How clean is your bottom?


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 Gravel looks natural and is reasonably cheap to buy. But it does need regular cleaning, especially if you have bottom-dwelling fish like catfish and loaches, that spend much of their lives in contact with the substrate. Gravel looks natural and is reasonably cheap to buy. But it does need regular cleaning, especially if you have bottom-dwelling fish like catfish and loaches, that spend much of their lives in contact with the substrate.
How clean is your bottom?

Gravel looks natural and is reasonably cheap to buy. But it does need regular cleaning, especially if you have bottom-dwelling fish like catfish and loaches, that spend much of their lives in contact with the substrate.

The type of substrate you decide on will have big effect on how much time you’ll need to spend on its maintenance. Our guide will ensure you stay on top of what’s on the bottom.


A couple of weeks into owning your set-up, you’re probably looking at the bottom of your layout and thinking ‘that doesn’t look right…’

Different types of substrate need different approaches when it comes to cleaning. If you’ve gone for bleached white sand under a barrage of intense lighting, you’ll probably need to be in there, sifting away daily. If you’ve gone in for a planting substrate, you might never clean it, once. 

Here’s how to deal with some of the more readily available substrates out there.

Planting substrates

Controversial, but if you have a tank decked out with high-end, high cost planting substrates like ADA Powersand, you either know what you’re doing or you’ve made a big mistake. 

Planting substrates are mainly designed to trap and slowly release nutrients to plant roots, and often come pre-loaded with food — that means ammonia. The moment you start trying to rake through them, you release those nutrients into the water column, and that in turn will lead to an outbreak of algae. 

How to clean them

  • Before going in the tank: Usually you don’t!
  • Once in the tank: Some aquascapers suggest removing a section of the substrate every few weeks or months, and cleaning before replacing. Others don’t. My own advice is to run a gravel cleaner about an inch above the surface of any exposed parts, so that you lift any waste without disturbing the substrate itself. 


  • Heaving with nutrients and perfect for almost all kinds of plant growth. 


  • Useless for burrowing catfish or excessively dirty tanks. 
  • Limited choice of colours and grain size. 
  • Often tends to have a slightly acidic (and rarely alkaline) influence on water chemistry.

Fine natural gravel

Some modern aquarists might be a bit sniffy about this ‘outdated’ substrate, but it still has its place — by which I mean it is a total breeze to clean. 

Gravels, and most famously the classic ‘Dorset pea gravel’ became a hobby staple during a time when tanks relied on undergravel filtration. Subsequently they have found themselves on the fringe of fashion, but many tank owners still persevere! 

How to clean it

  • Before going in the tank: Rinse thoroughly to remove any fine dust. A sieve is fastest, if you blast around 1 or 2kg at a time under a coldwater tap, shaking and swilling like chips in a fryer. Alternatively, place into a bucket and stir continuously while applying running cold water and letting the bucket overflow. Ensure the water is running off clean before draining and adding to the tank.
  • Once in the tank: Use a gravel cleaner with syphon to draw water out of the tank and plunge the gravel cleaner deep into the gravel at the same time. The water will lift the gravel, swill and rinse it, then when the gravel cleaner is lifted it will drop back out. A battery or air powered vaccum will do a similar job, but less effectively. You’ll need to do this at least every two weeks, though weekly is considerably better. Monitor how dirty the gravel is each time and adjust as needed.


  • The easiest gravel to clean by a mile. 
  • Inert in freshwater, rarely causes a slight alkaline elevation.
  • Looks good in many settings.
  • Cheap!
  • Hides obvious small particles of waste from view.


  • Awful rooting medium for most plants.
  • Can harm catfish bristles and burrowing species.
  • Improper cleaning will lead to nitrate spikes and disease hotbeds.

Silver sand

Silver sand is the choice for numerous biotopes, as it’s similar to substrates found in lakes and rivers the world over. It can be bought in almost any aquatic store, and similar looking substitutes like playpit sand are available where it isn’t. 

Despite some detractors claiming potential gut or gill problems associated with using it, it remains one of the most popular modern substrates going. 

How to clean it

  • Before going in the tank: Slowly, slowly is the key here. Place around 5–8cm depth in a bucket at a time, and stir continuously and vigorously while flushing with cold water. Note, this stage may take a long time, but you need to be thorough as it is hard to remove sand dust once it is in the tank. Don’t try putting it in a sieve as you’ll lose the lot!
  • Once in the tank: A gravel cleaner and syphon will just lift the sand out of the tank, though you can use that to your advantage. When particularly dirty, it may pay to remove some sand with a hose this way and rinse it as though going in the tank for the first time — just be careful to limit this to 25% of the total sand, in order not to disrupt filtration. Personally, I like to gently rake my fingers through silver sand on a weekly basis, allowing any muck to lift and drop back down to the surface. Then using a syphon hose, I skim just above the surface of the sand, removing the deposits. This method will result in a fractional loss of sand, which is cheap enough to replace as needed. 


  • Cheap.
  • Natural looking.
  • Great for catfish whiskers and fish that burrow.
  • Almost always inert, doesn’t affect chemistry.
  • Many plant roots love it.


  • Cannot be used for deep substrates as it can turn anaerobic.
  • Can look dirty very quickly.
  • Can find its way into filters easily.
  • Excitable fish may stir up a tank into a sandstorm.
  • Strong filter flows may move it, leaving craters and sand drifts.

Coloured gravels

Love them, hate them, ignore them, but coloured gravels are often part of the appeal for a new fishkeeper. Not all coloured substrates are the same, either in size, quality or durability, so even cleaning for the first use can be a disappointment.

Before anything, get some of your proposed gravel, put it in a jug with some water, give it a couple of days and test for ammonia. Some coloured gravels are reported to leach ammonia compounds, and if they do, I’d personally bin them — or you can soak them until it goes away. 

How to clean them

  • Before going in the tank: Rinse gently in a colander or sieve under gently running tapwater. In many cases, some of the colour will run off, leading the aquarist to panic and stop rinsing. You need to keep going until the water runs clear, but do be gentle! The same problem will arise if placing the gravel in a bucket and stirring while gently flushing. Note that some gravels come coated in a resin that will hold in the colour, and for these you can be vigorous, though paradoxically they’ll be amongst the cleanest out of the bag. 
  • Once in the tank: Gravel cleaners and syphons will need to be used at least weekly to keep coloured gravel clean. The lighter the colour, the quicker algae will start to smother it, and you may find that white gravel only lasts one or two days before needing syphoning again. Be particularly careful with black gravel as it can harbour a lot of solid waste without you noticing, and may turn your tank into a ticking time-bomb of sewage.


  • Pretty, if you like that sort of thing. 
  • Easy enough to clean once in place.


  • Some fish will freak out over bright substrates.
  • Some types may contain ammonia sources.
  • Colours may bleach over time.
  • Coarse grains will affect catfish and burrowing fish.
  • Can get dirty very fast.

Coral sand

Coral sand has a limited use these days, being restricted to marine set-ups, and hardwater tanks (usually African). It’s actually the product of fish that eat corals, and pass the tiny coral ‘sand’ fragments out in their faeces. 

Because it is riddled with calcium carbonate, it will make soft water hard, and subsequently alkaline. Never be inclined to use it in acidic tanks!

How to clean it

  • Before going in the tank: Place around 5–7cm of sand in a bucket and flush with cold water while stirring vigorously. Ensure all the sand is turned over as you do this. When the water eventually runs clear, the sand is ready for use. 
  • Once in the tank: Use a gravel cleaner and syphon weekly or fortnightly and clean as though you would fine gravel (see previous page). In between syphoning sessions, waste from the surface can be removed with a battery powered gravel vacuum, or by wafting a fine net above it and lifting out any waste.


  • Acts as a buffer in hardwater tanks.
  • Fine enough for some burrowing species such as eels.
  • Very attractive in the right setting.


  • Intense light will cause algae growth.
  • Useless in acidic and softwater tanks.
  • Some grades can be very dusty initially, requiring prolonged cleaning.
  • Fine particles are sometimes implicated in gill problems in some fish.

Top tips for healthier substrates

Never leave the roots of plants behind when extracting them, as they’ll decompose and churn out nitrates. Rather than pulling plants out, try digging them out. 

When cleaning substrates before adding them to your tank, use cold water instead of hot. Some substrates can give the illusion of cloudy run-off water when hot water is used, when in reality they are clean. Microbubbles may be a culprit here

Use nets to remove uneaten food and debris rather than letting it settle on the base.

For marine tanks, lay your sand out thinly on a tray and run over it with a powerful magnet before use. It’s rare, but occasional metal fragments in substrates are not unknown. 

The joy of snails! While poorly managed snail populations can become epidemics, having a few Malaysian trumpet snails among the substrate can help turn it over and prevent stagnant patches.