Black paint with "permanent" water spots

[Oldman]

My wife just bought an '06 4Runner. It's black and I've washed it and attempted to buff and wax it, but there are what appears to be water spots all over the car. Much more on the hood and roof than on the sides. I read where a 3 to 1 mixture of vinegar and water would remove them, but that didn't work. I used some cheap Turtle Wax polishing compound, but that didn't do the trick either.
I'm scared to be too aggressive because I've heard from so many that you can't use anything abrasive on a car with clear coat. The black paint is not scratched or faded, it's just spotted all over with what looks like mineral deposits from the water down here in the southeast.
Any help would be appreciated. I'll try anything and don't mind spending some time to make it look really nice for my bride.
Thanks guys,

[J Wikoff]

Try something called IronX. I used that recently to get iron dust off my car after a brake pad had worn away without the wear indicator letting me know. Kinda spend for a spray bottle full of stuff, but it does the job. I got the lemon scented version. Do it outside. It's potent.

[redfury]

I'd run it through a good car wash...like a car wash business, not a gas station car wash. I took my Bonneville that was just nasty from the garbage that falls off my cotton wood trees and is impossible to remove and it came out shining like a jewel afterwards. The car wash cost $26, but it was worth it ( cleaned inside and out ).

[jshow816]

Have you tried a claybar?

[00Beast]

I'd try a clay bar too.

[crash93ssei]

Try to get a couple good pictures, as close as possible to show it. Could be dealing with etching from acid rain.