Ask average fishkeepers what they know about anaerobic spots, and chances are, they will say “What?” and won’t have the slightest idea what it is. After all, the chances are slim that they will be affected by anaerobic spots.

What are they?

Anaerobic spots are areas in the aquarium that are deprived of oxygen; thus, they promote the culture of anaerobic bacteria. As we all know, anaerobic bacteria are harmful bacteria that thrive in oxygen-poor water. Once these bacteria are released in your tank, they can do a lot of damage to your water quality, thereby killing your fishes.

How are they made?

Nowadays aquariums are usually set up bare and devoid of any substrate or decorations. This allows for good water current to circulate around the tank, thereby ensuring the proper oxygenation of the entire tank. With these bare tanks, it would be almost impossible to create anaerobic spots in the aquarium. With water current freely flowing in the tank, no anaerobic spots in the tank are created.

However, put a flat rock or a tile at the bottom of the tank and this becomes a different ballgame. Between the tile and bottom of the tank is a small crevice that should be filled up by tank water. Despite having a strong current in the tank and the water generally being highly oxygenated, the water in this crevice becomes poorly oxygenated since it is trapped by the tile. Since there isn’t water flowing through the tight space, it is devoid of oxygen.

Once oxygen in the water is absent, anaerobic bacteria sets in. This is a classic example of an anaerobic spot in the aquarium. This area becomes conducive for anaerobic bacteria to thrive in. In no time, a healthy population of anaerobic bacteria will be created in this area. If for some reason, you lift out the tile, you will release the anaerobic bacteria trapped by the tile into the tank. This will be very harmful for the fishes and they could possibly die.

Strictly speaking, any décor in the aquarium can result in anaerobic spots. Once you put an object in a tank, the probability is high that anaerobic spots will be created. How detrimental the anaerobic spot is to your aquarium depends on the size of the anaerobic spot. If you put in a small rock, then it is expected that the anaerobic spot created will also be small, such that if anaerobic bacteria are released, the effects should also be minimal or may not even matter.

If you have a pile of rocks, big enough to prevent the water current from flowing though the crevices, then a huge anaerobic spot is created. Once the rocks are rearranged and the anaerobic bacteria are released, expect the anaerobic bacteria to destroy your water quality and put the lives of your fishes in danger.

How can you control anaerobic spots?

Granted that fishkeepers will surely create anaerobic spots in an aquarium, what should they remember to do in order to minimize the effects of the deadly anaerobic bacteria?

First and foremost is the size of the decorations. If your tank is sparsely decorated, then the danger is less; the denser or larger the decorations, the bigger the anaerobic spot created. The concern really is for those instances when big anaerobic spots are created. Very quickly I can enumerate the following instances where huge anaerobic sports are commonly created without the fishkeeper even knowing it:

Thick substrate

If you have substrate-like sand or gravel that is about 3 inches or thicker, then the bottom portions will be totally devoid of oxygen. Without the presence of oxygen, expect an anaerobic bacteria “farm” to create a tremendous amount of anaerobic bacteria along the whole bottom of your tank.

If for some reason your substrate is stirred up and the anaerobic bacteria released (for example, you decided to rearrange the tank and you upturned the substrate), expect the release of enough harmful bacteria that can kill the tank’s inhabitants. In case this happens, the best thing to do is do a 50% water change and increase aeration by adding an air stone run by a strong pump.

The best way of preventing this from occurring is to limit the thickness of your substrate to, at most, 2 inches. But if you are forced to have thick substrate, use gravel cleaners when doing your weekly water change.

The gravel cleaner is one of my favorite aquarium gadgets. Work out a siphon and dip the nozzle in the substrate then observe how gravel is turned over by spinning about in the nozzle and dirt is picked up and siphoned out. This prevents anaerobic spots from developing because substrate is kept oxygenated.

Another way is to “aerate” your substrate by introducing animals that burrow in or move the substrate. The Eartheaters or cichlids from the genus Geophagus that sift through the substrate looking for morsels to eat do an efficient job of “aerating” the substrate. They grab mouthfuls of substrate that exit through their gills. This stirs and oxygenates the substrate, thereby preventing anaerobic bacteria from developing.

The Malayan Snail and Assassin Snails are known burrowers and this behavior also allows oxygen from reaching the substrate bottom. Bottom active fish like Stingrays, Bichirs, some catfishes, some cichlids, and eels often get on our nerves when they rearrange the substrate. While they have destroyed our desig n for the tank bottom, their earth-moving activity is actually beneficial since it aerates the substrate and prevents anaerobic spots from developing.

Too much rockwork.

This kind of setup is quite popular with Lake Tanganyika and Lake Malawi Biotope tanks. Since both lakes are characterized by a rocky environment, fishkeepers duplicate this scene in their aquariums, with tanks filled with lots of rocks.

While this makes the fish feel at home in an environment that duplicates their natural home, too much rockwork hinders the flow of water and creates a lot of anaerobic spots. Each crevice created by the rocks piled one over the other will be a spot with poor oxygen and potentially a producer of anaerobic bacteria.

Adding a wavemaker may help by providing water current coming from different locations. But this does not guarantee it will be anaerobic spot-free. In fact, it is a sure thing that your setup will have lots of anaerobic spots. The best thing to do is to have regular water changes. Twice a week of 20% each should be fine.

In case the rockwork has been disturbed and anaerobic bacteria released, do a 50% water change and increase aeration.

3D Backgrounds

I am a big fan of 3D backgrounds because they make your tank look professionally done. But “looking” professionally done is very much different from “done professionally.” Those who know what they are doing know very well that sticking up a 3D background on the rear panel creates a serious anaerobic bacteria factory.

By putting spots of silicone along the back of the 3D background and sticking it to the rear panel, one creates a crevice that becomes oxygen free. This becomes an ideal home for anaerobic bacteria to thrive in. If you think it is just as easy as sticking the background up at the back, think again. Every time you do a water change, water that is full of anaerobic bacteria is released to the main tank as water is displaced from the small crevice between the 3D background and the rear panel of the main tank. Therefore, every time you do a water change, you actually poison your fish without you even knowing it.

The best thing to do is to do a 100% water-tight seal between the 3D background and the rear panel. This ensures the gap between the two is not filled with water; therefore it cannot create anaerobic bacteria.

Successfully installing 3D backgrounds can only be done with the tank totally dry. If someone tells you that he can install a 3D background while it still has fish in it, then you’re setting yourself up to fall for a sales pitch. Of course that person can install it, but you will just have to take the consequences. If you are to install a 3D background, do it right on the first and only time you do so.


Quite recently, I have noticed that some tanks have tiles on the tank bottom. The most common ones I have seen have 3 white tiles spread neatly and evenly at the bottom. This provides a white base at the bottom. Sometimes the rear panel is also adorned with the same tiles. This makes the tank look neat and nice—and potentially very dangerous.

As earlier mentioned, any crevice formed where water can seep through between the tiles and the glass panels will create anaerobic bacteria. Once you do a water change and displace the water from these crevices to your tank, you are poisoning your fish. To avoid the catastrophe above, do 100% sealing of the tiles and the tank panels.

Dead Canister Filters

The worst anaerobic bacteria factory I can think of is a dead canister filter. Canister filters are very efficient filter systems. They have a strong flow rate, thereby promoting a highly oxygenated environment for your beneficial bacteria to thrive. It has effective biomedia which beneficial bacteria can populate.

However, if there is a power outage, the canister filter is deprived of oxygen-rich water. Water in the hoses and the canister itself is stagnant. In 24 hours, all thriving beneficial bacteria will have died off and anaerobic bacteria will begin to conquer the “dead” canister filter. When electric power returns and the canister filter is up and running, brace yourself for a massacre in your aquarium. You have just released all the anaerobic bacteria from the canister filter to your tank.

Don’t worry because you will be alerted; even if you don’t see the anaerobic bacteria, you will definitely smell it from the canister. If there are brownouts that last more than 2 hours, it is best that you clean your canister filter. The design of the canister filter prevents oxygen from running through the system if it is turned off. Without oxygen, beneficial bacteria will die. In 2-3 hours the beneficial bacteria in the canister filter will have died from lack of oxygen. In a few more hours, they will have rotted—a few more hours, and anaerobic bacteria will have developed. Once power is back on, all of these harmful substances will be in the main tank if you didn’t clean your canister filter.

Think about it

Anaerobic spots can be present in your aquarium, and you have to be alert to know if there are certain spots in your tank than can be potentially dangerous. Observe your tank and think. Remember that so long as water is moving, it is highly oxygenated and therefore the possibility of anaerobic bacteria thriving is very low. But once water is stagnant, then be alert as anaerobic bacteria may develop.

Check your tank and ask

Are there areas where water cannot move freely? Should these areas have some water movement? Regular tank maintenance, of course, is always a great help. This not only cleans the tank by ridding it of toxic materials but circulates water in the tank as well.

While anaerobic spots in the tank may not be too obvious, it is worthwhile to assess your tank for these things. Look for areas that have low water movement, address the flow problem in these areas, and prevent the silent killer you have unknowingly created from conquering your tank.


This appeared in Animal Scene magazine’s December 2017 issue.