What Causes Aquarium Bacterial Blooms?

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Aquarium bacterial blooms are caused by a rapid increase in the microorganism population of your tank. They become so numerous that your tank water turns cloudy white or yellow. The germs are feeding on dissolved organic material from leftover fish food, poop, dead fish, and other sources. Once you’ve removed their food source, bacterial bloom cloudy water will fade away.

What are Fish Tank Bacteria?

All aquariums, no matter how clean, have bacteria and fungi floating in the water. And that is a good thing; microorganisms are an essential part of your aquarium ecosystem. They feed on dissolved chemicals and organic matter. Transmuting them into harmless substances like food for plants.

Some bacteria are pathogenic and will infect aquarium fish, causing diseases like fin rot, columnaris (cotton wool disease), and dropsy. Others are an essential part of your nitrogen cycle and convert ammonia into nitrite and nitrate.

Aquarium bacteria are necessary for fish tank health. They become a problem when they grow so numerous that the water turns milky.

Is Bacteria Bloom Bad for Fish?

Bacterial bloom in fish tank is a sign that some part of your ecosystem is out of balance. They are either bad or neutral, depending on the kind of bacteria and the source of that imbalance.

Aquariums that turn cloudy because of decaying food or dead fish are full of toxic compounds like ammonia and decay-causing bacteria. These same germs will infect your fish, which are being weakened by the poisonous chemicals in their environment.

One sign that you have a toxic bacteria bloom is to smell the water. A rotten egg aroma indicates the presence of anaerobic rot-causing bacteria.

In other cases, the imbalance is minor. Perhaps you overfed your fish one time or a fish died while you were on vacation. Your water may turn cloudy for a while but your fish are in non danger.

Bacterial Bloom During Cycle

A bacterial bloom in new tank is common. Your entire aquarium nutrient cycle is being established. Temporary cloudy water is not an issue so long as toxic bacteria aren’t present.

When cycling a new aquarium you should be tracking ammonia, nitrite, and nitrate levels on a daily basis. As long as parameters remain in the safe zone and your fish aren’t showing signs of stress, don’t do water changes. A large water change will disrupt or even reset your cycling process.

Bacterial Bloom After Cleaning Filter

Sometimes doing aquarium maintenance like cleaning your filter will cause a bacterial bloom. When this happens, you did not do anything wrong. The balance between nutrients and organisms was disrupted.

Large numbers of bacteria live inside of your filter. The cleaning may have purged a large number of them. Which gives the free floating bacteria in your water a change to become dominant.

In most cases, the balance fixes itself in a week. Filter bacteria numbers will reestablish themselves. As long as you aren’t overfeeding your fish they will consume their share of nutrients again, starving more of the cloudy water causing germs.

How Long Does Bacterial Bloom Last in Aquarium?

Bacterial blossoms last as long as the nutrient levels remain high. If you overfeed once but then feed as normal, the cloudy water resolves itself in most cases. The process will take a few days to a week, depending on the size of your aquarium.

Constant overfeeding will keep your water cloudy, however. Blooms caused by toxic bacteria may become self-sustaining even if you don’t overfeed, however. The poisons they produce can kill fish. As fish die, they release more food (and toxins like ammonia) into the water, sustaining the bacterial bloom.

How to Get Rid of Bacterial Bloom in Aquarium

Bacterial blooms are one of the easier water quality issues to reverse.

Do a Large Water Change

The first step is to do a large water change. Remove 30% to 50% of the tank’s water using a siphon hose. Do a thorough clean, digging deep into the gravel using your siphon hose to remove all rotting debris.

The digging action will also redistribute your gravel substrate so water will better penetrate it. Check behind and under decorations for dead fish, clumps of uneaten food, and other sources of bacteria food.

Reduce Tank Water Nutrient Levels

When we perform our water change, we are already reducing aquarium nutrient levels. Once we’re finished though, we have to keep levels steady. Otherwise, the bacterial bloom will happen again. What was the source of your bloom?

If you know you are overfeeding your fish then take steps to feed less. As a rule of thumb for small fish (under 3 inches), their stomach is about the size of their eye. Feed at most two to three times per day. Adult fish are fine with one or two feedings per day, skipping a meal once or twice per week.

For larger aquarium fish, feed once or twice per day. Give them enough that the stomach swells without leaving leftovers. Any leftover food should be swept up using a net or a small water change. Unless you have bottom feeding fish; they need to eat too.

Dead fish, dying plant leaves, and other sources of organic matter should be removed at once. General aquarium maintenance like water changes and filter cleaning should be done on a regular schedule.

One overlooked source of bacterial blooms is new pieces of driftwood. Some types of driftwood have a powdery exterior that will feed bacteria for a long time. Clean any new pieces with water and a sponge before adding them to your tank.

Increase Aquarium Aeration

One dangerous group of germs that will cause an aquarium bacterial blossom are anaerobic bacteria. These germs grow where oxygen levels are low or absent. In a healthy tank, they are found in small amounts deep in your substrate, where water circulation does not bring oxygen.

But during a bacterial bloom, aerobic (oxygen-loving) bacteria will reduce dissolved oxygen levels. Once this occurs, anaerobic bacteria will move into the water column. Low oxygen levels are already dangerous for your fish. But the presence of anaerobes is even more dangerous because they produce toxic hydrogen sulfide as waste.

Hydrogen sulfide has a distinctive rotten egg smell. If your aquarium water smells sulfurous then anaerobic bacteria have taken over. Even at this stage, you have options.

First, do a large water change of at least 50% of the aquarium’s volume. Follow all of the instructions above to clear debris from the substrate.

Refill the tank with dechlorinated water and then add an aquarium air stone. Oxygenating your water will kill any anaerobic bacteria left over. Air stones also create their own circulation current so oxygen will find its way down into your substrate.

Sand tends to compact over time, preventing this flow. So once per week, gently stir the substrate to keep it well oxygenated. You could also add pets like kuhli loaches, corydoras catfish, cichlids, or assassin snails that like to dig. Live plants also oxygenate sand substrates as they send their roots through it.


Aquarium bacterial blooms happen when microorganisms are so numerous that your water turns cloudy. Most are harmless indicators that they are feeding on nutrients like leftover food or a hidden dead fish. Water changes and proper feeding will clarify your aquarium water in a few days’ time. Keeping to a regular maintenance schedule (rather than large, infrequent water changes) will also prevent bacterial blooms in fish tank.


Bottled nitrifying bacteria are a great product for jump-starting your cycling process. It’s not possible to overdose on the bacterial concentration because the organisms feed only on nitrogenous waste products. If they run out of ammonia and other food, their numbers will drop to a level that is sustainable. It’s possible that as they start dying, decay-causing germs will feed on them. But any ammonia the decay-causers released will be eaten by your remaining nitrifying bacteria.

Biofilms grow in any mature, cycled aquarium. Tanks mature at around 6 months of age. Time and natural surfaces are the two best ways to grow biofilm in an aquarium. Live plants, rocks, and driftwood best grow biofilm. But the germs involved also grow on aquarium glass, gravel, filter tubes, and other surfaces.

Biofilm is a source of food for suckermouth catfish like plecostomus, dwarf otocinclus, and bristlenose plecos. Freshwater shrimp, mbuna African cichlids, and ramshorn snails also eat biofilm.

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