A slimy blue-green sheet is creeping across your substrate, climbing plant leaves, and smelling faintly like a swamp. This isn't algae at all — it's cyanobacteria, ancient photosynthetic bacteria masquerading as algae, and it plays by bacterial rules. That changes the treatment completely: what works on true algae often fails on cyano, and what kills cyano (antibiotics) would be absurd against algae. Identify it correctly, treat it as bacteria, fix the low-flow and organic conditions it exploits, and it leaves.
Identifying Cyanobacteria: The Three Tests
Test 1: Appearance
Cyano forms flat, slimy sheets or mats in blue-green, dark green, or sometimes reddish-brown. It spreads across substrate like a carpet, climbs glass in sheets, and coats plant leaves in a slimy film. Early colonies look like dark smudges; mature mats develop visible texture and may trap oxygen bubbles underneath (photosynthesis bubbles caught in the slime).
Test 2: The smell
Peel up a patch and sniff it. Cyanobacteria smells distinctly swampy, musty, or earthy — unmistakable once you've smelled it. No true aquarium algae smells like this. If it stinks like a pond, it's cyano.
Test 3: The peel
Cyano mats peel off in sheets, like wet tissue paper lifting off a surface. True algae smears, crumbles, or resists; cyano lifts as a coherent slimy layer. If it peels, it's bacterial.
Rule out: diatoms (brown dust, no sheets, no smell — see our diatom guide), green dust algae (thin film on glass, no mats, no smell — our GDA guide), and green spot algae (hard spots, not slime).
Why Cyanobacteria Appears: The Cause Map
Low flow / dead spots (the primary trigger)
Cyano thrives where water barely moves — behind hardscape, in carpet corners, along the front glass where the filter current doesn't reach. Stagnant micro-zones let it establish undisturbed. Tanks with a single gentle filter and dense hardscape are classic victims. If your cyano is always in the same still areas, flow is your problem.
Excess dissolved organics
Overfeeding, decaying plant matter, detritus-choked substrate, infrequent water changes — cyano feeds on dissolved organic waste more directly than true algae does. Neglected tanks get cyano; well-maintained tanks rarely do.
Low nitrates (the paradox)
Counterintuitively, cyano often blooms when nitrates read zero. Many cyanobacteria species fix atmospheric nitrogen, so they thrive precisely where true algae and plants starve for nitrogen. The ultra-lean, "clean" tank with undetectable nitrates is paradoxically vulnerable. If your nitrates are zero and cyano appears, the fix includes adding nitrogen — see our nitrogen deficiency guide.
Old or depleted substrate
Exhausted aquasoil or compacted, anaerobic substrate pockets release the organic compounds cyano loves. Deep, never-vacuumed gravel beds are reservoirs.
New tanks
Cycling and recently cycled tanks get cyano during the instability window — fluctuating bacteria, unsettled plants, immature flow patterns. Usually self-resolving as the tank matures, provided maintenance is consistent.
Treatment Protocol: Phase by Phase
Phase 1 — Manual removal (immediate)
- Peel and siphon every visible mat. Use the siphon to lift sheets — they come up easily. Do this before any chemical step; dead cyano rotting in the tank feeds the next wave.
- Gravel-vacuum the substrate thoroughly, especially under and around where mats grew. You're removing the organic reservoir.
- Trim smothered leaves — leaves coated in cyano slime rarely recover; remove them to export the biomass.
- Repeat every 2–3 days. Cyano regrows fast; stay ahead of it.
Phase 2 — Fix flow and organics (week 1)
- Eliminate dead spots: reposition the filter outlet, add a small circulation pump, or rearrange hardscape that's blocking flow. Every square centimeter should see gentle water movement.
- Deep-clean gently: vacuum detritus, rinse mechanical filter media in old tank water, remove decaying plant matter. Don't sterilize the biofilter — just remove the organic load.
- Increase water changes to 40–50% weekly during treatment. Dilution is your friend.
- Feed less: what fish eat in 60 seconds, once daily, until cyano is gone.
Phase 3 — Correct nitrates (week 1)
- Test nitrates. If zero (or near-zero) in a planted tank, dose nitrogen to maintain 5–10 ppm. This single step resolves a surprising number of cyano cases — you're removing its nitrogen-fixing advantage.
- Maintain complete fertilization otherwise; starving the tank helps nothing.
Phase 4 — Blackout (if phases 1–3 stall after 2 weeks)
A 3-day total blackout (tank fully covered, zero light) kills cyano effectively — bacteria have minimal energy reserves compared to plants. Keep filter and heater running, add an air stone, don't feed. After uncovering, do a large water change and siphon the dead mats. Plants tolerate 3 days of darkness well.
Phase 5 — Antibiotics (last resort)
Erythromycin kills cyanobacteria reliably because — remember — it's bacteria. But it's the nuclear option:
- It can harm your biofilter — the nitrifying bacteria are bacteria too. Dose precisely, monitor ammonia daily for two weeks after.
- It contributes to antibiotic resistance — a genuine ecological concern, not just hobbyist hand-wringing.
- It treats the symptom; cyano returns if flow, organics, and nitrates aren't fixed.
- Use only after manual + flow + nitrate correction + blackout have all failed, and only with a plan to fix the underlying causes simultaneously.
Hydrogen peroxide spot-treatment has limited effect on cyano — it damages surface mats but rarely penetrates to the base layer. Manual removal plus cause-correction outperforms chemicals here. And if your tank is fighting multiple issues at once — say cyano mats plus the leaf damage described in our plants dying after water changes guide — fix water quality first; everything else gets easier with clean, stable water.
Spot-treats cyanobacteria mats directly in the phase-by-phase protocol: 3% hydrogen peroxide.
Siphons the loosened cyano mats out of the tank during treatment: Aqueon siphon vacuum.
Cyanobacteria and Livestock Safety
Some cyanobacteria species produce cyanotoxins harmful to fish, shrimp, and even humans in sufficient concentration. In aquariums, severe, long-standing mats have been linked to livestock stress and unexplained deaths. Practical guidance:
- Don't let mats grow unchecked for weeks — remove them.
- If fish show distress (gasping, lethargy) coinciding with a heavy bloom, prioritize removal and water changes.
- Wash hands after handling mats. Don't ingest tank water during a bloom (good advice generally).
- The risk in typical hobby tanks is low, but it's real enough to treat cyano promptly rather than tolerating it.
Detoxifies ammonia/nitrite released when the cyano dies back: Seachem Prime.
Prevention: The Cyano-Proof Tank
- Flow everywhere — the single best prevention. No dead spots, no cyano footholds.
- Keep nitrates detectable — 5–20 ppm in planted tanks. Zero nitrates invite nitrogen-fixers.
- Regular detritus removal — vacuum visible waste, trim decaying leaves, don't let organics accumulate.
- Consistent water changes — 30% weekly, without fail. Skipped maintenance is the most common cyano invitation.
- Don't over-clean the biofilter — a crashed bacterial colony creates the instability cyano exploits. Rinse media gently, never replace it all at once.
Cyanobacteria in Shrimp Tanks
Shrimp tanks deserve special caution with cyano. Shrimp graze biofilm constantly, and they'll graze cyanobacteria mats too — ingesting whatever cyanotoxins the colony produces. While most hobby cyano strains are mildly toxic at worst, unexplained shrimp deaths coinciding with a heavy bloom should make you suspect the mats, not just water parameters.
Treatment adjustments for shrimp tanks: manual removal and flow fixes are unchanged and completely shrimp-safe. Blackouts are safe (shrimp handle darkness fine for three days). But be extra conservative with any chemical step — shrimp are far more sensitive to erythromycin's biofilter side effects than fish are, because even a minor ammonia spike is lethal to them. If you must use antibiotics in a shrimp tank, have a cycled quarantine container ready as a livestock refuge during treatment and recovery. In practice, shrimp keepers clear cyano with flow, vacuuming, and nitrate correction alone in the vast majority of cases — the nuclear option is rarely needed.
Frequently Asked Questions
Is blue-green algae actually algae?
No — cyanobacteria are photosynthetic bacteria, among Earth's oldest life forms. The misnomer stuck because they look and behave like algae in the aquarium. The distinction matters practically: algaecides target algae biochemistry and often fail on cyano, while antibacterial approaches (erythromycin) work on cyano but would be pointless against true algae. Identify first, then treat accordingly.
Will cyanobacteria kill my aquarium plants?
It smothers rather than poisons. Mats block light from leaves and trap detritus against them, causing the covered foliage to melt — which releases organics that feed more cyano. Remove mats promptly and trim smothered leaves; healthy uncovered growth recovers quickly. Long-ignored cyano can defoliate slow growers like anubias, so don't wait.
Why does cyanobacteria keep coming back in the same spot?
Because the conditions in that spot haven't changed — it's still a low-flow, detritus-collecting zone, possibly still at zero nitrates. Recurrence in one location is diagnostic: fix the flow to that specific area (redirect an outlet, add a nano pump, move the hardscape creating the eddy) and the cyano loses its foothold. Treating the mat without treating the spot guarantees a sequel.
Can I use a UV sterilizer against cyanobacteria?
Minimally effective. UV kills free-floating organisms, but cyano lives in attached mats — the sterilizer never touches the colony. UV helps prevent spread via waterborne cells during manual removal, but it won't clear an established mat. Spend the effort on flow, organics, and nitrates instead.
Is erythromycin safe for shrimp and snails?
Erythromycin at cyano-treatment doses is generally tolerated by shrimp and snails, but the biofilter risk threatens everything in the tank — an ammonia spike from damaged nitrifying bacteria kills shrimp faster than the antibiotic ever could. If you must use it, dose exactly, test ammonia and nitrite daily for two weeks, and have Prime or equivalent ready. And fix the underlying causes simultaneously, or you'll repeat the treatment.
Treat the Bacteria Like Bacteria
Cyanobacteria loses its mystery once you stop thinking of it as algae. It's a bacterium exploiting still water, organic waste, and zero nitrates — so you beat it with flow, cleanliness, and detectable nitrogen, backed by relentless manual removal. The keepers who clear cyano fastest aren't the ones with the strongest chemicals; they're the ones who aimed a powerhead at the dead spot and started vacuuming like they meant it.