Tips on How To Clean Aquarium Sand

Updated: Jan. 18, 2024

Cleaning aquarium sand is a cinch with a straightforward siphon, but these expert tips will ensure you don't disrupt your aquarium's delicate balance.

Sand is an aesthetically pleasing, affordable and practical substrate. It’s especially useful when you’ve got bottom-feeding or burrowing inhabitants in your tank. And, contrary to popular belief, cleaning aquarium sand isn’t difficult. All you need is a gravel siphon, and you’re good to go.

Professional aquarist Michelle Lowry says sand substrates are especially common in saltwater tanks, and the different uses depend on the tank setup. “Some coral reef keepers opt for deep sand beds to incorporate anaerobic breakdown of nitrogenous waste,” she says. “In other situations, there would be a shallow sand bed.”

The right cleaning technique depends on the depth of the sand. “The only reason cleaning the sand will cause an issue is if the sand bed is more than three inches deep,” says professional aquarist Chris Meckley.

Read on for expert-approved tips on how to clean aquarium sand safely and effectively.

Avoid Unnecessarily Deep Sand Substrates

Unless you opt for a deep sand bed for burrowing inhabitants, a particular aesthetic, or as an additional natural filtration system, it’s best to stick with around one to two inches.

Deep sand beds (typically over five inches) promote the growth of anaerobic bacteria that converts nitrate into harmless nitrogen.

“The first two to three inches of sand will be filled with aerobic bacteria, and anything below will be anaerobic [lacking in oxygen],” Meckley says. “If anaerobic bacteria are disturbed, this can cause issues in the main aquarium by releasing sulfur and other harmful compounds formed in the dead zone.”

That makes cleaning a deep sand bed much more open to pitfalls.

Siphon Thin Sand Beds During a Water Change

The easiest way to clean aquarium sand is with a gravel vacuum while changing out the water. “This way, the vacuum can just expel everything not wanted as water is drained,” Meckley says.

The steps below guide you through cleaning aquarium sand that’s no deeper than three inches.

1. Turn off filters and pumps

You don’t want filters running dry as the water levels lower.

2. Remove decorations

Tank decorations can harbor detritus on or under their surfaces, and removing them gives you a clear substrate surface to work with. Clean these items while they are out of the tank.

Leave live plants and fish in the tank where possible and carefully work around them. That way, you don’t have to worry about disturbing delicate roots or unnecessarily stressing inhabitants.

3. Siphon away surface debris

Grab your gravel siphon (aka a gravel or sand vacuum) to remove surface debris. Be aware the steps below are a guide for a basic pump siphon. Exact instructions vary depending on the siphon model you purchase.

  • Put the hose end of the siphon in a large bucket positioned below the tank.
  • Lower the suction end of the siphon into the water, being careful to avoid any small fish. Pinch the manual pump five times or so to start the water flowing into the bucket.
  • Hover the suction nozzle over the surface of the sand. Work methodically across the sand to pick up debris.
  • Once you’ve collected as much debris as you can, cover the top of the tube with your hand. This stops the suction action and saves debris from returning to the tank. Manually empty the remaining tube of water into the bucket.
  • Ideally, don’t let water levels drop by more than 25%. Introducing too much new water at once can be bad for your fish.
  • Depending on your tank size, you might not clean the full substrate before the water level gets too low. But you can always pick up where you left off during your next water change.

4. Return your tank to normal

Pop those cleaned decorations back into the tank. Slowly introduce new water. Don’t forget to turn on the filters and pumps.

Regularly Siphon Thin Sand Beds

Meckley says stirring things up at least monthly prevents the sand from absorbing a buildup of harmful phosphates produced during waste breakdown. It also keeps it from turning into a hard brick.

Exactly how often you siphon your sand depends on the tank size, the number of inhabitants and the type of sand.

“If it is coarse, it will need to be vacuumed or stirred more frequently, because it acts as a catch for anything small enough to fit between each piece of crushed coral or coarse sand,” Meckley says. “Fine sand has the same issue, but takes a little longer to catch enough particles.”

Clean a Deep Sand Substrate Carefully

When cleaning a deep sand substrate, it’s important to not disturb things below the surface. Doing so can release harmful compounds. Ensure the siphon is always above the surface of the substrate and never dug inside it. And don’t rake or stir.

Introduce Sand-Sifting Fish for Cleaning

Some sand-sifting tank inhabitants can aid in aquarium sand cleaning. These include catfish, sand-sifting gobies, loaches, cherry or ghost shrimp and ramshorn snails. They won’t replace siphoning, but can offer a helping hand.

Some burrowing microorganisms also expand the aerobic layer within deep sand beds and eat detritus at deeper levels. These include Californian blackworms, Malayan trumpet snails and planarian flatworms.

Always check that the species are suitable for the type and size of your aquarium and that they’re compatible with your existing tank dwellers.