How To Remove Fish Waste From An Aquarium

Last Updated on 2023-08-05

If you are wondering how to remove fish waste from an aquarium, then today is your lucky day! In this article, we’ll go over some of the best methods for removing wasted food, shed scales, and fish poop from your tank. Just be sure to create a regular schedule because a clean tank is absolutely vital for the health of your fish.

Let’s start with why this is so, and then we’ll move on to the steps that you will need to make this happen.

Why Is It So Important To Remove Fish Waste?

Fish waste can build up quickly. Fecal matter, urine, discarded scales, uneaten food; it all adds up and pollutes the water and the gravel floor of your beloved tank. Regular cleaning is therefore going to be critical, as failure to do so can cause the inhabitants of your tank to possibly sicken and die.

Below you’ll find the most important reasons why a clean tank is vital.

Clogged Equipment

As waste builds up in the water, your filter is forced to work just a bit harder. If you aren’t changing your filter at an increased pace, it runs the risk of clogging up. Scales, pellet bits, and fish food get sucked in until they reach a critical mass, and then you’ve got a problem.

If it happens when you are out of the house, it could be a very bad problem indeed.

Regular tank maintenance will help to ensure that your filter only has to do the work that it is rated for, and this is very important if you want to keep your fish both healthy and happy.

Ammonia, Nitrites, And Nitrates

Fish waste, be it poop, uneaten foods, or natural shedding, will have an enormous impact on water quality. Urine raises ammonia levels, and fish poop raises nitrites and nitrates, and your water must be closely monitored, or your fish will start to get sick.

While the nitrates are the least harmful and actually good for your plants, the nitrite and ammonia spikes can be fatal and will sicken the fish with the least tolerance to these levels first, with hardier fish soon to follow.

Cleaning your tank regularly is vital.

Increased Chance Of Disease

Fecal matter and the general uncleanliness of the water will promote the kind of bacteria that is not beneficial to your tank. Also, the general foulness increases the likelihood of diseases. Just think of it like you would with dogs or cats in your house. If you never cleaned up after them, everyone in the house will suffer from the smells, increased chances of infection, and likely get sick.

It’s the same for your fish. They need a clean home if they are going to thrive. The good news is that it is easy to set up a schedule for cleaning, and there are a number of methods that you might employ. Let’s take a look at these in the next 2 sections.

How Do You Remove Fish Waste From An Aquarium?

When it comes to ‘fish waste’, in this section, we’ll focus on wasted bits of food. These don’t break down the same as other ‘fish deposits’ and can play havoc with your water levels if they aren’t sufficiently dealt with. Some people will tell you ‘eh, they’ll eat it later’, but one look at their setups should tell you all that you need to know.

That waste needs to be removed, and below we’ve got the best ways to do it.

Aquatic Vacuums Are Worth Their Weight In Gold

A gravel vacuum is going to be the best and easiest way to do a little quick-cleanup on a regular basis. The gravel vacuum works by creating a ‘siphon effect’ that provides a small amount of suction for clearing up wasted food, fish poop, and more.

You can get them at most local pet stores and any aquarium supply, so save yourself a lot of time and go with an aquatic vacuum.

Consider Adding ‘Cleaner Shrimp’ To Deal With Excess Foodstuff And Algae

While snails are cute and might clean a little, they also produce more waste than they tend to clean. This is not the case with a number of species of ‘cleaner shrimp’. Red Cherry, Amano, and Ghost shrimps love to eat algae and fish pellets that their tankmates miss on the first go.

Adding a colony of shrimp to your tank is quite easy to do, and it means less cleaning of wasted food for you! You’ll still have to do some regular cleaning, but these little guys will definitely help with the wasted food and clean the algae off of your plants and glass in the bargain!

Clean It Up After Feedings With A Mesh Net

If you don’t have or want a vacuum, you can always make do with a mesh net, provided that the mesh is fine enough to make a difference. If you regularly clean this way, you can generally get away with just a little ‘spot cleaning’ by scooping up uneaten food with your mesh net.

Cleaning Gravel Manually

The manual way of cleaning up your aquarium gavel is basic but a little time-consuming. You’ll need a plastic bucket, and you’ll want to transfer your fish to a temporary tank for this process so that you do not stress them out.

Once the tank is vacated, simply scoop out the gravel into your bucket, after which you must fill it with warm water. You’ll need to shake up the gravel a bit to loosen up the waste, and holding the gravel in place, you pour out the warm water and repeat.

You should do this until the water involved remains relatively clear, and your gravel is clean. Return it to the tank and replace any displaced water, dechlorinate if your water has been treated, and reintroduce your fish carefully back to their newly-cleaned tank.

Preventative Maintenance: The 2 – 3-minutes Rule

Try to ensure that you aren’t overfeeding your fish so that you can save yourself additional maintenance. A good rule is the ‘2 – 3 minutes’ rule. Feed your fish in amounts that only take them 2 – 3 minutes to gobble up.

Once you’ve learned the ‘magic amount’, then less food will be ending up ignored on the bottom of your tank, and you’ve saved yourself some time and reduced the chances of unwanted fluctuations in your fishes’ water levels.

How To Remove Fish Poop From An Aquarium?

Now that we’ve gone over methods for dealing with the wasted fish food, we’ve got a section for dealing specifically with fish poop. Mind you; the best approach is just to take all of these cleaning recommendations into consideration to adopt a strategy for everything so that you can just clean it all at once.

To that effect, below, you will find a thorough cleaning method that will definitely deal with fish poop and other wastes in one fell swoop.

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Cleaning Fish Gravel Thoroughly Without A Vacuum

Manual cleaning is a great way to ensure that the environment is well and thoroughly cleaned. This should be done ideally every 2 weeks or after a water change so that the environment is always at its best, though times will vary depending on factors like ‘cleaning fish’ and the like, so use your best judgment.

Just keep the tank clean!

Prepare A Holding Tank

First, you will need to prepare a holding tank so that the cleaning process doesn’t frighten your poor fish into shock. You want a sterile tank that is free of chemicals and detergents to start with. No exceptions. Chemicals could sicken your transferred fish, so this step is vital.

Treat this process much like you would a water change, with new water making up about 50% of this tank’s water and water siphoned or otherwise transferred from your old tank making up the remaining 50%. This will help to ensure a comfy transfer. Adjust the new tank to a compatible temperature as well before transferring your fish.

Transfer Your Fish

Break out your mesh net, and it’s time to use a light hand and to carefully scoop up your fish and deposit them into the holding tank.

Take Out Decorations

Remove decorations, such as the classic treasure chest and other items that you have in your tank to spice up the aesthetics.

Unplug Your Equipment

Unplug your electrical equipment so that we don’t get undue stress with the gravel removal, and we are ready to proceed to getting that gravel clean.

Remove Gravel But Set Some Aside

Use a handy cup and start scooping out your gravel, placing most of it into a sieve. Save a cup or two of the gravel, placing it aside. This is important, as your tank naturally builds up colonies of beneficial bacteria, and we want to save this.

Sieve, Rinse, And Repeat

Start running clean water through your sieve, mixing up the gravel as you go so that the water will rinse the gravel thoroughly. Once the water sifts through the gravel and your sieve is clear, then the actual cleaning portion is complete.

Let It Dry And Mix The Old And New

Let your newly cleaned gravel have a little time to dry. Once it is fully dry, then we’ll want to mix it in with the gravel, which we put aside.

Return The Gravel And Decorations And Refill

Return the gravel to its original tank and add in your decorations back to where they go. Once everything is back in place, then you are ready to refill your tank with water back to its previous level and volume.

Dechlorinate The Water

As the cleaning process inevitably involves tap water, there is going to be residual chlorine in your gravel. This means that you will want to dechlorinate the water thoroughly before you put your fish back. Don’t turn the equipment back on during this part of the process so that your dichlorination agent will work its magic without disturbance or unintended filtration, diluting its strength.

Turn On The Equipment

Once the tank is dechlorinated, we’re almost done. Turn your equipment back on and let the water heat up to the proper temperatures so to ease the re-homing process on your fish.

Move Your Fish Back To Their Newly-cleaned Home

Transfer your fish back to their freshly cleaned home. If you have cleaner fish, such as a shrimp colony, be sure to follow an acclimation process such as the ‘drip method’ to make absolutely sure that the transfer doesn’t shock their systems, and you are done!


Now that you have the basics, here is a FAQ just to supplement some of what we have learned today. You’ll find the most commonly asked questions in the sections below.

Do Snails Eat Fish Waste?

Snails clear up some tank waste, but they don’t eat fish poop. They will mostly just consume wasted fish food and other impurities in your tank. That poop, however, is definitely not going to be eaten by your snails unless ingested by accident. In those cases, they’ll simply spit it out.

Do Shrimp Eat Fish Waste?

Shrimp, like snails, won’t eat poop, but they will eat wasted food and also dead fish. They might also eat the gelatinous coating on the bodies of snails, so this is something to keep in mind when deciding your tank inhabitants.

Do Algae Eaters Eat Fish Poop?

No. As their name suggests, they are mostly interested in your algae. Any accidental poop ingestion will be followed by spitting, just like with snails or shrimp.

Is Fish Waste Good For Plants?

Yes and no. A small amount, such as the waste produced by the Menhaden fish, is good and will promote plant growth. Too much, however, can have a bad effect on plant growth. Regular cleaning will help them get some use out of the fish waste without overdoing it.

What Breaks Down Fish Waste?

The ammonia from fish waste is broken down by bacteria in the tank, breaking it down into nitrites and further into nitrates. This is called a ‘nitrogen cycle’. Unfortunately, ammonia and nitrites are toxic to your fish, which is why monitoring water levels and routine cleaning are vital to the health of your fish.

Recap Time – Here Is What We Have Learned Today!

Cleaning your tank on a regular basis is ignored at your own (and your fishes) peril. If you hate cleaning, consider adding a colony of cleaner shrimp to help with the extra foodstuffs, and try managing the amounts that you use in feedings to minimize uneaten food amounts in your gravel.

Finally, regularly clean that gravel when you change the water or every 2 weeks and don’t forget to save the beneficial bacteria by keeping a cup or two of the old gravel. This will help to ensure that your tank environment is always at its best and keep your fish both happy and healthy!

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