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Tropical and Marine Fish Tanks

Common Issues When Cycling a Freshwater Aquarium

Cycling an aquarium is vital to keep healthy fish and plants, and most aquarists will agree that a 4 to 6 weeks cycling period before introducing fish is a good standard. There are several methods to cycle your aquarium safely, all of them involving a source of ammonia such as fish or fish food, bacterial colonies and a good testing kits. However, things not always go always to plan and the following are some common problems you can find when cycling an aquarium (and how to fix them).

My Aquarium Won’t Start Cycling

During a regular aquarium cycling process ammonia usually starts rising about 3 days after starting. If by day 5 you haven’t been able to measure any ammonia, and after discarding the possibility of a faulty test kit it’s time to consider whether your aquarium hasn’t started cycling at all.

This happens usually due to one of the following reasons:

  • There is no source of ammonia on hand
  • Something else is eating up the ammonia too fast for the bacteria to get to it
Cross-section through nitrifying bacteria   © Mary Ann Bruns, Center for Microbial Ecology, Michigan State University


It is a common mistake to just leave a functioning aquarium in the dark for weeks, hoping that bacteria will grow and colonize the filters and tank surfaces. While most fish stores will recommend running the aquarium for a day or two on just with water in order to ensure the filters and heaters are working properly, that won’t start the tank cycling on its own. Bacteria need ammonia to grow. If you haven’t add a source of ammonia, add one and test for nitrites after a day or two. Presence of nitrites means your aquarium has started cycling.

Another possible reason for the lack of ammonia is that the plants in the aquarium are disposing of it quicker than you can measure it.

It is very common for heavily planted aquariums to not have any significant ammonia or nitrites, as the plants will efficiently get rid of them. If after a few days there is still no ammonia (or the ammonia you introduced just disappeared, and there are no nitrites) you can either add more in order to leave something spare for the bacteria, or start adding fish slowly.

Fishless Cycling: Ammonia Not Dropping

Once your tank has started cycling, the next step is bacteria transforming ammonia into nitrites. However, if the ammonia is not dropping after a few days and you can’t detect nitrites on the water then something is wrong. Some of the most common causes of no nitrites but high ammonia (not including a faulty test kit) are:

  • pH is too low: At low pHs, under 6, ammonia will be mostly present as ammonium which the nitrifying bacteria can’t use. This means your bacteria colonies don’t have enough food to get established. Test kits increase the pH in order to measure free ammonia on the test sample, which means it will read as high ammonia when there is no actual ammonia in the water.
  • Chlorinated water: If you are not using a water conditioner before adding water to the aquarium the compounds on tap water may be disinfecting your tank and killing all the good bacteria. Always use a water conditioner on water changes even if you have no fish
  • Overzealous cleaning: Nitrifying bacteria live in the gravel, filters and decorations of your aquarium. If you clean too aggressively (hoovering all of the gravel of the aquarium) or change all the filters too often, you will be removing said bacteria before they have a chance to establish and deal with the aquarium ammonia. Only clean a third of the aquarium on each water change, and don’t change all the filters at once. Always leave some of the old medium in place so bacteria is seeded on the replacements.

Algae Bloom During Aquarium Cycling

Algae are usually an unsightly presence on an aquarium, but they are not necessarily fatal. However, an aquarium in the middle of a fishless or silent cycling process can be the perfect growing environment for all sorts of ugly and difficult to remove algae. The reason for this is that algae just loves ammonia, just like any other plant.

If you are fishless cycling your aquarium and suffer from algae problems, start with turning off the lights. No light = no algae, and the nitrifying bacteria won’t even notice. Be careful not to place an aquarium near a window where natural light will just encourage algae growth.

For planted aquariums, algae are a common problem brought on by the use of fertilisers (algae love phosphates and ammonia even more than just ammonia) and you can’t just turn off the lights. However, you can make sure your plants don’t get more than 10h of light a day to avoid encouraging algae bloom. Plants will directly compete with algae for nutrients and so if you avoid over-fertilising the aquarium algae will naturally die. Using substrate fertilisers instead of liquid ones, and incorporating a CO2 injector will also help.

In order to cycle your aquarium with plants it is best to choose plants that don’t require much light and are quick growers, as they will dispose of nutrients quicker and compete directly with algae. For example, Java fern, Java moss and Water wisteria are quick growers that won’t require much light. A good carbon filter will also help get rid of the extra phosphates.

As soon as your aquarium is safe, it is time to add fish to it. Make sure your first fish are algae eaters, such as a catfish or siamese algae eaters, as they will munch on even green haired algae. It may take a while to clean up your aquarium after cycling, but biological algae control is much less likely to unbalance your setup.

Ammonia Levels Are Too High! Fish Are Dying!


API Freshwater Master Test Kit

If you are doing a fish-in cycle, sometimes all the water changes in the world won’t keep an overstocked tank from having too much ammonia. In cases like this, using a water conditioner which binds Ammonia, such as Seachem’s prime, can be your fish salvation. Prime conditions the water and binds the ammonia into a compound that bacteria can feed on, but which is safe for the fish. A water change of 50% and a heavy dose of Prime every 2 days can keep the ammonia under control until the bacteria catch up. If you are not adverse to buying additional products, using bio-start additives with live bacteria can also help the aquarium to catch up with the ammonia production.

Another alternative is lowering the pH of your aquarium under 7, as this way ammonia will only be present in its non-harmful form: ammonium. This can be easier said than done. Peat moss and driftwood will naturally lower the pH of your aquarium, but you must keep in mind that fish are very sensitive to sudden pH changes so this method will only work if other short-term ammonia control methods are used first, or if your pH was naturally close to 7 to start with.

Nitrate Levels Aren’t Rising Significantly

Ammonia levels rise as soon as organic matter is added to the tank and starts to decay, however Nitrate rising is the first sign that your aquarium is starting to cycle. However, sometimes in an unplanted aquarium nitrate levels remain stubbornly at 0, and ammonia is not processed.

If you are doing a fishless cycle remember that you still need to use a water conditioner or RO water. Even if there is nothing on your tank besides gravel and water, bacteria are still living beings who don’t appreciate the chlorine and heavy metals present in tap water. You may have some bacteria, but you are killing it every time you make a water change.

Regarding water changes, if you clean up the gravel using a gravel cleaner you may be taking all the good bacteria away with you. Nitrifying bacteria will not only colonise the filter, but also every surface in the aquarium. Try cleaning only a third of the gravel each time you perform a water change, so the bacterial colonies have a chance to establish themselves.

You don’t need to add bacteria to the aquarium in order to start the cycle, because there is bacteria everywhere and it will find its way into the aquarium. However, you must make sure you don’t kill or remove it before it can become established.

My Aquarium Has Started Cycling Again

At some point, testing the water results in no ammonia and no nitrites, and your aquarium has cycled. Until you add more fish, and the subsequent ammonia spike has your running for the buckets to perform an emergency water change. Can a cycled aquarium start cycling again? The answer is yes.

Remember, the cycling process is just encouraging the growth of enough bacterial colonies to deal with the bioload of the aquarium. If you have very small bioload, for example, just a few danios, you will have just enough bacterias to deal with the waste produced by them. If you suddenly add all of your remaining fish stock, the bacteria won’t be able to cope and the ammonia will spike, killing your fish.

The only solution to this is to avoid mini-cycles by stocking your tank slowly. As tempting as it is to drop a lot of fish on your big aquarium, they will be much happier if you just add a few each week and feed them sparingly until they feel at home.

Those are some common issues when cycling an aquarium, but each tank is different. What are your tricks to get your aquarium to cycle successfully?


  1. Help please.

    How many platys should be used to cycle a 10 gallon tank? I have two in there for three weeks and Ammonia never goes over .25.



  2. I have had my 2 foot by 1 foot tank since feb I hag just plants for a few weeks, added 6 Molly and the plants and fish doing well. Snails came with the plants and growing, my fish even had babies and o have 3 fry. Added 4 Molly and 2 cat fish yesterday. 1 Molly died due to stress I think. Still showing no signs of nitrites but my plants are growing like crazy

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