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I believe what you are describing is mold. In the beginning of the season I use my one gallon pump sprayer with 1 cup of bleach, a small amount of boat soap and fill the balance with water. I spray this mixture on the deck and gunnels and then hit it with my 2200psi power washer. The crud just jumps off the boat. In the absence of a power washer I've used a stiff deck brush and have had great results as well. This mixture has never done any harm to the gelcoat, stainless or the varnished wood surfaces. Give it a try, I think you'll have similar results.

Norm