A pond works best with a balanced 5-part ecosystem. Biological filtration, mechanical filtration, Rock/Gravel, fish, and plants make up this recipe. Beneficial Bacteria used regularly with a proper filtration system should keep your pond clean. Beneficial Bacteria colonizes on the rocks and gravel in the pond. This Beneficial Bacteria breaks down complex organic compounds that sink to the bottom of the pond. Without the rocks and gravel on the bottom of the pond, you would not have the large quantity of bacteria in this location to help breakdown and digest the organic material. Over the same time period, ponds with the balanced 5-part ecosystem will have less organic material at the bottom of the pond than a bare-bottomed liner pond.