How to Change the Substrate in the Tank

Changing the substrate in the tank is one of the most dreadful and stressful experience not only for the fish and shrimp but for the hobbyist as well. If you have had the ‘pleasure’ of doing it before, you can understand the scope of potential problems it can cause and why we often keep putting this off.

Unfortunately, lots of people do not understand that changing the substrate can disrupt the nitrogen cycle in the tank or put it through a mini-cycle as the bacterial levels build up again.

In this article, I will talk about different ways of how to change the substrate in the tank step-by-step, pros and cons, and what we can do to increase the chances of doing it successfully.

However, before we jump into discussions, I need to start off with some basic explanations regarding beneficial bacteria and ‘mini’ cycles. It can be especially helpful for those who are new to this hobby.

What are the Beneficial Bacteria in the Tank?

Ammonia is released by fish, shrimp, snails, etc. as waste products, which produce ammonia. Beneficial bacteria are used to cycle our tank because these bacteria eat ammonia and nitrites products. So, the accumulation of high concentrations of ammonia and nitrites, which is toxic to fish and other aquatic organisms, is prevented by nitrifying microorganisms (Beneficial bacteria). This is called a nitrogen cycle.

Basically, the nitrogen cycle is THE MOST important process in the aquarium. It refers to the establishment of beneficial bacterial colonies. Therefore, our goal is to keep it as stable as possible.

There are many species of beneficial bacteria but all of them can be divided into two main categories:

AOB (Ammonia Oxidizing Bacteria, Nitrosomonas sp.) that converts our ammonia into nitrites.
NOB (Nitrite Oxidizing Bacteria, Nitrospira ) that converts our nitrites into nitrates.

However, sudden and big changes in the tank can disrupt this cycle, and harm the beneficial bacteria. Depending on how badly those beneficial bacteria were hurt, we can have a so-called mini-cycle, or in the worst-case scenario, even the cycle crash.

Read more about it in my article – Everything about Beneficial Bacteria in Aquariums.

What is a Mini-Cycle in the Tank?

Mini-cycle (also know as New tank syndrome) is the result of an insufficient amount of beneficial bacteria compared to the existing bioload in the tank.

We can often see mini-cycles in newly set-up aquariums when they are caused during the introductory phase by adding too many fish at once.

That is why it is never recommended to fully stock the tank right after the cycling process. We have to keep in mind that the tank is not established and that the bacteria colony is not large enough yet to consume a lot of bioload.

Although in a well-established tank it is a lot harder to cause these mini-cycles to occur, it can still happen if we remove some part of nitrifying bacterial colonies from the tank.

How long does mini-cycle last?

In most cases, mini-cycles last anywhere from a few days to a few weeks. Mini-cycling is different for each tank, just like cycling.

Where Does Beneficial Bacteria Live?

There are two popular misconceptions regarding beneficial bacteria:

They exist in the water column of the tank. This is wrong.
They exist in the filter of the tank. This is also wrong to some degree.

Beneficial bacteria attaches itself to any surfaces throughout the aquarium, it is on the décor, live or fake plants, driftwood, rocks, tubes, heaters, glass, substrate, and, of course, in the filter of your tank.

Every other surface you may have within your aquarium targets for bacterial growth.

Although it is true that the majority of your bacteria is living in your filtration system, it does not always mean that it can be enough to handle all the bioload in the tank by itself.

The substrate also covers a huge portion of the tank, therefore, changing the substrate in the tank can be detrimental to the aquarium’s bacterial colonization because it is going to be a big hit to the nitrogen cycle.

Two Ways of Changing the Substrate in the Tank

Changing the substrate is a very debatable topic. Even though everybody does it their own way, there are 2 main techniques of doing it:

1. Partial substrate change.

This method is often used with large tanks, or when it is not possible to relocate the livestock. Therefore, people change 1/3 or ¼ of the substrate once every week.

PROS	CONS
Suitable for any tank	The process may last for weeks
Safer	Very messy
Does not require a holding tank	Very stressful for the fish

2. One-time substrate change.
This method cannot be used in all tanks. The main advantage is that it can be done in one hour with good preparation.

PROS	CONS
Suitable for small to medium sized tanks	Risky
Fast	Requires a holding tank
Less messy	Stressful for the fish

Preparation Tools

To change the substrate, you need to have a plan and a checklist of materials you need.

New substrate (Sand, gravel, soil, or dirt)
Quarantine or holding tank (large enough to keep all your fish, shrimp, snails, etc.).
Aquarium water buckets or canisters.
Buckets with dechlorinated water.
Nets.
Large sieve.
Buckets for the old substrate.
Scoop or small dustpan to remove the old substrate.
Spray bottle.
Tweezers.
Siphon (for example, the Python water changer (link to check the price on Amazon).
Water treatment (for example, Seachem Prime, Seachem Stability, or similar products).

Preparation Tips

Whenever it is possible, install the second filter in the main tank 2 weeks before that. This time will be enough for bacterial colonization. Consider it as your safety net.
Do not feed fish the day before you decide to change the substrate. It will reduce the amount of waste produced in the quarantine or holding tank.
Do not change the substrate in the tank in the evening. If anything goes wrong, it will be harder to fix.
Make sure not to clean filter sponges or other filtration components at the same time! It will reduce the amount of beneficial bacteria. Even more, I would not recommend cleaning it at least 2 weeks before that as well.
Prepare your new substrate. It must be clean and free from any detritus. If you do not do that, expect to have milky water for weeks!

Important: We can often see that the substrate is marketed as “pre-rinsed” or “pre-cleaned” by manufacturers. DO NOT trust them. Even though the substrate itself can be clean, their bags often contain dust, debris, grit, or other residues from the workshop it was packaged in. We do not want any of that in our tanks.

How to Prepare Sand for a Tank

If you forget to rinse your sand, your tank can turn into an uninhabitable cloudy mess. It’s normal for sand to take some time to settle to the bottom of a tank. However, it will take way longer for the sand to settle if you forget to rinse it.

When I was a beginner trying out sand, I made the mistake of not rinsing my sand before adding it to the tank. My sand never settled naturally and I ended up removing it entirely to try again.

The rinsing process to clean sand is really easy.

First, you take your sand and sieve it into a bucket.
Next, fill the bucket with water. Go ahead and pour out the water. The water should start out cloudy and gradually become cleaner as you continue to rinse the sand.
Be careful not to lose your sand during the rinsing process.
Repeat the process by adding and dumping water until the water starts running out clear.
Important: When you think that sand is absolutely clean – rinse it again! I am completely serious. Sand has lots of tiny detritus particles. This is not funny to have sand-storms in the tank.

Depending on how much sand you have, it usually takes from 15 minutes to 1 hour.

How to Prepare Gravel for a Tank

Place a sieve, over the bucket, and fill it half full of gravel.
Start pouring water over the gravel in the sieve, while gently shaking it. Do it until the water runs clear and you are satisfied with the result.
Place the gravel into the bucket.
Fill the bucket with tap water. The water should completely cover the gravel.
Stir and move the gravel around (use a stick if necessary).
Leave it in the bucket for 5 – 10 minutes. It will soften up any dust and debris that may be on the gravel.
Note: If you have some serious doubts regarding the gravel or you picked it yourself (do not do that!), use a bleach. Mix bleach and water in the proportion of 1:10. Do not soak gravel in bleach more than 15 minutes, it may start breaking due to the chemical reaction. Rinse the gravel several times with tap water to make sure all the bleach be washed away.

How to Prepare Soil for a Tank

First of all, you need to do your research because some products can leach ammonia. Therefore, before changing the substrate in the tank, we have to get rid of it.

Place the soil into the buckets.
Fill the buckets with tap water. The water should completely cover the soil.
Rinse it in the buckets. Stir in very vigorously! Ideally, you need to do it at least 2 times a day because ammonia concentrates in the lowest section of the substrate.
When your test kit (see the price on Amazon) reads 0, you need to wait at least 1 week before using it. (Keep stirring it at least 1 time a day).

For example, if you check my article “Top 5 Substrates For Planted Aquariums” you will see that many products leach ammonia.

Changing the Substrate in the Tank

Once everything is ready and all preparations are done, it is time to actually change the substrate in the tank.

Drain half of the water into your buckets.
Take out driftwood, rocks, decorations from the tank and place them in the buckets with the aquarium water.
Remove your fish, shrimp, snails, etc. to the quarantine or holding tanks.
Cover the quarantine tank with a blanket to reduce the stress of your pets.
Move your filter to the buckets with the aquarium water.
Move plants to the buckets with the aquarium water.
Note: If there are many small fish and/or shrimp in the tank, we might have to remove plants before removing the animals. It can be close to impossible to catch them in the plants. The problem, though, it will make water cloudier, making them also hard to catch.
Vacuum the old substrate in the tank really thoroughly. Otherwise, it can turn the water really murky.
Drain the rest of the water to other buckets.
At this stage, there should be nothing left in the tank but the old substrate.
Use a scoop or a small dustpan to remove the current substrate.
If you see that the process takes more time when you expected. Use a spray bottle with the aquarium water (or dechlorinated water) to spray the inside walls of the tank. It will help beneficial bacteria to survive.
DO NOT clean the inside walls of the tank!
Add a new substrate to the tank.
We are ready to start filling the tank with the water. Put something (for example, I use an ordinary plate) on the substrate to prevent any disturbance.
Use new dechlorinated water to fill the tank.
Add driftwood, rocks, décor.
Move back your plants. Use tweezers if you need to root them.
Install filtration and lighting.
Add Seachem Stability (or similar products) to compensate for the loss of beneficial bacteria.
Done

When should we add our pets back?

Check your water parameters for the next week before adding the animals. Depending on the substrate, it may leach ammonia even after it was at 0 in the bucket.

That is why it is very important that the quarantine or holding tank should be cycled as well! We never know how long we will have to keep them there. If it is not cycled, everything will die there.

Can We Change the Substrate without Quarantine Tank?

In some cases, people do not have another cycled tank to keep their fish for a week or more. What can they do?

Generally, you can only hope for the best that the filter has enough beneficial bacteria to avoid mini-cycle.

The algorithm of changing the substrate remains the same. Except that all animals should be put back in the main tank right after the process is done. In addition:

Cover the tank with a blanket to reduce the stress level.
Do not feed them this day.
Use any water conditioner (like Seachem Prime or similar) to bind ammonia and prevent any spikes.
Regularly test your water to see if the cycle has crashed. You may have to do daily water changes to reduce nitrates, etc. in the tank.
Note: If you keep shrimp, big, and (or) frequent water changes can cause molting problems.
Larger tanks have more chances to avoid mini-cycles. The main advantage of the larger system is that the more water volume and the more surface area you have, the more forgiving it will be.

Can I use Old Water After Changing the Substrate?

People often use old water after changing the substrate. Is it reasonable?

I do not think so.

As I have already said, the water actually does not hold the beneficial bacteria so you do not need to keep it. The only reason to use it – because our animals are already acclimated to it. However, this argument is valid only for a short period of time.

Bottle Trick with Sand

This trick can be used only when we are partially changing the substrate in the established tank.

Take a plastic bottle and fill it with sand (about 2/3).
Submerge the bottle into the aquarium and let the water fill the rest of the volume.
Turn the bottle over and let the sand come out from the bottle exactly where you want it to be.
While the sand comes out, it is replaced by water. When water goes through the sand it rinses it and keeps all the detritus in the bottle.
Carefully remove the bottle with dirty water.

Trick with Active Substrates for Shrimp Tanks

Some shrimp species (mostly Caridina species like Crystal shrimp, Blue bolt shrimp, etc.) require active substrate. Active (buffered) substrate means that the substrate alters water chemistry (pH).

The buffering capacity of the water (KH) neutralizes the acidic soil.

Depending on how much of a buffering system in the water, the active substrate may last from several months to 2 years. Nonetheless, eventually, any active substrate stops being active and becomes inert.

In order to avoid the problem of changing the substrate, or at least make it simpler, some professional shrimp breeders use a bare bottom tank (or very thin inert substrate) with a large pot filled with active substrate.

Therefore, every time they need to remove or change the substrate in the shrimp tank, they simply take out the pot and replace it with another one.

If you decide to use this trick, DO NOT forget to prepare the soil beforehand! It may leach ammonia. In addition, you need to have some beneficial bacteria as well, otherwise, you may get a mini-cycle.

Although it may not look really nice. Nonetheless, it is efficient and it works.

In Conclusion

Changing the substrate in the tank can be a real pain, especially in large aquariums. If we do not do it the right way, the tank may take months to balance back out. It is a big job and I would not advise doing it without meticulous preparation.