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How To Clean Fish Tank Gravel: Three Proven Methods

Gravel is one of the most common aquarium substrates. It is pretty, looks natural, allows plants to grow freely, and provides surface aplenty for beneficial bacteria to live. It is not without its drawbacks, but the benefits it adds to any aquatic ecosystem are numerous.

Arguably, one of the greatest gravel pros is the ease with which it can be cleaned.

There are three main ways to go about it. In order of easiness and least disturbance for the fish, here’s how to clean fish tank gravel:

  1. With a gravel vacuum
  2. By removing parts of it and rinsing them before returning them back 
  3. By stirring the water to make the debris and mulm float before removing them from the water column.

Before we examine each method in detail, let’s clarify a couple of things regarding aquarium maintenance in general and gravel cleaning in particular.

Should I Clean the Gravel in My Fish Tank?

Gravel is great at absorbing biowaste. After pebbles, it is the most porous substrate. That allows the fish poop, decaying plants, and uneaten food to enter the spaces between the tiny stones that comprise the gravel substrate.

This intrinsic quality of the gravel has two massive benefits:

  1. It absorbs plenty of nutrients that root-feeding plants can feed upon. With gravel and livestock, you can grow lots of demanding plants without additional fertilization.
  2. The fish tank stays (seemingly) clean for a very long time. Compared to bright, fine sand that shows signs of dirtiness within days after cleaning, gravel absorbs biowaste tremendously well.

Now, the second point can make you wonder whether you should clean your gravel at all. Generally speaking, you should clean it every now and again.

A well-established, stable ecosystem, with a thick substrate layer (more than six centimeters or three inches) may need no gravel cleaning whatsoever. Inert substrates like gravel and sand still make an excellent home for beneficial bacteria. Together with plants, these bacteria provide suburb natural filtration.

There is more to establishing a self-sufficient ecosystem, but knowing this will help you understand the dynamics of gravel cleaning outlined below.

How Often Should I Clean My Gravel?

While water changes, particularly in newly established tanks, should happen with relative regularity, they shouldn’t necessarily involve complete gravel vacuuming. 

You should vacuum the substrate to control the buildup of mulm but don’t try to vacuum the entire bottom of your tank at once. Vacuuming removes fish poop and other waste but also bacteria. Extracting too many beneficial bacteria at once is likely to result in ammonia spikes. See, these bacteria are beneficial because they consume ammonia, transforming it into less harmful substances.

But how often should you clean your gravel?

If you change your water every week, gravel a third of the tank deeply and scoop the top layer of the rest to remove large debris and mulm. Clean carefully in current shadows, places where waste accumulates. If you clean every other week, you could go deeper in about half the tank.

When the aquarium is better established, after 6 months have passed, you can halve the gravel vacuuming efforts. And once a full year has lapsed, assuming you have a thriving, balanced ecosystem, deep gravel vacuuming can cease completely or be done every other month or so.

To gauge how things progress without regular gravel cleaning, test regularly for changes in ammonia and nitrite levels regularly. Observe the livestock for signs of stress — learn how to distinguish them here — and algae levels.

How to Clean Fish Tank Gravel

Technically speaking, there is no way to clean your tank without some sort of tool. Fishkeeping is one of the techiest — or tech-heaviest? — pet-related hobbies. All the same, the equipment needed is extremely affordable and easily accessible.

You can clean your gravel substrate with a gravel vacuum, a metal cup and running water, or with a hand and hose.

Whichever method you choose, here are a couple of preparatory steps you must follow any time you conduct a water change:

  1. Prepare the scene — Bring a bucket or another vessel for the dirty water. Take along a towel or a mop as well, as some drops are bound to spill during water changes.
  2. Turn off all submerged devices — Unplugging filtration systems and heater is an absolute necessity when maintaining your aquarium. It is a non-negotiable safety step for you and for the equipment in question. You can leave the light on to see better what you are doing. If it is submerged, turn it off, move it out of the way (mount it on the back wall of the tank, for example), and turn it on to help you in the maintenance.
  3. Wash your hands well — Make sure no trace of soap remains.

1. How to Use Gravel Vacuum

With the basics out of the way, here’s how each method works in practice.

The gravel vacuum is the most straightforward way to clean your substrate. It is a simple plastic siphon attached to a tube.

It allows for deep cleaning of specific locations and top-cleaning wherever you want while reducing the water column. You can regulate the depth of sucking as well as the territory covered to perfection.

What’s more, the gravel vacuum disturbs your fish much less than the other two methods. It is an inexpensive but extremely helpful tool for water changes and overall maintenance.

Mostly all gravel siphons have instructions on how to get them going, but here are the steps you should follow at a glance.

  1. Prepare the aquarium surroundings.
  2. Turn off electric equipment.
  3. Be clean.
  4. Submerge the siphon — Put the siphon underwater. Some models have hand pumps to get going, others are equipped with battery-powered motors, while the simplest variations require some lung power. Make sure to place the bucket for dirty water lower than the aquarium, then start the water flow, as indicated by the instructions on your vacuum device. In case it requires you to suck some water into the tube to get it going, be careful to not drink any fish tank water. 
  5. Vacuum the chosen location — Place the siphon wherever you wish to clean well. Keep it there for a few seconds to absorb all the debris. For deep cleaning, shovel the siphon into the gravel and let it suck everything out. When ready to move on, break the water flow intensity through a switch, if available, or by doubling the tube. This will release the stones sucked by the siphon back to their place.
  6. Take the siphon out — When the bucket for dirty water is getting full, turn the siphon upside-down and take it out of the tank. This way, no dirty water or debris will return to the tank. Since all gravel vacuums have a netting that prevents larger particles or livestock from being sucked, some garbage can be stuck there. To release it, just submerge the siphon into the dirty water, and give it a couple of shakes.

That’s about it. Gravel vacuuming with a siphon is very easy and efficient.

Tips for Using Gravel Vacuum

Let’s clarify a couple of things about gravel vacuums.

First off, it is by far the best way to clean your tank. Be it pebbles, sand, enriched soil, or even a bare bottom tank, the vacuums take care of business with minimal disturbance. There is no need to take fish out.

Still, you should pay attention.

Be careful to not uproot live plants and not to suck fry or other small inhabitants of your aquarium. They might dart into the siphon as it extracts mulm — some of the stuff that goes into it may taste good!

Another important point is to choose an area for deep vacuuming, i.e., an area where you’d suck the gravel into the siphon for a thorough cleaning.

You shouldn’t vacuum the entire bottom of the tank deeply. Cleaning way too much, washing thoroughly ALL the filters at once, or removing too much water is likely to lead to imbalances that can spike the stress levels of your fish.

Instead, focus on a third or half of the bottom and clean it well. Tackle another part the next time you use the siphon.

Clean places where debris accumulates naturally. In any larger fish tank, there are places where the filtration is less effective. Be it behind a pile of rocks or pretty driftwood, hardscape and plants inevitably disturb the water flow created by the filtration systems. Such places are rather obvious because the waste is visible.

Place the vacuum there and keep it in place for a while. It takes a few seconds to start extracting all the heavy particles stuck there.

2. Clean with a Cup and Running Water

If your gravel vacuum breaks or you feel like experimenting, there are other ways to clean the gravel.

Cleaning with a cup is a deep-cleaning method that also allows you to target sections of the bottom, but it doesn’t work well around hardscape and, especially, live plants. Often, the end result of slightly disturbed bottom-scape calls for lengthy tinkering with a rake to arrange it all again.

All the same, it is simple and straightforward.

Grab a clean cup, preferably an oldskool metal vessel (as it won’t ever break), and go for it.

Here’s how:

  1. Prep the scenery.
  2. Unplug all submerged electric devices.
  3. Clean your hands.
  4. Grab the cup and fill it up carefully with the gravel patch you wish to wash.
  5. Place the gravel into a metal sift and wash it thoroughly under running water.
  6. Rinse and repeat.

This method is fairly straightforward and doesn’t disturb the fish that much. They’ll be fine staying in, even though the returning clean gravel could be a bit scary.

Just like vacuum gravel, using a cup is great for deep cleaning. In fact, you can clean the gravel even better than with a siphon. However, the cup method is rather poor for substrate-surface cleaning. It is also slower and messier.

On top of that, it doesn’t really help with the water change.

All the same, it is an alternative that can help you when a gravel vacuum is unavailable.

3. Hand, Hose, and Waves

If you have no gravel vacuum or cups (or glasses even), but a cleaning session is an absolute must, you can make do with a hose or tube and nothing more.

The principle is simple: disturb the bottom of the tank and let the debris float, then such it out of the water column.

The thing is that waving your hand and sending the mulm and debris floating into the water column is extremely messy and stressful for the fish. You’ll have to suck garbage out of the water column with lowered visibility, which makes you dangerous for the fish.

If this is your preferred method of gravel cleaning, it is best to take fish and other livestock to a hospital tank for the duration.

This way of cleaning is the most inefficient and the most stressful for all involved. It doesn’t do much for waste stuck under the top substrate layer and sucking out all the floating garbage is a tall order. Most likely, some 20%-40% will stay in the water column before settling back onto the bottom.

Add to that the fact that it’s best to remove any livestock beforehand and you end up with tons of work that brings dubious results.

If all you have is a hose, it is much better to use it as a gravel vacuum. It won’t be as efficient and thorough as the real deal, but it will clean the top of the substrate while helping you change the water. What’s more, it won’t make a total mess of things and will save you the trouble of taking the fish out.

Whatever stones are sucked in by the hose can be put back in easily.§


So, there you have it, three tested and proven methods to clean your fish tank gravel.

When I say proven, the last of them is proven to be a very bad idea, overall. It is best to get a siphon and put it to good use. They cost next to nothing and will make your life so much easier.

A gravel vacuum will help you clean your tank without stressing out the fish or disturbing the aquascape in any major way.

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