepers call red slime is a mat that grows where dissolved organic matter and unused nutrients are building up faster than the tank removes them. In practice that comes down to a handful of causes: feeding and waste outrunning your export, flow that lets detritus settle instead of lifting it into the filter, source water that is not as clean as assumed, filtration media that is no longer keeping up, a tank that was recently disturbed, and light or gas exchange that has drifted away from where it was. A low nitrate or phosphate reading does not rule it out — the mat can be taking nutrients up as fast as they appear. Find the cause first, then change one thing at a time and re-measure.

It is bacteria, not algaeThat is why algae-focused fixes and herbivores usually leave it alone.
It grows on build-upThe mat appears where organics and unused nutrients are accumulating, not at random.
Zero readings do not rule it outA mat can strip nutrients out of the water as fast as your kit can measure them.
Change one thing, then re-measureOne confirmed change with a before-and-after reading teaches you something you can use again.

Handle it carefully

Some cyanobacteria produce compounds that are harmful to other tank life, and keeper reports of losses after a heavy mat are common. Keep your hands out of the water where you can, wear gloves when you must reach in, do not scrub the mat into the water column, ventilate the room, and wash up afterwards. This page explains what causes it and how to work through it. It is not a treatment protocol.

What cyanobacteria actually is

Three things worth knowing before you try to get rid of it.

A photosynthetic bacterium, not a plant

It makes its own food from light, so a mat can spread across a surface that looks bare to everything else. Because it is not an algae, the grazing animals and algae-focused fixes keepers reach for first frequently leave it untouched.

A mat that grows on what is left over

It forms where dissolved organic matter and unused nutrients collect on a surface. That is why it turns up in the same corners, the same patch of sand and the same low-flow pockets each time. It is a symptom of an accumulation, not an organism that arrived from nowhere.

Fast to appear, slow to leave

It can cover a surface quickly once conditions suit it, and it commonly returns within days of being siphoned out if nothing about the tank has changed. Removing the mat is cleaning; removing the cause is the part that lasts.

The causes, in the order they usually turn out to be the reason

Work down this table with your own tank in front of you. Most tanks turn out to be more than one row.

Cause	What you would typically see	How to check it on your own tank	First move
Organic matter building up faster than the tank exports it	A mat that returns within days of being removed, in the same places. Water that looks slightly dull or has a film on the surface.	Write down what goes into the tank in a normal day — food, additives, anything that died and was left in. Then look at how much of it your filtration and water changes actually take back out.	Cut back to what the tank actually eats in one sitting, and siphon out what settles instead of leaving it to break down.
Flow that lets detritus settle instead of lifting it	A mat that starts in low-flow pockets — behind rockwork, along the sand at the back, under a branch, in a corner the return does not reach.	With the pumps running as normal, watch where food and waste travel in the first minute after feeding. Wherever it lands and stays is where the mat starts.	Adjust existing flow so settled material stays in suspension long enough to reach the filter, rather than adding more equipment.
Source water that is not as clean as assumed	A mat that keeps coming back even though the display tank's own numbers look reasonable, or a mat that appeared after a change in water source.	Test the water you use for changes and top-off with the same kits you use on the tank, and compare. Check the cartridges or resin you rely on rather than trusting the date on the label.	Fix the source water before treating the display tank, because the cause may be upstream of the tank entirely.
Filtration media that is no longer keeping up	A mat that spreads in slow steps over weeks. Mechanical media that is dark, clogged or overdue. Surfaces inside the sump or filter compartment that feel slick.	Open the filter and look, rather than remembering. Check mechanical media, chemical media and the compartment surfaces you never normally touch.	Clean or replace what is exhausted and clear the detritus out of the compartments, then watch whether the return rate to the display changes.
A tank that was recently disturbed	A mat appearing within weeks of new sand, new rock, a move, a livestock change or a filtration change.	Think back through the last few weeks and write down everything that changed. A disturbance that stirred up settled material is a common trigger.	Hold everything else steady and let the system settle before changing another variable on top of it.
Light or gas exchange that has drifted	A mat on surfaces that face the light, or a mat that appeared after a lighting change, a lamp aged, or the tank was covered for longer than usual. Surface film and sluggish water movement at the top.	Check the light schedule you are actually running against the one you meant to run, and look at how much the water surface moves.	Put the light schedule back to where it was and improve surface movement, then leave it there long enough to see a trend.

No single row decides it, and the order is a starting point rather than a rule. If two or more rows fit what you are seeing, start with the one you can check most cheaply — usually flow or what you are putting into the tank.

Find your cause in six checks

Run these once, in this order, and write the answers down. They use things you already own.

1. Map where it growsAny time, with the pumps running as normal.
Mark every patch on a photo or a sketch. If the patches are all in low-flow pockets, start with the flow row in the table above.
2. Test the parameters you normally trackSame hour, same day, with your own kits.
Salinity, alkalinity, nitrate, phosphate and temperature. Log the values with the date next to them. A single reading is not a trend, and a surprising one is a reason to re-test, not to act.
3. Re-test anything that looks wrongImmediately after the first test.
Run the same kit a second time, and check it against your reference solution if you keep one. Confirm the reading before you change the tank because of it.
4. Test your source waterAfter the tank's own tests.
Run the same kits on freshly mixed water and on your top-off water. If the number is already there before it reaches the tank, the first move belongs upstream.
5. Look inside the filterOnce, with the pump off.
Mechanical media, chemical media, the sump floor, the compartments you do not normally open. Note whether anything is dark, clogged, overdue or slick to the touch.
6. Write down the last thing that changedAfter the five checks above.
Feeding, livestock, new sand or rock, a move, a media change, a lighting change. If the mat appeared within weeks of one of them, that is where to look first.

Repeat before you act

Run the checks on at least two separate days before you decide. A single reading on a single afternoon is how most wrong conclusions get made, and a mat that is being stripped of nutrients by its own growth can look like a tank with no problem at all.

Which cause is most likely yours?

Answer in order. Stop at the first question you answer yes to, and start there.

Start here

There is a dark red-brown mat on sand, rock or glass, and it comes back after you remove it.

Question 1

Is it concentrated in low-flow pockets — behind rockwork, along the back of the sand, in a corner your return does not reach?

Yes → Outcome: Start with the flow row. Adjust what you already have, then watch whether material still settles in the same places.

No → Continue to question 2.

Question 2

Did the mat appear within a few weeks of something changing — new sand or rock, a move, a livestock change or a media change?

Yes → Outcome: Start with the recent-disturbance row. Hold everything else steady and let the system settle before you change anything else.

No → Continue to question 3.

Question 3

Do the tank's own tests come back at or near zero for the nutrients you track?

Yes → Outcome: Do not assume there is nothing there. Re-test to confirm, then test your source water and look inside the filter before deciding the tank is short of anything.

No → Continue to question 4.

Question 4

Has anything about the light or the water surface changed recently — a new schedule, an aged lamp, a covered tank, a still surface?

Yes → Outcome: Start with the light and gas exchange row. Put the schedule back where it was and improve surface movement.

No → Outcome: Start with the organic build-up row and the filter check. Reduce what goes in, siphon out what settles, and clean what is exhausted — then re-measure before changing anything else.

This chooser narrows down where to look. It does not identify the organism. Confirming that needs a microscope.

The order that works

Seven steps, in this order. Do not skip to the last one.

Confirm what you are looking at
Cyanobacteria, dinoflagellates and a heavy diatom film all read as brown growth at a glance and they need different responses. Before you change anything, make sure the mat you have is the mat you think you have.
Record your own numbers first
Test and log the parameters you normally track with your own kits, on the same day, with the date written next to the values. Those numbers are your baseline, and without them you cannot tell whether anything you do next helped.
Remove only what you can reach, gently
Siphon the mat out during your normal maintenance, using the siphon to take water out at the same time. Run a fine filter pad or floss in the flow path to catch what lifts off, and change it out. Do not scrub or blast the mat into the open water.
Fix the physical cause you found
Work the row your checks pointed at: what goes into the tank, where the flow lets material settle, the source water, the media, the light schedule, or simply letting a recently disturbed system settle.
Change one variable, then wait
Pick a single thing to adjust, change only that, and leave it alone long enough to see what it did. Several days of the same checks is a reasonable minimum before the next change.
Re-test on a fixed schedule
Test at your normal cadence and log each result next to the previous one, so you are reading a trend rather than a single number. This is the step that tells you whether step four actually worked.
Escalate with evidence
If the mat holds after the low-risk moves, get it identified under a microscope and get a second opinion before using any product. Bring your log and your photos with you.

Mistakes that make it worse

These six are the ones that cost the most time.

Treating it as an algae problem

It is a bacterium. The grazing animals and algae-focused fixes keepers reach for first frequently do nothing to it, and the weeks spent on them are weeks the actual cause keeps running.

Dosing a product before finding the cause

Anything strong enough to knock a mat back in the water column also reaches your invertebrates, your corals and your filter community. Do not add anything until you have found the cause and confirmed what you are looking at.

Scrubbing or blasting the mat into the water column

It spreads to new surfaces, and it puts whatever the mat contains into the water you are leaning over. Siphon it out instead of scrubbing it loose.

Making a very large water change

A big change is not a reliable fix for a mat, and it swings the parameters you spent the previous weeks stabilising. Keep your normal routine and use it to siphon.

Changing several things at once

When you change three variables and the mat recedes, you have learned nothing you can use next time. Change one, measure, then decide.

Turning the lights off and calling it fixed

A dark period can knock the visible mat back without changing anything that caused it, and everything in the tank that depends on light pays the price. Treat it as one measured change with a before-and-after log, not as a cure.

Edge cases worth knowing

Six situations where the standard checks need a caveat.

Both nutrients read zero

A zero reading is not always the whole story, because a fast-growing mat is taking nutrients up as quickly as they appear, and some cyanobacteria can use nitrogen sources your kit does not measure. Confirm the reading with a second test method before you treat a low number as proof that nothing is there — and do not start adding anything on the strength of it.

It keeps coming back in exactly the same spot

That pattern points at a local cause rather than a tank-wide one: a dead spot in the flow, a pocket of settled detritus, or a surface that stays coated. Fix the spot, not the whole system.

It is growing on the corals

Priority one is the coral, not the mat. Keep the parameters you track stable, do not scrub coral tissue, and do not stack several interventions to get rid of it faster. Siphon around the colony rather than over it.

It appeared right after a change

New sand, new rock, a move, a media swap and a lighting change all stir up or shift what the system was previously handling. Hold everything else steady and give the tank time to settle before adding another change on top.

Something has died, or the livestock look wrong

Remove anything dead promptly, move or isolate what you can, keep your hands out of the tank where possible, wear gloves when you must reach in, ventilate the room, and wash up afterwards.

You are considering a chemical or an antibiotic

Do not add either before the organism has been identified and the cause has been found. Treatments aimed at a mat in the water column reach the rest of the tank too, and a treatment that works on the wrong problem costs you the livestock you were protecting. If you do use one after confirming the identification, follow the manufacturer's instructions exactly, do not exceed them, and do not run two products that do the same job at the same time.