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Cyanobacteria blooms are among the most frustrating problems for aquarium keepers. They spread fast, smother plants and corals, trap debris, and make a tank look and smell bad. The good news is that you can beat cyanobacteria with a clear plan that addresses both the visible slime and the root cause. This guide explains what cyanobacteria is, why it shows up, how to remove it safely, and how to prevent it from returning. Everything here is written in simple language, so even beginners can follow along with confidence.
What Is Cyanobacteria?
Not Actually Algae, Even If It Looks Like It
Cyanobacteria are photosynthetic bacteria, often called blue-green algae (BGA). Despite the nickname, they are not true algae. They can appear in many colors: deep green, dark red or maroon, purple, brown, or even black. They grow as slimy sheets or mats that slide over glass, substrate, rocks, driftwood, and plant leaves.
Unlike most algae, cyanobacteria can fix nitrogen in some conditions, which means they can survive in low nitrate water. They grow quickly under bright light and with available nutrients, especially dissolved organics and phosphate.
How Cyanobacteria Looks and Smells
Most hobbyists first notice a shiny, slippery film that looks like wet cling wrap. If you gently wave your hand near it, it may lift off in sheets. It often has bubbles trapped underneath during the day because photosynthesis creates oxygen. Many aquarists also report a musty or swamp-like smell. These clues help confirm it is cyanobacteria rather than normal algae.
Freshwater vs. Saltwater Cyanobacteria
In freshwater tanks, cyanobacteria often appears as green or dark green mats on the substrate, near dead zones with low water flow, or on slow-growing plant leaves. In saltwater tanks, it commonly shows up as red or burgundy “red slime” on sand, rocks, and around low-flow areas. Some marine strains can be more toxic to invertebrates and corals, so quick action is important.
Why Does Cyanobacteria Appear?
Excess Nutrients and Imbalance
Cyanobacteria thrives on dissolved organic compounds and phosphate. Overfeeding, infrequent water changes, dirty filters, and decaying plant or food waste release organics that fuel growth. An imbalance can be just as important as a surplus. For example, in planted tanks, very low nitrate with relatively higher phosphate often invites cyanobacteria to take over.
Too Much Light or the Wrong Light
Long photoperiods, intense lighting, and light that hits the tank from a window encourage blooms. Old bulbs with shifted spectrum can also promote nuisance growth. Cyanobacteria responds quickly to strong light, especially when nutrients are available.
Low Flow and Dead Zones
Areas behind rockwork, under hardscape, or in corners with weak circulation collect detritus and become low-oxygen pockets. Cyanobacteria loves stagnant zones. Improving flow is one of the simplest and most effective adjustments you can make.
Dirty Substrate and Trapped Detritus
Waste that sinks into sand or gravel breaks down and leaks nutrients back into the water. Without regular vacuuming or gentle stirring, the bottom of the tank can become a nutrient bank that continually feeds cyanobacteria.
New Tank Syndrome and Unstable Biofilters
In young aquariums, the beneficial bacteria community is still developing. Ammonia spikes, unstable nitrification, and organic swings create perfect conditions for cyanobacteria to grab hold. In these tanks, patience and gentle, regular maintenance are key.
Old Tank Syndrome and Neglected Maintenance
In older setups, a long period without deep cleaning can lead to a slow buildup of organics in the substrate and filter. Even if water tests look “OK,” the internal nutrient load can be high. Cyanobacteria often shows up in these tanks because the underlying balance has shifted.
Source Water Quality and Silicates
Tap water can add phosphate, nitrate, and silicate. A good water conditioner does not remove phosphate or silicate. If your tap is nutrient-rich, cyanobacteria will have an easy time. Using RO/DI water for marine tanks and sensitive freshwater setups reduces this risk.
Carbon Dosing and Nutrient Skews in Marine Tanks
In reef aquariums, aggressive carbon dosing (like vodka, vinegar, or commercial products) can drive nitrate very low while leaving phosphate measurable. This imbalance often encourages cyanobacteria. It is important to tune dosing and keep both nitrate and phosphate within balanced, non-zero ranges.
Very Low Nitrate in Planted Tanks
Planted aquariums sometimes run into cyanobacteria when nitrate is too low. Plants slow down, organic waste accumulates, and cyanobacteria steps in. Keeping nitrate and phosphate in a stable ratio helps plants outcompete BGA.
How to Diagnose a Cyanobacteria Bloom
Visual Clues and Smell
Look for shiny sheets or slimy mats that peel off in thin layers. Watch for oxygen bubbles trapped underneath during the light cycle. Note any earthy, swampy smell. These signs strongly suggest cyanobacteria.
The Paper Towel Test
Gently remove a small patch and lay it on a white paper towel. Cyanobacteria will smear and stain more like paint than fibrous algae. It usually pulls off in continuous sheets rather than in strands.
Test Your Water Parameters
Measure ammonia, nitrite, nitrate, phosphate, and pH. In freshwater planted tanks, nitrate near 5 to 20 ppm and phosphate near 0.1 to 0.5 ppm is usually healthy for plants and discourages cyanobacteria. In reef tanks, many hobbyists aim for nitrate between 2 to 10 ppm and phosphate between 0.03 to 0.1 ppm. Zero readings for nitrate with measurable phosphate often correlate with cyanobacteria blooms.
Map the Bloom Location
Where cyanobacteria starts can point to the cause. On substrate and low-flow corners suggests poor circulation and trapped detritus. On slow plant leaves suggests low nitrate and decaying organics. On rock faces with intense light suggests too much light or photoperiod.
Immediate Actions to Slow the Spread
Manual Removal Done Right
Use a siphon tube and gently lift sheets while sucking them out. In marine tanks, turning off pumps during removal helps you capture more without spreading. In planted tanks, be careful not to uproot plants while you vacuum the surface. Remove as much as you can, but do not stir it into a fine cloud, as this can spread cells.
Reduce Feeding Without Starving Fish
Feed small portions that are fully eaten in under one minute. Skip a day or two if fish are healthy. For reef tanks, reduce liquid foods and target feeding until the bloom is controlled.
Adjust Light and Consider a Short Blackout
Shorten the photoperiod to 6 to 7 hours temporarily. For stubborn cases, a 2 to 3 day blackout can help in freshwater tanks. Cover the tank to block all light and maintain good aeration. In reef tanks, blackouts can stress photosynthetic corals, so use shorter periods and monitor livestock closely.
Increase Flow and Aeration
Re-position powerheads or filter outlets to eliminate dead spots. Aim for gentle movement across the substrate. Add an airstone or increase surface agitation to boost oxygen, especially if you plan to use any medication that can reduce oxygen levels.
Deep Clean Strategy: Reset the Organics
Gravel Vacuum and Sand Care
In gravel tanks, perform a careful deep vacuum in sections to remove trapped waste. Avoid over-cleaning the entire substrate at once if your tank is heavily stocked or very new. In sand tanks, gently stir the top layer and siphon off loosened debris. Do not disturb deep sand beds in reef tanks unless you understand the risks; they can release toxins if disrupted.
Filter Service and Rinse Technique
Rinse mechanical media like sponges and filter floss in a bucket of tank water during a water change. Replace or rinse any clogged floss weekly until the bloom subsides. Avoid over-cleaning bio-media. You want to preserve beneficial bacteria while removing gunk.
Clean Hardscape and Plant Leaves
Use a soft brush to gently wipe rocks and décor while siphoning away loose mats. For plants, remove affected leaves if heavily coated. Healthy new growth will replace them once conditions improve.
Water Change Schedule
Perform 30 to 50 percent water changes over several days rather than one very large change in a single day. Consistent, moderate changes export nutrients without shocking your system. Use matched temperature and, for marine tanks, carefully matched salinity and alkalinity.
Treatment Options: Chemical and Non-Chemical
When to Use Medication
If manual removal and deep cleaning reduce but do not eliminate cyanobacteria, or if the bloom keeps returning quickly, a chemical treatment can help reset the tank. Always increase aeration, monitor livestock, and plan follow-up maintenance to prevent a quick comeback.
Freshwater Tanks: Erythromycin Guidance
Erythromycin is an antibiotic that targets many cyanobacteria. Follow the product’s instructions carefully. Typical courses last 3 to 5 days. Remove chemical media like carbon during treatment. Increase aeration because die-off can reduce oxygen. Watch ammonia and nitrite daily because antibiotics can stress the biofilter. After treatment, perform a large water change of 40 to 50 percent, add fresh carbon to remove residues, and consider re-seeding with a beneficial bacteria product. Do not use antibiotics casually; fix the underlying cause or the bloom will return.
Marine Tanks: Red Slime Treatments and Skimmer Management
Products marketed for red slime (often erythromycin derivatives or similar) are common in reefkeeping. Before dosing, turn off UV and remove carbon. Many products cause your protein skimmer to over-foam; some directions suggest turning the skimmer off or venting it to a waste bucket. Strongly increase aeration. Follow the full treatment time and do not overdose. After treatment, perform a water change, restart carbon, and slowly bring your skimmer back online. Keep a close eye on corals and invertebrates for stress.
Hydrogen Peroxide Spot Treatment
Careful spot dosing can weaken cyanobacteria in both freshwater and marine tanks. Use a syringe to apply small amounts directly onto mats, with filters temporarily off. Typical spot doses range around 1 mL of 3 percent hydrogen peroxide per 10 gallons per session, but always start low, observe livestock, and do not combine with other oxidizers. Wait 10 to 15 minutes, then restart flow. Repeat every few days if needed.
UV Sterilizers: Helpful but Limited
UV sterilizers can reduce free-floating bacteria and algae, but cyanobacteria mostly lives on surfaces. UV can help prevent green water and can contribute to overall stability, yet it will not remove established mats. Use UV as part of a broader plan, not a standalone cure.
Rebuilding the Microbial Community
After a bloom or medication, adding a trusted beneficial bacteria product can help reset the biological balance. These products do not magically fix the problem, but they help your filter and surfaces repopulate with microbes that process waste and compete with cyanobacteria.
Long-Term Prevention and Balance
Target Nutrients, Not Zero Nutrients
In freshwater planted tanks, keep nitrate between 5 and 20 ppm and phosphate between 0.1 and 0.5 ppm. In reef tanks, aim for nitrate between 2 and 10 ppm and phosphate between 0.03 and 0.1 ppm. Avoid chasing zero; zero nitrate with detectable phosphate is a classic cyanobacteria trigger.
Lighting Schedules That Support Balance
For freshwater, 6 to 8 hours of strong light is often enough, especially if plants are not heavily demanding. For reef tanks, use a balanced schedule with ramp-up and ramp-down and avoid excessive white light intensity. Replace old bulbs and adjust LED intensity slowly. Prevent direct sunlight from windows touching the aquarium.
Flow and Circulation Goals
Freshwater community tanks generally do well with 5 to 10 times turnover per hour through the filter and added circulation. Reef tanks usually benefit from 20 to 40 times turnover, depending on coral type. The goal is gentle, consistent movement across all surfaces and the substrate to keep detritus suspended for filtration.
Feeding Practices to Limit Waste
Feed less than you think. For fish, offer amounts that disappear in under a minute and remove uneaten food. For reefs, target feed corals sparingly and avoid overuse of powdered or liquid foods. Rinse frozen foods to avoid adding excess phosphate-rich juices.
Grow Competitors: Plants and Macroalgae
In freshwater, fast growers like stem plants or floating plants help absorb nutrients and shade surfaces. In marine tanks, a refugium with macroalgae like chaetomorpha reduces nutrients and stabilizes the system. Healthy competitors make it harder for cyanobacteria to dominate.
Use Clean Source Water
If your tap water has high phosphate or nitrate, consider RO/DI water. For reef tanks, RO/DI is strongly recommended. For freshwater, RO/DI mixed with a remineralizer gives you control over hardness and pH while reducing unwanted nutrients.
Build a Maintenance Routine
Plan weekly or biweekly tasks: clean prefilters and floss, vacuum substrate sections, wipe glass, change 20 to 30 percent of water, and check flow. Small, regular actions beat big, rare cleanings. Keep a simple log so you can spot trends before problems appear.
Quarantine and Dip New Additions
New plants, rocks, and corals can carry cyanobacteria or other pests. In freshwater, dip plants to remove hitchhikers. In marine tanks, cure rock and quarantine corals when possible. Reducing surprises helps you keep control.
Track Your Tank
Record test results, feeding amounts, dosing, and any changes you make. When blooms happen, notes make it easier to find the cause. Stability is the foundation of a clear tank.
Example Action Plans You Can Follow
7-Day Rescue Plan for Freshwater Tanks
Day 1: Siphon out as much cyanobacteria as possible. Perform a 40 percent water change. Clean filter floss and rinse sponges in tank water. Reduce light to 6 hours. Increase aeration.
Day 2: Test nitrate and phosphate. If nitrate is near zero but phosphate is measurable, lightly dose nitrate to reach about 10 ppm if you keep plants. Feed lightly and remove any decaying leaves.
Day 3: Vacuum another section of substrate. Adjust flow to reduce dead spots. Consider a 2-day blackout if the bloom is still aggressive.
Day 4: If blacking out, keep lights off and maintain aeration. Do not feed or feed very lightly. Ensure fish are not gasping and water temperature is stable.
Day 5: End blackout. Manually remove weakened mats. Perform a 30 percent water change. Replace filter floss if dirty. Consider adding beneficial bacteria.
Day 6: Observe. If cyanobacteria is returning fast, consider a carefully dosed erythromycin course while closely monitoring ammonia and nitrite. Increase oxygenation during treatment.
Day 7: Water change of 40 percent and restore a normal but shorter light schedule. Resume balanced fertilization for plants, keeping nitrate and phosphate in target range. Continue weekly substrate cleaning in sections.
7-Day Rescue Plan for Reef Tanks
Day 1: Siphon cyanobacteria off sand and rock during a 30 to 40 percent water change. Turn off carbon and UV if you plan to medicate later. Clean filter socks and mechanical media. Increase flow across the sandbed.
Day 2: Test nitrate and phosphate. If nitrate is ultra low but phosphate is not, ease back on carbon dosing and nutrient removers. Target nitrate to at least 2 ppm, and avoid stripping phosphate below 0.03 ppm.
Day 3: Gently stir small sand areas and siphon loosened detritus. Reduce white light intensity and total photoperiod for a few days. Keep corals observed for stress.
Day 4: If cyanobacteria remains strong, use a trusted red slime remover at the recommended dose. Turn off UV and remove carbon. Increase aeration and manage the skimmer according to product directions.
Day 5: Continue aeration. Watch fish and inverts closely. Avoid feeding heavily. Check pH and alkalinity remain stable.
Day 6: Perform a 30 to 40 percent water change. Add fresh carbon. Restart UV if you use one. Slowly bring your skimmer back; be prepared for extra foam.
Day 7: Reassess nutrients and flow. Consider adding a refugium light cycle or increasing macroalgae mass. Maintain higher but balanced nutrients rather than zeroing them out.
Common Mistakes to Avoid
Only Treating the Symptom
Scraping slime away without fixing feeding, flow, and nutrient balance leads to quick returns. Always pair removal with root-cause changes.
Overusing Antibiotics
Antibiotics can help but may stress your biofilter. If you use them, increase oxygen, monitor ammonia and nitrite, and follow with large water changes and bacterial re-seeding. Do not repeat treatments back-to-back without investigating causes.
Running Lights Too Long
Extending light hours to enjoy the tank often fuels cyanobacteria. Keep a consistent schedule and avoid direct sunlight.
Ignoring Low Flow Pockets
Dead zones are cyanobacteria’s favorite place. Adjust powerheads and return outlets so waste cannot settle easily. Watch how food and bubbles move to find weak areas.
Starving the Tank of All Nutrients
Chasing zero nutrients harms plants and corals and can give cyanobacteria an edge. Aim for stable, non-zero targets and balance between nitrate and phosphate.
Stirring Without Siphoning
Stirring mats into the water without siphoning spreads spores. Always pair brushing or stirring with active removal and a water change.
Health and Safety Notes
Handle With Care
Some cyanobacteria species can release toxins that irritate skin or harm pets if ingested. Wear gloves during removal, avoid touching your face, and wash hands after maintenance. Keep pets away from siphoned waste and used towels.
Protect Oxygen Levels
Die-offs consume oxygen. Any blackout or medication must be paired with added aeration. Watch for fish breathing fast or gathering at the surface, and respond with immediate water changes and increased air.
Quick Troubleshooting Guide
If It Keeps Coming Back Fast
Re-check feeding and change smaller amounts more often. Confirm that flow reaches the substrate. Verify your test kits are accurate and not expired. In marine tanks, rebalance or pause carbon dosing. In planted tanks, ensure nitrate is not zero and that plants are actively growing.
If Plants or Corals Look Unhappy
Reduce drastic changes and stabilize. Keep light moderate. Ensure nutrients are present but controlled. Address cyanobacteria step by step rather than trying everything at once.
If You Are Unsure About Medication
Give manual removal, cleaning, flow improvement, and light adjustments a full week. Many blooms fade with better husbandry. Medication is a useful tool, but not always necessary.
Conclusion
Win the Battle by Balancing the System
Cyanobacteria blooms are a sign that the aquarium’s balance has tilted. While the slimy mats are the obvious problem, the real solution lies in controlling nutrients, improving flow, and keeping a steady routine. Start by manually removing as much as you can, clean filters and substrate, shorten lighting, and increase aeration. Test water and adjust nitrate and phosphate to healthy, non-zero targets. If needed, use a careful course of treatment, and then rebuild your beneficial bacteria.
With steady habits and small, consistent improvements, cyanobacteria loses its grip. Your plants, corals, and fish will look better, your water will smell clean, and the tank will become easier to maintain. Focus on balance more than quick fixes, and you will not only remove cyanobacteria—you will prevent it from returning.