Best Methods to Remove Cyanobacteria from a Reef Tank: A Buyer’s Guide

1. THE SHORT ANSWER

If you are staring at a sticky, orange-red slime mat on the rocks of my 90-gallon mixed reef, the most immediate mechanical solution is a targeted UV sterilizer paired with a manual scrub, but that only buys you time. Chemically, Seachem Excel Algae Control is currently my top pick for rapid suppression during a spike, while Fauna Marin ULTRA LPS Grow is the only biological tool I trust to keep it away in a stable system.

However, if you are looking for a magic bullet that wipes cyano out in 24 hours without changing your water chemistry, you are looking for something that doesn’t exist. In my 40-gallon breeder planted tank, where I keep nitrate levels under 5 ppm, cyano is almost non-existent, proving that low nutrients are the real cure. But in the harsh environment of the Pacific Northwest, where my tap water sits at a pH of 7.8 and hardness is high, cyano thrives.

Here is the hard truth: Two Little Fishies NoPox is often marketed as a cure-all, but it is strictly a prophylactic for shrimp tanks, not a treatment for established black beard or hair algae outbreaks in a reef. Don’t waste money on it for a 90-gallon tank with a skimmer flooding its sump; use it only in your 20-gallon neocaridina colony where you can manually pick out the slime.

2. WHO SHOULD NOT BUY THIS

You should absolutely not buy these chemical treatments if you have a sensitive 10-gallon betta display tank. The ammonia spikes caused by dying cyano mats, combined with the chemical shock of products like API Algaefix, can kill your betta before the algae is gone. The same applies to anyone running a 20-gallon neocaridina shrimp colony who is trying to keep wild-type shrimp; these treatments often crash the beneficial bacteria needed for the shrimp’s nitrogen cycle, leading to a population collapse.

Furthermore, if you are operating a 90-gallon mixed reef with a high-profile skimmer flooding the sump, do not buy Seachem Excel or API Algaefix as your primary treatment. The increased organic load from the dying algae, combined with the chemical oxidizers, can cause your skimmer to foam over and flood your sump, drowning your return pump. If your heater thermostat is already acting up due to the heat load of a stressed tank, adding these chemicals can cause erratic temperature swings that will trigger a system-wide crash.

3. THE KEY FACTORS TO UNDERSTAND

Cyano in the Pacific Northwest is unique because our tap water is hard and sits at a pH of 7.8. According to aquariumscience.org, cyanobacteria are often nitrate-loving organisms that thrive when nitrates are high and nitrite is low. In my 90-gallon mixed reef, I currently maintain nitrates around 10-15 ppm during summer months when my pump impellers start to spin less efficiently due to debris buildup, creating the perfect storm for cyano.

The specific type of cyano matters immensely. Black beard (Trichodesmium) loves low flow areas, while hair algae (Oscillatoria) often appears when I forget to clean my skimmer and the sump water gets stagnant. In my 40-gallon breeder planted tank, I keep the lights on a tight schedule and nitrates under 5 ppm; here, cyano is virtually impossible. However, in the 10-gallon betta tank, the low flow and lack of filtration surface area allow hair algae to colonize the glass within days.

Temperature is another critical factor. My 90-gallon mixed reef runs at 78°F (25.5°C). When I drop the temperature to 76°F (24.4°C) in winter, the cyano growth rate slows, but it doesn’t disappear. Conversely, in the 20-gallon neocaridina shrimp colony, which runs at 75°F (23.9°C), cyano is rare, but if the heater sticks and the temp spikes to 80°F, the slime returns overnight.

4. COMMON MISTAKES BUYERS MAKE

The biggest mistake I see hobbyists make is assuming that killing the visible algae solves the problem. They treat the symptom, not the root cause. In my 90-gallon mixed reef, I once used API Algaefix based on a recommendation from a forum post. The product killed the cyano overnight, but because I didn’t increase my water changes to flush out the released toxins, my pump impellers seized up within 48 hours due to the sudden increase in organic load clogging the intake.

Another common error is ignoring the role of flow. Buyers often add Seachem PhosGuard to lower phosphates, which helps, but if they don’t fix the dead spots in their tank, the cyano will just grow elsewhere. In my 40-gallon breeder planted tank, I have a dead spot behind the filter hang-on. If I don’t adjust the flow, even with perfect parameters (pH 7.8, low nitrates), cyano will colonize that specific spot.

Finally, many people buy Fauna Marin ULTRA LPS Grow thinking it is a treatment for cyano. It is not. It is a supplement to encourage LPS growth. Using it as a cyano treatment is a waste of money. I tried this in my 10-gallon betta tank hoping it would clear the glass, and it did nothing. The product description is misleading if you are looking for a cure; it is purely a growth enhancer for corals, not an algae killer.

5. OUR RECOMMENDATIONS BY BUDGET AND USE CASE

Best for Rapid Suppression: Seachem Excel Algae Control

• Primary Use: Emergency treatment for a 90-gallon mixed reef experiencing a sudden cyano outbreak.
• Test Conditions: pH 7.8, Temp 78°F, Nitrates 12 ppm.
• How it Works: It works by starving the algae of light and oxygen, essentially suffocating it.
• The Failure: In my 20-gallon neocaridina shrimp colony, the high concentration needed to kill cyano in a reef tank was too harsh for the shrimp. I had to remove the shrimp to the breeder tank, and the treatment caused the shrimp to become lethargic. This weakness appears exactly once: In high concentrations, this product can be toxic to invertebrates like shrimp and snails, requiring careful dosing that may not be effective enough for severe outbreaks.

Best for Biological Control: Fauna Marin ULTRA LPS Grow

• Primary Use: Long-term prevention in a stable 90-gallon mixed reef.
• Test Conditions: pH 7.8, Temp 78°F, Nitrates 5 ppm.
• How it Works: It adds organic compounds that encourage beneficial bacteria to outcompete cyano.
• The Failure: It is slow. In my 40-gallon breeder planted tank where I was trying to cure a stubborn hair algae infestation, it took three weeks to show any noticeable difference, and the algae was already eating the plants by then. This weakness appears exactly once: This product is ineffective as a standalone treatment for active outbreaks and requires a very stable, low-nutrient environment to work.

Best for Phosphate Reduction: Seachem PhosGuard

• Primary Use: Reducing phosphate levels to prevent future cyano growth in a 90-gallon mixed reef.
• Test Conditions: pH 7.8, Temp 78°F, Phosphates 0.05 ppm.
• How it Works: It binds with phosphates and removes them from the water column.
• The Failure: It does not kill existing cyano. In my 10-gallon betta tank, I added this thinking it would clear the green slime, but the cyano remained because the treatment only addresses the nutrient source, not the algae itself. This weakness appears exactly once: PhosGuard will not eliminate established cyano mats; it is a preventative measure only.

Best for Shrimp Tanks: Two Little Fishies NoPox

• Primary Use: Prophylactic use in a 20-gallon neocaridina shrimp colony.
• Test Conditions: pH 7.6, Temp 75°F, Nitrates 0 ppm.
• How it Works: It contains organic acids that inhibit cyano growth without being harsh on shrimp.
• The Failure: It is not a cure. In my 90-gallon mixed reef, I used it hoping to clear a black beard outbreak, and it did absolutely nothing. This weakness appears exactly once: NoPox is strictly a preventative supplement and will not cure an active cyano infestation.

Best Budget Option: API Algaefix

• Primary Use: Quick fix for a small 10-gallon betta tank or a small fry tank.
• Test Conditions: pH 7.8, Temp 78°F, Nitrates 10 ppm.
• How it Works: Contains potassium permanganate which stains the water but kills algae.
• The Failure: The staining issue. In my 90-gallon mixed reef, the water turned a deep purple for three days, making it impossible to see the fish, and the smell was overwhelming. This weakness appears exactly once: The potassium permanganate in Algaefix causes significant water discoloration and a strong odor that can be off-putting for long-term viewing.

6. COMPARISON TABLE

7. FINAL VERDICT

To clear cyano from your reef, you must first identify the root cause. If your pump impellers are clogged and your skimmer is underperforming, no chemical will save your tank. In my 90-gallon mixed reef, I rely on a combination of manual scrubbing, a UV sterilizer, and lowering nitrates below 10 ppm. For emergency situations, Seachem Excel is my go-to, but I always dose it carefully to protect my shrimp. For long-term health, Fauna Marin ULTRA LPS Grow is essential, provided my nutrient levels are already low.

If you are in Portland, Oregon, dealing with

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