How To Clean Fish Poop & Fish That Eat it! [GROSS!]

Estimated read time 13 min read

In this article, you’ll learn how to clean up the fish poop that’s been collecting at the bottom of your aquarium.

We’ll also explain why it’s important to clean it up, why you might have too much fish poop, and even some of the benefits if you can believe that.

Let’s begin.


What Is The Difference Between Fish Poop & Other Waste In Your Aquarium? 

An aquarium may be a small part of your home, but for the fish inside, it is their home. It’s their whole world, and it tends to be inherently messy.

In nature, the fish eats and excretes in the same environment, but it tends to be either a moving body of water (river, tributaries, etc.) or a massive body of water (lake, pond, etc.).

Since fish poop is distributed over a large area, it doesn’t contaminate the water extensively.

On the other hand, an aquarium is a small, enclosed environment, and fish poop is just one type of waste found there.

So before you learn how to clean fish poop and its contribution to an aquarium’s contamination (something your filter fights against 24/7).

It’s essential to understand the different waste types that “grace” your aquarium with their “nasty” presence and how they are separate from fish waste.

There are two core categories of waste in your aquarium:

Organic Waste

Any waste from living things and organic elements (food mostly) is considered organic waste in your aquarium.

By that definition, fish poop is organic waste. Other forms of organic waste include:

  • Fish pee (it’s more diluted for freshwater fish compared to saltwater)
  • Dead plant matter (if you have a planted aquarium)
  • Leftover food (which decomposes over time)
  • Dead fish and other organisms that are not removed from the aquarium
  • Algae

The difference between fish poop and other organic waste mainly pertains to how long it takes the beneficial bacteria to decompose it and how rapidly it contaminates the water.

It’s also important to note that fish poop might be helpful in some scenarios, but that doesn’t mean you can leave it all there and don’t care about cleaning at all.

Inorganic Waste

Inorganic waste is what doesn’t quickly decompose in the water.

Bits and pieces of plastic ornaments in the aquarium might technically be an inorganic waste, but they don’t usually impact the chemical balance of the aquarium.

But the real danger of inorganic waste comes from what organic waste decomposes into, i.e., ammonia, nitrate, and nitrite, three inorganic compounds which can be harmful to the fish in large quantities.

The significant difference between fish poop and inorganic waste is that fish poop might not be harmful to the fish or other organisms in its raw form.

But in their natural form, the inorganic waste can be deadly to the fish, especially if the nitrogen cycle is disturbed.

Related: Learn How To Remove Ammonia From Your Fish Tank

Why Might You Have A Lot Of Fish Poop?

There are two reasons you might have a lot of fish poop (apart from the fact that you are not cleaning your aquarium as frequently as you should)

One is qualitative and one quantitative.

The qualitative factor is the type of fish you have in your aquarium and the type of food you use.

Some fish tend to produce more waste than others (if we compare them weight to weight).

Oscars, Plecos, Goldfish, and Clown Loaches are some of the most aggressive waste producers.

Similarly, each fish has its favorites when it comes to feeding. Even among omnivores, who technically eat everything, some might prefer live or frozen feed over flakes and food pallets.

The more they eat and digest, the more of their “mess” you’ll have to clean up.

However, uneaten or partially eaten food can be just as (if not more) contaminating for the aquarium.

But even the qualitative factor is reliant upon the quantitative one, i.e., excess food.

The more food you use, the more fish waste you’ll have.

Plecos are aggressive algae eaters, and they consequently produce more waste.

Your feeding frequency and the amount will depend upon the kind of fish you have.

Lazy fish that stick to the bottom and don’t move around a lot might not need as much food as small, active fish that keep zipping around the aquarium.

Based on the size and activity of your fish, you may need to feed them once or twice a day, but only enough feed that they can finish in three to five minutes.

The case would be different for algae eaters.

If there is a lot of uneaten food accumulating on the substrate, it might indicate that you are overfeeding your fish, which can cause more insidious problems than a large quantity of fish poop.

A high fiber diet and digestive problems can also cause the fish to poop more.

How Much Fish Waste Is Okay?

It depends on the aquarium’s size, the fish you have, stocking, whether it’s planted or not, how healthy is the nitrogen cycle, and a few other factors.

In an ideal world, you might not let any fish waste accumulate at all.

But we don’t live in an ideal world.

Also, suppose you disturb the gravel and your whole tank to get every speck of fish waste out of the aquarium.

In that case, it might be counterproductive because instead of leaving relatively harmless waste on the gravel, you will be disturbing the cycle and bacteria growth surfaces.

Then there is the fish—some fish like relatively cleaner water and higher oxygen levels.

Suppose there is too much fish waste being decomposed by good aerobic bacteria (that consumers oxygen).

In that case, it might not be suitable for your fish unless you are pumping an adequate amount of oxygen in the aquarium to make up for it.

Your filtration system keeps some of the most toxic effects of decomposing fish waste at bay.

So there is no one-size-fits-all answer to this question.

However, a good practice is that you shouldn’t let the muck (of which fish waste is just one element) pile up so much in the gravel that it starts changing the water’s color and odors start exuding from your tank.

The problem with “accumulating” fish waste is that in most cases, you can’t because it starts to decompose.

But some solid fish waste remains on display on your substrate and becomes part of the general much.

If you have plants, the nitrates your decomposed feed converts into will act as their natural fertilizer.

So in a planted tank, you might be able to hold on to (though we highly recommend that you don’t) fish waste for more extended periods.

Generally, a good practice is to do weekly partial water changes and vacuum the substrate to take as much food waste and fish waste out of the tank as possible.

The fish waste that accumulates between weekly changes is generally okay.

How To Clean Fish Poop In Your Aquarium

Once you have decided to clean up the mess your friends have made in the aquarium, you may have to take a different approach depending on where the fish poop is:

From Sand

One way to remove fish poop off of sand substrate is to vacuum it out.

You can’t vacuum sand the same way you do gravel because if you dig too deep with your vacuum head, it will start pulling in the sand grains as well.

But the good news is that thanks to the compactness of the sand, not a lot goes deep in the substrate anyway.

You can get around it by sucking in the sand and pinching the intake tube to let it settle or by using a filter in the intake part.

You can also scoop the fish poop out of the sand, but it takes time and effort and will spook your fish.

A Turkey baster is another good option for sucking up fish poop from the sand.

You can also stir the sand up before cleaning, and the fish poop (being lighter) will settle after the sand.

Then you can skim your vacuum over the substrate and remove the fish poop.

A combination of a powerhead to create enough flow and a powerful filter usually takes care of the fish poop automatically.

Still, you might have to manually do the “nook and crannies” where it accumulates.

From Gravel

With gravel, going deep with your gravel vacuum is the key.

Like uneaten food, fish poop (especially the fragments that are already partially decomposed) tends to fall below and get trapped under the gravel pieces.

Thorough vacuuming to get everything that’s not supposed to be in the gravel out is how to clean fish poop from gravel.

Get It Off Plants

If your fish have the nasty habit of going brown in the green, you might have to scrape it off (wherever you can) without disturbing the plant too much or uprooting it from the substrate.

A few things you can do are:

  • Use a tiny vacuum to siphon off fish poop from plants and tight spots.
  • Redirect/use a powerhead to create a flow from the plants blowing out in the open; it might move the fish poop away from plants.
  • Turkey baster work just as well as small/tiny vacuum.
  • Tie a chopstick to your siphon’s head, sticking it out an inch or so. Use it to gently prod (or violently beat off) the fish poop away from the plant and into the suction.
  • Stir up the plants and the substrate underneath to chuck the fish poop off it and in the open water/substrate where the poop can siphon it off more effectively.

Video: How To Remove Fish Poop From An Aquarium

In this video, Simple Reef life shows you how he gets rid of all that gross in his fish tanks.

Is Fish Poop Good For Aquarium Plants?

The answer to this question is both yes and no.

The fish poop decomposes into nitrates which act as an Aquarium Plant Fertilizer. That’s the concept of aquaponics.

But if most of the fish poop is decaying away from the plant roots where they can’t absorb the nitrates, then it might simply be overloading your nitrogen cycle.

Root-feeding plants win in this area.

It also depends upon the substrate. If you have root feeders with gravel substrate, then fish poop might act as tiny root tabs if they decompose at or near the roots.

For sand, the fish poop might simply be lying and rotting on the substrate surface, releasing nitrates into the water, only a limited amount of which might be absorbed by the plants (based on planting density and plant type).

How good fish poop is for aquarium plants should always be contrasted against how bad it is for your fish.

How To Get Rid Of Fish Poop Without Removing Water From Your Fish Tank.

If you are not doing a water change and are planning to remove fish poop without removing any substantial amount of water, you still have a few options:

  • Physically scoop the poop out (people do it for their dogs and cats, fish should have equal rights!).
  • You can stir up the substrate (or use a powerhead to blow it away), especially around the areas where the fish waste is lying, and the filter will suck it up.
  • The right-sized turkey baster might help you spot clean fish poop without removing too much water from the tank.

Do Fish Eat Poop?

No. Why would they? It’s stuff they have explicitly expelled from their body because they couldn’t draw any valuable nutrients from it.

And one fish won’t eat another fish’s poop for the same reason (apart from the obvious, that it’s disgusting), i.e., it might not offer any nutritional value.

Types Of Fish That Will Eat Poop

You might see some fish nibble on fish waste, especially if it’s floating in the water before settling on the substrate because they tend to attack any floating bits of food, but once they realize what they’ve done, they usually spit it back out right away.

Fish like Corydoras and Plecos (the avid algae-eaters) are said to eat fish poop, but that’s a common misconception.

People think that because they are cleaners and bottom feeders, they might eat fish poop as well, but they only stick to uneaten food, algae, or bits of dead plants.

Types of Snails That Will Eat Poop

There are conflicting opinions in this regard, but a few snails, like Bladder snails and Malaysian Trumpet snails, are known to eat fish poop.

People who believe snails eat fish poop claim that it’s part of their natural cycle as scavengers, i.e., breaking down fish poop into more easily decomposable snail poop.

People against the idea of snails eating poop believes that as scavengers, snails might munch on anything and everything they can get their mouths on, but they might not be able to process fish waste just as fish can’t.

But the problem of the poop will remain the same (albeit at a different snail/scale) because snails would produce poop as well.

It’s up to you whether you are more interested in cleaning up fish poop or snails.

Best Fish Tank Poop Cleaner


All aquarists agree that you, the keeper, protector, i.e., the “Aquaman” (or woman) of your aquarium, is the best fish tank poop cleaner.

All you will need in most cases is a siphon vacuum.

For some heavily planted tanks (or for tanks with sand substrate), you might consider going with a turkey blaster or small vacuum for more accurate/pinpoint poop cleaning.

But remember that even if you have a good cleanup crew (fish and snail that break down detritus and food waste) and a strong filtration system, one of the best ways to keep your tank clean is partial water changes and vacuuming.

It will help you eliminate all the accumulating muck, including fish waste, off the substrate.

Poop FAQ

How many times a day does a goldfish poop?

The frequency depends quite a bit on diet, size of the fish, and overall environment of the aquarium, but a healthy goldfish might poop somewhere between five and eight times a day.

Do algae eaters eat fish waste from the bottom of the tank?

No. They might appear to be consuming/eating it when they are sifting through the debris, but they can’t process it and usually spit it out.

What happens to fish poop in the aquarium?

Most of it is decomposed.

Some relatively substantial elements take months to deteriorate, and they should be vacuumed or scraped away so they don’t contaminate the water.

What color is fish poop?

The color depends upon the diet (factors like food coloring used in the palette) and the health of your fish.

A healthy fish should have brown color poop, while white or yellowish poop might mean an infection or a digestive disorder.

Apart from color, the difference in shape and consistency can also indicate a problem.

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