rust spots after 1st year

last summer was the first year my car was on the road, it was a really wet year and i drove in the rain several times. anywhere that the water was able to lay on or got between such as leaf springs, small holes or pinch welds there is iron/rust spots. i would like to try cleaning this off but can't seem to find anything that really works. i tried varsol, gas and cleaner/polish. i would like to use CLR but i'm sure that would eat paint. anyone have any ideas?