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Fishes are cute - you can look at them all day long. Do you know what's not so cute? Their waste.

One look at fish waste, and you may feel the irresistible huge to get it out of your aquarium as soon as possible. The sight is worse if you have fine light-colored sand.

The problems don't stop with the appearance. Like most kinds of animal poop, fish waste may be unsafe for some of the creatures in your aquarium.

Unfortunately, we can't stop our fish from passing waste, can we? Your best option is to remove the waste. If you've ever tried, you will notice that this too can be tricky.

So, how do you do it?

This guide will answer all your burning questions about fish poop and the methods to remove it from your aquarium. Yes, it's possible to have an aquarium free of fish waste and other impurities so that it remains clean and beautiful.

Read on to find out how to remove fish waste from aquariums, plus everything else you need to know about fish poop and keeping your fishes safe.

Is Fish Waste Harmful? 

This is probably the question at the top of your mind, and the answer is a little complicated. We'll examine how harmful fish waste is to fishes and the aquarium plants since fishes aren't the only aquarium occupants.


Fish waste constitutes not only fish poop but also uneaten food and other deceased fish. On the one hand, fish poop is not harmful to fishes because it isn't a source of toxic ammonia (all the ammonia would've already been excreted from the gills).

On the other hand, uneaten food and all the other organic leftovers will decay and produce ammonia spikes that can harm your fishes.

Aquarium Plants

Fish poop decays in the substrate and will boost the growth of some of your aquarium plants. This is not to say they can be used as subs for fertilizers because they won't perform.

Here’s the deal:

Most fish waste is harmful to fishes, and fish poop only helps aquatic plants grow, which will not solve your fish waste problem.

Why Do You Need to Remove the Fish Waste? 

Keeping your aquarium clear of fish waste is necessary for the following reasons:

Reduces the concentration of harmful compounds

In the nitrogen cycle, ammonia turns to nitrite, and this will in turn to nitrate. Ammonia and nitrite are harmful to fish, and most aquarium ecosystems don't have the ideal conditions to handle nitrate.

Bacteria colonies in your fish tank can help convert the harmful compounds to nitrate, which isn't as harmful to fish as the other substances. Regular water changes remove nitrates, and unless you have a large concentration of them, you have nothing to worry about.

Replenishes Important Minerals

In fishes’ natural habitat, there is a constant supply of nutrients, vitamins, and minerals. The filter in your aquarium will remove these essential elements, or they will reduce gradually as your aquarium inhabitants use them to grow.

If fishes are left in the water with either a high or low supply of minerals, it can lead to osmotic stress, then osmotic shock, and ultimately death. Changing the water will give your fishes the fresh supply that they need for growth.

Gets Rid of Decaying Waste materials.

Organic matter is any waste that is a natural by-product of having a tank of fish that is fed regularly. Food waste and other organic issues get broken down in your tank to release phosphates, toxic nitrogenous products, and harmful chemicals.

These harmful substances will reduce the water quality and, in some cases, make the environment acidic. pH swings and the buffering capacity of the water will also be affected.

Step-By-Step Guide to Removing Fish Waste

Before we break down the steps, you need to get all your equipment ready, which include:

  • A dedicated bucket of about 5 gallons
  • Thermometer
  • Filter media
  • Water conditioner (Chlorine remover)
  • Filter brush
  • Water testing kit
  • Old bath towels
  • Algae pad/magnet
  • Paper towels
  • Siphon gravel vacuum
  • Razorblade
  • Lime remover/glass cleaner
  • Bleach

Freshwater Aquariums

  1. Fill a bucket of water and add a water conditioner. It would be best if you did this the night before so the chlorine would have evaporated and the water will be safe for your fish.
  2. Check the water the next day for parameters such as hardness, temperature, and pH to ensure it matches your aquarium and fishes.
  3. Position your water heater properly and turn off your filter.
  4. Use your algae pad to clean the glass by rubbing it across. Try not to scrub it too hard.
  5. Remove the decorations and use boiling water or bleach to clean them, thereby killing the beneficial bacteria.
  6. Siphon the water into the bucket and while you do this, go through the gavel to clear out as much waste as you can.
  7. If you use sand, use the hose part of the vacuum and keep it at a distance of 1 inch to the surface to get all the waste.
  8. Rinse your filter in the tank water you drained from the aquarium.
  9. Use a thermometer to confirm that the temperature of the treated water is correct for your tank.

Saltwater Aquariums

  1. Buy RO/DI water from your fish store or a system that produces the water. Only use tap water if you have only fish in your aquarium, and the supply is perfect. Also, make sure the Total Dissolved Solids test is between 0-10.
  2. Dechlorinate the water and add a salt mix with a brand you trust. Use a heater and powerhead to add moving warm water to your salt mix.
  3. Leave the water treatment till the next day to let the salts dissolve properly.
  4. Unplug all the electrical elements of your aquarium and remove any ornaments or decorations. You should also remove all artificial plants.
  5. Clean the gravel and drain the water with a siphon gravel vacuum attached to a hose. Block the tube end to reduce the siphoning speed and ensure the gravel does not enter the tube.
  6. Place a magnet of the magnetic algae cleaner on the inside and the other magnet on the outside of the aquarium. Drag the outer magnet around so the inner magnet removes the algae.
  7. Remove the filter and rinse it in the bucket of water you just removed from your tank.
  8. Replace the water with the already treated one, ensuring the salinity, pH, and temperature matches the tank.


Do Some Fish Species Eat Waste? 

Clean-up crews are fishes you put in the tank to clear the waste in it, such as deceased fish and uneaten food. Contrary to popular opinion, these fishes don't eat poop or serve as substitutes for cleaning the tank.

Examples of such fishes are shrimp, corydoras, snails, and plecos. If they are compatible with your tank, you can add them to make your cleaning easier and reduce the dirt in your tank.

Clean-up crew also eat the organic leftover, which would otherwise turn to ammonia that could be harmful to your fishes. 

What’s the bottom line?

Don't add clean-up crews to your tank if you're looking for ways to remove poop from your aquarium because they also produce poop.

You can add a clean-up crew if you notice a lot of leftover food settling at the bottom of your tank. The fishes will help you clear that out and keep your aquarium looking relatively clean.

How to Reduce Fish Waste in My Tank

Still, having a lot of fish waste in your tank after regular cleaning? Here are some factors that determine the amount of fish waste in your aquarium so you can reduce them.

Amount of Food you Feed Them.

You should either reduce the frequency at which you feed your fish or limit the amount of food you provide them. Any of both options will ensure that your fish get what they need to survive without building up leftovers in your tank.

It will also reduce the amount of poop the fishes release into the tank. Small fish fishes only need to be fed once a day, and it should be an amount that they can finish in 5 minutes or less.

Larger tropical fish may need to eat twice a day but only give them a quantity to finish in 3 minutes or less.

Type of Food

Some foods are digested faster than others and will result in more waste from your fishes. Also, fish will eat more of their favorite foods than others.

How Can Intake Sponges and Flow Help with Fish Waste?

You may use intake sponges to reduce the fish waste in your tank by adding them to the filter intake. This way, you can alter the flow in your tank as you wish.

If you have a bigger aquarium, powerheads will work fine to help change the flow to the direction you want. Small water pumps with suction cups are a good alternative if you don't have a large aquarium.

Changing the flow will help you direct the fish waste in your tank towards the filter intake. This way, you can remove the intake sponge and wash to remove the fish waste.

Here’s the catch:

You should only increase the flow if you have fishes that can handle more flow.

What Does Fish Waste Look Like? 

Fish poop will vary depending on your fish species, but they usually look gross and ugly. They will be more visible in your aquarium if you have light sand. Sometimes the poo of your fish could also match what they have been eating.

How Do I Select a Gravel Vacuum? 

There are many options in the market for a gravel vacuum. It gets confusing when you try to figure out which will work best for you. Here are a couple of tips to help you select one:

  • Cost: Some are expensive, but you can get a cheaper vacuum so long as it's functional.
  • Size: If your tank is big, you'll want to go for a longer one so you can reach the base of your tank.
  • Material: Go for one made with simple and easy to clean materials.

Why Do Fish Eat Other Fishes Poop Sometimes?

As stated above, fish does not usually eat other fish poop, but there are rare cases. Fish tend to eat many of the substances they see floating in the aquarium, mistaking them for food. Sometimes, this includes poop.


There's no need to worry. If your fish eats anything that isn't food, they'll most likely spit it back out, including any fish poop they may have swallowed.


There you have it! Now you have all you need to know about fish waste and how to handle it. This guide should help you keep your aquarium free from any waste as long as you follow the steps described and regularly clean it.

Next time you want to clean your tank, you should have no problem selecting a gavel vacuum and identifying the fish waste in your tank. You can also use the intake sponges to reduce the waste flowing in your tank. This hack will make cleaning your aquarium a lot more convenient.

About the author 


My name is Eric. I'm the owner of snugaquarium.net and a writer with a passion for aquariums and fish-keeping. I love to watch the three different species of freshwater fish floating around in my homemade aquarium in my spare time.

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