Good question.
Fertilizer should be applied to clear water each spring when water temps are consistently above 60 degrees. The clearer the water, the more fertilizer you need. Phosphorus is the key limiting ingredient needed to promote plankton growth. The goal in not to prevent algae, but to create a plankton bloom, which shades sunlight off the bottom of the pond, which helps prevent rooted plant growth.
When your pond flushes, judge when to fertilize by water clarity. Clear water with deep visibility needs the most fertilizer. Fertilizer rates are determined by how far down you can see, and to some degree, your water chemistry.
