How to Keep Your Aquarium Sand Clean

Want to use sand substrate in your aquarium, but you’re afraid it’ll be hard to clean? Not a problem! Keep reading as I share my easy tips and tricks for keeping your sand clean and animals healthy.

Recently, I released a post explaining the first steps for setting up a planted tank with sand substrate. Several people asked, “How in the world do you keep that sand clean? Won’t it just get sucked up by the siphon if you try to vacuum it?” Great question! I had the same worries when I first switched from gravel to sand because no one wants to use a substrate that’s hard to clean and could trap excess waste that might harm your fish. But after I teach you a few simple techniques, you’ll realize that there’s nothing to it and it’s just like cleaning gravel… almost. 😉 (By the way, I’m going to be talking about using a siphon to vacuum your aquarium substrate, so if you don’t know what that is or how to use one, definitely check out my water changing article.)

Select the Right Sand

Okay, first off, let’s talk about sand selection. Not all sands are created equally, and if you’re using a very fine, lightweight sand, it’s going to get sucked up more easily in your siphon and you may have to add some more sand occasionally. In fact, word to the wise, you’ll also want to prevent sand from getting sucked up by your hang-on-back or canister filter and ruining the motor – which is exactly what happened to my first AquaClear filter. To prevent that from happening, buy a prefilter sponge (which looks like a cylinder with a hole on one side), and stick it on end of your filter’s intake tube. The added bonus it that it’ll grow beneficial bacteria and prevent any fish or plant leaves from getting sucked up too!

I’ve never had any trouble with aggressively vacuuming my substrate because I use the heavier generic-brand sand sold by Petco and PetSmart. Side note, but I prefer black sand versus a lighter color because fish waste doesn’t seem to show up as much. Some people might say, “Well, why don’t you get a brown colored, natural-looking sand to really hide that mulm?” Personally, I think the fish and plants just seem to really pop against a black background and substrate, so that’s why I prefer it.

Large-grained black sand from Petco

As I was saying before, the Petco sand has large particles that rarely get sucked up because they’re too heavy to make it all the way up the tube. The only time I’ve had problems with this is if I’m using my mini siphon, which is about six inches tall. It seems that the tube portion is just short enough to suck up the sand if I’m not paying attention.

How to Vacuum Sand Substrate

So, how do you deal with sand that keeps getting sucked up in the siphon? Okay, there are three common methods.

Method 1: Hoover above the sand
If your sand is super fine, don’t stick your siphon tube into it. Instead, use the tube to gently swirl water above the sand and then suck up any detritus that floats up into the water column. The great thing about this method is that you’re not really disturbing your aquascape. The sand is still nice and smooth and undisturbed. However, I believe Rachel O’Leary likes to use a chopstick to stir up the substrate a bit and then hover above with her siphon to suck up whatever gets loosened.

Method 2: Vacuum the sand like gravel
If you’ve got a heavier sand like me and really want to get a deeper cleaning, gravel vacuuming is the way to go. What do I mean by that? Just stick the tube down into the sand like an inch or so, suck up some waste, and then when you lift up the tube, the heavier sand particles will fall while the lighter brown detritus continues to rise. Easy peasy! Just like vacuuming regular gravel. I like to systematically clean the tank bottom in a grid-like pattern: vacuum, raise and release, vacuum, raise and release – rinse and repeat until I’ve cleaned about half the tank. And then next week, I’ll clean the other half or wherever looks dirtiest.

Method 3: Crimp the siphon hose
The final method is really useful for my shrimp tank. Honestly, this should be my easiest aquarium to clean because I don’t have to wipe off any algae since it provides extra grazing areas for my shrimp. (Pro tip: use razor blades for algae scrapping to avoid scratching the walls up with sand grains.) Unfortunately, I have a really hard time not sucking up the millions of tiny, clear shrimp babies crawling everywhere. It’s incredibly stressful! So, this principle works for both sand particles and any live animals you don’t want to suck up. Just vacuum like normal, but if I see any baby shrimp in the tube, I clamp down on the hose to stop the flow and wait for the shrimplet to eventually crawl its way out. This works for sand as well. Vacuum, crimp the hose, vacuum some more, and then crimp it to stop. It’s like magic!

More Maintenance Tips for Sand

As awesome as these techniques are, they’re not perfect and some grains may accidentally get sucked up anyway. Because of that, my husband Mr. Gamer really doesn’t want me pouring the wastewater down our sink or toilet and accidentally clogging up our plumbing. Instead I just dump it onto our lawn or use it to water our plants. Win-win situation!

As you refill your aquarium, just realize that sand can be easily disturbed if you aim the hose right at it, so lots of people use plastic bags or colanders to lessen the water pressure and prevent their aquascape from moving around. However, my aquariums are tall enough where I can just aim the spout at a tank wall or maybe some décor to help dissipate the flow.

In fact, in my 20-gallon tank, I’m trying to maintain a gentle slope in the substrate where the sand is lower in the front and higher in the back, kinda like stadium seating for the plants. However, gravity and my nosy kuhli loaches tend to flatten the sand over time, so I usually take the opportunity during water changes to manually rebuild my little hill as needed. Boom! Clean tank, clean sand… looks great for about 20 seconds until my fish mess it up again. 😜

Does Sand Substrate Cause Toxic Hydrogen Sulfide Gas?

I know there's been some discussion about deep sand beds potentially creating an environment for anaerobic bacteria to grow and producing pockets of deadly hydrogen sulfide gas. I’m not really worried about it with my Shy Guys jungle tank because a) my substrate isn’t that deep (like 3 inches at most) and b) I regularly stab root tabs into my substrate, which messes up sand a bit. Plus, Jason from Prime Time Aquatics, who happens to be a college professor of microbiology, says he’s actually seen hydrogen sulfide bubbles coming from some of his tanks but he’s also running a lot of sponge filters so it’s never really bothered any of his fish.

If you want to learn about my whole process for setting up a planted tank with sand substrate, check out the series here. Take time to enjoy your aquariums and I’ll see you in the next post!

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