Substrates for Amphibians & Reptiles

Posted by in Terrariums and Housing

What is a substrate and what does it do?

A substrate is the material in the bottom of the cage. The substrate’s most basic function is to absorb waste produced by your pet. Substrates also serve other purposes, such as:

  • Retain moisture and maintain humidity levels
  • Offer padding against a hard plastic or glass bottom
  • Provide cover/shelter for burrowing and terrestrial species
  • Buffer a heat source placed under the enclosure

What’s the best substrate to use?

This depends on the reptile or amphibian you keep. A species from the desert needs a different kind of substrate than a species from the rainforest. It is also important to consider your pet’s feeding needs. Substrates can be ingested and cause impactions and blockages, so using the wrong kind can be dangerous.

Simple Substrates vs. Natural Substrates

I have divided commonly used herp substrates into two categories: those that are used because they are practical (simple substrates) and those that are organic and improve the way a setup looks (natural substrates).

In the best situation these two categories overlap and the most attractive substrate is also the most practical, but sometimes this is not the case. You will have to consider the needs of your pet, how often you plan to clean the cage, how the rest of the enclosure is set up, and the cost involved when deciding what to use.

Jump To: Bare-bottom | Paper towels and newspaper |  Reptile carpeting, mats, and liners | Aspen and Carefresh beddings | Moss | Soil blends | Coconut husk fiber | Coconut husk chunks | Fir bark | Cypress mulch |  Leaf litter | Sand | Gravel

Part 1: Simple substrates

Bare bottom

Sometimes you don’t need to use any substrate at all. For arboreal species that spend almost all of their time above ground, a bare bottom can be the easiest option. In this case, a drain is fitted in the bottom of the enclosure and the whole cage hosed out with water for easy cleaning.

A bare bottom is also a good option for many aquatic reptiles and amphibians. Aquatic turtles are especially well-suited to live in an aquarium without a substrate.

Pros: easy to clean, no risk of animal ingesting substrate

Cons: requires frequent maintenance, does not offer cover or help maintain humidity levels, can be aesthetically unpleasing

Best for: Aquatic turtles like red-eared sliders, cooters and painted turtles, the water section of setups for semi-aquatic amphibians like bullfrogs or leopard frogs, highly arboreal species like chameleons and certain tree frogs (red-eyes, monkey frogs, etc.)

Paper towels and newspaper

Using a layer of paper towels or newspaper is a good option for a simple setup as long as you don’t mind changing them frequently. They may need to be changed as often as daily in some situations.

Paper towels are the preferred substrate for many reptiles. For species that need high humidity, create humid microclimates in the cage by using other moisture retentive substrates, such as moss, under shelters on top of paper.

For amphibians, use only plain paper towels without colors because dyes could be harmful. Also, pay close attention to how wet or dry the paper towels are. Wet, soiled paper towels are a breeding ground for unwanted bacteria and will lead to health problems.

Paper towels are not well-suited for burrowing reptiles or amphibians. They also are not the best choice for especially large or active animals, which will turn a substrate of paper into confetti. For these species, go with reptile carpeting or mats instead.

Pros: easy to clean, inexpensive, hygienic

Cons: need to be replaced frequently, may not hold enough moisture for some species, aesthetically unpleasing

Best for: Popular pet snakes and lizards including corn snakes, kingsnakes and milk snakes, leopard and crested geckos, and bearded dragons. Can be used for almost any reptile and works well for some pet amphibians like White’s tree frogs and young pacman frogs.

Reptile carpeting, mats, liners, and similar products

A bearded dragon basking over cage carpet for reptiles

Cage carpet is best-suited for reptiles from arid environments

Another simple substrate option is reptile carpeting and reptile mats. These products are used more or less like newspaper but have the advantage in that they don’t need to be thrown away afterwards. Instead, it’s best to have two pieces of carpeting or mats so that when one is soiled it can be replaced with a clean one while the other is washed and then dried.

Reptile carpeting is not suitable for use with amphibians.

Pros: easy to clean, more attractive than newspaper

Cons: requires frequent cleaning, not suitable for species that require a moist or humid environment

Best for: Pet reptiles when newspaper or paper towels are undesirable.

Aspen Bedding, Carefresh, and other small animal bedding

A ball python and aspen bedding

One of the best substrates for snakes is aspen bedding

The last of the simple substrate options that I feel I should mention are beddings typically used for guinea pigs, hamsters, mice and other small pets. Some of these substrates are also great options for keeping snakes, notably aspen shavings and bedding made from recycled paper products such as Carefresh. While a good option for snakes, small animal bedding is not suitable for most other reptiles. It also is not appropriate for amphibians because most small animal bedding spoils when wet. An exception may be using moist recycled paper-based bedding for caecilians.

Pros: absorbent, controls odor, snakes can burrow in it

Cons: spoils if moist (so not good for species that require constant high humidity)

Best for: Snakes!


Phyllobates terribilis on sphagnum moss

Sphagnum moss as a substrate for a juvenile dart frog

Many types of moss are available at pet stores and garden centers. Some of these are purely ornamental—they are not to be used as a substrate but rather as accents or décor within a terrarium.

Other mosses are marketed as good substrates for reptiles and amphibians but are not so. This is especially true of green mosses sold at pet stores in bricks or bales. This green moss has a tendency to mold and is not as good at holding moisture as the best kind of moss: sphagnum moss.

Sphagnum moss is brown, tan, or pink in color. It grows in bogs and decays into a soil additive called peat moss. Sphagnum moss can be used alone as a substrate for many amphibian species and certain lizards. It is also good for placing under shelters and hides on top of other substrates to provide humid microclimates.

To use sphagnum moss as a substrate, take a handful of dry moss and ring it out under water. It will absorb the water like a sponge. Note that sphagnum moss is acidic. For this reason, it is not a great substrate for terrestrial and burrowing amphibians. Sphagnum moss can also be ingested and potentially cause impactions. This is a greater risk if it is not kept moist and padded down tightly on the bottom of the enclosure.

Pros: holds moisture well, creates a humid environment, looks natural

Cons: certain types of moss spoil easily, can be swallowed and cause impactions, sphagnum moss is acidic

Best for: Frogs and toads. For other pets, place clumps of moist moss around the enclosures to create humid areas.

Soil blends

Numerous soil mixtures are available at pet stores. There are also soil substrate “recipes” to make your own from ingredients available at garden centers. Different soils have different qualities, so it can be difficult to evaluate their suitability for use as a substrate. Always avoid soils with rocks, perlite, or vermiculite. Soil blends sold for reptiles and amphibians from pet suppliers are the safest option.

Soils work well for terrestrial and burrowing species from humid or tropical environments. It is important to pay attention to the moisture content of soil. Sometimes you will want to use a drainage layer of gravel or other material underneath so the soil doesn’t become waterlogged in particularly humid environments.

Pros: natural appearance, live plants can be grown directly in it, long-lasting if not overly wet, can be used to create a tropical terrarium

Cons: if too wet will spoil, some types may irritate the skin of certain amphibians (pay attention to what is in it), can potentially cause problems if ingested

Best for: Terrestrial frogs, toads, and salamanders, as well as some geckos. Soil is a good substrate for species that burrow and live in humid environments.

Coconut husk fiber

A large adult African bullfrog on a substrate of coco fiber

Coconut husk fiber as a substrate for an African bullfrog

Found for sale in a dry compressed brick, coconut husk fiber is made from the ground up fibers of coconuts. These hairy fibers are called coir. When placed in water, the dry brick expands into an excellent substrate for reptiles and amphibians. If you keep up on spot cleaning, coconut husk fiber does not need to be replaced often. Coconut husk fiber also holds moisture well. Mix it with other components like sphagnum moss, sand or soil to create a substrate blend that works for your pet.

Pros: long-lasting, holds moisture well, does not spoil easily, generally safe if swallowed

Cons: can irritate amphibians if not given time to fully expand and settle before use, will spoil if saturated with water for extended periods

Best for: Most species with the exception of those from dry or arid environments. It is an especially good substrate for terrestrial amphibians when used in conjunction with sphagnum moss and leaf litter. Also good for terrestrial turtles and tortoises.

Coconut husk chunks

Similar to coconut husk fiber, coconut husk chunks are also available in a dry compact brick. They consist of the hairy coconut fibers around the shell of a coconut that have not yet been ground.

Coconut husk chunks have similar properties to coconut husk fiber, but because they are larger they may be more prone to causing problems if ingested so take care with which species you use coconut husk chunks with. Often their best use is when mixed with coconut husk fiber or a soil. When mixed with other substrates, coconut husk chunks help improve drainage in a tropical terrarium. They also are a more natural looking alternative to small animal bedding for many snakes.

Pros: same as coconut husk fiber, a good alternative to cypress mulch

Cons: potential to be ingested

Best for: When used alone, coconut husk chunks are best for reptiles. Most snakes, lizards, terrestrial turtles and tortoises that are not from dry arid climates live well on it. Mix with coco fiber or soil for amphibians.

Leaf litter

More often collected than purchased, leaf litter can form the bulk of the substrate for some amphibians and reptiles. It works especially well when placed over a soil mixture, coconut husk fiber, or other natural substrate. Live oak and magnolia leaves are most often used.

Leaf litter can be used as is, but there is a risk that pests or infectious diseases could be introduced with freshly collected leaves.

Dendrobates tinctorius on magnolia leaves in a terrarium

Leaf litter over a soil mixture in a vivarium for dart frogs

Instead, consider washing leaves under hot water and then letting them air dry in the sun for several days. You can also microwave leaf litter to kill pests.

Pros: natural appearance, provides cover for small herps, good addition on top of soil/coco husk fiber

Cons: potential to introduce unwanted pests, diseases, or chemical pollutants such as herbicides and pesticides

Best for: Amphibians, especially salamanders and terrestrial frogs and toads. Leaf litter can be placed over a bare-bottom in tree frog enclosures to improve the appearance of the setup or used on top of soil or coconut husk fiber in more traditional amphibian housing.

Fir bark

Fir bark was once the only natural substrate option marketed specifically for reptiles and amphibians. Often called by the popular brand name reptibark, fir bark looks natural and can help retain humidity in an enclosure. It is not appropriate for all species, however, being best reserved for use with snakes or certain terrestrial turtles and tortoises from humid environments.

The main issue with fir bark is that it is particular easy for amphibians and lizards to accidentally ingest while feeding. In my opinion, coconut husk fiber chunks are usually a better option in almost all situations, although fir bark can work well when mixed with soil or coconut husk fiber. In this way it serves a similar role as coconut husk chunks, helping break up the substrate and improving drainage.

Pros: readily available at pet stores, aesthetically pleasing substrate for snakes

Cons: causes impactions if ingested, does not retain moisture as well as other natural substrates, can be dusty

Best for: Fir bark can be used successfully for many snakes and some tortoises, but there are usually better substrate options.

Cypress mulch

Cypress mulch is another substrate for reptiles and amphibians made from wood. Widely available at pet stores and garden centers, cypress mulch works better in moist or humid conditions than fir bark. It can be used successfully with many amphibians, turtles, tortoises, and lizards.

Unfortunately, cypress mulch is not sourced in a sustainable manner. Cypress logging in the southeast United States damages wetlands and important amphibian and reptile habitat.

Pros: withstands wet and humid conditions, looks natural, does not spoil quickly when wet

Cons: unsustainable wood product

Best for: None. Because cypress mulch is made in a way that damages wetlands, it is best passed by for more sustainable bark substrates such as coconut husk chunks.

Sand (calcium sand, play sand, etc.)

Fine sand as a substrate for Stenodactylus geckos

Fine sand as a substrate for Stenodactylus geckos

Sand can be used alone as a substrate for some reptiles from arid regions. Some people use regular old play sand, but be careful to check it for rocks or debris that could cause problems if ingested. This is especially important for lizards kept on sand.

There are also sands made from calcium carbonate specifically for reptiles. These products are safer to use than sand because if accidentally ingested your pet is less likely to have an issue with impaction.

Sand should not be used on its own with amphibians, although it can be mixed with soils to form a more natural substrate. When added to soil mixtures, sand helps the substrate hold its form.

Pros: natural appearance for reptiles from arid regions

Cons: quality varies depending on type and may need to be cleaned, can cause impactions if accidentally ingested

Best for: Desert reptiles. When mixed with soil or coconut husk fiber, sand can also form part of the substrate for geckos, skinks, certain snakes and tortoises, as well as some amphibians.

Gravel, Stones, and Rocks

Many types of gravel, rocks, and stones are available for pet reptiles. Be careful when using rocks as a substrate. If swallowed they will be difficult for your pet to pass and will cause an impaction.

To avoid blockages, use stones that are too large for your pet to swallow. Many species that can live well

Turtles in an aquarium on a gravel substrate

Gravel substrate for aquatic turtles. It is important that stones are too large to be ingested.

on a bare-bottom also can be kept on large stones or river rocks, and these can enhance the appearance of the enclosure.

Aquarium gravel should almost always be avoided. The exception is when it is used under another substrate as a drainage layer, or with certain small aquatic species in an aquarium. Do not use small grade gravel with aquatic turtles or large amphibians, go for the big stuff. The rocks should always be too large to swallow.

Pros: readily available, natural appearance, can add surface area to aquatic areas to increase room for beneficial bacteria to grow

Cons: dangerous if swallowed, heavy

Best for: Large river stones and rocks are okay for some tree frogs and aquatic turtles. Most other reptiles and amphibians are best kept on other substrates.