Construct your pond with enough depth to control the growth of algae and waterweeds, which are any submerged or floating aquatic plants. The most shallow areas of your pond need to be at least 3 feet deep, because weeds grow in shallow areas.
Fence in livestock if you build your fish pond on the same land where it feeds. Don't allow livestock to drink water from your fish pond. Livestock waste is a major source of pond pollution, which can lead to roots growing on the bottom of the pond.
Install a pump and filters. The pump should keep the water in the pond circulating 24 hours a day. Algae and other weeds grow best in stagnant water. You can get an ultraviolet filter if you want to use light to kill roots, or a biological filter if you want to put beneficial organisms into your pond water to destroy algae and other pests. Filters may take a couple of months to become effective, if you have a large-scale problem.
Check your pond regularly. Remove algae and other weeds as soon as you see them. You can use your hands to pull up algae by the roots, or you can use a net or water skimmer to pull it out of the water.