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A simple guide on how to clean sand substrate in aquarium

Should the sand substrate in your aquarium be cleaned? Yes is the correct answer. Well, this is not an un-common concern with most beginner fish keepers setting-up a fish tank with sand bottom. Now, the question answer to is; do I know how to clean the sand substrate in my aquarium?

Now, cleaning is essential regardless of whether your tank has sand or gravel substrate. Without this, your tank will suffer poor water quality issues and your filters may not offer much help. You surely don’t want such an unhealthy habitat for your pet.

How to clean sand substrate in aquarium

Well, you may have stumbled on scary write-ups on how difficult sand substrate cleaning is, don’t fall for that. It is equally easy to clean just as gravel cleaning.

Why should you clean aquarium sand?

After feeding your pet fish, the only obvious place for the uneaten foods is on the substrate. That’s where fish’s excrement will be too besides other detritus; say of fallen leaves and dead roots from the aquarium plants.

If the waste build-up is left on the aquarium sand to rot, toxic compounds therefrom will obviously pollute the tank waters. Ammonia is particularly one of the results.

As a result, how to clean the sand substrate is one critical aspect in aquarium maintenance. Cleaning will ensure the aquarium sand bottom retains its natural looks besides being a healthy habitat for fish.

How to clean sand substrate in aquarium:

Here, we’ll look at how to clean aquarium sand as well as how to keep the sand clean.  Further, we’ll also discuss how to clean substrate sand with both a siphon and without it.

How to vacuum sand in aquarium:

As a fish keeper who has experimented with both sand and gravel substrates, I rank sand bottomed aquarium higher than the alternative. While debris will sink through the gravel, the same will remain on top of substrate. This makes it even easier to clean especially with experience.

Having said that then, vacuuming substrate is perhaps the best way to clean aquarium sand.

Now, if you’re not too inexperienced, I suppose you are asking; “how do you vacuum aquarium sand?”

Well, with these easy steps, you’ll effectively do it;

  • Firstly, either unplug or switch off all the appliances in the tank such as filters, heaters or even pumps if any. Don’t be too worried of the effect to your pet(s). The cleaning exercise will only last for a short time to have any effect on them. Besides, safety precaution.
  • You may also want to take this time to clean the aquariums decorations. Therefore, gently remove them. In addition, plants can also be removed to allow good working space.    
  • Having done that, now gently rake the sand (you could use your fingers) from one end of the tank to the other. This will ensure you cover every part of the aquarium. The goal is to upturn all the sand.

The effect of this is that all the waste will be laid bare on the surface. As you stir the sand, water will obviously turn cloudy. Allow 5 – 10 minutes for the water to clear off. By this time, the debris will be easily visible on the sand surface.

However, before raking, you may consider running the siphon over the sand to pick what’s already on top. That however is an option when already too much waste is sitting on the sand.

This reduces chances of covering what’s already on the surface when upturning the substrate.

  • Now, gently lower a siphon (preferably with a large barrel) to just about ½ inch above the substrate. From that level and at a slight tilted angle, gently swirling the siphon across the breadth of the sand and vacuum out all the debris.

Just be careful not to lower the siphon too close to the substrate lest you suck up the sand instead of the intended waste.

  • Now, with your fingers again, spread out the sand well round the tank. This prevents anaerobic conditions developing from where-in decay of trapped waste could happen. This happens because fine sand compacts particularly with deep sand bends, trapping debris.

A black layer caused by the anaerobic bacteria resulting from the trapped and decaying debris forms.

Subsequently, it’ll be releasing toxic compounds to the water which are lethal to the fish. That’s besides the foul smell which will be emanating from the tank too.

  • You can now replace the decorations after cleaning.

Finally, when satisfied that all the waste has been removed, you may consider a good filter rinsing. Why you ask? Well, on the raking of the sand, it will pick so much of debris. That is ONLY if the filter is on when stirring the sand (mostly common with experienced aquarist who just dives into raking sand).

After you have everything in place, you can now turn on all appliances; the filter, lighting, heater and pumps if any.

How to clean aquarium sand without siphon:

If yet to hack the art of using a siphon or you don’t have one, well, how to clean substrate shouldn’t stress you too much.

Just get yourself a turkey baster. With this, you are able to aim and pick particles on the sand substrate.

The down side of it is that, it is a rather slow way of cleaning your aquarium sand. You’ll have to be patient to pick a particle at a time unlike the siphon.

Following this therefore, this aquarium sand cleaner is mostly not ideal for big and heavily stocked aquariums. Instead, it is most suited for heavily planted/decorated tanks or a nano tanks. Would work very well for you goldfish bowl or 5 gallon tank.

Another technique to clean aquarium sand without siphon is by stocking freshwater sand cleaning fish.

These aquarium sand sifting fish are bottom dwellers that scavenge for food on the substrate. As they sift on the sand bend, they clean it by eating up the uneaten foods and any matter, among them fish poop.

A good note however is that they can’t live on that only. You’ll have to supplement that with sinking foods.

Whilst they are good cleaners, dirty substrate nonetheless can cause them infections particularly affecting their whiskers/barbels. As a result therefore, you’ll still need to employ other effective ways on how to keep aquarium sand clean.

In addition, avoid course sand and use fine sand instead. Further, all sharp objects must be removed because they can hurt the underbelly of the fish. That’s besides decapitating the barbels.

Some of these effective cleaner fish include small bodied catfish like suckermouthed and Corydoras.  Other good aquarium cleaners that can be stocked in a community fish tank with fish are shrimps and snails.

How often should you clean the sand substrate in the aquarium?

To keep aquarium sand clean, occasional substrate cleaning is a must. As a result therefore, a workable schedule should be in place. That said, it’s most convenient with many fish keepers to vacuum the substrate when doing water change.

However, how often you do it is also dependent on factors like the size of the tank as well as the size of your pet stocks. A bigger tank may not easily get messy. Likewise, a less stocked tank. It is up-to you to find what work best for you depending on these factors.


How to clean sand substrate in aquarium is an important skill as much as how to keep substrate sand clean. This will ensure reduced chances of toxins building up in the fish tank which is unhealthy.

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