Stop the source of the rust perhaps by painting or replacing the nails (with
copper) and the stains will fade in a year or two. The rust stain is just
particles trapped on the shingle surface not actual rusting of the shingle
so a rust cleaner like CLR will have limited effect (except by virtue of the
soap it also contains). Plain old dish soap and a garden hose would be how
I would start. Don't spray too hard or the grit will come off too much and
you'll wish you had left it alone.
A good hardware or paint store will have oxalic acid. It is used and
sold as wood bleach. Oxalic acid, dissolved in water will react with
the (insoluble) red iron oxides that we call rust to form iron oxalate
which is soluble in water and therefore just washes of. You will need
to keep the area you are trying to clean wet with the oxalic acid
solution until the rust stain disappears. Protect any bare wood or it
will be bleached. Although found in most green leafy vegetables in
small quantities oxalic acid is poisonous.
As an aside, I have considerable iron in my water. The housings of my
water filters get to look pretty gross when as they turn brown with
rust. Last week I took one off, dropped it in a bucket filled with
water and about a quarter cup of oxalic acid. About an hour later I had
a crystal clear water filter housing.
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