Since wildlife ponds are not generally cleaned on a regular basis, covering the bottom with rocks or gravel is perfectly fine. In fact, it provides tiny openings that encourage microbial life to bloom. These microbes help keep the water clean and healthy, in addition to offering food supplies for the tiniest forms of life. Rocks on the bottom create a more natural look that is appealing both to wildlife and the humans watching them. If larger animals like raccoons or deer climb into the water or dig around in it, a layer of gravel will keep them from accidentally damaging the liner.
There’s no negatives to using gravel in a pond aside from the difficult of dredging the pond to remove sludge. While sludge is an unattractive problem in decorative and swimming ponds, it’s a positive part of a wildlife habitat pond instead. It’s rarely removed unless it’s starting to fill the pond in to the point of lost volume. Whether you prefer smooth pea gravel or larger chunks that create a lot of habitat space, all of these materials have a place in any well designed wildlife pond.
