How to Change Out Your Substrate

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Start with a good foundation for a healthy and vital tank.

Many people will start their aquarium and over time will develop a different taste for how they want to have the tank decorated. Often times one of the first things you will want to do is to change out your substrate. What makes this task so unique vs. other redecorating processes is that you’re not just changing out how the tank looks your also affecting a very big portion of the tanks bacteria filtration system. It’s hard to top the raw surface area your substrate has for growing the ammonia and nitrite consuming bacteria that ever tank needs to be successful.

Regardless if this is a saltwater aquarium or a freshwater system the procedure for changing out your substrate will be the same. The types of substrate you’re dealing with will be different but the actual process will work for either style of aquarium.

The first step in this process is selecting the new substrate. If you’re going to go with a sandy style substrate then you might want to check out our sand depth calculator to get estimation as to how much sand you will need/want for a given depth. It would also be a good idea to have handy some water for a water change when this process is complete. The reason is your water is going to be quite dirty from disturbing the old substrate.

Once you have selected your substrate it’s a good idea to rinse it off to remove any rock dust or dirt that might have gotten on the gravel during the bagging and shipping process. If your doing saltwater you might elect to not rinse your sand substrate in order to maximize the particle size in the sand bed. To rinse your substrate it’s easiest to get a bucket (5 gal capacities) and fill it no more than 1/2 full of your gravel/sand. Then take the bucket outside and put your garden hose in the bucket and turn it on. Fill the bucket full of water and at the same time mix up and stir the gravel. The water spilling over the sides of the bucket should be cloudy. After a few min the water should start to clear up and once it’s relatively clean you can set that gravel/sand aside to prepare more.

Now that you have your rinsed gravel/sand ready you can begin the process of changing out your substrate within the tank. The first thing to do is to shut down your pumps. This process is going to dirty up the water to some degree so no need to make it so bad you can’t see whets going on. Given that your current substrate is doing the bulk of the ammonia and nitrite removal it’s a good thing to not change it all out at once. Instead change your substrate out over time by doing 1/2 of the tank one day and the other half after a week or two’s time. The reason we are doing this in stages is to allow the bacteria to migrate and reproduce in enough quintiles that it will repopulate the new substrate so as you do not experience a noticeable ammonia spike.

When replacing 1/2 of the substrate you have two options. First you can remove the old substrate from that half of the tank OR you can move it all to 1 side of the tank. Remove any rock or other decorations from the side of the tank you plan on working on. If you’re going to remove the substrate then get a bucket and a scoop of some kind and carefully scoop out the old substrate from the section of tank you are going to work on. Another process if you have a light weight substrate like very small pebbles or crushed coral is to get a small diamater hose (1″) and start a sypohon and syphon out the old substrate. This will help keep the tank water clean and at the same time allow you to do a water change when the process is done. We want to work slow because we don’t want to dirty the water up to much at this point because we have lot of work yet to do.

Once you have either moved the substrate all to 1 side OR taken all of the substrate out of the part of the tank your working on its time to put the new substrate in the tank. If its gravel you can use the same scooper and gently lower the new substrate down to the bottom of the tank and spread it out until you have the desired depth you want.

If you’re putting in a sand style substrate you won’t be very successful by lowering the sand in the water surface because the sand is so light. Instead try one of the following methods. Use a large plastic bag (like a Ziploc freezer bag) and fill the bag with sand and seal the bag closed. Lower the bag to the bottom of the tank and then gently open a portion of the bag and slowly pour out the sand. The other method involves making a long funnel out of a 2 ltr bottle or a couple of 2 ltr bottles. Cut the bottom off a 2 ltr bottle and if you need to make the funnel taller chop the top and bottom off another bottle and insert the extension onto the other bottle. Then put the cap on the bottom. Fill this up with sand and slowly lower it to the bottom of the tank. Take the cap off and the sand should flow out the bottom of the DIY funnel.

Once you have the new gravel/sand in the aquarium the water is probably going to be fairly dirty and cloudy. Your fish will be ok with this for the short term (think about a tropical storm on the shallow ocean reefs). You can aid in helping clear up the water by doing a 20% or so water change at this time as well. Once you have the new water into the tank put your decorations/rocks back where you would like them to be and power up your pumps.

Repeat the above stages after two weeks and you should experience little ammonia or nitrite spikes by doing this in two stages.

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