Putting any material on the bottom of the pond helps give it a natural look, but it also complicates maintenance over the years. Rocks, gravel, sand, and mud are all commonly added to koi ponds in particular to harbor the bacterial life necessary to keep water quality high. They also help hold down the liner so that water or gas that becomes trapped underneath it can’t push the material up. However, the uneven surface of gravel or sand means that sludge and muck becomes trapped between pieces of material. If you want a completely clean pond and need to control water quality for healthy fish, you should leave the liner uncovered so you can vacuum it with a pond cleaner.
Koi ponds in particular tend to rely on bottom filters and circulation systems that help keep waste from building up. When you cover these filters with layers of sand or gravel, circulation drops significantly to leave the water high in nitrates and low in oxygen. While some koi keepers recommend rock and other material for lining a pond for the bacterial benefits, others swear against it for the difficulty of keeping the pond clean. You’ll have to decide what’s right for your situation.
