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2.5.1. Fish-in Cycling Science

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Author : David Bogert

Published :

Time To Read :
7 minutes
Difficulty : Level 7

Excerpt :

This article goes into some depth on the science of doing a cycle on an aquarium where there are fish in that aquarium.
The PETA folks and other well-meaning hobbyists will rail against “fish-in cycling” as being “mean and cruel”. They say fish-in cycling will hurt, damage, or even kill the fish. They have a point in certain rare cases. If beginners in the hobby know enough to only put in a few fish and only fed a small amount of food to those fish, fish-in cycling would be fine.

Fish in Cycling can VERY RARELY Kill Fish

But typically beginners are not knowledgeable. They sometimes overstock new tanks and they almost invariably overfeed their fish. This combination can VERY RARELY kill fish over weeks. Note that the killer is generally either bacterial toxins or nitrite, not ammonia.

picture of an aquarium fish Melanochromis auratus female
Melanochromis auratus female

There is another mechanism that can kill fish. If a filter is not mature enough to remove ammonia from the water it is also not mature enough to remove something called “dissolved organic compounds” (or DOCs) from the water.

So there ends up being a cascade:

  • leftover food and feces form dissolved organic compounds (DOCs)
  • dissolved organic compounds feed bacteria in the water column
  • fish devote a lot of their immune system to fighting these bacteria in the water column
  • the bacteria also produce toxins
  • the bacteria use up oxygen in the water
  • the fish’s immune system can’t keep up with the bacteria load, the toxins, and the low oxygen level and a pathogen gets through to infect the fish
  • and the fish die

This cascade is why fish can die in water with only small spikes in ammonia and/or nitrite.

Buccochromis spectabilis
Buccochromis spectabilis

When a batch of new fish is put into a new tank that hasn’t been cycled sometimes a lot of them will die overnight. And the small ammonia reading in the aquarium will be blamed for the deaths. There are a lot of reasons for fish to die overnight and ammonia poisoning is not one of them. Those reasons are reviewed in this link

1.6. Rapid Fish Deaths

Many experienced fishkeepers recommend fish-in cycling as the best method of cycling because of its simplicity. These fishkeepers included Cory of Aquarium Co-op, probably the most knowledgeable fishkeeper in the business. So this method is not to be lightly dismissed. As long as one doesn’t feed too much or get too many fish, fish-in cycling works well. The problem is that many newcomers don’t know what “feed too much” or “too many fish” mean, which can, VERY RARELY, be a disaster.

picture of an aquarium fish Melanochromis auratus male
Melanochromis auratus male


Fish-in cycling is not done by experienced fishkeepers because the level of fish that can be handled at the end of cycling with a fish-in cycle is much fewer than the level that can be safely handled by a properly done fish-less cycle. Properly done fish-in cycling rarely goes above 0.5 ppm ammonia whereas fishless cycling can hit 4 to 20 ppm ammonia, depending on how it is done. So fishless cycling gives one much larger beneficial bacteria colonies able to handle much larger and many more fish.

Fishless cycling can also be done in half to one-fourth the time it takes to do fish-in cycling. And the water can be crystal clear and very healthy for the fish with fishless cycling. With fish cycling, the water is typically pretty “dull” and not crystal clear. This type of “dull” water is not healthy for the fish.

Melanochromis maingano
Melanochromis maingano

The Advice for a Beginner

It is very common for a newcomer to the hobby to find themselves with a brand new aquarium and some fish sold to them by the fish store. It is also very common for some know-it-all “fish police” on social media to tell the newcomer their fish are going to die and that they should have known better than to do that. If you find yourself in this position know that your fish will probably survive just fine.

I’ve been in the hobby for fifty years. I set up many tanks years ago and just put in water conditioner and then just dumped the fish in. And the fish did just fine. I used under-gravel filters. The water got cloudy for a few weeks. I ignored it and let Mother Nature do her thing with no water changes, no bacteria-in-a-bottle, and no chemicals. And the water cleared at four to six weeks and all was well. I got brown algae on all my ornaments and I learned to live with it.

But the little book on “How to Set Up an Aquarium” I got with my first aquarium said that beginners often overfeed fish, which can kill them. So I took that advice to heart and fed my first aquarium quite lightly. And I only added a few small fish. So so long as the newcomer feeds only small amounts of food to a small number of fish during fish-in cycling they will be just fine. And I know, I hear the howls of protest: “that’s old technology and is no longer true”.

Isn’t it amazing how what you did fifty years ago many times and it worked fine no longer works? I guess the fish have evolved with the technology.

picture of an aquarium fish Melanochromis chipokae female
Melanochromis chipokae female

Why Fish-in Cycling Works

The reason fish-in cycling can work is that ammonia and nitrite are just not as poisonous as we have all been led to believe. Levels of ammonia need to get to at least 32 ppm at 7.0 pH before there is a possibility of any long-term damage. Nitrites are much more of a concern as at a pH of 7.0 even 1 ppm nitrite is a concern. The “alarm” levels below are when one needs to get concerned.

Ammonia and nitrite toxicity is very dependent on pH. The most accurate way to illustrate the toxicity of ammonia is a chart derived from the University of Florida ammonia toxicity chart (Publication #FA16, “Ammonia in Aquatic Systems”, Ruth Francis-Floyd).

pH of the waterAPI Ammonia test in ppmAPI nitrite test in ppm
Nitrate alarm level is greater than 80 ppm.
Nitrate toxic level is greater than 440 ppm.

To use the chart, first, measure your pH. Find the pH in the left column. Read across as to the toxicity level with the API test. If one’s pH is 7.6 one should be “Alert” at 2 ppm and watch things, “Alarmed” at 8 ppm and do water changes, and fish will start dying (“Toxic” level) at 20 ppm. To read the API test kit at those levels one must dilute the water by a factor of ten and then multiply the results by ten. . There are dozens of other very similar charts by other university researchers. These numbers will shock most hobbyists but they are accurate.

Now we do not recommend going above 2 to 4 ppm ammonia with fish in cycling. The ammonia typically won’t be toxic but the bacteria that accompany that high ammonia levels will be toxic due to the cascade shown above.

Otopharynx ovatus Chilumba
Otopharynx ovatus Chilumba

There is another graph currently being circulated on social media forums. This graph is horribly inaccurate. If these recommendations were followed one would never be able to complete cycling a fish-in aquarium cycle. And the number of water changes one would subsequently have to do to keep nitrates down will drive anyone out of the hobby. This sort of misinformation is rampant on social media:

Incorrect aquarium water change recommendations
Incorrect aquarium water change recommendations

Let’s assume the pH of one’s aquarium is 7.4. Then the level where major water changes are “required” per this “one size fits all” chart is 4% the level of ammonia, 25% the nitrite, and 25% the nitrate the recommendations of all the aquaculture research centers in the world. This “one size fits all” chart is completely at odds with what the University of Florida and about a dozen different universities are recommending as to the safety levels of various toxins in an aquarium. It is just bogus information. Sorry, can’t sugarcoat this. I do suspect that this chart makes a lot of profit for Seachem from sales of Prime ….. hhhmmmm… ???

Here is a link to many university papers on the topic of toxicity of these compounds:

5. Ammonia, Nitrite, Nitrate, and Chlorine Toxicity

Pelvichromis kribensis
Pelvichromis kribensis

Belief Perseverance Effect

Now there is a psychological phenomenon called the “belief perseverance effect” which is very strong. “Belief perseverance effect,” says that if someone believes that small amounts of ammonia can kill fish overnight and fish-in cycling is cruel to fish, they will rationalize and support that belief no matter what.

Nothing dies harder than a lie that people want to believe


There is no way any evidence, testing, or scientific papers from reputable Universities can penetrate the brick walls that the belief perseverance effect puts up in the mind. So we won’t try.