1. Diatoms, The New Tank Brown Film

Diatoms are the first algae almost every reef tank experiences, and the one
beginners panic about most unnecessarily. They appear as a brown, rust-colored,
or tan powdery film covering the sand, glass, and rock surfaces, typically
starting 2–4 weeks after setup and clearing on their own 4–8 weeks later.

What Causes Them

Diatoms are silica-based organisms, they build their cell walls from dissolved
silicate. New tanks have elevated silicate from several sources: fresh aragonite
sand leaching silicates, tap water used for mixing (if not using RODI), and
uncured rock releasing dissolved minerals. Diatoms exploit this temporary
silicate availability and colonize every surface.

As the tank matures, silicate is consumed, the RODI water used for top-offs
and water changes contains no new silicate to replenish it, and the diatom
population collapses. Competing algae and the clean-up crew then consume
the remaining diatoms.

How to Identify Them

• Brown, tan, or rust-colored film, wipes off glass easily and smears rather than scraping
• Appears on sand, glass, and rock simultaneously
• Appeared in the first 2–6 weeks of the tank’s life
• Sand looks uniformly brown rather than white or cream
• No smell

What to Do

Mostly: wait. Diatoms in a new tank are a maturation phase, not a problem
requiring intervention. Specific actions that help:

• Confirm you’re using RODI water, tap water continuously replenishes silicate and can extend the diatom phase for months. If using tap water, switch to RODI immediately.
• Add a clean-up crew after cycling, turbo snails, cerith snails, and nassarius snails consume diatoms aggressively. A 20-gallon tank with 15–20 snails will clear a diatom bloom noticeably faster than a tank without them.
• Wipe the front glass weekly, doesn’t prevent diatoms but keeps the tank visible while the phase passes.
• Don’t add GFO or chemical treatments, diatoms clear on their own. Adding GFO at this stage crashes phosphate which can trigger dinoflagellates, a far more difficult problem.

Timeline

4–10 weeks from first appearance to clearing. If diatoms persist beyond
10–12 weeks in a tank running RODI water, test the RODI output for silicate, a depleted DI resin can allow silicate through even when TDS reads low.

2. Green Hair Algae, The Nutrient Problem Made Visible

Green hair algae (GHA) is the most common persistent algae problem in
established reef tanks. It grows as bright green filaments, from a few
millimeters to several centimeters long, on rock, the glass, sand edges,
and the base of corals. In a heavy outbreak, it covers the entire rockwork
in a green carpet that smothers corals and makes the tank look neglected.

GHA is a direct indicator of elevated nitrate and/or phosphate. It doesn’t
appear in tanks with genuinely low, stable nutrients, it grows because
the nutrient load is feeding it. This is the most important thing to
understand about GHA: removing it manually without addressing the nutrient
cause produces regrowth within days.

What Causes It

• Elevated nitrate (above 5–10 ppm in a reef)
• Elevated phosphate (above 0.05 ppm)
• Overfeeding, the most common root cause in beginner tanks
• Insufficient nutrient export, skimmer not performing, filter floss not changed frequently enough, infrequent water changes
• Tap water use, adds nitrate and phosphate with every top-off and water change
• Too-long photoperiod, 14+ hour lighting fuels algae growth

How to Identify It

• Bright green, individual filaments, not a flat film, distinct strands
• Can be pulled off rock by hand and comes away in clumps
• Grows on rock surfaces, around coral bases, on glass
• Returns quickly after manual removal if nutrients are not addressed
• Test: nitrate above 10 ppm and/or phosphate above 0.05 ppm confirmed

How to Get Rid of It, Address the Source First

1. Test nitrate and phosphate. Get specific numbers.
   GHA typically appears when nitrate is above 5–10 ppm or phosphate is
   above 0.05 ppm. You need to know where you are before you can track
   improvement.
2. Reduce feeding. If you’re feeding once or twice per day,
   reduce to small amounts 2–3x daily, only what fish consume in 2 minutes.
   Skip one day per week. Thaw frozen food in a cup and strain the liquid
   (which is high in phosphate) before adding the food to the tank.
3. Replace filter floss immediately and then every 5 days
   going forward. Old filter floss is a net nutrient source, it adds
   phosphate and nitrate back to the water faster than it removes them.
4. Increase water change frequency temporarily, 10–15%
   twice per week until nitrate and phosphate are back in range. Then return
   to bi-weekly once stable.
5. Check skimmer output. A skimmer running wet or producing
   minimal skimmate is failing to export dissolved organics. Adjust the
   output valve, clean the neck, and verify the operating water depth is
   correct.
6. Reduce photoperiod to 10 hours maximum while the outbreak
   is active. GHA needs light to grow, less light slows its growth rate
   while you address nutrients.
7. Manually remove GHA by hand or with a toothbrush once
   nutrients are trending down. Remove as much as possible physically, this reduces the biomass that nutrients have to feed and accelerates the
   clearing. Siphon the removed algae out with the water change.
8. Add a clean-up crew that eats GHA, emerald crabs,
   turbo snails, sea hares, and lawnmower blennies all consume GHA actively.
   They’re a complement to nutrient reduction, not a substitute for it.

Timeline to Resolution

4–8 weeks with consistent nutrient reduction and weekly manual removal.
GHA that’s been present for months in a heavily nutrient-loaded tank can
take 2–3 months to fully clear. Tanks that address nutrients aggressively
and early clear significantly faster.

Why It Keeps Coming Back

If GHA returns within days of manual removal, nutrients have not been
adequately addressed. Test again. The return rate of GHA is a direct
measure of how much excess nutrient the tank is carrying, fast regrowth
means significant excess. Very slow regrowth means you’re close to the
right balance.

3. Cyanobacteria, The Red Slime That Isn’t Actually Algae

Cyanobacteria (cyano) is technically a photosynthetic bacteria, not an
algae, but it behaves like one and is treated as an algae problem in
reef keeping. It appears as a red, dark maroon, purple, or occasionally
blue-green slimy sheet that covers the sandbed, rock surfaces, and low-flow
areas of the tank. It lifts off in sheets when disturbed and has a
distinctive unpleasant smell.

Cyano is one of the more persistent reef tank problems because it has
multiple possible causes that aren’t always obvious, and because the
same conditions that produce it also make other approaches less effective.

What Causes It

• Low flow / dead spots, the most common cause. Cyano thrives in areas of minimal water movement. It’s almost always most severe in the areas of the tank with the least circulation.
• Elevated nutrients, particularly elevated dissolved organic carbon (DOC), nitrate, and phosphate
• Imbalanced nutrient ratio, specifically, low nitrate relative to phosphate. Cyano can fix its own nitrogen from the water, meaning it can thrive even when nitrate is low if phosphate is elevated. This is why cyano sometimes appears in ultra-low-nitrate tanks that seem otherwise clean.
• New tank maturation, cyano is extremely common in the first 2–4 months of a new tank as the biological system establishes
• Old or insufficient substrate, a sandbed that hasn’t been disturbed in years can develop anaerobic pockets that contribute to cyano formation at the surface

How to Identify It

• Red, dark maroon, or purple slimy coating, distinct from brown diatoms which are a dry film
• Lifts off surfaces in sheets when disturbed by a powerhead or siphon
• Distinctive musty, unpleasant smell
• Air bubbles sometimes trapped underneath the sheet
• Returns to the same low-flow spots after removal
• May cover large areas of sand surface overnight

How to Get Rid of It

1. Increase flow in affected areas. This is the first and most
   important intervention. Reposition the wavemaker to direct more flow toward
   the cyano-affected areas, or add a small secondary powerhead aimed at
   persistent spots. Cyano cannot establish on surfaces with adequate water movement.
2. Physically remove it with a siphon during water changes, target cyano-covered areas directly and siphon it out. Don’t blow it around
   with a powerhead unless you’re simultaneously siphoning, dispersed cyano
   spores settle in new locations and expand the outbreak.
3. Increase water change frequency, 10% twice per week
   for 3–4 weeks to export nutrients.
4. Check and improve skimmer output, cyano is strongly
   associated with elevated dissolved organics that a well-functioning
   skimmer should be removing.
5. Reduce photoperiod to 8–10 hours temporarily while
   the outbreak is active.
6. If cyano persists after 4–6 weeks of the above:
   consider a targeted treatment with Chemiclean (Boyd Enterprises) or
   a similar cyano-specific treatment. Follow the instructions precisely, Chemiclean requires removing activated carbon during treatment and
   running heavy aeration. It’s effective but should be a last resort
   after addressing flow and nutrients, not a first response.

Why Cyano Is Especially Difficult

Cyano can fix atmospheric nitrogen from the water, meaning it can feed itself
even when nitrate is very low. A tank that crashes nitrate to undetectable
levels without managing phosphate and DOC may actually make cyano worse by
removing nitrate competition while phosphate remains. If cyano appears in a
tank with very low nitrate, the fix may be slightly raising nitrate (to 2–5
ppm) while simultaneously reducing phosphate, rebalancing the ratio rather
than simply reducing all nutrients.

4. Bubble Algae, Controlled Removal Is Everything

Bubble algae (Valonia and related species) appears as round, shiny green
bubbles attached to rockwork, frag plugs, and epoxy. Individual bubbles
range from 2mm to 20mm in diameter. It’s not toxic and doesn’t directly
harm corals or fish, but left unmanaged, it spreads across rockwork,
gets between coral frags and their substrate, and eventually occupies
significant rock surface area that corals can’t colonize.

What Causes It

Bubble algae is almost always introduced with live rock, frags, or corals
from another tank or a fish store. It doesn’t spontaneously generate, it arrives as spores or small colonies and establishes on the rockwork.
Elevated nutrients encourage its spread but don’t cause initial colonization.

How to Remove It, The Most Important Detail

Bubble algae removal technique matters enormously. Each bubble is a single
large cell containing thousands of reproductive spores. A bubble
that’s popped or crushed inside the tank releases those spores directly
into the water, spreading the outbreak far more aggressively than
if the bubble had been left alone.

1. Remove the bubble intact, use tweezers or your fingers to peel it off the rock at its attachment point without puncturing it
2. Place it directly into a container or bag before removing it from the tank, don’t let it float free in the water column
3. Dispose of it outside the tank, not back in with the siphon water
4. For bubbles that are inaccessible or likely to pop during removal, consider removing the affected rock from the tank and scrubbing it in saltwater outside the display before returning

Biological Control

Emerald crabs (Mithraculus sculptus) eat bubble algae and are one of the
most effective biological controls available. Add 1–2 emerald crabs per
20 gallons in a tank with an active bubble algae problem. They’re
reef-safe in most cases, the occasional individual develops a taste for
coral tissue, which is unusual but worth monitoring.

Ongoing Management

Bubble algae rarely disappears completely once established, the goal is
keeping the population small through regular manual removal and biological
control. Inspect rockwork during weekly maintenance and remove any new
bubbles before they grow large enough to be difficult to extract intact.

5. Turf Algae, The Stubborn One

Turf algae grows as a dense, short, matted layer of filamentous algae on
rock surfaces, typically appearing after a green hair algae phase as the
tank matures. It looks like a rough, carpet-like coating in shades of green,
brown, or grey. Unlike GHA which can be pulled off in clumps, turf algae is
anchored into the rock surface and requires mechanical removal.

What Causes It

Turf algae is driven by the same elevated nutrients as GHA, but it’s more
physically resilient and harder to remove because its holdfasts penetrate the
rock surface. It typically appears in established tanks where GHA has been
present for a while and where the algae population has shifted to a more
established, lower-growth form.

How to Remove It

• Mechanical scrubbing: Use a stiff-bristled toothbrush or a wire brush to scrub affected rock surfaces. This must be done in tank water, scrubbing in air kills the rock’s biological function. The scrubbing loosens the algae from its holdfast so it can be siphoned out.
• Scrub and immediately siphon, scrub a section of rock and immediately siphon the dislodged material out of the water before it can resettle. Do this section by section during water changes.
• Sea hares (Dolabella auricularia) are among the most effective biological controls for turf algae, large, fast-moving herbivores that consume turf algae rapidly. They require return to a fish store or trade after the algae is consumed as they typically starve in tanks without sufficient algae.
• Urchins (tuxedo urchins, long-spine urchins) graze rock surfaces continuously and are effective long-term turf algae controls, but they’ll also rearrange your rockwork and can damage coral if they knock things over.

Why It’s Harder Than GHA

Turf algae’s anchoring system means nutrient reduction alone doesn’t clear it
once established, the physical biomass is attached and doesn’t die off
quickly even when nutrients drop. Manual removal combined with nutrient
reduction is required. Expect 2–4 months of regular scrubbing to clear
a significant turf algae infestation.

6. Dinoflagellates, The Most Difficult Reef Algae Problem

Dinoflagellates (dino) are the most difficult algae problem in reef keeping
and the most commonly misidentified. They appear as a golden-brown, stringy
or mucus-like coating with visible air bubbles trapped inside or underneath, covering the sand surface, glass, and rock with a slimy film that looks
partially transparent and bubbly. Some species are toxic to fish and corals.

Dino is paradoxically a problem of too little nutrients rather than
too many, it thrives in ultra-low nutrient environments where it has less
competition from other algae. This is what makes it so counterintuitive and
why the standard “reduce nutrients” advice that works for GHA and cyano
often makes dino worse.

What Causes It

• Ultra-low nutrient environments, tanks where nitrate and phosphate have been driven to undetectable levels through aggressive GFO use, heavy skimming, and minimal feeding
• New tanks, sometimes appears during initial maturation before the full microbial community establishes
• Imbalanced microbial diversity, dino appears when the competitive microbial community that would normally outcompete it is absent or suppressed
• Extended high-intensity lighting, dino is photosynthetic and long photoperiods give it more energy than competitors in nutrient-poor conditions

How to Identify It

• Golden-brown, translucent, slimy or stringy coating, distinct from the opaque brown of diatoms
• Air bubbles visible inside or trapped underneath the film, a distinctive feature
• Appears to disappear at night and reform during the day (strongly photosynthetic)
• Lifts off in stringy sheets rather than the flat sheets of cyano
• Sand grains may appear to be coated and slightly raised from the surface
• May cause corals to close or fish to show mild irritation if toxic species are present
• Nitrate and phosphate test at or near zero in affected tanks

How to Treat It, The Opposite of Most Algae Advice

Dino treatment is counterintuitive because the cause is different from
other algae. The goal is to raise nutrients slightly and increase microbial
competition, not reduce nutrients further.

1. Remove GFO immediately if running it. GFO-driven phosphate
   crash is one of the most common dino triggers. Stop all phosphate removal
   media.
2. Increase feeding, deliberately raise nitrate to 2–5 ppm
   and phosphate to 0.02–0.05 ppm. Test daily to track where parameters are
   moving. The goal is a low but detectable nutrient level, not zero.
3. Blackout treatment: Turn off all lights for 3 consecutive
   days. Dino is photosynthetic and a blackout starves it of energy while
   non-photosynthetic competitors survive. This is often the most effective
   single intervention, but it requires temporarily removing corals or
   supplementing them with a coral food during the blackout.
4. Increase microbial diversity, add a bottle of diverse
   bacteria inoculant (Prodibio, Brightwell MicroBacter7) to reintroduce
   competing microbial populations that suppress dino.
5. Manual siphoning during lights-on period, dino floats
   toward the light surface during the day. Siphon it out aggressively
   during this window daily.
6. Raise pH above 8.3 temporarily, higher pH (8.4–8.5)
   is hostile to many dino species. Kalkwasser dripped in the evening
   raises the pH peak without crashing alkalinity.
7. UV sterilization, running a UV sterilizer on a recirculating
   line kills free-floating dino cells and significantly reduces population
   between manual removals.

Timeline

Dino outbreaks are measured in months, not weeks. Most successful treatments
take 6–12 weeks of consistent intervention before the population collapses.
Partial improvement followed by regression is common, persistence is required.
If dino is confirmed toxic (fish flashing, corals closing in affected areas,
visible slime on fish), increase urgency of treatment and consider a temporary
removal of affected livestock to a quarantine tank.

7. Coralline Algae, The One You Want

Coralline algae is calcified encrusting algae that grows as pink, purple,
lavender, or white hard crusts on rockwork, the back glass, and equipment
surfaces. It’s a positive indicator of tank health, it requires stable
alkalinity, calcium, and magnesium to calcify properly, and its presence
confirms the chemistry is where it needs to be.

Coralline also outcompetes nuisance algae for rock surface area, a rockwork
heavily colonized by coralline has less surface available for GHA, turf algae,
and cyano to establish.

How to Encourage It

• Maintain alkalinity at 8–10 dKH, calcium at 400–450 ppm, and magnesium at 1250–1350 ppm, the same parameters that keep corals healthy
• Use rock that arrives pre-seeded with coralline, live rock from established reef systems arrives with coralline already present; it spreads to new rock surfaces over weeks to months
• Don’t scrape the back glass, let coralline colonize it freely as a natural background
• Scrape only the front viewing glass with a razor blade; leave side glasses and back glass alone

Coralline Turning White

Coralline that bleaches from purple/pink to white is losing its zooxanthellae, usually from elevated alkalinity, low magnesium, or pH instability. Test all
three parameters and correct. White coralline will recolor once chemistry is stable.