Once infected, a pond will be difficult to uninfect.
As
@jim mcnamara said, sterilizing the rocks but leaving the water alone will probably not do much.
Depending on details like: the size of the pond, what might be in it worth preserving, and how you treated it, I would consider starting over.
Even smaller more controlled situations like aquaculture water system are difficult to uninfect.
Ponds or water systems can be fitted with UV "Sterilizers" or treated with ozone (O
3) generators to treat pumped water, but there will still be unaffected microbes in the water since it is not pumped all at once. Removing the water or bleaching the water in the pond may kill the unwanted microbes (if other debris that might react with the chemicals are removed), but would also kill possibly desired occupants.
Another approach often taken with (large) ponds is to drain them and let them dry out for an extended period of time. This kills some stuff and also promotes oxidation of organics in the bottom muck (more oxygen in air than in water). Treatments like this are used periodically to ward-off eutrophication.
Less extreme treatments could be using iodine or potassium permanganate.
You might try contacting the source of your treatment to see what they recommend. An aquaculture extension service might also be of help. There may also be aquaculture societies of various kinds around in your area.