You’ll find many websites claiming that vinegar is a safe and cheap way to keep algae from taking over your pond. Unfortunately, this isn’t true. Vinegar isn’t good for controlling algae or preventing it from growing, nor is it a safe way to change the pH of the pond’s water. It’s not too damaging if you only have plants, but acetic acid is very harmful to fish like koi. Their sensitive gills can’t take this kind of acid being mixed into the water in the volumes recommended for algae control. Even if you plan to remove your fish while mixing in the vinegar, lingering compounds will still hurt them when you add them back.
Vinegar is acceptable to use for killing algae and cleaning a pond when it is drained. The acidic is good at lifting away the stubborn algae deposits and stains without damaging the liner material. When used in this way in limited amounts, the leftover vinegar residue won’t hurt the fish or change the pH of the water. However, this isn’t the way most homeowners plan to use vinegar to kill algae. Don’t dump it into a filled pond, even in small amounts, to avoid damage to sensitive plants and fish.