hmm- I might try CLR on a cloth first - if it's rust, you might jsut be able to neutralize it.

if they're algae stains ( not uncommon ) bleach will do the same thing (not on the same day, though- those are two chemicals I don't like keeping in the same cabinet!)

I would suspect that your local pool place would know what kind of paint would be best to use on your above-ground, depending on whether the outer shell is metal or fiberglass.