Fluconazole: The Aquarium Algae Magic Bullet

Fluconazole: Aquarium Algae Killer That Works

Aquarists around the world, rejoyce! After years of struggling to find a treatment for just about all aquarium algae types. Have you ever tried an effective aquarium algae cleaner that worked? Have you tried adding algae eating fish only to be disappointed that they didn’t like the taste? Do you have aquarium algae growing on your rock, decorations or corals? I’ve been in this hobby for four decades and i’ve tried everything from aquarium algae scrapers to manual removal to fish and invertebrates and everything in-between. Including actual pond algaecides. Aquarists just like us have fought long and hard with pest species of aquarium plants and the hobby has needed a safer, yet effective, treatment.


The use of Fluconazole has an interesting back story. It was discovered accidentally by an aquarist from South America that purchased some Fluconazole as a treatment for a fungal infection in his fish. That is Fluconazole’s primary use, to treat fungal infections in fish that live in marine aquariums with sensitive corals and invertebrates in them. As he added the treatment, he began to notice something really odd. All of his bryopsis, a very problematic fast growing saltwater pest algae, turned pinkish white, melted and died. Then, he shared this information with his local aquarium group and they tried it on their problem algaes, even dusty algaes disappeared. The news went viral.  People around the world began trying out Fluconazole, an anti-fungal medicine, for treating their problem pest algaes. Surprisingly, it worked!

How Does It Work?

Studies are currently being conducted on Fluconazole’s method of action, but the current hypothesis is that fluconazole somehow intereferes with the photosynthetic processes in lower order plants but isn’t able to penetrate coral tissues or the cellulose of higher order plants. In fact, increasing the light exposure during treatment speeds up the process of wiping out problem algae. Pest aquarium algaes fall into that group of lower order plants as most of them are colonial in origin. Think more like a big group of single celled algae all working together. Even aquarium algae growing on plant leaves can be treated, such as the dreaded black beard algae.

How do you use Fluconazole?

After doing some homework on FluconazoleI decided to try it for myself. I’d been having problems with aquarium algae on glass and on my rock work in my reef tank and it’d been a losing battle. I’d remove it and it would grow right back. So, I went to amazon and bought that very same bottle of reef flux fluconazole. The first step in the treatment is to remove any chemical media from your aquariums. This means any active carbon or purigen or similar chemical medias need to be out of the water so that the medication can stay in suspension in the water. During the initial 72 hours after your first dose, do not run your skimmer. After that, running a skimmer is just fine and in fact encourage for saltwater and reef tanks. As the algaes melt, the skimmer will help remove some of the gunk.

The first dose of fluconazole I used was 4 mg per gallon. For a 30 gallon tank, that was 120 mg. The capsules pull apart easily. Dump the contents of each capsule into a plastic cup half filled with tank water and use one capsule per ten gallons (for 20% initial dose). Mix until dissolved. Add cup of fluconazole tank water to a sump area or broadcast throughout the main tank in high flow areas. Next, crank up the lights and make sure all of the algae gets a sunburn.

Single celled algaes will disappear first. Aquarium algae on glass will melt away in the first 24 hours. Bryopsis and other turf algaes will begin to melt after a week. Aquarium algae on rocks and corals will be neary eliminated after three weeks. Even the dreaded valonia bubble algae and black beard algae growing on aquarium plants will eventually begin to turn white, pink and die. 

After three weeks, perform a 25% water change and evaluate your tank’s algae condition. If a repeat dose is necessary, consider adding another dose at the 4mg per gallon level (one capsule per 10 gallons) to the water change replacement water and repeat the process. To prevent the algae growing back, consider adding a maintenance dose of 2 mg per gallon in your water changes.

After your algae problem is back under control, you can add your chemical media back to the tank and discontinue dosing.

Is Fluconazole Safe?

In my experience, Fluconazole is safe to use in reef tanks and freshwater aquariums filled with sensitive corals and invertebrates. My corals, shrimps, starfish and urchins and live plants suffered zip zero problems from the treatment and i’m much happier not to be constantly doing battle with algae. My tanks are teeming with copepods, amphipods and beneficial annelids (worms).


This treatment can be harmful to macro algaes such as ulva (sea lettuce), caulerpa and chaetomorpha. Certain ornamental mosses such as marimbo might also be affected. If you’re uncertain, don’t dose without removing and quarantining your  lower order plants.


Member: A.K.A., A.C.A, N.A.N.F.A., S.K.S..

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