Colorful gravel and a few pebbles

How to Choose Substrate for Aquarium: A Working Framework

Substrate is the very foundation of an aquarium. The bottom of the tank determines the overall look and feel of the slice of nature you are going to install in your home.

Aesthetics aside, each substrate has unique properties that include whether and by how it impacts the water quality, and also its maintenance requirements.

It is impossible to tell you which substrate is the best because the perceived value of its innate qualities depends heavily on personal circumstances and preferences. The best I can do is give you an evaluation tool, a series of questions that form a framework inspired by your vision for your new fish tank.

Here’s how to choose substrate for aquariums with fish and other livestock. Note down the following questions:

  • Am I ready and willing to provide regular maintenance?
  • Do I like how it looks?
  • Do I like how my fish look atop this substrate?
  • Does it fit in my budget?
  • Does it work with the fish I want to keep?
  • Do I want live plants?

The questions aren’t listed in order of importance. Over time, your ideas and interests in the hobby will evolve.

At first, you may choose a substrate that fits the fish you want to keep. Maybe you will start creating your own substrate mix. Yet another tank could grow from an idea about a specific hardscape, and that would inform the species the aquarium could host.

That’s why things like comparing in absolute terms bare bottom tanks vs. gravel aquariums don’t make much sense. Is bare bottom better than gravel? In certain scenarios, like hospital or breeding tanks, bare bottom tank is the perfect choice. In others, gravel is the clear winner.

That’s why you can use the famous standard array outline the character you envision for your new fish tank. Your perspective may — and likely will — change over time and the emphasis you assign to each question will shift accordingly.

These are the values of the standard array: 15, 14, 13, 12, 10, 8.

Assign the points as you see fit among the six main questions. It is a mental exercise that will help you choose the substrate that best matches your level of experience, vision for the tank, budget, and more.

The standard array works for each substrate in this guide, as well. Each of them has six characteristics, so you can grade their appeal to you easily. What’s more, the substrates are split into six categories.

You get the drill.

Here are the most common substrate types, starting with the simplest of them all: no substrate tank.

Bare Bottom Tanks

Bare bottom tanks are minimalist setups with several clear advantages:

  • Very easy to clean — With an adequate filtration system, bare bottom tanks hardly need any cleaning or extensive maintenance sessions. That’s what makes them a very good option for large and polluting species like goldfish.
  • Stable water parameters — No substrate means eliminating a huge factor in the aquatic ecosystem. Bacterial life and accumulated waste are forces to be reckoned with both in nature and in a fish tank. Properly filtrated bare bottom tanks can maintain constant water parameters. That’s why they are excellent for breeding and hospital tanks, as well as for sensitive fish species like loricaria.
  • Visually striking — Bare bottom tanks can be striking through a marvelous fish that moves around freely in all its glory or by an accentuating light or even a captivating piece of hardscape. It is true that tanks with no or minimal decor are an acquired taste for many, but if minimalism is put to work, the results often are striking or quietly enchanting.
  • Potentially cheaper — While bare bottom tanks need good filtration, that doesn’t necessarily mean expensive equipment. A submersed pump and a sponge filter could do the job in certain tanks. Bare bottom setups, even if they have some decoration, allow much better water flow compared to a fully planted tank, for instance, so a weaker mechanical filter can work unobstructed. And then you don’t have to buy substrate making bare bottom tanks technically the cheapest alternative to gravel or sand. Of course, most inert substrates like gravel or sand could be very affordable or even free.

And while bare bottom tanks have even more, subtler advantages, they do come short in a couple of instances. Here are the main cons of a bare bottom tank.

  • Some fish and snails prefer substrate — Many bottom-dwelling fish spend their time foraging through the substrate. Corys sift sand through their gills and Malaysian trumpet snails burrow in during the day.  Many other species need places to hide under to feel at ease.
  • Will always need care — While bare bottom tanks require minimal care, they need it at all times. Their most glaring limitation is the inability to create an ecosystem in a box. Without working filtration, they accumulate waste more quickly than a tank full of plants in sand or gravel.

Here you have the six pros and cons of bare bottom tanks. The categorization is biased, of course — looks can be a huge advantage for a bare bottom tank enthusiast.

You can distribute the standard array here, too, to craft an outline of your attitude toward tanks without substrate. My detailed guide on bare bottom tanks provides additional insight into their merits and limitations.

Inert Substrates: Sand, Gravel, Pebbles and Rocks

Budding aquarists usually have success with sand or gravel, two of the prettiest and most accessible substrates in the hobby.

Sand, gravel, pebbles, and lava rock are called inert substrates because they don’t impact the water quality in any way. But soon after they are introduced to the aquarium, these substrates will be teeming with invisible bacterial life. Over time, the sand irregularities and the tiny cracks within the gravel will fill up with mulm that will transform into underwater soil.

Inert substrates can support plenty of plant life in a fish tank, but they will benefit from a boost of root tabs or liquid fertilizers early on.

Here are the most popular inert substrates in a nutshell:


Small gravel without sharp edges is the go-to option for many fishkeepers. Its variety of colors and shapes ticks the box for looks, but there’s more to gravel than initially meets the eye.

Gravel substrate pros:

  • Visually diverse and appealing — Gravel comes in many shades and forms. 3-9mm size is appropriate for most fish. Avoid brightly colored gravel unless you want to re-make the aquarium in the near future. Pink, blue, green, yellow, and other bright colors don’t stick for too long once the gravel is underwater. What’s more, darker substrates make most fish colors stand out.
  • House bacterial life — Gravel can play a significant part in the nitrogen cycle. Its bacterial life is among the biggest benefits of this substrate. Typically, gravel provides more surface for bacteria than sand.
  • Provides room for rooting plants — Root feeders grow well in gravel. Their roots can spread out, creating larger foot chains. What’s more, plants in gravel are much harder to uproot than species planted in sand or aquasoil.
  • Gravel is very affordable — Whether at the hardware store or the pet store, gravel is among the cheapest purchases you can make. From a hardware store, it typically costs less but needs more intense rinsing. Of course, you may be lucky enough to have access to gravel even for free. I collected my first gravel substrate from the vicinity of a nearby stone quarry.

As for disadvantages, gravel has a few things to consider.

  • Gravel is not ideal for all fish — Some popular fish species prefer sand. Corydoras love sifting sand through their gills. Kuhli loaches are yellow and shy but dream big; they have their Shai-Hulud moments by fiercely burrowing into the sand.  Additionally, brightly colored gravel or sand could affect the coloration of your fish.
  • Initial inertness — Gravel comes devoid of nutrients for plants. Many plant species can and will survive and eventually thrive in gravel because it slowly fills up with soil. Biowaste and decaying matter become mulm and then aquatic solid, but it takes 6-12 months or more. Early on, gravel could use root tabs or liquid fertilizers to ignite plant growth.

See, gravel is awesome. It’s one of the best options for starting aquarists. It is relatively easy to clean and planted plants stay planted.

But some fishes and snails simply prefer sand.

Sand Substrate

Sand shares many of the same pros as gravel:

  • Visually amazing — Variety of colors and sizes make sand fit in many tanks. Slightly coarser sand is better as it is less likely to enter a mechanical filter. It is also less prone to compacting. Tiny sand can become too tightly pressed by the water pressure, hampering root expansion in plants.
  • Provides natural filtration — Just like gravel, sand houses many beneficial bacteria that break down fish and other waste.
  • Maintains its looks — Sand needs cleaning but with simple siphoning, it can remain as vibrant and clear as when you put it in. And while it can accumulate waste on top, a cleaning crew of snails, suckerfish, and shrimp can rummage through sand much more efficiently than through gravel, leaving less waste unattended.
  • Extremely affordable — Sand is very cheap. It can come for free, too, but collect only from clear sources. Some riverbeds are very polluted by human activity making their sand or small pebbles unsafe for fish tanks.

Sand is the favorite substrate for several fishes and snails. Kuhli loach, all corydoras species, and Loricaria lata all love sand. Malaysian trumpet snail is a good borrower and will find its way into finer gravel too, but sand makes it so much easier to find a place to sleep.

Sand is one of the best substrates out there, but it has a few drawbacks.

Sand substrate cons:

  • Not ideal for all fish — Oscars and cichlids like to interact with sand. So much so that if left unchecked, they can aquascape the hell out of your fish tank.
  • Tricky with fine sand — Fine sand can be sucked up the gravel vacuum easily unless the vac is long and narrow. Also, bright sand makes debris and fish waste quite obvious. Sand isn’t as porous as gravel, so a lot of the waste will stay atop.

Pebbles and Lava Rocks

Small and even medium pebbles can be collected from clean rivers. They are very pretty and fish species that like fast-flowing water often feel right at home with pebbles. Hillstream loaches come to mind.

Lava rock is another excellent substrate choice. Their unevenness provides ample surface for bacteria to colonize.

In terms of pros, pebbles and rocks boast the following:

  • Look great
  • Powerful biofiltration — Lava rock in particular can house loads of beneficial bacteria.
  • Goldfish like pebbles — Even though small pebbles (or gravel) could be a choking hazard, goldfish like to “chew” on them. If you keep several goldfish and don’t want to have a bare bottom tank, covering the bottom with river stones is a good solution. A thin layer of pebbles will remain easy to clean while enhancing the aesthetics of the aquarium.
  • Lava rock is light — This is especially handy with large aquariums that need a lot of stones to cover the entire bottom.

The cons of pebbles and lava rock aren’t many but exist:

  • Not ideal for all types of fish — Sand-lovers like cory catfish wouldn’t be that happy among pure rock bottom.
  • Can accumulate a lot of waste — Small pockets can form underneath the pebbles. Over time, they can become waste pits that can affect water parameters and microbial life in the tank. To prevent this, caulk the pebbles with sand as you lay them on the bottom. Regular cleaning routine and good filtration will take care of the rest.

These are the most common inert substrates for building a fish or a planted tank. However, there are ways to make your substrate active so that it can contribute to plant and fish tank at all times.

Active Substrates

Active are substrates that contain chemical elements that affect water quality.

The two main types of active substrates are soil — potting soil, soil from the garden — and special aquarium soils. Both active substrates change water parameters because they contain decaying matter and chemical compounds that serve as nutrients to help plants grow.

Aqua soils and potting soil affect the entire aquarium, though, not only the plants. That makes setting up and maintaining a topsoil aquarium or a fish tank with specialized soil more challenging.

The inexperienced hobbyist can start their journey toward understanding the underwater mysteries by exploring the excellent Walstad method:

However awesome active substrates may be, they come with their own set of challenges. Here are the main pros and cons of active substrates.

Topsoil Aquarium

Gardening soil is an excellent promoter of plant growth. It can work its magic even underwater, fully submersed, and capped off with a healthy layer of sand.

Here are the main benefits of topsoil aquariums:

  • Promotes organic life — Soil, even used sparingly, can bring a lot of nutrients into the tank. Many will go to the plants. But microscopic creatures like daphnia and scuds are also very likely to appear. Natural water sources teem with such small critters that often become fish food.
  • Less maintenance in the long term — Soil can go a long way in establishing an ecosystem that requires next to no maintenance once it matures. Early on, just like with commercially produced aqua soils, regular water changes are necessary but over time you can go even without mechanical filtration.
  • Plants love it
  • Very affordable — Whether you grab a bag of organic potting soil or scoop some dirt from your garden, soil is extremely affordable. It must be capped with sand (or gravel, but sand provides better coverage), but sand also costs next to nothing or, indeed, nothing.

Soil is great but it comes with a couple of caveats that make it a bit harder to work with.

Here are the main disadvantages of topsoil fish tanks:

  • Soil will affect the water parameters — Soil interacts powerfully with the water. A newly set up dirt tank, especially when made with unknown soil, must be tested regularly for ammonia, nitrates, and nitrites. Once the nitrogen cycle is complete, the parameters should be stable, but regular testing early on (once a week for 6-8 weeks should do) and patience are a must.
  • Dirt can make the water muddy — This happens if the soil is not capped well or during maintenance. Aggressive siphoning can disturb the capping layer, releasing dirt particles into the water column. It is also very likely that in the first weeks or even 2-3 months in, the water to be slightly brackish. Organic, living soil contains a lot of decomposing matter that will release tannins. Now, tannins are great but not everyone likes how they look. Here’s how you can tackle them.

Dirted tanks are an exciting way to get a lushly planted tank with minimal monetary investment, but you must proceed with care and curiosity.

Patience is a virtue with types of gardening.

There is plenty to read and watch out there if you want to understand how they work. My detailed guide will help you understand how to set up a dirted aquarium and its unique dynamics.

Enriched Aquatic Soils

Commercially produced aquatic soils are more targeted and less messy than potting soils. They share most of the same benefits:

  • Excellent for plants — Aqua soils contain certain types of nutrients. Different labels are good for different setups, though, whereas organic potting soil could provide a more rounded supply of nutrients.
  • Great for bacterial life — Most commercially sold soils are baked into granules the size of a green pea or smaller. In other words, they are very much like gravel in overall size. That provides plenty of surface for bacterial growth.
  • Look good — While not as visually diverse as sand or gravel, aqua soils are pretty. Of course, pockets of the stuff can be buried under inter substrate, for better visuals and control of the active substrate.
  • Consistent results — Nutrient-rich aquatic soils will produce the same results time and again. Unlike soil collected from the backyard, their chemical composition doesn’t change over time. Indeed, if you use the same brand of potting soil for a dirted tank, the results can be predicted to a great extent, but aqua soils very much guarantee consistency.

Nutrient-rich soils are great for planted tanks, but they aren’t ideal for beginners. Here are the two main cons of aqua soils:

  • Costly — Hands down the most expensive substrate you can find. Different labels come at different prices but they are costlier than inert substrates or potting soil.
  • Affect water parameters — Aqua soils are made to change the water parameters. The nutrients they release are great for plants but could be dangerous for livestock. Early monitoring and maintenance are necessary. Some experience working with them helps a lot. Aqua soils are very potent and can lead to algae blooms, so regular water changes (daily the first week, every other day the second, once at week four) are necessary to remove the excess nutrients.

Enriched aquarium substrates can produce great results with the proper maintenance and dedication, but they are more demanding than inert substrates and even potting soil if done correctly.

How to Choose the Substrate for Your Aquarium

Use the information in this guide to get a feel of the different substrate types. Go in the specific guides on gravel, sand, bare bottom, and dirted tanks to understand things even better.

Then use the standard array to assign values to each question that forms the decision-guiding framework. To dive deeper, you can grade each type of substrate individually and determine the value its qualities bring to your fish tank.

It is entirely possible to mix substrates, too, even though that’s slightly more complicated than going with a single type.

See what matters to you in terms of visuals, maintenance, species you want to keep, and budget. Finding the answers to these questions will help you choose the right substrate for your aquarium

Similar Posts

Leave a Reply

Your email address will not be published. Required fields are marked *