My new tank is covered in brown/green/red algae — is something wrong?
When: During and shortly after cycling — the first 3-6 months of a new tank
Short answer: Almost certainly nothing is wrong. Every new reef tank goes through the "ugly phase" — a normal, expected 3–6 months of brown, green, and sometimes red blooms as the system matures and finds balance. It looks like failure and it isn't. The worst thing you can do is panic and start ripping the tank apart; that usually makes it last longer.
The details — what you're seeing, in order
Diatoms (brown film) — weeks 1–3. A brown dusty film on glass, sand, and rock. Caused by silicates leaching from new dry rock, new sand, or lower-quality source water. Self-limiting: do essentially nothing. Wipe the glass, let snails graze it, and it fades in 2–4 weeks. If it persists past two months, test your RO/DI water for silicates.
Cyanobacteria (red slime) — weeks 3–6. Red, purple, or black slimy sheets, sometimes with bubbles and a musty smell, in low-flow, detritus-heavy spots. Fix the cause: increase flow to kill dead spots and siphon it out during water changes. Spot-treat stubborn patches with 3% hydrogen peroxide by syringe. Chemical removers (Chemiclean) treat the symptom, not the cause.
Green hair algae (GHA) — weeks 4–8. Green filamentous algae on the rocks, fueled by the elevated nutrients a young tank leaches. Manual removal, add herbivores (turbo snails, emerald crabs, urchins), and be patient — it recedes as nutrient export matures.
Dinoflagellates (dinos) — weeks 4–12, not every tank. Brown/golden stringy "snot" with bubbles that often disappears at night and returns after lights on. Counterintuitively, dinos are a too-clean-water problem. If yours are the substrate-attached type: raise nutrients (nitrate to 10–15 ppm, phosphate to 0.08–0.1 ppm), do a 3-day blackout, dose diverse bacteria, and add a carbon source for a week. Free-swimming dinos respond to strong UV.
The numbers
| Bloom | Typical onset | Duration | What to do |
|---|---|---|---|
| Diatoms | Weeks 1–3 | 2–4 weeks | Nothing; wipe glass, let snails graze |
| Cyanobacteria | Weeks 3–6 | 2–8 weeks | More flow, siphon out |
| Green hair algae | Weeks 4–8 | 4–12 weeks | Manual removal + herbivores + patience |
| Dinoflagellates | Weeks 4–12 (some tanks) | 2–8 weeks | Raise nutrients / UV / blackout |
| Whole ugly phase | Starts week 1–2 | 3–6 months total | Patience |
Common mistakes
- Panicking and "resetting" the tank. Tearing down rock, deep-cleaning, big chemical interventions — this destabilizes the young system and prolongs the ugliness.
- Chasing zero nutrients. Ultra-clean water invites dinos, which are harder to beat than ordinary algae. A little nitrate and phosphate is healthy.
- Skipping a clean-up crew. Snails and hermits are your unpaid diatom/algae labor.
When to worry
- Normal: Brown, then a bit of green, then some red slime, over the first few months. This is the tank maturing. As Reef Builders puts it: *"it is not time to panic or rush as that typically only makes things worse."*
- Worry: Blooms that are still worsening after ~6 months, or dinos smothering coral — those warrant a targeted plan (source-water test, nutrient management, UV), not a teardown.
What's next
Keep going: a clean-up crew is the first livestock you add — first-steps-after-cycling.
- Reacting to normal algae by tearing down the tank or dosing chemicals in a panic
- Reef Tank Cycling Research (internal)
- Reef Builders — Managing the Ugly Stage of a New Reef Tank