If they are etched into the paint then you'll have to use a polish to get them out. There is a thread about this currently on this forum:
http://autopia.org/forums/showthread.php?s=&threadid=47298
Note that I've never used CLR , but if you want to try it here is a post I copied from
turbomangt on this subject a while back:
"CLR removes hard water spots in seconds
It is found in any hardware store, it removes mineral deposits, hard water stains, and rust. I have used it on paint for water spots, comes right off. Not sure what the letters stand for.
(edit: CLR stands for Calcium, Lime, and Rust. It's a good product for dissolving those things.)
My experience using it came when I could not for the life of me get some tough water spots off the car. Then the distributor from Ardex told me about the CLR, it seems the mineral deposits need to be broken down in the hard water, or dissolved would be a better term. I used it on a section of the car, and it came off instantly. Ardex rep said it was safe on the paint. But I never gave a car a bath with it. I would take a terry towel and use it on a section of the problem area a little at a time. It is expensive so you don't want to waste it. A little I think would be effective, but plan on taking some time."
HTH