The amount of vinegar you would have to add to affect the algae would be harmful to your koi, which require a balanced pH. Also, vinegar is a quickly metabolized nutrient in a mature pond, and will lead to increased microbial growth, which is probably not what you're looking for. Although there are chemicals that you can add to kill algae, they will destabilize the ecosystem and are only temporary measures.
Most effective is to lower the phosphate and nitrogen load in the system. This means not overfeeding, removing decaying debris, and exporting nitrogen (fish waste) somehow. Options include active filters, plant life, nitrogen absorbers such as straw bales, and water changes with dechlorinated water.
Come visit us in the Ponds and Water Gardening forum for advice. Algae is a common issue, and there are many ways that our members handle it. We'd love to hear about your experiences.
http://garden.org/forums/view/...
