Articles Setting up an aquarium

Choosing an aquarium substrate

February 8, 2015
caviar sand

There are many types of aquarium substrate to choose from nowadays; substrate choices range from neon colored gravel to all natural looking sand types. The substrate is an important place for beneficial bacteria to grow but choosing the right type can be a bit of a challenge, as each substrate type has a different effect on your aquarium and fish. 

Keep reading for a list of the most common aquarium substrate types and their pros and cons, which will hopefully help make the choice a bit easier!


Gravel is probably the most commonly used aquarium substrate. It’s available in many particle sizes and shapes and is often dyed in bright, artificial colors. There is a type of gravel for almost every setup – with a few exceptions.

If you’re thinking of using gravel, consider your stock first. Be sure to check which substrate the fish you’re interested in will do best on. Some species, like Corydoras catfish, like to sift through the substrate to find their food. Gravel will make this quite difficult for them, and sharp gravel may even damage their delicate barbels and cause rot.

Other aquarium fish, like Kuhli loaches, like to burrow into the substrate and have delicate bellies that may get damaged by sharp gravel. Using sand is not absolutely necessary for these species, but it will allow them to show their natural bevior. One species that should not be kept on gravel at all is the ever-popular goldfish; gravel can get stuck in their throat and you may end up having to take it out with a pair of tweezers, which obviously causes the fish a lot of stress.

Another point to keep in mind if you’re considering gravel, especially bigger sizes, is the fact that dirt particles and uneaten foods will be quite difficult to remove. They can build up and cause bad water quality when the gravel is disturbed after a longer time. If you do decide to go with gravel, especially with the fish species mentioned above, a smaller, polished type is probably your best bet! Natural colors will be appreciated.

Vacuum Cleaner
Gravel is not suitable for goldfish. Vacuum Cleaner by bensonkua


Although sand is not a first choice for most fishkeepers, I personally prefer it. When used correctly, sand is a great substrate that causes no problems. Dirt particles stay on top of it instead of falling between the grains, so cleaning will be much easier.

Slightly coarser sand with a medium grain size like river sand works best, as this has a much smaller chance of becoming anaerobic and causing ammonia spikes when it’s disturbed after a long time. Sand types with very small grain sizes, like play sand, should be avoided unless you’re only using a very thin layer! Using sand that is too fine is the reason many fishkeepers have bad experiences with this type of substrate. It can become compacted and anaerobic and live plants will not be able to develop their root systems properly.

Plants will do well in sand with a larger grain size, and bottom feeders like loaches, goldfish and catfish will appreciate it. If you’re worried about your sand becoming anaerobic, be sure to disturb it once in a while during cleaning and avoid using a thick layer. Malaysian trumpet snails can also be of help here; they burrow in the substrate, thereby disturbing it on a regular basis.

How to choose the best substrate type for your aquarium

Crushed coral, aragonite

Crushed corals and aragonite are two substrate types that are not usually used in most aquarium setups. They harden the water and act as a pH buffer; the pH will be raised and stabilized without using any chemicals. This is not required and even unwanted in regular tropical aquariums, because most tropical fish need a lower pH.

However, if you’re interested in keeping African Cichlids or a brackish aquarium you may end up needing one of these substrates! Though crushed coral is traditionally recommended at many aquarium stores, the (slightly more expensive) aragonite seems to be preferred by most fishkeepers because crushed coral can trap dirt and can eventually cause problems with your water quality. You can buy aragonite online here.

Marbles, river rocks, lava rock

Bigger (decorative) rocks and marbles are sometimes used as a substrate. While these are all suitable for use in your aquarium, it may be best to just use them as decorations instead. Dirt can get trapped between rocks/marbles quite easily, and in some cases fish may even get stuck between rocks.

Smooth rocks and marbles are not a good place for beneficial bacteria to grow in. They can, however, be scattered across the regular substrate for a decorative effect. Lava rock substrate would great for beneficial bacteria but lava rock is better suited for use as biological filter material inside your filter or as part of your hardscape.

Plant substrate

If you’re interested in keeping live plants, you can consider a substrate which contains extra nutrients, like Eco-Complete, for your plants to grow. However, they are not absolutely necessary to achieve a lush green setup. Most plants do just fine without a special substrate.

While an enriched substrate can be used as a “main” substrate, there are also extra plant nutrients that should go under your regular gravel or sand, like laterite. These are not necessary for good plant growth either, but can definitely help! Just be careful when planting, as you may accidentally stir up the laterite and cause cloudiness.

No substrate

Although using substrate has many advantages, there are a few situations where a “barebottom” aquarium may be preferred. Many goldfish keeper choose not to use a substrate because this makes cleaning much easier. Goldfish are very messy fish and with the amount of water changes required a barebottom tank may be more convenient.

Keeping live plants is a challenge in a barebottom aquarium, but with some creativity it’s certainly possible. When you’re setting up a hospital tank, breeding tank or display tank it’s also not necessary to add substrate.

If you have tips or questions about choosing a substrate, be sure to leave a comment below. Happy fishkeeping!

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  • Reply MARY BETH MABE July 30, 2017 at 2:24 am

    I have been reading several of these articles and am glad to have found a simple neutral site to read info from. I also have been watching Pectec, Dustin’s Fish, Rachel O’Leary. The DIY fishkeeper, Serpa Design, and a few others. I would like an advice list on this idea for a new tank/ new to the hobby after 20 years away.
    I want a planted tank, with either plant substrate or soil that is capped by pea gravel / larger sized sand in the natural colors in the clay flower pots. I want to use clay flower pots as my hiding spots on their sides. A few rocks to make a little cliff image, and maybe one or two small little figurines/ornaments. I would use Hornwort, Crypt, and a few others I can’t think of the name of but are low light and common.
    I want 5 Glowlight tetras and 5 Neon tetras, 3 panda Cory, a few nerite snails, and maybe a few ghost shrimp. 10 gal tank with a <20 gal filter and a heater. Please tell me if I am on the right track. thank you.

    • Reply Mari July 30, 2017 at 12:19 pm

      Hi! Glad to hear you appreciate the site 🙂

      Your plan sounds good plant-wise, the stock is unfortunately not great for a 10 gallon. Neons, glowlights and panda Cories all get too large for a 10 gallon and the school sizes are too small, all should be kept in groups of at least 8. So I’d scratch those altogether and find other fish you like. Ghost shrimp and nerite snails are fine.

      In a 10 gallon you have to be super careful with stocking; I would personally stick to one fish species with a few inverts. I’ve got an article about stocking a 10 gallon tank here that contains pretty much everything you need to know. Off that list I especially love the dwarf puffer. Dwarf crayfish are also a lot of fun to keep. If you really want schooling fish then I’d go for 10+ mosquito rasbora.

      I hope that helps! Good luck 🙂

  • Reply Jenny February 8, 2015 at 10:19 pm

    I have a 10 gallon aquarium with sand and plants and I was wondering what is the best way to clean the sand? If I use a siphon on it, the sand just comes up with the waste. The waste seems to fall down in Below my sand and if I stir up the sand and let it settle before siphoning off the top, I feel like I’m not getting all of the waste.

    Is there a better way of cleaning sand?

    • Reply Mari February 9, 2015 at 2:06 pm

      This is going to be super hard to explain as I’m not at home and I can’t take photos, but we found a rather unorthodox solution to this. To clean the sand, we attached a fondue fork without the handle (so basically a long iron pin) to our siphon with tie wraps. The fork sticks out about an inch further than the siphon, which makes it possible to sift through the sand with the pin and then immediately and automatically siphon off the waste that comes up. You get almost no sand because it’s heavier than the waste and won’t come up as far. I hope it makes sense explained like this but it works quite well! The dirt usually collects in a few places so it’s pretty easy like this.
      This video also uses a pretty good method.
      Hope that helps a bit!

      • Reply Jenny February 9, 2015 at 5:34 pm

        Ok! That does make sense! I’ll have to try that! Thank you so much! I’ve been wondering about an easier way for a long time and none of my other friends that have fish have sand.


        • Reply Mari February 9, 2015 at 10:06 pm

          Glad you managed to figure out what I meant, haha. I think it’s a lot more effective than when you just siphon off the waste at the top, and disturbing the sand once in a while is also good for preventing compaction. 🙂

          • ALvin Yao February 23, 2015 at 9:03 am

            you could also install and/or make an undergravel jet system.

          • Mari February 24, 2015 at 11:30 am

            I unfortunately don’t think that would work very well with a sand substrate! Water is not able to pass through the sand.

          • ALvin Yao February 24, 2015 at 11:43 am

            It works with pool filtration sand……I think

      • Reply Aeon March 3, 2015 at 3:23 am

        thats an awesome idea thanks

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