I have a planted tropical community tank which has a layer of roughly 3cm of fine sand substrate. I've read a lot about anaerobic gas build-up in the substrate where it is not regularly turned over and moved. When I shift the sand I get very small bubbles rising. This has been happening for a while and it doesn't seem to have a negative impact on my tank.

I've read from various, different sources that anaerobic gas (Hydrogen Sulphide) can prove toxic to fish but I've so far, not found this happen in practice (my fish are fit and healthy).

Some of the 'solutions' to this problem, suggested with varying levels of controversy across the internet, include:

  • Having a thin layer of substrate
  • Using gravel not sand
  • Regularly disturbing the sand to stop the build up
  • Increasing water changes to handle the toxic nature of the gas
  • Get snails to stir up the sand

None of these necessarily seem like a perfect solution. In a planted tank, I rely on having enough substrate to create a stable foundation for the plants. Compost/sand definitely seems to grow them best. Gravel lets us easily stir through it to remove any of detritus that is underneath but doesn't hold plant roots well (at least in my experience). I also have some snails which live in the substrate and I would assume that they help stir the substrate up.

With all this in mind:

What is the best way to prevent anaerobic gas build-up in a planted aquarium, assuming it is in issue?

Image of gas bubbles/snails in substrate

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    this might be a stupid comment but fresh water mussels do walk around in the sand and this is what you want i belive,you will proably ned to put the plants that do come loose down in the sand again from time to time,and the tank needs to be 150liters+ depending on the size of the mussels. Commented Aug 27, 2017 at 16:36
  • I'd probably prefer not adding other animals to my tank. I'm more looking for a way to prevent this or if there is some other technique that I'm yet to try that has proved successful for someone else.
    – Henders
    Commented Aug 29, 2017 at 8:22
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    i do understand you not wanting to put more animals in the tank,the trouble is your question is more complicated then it looks at first,i did consider a lot of options but none of them was any good. Commented Aug 29, 2017 at 8:56
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    H2S is toxic to about any animal. I don't release the H2S by stiring the gravel /sand in my aquariums . Commented Aug 31, 2017 at 1:39
  • @blacksmith37 If you are regularly stirring your gravel, this means that it can't build up so there is nothing to actually release, right? I'm just not sure how to do this with a planted aquarium... The roots run around the tank quite a bit.
    – Henders
    Commented Aug 31, 2017 at 8:11

2 Answers 2


I am going to provide my insight to hopefully serve as a complement to existing answer and comments because I think this is an interesting question.

In addition to perfectly valid methods already mentioned, an additional approach for H2S management in aquarium could be also controlling amount of foods with a significant load of sulfur-containing amino acids (methionine and cysteine) being fed.

Methionine is an essential amino acid, so one shouldn't attempt eliminating it completely from fish diet because that would ultimately lead to fatal malnutrition.

On the other hand one should keep in mind that sulfur-containing amino acids are used as substrates for hydrogen sulfide production in anaerobic conditions - and for that reason, make sure that such foods aren't being carelessly fed in excess. Stagnant, fine, deep substrate mixed with decomposing chunks of uneaten, high in sulfur-containing amino acids food in a warm, tropical aquarium is in this context a perfect environment for H2S production.

For example, some fish foods are sold in an "ovo" version, which means an egg-based or egg-enriched version with strengthening properties meant for feeding young and growing up fish - and egg proteins are exceptionally high in sulfur-containing amino acids, which is also simultaneously the exact reason why the disagreeable odor of H2S is associated with the odor of rotten eggs. My approach for the H2S management in the tank would be in essence making sure that foods like that are used in carefully controlled amounts, or not used at all if it's not really needed.

Also some specific plant foods like cabbage, broccoli, cauliflower and Brussels sprouts are high in sulfur-containing amino acids so please be careful and stay informed if you plan on feeding them to your fish. In the tangentially relevant Q&A Trond Hansen explains why it is bad to overfeed this type of food, using the case of sea lettuce.

Generally in this context it would be helpful to always carefully study and accurately determine the amino acid nutritional profile of any type of food being fed, but in practice it could often prove to be unreliable or tedious.

And something about hydrogen sulfide itself: yes, this is a naturally occurring compound and it's used in minuscule amounts as a signaling molecule in living organisms - for this reason there exists a metabolic pathway for neutralizing minuscule amounts of it. But it becomes easily overwhelmed with relatively small amounts of H2S, and H2S interferes with cellular respiration, hence it's high toxicity - which is actually comparable to the toxicity of carbon monoxide and hydrogen cyanide.

Stirring the substrate, either performed manually or by snails as mentioned in others' answer/comments is also an efficient method of H2S management - but actually it's main goal is not releasing H2S from the substrate but rather mixing oxygen-rich water into it - oxygen presence enables aerobic metabolism in substrate inhabiting bacteria and thus disables H2S production, which occurs in anaerobic conditions.

In addition to snails, there also exists an interesting genus of fish Acanthopsis choirorhynchus which is apparently named commonly as horseface loach. It is known for its behavior of being noticeably mobile and also completely burrowing itself in the substrate, being exceptionally efficient in frequently stirring it and thus preventing anaerobic conditions arising. For these reasons, in my native language it is also somewhat erroneously named as what could be roughly translated as "mud-eater" or "slime-eater". It could be a wise choice to include this fish if your tank has appropriate type of substrate for it. However, keep in mind that this fish is so aggressive in it's mobility that it tends to uproot plants.

My general source was Wikipedia.


Had this worry some years ago. My solution: use a chopstick or the blunt end of a wooden skewer and run it through the substrate every other day. I never had an issue with a build up of toxic gases. By the way, small bubbles are not a cause of concern; it would have to be a bubble the size of an orange that would be and you'd smell it too.

  • I would have thought the opposite in terms of bubble size. To dissolve gas in water, the smaller the bubble, the better it dissolves. Do you think the chopstick would work with a planted tank? I think I'd end up pulling up a bunch of roots with it instead...
    – Henders
    Commented Nov 29, 2017 at 23:09
  • Completely understand your reasoning about bubble size and how smaller dissolves better in water. When I mentioned smaller bubbles are not a cause of concern, a major concern is what I should have said. That's is because a bigger bubble is going to be a bigger build up and when that bigger bubble is released, that's a bigger amount of toxic gas to deal with. when you're at that stage of having BIG bubble of anaerobic gas being released, then your not only does the tank substrate really needs stirring up but most likely there's been some fish casualties.
    – Jarl Axle
    Commented Nov 30, 2017 at 18:28
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    Also, I never dragged the chopstick through the substrate (sand in my case at the time) but rather carefully stirred the sand in small circular areas. Think size of a quater. Later when I had more plants and switched to the skewer, those circular stirrings were about the size of a toothpaste cap.
    – Jarl Axle
    Commented Nov 30, 2017 at 18:34

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