How to Replace Aquarium Substrate

If you ever decide to replace the substrate in an aquarium after it is running, you may find a lot of conflicting information out there about exactly how to do it. Some will say to take the fish out, others won’t. Some will say to do it in stages, others will say to do it all at one time. I have done it countless times in my own tanks and the tanks of my clients, as well as instructed many customers on how to do it in their own tanks, and I hope this how-to article will help make the transition smooth and as simple as possible.

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This article is written specifically for replacing old gravel with Estes Marine Sand. Some of the specifics in this article may not apply to you if you are not making this particular replacement, but the overall process is still the same.

Replace All of the Substrate at the Same Time

Do it all at once. Don’t do it in sections, especially not taking some of the old out and putting some of the new in using a divider to separate the new from the old, that is tedious and most likely isn’t going to work nearly as well as it sounds like it will.

The idea behind doing it in sections is to avoid removing too much of the nitrifying bacteria at one time. However, the bacteria live in your filter, not evenly throughout the tank. Effectively all of the bacteria are in the filter. I know this because countless times I have moved entire setups from one tank to another (usually as part of an upgrade in the size of the tank) and moved the fish, filter, and nothing else, and I have not had any issues with the tank uncycling or going through a mini-cycle or anything like that. I have done this over and over and not once had a tank thrown out of balance because of this. I know this is the exact opposite of what people on forums will tell, they’re wrong. Ask them if they’ve ever tried it, they will say “Of course not, it would take out all your beneficial bacteria.” So I ask, if they’re so right, why hasn’t that ever happened in tanks when I’ve swapped out the entire substrate all at once? It’s theoretical. It’s well-intentioned, but it’s completely baseless (which is way too common in our hobby). By moving the fish (the entire bioload) and the filter (the bacteria for that entire bioload) at the same time, the new setup will instantly cycle for that exact bioload of fish. Removing the entire substrate can stir up all sorts of debris and waste, so it is still a good idea to do an extra water change or two in the week following such a release of extra nutrients.

This is not to say there are bacteria in the filter and the rest of the tank is sterile, this is not the case at all. If there is truly enough filtration, then the bacteria will have more than enough surface area and flow to have enough bacteria for the entire tank’s bioload in the filter. Like every organism ever, the bacteria do not simply spread out evenly. They concentrate where their needs are best met, specifically where their limiting factors are best met. In our aquariums, the limiting factors are food supply (ammonia and nitrite) and oxygen. Where is there the most food supply and oxygen? In the filter, of course, where the conveyor belt of high water flow brings them a constant supply of both (like a buffet where the food comes to you). They do not have this opportunity and then spread out evenly across every surface area of the tank (on the glass, decorations, or sit in the relatively passive flow of water across the substrate). They concentrate where their needs are best met. If there was enough of a food supply, then they would also grow in heavier populations in other parts of the tank, but that is simply not the case. The reality is that the bacteria in the filter outcompete bacteria elsewhere because the ammonia and nitrite, along with the oxygen needed to process it, are handed to them on a silver platter by the flow and there’s simply not enough leftover to allow significant populations of bacteria elsewhere  in the tank. If your filtration is inadequate due to weak flow, or a biomedia with too little surface area, or anything else that may prevent a large, complete colony of bacteria from growing and thriving long term, then in some tanks there may be some significant populations of bacteria elsewhere in the tank, but this is rare and should be corrected as a separate issue.

Do Not Take the Fish Out

Many people feel the need to remove the fish during a substrate replacement. This is not necessary and will actually be more stressful for the fish. This is not to say that keeping them in the tank isn’t stressful, but taking them out, letting them sit in buckets for an hour or two (or longer) while you work, letting the buckets cool, letting them sit in buckets which usually aren’t aerated, then having to acclimate them back to their own tank is simply more stressful. Leave them in the tank. While you scoop out the old substrate or get the new sand to settle at one end, they will hang out at the other end.

There are exceptions though. Really small fish that would be easy for you to miss, fish that will timidly hide instead of fleeing from your hand, fish that burrow into the substrate, etc. should be removed. Maybe you have some loaches but the other fish will avoid you, simply remove the loaches (good luck catching them by the way). 

Vacuum the Old Gravel

The day before the replacement, do a thorough gravel vacuuming and water change. This helps get as much of the extra debris out of the old gravel as possible. On the day of the replacement, do the same thing only do not refill the tank. It is while the water is low that you will complete the replacement.

Remove the Old Gravel

After you have vacuumed the gravel and while the water is still low, you will remove the old gravel. I usually use a fish specimen container to scoop out the old substrate. These are the plastic containers that hang on the outside of a tank that fish stores use to catch and bag fish. These are available to be purchased and make a handy tool for any aquarist anyway. They are large, heavy-duty, and have a flat edge perfect for scooping out old gravel. The next best thing is some sort of heavy-duty dustpan or plastic shovel/scoop. Old gravel can be used for a lot of things such as potting plants, erosion control, walkways, etc. If you have a use for it, then save it. Otherwise, just bag it up and throw it away. You will have to get in and remove the last few pieces of gravel by hand, but it’s worth the time to get it all out. If you go through all the work and then see a piece of old gravel in there, it will drive you nuts.

Adding the New Sand

Once you have the gravel out, you can let the tank sit still for a few minutes and any debris that settles to the bottom can quickly and easily be vacuumed out before you pile sand on top of it. I usually do a half-and-half mix of black and white sand. I usually stand all the bags of sand upright in the box, cut off a corner on each one, then add the sand one bag at a time alternating between black and white. I don’t want to add all the white then add all the black, it will be harder to mix completely.

The only bad thing about Estes Marine Sand is that because it has the polymer/ceramic coating it doesn’t sink immediately, it clings to the surface of the water (including bubbles). This means that once it is added you need to take some time to get it to settle. A lot of it will cling to the surface, and some will cling to bubbles. Some of the bubbles will have so much sand clinging to them that they will sink. So for 15-20 minutes in most tanks, you will need to pat the surface, stir up the bottom (this releases trapped bubbles and mixes the colors), then pat the surface, stir the bottom, pat the surface, stir the bottom, etc. If you can see the bottom of the tank from inside the stand, take a look to find spots that still need to be mixed. It won’t be perfect, but you will get most of the sand settled in 15-20 minutes. Once you do, you can refill the tank and start the filters again, then you are done.

Estes Marine Sand may discolor the water a little, but it is minimal and will clear up within a day or so, especially with a water change. It requires no cleaning or rinsing before being added to the tank.

This is the method I have used countless times and have never had any issues. The fish live without any illness or signs of stress. The replacement is isolated to one session of work and then it is done.

Other Articles You May Be Interested In

Sand as a Superior Substrate

Cycling and Understanding the Good Bacteria

Filter Media Types Guide

Water Changes and Water Quality