Purchase a herbicide containing glyphosate, such as Aqua Neat or Rodeo. Aqua Neat and Rodeo are designed for aquatic use, and thus will not injure wildlife if the chemical gets into the pond. Alternatively, you can purchase a natural herbicide. Natural herbicides include vinegar and corn gluten. Natural herbicides are non-selective and thus will kill everything they come in contact with, including desirable plants and grasses.
Pour the herbicide into a watering can.
Sprinkle the herbicide over the weeds. You can use a compressed air sprayer or sprayer attached to a garden hose as an alternative to a watering can. However, these two methods increase the risk that the herbicide will drift into the pond.
Pull any remaining weeds by hand. When pulling weeds by hand, be sure to remove the entire root to prevent future growth. Consider using a hand-held hoe if you want to avoid spending hours bent over on your hands and knees.
Do not fertilize the area around the pond. Fertilizing is a common technique employed to prevent future weed growth. However, most fertilizers contains phosphorus, a chemical which can run off into the pond and harm wildlife.