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How Do I Clean My Aquarium? Part 1: Cleaning the Gravel.

Cleaning the gravel or substrate of your fish tank is an important step in the regular maintenance of most aquariums. I say most aquariums, because I have a planted tank with a gravel bed I do not touch at all. As part of a self-sustaining experiment, this tank’s pea-gravel substrate bed remains undisturbed, allowing it to accumulate waste and nutrients for root growth, as well as cultures of anaerobic bacteria for nitrate reduction. I’ve also never done a water change on this tank, but that's all for a different post. Check out the Simple CO2 Setup posts for photos of the 38 planted self-sustaining tank.

Why Clean the Gravel?

Most aquarium setups require regular gravel cleaning. The gravel bed is where most waste accumulates if it is not taken up by the filter. If this waste is left to decompose, it will deposit nitrates and phosphates into the water column. This causes decreased fish health, stunted growth, susceptibility to disease and infections, and increased algae growth.

When to Vacuum the Gravel

Because the aquarium siphon is designed to pull water from the tank while vacuuming the gravel, you can accomplish both a water change and a gravel cleaning simultaneously. The trick is to regulate the flow of water from the siphon in such a way so you don’t pull too much water from the tank before you’re done vacuuming the gravel or vice versa.

How to Vacuum Aquarium Gravel

Regardless of whether you're vacuuming a gravel bed, sand bed, or a bare bottom tank, you’ll start the process the same way. First, you’ll need some supplies. Five gallon buckets are ideal for most aquarium jobs and work well for emptying tank water into. They are large enough to hold quite a bit of water, but small enough to be able to easily lift and transport. Alternatively, some hobbyists opt for a hose attached to their siphon with enough length to reach a bathtub or outside garden (freshwater only). Either way, the end of the hose, whether in a bucket or trailing outside, will have to rest below the aquarium so gravity can siphon the water effectively. Another option is to purchase a hose system that attaches to your sink. These setups use the negative pressure from the flowing sink to siphon the water from your tank, so the end of the hose doesn’t have to be below the tank, as it's not siphoned via gravity.

Starting the Siphon

Once you choose what your water will empty into, you can now decide how to start the siphon. There are plenty of siphons available with self-starting hand pumps and even motorized pumps that will start the siphon for you. Alternatively, the age old method of pulling air from the end of the hose using negative pressure from your lungs while the siphon head is submerged underwater is always an option. I don’t recommend this method due to the potential for water in the mouth, and spillage as you quickly thrust the hose end back toward the empty bucket. This method also doesn’t work if your hose end is outside or at a drain in another room.

My favorite method for starting the siphon goes as follows. Stand in front of the tank with the hose end either in a bucket, bathtub, or outside. Hold the siphon head in one hand and grab the siphon hose in front of you with the other hand. With this hand, fold the siphon hose over itself and pinch it closed so no water or air can pass through. Then, holding the siphon head with the opening facing up, submerge it in the tank so it fills with water. Lift the siphon head from the tank so the water fills up the hose to the point where you are pinching it closed with your other hand. Next, return the open-end-up siphon head into the tank and re-submerge with the open end facing up and refill it again to the top. Then, slowly tip the siphon head over, while submerged, so the open end faces down. Finally, unpinch the hose and watch as the water moves down the hose and into the bucket. There shouldn’t be any air in the hose from the point you pinched it to the siphon head. Because there is no air in the siphon, as gravity pulls the water into the bucket it will continue to pull whatever fluid, in this case water, is at the opening of the siphon head. This “completes” the siphon and water will begin to flow from the tank, through the entire hose and into the bucket.

If at any time, too much air is allowed to enter the siphon head and then the hose, it will “break” the siphon. This happens because the water being pulled through the hose can’t pull more water from the tank due to the air breaking the hydrophilic connection.

Large Gravel

Once your siphon is started, choose a corner and systematically dig the siphon head into the gravel. Allow the flow of water to pull detritus and waste from the gravel until the water is clear within the siphon head, then pull the siphon head up and over to the next patch of gravel. Continue this process until every square inch of exposed gravel has been vacuumed.

If at any time you are pulling too much water from the tank too quickly, or the flow is powerful enough where it is pulling gravel into the hose, simply pinch the hose with your other hand to adjust the flow rate. You may find yourself pinching the hose each time you dig into the gravel and releasing as you pull the siphon head from the gravel. Eventually, you’ll find a pattern that works for your tank and siphon setup.


Vacuuming sand is a little different due to the fine grains and light weight. It’s easy for sand to travel into the hose with the siphoned water. If the sand is fine enough, most of the detritus will sit on the top of the sand bed. This makes it easy to float the siphon head over the top of the sand bed and pick up just the waste. By pinching the hose you can regulate the strength of the flow and slow it down if too much sand is picked up.

Alternatively, you can pinch the siphon head into the sand bed like with gravel, and repeatedly pinch and unpinch the hose to pull the detritus from the sand while allowing the sand to sink back down to the bottom of the siphon.

With either method, it is a good idea to disturb the sand bed regularly. Sand beds can become anaerobic to the point where hydrogen sulfide pockets build up. If these pockets reach a high enough concentration and release into the aquarium water, they can become toxic to fish and invertebrates. Hydrogen sulfide pockets tend not to build up in undisturbed gravel as the spaces in-between the gravel are large enough to allow gas to escape.

Dead Spots

Unless you have perfect flow, there will be spots in your aquarium where flow is slowest. These areas are where waste and detritus accumulate and are known as dead spots. With sand beds, the waste will accumulate on top, and with gravel, it will sink into the substrate. Be sure to vacuum these spots diligently to remove the waste build up.

Try experimenting with your powerheads' flow and location, to reduce dead spots. In some reef aquariums with wavemakers or controllable powerheads, aquarists will set the powerhead to pulse on and off quickly. This creates a pulsing wavelike motion in the water column, causing the accumulated waste in dead spots to flush out and into the tank where the filter can collect it. This effect is usually done once a day.

When am I Done Vacuuming?

You're done vacuuming when you have removed as much waste as you can, or when you have reached your 25-30% water change. Start vacuuming in the dirtiest locations first to remove as much as possible before you reach your 25% water change limit. It’s okay if some waste is left in the tank, the filter may collect some as it floats around in the water column. The key is to not skip gravel vacuuming. That is how you get waste buildup past the point of being able to remove enough of it with each 25% water change.

With proper filtration and regular vacuuming, you will find the substrate is clean with just one or two passes, and you'll be finishing the water change with the siphon just sitting in the water column as it finishes siphoning the regular 25% water change.


As always, try different methods when you perform your water change and gravel cleaning. Different sized siphons, hose lengths, or water disposal methods may serve your aquarium better than others. You never know what technology or methodology will make your life easier.

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