How to Replace Aquarium Substrate

Kissing Gold Fish near aquarium gravel

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Replacing aquarium gravel in an established tank is debated because of the potential impact on the bacterial colonies that neutralize wastes in the tank. Some feel that most beneficial bacteria live in the substrate, and therefore the gravel should be disturbed as little as possible. Others believe the lion's share of beneficial bacteria lives in the filter medium rather than the substrate.

Where Does Bacteria Live?

Beneficial bacteria live on many surfaces within the aquarium. Therefore removing anything, be it rocks, gravel, plastic plants, or the filter media, will have some impact on the bacterial colonies. Does that mean nothing can ever be removed from your aquarium? Certainly not!

Armed with a water test kit and the knowledge of what to look out for, you can successfully change your gravel to something more appealing to you as well as to your fish (blue gravel isn't the norm in nature—your fish will probably enjoy the change to a more natural colored substrate).

Planning Ahead

To replace aquarium gravel, you should plan. A checklist of tasks and materials needed is a good idea to ensure all your bases are covered. See the checklists below.

Because changing gravel can be invasive, it's advisable to move the fish into a temporary holding tank. If you don't have a spare tank, purchase a 10-gallon tank. It only costs about $10 and can be used as a hospital or quarantine tank later. If you absolutely cannot afford a spare tank, the next option would be to use a clean 5-gallon bucket that has never had detergents or chemicals in it.


Time your gravel change day so that it is not immediately following a filter change or cleaning. This will allow the bacteria in the filter media to stabilize before you challenge them with changes. A few days before you plan to change the gravel, top off your tank completely. Test the water to ensure the ammonia and nitrite levels are zero. If they aren't zero, address that problem before attempting a gravel change.

On the day before the big change, do not feed your fish. This will cut down on the wastes produced in the holding tank (nothing in means little goes out). Also on the day before the gravel change, review your checklist to ensure you have everything you need.

Set up Holding Tank

Start the process by rinsing the new gravel until the rinse water runs clear. Then set up a holding tank as close to the main tank as possible. This will allow you to transfer the fish from one tank to the other readily. Next, temporarily turn off the filter in the main (29-gallon) tank. Perform the next few steps quickly, so the filter is only turned off for a short period.

Siphon off enough water from the main tank to fill the 10-gallon holding tank about two-thirds of the way full. Then remove any live plants, rocks, and other decorations from the main tank and put them in the holding tank. This will preserve the bacteria growing on the rocks, etc. However, if you have large items, you may not have room to put them in the holding tank. Keep in mind that you'll need room for the fish, which you are now ready to move from the main tank.

Move Fish

Quickly net the fish and move them to the holding tank. Because the water in the holding tank is from the original tank, you do not need to acclimate them—they can be moved directly over. Once you have moved the fish, cover the holding tank so none of your finned friends can jump out. If you don't have a regular hood or cover for the holding tank, a newspaper or piece of cardboard will do. Add enough aged or treated water to the main tank to allow the filter to run, and then turn the filter back on.

Note: Don't fill the main tank, as you need space to move back the rocks, plants, and decorations. You are now ready to swap the gravel.

Replace Gravel

Scoop out the old gravel and place it into buckets. Once all the old gravel has been removed, vacuum any debris from the bottom of the tank then put the new gravel in. After the new gravel has been added, you can move your rocks, plants, and decorations from the holding tank back to the main tank. Lastly, move your fish from the holding tank back to the main tank.

Leave the lights off for the rest of the day, and add some stress coat to the water to help ease the stress on your fish. Feed the fish sparingly the first day, then normally after that. Although your gravel swap is done, it is important to monitor the water for ammonia and nitrite spikes. Odds are you'll have at least a small spike.

After the Change

Three days after the gravel change, test the water for ammonia. If it is zero, wait another three days and test again. If it is still zero, repeat the test after one week just to be on the safe side. If the test shows an ammonia spike, treat the tank as if it were a newly set up aquarium, which means frequent testing and water changes until the ammonia and nitrite levels fall to zero.

Materials Needed

  • New gravel
  • Holding tank (10-gallon leader is a good choice)
  • Cover for holding the tank
  • Siphon
  • Nets
  • Buckets for the gravel
  • Clean cup to scoop gravel
  • Stress coat/water treatment

Tasks to Do in Advance

  • At least two weeks ahead: Clean filter
  • Two days ahead: Top off the water in the tank
  • One day ahead: Test water for ammonia and nitrite
  • One day ahead: Stop feeding the fish
  • Day of change: Set up the holding tank
  • Day of change: Wash gravel

Changing the Gravel

  1. Turn filter off on the main tank.
  2. Fill holding tank 2/3 full of water from the main tank.
  3. Remove rocks, plants, and decorations and place them in a holding tank.
  4. Move fish from the main tank to the holding tank and cover the tank.
  5. Add enough water to the main tank to allow the filter to run.
  6. Turn the filter back on in the main tank.
  7. Scoop old gravel out of the main tank.
  8. Add new gravel to the main tank.
  9. Move rocks, plants, and decorations to the main tank.
  10. Move fish back to the main tank.