My '97 Civic had the rust at the quarter panel joint by the left rear wheel. I started sanding away the rust, ended up with a hole in the steel. Just FYI, I think there's a good chance that's what you'll find. Once you clean away all the rust you can paint + Bondo, or you can weld it.
I like the advice to clean from the inside also by removing the interior panel. BUT I think at least in my '97 Civic it's a "chamber", you can't get to it from the other side. Yours is the generation before mine, maybe you can get to the back side of it.
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Coast long and prosper.
Driving '00 Honda Insight, acquired Feb 2016.
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