Best Pond Substrate for Outdoor Fish Ponds

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Most pet fish live in either an indoor tank or outdoor pond. We already covered what the bottom of your tank should look like, but what is the best pond substrate? Ponds are much more diverse than tanks and can come in a variety of shapes, layouts and “all natural” finishes. What is the “healthiest” bottom for your pond is essentially the easiest to clean = nothing.

Options for Pond Substrate

Gravel/Small Rocks

Pros: This pond substrate is the most eye appealing of them all. It breaks up the industrial look of a synthetic fish environment and can provide hold for and uncontained plants.

Cons: You will need to stir the gravel/small rocks frequently to keep them from cementing together. A pond vacuum will be of little use and will keep collecting all these small stones. This substrate collects lots of debris and is hard to clean. If the substrate is deeper than 3″, you run the risk of anaerobic bacteria production once they are cut off from the oxygen in the water. This can create pockets of hydrogen sulfide that can kill fish if mixed into the water supply.

Large Rocks

Pros: Another aesthetically appealing bottom pond substrate. Larger rocks are more suitable to a “river” appearance.

Cons: Your pond vacuum will work slightly better if the substrate is too large to fit up the hose. If the stones are too heavy, you will have a very hard time cleaning between them. Multiple layers of stones will be more likely to collect debris than only one layer of rocks. This layering effect can contribute to cementing of rocks together and formation of hydrogen sulfide producing anaerobic bacteria. Adding rocks on top of a liner, either sheet plastic or sprayed, will erode through the liner faster and require replacement.

Plastic Liner

Pros: A liner bottom is one of the easiest substrates to keep clean. They work well with a bottom drain.

Cons: Pay special attention to the thickness of your liner. Thinner liners may be more economical, but they will not last as long as thicker liners. They are prone to tears from rocks, root growth and boots. They are not as aesthetically pleasing and deep folds can potentially trap fish. Learn more about the types of available pond liner.

Concrete/Spray Liner

Pros: Concrete bottoms with a spray-applied liner are very easy to keep clean. They are more durable than simple liner ponds. Leaks from tears are not an issue as this type of bottom stands up well to abuse from rocks and boots.

Cons: This is one of the most expensive pond substrate options for fish ponds. If your concrete is not mixed properly, you will lose chunks of your bottom, leading to leaks. They are susceptible to earthquake damage if this is an environmental concern. Be sure both your concrete mix and spray liner are appropriate for usage with fish. You cannot change the shape of your pond or add any underwater features later with this substrate.

Plants/Mud/Bog/”All Natural” Pond Substrate


Cons: Your lack of cleaning effort creates a dangerous health hazard to your fish. Dense planting and layers of debris and fish waste create layers of bacteria that lose contact with oxygen in the water. These anaerobic bacteria use sulfur as a food source. If you mess around in the muck or your fish try to flash on this surface, you will release hydrogen sulfide and kill all your fish.

It is impossible to recreate a native environment in a synthetic fish system. “All natural” systems in wild environments use multiple species working together to balance waste management. In a man-made pond, you are missing many of these critical elements. Do your regular maintenance!

A bare bottom is the best pond substrate?

Yes, a plain bottom is aesthetically unpleasing, but a bare bottom pond is easiest for most owners to clean. Whatever substrate you have, rocks or stones or something else, as long as you clean it regularly, it is fine for your fish. If you don’t clean it regularly or thoroughly, pockets of anaerobic bacteria can start to grow, and it their ever disturbed, release hydrogen sulfide that can kill all your fish. However, we have come to find that most pond owners don’t clean their substrate regularly. Having a plain bottom makes cleaning easier! Who doesn’t like that?

How do I clean my pond bottom?

The easiest way is by using a pond vacuum. These items are specially designed to make cleaning ponds easy. Think of it similarly to a pond-size gravel siphon. If you don’t have access to a vacuum, use a long brush or stick to stir up the substrate on a regular basis. This will bring oxygen deep into the cracks and crevices, preventing anaerobic bacteria formation.

For more information on pond cleaning, use our handy checklist so all your daily, weekly, monthly and yearly tasks get done on time. Remember: water quality is the #1 influence on fish health! Regular maintenance is the best thing you can do to keep your pond healthy.

“But my ‘all natural’ mud bottom is just like their natural environment so it’s better for my fish.”

Like we said, whatever works for you and keeps your fish healthy is fine by us. Just keep in mind that trying to mimic a “wild” system in an artificial environment is usually incomplete. Most “wild” setups include multiple types of fish, invertebrates and commensals working together to make their environment hospitable for all. There is usually a constant flow of water, so unless your pond has a leak or your have the funds to set up a constant overflow, this is harder to maintain. Also, wild systems will lose fish constantly to predators and other diseases that you do not want to subject your pet fish too. Just because it is “all natural,” doesn’t mean it’s better.

Deep pockets of muck, if left undisturbed for long periods of time, can start to culture anaerobic bacteria. Rather than using oxygen as a fuel source, these bacteria use sulfur. If these bacteria are disturbed by an errant vacuum or flashing fish, they can die and release hydrogen sulfide. Your pond will smell like rotting eggs and your fish can die from this toxic substance. If you are sure how deep your muck is, get your fish out of the way first!

Most outdoor fish, meaning koi and goldfish, have been bred over centuries to live in artificial environments. They are poorly suited to living in the wild because brightly colored fish are easiest to spot and eat. Don’t pretend to go “all natural” because you don’t want to clean your pond. If you don’t want to do it, hire someone to do it for you. Providing your fish a clean and healthy environment is the contract you signed when you picked them out at the store.

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