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If you have ever woken up to find a shiny, slimy sheet spreading over your sand, rocks, or glass, you are probably looking at cyanobacteria. Many hobbyists call it “blue-green algae” in freshwater tanks or “red slime” in saltwater tanks. It grows fast, looks terrible, and can stress your fish, plants, and corals. The good news is that a cyanobacteria bloom is fixable. With a few steady changes, you can clear it up and prevent it from returning. This guide explains what cyanobacteria is, how to recognize it, why it happens, and exactly how to get rid of it safely.
What Is a Cyanobacteria Bloom?
Cyanobacteria are photosynthetic bacteria. They are ancient organisms that use light to grow, much like plants do. In aquariums, they often appear as a smooth, slimy sheet that spreads over surfaces. The color can vary: deep green, blue-green, dark red, burgundy, brown, or even purple. In marine tanks, the red or maroon version is common, which is why many reef keepers call it red slime.
Unlike typical algae that grow as filaments or fuzzy patches, cyanobacteria form cohesive mats. These mats can trap gas bubbles during the day (oxygen produced from photosynthesis). At night, cyanobacteria respire and use oxygen, which is why heavy blooms can reduce oxygen available to fish and invertebrates after the lights go out.
How It Behaves in Aquariums
Cyanobacteria tends to bloom where conditions favor it: low water flow, excess nutrients, long light periods, and dirty surfaces. It loves to start on sand, dead spots, and the edges of rocks or decorations. It spreads quickly, sometimes within days. It can peel off in sheets when you siphon it, and it often has a distinctive earthy or swampy smell.
Why It Matters
While not every cyanobacteria species is toxic, many produce compounds that irritate tank inhabitants. Thick mats can smother plant leaves and coral tissue. Heavy blooms can also cause oxygen dips at night, leading to stress, panting fish, and in extreme cases, livestock losses. Even when it does not outright harm animals, it signals an imbalance in your system that needs attention.
How to Identify Cyanobacteria vs Similar Problems
Correct identification saves time and prevents using the wrong fix. Here are simple ways to tell cyanobacteria apart from look‑alikes.
Visual Clues
Cyanobacteria forms smooth, slimy, wet-looking sheets. It rarely looks like hair. The color ranges from emerald green to maroon or even dark purple. You may see many tiny bubbles caught underneath during the day. It often starts on sand and flat surfaces, then creeps up onto nearby rocks or plant leaves.
The Peel Test and Smell Test
Try gently lifting an edge with a siphon hose or card. If it lifts easily in a sheet or peels away as a thin film, that points to cyanobacteria. A musty, earthy, or swampy smell is another strong clue.
Common Look-Alikes
Green hair algae looks stringy or fluffy, not slimy. It does not peel in sheets. Diatoms (brown dust on new tanks or on silica-rich water) wipe off like powder and do not form slimy layers. Dinoflagellates in saltwater can make snotty strings with bubbles, but they often look more gelatinous and less sheet-like; they frequently worsen when nutrients are extremely low and often return quickly after lights-out. Green water is free-floating algae that turns the water green; cyanobacteria mats sit on surfaces instead of tinting the water.
What Triggers a Bloom?
Cyano blooms are almost always a sign that the tank environment favors them over other microorganisms. These are the most common triggers.
Excess Nutrients and Imbalance
High dissolved nutrients, especially phosphate and dissolved organics, fuel cyanobacteria growth. A classic trigger is an imbalance where nitrate is near zero while phosphate is measurable. Many cyano species can thrive when nitrate is limited, especially if there is plenty of phosphate and organic waste. Overfeeding, decaying food, and dead plant matter are common sources.
Low Water Flow and Dead Spots
Stagnant areas allow detritus to settle and create low-oxygen microenvironments. Cyanobacteria often starts in those quiet corners or under decorations where waste accumulates. On sand beds, small “dead spots” become cyanobacteria starting zones.
Old Light Bulbs and Too Much Light
Light fuels photosynthesis. Very long photoperiods and old bulbs (that have shifted spectrum toward the red range) can encourage cyano growth. Tanks that receive direct sunlight also tend to get blooms on the sunlit side.
New Tank Syndrome or Disrupted Biofilter
New aquariums and tanks that have had recent deep cleanings, big filter changes, or large media replacements often see cyano because the beneficial microbes are not yet stable or were disturbed. Cyanobacteria can colonize quickly and fill the gap.
Source Water Quality
Tap water can introduce phosphate, nitrate, and silicate. Using untreated tap for water changes and top-offs can slowly push nutrients too high. In saltwater, using RO/DI with good cartridges and low TDS helps prevent this.
Dirty Substrate and Trapped Detritus
Uneaten food and fish waste sink into gravel and sand. Without regular maintenance, this detritus breaks down and feeds cyano. Over time, even clean-looking tanks can accumulate enough hidden waste to trigger a bloom.
Test and Observe First
Before you act, gather information. Test nitrate and phosphate. Reliable, low-range test kits matter here, because small differences are important. In freshwater, a beginner-friendly goal is often nitrate around 10 to 20 ppm and phosphate in the 0.1 to 0.3 ppm range for planted tanks. In reef tanks, many hobbyists aim to maintain nitrate around 2 to 15 ppm and phosphate around 0.02 to 0.1 ppm. Zero is not ideal; a bit of nutrient stability helps prevent cyano and dinoflagellates.
Look for low‑flow areas. Map where the cyano starts. Note your photoperiod and whether sunlight hits the tank. Check your filter maintenance schedule. If you use RO/DI, confirm your TDS and cartridge condition. This short audit tells you which steps will matter most for your setup.
Step-by-Step Plan to Remove Cyanobacteria
The best results come from combining manual removal with small, steady improvements to flow, nutrients, and maintenance. Follow these steps, and avoid making many large changes at once.
Step 1: Manual Removal and Siphoning
Physically removing as much as possible weakens the bloom and reduces the load on the system. Use a small-diameter siphon tube to lift the mats gently off the surface. On sand, hover the tube just above the cyano and let it flow into the hose. On rocks and decorations, loosen an edge with a card or turkey baster and siphon it away. Clean mechanical filter media shortly after, so trapped cyano does not decay in the filter.
If the bloom is heavy, split the work over several days to avoid large changes in water chemistry. A partial water change after siphoning helps export dissolved nutrients and spores.
Step 2: Improve Oxygen and Flow
Increase surface agitation and circulation to reduce dead spots. In freshwater, reposition the filter outflow or add a small powerhead aimed across the substrate. In saltwater, adjust wavemakers to gently move water along the sand and behind rocks. The goal is to keep detritus suspended long enough to be removed by the filter, not to blast fish or corals.
Better oxygenation helps fish and invertebrates at night when cyano consumes oxygen. An airstone in freshwater or slight skimmer wet-skimming in marine systems can boost gas exchange.
Step 3: Fix Nutrients
Reduce overfeeding. Feed small amounts your fish finish in under a minute, once or twice a day depending on species. Rinse frozen foods to remove juices that add phosphate.
In freshwater planted tanks, cyano often strikes when nitrate is too low. If nitrate is near zero, carefully raise it to a stable level with a quality fertilizer, and ensure plants have enough macro and micronutrients. Healthy plants outcompete cyano over time. Maintain CO2 at a stable level if you inject it.
In marine tanks, aim for a small but steady amount of nitrate and phosphate rather than chasing zeros. Consider adding or tuning your refugium and macroalgae growth. Use protein skimming to remove dissolved organics. If phosphate is high, use a phosphate remover media in a reactor or filter, but change it slowly to avoid shocking corals. Overshooting and stripping nutrients to zero can replace cyano with dinoflagellates, so adjust in measured steps.
Step 4: Adjust Lighting
Shorten the photoperiod during the recovery period. For freshwater planted tanks, consider running 6 to 8 hours of light temporarily, then gradually return to 8 to 10 hours when things stabilize. For reef tanks, 7 to 9 hours of the main lighting is common. Avoid direct sunlight on the aquarium. If bulbs are old and have shifted spectrum, replace them. On LED systems, avoid sudden increases in intensity; use gradual ramping and appropriate spectrum.
A full blackout can help in stubborn cases. Cover the tank to block all light for two to three days, keeping good aeration and normal filtration. This weakens photosynthetic cyano, but it works best combined with manual removal and nutrient correction, or the bloom can return.
Step 5: Deep Clean Filtration and Substrate
Clean mechanical filter pads or floss every few days during a bloom, then weekly. Rinse or squeeze sponges in tank water to preserve beneficial bacteria. Do not replace all media at once; keep your biofilter stable.
Vacuum debris from the top layer of gravel or sand. In freshwater, a gravel vacuum works well. In saltwater with a shallow sand bed, gently siphon the surface layer to remove detritus. For deep sand beds, avoid deep stirring to prevent releasing trapped gases; focus on the top surface and improve overall flow instead. Regular small water changes help export the fuel cyano needs.
Step 6: Use Chemical Aids Carefully
Sometimes, even with good husbandry, a mature bloom needs an extra nudge. Chemical aids can help, but use them responsibly and only after addressing the root causes.
In freshwater, low-dose hydrogen peroxide can be effective. A common conservative approach is about 1 milliliter of 3% hydrogen peroxide per 10 gallons per day, for up to three days, with increased aeration. For spot-treating, you can temporarily pause flow and gently apply a small amount with a syringe to affected areas, then resume circulation after a few minutes. Avoid dosing directly on fish, shrimp, or sensitive plants. Observe livestock closely.
In marine tanks, commercial cyanobacteria removers are widely used. Follow the product’s directions exactly. Increase aeration and be ready for your protein skimmer to overflow after treatment. Remove carbon and phosphate media if the instructions say to do so, and perform the recommended water change after the treatment period. Antibiotic-style treatments can stress beneficial microbes if misused, so do not rely on them as the only fix. If root causes remain, the bloom will return.
Special Notes for Different Setups
Freshwater Planted Tanks
Planted tanks often see cyano when nitrates are too low and phosphate or organic waste are relatively high. Counterintuitively, adding nitrate fertilizer to reach a stable 10 to 20 ppm can help plants outcompete cyano. Ensure adequate potassium and micronutrients, and provide stable CO2 if you use it. Keep good flow around the substrate and under hardscape where debris collects. Prune dying leaves so they do not decay and feed the bloom.
Freshwater Non-Planted or Low-Tech Tanks
Focus on feeding control, regular gravel vacuuming, filter maintenance, and improved circulation. Most of the time, consistent water changes and reducing waste solve the problem. If your tap water is high in phosphate or nitrate, consider using RO water for changes or mixing RO with tap to lower nutrient inputs.
Saltwater Reef and FOWLR
A stable, small amount of nitrate and phosphate is healthier than zero. Tune your skimmer, consider a refugium, and use moderate phosphate control media without stripping the tank. Adjust flow to reduce dead spots along the sand and behind rock structures. Clean and maintain the protein skimmer and mechanical filters regularly. If you use a cyano remover, maintain heavy aeration and follow up with a water change. After clearing the bloom, keep nutrients stable to prevent a swing into dinoflagellates.
Ponds and Outdoor Systems
Sunlight and warm temperatures fuel cyanobacteria outdoors. Shade the water where possible, limit fish load and feeding, and improve mechanical filtration and circulation. Aquatic plants can help compete for nutrients. Use water changes carefully, as ponds are large; focus on reducing nutrient inputs and removing organic debris.
Prevention Checklist and Weekly Routine
Prevention is about balance and consistency. Feed sparingly and observe how much your fish truly need. Clean mechanical filter floss or pads often so trapped waste does not rot. Rinse biomedia in tank water only when it slows flow, not to make it look “new.” Maintain steady flow across the entire tank, and reposition powerheads if you notice dead spots or accumulating debris.
Keep a steady photoperiod. Replace old bulbs before their spectrum drifts. Avoid placing tanks in direct sun. If you use RO/DI, check TDS and replace cartridges before they are exhausted. During weekly maintenance, siphon the top of the substrate, remove visible debris, and perform small, regular water changes instead of big, rare ones.
In planted tanks, maintain a balanced fertilization schedule so plants are never starved. In reef tanks, test nitrate and phosphate periodically and aim for stability inside a reasonable range, not zero. Consider occasional dosing of beneficial bacteria to diversify your biofilter, especially after major changes or medication.
Troubleshooting Scenarios
It Keeps Coming Back Every Week
Recurring blooms usually mean a persistent source of nutrients or a dead spot. Track where it starts and improve flow there. Clean prefilters and floss more often. Rinse frozen foods. Confirm your photoperiod and reduce it temporarily. Verify that your test kits are not expired and that your source water is low in nutrients.
Nitrate Is Zero but Phosphate Is Measurable
This imbalance often favors cyano. In planted tanks, raise nitrate to a stable level. In reef tanks, lightly increase feeding or reduce aggressive phosphate removal so nitrate and phosphate rise together, then stabilize both inside a reasonable range. Do this slowly and watch corals or plants for response.
Cyano After Medication or Deep Cleaning
Antibiotics and deep filter cleanings can knock back beneficial microbes. Cyanobacteria can rush in during the gap. Re-seed with a trusted bacterial product, avoid over-cleaning next time, and maintain good aeration and moderate nutrients while the biofilter recovers.
Blackout Worked but It Returned
Blackouts weaken the bloom, but if nutrients, flow, or maintenance are not addressed, cyano will return. Combine blackouts with manual removal, better circulation, waste reduction, and stable nutrient levels.
New Sand or Rock Triggered a Bloom
New surfaces collect biofilms and detritus. Increase flow on the new area and siphon gently during the first weeks. The bloom usually fades as the tank microbiome stabilizes and you maintain good export.
Safe Use of Additives and Equipment
Activated carbon helps remove organic compounds that cyano can feed on. Replace it regularly so it does not become a nutrient source. Phosphate removers are helpful but should be used in moderation. Large, sudden drops in phosphate can stress corals and plants and promote other pests. A UV sterilizer can reduce free-floating microbes, which may help indirectly, but it will not remove mats on surfaces; it works best as part of a broader plan.
When using any chemical treatment, increase aeration, follow instructions exactly, and perform the recommended water change afterward. Monitor fish and invertebrates closely for stress, and pause treatments if anything looks wrong. Remember that chemistry alone cannot keep cyano away; balanced husbandry does the long-term work.
How Long Will It Take to Clear?
Small blooms often improve within a week with manual removal, better flow, and reduced feeding. Moderate cases usually take two to four weeks to fully stabilize, especially if you are adjusting nutrients carefully. Stubborn, long-running blooms can take longer and may require a one-time chemical assist. If you keep changes consistent and avoid big swings, the tank will find a healthier balance and the cyano will fade.
Key Takeaways
Cyanobacteria is a symptom of imbalance, not a random curse. It thrives on extra nutrients, low flow, and long or poor-quality light. You beat it by removing the mats, improving oxygen and circulation, stabilizing nutrients, keeping a steady photoperiod, and maintaining clean filtration and substrate. Chemical tools can help in tough cases, but they are most effective when you also correct the underlying causes.
Conclusion
A cyanobacteria bloom looks intimidating, but you can win against it with simple, steady steps. Start by siphoning the mats, then strengthen flow and aeration. Adjust feeding and nutrient balance, shorten the light schedule for a while, and clean your filter and substrate more consistently. If needed, use a careful, well-aerated treatment once to push the bloom over the edge. Most of all, keep things stable. Over a few weeks, you will see less slime, clearer surfaces, and a tank that stays cleaner between maintenance. With patience and balance, cyanobacteria becomes a short chapter in your aquarium journey—not the whole story.